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https://api.github.com/repos/materialsproject/pymatgen/issues/2825
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PR_kwDOACgets5JCjOK
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Fix pre-commit.ci isort error
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[
"\n[](https://coveralls.io/builds/56525588)\n\nCoverage: 78.875% (-0.5%) from 79.414% when pulling **332e26ee51fcd9ee70d44076754afb7fe9756b06 on fix-precommit-ci-isort** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n"
] | 2023-02-01T19:45:47
| 2023-02-01T23:01:15
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2023-02-01T22:58:06Z
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MEMBER
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Error is due to https://github.com/PyCQA/isort/pull/2078.
Updating `black` also introduced some formatting changes.
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I_kwDOACgets5dajln
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The hkl index outputted by XRDCalculator is incorrect.
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[
"I am not able to reproduce this error. Here is the XRD pattern that I get from the latest pymatgen. As far as I can tell, the labelling of the peaks corresponds to the VESTA ones.\r\n\r\n\r\n\r\nFor future reference, I would prefer if you provide a structure file and code example to reproduce any reported errors. Since we don't have access to other third party apps, we can't reproduce what happens there.",
"Thank you for your quick response.\r\n\r\nThe CIF file and Python code used are as follows.\r\n\r\n\r\n---\r\n## CIF file\r\n[alpha-Fe2O3_fiz15840.zip](https://github.com/materialsproject/pymatgen/files/10575493/alpha-Fe2O3_fiz15840.zip)\r\n\r\n\r\n## My Python code\r\n```python\r\nfrom os.path import dirname, basename\r\nimport pandas as pd\r\nimport numpy as np\r\nfrom scipy.special import wofz\r\n\r\nfrom pymatgen.io.cif import CifParser\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\n\r\n# setting --------------------------------\r\nx_str = 10 # /deg (start of X range)\r\nx_end = 120 # /deg (end of X range)\r\n\r\n# Debye-Waller factor\r\nDWF = {\"Fe\": 0.15, \"O\": 0.6}\r\n# ----------------------------------------\r\n\r\n\r\ndef voigt(x, amp, pos, fwhm, shape):\r\n \"\"\"\r\n x: x data\r\n amp: amplitude(peak height)\r\n pos: peak center\r\n fwhm: Full Width at Half Maximum\r\n shape:\r\n \"\"\"\r\n tmp = 1 / wofz(np.zeros((len(x))) + 1j * np.sqrt(np.log(2.0)) * shape).real\r\n tmp = (\r\n tmp\r\n * amp\r\n * wofz(\r\n 2 * np.sqrt(np.log(2.0)) * (x - pos) / fwhm\r\n + 1j * np.sqrt(np.log(2.0)) * shape\r\n ).real\r\n )\r\n return tmp\r\n\r\n\r\ndef sum_voigt_peaks(pat, x_str, x_end):\r\n x = np.arange(x_str, x_end, 0.01)\r\n calc_y = np.zeros(len(x))\r\n\r\n N = len(pat.x)\r\n fwhm = 0.06\r\n shape = 0.5\r\n for i in range(N):\r\n pos = pat.x[i]\r\n amp = pat.y[i]\r\n calc_y += voigt(x, amp, pos, fwhm, shape)\r\n\r\n return x, calc_y\r\n\r\n\r\ndef output_hklTable(pat, f):\r\n d_space = pat.d_hkls\r\n _hkl = pat.hkls\r\n\r\n hkl_index = [i[0][\"hkl\"] for i in _hkl]\r\n m = [i[0][\"multiplicity\"] for i in _hkl]\r\n dict = {\r\n \"hkl\": hkl_index,\r\n \"multiplicity\": m,\r\n \"d\": d_space,\r\n \"2theta\": pat.x,\r\n \"Int\": pat.y,\r\n }\r\n df = pd.DataFrame(dict)\r\n df.index = df.index + 1\r\n d_name = dirname(f)\r\n f_name = basename(f).replace(\".cif\", \".csv\")\r\n df.to_csv(\r\n d_name + \"\\\\hkl_\" + f_name,\r\n encoding=\"utf-8\",\r\n index=True,\r\n )\r\n\r\n\r\ndef output_XRDpattern(pat, f):\r\n x, y = sum_voigt_peaks(pat, x_str, x_end)\r\n dict = {\"2theta\": x, \"Int\": y}\r\n df = pd.DataFrame(dict)\r\n d_name = dirname(f)\r\n f_name = basename(f).replace(\".cif\", \".csv\")\r\n df.to_csv(\r\n d_name + \"\\\\prof_\" + f_name,\r\n encoding=\"utf-8\",\r\n index=False,\r\n )\r\n\r\n\r\ndef main():\r\n f = r\"D:\\alpha-Fe2O3_fiz15840.cif\"\r\n parser = CifParser(f)\r\n structure = parser.get_structures()[0]\r\n lat = XRDCalculator(\r\n wavelength=1.54056,\r\n debye_waller_factors=DWF,\r\n )\r\n pat = lat.get_pattern(structure, scaled=True, two_theta_range=(x_str, x_end))\r\n\r\n output_hklTable(pat, f)\r\n\r\n output_XRDpattern(pat, f)\r\n\r\n\r\nif __name__ == \"__main__\":\r\n main()\r\n\r\n```",
"I'd like to point out a clear mistake@pymatgen: 2022.0.17.\r\n\r\nThe below information was learned from an expert in crystallography.\r\nThis mistake is a commonly seen even in well-known journals like JACS.\r\n \r\n---\r\nThe term 'pat.hkls' in the code above corresponds to:\r\n- Incorrect: index (hkl)\r\n- Correct: index hkl\r\n Parentheses are NOT required.",
"@Higomon I cannot reproduce this error. The following code with the latest pymatgen:\r\n\r\n```python\r\nfrom pymatgen.core import Structure\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\nfe2o3 = Structure.from_file(\"gamma-Fe2O3_fiz15840.cif\")\r\nxrd = XRDCalculator()\r\npat = xrd.get_pattern(fe2o3)\r\nfor hkl, d_hkl in zip(pat.hkls, pat.d_hkls):\r\n print(f\"{hkl[0]['hkl']}: {d_hkl}\")\r\n```\r\n\r\nproduces \r\n\r\n```\r\n(1, 0, -1, 2): 3.685515645479806\r\n(1, 0, -1, 4): 2.702803854252989\r\n(2, -1, -1, 0): 2.519\r\n(0, 0, 0, 6): 2.2953333333333332\r\n(2, -1, -1, 3): 2.2083785301414456\r\n(2, 0, -2, 2): 2.0796505109689116\r\n(2, 0, -2, 4): 1.842757822739903\r\n(2, -1, -1, 6): 1.6966200256087358\r\n(3, -1, -2, 1): 1.6373761063233816\r\n(3, -1, -2, 2): 1.6037256011439684\r\n(1, 0, -1, 8): 1.6013563379925253\r\n(3, -1, -2, 4): 1.4872776183689425\r\n(3, 0, -3, 0): 1.4543453280886673\r\n(3, -1, -2, 5): 1.414875898650733\r\n(2, 0, -2, 8): 1.3514019271264945\r\n(1, 0, -1, 10): 1.3133259704931688\r\n(2, -1, -1, 9): 1.3078237953427998\r\n(3, -1, -2, 7): 1.2638308057577687\r\n(4, -2, -2, 0): 1.2595\r\n(3, 0, -3, 6): 1.2285052151599352\r\n(4, -2, -2, 3): 1.2146149027377362\r\n(4, -1, -3, 1): 1.2054441452139546\r\n(4, -1, -3, 2): 1.191825624400629\r\n(3, -1, -2, 8): 1.190852222477705\r\n(2, 0, -2, 10): 1.164552105283258\r\n(0, 0, 0, 12): 1.1476666666666666\r\n(4, -1, -3, 4): 1.1416302174754414\r\n(4, -1, -3, 5): 1.1078859219073478\r\n(4, -2, -2, 6): 1.1041892650707228\r\n```\r\n\r\nThis is exactly what it should be. The code you have is too complicated for this purpose. \r\n\r\nFor future reference, pls do not quote \"an expert in crystallography\". If the expert wishes to report the error, they should file an issue report with a detailed explanation as to why they think the output is wrong. ",
"Sure, with the code you presented, I can reproduce it the same way. \r\n\r\nHowever, with the following code, it will be as I said.\r\n\r\n### Environment:\r\nI tried to install the latest version through pip and conda, \r\nbut it couldn't be installed due to errors.\r\n\r\n\r\n### My Code\r\n```python\r\nfrom pymatgen.io.cif import CifParser\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\n\r\nparser = CifParser(\"alpha-Fe2O3_fiz15840.cif\") # <-- just changing the file name, it's the same file.\r\nfe2o3 = parser.get_structures()[0]\r\nxrd = XRDCalculator()\r\npat = xrd.get_pattern(fe2o3)\r\nfor hkl, d_hkl in zip(pat.hkls, pat.d_hkls):\r\n print(f\"{hkl[0]['hkl']}: {d_hkl}\")\r\n```\r\n\r\nprint\r\n```\r\n(1, 1, 0): 3.6855156454798053\r\n(1, 1, 2): 2.7028038542529886\r\n(2, 1, 1): 2.5190000000000006\r\n(0, 0, 2): 2.295333333333333\r\n(2, 1, 2): 2.208378530141446\r\n(2, 2, 2): 2.079650510968912\r\n(2, 2, 0): 1.8427578227399026\r\n(2, 1, 3): 1.6966200256087358\r\n(3, 2, 2): 1.6373761063233818\r\n(3, 2, 1): 1.6037256011439682\r\n(1, 0, 3): 1.6013563379925249\r\n(3, 2, 3): 1.4872776183689427\r\n(3, 3, 2): 1.4543453280886673\r\n(3, 1, 3): 1.414875898650733\r\n(2, 2, 4): 1.3514019271264943\r\n(1, 1, 4): 1.3133259704931686\r\n(2, 1, 4): 1.3078237953427996\r\n(3, 2, 4): 1.2638308057577687\r\n(4, 2, 2): 1.2595000000000003\r\n(3, 3, 4): 1.2285052151599352\r\n(4, 2, 3): 1.2146149027377364\r\n(4, 3, 2): 1.2054441452139546\r\n(4, 3, 3): 1.191825624400629\r\n(3, 1, 4): 1.1908522224777047\r\n(2, 0, 4): 1.1645521052832577\r\n(0, 0, 4): 1.1476666666666664\r\n(4, 3, 1): 1.1416302174754414\r\n(4, 3, 4): 1.1078859219073478\r\n(4, 2, 4): 1.104189265070723\r\n```",
"Your python version is probably old. Pls upgrade your python version to at least 3.9 or 3.10 and reinstall pymatgen. 2022.0.x is too long ago and no longer supported. ",
"Even with the latest pymatgen, the incorrect index is still being produced.\r\n\r\nIn the reliable ICDD, the index is indicated by three elements of hkl. \r\nTherefore, if possible, it is desired that pymatgen also align with it. \r\n\r\nIf either the trigonal or the rhombohedral system can represent the crystal,\r\nit is desired to indicate the hkl index of the trigonal system.\r\n\r\n## Environment:\r\n- OS: Ubuntu 20.04.5 LTS\r\n- Python: 3.9.13\r\n- pymatgen: 2023.1.30\r\n\r\n## My Code\r\n```python\r\nimport sys\r\nsys.path.append('/home/Higomen/py_envs/py39/venv/lib/python3.9/site-packages')\r\nfrom pymatgen.io.cif import CifParser\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\n\r\nparser = CifParser(\"alpha-Fe2O3_fiz15840.cif\")\r\nfe2o3 = parser.get_structures()[0]\r\nxrd = XRDCalculator()\r\npat = xrd.get_pattern(fe2o3)\r\nfor hkl, d_hkl in zip(pat.hkls, pat.d_hkls):\r\n print(f\"{hkl[0]['hkl']}: {d_hkl}\")\r\n```\r\n\r\nprint\r\n```\r\n(1, 1, 0): 3.685515645479806\r\n(1, 1, 2): 2.7028038542529895\r\n(2, 1, 1): 2.5190000000000006\r\n(0, 0, 2): 2.295333333333333\r\n(2, 1, 2): 2.208378530141446\r\n(2, 0, 0): 2.079650510968912\r\n(2, 2, 0): 1.842757822739903\r\n(2, 1, 3): 1.6966200256087358\r\n(3, 2, 2): 1.6373761063233818\r\n(3, 2, 1): 1.6037256011439687\r\n(1, 0, 3): 1.6013563379925249\r\n(3, 2, 3): 1.4872776183689427\r\n(3, 0, 1): 1.4543453280886676\r\n(3, 1, 3): 1.4148758986507333\r\n(2, 2, 4): 1.3514019271264948\r\n(1, 1, 4): 1.3133259704931683\r\n(2, 1, 4): 1.3078237953427998\r\n(3, 2, 4): 1.263830805757769\r\n(4, 2, 2): 1.2595000000000003\r\n(3, 3, 4): 1.2285052151599354\r\n(4, 2, 3): 1.2146149027377364\r\n(4, 1, 2): 1.2054441452139548\r\n(4, 3, 3): 1.191825624400629\r\n(3, 1, 4): 1.190852222477705\r\n(2, 0, 4): 1.1645521052832577\r\n(0, 0, 4): 1.1476666666666664\r\n(4, 3, 1): 1.1416302174754416\r\n(4, 3, 4): 1.1078859219073478\r\n(4, 2, 4): 1.104189265070723\r\n```",
"Pymatgen calculates the XRD pattern based on the structure provided. If you want the tribunal structure, you have to provide it with that structure and set the primitive =False option. This has nothing to do with the XRDCalculator itself. ",
"This bug is serious and should be made publicly available. \r\n\r\nDespite its existence, I still view pymatgen as an excellent open-source software.\r\n\r\n\r\n---\r\n## Reference\r\n\r\n\r\n\r\n## Environment:\r\n- OS: Ubuntu 20.04.5 LTS\r\n- Python: 3.9.13\r\n- pymatgen: 2023.1.30\r\n\r\n\r\n## pymatgen.core.structure module \r\n### primitive option *True* | from_file() \r\n```python\r\nfrom pymatgen.core import Structure\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\n\r\nfe2o3 = Structure.from_file(\"alpha-Fe2O3_fiz15840.cif\", primitive=True)\r\nxrd = XRDCalculator()\r\npat = xrd.get_pattern(fe2o3)\r\nfor hkl, d_hkl in zip(pat.hkls, pat.d_hkls):\r\n print(f\"{hkl[0]['hkl']}: {d_hkl}\")\r\n```\r\nprint\r\n```\r\n(1, 1, 0): 3.685515645479806\r\n(1, 1, 2): 2.7028038542529895\r\n(2, 1, 1): 2.5190000000000006\r\n(0, 0, 2): 2.295333333333333\r\n(2, 1, 2): 2.208378530141446\r\n(2, 0, 0): 2.079650510968912\r\n(2, 2, 0): 1.842757822739903\r\n(2, 1, 3): 1.6966200256087358\r\n(3, 2, 2): 1.6373761063233818\r\n(3, 2, 1): 1.6037256011439687\r\n(1, 0, 3): 1.6013563379925249\r\n(3, 2, 3): 1.4872776183689427\r\n(3, 0, 1): 1.4543453280886676\r\n(3, 1, 3): 1.4148758986507333\r\n(2, 2, 4): 1.3514019271264948\r\n(1, 1, 4): 1.3133259704931683\r\n(2, 1, 4): 1.3078237953427998\r\n(3, 2, 4): 1.263830805757769\r\n(4, 2, 2): 1.2595000000000003\r\n(3, 3, 4): 1.2285052151599354\r\n(4, 2, 3): 1.2146149027377364\r\n(4, 1, 2): 1.2054441452139548\r\n(4, 3, 3): 1.191825624400629\r\n(3, 1, 4): 1.190852222477705\r\n(2, 0, 4): 1.1645521052832577\r\n(0, 0, 4): 1.1476666666666664\r\n(4, 3, 1): 1.1416302174754416\r\n(4, 3, 4): 1.1078859219073478\r\n(4, 2, 4): 1.104189265070723\r\n```\r\n\r\n### primitive option *False* | from_file() \r\n``` python\r\nfrom pymatgen.core import Structure\r\nfrom pymatgen.analysis.diffraction.xrd import XRDCalculator\r\n\r\nfe2o3 = Structure.from_file(\"alpha-Fe2O3_fiz15840.cif\", primitive=False)\r\nxrd = XRDCalculator()\r\npat = xrd.get_pattern(fe2o3)\r\nfor hkl, d_hkl in zip(pat.hkls, pat.d_hkls):\r\n print(f\"{hkl[0]['hkl']}: {d_hkl}\")\r\n```\r\n\r\nprint\r\n```\r\n(1, 0, -1, 2): 3.685515645479806\r\n(1, 0, -1, 4): 2.7028038542529895\r\n(2, -1, -1, 0): 2.5190000000000006\r\n(0, 0, 0, 6): 2.2953333333333332\r\n(2, -1, -1, 3): 2.208378530141446\r\n(2, 0, -2, 2): 2.079650510968912\r\n(2, 0, -2, 4): 1.842757822739903\r\n(2, -1, -1, 6): 1.6966200256087358\r\n(3, -1, -2, 1): 1.6373761063233816\r\n(3, -1, -2, 2): 1.6037256011439684\r\n(1, 0, -1, 8): 1.6013563379925253\r\n(3, -1, -2, 4): 1.4872776183689427\r\n(3, 0, -3, 0): 1.4543453280886676\r\n(3, -1, -2, 5): 1.4148758986507333\r\n(2, 0, -2, 8): 1.3514019271264948\r\n(1, 0, -1, 10): 1.3133259704931688\r\n(2, -1, -1, 9): 1.3078237953427998\r\n(3, -1, -2, 7): 1.263830805757769\r\n(4, -2, -2, 0): 1.2595000000000003\r\n(3, 0, -3, 6): 1.2285052151599354\r\n(4, -2, -2, 3): 1.2146149027377364\r\n(4, -1, -3, 1): 1.205444145213955\r\n(4, -1, -3, 2): 1.1918256244006291\r\n(3, -1, -2, 8): 1.190852222477705\r\n(2, 0, -2, 10): 1.164552105283258\r\n(0, 0, 0, 12): 1.1476666666666666\r\n(4, -1, -3, 4): 1.1416302174754416\r\n(4, -1, -3, 5): 1.1078859219073478\r\n(4, -2, -2, 6): 1.104189265070723\r\n```",
"I am not sure what you are referring to. The primitive = False output is the same as the reference output. Eg (102) and (012) are equivalent in the hexagonal setting. There is no bug here. ",
"VESTA imports the same CIF file and outputs hkl, which is shown in the topmost image.\r\nThe output of VESTA is, of course, the same as ICDD. \r\n\r\nWhy is pymatgen different?",
"Pls refer to a crystallography textbook on equivalent miller indices. For example, (100), (010) and (001) are all equivalent in a cubic crystal. There is no specific convention. ",
"In the widely recognized crystallography text by Professor Cullity,\r\nthe index on top of X-ray diffraction peaks do NOT have brackets (refer to Cullity's book or page 366 at the URL). \r\n\r\nIt is important to differentiate between the X-ray diffraction refractive index (hkl index) and the mirror index.\r\n\r\n## Ref.\r\nB. D. Cullity, _Elements of X-ray diffraction_, (1980).\r\nhttp://s1.iran-mavad.com/pdf96/X-RAY%20DIFFRACTION%20Cullity_iran-mavad.com.pdf",
"Feel free to remove the brackets if you wish. I am not replying to the is thread further given that the bug that is claimed doesn't exist. ",
"It is important to differentiate between the X-ray diffraction refractive index (hkl index) and the mirror index.\r\n\r\nThis is not a claim, but simply an observation of an error made as a chemist who loves science.\r\n\r\n"
] | 2023-02-02T03:11:50
| 2023-02-04T14:36:20
|
2023-02-02T15:09:39Z
|
NONE
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# Describe the bug
An XRD expert, as pointed out on Twitter (https://bit.ly/3X4RFfa),
the hkl index is obviously incorrect as shown in the attached image.
We hope for improvement.
# Screenshots
---
# Environment:
- OS: Windows 10 Pro 22H2, build 19045.2486
- Python: 3.9.13
- pymatgen: 2022.0.17
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I_kwDOACgets5da7Je
| 2,827
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Is the Debye-Waller correction in XRDCalculator correct?
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[
"Could you share a reference for the expression in the exponential? I'm not an expert in XRD but can help out if I have a resource to look at.",
"Thank you for your reply.\r\n\r\nI only have the text written in Japanese by Fujio Izumi.\r\n\r\nInstead, I asked ChatGPT4, and the answer is below.\r\nI'm no expert in crystallography, but the following seems to be a reasonable answer.\r\n\r\n\r\n---\r\n## *Isotropic* Debye-Waller factor\r\nIn X-ray diffraction, the Debye-Waller factor (also known as the temperature factor) accounts for the reduction in diffracted intensity due to atomic vibrations. It's typically denoted as B, and it's related to the mean square displacement of atoms, <u²>, via the equation:\r\n\r\n```\r\nB = 8π²<u²>\r\n```\r\n\r\nThis factor is applied to the scattering intensity of X-rays using the formula: \r\n\r\n```\r\nI = I0 exp(-2Bsin²θ/λ²)\r\n```\r\n\r\nwhere:\r\n- I is the scattered intensity\r\n- I0 is the initial intensity (at 0°, or when the temperature effects are ignored)\r\n- B is the Debye-Waller factor\r\n- θ is the scattering angle\r\n- λ is the wavelength of the X-ray\r\n\r\nHere, B assumes isotropic vibrations, i.e., atoms vibrate equally in all directions, which may not be the case in many real-world applications.\r\n\r\n\r\n## *Anisotropic* Debye-Waller factor\r\nThe Debye-Waller factor (B) assumes isotropic vibrations, i.e., that atoms vibrate equally in all directions. However, in many real-world cases, atomic vibrations can be anisotropic, meaning they vary depending on the direction.\r\n\r\nIn cases of anisotropic vibrations, the Debye-Waller factor is replaced by an anisotropic displacement parameter (ADP), also known as anisotropic temperature factor. This anisotropic factor is usually expressed as a symmetric 3x3 tensor (matrix):\r\n\r\n```\r\nU =\r\n| U11 U12 U13 |\r\n| U12 U22 U23 |\r\n| U13 U23 U33 |\r\n```\r\n\r\nEach element of this matrix represents mean-square displacement along specific crystallographic directions.\r\n\r\nWhen this anisotropic displacement parameter is incorporated, the intensity equation becomes:\r\n\r\n```\r\nI = I0 exp[-2π²(h²a²U11 + k²b²U22 + l²c²U33 + 2hkabU12 + 2hlccU13 + 2klbc*U23)]\r\n```\r\n\r\nwhere:\r\n- h, k, l are Miller indices\r\n- a*, b*, c* are reciprocal lattice vectors\r\n\r\n\r\nThis allows for more accurate modeling of atomic vibrations in X-ray diffraction studies, particularly in real-world cases where these vibrations are likely to be anisotropic.\r\n\r\nPlease note that the above form is a general form and may take different forms depending on the specific crystal structure or experimental conditions."
] | 2023-02-02T05:19:42
| 2023-06-03T13:52:36
|
NONE
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# Describe the bug
I am not an expert in XRD.
An XRD expert on Twitter(https://bit.ly/3jhhoDi) pointed out that
rough X-ray diffraction intensity calculations ignoring Debye-Waller factors are not valid.
Therefore, I tried simulating by changing the Debye-Waller factors as shown in the attached figure. Even when I raised the Debye-Waller factor of iron, the intensity seems too high on the high-angle side compared to the VESTA results.
Is the target formula (line 243) of xrd.py correct?
By referring to the expert's book on XRD, I modified it as follows and got reasonable results.
```
pi2 = np.pi ** 2
243: dw_correction = np.exp(-2 * pi2 * ndwfactors * s2)
```
I would like the expert to verify this.
## pymatgen.analysis.diffraction.xrd module
xrd.py
```
243: dw_correction = np.exp(-dwfactors * s2)
```
# Environment
- OS: Windows 10 Pro 22H2, build 19045.2486
- Python: 3.9.13
- pymatgen: 2022.0.17
# CIF file
[gamma-Fe2O3_fiz15840.zip](https://github.com/materialsproject/pymatgen/files/10564905/gamma-Fe2O3_fiz15840.zip)
---
# Code
```
from os.path import dirname, basename
import pandas as pd
import numpy as np
from scipy.special import wofz
from pymatgen.io.cif import CifParser
from pymatgen.analysis.diffraction.xrd import XRDCalculator
# setting --------------------------------
x_str = 10 # /deg (start of X range)
x_end = 120 # /deg (end of X range)
# Debye-Waller factor
DWF = {"Fe": 0.15, "O": 0.6}
# ----------------------------------------
def voigt(x, amp, pos, fwhm, shape):
"""
x: x data
amp: amplitude(peak height)
pos: peak center
fwhm: Full Width at Half Maximum
shape:
"""
tmp = 1 / wofz(np.zeros((len(x))) + 1j * np.sqrt(np.log(2.0)) * shape).real
tmp = (
tmp
* amp
* wofz(
2 * np.sqrt(np.log(2.0)) * (x - pos) / fwhm
+ 1j * np.sqrt(np.log(2.0)) * shape
).real
)
return tmp
def sum_voigt_peaks(pat, x_str, x_end):
x = np.arange(x_str, x_end, 0.01)
calc_y = np.zeros(len(x))
N = len(pat.x)
fwhm = 0.06
shape = 0.5
for i in range(N):
pos = pat.x[i]
amp = pat.y[i]
calc_y += voigt(x, amp, pos, fwhm, shape)
return x, calc_y
def output_hklTable(pat, f):
d_space = pat.d_hkls
_hkl = pat.hkls
hkl_index = [i[0]["hkl"] for i in _hkl]
m = [i[0]["multiplicity"] for i in _hkl]
dict = {
"hkl": hkl_index,
"multiplicity": m,
"d": d_space,
"2theta": pat.x,
"Int": pat.y,
}
df = pd.DataFrame(dict)
df.index = df.index + 1
d_name = dirname(f)
f_name = basename(f).replace(".cif", ".csv")
df.to_csv(
d_name + "\\hkl_" + f_name,
encoding="utf-8",
index=True,
)
def output_XRDpattern(pat, f):
x, y = sum_voigt_peaks(pat, x_str, x_end)
dict = {"2theta": x, "Int": y}
df = pd.DataFrame(dict)
d_name = dirname(f)
f_name = basename(f).replace(".cif", ".csv")
df.to_csv(
d_name + "\\prof_" + f_name,
encoding="utf-8",
index=False,
)
def main():
f = r"D:\gamma-Fe2O3_fiz15840.cif"
parser = CifParser(f)
structure = parser.get_structures()[0]
lat = XRDCalculator(
wavelength=1.54056,
debye_waller_factors=DWF,
)
pat = lat.get_pattern(structure, scaled=True, two_theta_range=(x_str, x_end))
output_hklTable(pat, f)
output_XRDpattern(pat, f)
if __name__ == "__main__":
main()
```
---
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[
"Thanks for reporting this. I just pushed a fix. For some reason, jQuery disappeared from current pymatgen docs. @janosh is this related to the update of the docs you did recently?",
"@shyuep Don't think so but maybe I missed something? Last time I updated the docs was for the [v2023.1.9 release](https://github.com/materialsproject/pymatgen/releases/tag/v2023.1.9) (https://github.com/materialsproject/pymatgen/pull/2798). Lots of changed lines but I didn't spot a `jquery` removal in there.",
"Thank you for the quick fix. For me, the search bar is working again!"
] | 2023-02-02T15:07:08
| 2023-02-02T16:05:12
|
2023-02-02T15:16:48Z
|
NONE
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When I go to the pymatgen website(https://pymatgen.org/) and type a search term in the search bar, the search never finishes.
This occurs under firefox version: Mozilla Firefox version mint-001 - 1.0 109.0.1(64-bit)
as well as under Chromium version: 109.0.5414.119 (Official Build) for Linux Mint (64-bit)
|
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I_kwDOACgets5dh83k
| 2,829
|
__init__() got an unexpected keyword argument
|
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[
"As the error states, `inter_cutoff` is not a variable of the `CrystalNN` class. You can see the variable names here: [link](https://github.com/materialsproject/pymatgen/blob/v2023.3.10/pymatgen/analysis/local_env.py#L3772). You want to use `distance_cutoffs` instead which has to be a tuple with 2 values.\r\n\r\nI think this issue can be closed.",
"Thanks @peterschindler for answering this."
] | 2023-02-03T04:10:00
| 2023-05-19T20:18:47
|
2023-05-19T20:18:37Z
|
NONE
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Hello everyone, I am a freshman in pymatgen. Recently, a colleague share with me the following script to generate all tetrahedral sites in a bcc unit cell
```py
from pymatgen.core import Structure
from pymatgen.core import Lattice
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pymatgen.analysis.local_env import CrystalNN
bcc = Structure.from_spacegroup("Im-3m", Lattice.cubic(2.8), ["Fe"],
[[0, 0, 0]])
##-- Get the tetrahedral interstitial sites
nn = CrystalNN(inter_cutoff=2.0)
tetrahedral_sites = nn.get_nn_sites(bcc, target_site_type="Tetrahedral")
##--- Get all possible interstitial configurations
for site in tetrahedral_sites:
bcc.make_supercell(3)
for i, frac_coords in enumerate(site.frac_coords):
bcc.append("Fe", frac_coords, coords_are_cartesian=False)
```
However, I am, getting the following error:
```py
Traceback (most recent call last):
File "/home/jucego333/newstructure/new1.py", line 13, in <module>
nn = CrystalNN(inter_cutoff=2.0)
TypeError: __init__() got an unexpected keyword argument 'inter_cutoff'
```
I have followed each step concerning the installation of pytmagen in linux.
Can anybody give a hand with this?
|
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PR_kwDOACgets5JP1Im
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Avoid adjusting input entries in mixing schemes.
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[
"\n[](https://coveralls.io/builds/56608789)\n\nCoverage: 74.3% (-5.2%) from 79.463% when pulling **7606c36e7b268a9de33ba0531ffb7693a03f094f on peikai:EntriesCopy** into **c6f9bba0cf6d3040d630cf083da2d1963a658e6c on materialsproject:master**.\n",
"The usage of process_entries() method needs attention. It only returns the entries that have been processed, not always the complete set of adjusted entries. If input entries have contained energy adjustments, they would not be processed again, and even would not be shown in the results that are returned (if process_entries(clean=False)). \r\n\r\nIn the case, processed_entryList = compatibility.process_entries(entryList, clean=True), entryList will be changed as well.\r\nIn the case, processed_entryList = compatibility.process_entries(entryList, clean=False), processed_entryList may not have a complete set of entries, if there are some entries containing energy_adjustements in entryList.\r\n\r\nI would close this PR, to avoid changing this usage.",
"This PR is renewed in #2841."
] | 2023-02-04T00:59:07
| 2023-02-12T05:37:40
|
2023-02-04T04:14:23Z
|
CONTRIBUTOR
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Here to submit changes to avoid change input entries in place.
In both of GGA/GGA+U and GGA/GGA+U/R2SCAN mixing processes, the methods below not only return adjusted entries, but also change input entries in place. Is it necessary? I think this may cause bugs in programming.
MaterialsProjectDFTMixingScheme.process_entries()
entries.compatibility.process_entries()
Thanks!
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Avoid adjusting input entries in mixing schemes.
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[
"I've run into the same problem. I definitely agree that API could be improved. But it would be a substantial change, so not something to do on a whim. I think any modifications would need the green light from @shyuep, @mkhorton and @rkingsbury.",
"I agree, the process_entries() still works if people use with awareness, i.e., keeping clean=True and aware of entries would be changed in place when building phase diagrams. I've noticed there is a warning in up-to-date documents. ",
"I agree the API can be improved. I believe the current behavior of `process_entries` was intended to emulate the historical behavior (see #1826 when we updated the Compatibility API) - i.e., it both processes entries in place and returns the processed entries. This is partly due to the fact that the energy corrections are carried as attributes to the entries, so in some sense it makes sense to process them in-place. Note, however, that any entry which raises a `CompatibilityError` is _not_ returned by `process_entries`. This was again trying to emulate historical behavior, where any \"incompatible\" entries would be excluded from the returned list.\r\n\r\n> In the case that running processed_entryList = compatibility.process_entries(entryList, clean=False), it only returns the entries that have been processed, not always the complete set of adjusted entries.\r\n\r\nI was not aware that this was the case, and it's not intended behavior. The only thing `clean` is supposed to do is to control whether or not the `energy_adjustment` attribute of an entry is cleared before processing or not.\r\n\r\nIn any case, I'm not opposed to changes that reduce potential for confusion or errors, and I think they could be made with relatively little effort (although we'd need to coordinate them with Builder logic in `emmet` `ThermoBuilder` to make sure). I'd be happy to comment on PR with proposed changes.\r\n",
"> In any case, I'm not opposed to changes that reduce potential for confusion or errors, and I think they could be made with relatively little effort\r\n\r\nPerfect! @peikai If you want to submit a PR, I think you'll get plenty of feedback. Maybe a good first step would be to always return the full list of passed entries, regardless of whether they were corrected or not. And might be good to have an `inplace` flag. Should it default to `False` to keep with current behavior or to `True` meaning always return copies and leave originals untouched? I'm leaning towards the former for speed.",
"> Maybe a good first step would be to always return the full list of passed entries, regardless of whether they were corrected or not. \r\n\r\nSo this change would likely cause a lot of problems. Part of the core idea behind `process_entries` is that it _only_ returns entries that are \"valid\" within a particular `Compatibility` scheme. This is essential for properly constructing phase diagrams and things. For example, if you pass a collection of LDA, GGA, and GGA+U entries to `MaterialsProjectCompatibility2020` and run `process_entries` on it, the class needs to make sure the LDA entries are discarded. So I think its important, as a design principle, that `process_entries` only return the right entries. Technically speaking, this means entries that don't raise a `CompatibilityError` when passed to `get_adjustments` .\r\n\r\nThat said, to extend the above example, _any GGA or GGA+U_ entry should be returned, even if its correction is zero. That should be the current behavior, but if its not we should investigate.\r\n\r\n> And might be good to have an `inplace` flag. Should it default to `False` to keep with current behavior or to `True` meaning always return copies and leave originals untouched? I'm leaning towards the former for speed.\r\n\r\nI like this idea\r\n",
"@peikai In general, there should be only one valid entry list during use. I am fine if the code is changed to avoid changing the original entry list. But the general idea is that you should not be using the original entry list after processing in the first place. I am not clear of the use case where both the original and processed entry list are both used in an analysis.",
"> So this change would likely cause a lot of problems. Part of the core idea behind process_entries is that it only returns entries that are \"valid\" within a particular Compatibility scheme.\r\n\r\nAh, I was not aware of this. I thought that is left to the user to handle correctly. Good to know.",
"> > In the case that running processed_entryList = compatibility.process_entries(entryList, clean=False), it only returns the entries that have been processed, not always the complete set of adjusted entries.\r\n> \r\n> I was not aware that this was the case, and it's not intended behavior. The only thing `clean` is supposed to do is to control whether or not the `energy_adjustment` attribute of an entry is cleared before processing or not.\r\n\r\n@rkingsbury, because some entries might have already contained adjusted energy. If `clean=False`, these entries with correct adjustment would not be processed again by the method, thereby missing in processed_entryList, then missing in subsequent phase diagrams built with them. This may happen in both of `compatibility.process_entries()` and `MaterialsProjectDFTMixingScheme().process_entries()`.\r\n\r\n@shyuep, I intended to generate and compare the phase diagrams built with GGA/GGA+U (Mixed) scheme and GGA/GGA+U/R2SCAN (Mixed) scheme in one file. Then I found the input entries are changed in place that could not be reused, and processed entries could possibly not a complete set of entries having adjusted energy.\r\n\r\nThanks all.",
"> @rkingsbury, because some entries might have already contained adjusted energy. If `clean=False`, these entries with correct adjustment would not be processed again by the method, thereby missing in processed_entryList, then missing in subsequent phase diagrams built with them. This may happen in both of `compatibility.process_entries()` and `MaterialsProjectDFTMixingScheme().process_entries()`.\r\n\r\nHmm, I see. I agree those entries would not be processed again, but they really should be passed through to the returned list. If not, I think that is a bug that we should fix. Thanks for investigating; can you provide a minimal example?\r\n\r\n> @shyuep, I intended to generate and compare the phase diagrams built with GGA/GGA+U (Mixed) scheme and GGA/GGA+U/R2SCAN (Mixed) scheme in one file. Then I found the input entries are changed in place that could not be reused, and processed entries could possibly not a complete set of entries having adjusted energy.\r\n\r\nYes, for this use case you should maintain two separate copies, because the GGA/GGA+U entries will require different corrections in the regular vs. the R2SCAN mixing scheme. Note that you may have to use `.deepcopy` to ensure your two lists aren't actually pointing to the same underlying entries.",
"@rkingsbury, I read source codes again. The `process_entries()` method returns all entries having (correct) adjusted energy indeed. I misinterpreted the effect of `pass` command of it.\r\n\r\nJust ignore the second fixing request below.\r\n\r\n> In the case that running **processed_entryList = compatibility.process_entries(entryList, clean=False)**, it only returns the entries that have been processed, not always the complete set of adjusted entries. If input entries have contained energy adjustments, they would not be processed again, and even would not be shown in the results that are returned, which might cause missing entries in phase diagrams, when using them to create phase diagrams.\r\n",
"> > And might be good to have an `inplace` flag. Should it default to `False` to keep with current behavior or to `True` meaning always return copies and leave originals untouched? I'm leaning towards the former for speed.\r\n> \r\n> I like this idea\r\n\r\nThanks, @janosh @rkingsbury. A new PR #2841 has been opened to add the inplace flag.",
"The PR has been merged."
] | 2023-02-04T05:06:26
| 2023-02-13T06:39:13
|
2023-02-13T06:39:12Z
|
CONTRIBUTOR
|
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The usage of process_entries() method needs attention.
In the case that running **processed_entryList = compatibility.process_entries(entryList, clean=True),** entryList will be changed as well. The method not only returns adjusted entries, but also change input entries in place. Is it necessary? I think this may cause bugs in programming and affect subsequent usage of input entries.
In the case that running **processed_entryList = compatibility.process_entries(entryList, clean=False)**, it only returns the entries that have been processed, not always the complete set of adjusted entries. If input entries have contained energy adjustments, they would not be processed again, and even would not be shown in the results that are returned, which might cause missing entries in phase diagrams, when using them to create phase diagrams.
I've ever created a PR, but then closed it to avoid changing the usage style.
https://github.com/materialsproject/pymatgen/pull/2830
|
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| 1,571,667,129
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I_kwDOACgets5drby5
| 2,833
|
CifWriter writes standard-incompliant chemical formulae and cell formula
|
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[
"Thanks for reporting this. But I would like to understand what is the actual implication of this beyond \"non-standards\" compliance. Does it affect the use of the CIF in any software out there?\r\n\r\nI am happy for someone to write a PR to fix this. But unless there is a pressing compatibility problem, I don't foresee being able to spend time to work on this.",
"Thank you for your reply.\r\nSo far I have no software problems related to elemental order of `_chemical_formula_sum` and to discrepancy among `_cell_formula_units_Z` and `_chemical_formula_sum`/`_chemical_formula_structural`, but the latter is, I believe, incorrect."
] | 2023-02-05T23:47:24
| 2023-02-14T06:29:05
|
CONTRIBUTOR
|
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**Describe the bug**
A clear and concise description of what the bug is.
Chemical formulae-related items written by `CifWriter` do not comply with the specification.
**To Reproduce**
Steps to reproduce the behavior:
Run the following script (POSCAR of CH₃NH₃PbI₃ from <https://materialsproject.org/materials/mp-1194604/>):
```python
#!/usr/bin/env python3
import pymatgen.core
import pymatgen.io.cif
import pymatgen.io.vasp
def main():
print("#", pymatgen.core.__version__)
s = pymatgen.io.vasp.Poscar.from_string(
"""H24 Pb4 C4 I12 N4
1.0
8.6500830000000004 0.0000000000000000 0.0000000000000005
0.0000000000000014 8.9913910000000001 0.0000000000000006
0.0000000000000000 0.0000000000000000 13.1226540000000007
H Pb C I N
24 4 4 12 4
direct
0.3037930000000000 0.4412980000000000 0.2500000000000000 H+
0.1962070000000000 0.9412980000000000 0.2500000000000000 H+
0.6962070000000000 0.5587020000000000 0.7500000000000000 H+
0.8037930000000000 0.0587020000000000 0.7500000000000000 H+
0.4531830000000000 0.3445690000000000 0.1812530000000001 H+
0.0468170000000000 0.8445690000000000 0.3187469999999999 H+
0.5468170000000000 0.6554310000000000 0.6812530000000001 H+
0.9531830000000000 0.1554310000000000 0.8187469999999999 H+
0.5468170000000000 0.6554310000000000 0.8187469999999999 H+
0.9531830000000000 0.1554310000000000 0.6812530000000001 H+
0.4531830000000000 0.3445690000000000 0.3187469999999999 H+
0.0468170000000000 0.8445690000000000 0.1812530000000001 H+
0.4961490000000000 0.6095140000000000 0.1858000000000000 H+
0.0038510000000000 0.1095139999999999 0.3141999999999999 H+
0.5038510000000000 0.3904860000000000 0.6858000000000001 H+
0.9961490000000000 0.8904860000000000 0.8141999999999999 H+
0.5038510000000000 0.3904860000000000 0.8141999999999999 H+
0.9961490000000000 0.8904860000000000 0.6858000000000001 H+
0.4961490000000000 0.6095140000000000 0.3141999999999999 H+
0.0038510000000000 0.1095139999999999 0.1858000000000000 H+
0.3604920000000000 0.4782410000000000 0.7500000000000000 H+
0.1395080000000000 0.9782410000000000 0.7500000000000000 H+
0.6395080000000000 0.5217590000000000 0.2500000000000000 H+
0.8604920000000000 0.0217590000000000 0.2500000000000000 H+
0.5000000000000000 0.0000000000000000 0.0000000000000000 Pb2+
0.0000000000000000 0.5000000000000000 0.5000000000000000 Pb2+
0.5000000000000000 0.0000000000000000 0.5000000000000000 Pb2+
0.0000000000000000 0.5000000000000000 0.0000000000000000 Pb2+
0.4259970000000000 0.4084900000000000 0.2500000000000000 C2-
0.0740030000000000 0.9084900000000000 0.2500000000000000 C2-
0.5740030000000000 0.5915100000000000 0.7500000000000000 C2-
0.9259970000000000 0.0915100000000000 0.7500000000000000 C2-
0.5692760000000000 0.9730720000000000 0.2500000000000000 I-
0.9307240000000000 0.4730720000000002 0.2500000000000000 I-
0.4307240000000000 0.0269280000000000 0.7500000000000000 I-
0.0692759999999999 0.5269280000000000 0.7500000000000000 I-
0.3263700000000000 0.6794470000000000 0.0175740000000000 I-
0.1736300000000000 0.1794470000000001 0.4824260000000000 I-
0.6736300000000000 0.3205530000000000 0.5175740000000000 I-
0.8263700000000000 0.8205530000000000 0.9824260000000000 I-
0.6736300000000000 0.3205530000000000 0.9824260000000000 I-
0.8263700000000000 0.8205530000000000 0.5175740000000000 I-
0.3263700000000000 0.6794470000000000 0.4824260000000000 I-
0.1736300000000000 0.1794470000000001 0.0175740000000000 I-
0.4788280000000000 0.4539980000000000 0.7500000000000000 N3-
0.0211720000000000 0.9539980000000000 0.7500000000000000 N3-
0.5211720000000000 0.5460020000000000 0.2500000000000000 N3-
0.9788280000000000 0.0460020000000000 0.2500000000000000 N3-
"""
)
w = pymatgen.io.cif.CifWriter(s.structure)
print(w)
if __name__ == "__main__":
main()
```
Output is as follows:
```
# 2022.11.7
# generated using pymatgen
data_H6PbCI3N
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 8.65008300
_cell_length_b 8.99139100
_cell_length_c 13.12265400
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural H6PbCI3N
_chemical_formula_sum 'H24 Pb4 C4 I12 N4'
_cell_volume 1020.63119132
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
H H0 1 0.30379300 0.44129800 0.25000000 1
H H1 1 0.19620700 0.94129800 0.25000000 1
H H2 1 0.69620700 0.55870200 0.75000000 1
H H3 1 0.80379300 0.05870200 0.75000000 1
H H4 1 0.45318300 0.34456900 0.18125300 1
H H5 1 0.04681700 0.84456900 0.31874700 1
H H6 1 0.54681700 0.65543100 0.68125300 1
H H7 1 0.95318300 0.15543100 0.81874700 1
H H8 1 0.54681700 0.65543100 0.81874700 1
H H9 1 0.95318300 0.15543100 0.68125300 1
H H10 1 0.45318300 0.34456900 0.31874700 1
H H11 1 0.04681700 0.84456900 0.18125300 1
H H12 1 0.49614900 0.60951400 0.18580000 1
H H13 1 0.00385100 0.10951400 0.31420000 1
H H14 1 0.50385100 0.39048600 0.68580000 1
H H15 1 0.99614900 0.89048600 0.81420000 1
H H16 1 0.50385100 0.39048600 0.81420000 1
H H17 1 0.99614900 0.89048600 0.68580000 1
H H18 1 0.49614900 0.60951400 0.31420000 1
H H19 1 0.00385100 0.10951400 0.18580000 1
H H20 1 0.36049200 0.47824100 0.75000000 1
H H21 1 0.13950800 0.97824100 0.75000000 1
H H22 1 0.63950800 0.52175900 0.25000000 1
H H23 1 0.86049200 0.02175900 0.25000000 1
Pb Pb24 1 0.50000000 0.00000000 0.00000000 1
Pb Pb25 1 0.00000000 0.50000000 0.50000000 1
Pb Pb26 1 0.50000000 0.00000000 0.50000000 1
Pb Pb27 1 0.00000000 0.50000000 0.00000000 1
C C28 1 0.42599700 0.40849000 0.25000000 1
C C29 1 0.07400300 0.90849000 0.25000000 1
C C30 1 0.57400300 0.59151000 0.75000000 1
C C31 1 0.92599700 0.09151000 0.75000000 1
I I32 1 0.56927600 0.97307200 0.25000000 1
I I33 1 0.93072400 0.47307200 0.25000000 1
I I34 1 0.43072400 0.02692800 0.75000000 1
I I35 1 0.06927600 0.52692800 0.75000000 1
I I36 1 0.32637000 0.67944700 0.01757400 1
I I37 1 0.17363000 0.17944700 0.48242600 1
I I38 1 0.67363000 0.32055300 0.51757400 1
I I39 1 0.82637000 0.82055300 0.98242600 1
I I40 1 0.67363000 0.32055300 0.98242600 1
I I41 1 0.82637000 0.82055300 0.51757400 1
I I42 1 0.32637000 0.67944700 0.48242600 1
I I43 1 0.17363000 0.17944700 0.01757400 1
N N44 1 0.47882800 0.45399800 0.75000000 1
N N45 1 0.02117200 0.95399800 0.75000000 1
N N46 1 0.52117200 0.54600200 0.25000000 1
N N47 1 0.97882800 0.04600200 0.25000000 1
```
Focus on the lines
```
_chemical_formula_structural H6PbCI3N
_chemical_formula_sum 'H24 Pb4 C4 I12 N4'
_cell_formula_units_Z 4
```
**Expected behavior**
A clear and concise description of what you expected to happen.
The lines must be
```
_chemical_formula_structural '(C H3 N H3)4 Pb4 I12'
_chemical_formula_sum 'C4 H24 I12 N4 Pb4'
_cell_formula_units_Z 1
```
or
```
_chemical_formula_structural '(C H3 N H3)1 Pb I3'
_chemical_formula_sum 'C1 H6 I3 N1 Pb1'
_cell_formula_units_Z 4
```
- [ ] The elemental order of `_chemical_formula_sum` is wrong
- [ ] IIUC the numbers of elements in `_chemical_formula_structural` and `_chemical_formula_sum` must be the same; the above `_chemical_formula_structural`’s are for illustration, and it would be difficult to write them as such, though
-----
From [\_cell\_formula\_units\_Z](https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Icell_formula_units_Z.html):
> The number of the formula units in the unit cell as specified
> by _chemical_formula_structural, _chemical_formula_moiety or
> _chemical_formula_sum.
From [\_chemical\_formula\_structural](https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ichemical_formula_structural.html):
> See the \_chemical\_formula\_[] category description for the rules
> for writing chemical formulae for inorganics, organometallics,
> metal complexes etc., in which bonded groups are preserved
> as discrete entities within parentheses, with post-multipliers
> as required. The order of the elements should give as much
> information as possible about the chemical structure.
> Parentheses may be used and nested as required. This formula
> should correspond to the structure as actually reported,
> i.e. trace elements not included in atom-type and atom-site
> lists should not be included in this formula (see also
> \_chemical\_formula_analytical).
From [\_chemical\_formula\_sum](https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Ichemical_formula_sum.html):
> See the \_chemical\_formula\_[] category description for the rules
> for writing chemical formulae in which all discrete bonded
> residues and ions are summed over the constituent elements,
> following the ordering given in general rule (5) in the
> \_chemical\_formula\_[] category description. Parentheses are not
> normally used.
From <https://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Cchemical_formula.html>
> (5) Unless the elements are ordered in a manner that corresponds
> to their chemical structure, as in
> \_chemical\_formula\_structural, the order of the elements within
> any group or moiety depends on whether carbon is present or
> not. **If carbon is present, the order should be: C, then H,
> then the other elements in alphabetical order of their
> symbol. If carbon is not present, the elements are listed
> purely in alphabetical order of their symbol.** This is the
> 'Hill' system used by Chemical Abstracts. This ordering is
> used in \_chemical\_formula\_moiety and \_chemical\_formula\_sum.
(emphasis mine)
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Environment (please supply relevant versions and platform info):**
- OS: (e.g. Mac, Windows, Linux): EndeavourOS
- Version (e.g. 2022.11.17): 2022.11.7
**Additional context**
Add any other context about the problem here.
|
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| 1,573,482,531
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PR_kwDOACgets5JY0Lb
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[pre-commit.ci] pre-commit autoupdate
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[] | 2023-02-07T00:13:11
| 2023-02-07T00:15:35
|
2023-02-07T00:15:28Z
|
CONTRIBUTOR
|
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<!--pre-commit.ci start-->
updates:
- [github.com/MarcoGorelli/cython-lint: v0.11.1 → v0.12.4](https://github.com/MarcoGorelli/cython-lint/compare/v0.11.1...v0.12.4)
<!--pre-commit.ci end-->
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PR_kwDOACgets5JdmFp
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Add keyword `check_occu: bool = True` to `CifParser.get_structures()`
|
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[
"Could you move the test into the existing [`pymatgen/io/tests/test_cif.py`](https://github.com/materialsproject/pymatgen/blob/master/pymatgen/io/tests/test_cif.py)? And add the new kwarg to the doc string? Would be great to have a sentence in there explaining when this might be useful.",
"Hello @janosh, My most resent pull request has been sitting for a while and not running any tests. It says it needs maintainer approval. Regarding your doc string comment. There is an explanation in the get_structures doc string. There isn't one in the _get_structure doc string as none of its other arguments were explained there either. ",
"@janosh, I've addressed the changes you wanted. It says it needs approval before running the tests again. Do you know why sometimes it runs the tests automatically and sometimes it doesn't? ",
"> @janosh, I've addressed the changes you wanted.\r\n\r\nThanks!\r\n\r\n> Do you know why sometimes it runs the tests automatically and sometimes it doesn't?\r\n\r\nGitHub doesn't auto trigger workflows on PRs from 1st time contributors as a security measure.",
"@janosh I'm not sure what happened with my most recent commit. It failed in the linting step and is giving over 450 errors, mostly in files I've not worked with at all. Do you have any suggestions on the best way to proceed with this?",
"If you merge the `master` branch into your PR, the errors should disappear.",
"@janosh This is waiting for approval again. I think the issues have been resolved.",
"@janosh waiting for approval to run the tests.",
"hello @janosh, the pull passes most of the tests but fails two of them. In both the issue is that it can't find the file. I emulated the syntax used in the other test functions so I am not sure what is going wrong. In both fails I believe the file directory is wrong. I'm unsure why its looking in different directories for those tests considering it worked for the majority of them.",
"It fails because you did not commit your `Skip_checks_test.cif` file to the repo. Naturally, that file does not exist on Github.....",
"@janosh Okay looks like this is ready to go.",
"@janosh looks like it is waiting for approval again.",
"## [Codecov](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) Report\nPatch coverage: **`86.66%`** and project coverage change: **`-0.58%`** :warning:\n> Comparison is base [(`ac14c88`)](https://app.codecov.io/gh/materialsproject/pymatgen/commit/ac14c8840c5da76e4b69ef0cd0660018f7a551e8?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.63% compared to head [(`6c32804`)](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) 74.06%.\n\n<details><summary>Additional details and impacted files</summary>\n\n\n```diff\n@@ Coverage Diff @@\n## master #2836 +/- ##\n==========================================\n- Coverage 74.63% 74.06% -0.58% \n==========================================\n Files 230 230 \n Lines 69403 69426 +23 \n Branches 16161 16169 +8 \n==========================================\n- Hits 51802 51422 -380 \n- Misses 14528 14959 +431 \n+ Partials 3073 3045 -28 \n```\n\n\n| [Files Changed](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject) | Coverage Δ | |\n|---|---|---|\n| [pymatgen/io/cif.py](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject#diff-cHltYXRnZW4vaW8vY2lmLnB5) | `92.01% <86.66%> (-0.15%)` | :arrow_down: |\n\n... and [7 files with indirect coverage changes](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject)\n\n\n</details>\n\n[:umbrella: View full report in Codecov by Sentry](https://app.codecov.io/gh/materialsproject/pymatgen/pull/2836?src=pr&el=continue&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject). \n:loudspeaker: Have feedback on the report? [Share it here](https://about.codecov.io/codecov-pr-comment-feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsproject).\n",
"@janosh I believe everything is working as it should now. I added the description you wanted as well. "
] | 2023-02-07T19:32:20
| 2023-08-22T01:34:16
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2023-08-22T01:34:16Z
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CONTRIBUTOR
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If `check_occu=False`, site occupancy will not be checked, allowing unphysical occupancy != 1. Useful for experimental results in which occupancy was allowed to refine to unphysical values. Warning: unphysical site occupancies are incompatible with many pymatgen features.
|
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I_kwDOACgets5d9nJb
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|
Inconsistent behavior for calculating charge
|
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[
"A Structure's charge can be different from the sum of the oxidation states (e.g., if you are doing electron or hole doping of the structure).\r\nIn this case, the reason is that the API sets the charge. I am not sure why this is the case. @munrojm can you check? As far as I know, MP does not do non-neutral structure computations.\r\nI added a method called `unset_charge` to structure. This sets the charge to None, which ensures that the correct method is called to compute the charge on the fly. I also added a warning when the structure charge is different from the formal sum of oxidation states.",
"Sorry, a little confused here. Why should the charge be 0.1 in this case? I can confirm that the API simply pulls the charge in directly from the DB and does not change it. As far as I understand, you are correct and we do not do any non-neutral calculations.",
"He did substitutions. If you sum the oxidation states of the substituted structure, it is 0.1. That is the default behavior if the charge is not set. I am not sure why the charge is set in the API. ",
"Gotcha, I understand now. Looks like the serialized `Structure` objects within the core materials collection have the charge explicitly as zero. Not sure at what point in the pipeline (parsing or running builders) this happens, but it is being set somewhere. We can change this if it conflicts with the expected use in pymatgen and is of big concern."
] | 2023-02-08T16:26:47
| 2023-02-11T01:55:13
|
2023-02-08T16:53:57Z
|
NONE
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**Describe the bug**
The structure.charge function sometimes does not print the right charge
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.ext.matproj import MPRester
with MPRester("kVbufThFdGlpePa0IbqjnimfyIHc5Ng2") as m:
# Structure for material id
str_test = m.get_structure_by_material_id("mp-1138") # learn it online to see what it does
str_test.add_oxidation_state_by_element({'Li':1,'F':-1})
rp_dict2 = {'Li+':{'Li+':0.6,'Mn3+':0.2,'Ti4+':0.2},'F-':{'O2-':0.9,'F-':0.1}}
str3 = str_test.copy()
str3.replace_species(rp_dict2)
print(str3.charge)
```
The charge should be 0.1 but I get 0 as output
|
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I_kwDOACgets5d_Hdn
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|
Primitive matrix for trigonal structure has negative determinant
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[
"I think a simple solution would be to multiply the lattice matrix and vectors by -1?"
] | 2023-02-08T21:31:16
| 2023-02-12T15:38:07
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2023-02-12T15:38:07Z
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CONTRIBUTOR
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For certain structures, pymatgen's `SpacegroupAnalyzer.get_conventional_to_primitive_transformation_matrix()` is returning a matrix with a negative determinant, which is causing issues when trying to use this transformation matrix in codes like `phonopy`. I know that the symmetry elements for trigonal space groups are especially tricky, and I see that there have been multiple issues in the past with trigonal or hexagonal rhombohedral cells.
For example, As in the R-3m spacegroup (166) with mpid mp-11.
```
import numpy as np
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
# conventional poscar downloaded directly from MP
structure = Structure.from_file("POSCAR")
sga = SpacegroupAnalyzer(structure)
conv_to_prim_trans_matrix = sga.get_conventional_to_primitive_transformation_matrix()
print(conv_to_prim_trans_matrix)
array([[-0.33333333, 0.33333333, 0.33333333],
[ 0.66666667, 0.33333333, 0.33333333],
[-0.33333333, -0.66666667, 0.33333333]])
trans_matrix_det = np.linalg.det(conv_to_prim_trans_matrix)
print(trans_matrix_det)
-0.3333333333333333
```
`Phonopy/spglib` are able to find a primitive matrix with a positive determinant.
Any ideas how to fix this?
|
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I_kwDOACgets5d_NVL
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|
StressTest.test_properties uses equality for floating point comparison
|
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[] | 2023-02-08T21:55:11
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2023-02-13T17:40:03Z
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CONTRIBUTOR
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**Describe the bug**
StressTest.test_properties in analysis/elasticity/tests/test_stress.py uses equality '==' to test mean_stress values at https://github.com/materialsproject/pymatgen/blob/134722b20ca24e6ff3d01aaa194fb51e296966b6/pymatgen/analysis/elasticity/tests/test_stress.py#L21 . This inevitably fails since the numbers are floating point, see e.g. https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=hurd-i386&ver=2022.11.7%2Bdfsg1-7&stamp=1675882439&raw=0
Floating point comparison needs to be used instead, such as `isclose()`, or more likely `pytest.approx()` which is used in the very next line.
**To Reproduce**
Steps to reproduce the behavior:
1. `pytest-3 -v -k test_properties pymatgen/analysis/elasticity/tests/test_stress.py` on affected systems (e.g. hurd-i386)
2. See error
**Expected behavior**
Unit tests should pass.
**Screenshots**
https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=hurd-i386&ver=2022.11.7%2Bdfsg1-7&stamp=1675882439&raw=0
```
=================================== FAILURES ===================================
__________________________ StressTest.test_properties __________________________
self = <test_stress.StressTest testMethod=test_properties>
def test_properties(self):
# mean_stress
> assert self.rand_stress.mean_stress == 1.0 / 3.0 * (
self.rand_stress[0, 0] + self.rand_stress[1, 1] + self.rand_stress[2, 2]
)
E assert 0.10886349886048481 == ((1.0 / 3.0) * ((0.8483290292899243 + 0.5551653459300319) + -1.0769038786385017))
E + where 0.10886349886048481 = Stress([[ 0.84832903 0.84625727 0.4736945 ]\n [ 0.58605031 0.55516535 -0.19111055]\n [ 0.06861778 -0.77199009 -1.07690388]]).mean_stress
E + where Stress([[ 0.84832903 0.84625727 0.4736945 ]\n [ 0.58605031 0.55516535 -0.19111055]\n [ 0.06861778 -0.77199009 -1.07690388]]) = <test_stress.StressTest testMethod=test_properties>.rand_stress
.pybuild/test_python3.11/pymatgen/analysis/elasticity/tests/test_stress.py:19: AssertionError
```
**Environment (please supply relevant versions and platform info):**
- OS: GNU Hurd-i386
- Version 0.9
**Additional context**
I haven't made a comprehensive review to confirm if other tests using `==` for floating point comparison, perhaps there are others. But a quick look sees other tests using `pytest.approx()`
Test on pymatgen 2022.11.7 but the failing code is still in git HEAD.
|
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| 1,577,251,120
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I_kwDOACgets5eAvEw
| 2,840
|
PatchedPhaseDiagram.get_decomp_and_e_above_hull() performance bottle neck
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[] | 2023-02-09T05:09:38
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2023-02-12T17:08:34Z
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MEMBER
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This `if` statement in `PatchedPhaseDiagram.get_decomp_and_e_above_hull()` scales very poorly with the size of the `stable_entries` `set`.
https://github.com/materialsproject/pymatgen/blob/134722b20ca24e6ff3d01aaa194fb51e296966b6/pymatgen/analysis/phase_diagram.py#L741-L747
For a PPD constructed from all entries in MP, `PatchedPhaseDiagram.get_hull_energy_per_atom` is more than 100x faster than `get_decomp_and_e_above_hull`. Almost all of that time is spent on evaluating `entry in self.stable_entries`.
```py
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram
from pymatgen.ext.matproj import MPRester
all_mp_computed_structure_entries = MPRester().get_entries("")
ppd_mp = PatchedPhaseDiagram(all_mp_computed_structure_entries, verbose=True)
# this is fast, ~200 iterations / sec
ppd_mp.get_hull_energy_per_atom(x.composition for x in all_mp_computed_structure_entries[:1000])
# this is slow, ~2 iterations / sec
ppd_mp.get_decomp_and_e_above_hull(all_mp_computed_structure_entries[:1000])
```
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PR_kwDOACgets5JyZLO
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Add inplace flag to select whether to adjust entries in place
|
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[] | null |
[
"@peikai Really nice work! Thanks for adding tests. 👍 ",
"Great :clap:"
] | 2023-02-12T05:29:05
| 2023-02-13T06:43:05
|
2023-02-12T16:58:04Z
|
CONTRIBUTOR
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With regard to the discussion in #2832, this PR is submitted to avoid always adjusting entries in place.
- A flag `inplace` is added into `process_entries` method for several compatibility schemes, including `Compatibility()`, `MaterialsProjectDFTMixingScheme`, and `MaterialsProjectAqueousCompatibility`. If `inplace = False`, entries will be processed on a copy.
- Corresponding unittests have also been added.
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PR_kwDOACgets5Jy9zc
| 2,842
|
Default `check_stable` to `False` in `PatchedPhaseDiagram.get_decomp_and_e_above_hull()` for speed
|
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[] | 2023-02-12T16:22:56
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2023-02-12T17:08:33Z
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MEMBER
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Closes #2840.
|
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I_kwDOACgets5eTXKY
| 2,843
|
It should be possible to use a setter for coords on a neighbor object
|
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[
"Well, Neighbors are essentially container objects that bypass some of the checks that PeriodicSite runs by default. It is meant to be a unchangeable storage. If you prefer sites that are modifiable, I suggest you convert the neighbor objects to site objects (the information are all the same, you just need to run PeriodicSite(...) with the correct parameters. After that, you can make as many changes as you wish. It is just a single line of code."
] | 2023-02-13T11:02:57
| 2023-02-13T16:30:33
|
2023-02-13T16:30:33Z
|
NONE
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**The problem**
If I get all the ligands around a central cation using the structure method `get_neighbors`:
```
ligands = structure.get_neighbors(core_site,3.0)
```
and I then want to change the position of one of these ligands, i.e.:
```
ligand = ligands[0]
new_coords = ligand.coords
new_coords[2] = new_coords[2] + 0.001
ligand.coords = new_coords
```
An attribute error occurs. I may be mistaken, but I think this is because this is a neighbor object, not a PeriodicSite object, and the setter for `coords` doesn't apply to the PeriodicSite object which the neighbor object relates to.
**Describe the solution you'd like**
Neighbor objects should have a setter for coords which will update both themselves, and the coords for the PeriodicSite object they relate to.
Note that some thought will need to be given to periodicity. I.e., if a neighbor of the core_site occurs in a neighbouring unit cell, the new code needs to make sure that the new site coordinates are corrected to make sure the change occurs within the main unit cell, but in a way that will mean the version of the PeriodicSite occurring in the unit cell where the neighbor object occurs, will be in the location the user intends when setting the coords of the neighbor object.
**Describe alternatives you've considered**
End user could write more complex code than is necessary
|
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| 1,582,350,680
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PR_kwDOACgets5J2ZyZ
| 2,844
|
Modified dosplotter
|
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[
"Thanks @kaueltzen! 👍 ",
"Let me know when this is ready to merge.",
"Hey @janosh , this is ready to merge(:",
"`mypy` is failing. you can try and fix the errors or (if that's too much hassle) decorate the plot function with\r\n\r\n```py\r\nimport typing\r\n\r\n@typing.no_type_check\r\n```",
"Thanks, I decorated the get_plot method. If required, I can look into fixing the mypy errors when I have more time.",
"GitHub actions are currently down https://www.githubstatus.com. Hopefully, tests will run later today.",
"Yeah! @kaueltzen 's first pymatgen contribution!",
"Congrats @kaueltzen! Very nice work even including tests in your first PR. 👏 "
] | 2023-02-13T13:23:38
| 2023-03-29T17:42:40
|
2023-03-29T17:26:21Z
|
CONTRIBUTOR
|
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- added arguments in Dosplotter class to plot DOS w. inverted axes (as common in chemistry) and to plot beta spin channel w. dashed line
- debugged CohpPlotter class: limit determination and display of energy axis
- added tests for automatic limit determination in DosPlotter class (especially to test if DOS and energy axis outputs are the same for inverted and non-inverted case)
|
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| 1,583,064,736
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I_kwDOACgets5eW6ag
| 2,845
|
get_neighbors() function does not give different results when coordinates of PeriodicSites are changed
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[
"I have gone down a different route. I use `input_cell.remove_sites()` to remove the site, and then `input_cell.insert()` to add the same site with different coordinates. this seems to work"
] | 2023-02-13T21:07:44
| 2023-02-13T21:33:02
|
2023-02-13T21:33:02Z
|
NONE
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**Problem**
Changing the coordinates of a `PeriodicSite` within a structure does not change the coordinates of that `PeriodicSite` object shown elsewhere.
For instance, if I have a structure object `input_cell` containing several sites, where `input_cell[0].coords` is [0,0,0], and I then change it as follows:
```
input_cell[0].coords[2] = 0.01
```
If I were to then do `print(input_cell[0]).coords` I would get [0,0,0.01] as expected. However, if I were to do simply `print(input_cell)` or if I were to use the `get_neighbors` method on a different site (i.e. `input_cell.get_neighbors(input_cell[1],2.5)`), then the original unmodified coordinates ([0,0,0]) would be printed or stored as coordinates in the resulting neighbor object.
I am trying to run a simulation which updates the coordinates of sites as above, but will only work if `get_neighbors` is updated when I change the coordinates of sites. This is not currently happening. I'd be grateful if anyone could either push a fix to pymatgen, or advise me on a way to make `get_neighbors` reflect the changes I make to site coordinates (for instance, can I "refresh" the structure object somehow so it will update all the sets of coordinates?)
**Describe the solution you'd like**
Either push a fix to pymatgen, or advise me on a way to make `get_neighbors` reflect the changes I make to site coordinates
**Describe alternatives you've considered**
Without this, I am not sure how I can get my simulation to work using pymatgen.
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PR_kwDOACgets5J_X3w
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Document difference between Composition.get_el_amt_dict() and Composition.as_dict()
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[] | 2023-02-15T00:24:07
| 2023-02-15T00:45:08
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2023-02-15T00:45:07Z
|
MEMBER
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PR_kwDOACgets5KEDJD
| 2,847
|
Add Ruff linter
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[
"Awesome 😍",
"I replaced `flake8` and `pylint` with `ruff` in `.github/workflows/lint.yml`. Great news. That action used to take ~9 mins before and runs in 3.\r\n\r\nThe main time hog left now is `mypy` (which I update from 0.991 to v1 which supposedly is 40% faster). Before, the longest running step was `pylint`. `ruff` literally takes 1 second.\r\n\r\n**Before**\r\n\r\n\r\n**After**\r\n\r\n"
] | 2023-02-15T19:16:05
| 2023-02-19T15:57:58
|
2023-02-19T15:57:57Z
|
MEMBER
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This PR adds Ruff as a new linter to be run in pre-commit.ci. Ruff is written in Rust and about 100x faster than our existing linters written in Python. Unlike `flake8`, it also auto-fixes many violations. It takes less than a second to check the entire pymatgen codebase:
```sh
time ruff check . --no-cache
ruff check . --no-cache 0.88s user 0.07s system 757% cpu 0.126 total
```
Thanks to @munrojm for introducing me to Ruff.
Plan is to to remove most of our existing linters in favor of running Ruff exclusively. We should get the same code QA at a huge reduction in wait time. Quoting from the [Ruff readme](https://github.com/charliermarsh/ruff#how-does-ruff-compare-to-flake8):
> Ruff also re-implements some of the most popular Flake8 plugins and related code quality tools natively, including:
>
> [autoflake](https://pypi.org/project/autoflake/) (https://github.com/charliermarsh/ruff/issues/1647)
> [eradicate](https://pypi.org/project/eradicate/)
> [flake8-2020](https://pypi.org/project/flake8-2020/)
> [flake8-annotations](https://pypi.org/project/flake8-annotations/)
> [flake8-bandit](https://pypi.org/project/flake8-bandit/) (https://github.com/charliermarsh/ruff/issues/1646)
> [flake8-blind-except](https://pypi.org/project/flake8-blind-except/)
> [flake8-boolean-trap](https://pypi.org/project/flake8-boolean-trap/)
> [flake8-bugbear](https://pypi.org/project/flake8-bugbear/)
> [flake8-builtins](https://pypi.org/project/flake8-builtins/)
> [flake8-commas](https://pypi.org/project/flake8-commas/)
> [flake8-comprehensions](https://pypi.org/project/flake8-comprehensions/)
> [flake8-datetimez](https://pypi.org/project/flake8-datetimez/)
> [flake8-debugger](https://pypi.org/project/flake8-debugger/)
> [flake8-django](https://pypi.org/project/flake8-django/) (https://github.com/charliermarsh/ruff/issues/2817)
> [flake8-docstrings](https://pypi.org/project/flake8-docstrings/)
> [flake8-eradicate](https://pypi.org/project/flake8-eradicate/)
> [flake8-errmsg](https://pypi.org/project/flake8-errmsg/)
> [flake8-executable](https://pypi.org/project/flake8-executable/)
> [flake8-implicit-str-concat](https://pypi.org/project/flake8-implicit-str-concat/)
> [flake8-import-conventions](https://github.com/joaopalmeiro/flake8-import-conventions)
> [flake8-logging-format](https://pypi.org/project/flake8-logging-format/)
> [flake8-no-pep420](https://pypi.org/project/flake8-no-pep420)
> [flake8-pie](https://pypi.org/project/flake8-pie/)
> [flake8-print](https://pypi.org/project/flake8-print/)
> [flake8-pyi](https://pypi.org/project/flake8-pyi/)
> [flake8-pytest-style](https://pypi.org/project/flake8-pytest-style/)
> [flake8-quotes](https://pypi.org/project/flake8-quotes/)
> [flake8-raise](https://pypi.org/project/flake8-raise/)
> [flake8-return](https://pypi.org/project/flake8-return/)
> [flake8-self](https://pypi.org/project/flake8-self/)
> [flake8-simplify](https://pypi.org/project/flake8-simplify/) (https://github.com/charliermarsh/ruff/issues/998)
> [flake8-super](https://pypi.org/project/flake8-super/)
> [flake8-tidy-imports](https://pypi.org/project/flake8-tidy-imports/)
> [flake8-type-checking](https://pypi.org/project/flake8-type-checking/)
> [flake8-use-pathlib](https://pypi.org/project/flake8-use-pathlib/)
> [isort](https://pypi.org/project/isort/)
> [mccabe](https://pypi.org/project/mccabe/)
> [pandas-vet](https://pypi.org/project/pandas-vet/)
> [pep8-naming](https://pypi.org/project/pep8-naming/)
> [pydocstyle](https://pypi.org/project/pydocstyle/)
> [pygrep-hooks](https://github.com/pre-commit/pygrep-hooks) (https://github.com/charliermarsh/ruff/issues/980)
> [pyupgrade](https://pypi.org/project/pyupgrade/) (https://github.com/charliermarsh/ruff/issues/827)
> [yesqa](https://github.com/asottile/yesqa)
|
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| 1,587,497,232
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PR_kwDOACgets5KHth1
| 2,848
|
Manually update OPTIMADE database aliases and add option to refresh on init
|
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[] | 2023-02-16T11:19:18
| 2023-02-19T15:39:42
|
2023-02-16T17:14:51Z
|
CONTRIBUTOR
|
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## Summary
Currently `OptimadeRester` defaults to an outdated list of OPTIMADE database URLs (several of which fail) and the design of the class is such that refreshing these aliases can only be done post-init which means they will not be used if the user provides their own filtered list of aliases, without doing some extra work.
This PR refreshes the vendored list of aliases (which should be much more stable now since their initial addition 2 years ago), and also adds the option to refresh the aliases on initialization of the class.
This currently affects the pymatgen OPTIMADE tutorials at https://github.com/Materials-Consortia/optimade-tutorial-exercises.
|
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I_kwDOACgets5e0Asg
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|
Can't install on Python 3.11
|
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[] | null |
[
"3.11 is not officially supported at the moment as it is a bit new. We are working on it.",
"Related issue #2710 and PR #2714",
"Thanks for the information. I would like to add that the same problem was also present on my laptop which runs Fedora 36 (python 3.10). So, I am guessing that it will be first fixed for 3.10 and then for 3.11? ",
"> Thanks for the information. I would like to add that the same problem was also present on my laptop which runs Fedora 36 (python 3.10). So, I am guessing that it will be first fixed for 3.10 and then for 3.11?\r\n\r\n@adosar in your specific case, it looks like you are using your system Python (i.e., one that comes from Fedora itself) to construct your virtual environment. To get around this issue, you need to install the development version of the Python package for Fedora, with something like `yum install python-dev`. \r\n\r\nThis will then allow pip to compile the C-extensions that come with pymatgen (see below that we can also ask that these builds get made in the CI of this package, so that everyone on Linux can just install them without recompiling -- I've had no trouble building these wheels myself of pymatgen for Python 3.11 but as @shyuep suggests there maybe outstanding compatibility issues that I haven't run into). \r\n\r\n*Another option would be to decouple your \"science Python\" from your system Python by using tools like conda, pyenv etc. to manage separate Python executables for each virtual environment -- people have many opinions on this and the \"best tool\" changes year on year, so just treat this as something you could consider investigating...*\r\n\r\n-----\r\nThis has made me notice that currently wheels are not being built for Linux on release. Is this intentional (@shyuep @janosh)?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/13a860aab7cbf914c1aaedfa5b06a703211de202/.github/workflows/test.yml#L104",
"> currently wheels are not being built for Linux on release\r\n\r\n@ml-evs I noticed this as well but don't know the reason. I assume it's just lack of time to implement. There's an open PR for linux wheels #2800.",
"I would've thought that simply adding `ubuntu-latest` to the build matrix line would get you most of the way (that's how I build wheels at least -- understand there must be additional complexities here). It looks like this is what used to be done, until https://github.com/materialsproject/pymatgen/commit/f4959c1a2b6bc1bd744f41888b97383def8d1993",
"For Fedora users:\r\n(Fedora 36 here but of course can work with newer releases)\r\n`sudo dnf install python3.9`\r\n`python3.9 -m venv <venv-name>`\r\n`source <venv-name>`\r\n`pip install wheel`\r\n`pip install pymatgen`\r\n\r\nInstallation had no problems.",
"@ml-evs Ah, [looks like](https://github.com/materialsproject/pymatgen/actions/runs/4248894628/jobs/7388717234#step:4:2501) because of the compiled C extensions in `pymatgen`, uploading a Linux wheel isn't straightforward and [needs to go through `manylinux`](https://stackoverflow.com/a/59586096) like #2800 is attempting.",
"Now `pymatgen` can be easily installed on `python3.10` with pip (works flawlessly in Fedora 36).",
"Great. Thanks,",
"> Great. Thanks,\r\n\r\n@shyuep Haven't tried it yet to `python3.11` though. Can you please leave it open untill it works also on `python3.11`? Thanks!\r\n\r\n",
"Sure.",
"I have tried it also in Fedora 37 with Python 3.11.2 and works flawlessly. Just `pip install pymatgen`.",
"@adosar Thanks for confirming."
] | 2023-02-19T13:43:21
| 2023-05-19T20:19:51
|
2023-05-19T20:16:47Z
|
NONE
|
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I am trying to install pymatgen on a clear virtual environment on Fedora 37.
`python -m venv <virtual-environment-name>`
`source <virtual-environment-name>`
`pip install wheel`
`pip install pymatgen`
But I get the error shown on the attached image.
|
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PR_kwDOACgets5KSbza
| 2,850
|
Fix auto-fixable pydocstyle errors through ruff
|
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[] | 2023-02-19T16:25:15
| 2023-02-19T17:48:41
|
2023-02-19T17:30:26Z
|
MEMBER
|
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Would be good in the long run to enable `pydocstyle` (rule class "D" in `ruff`) across the whole code base but at the moment, there are too many existing errors to fix them all. This is just a swing at fixing all the auto-fixable ones with
```sh
ruff check . --fix-only --select D
```
|
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PR_kwDOACgets5KS-K8
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Run pyupgrade and flake8-simplify through ruff
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[] | 2023-02-20T00:26:52
| 2023-02-20T23:18:52
|
2023-02-20T23:18:50Z
|
MEMBER
|
{
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|
```diff
[tool.ruff]
select = [
"B", # flake8-bugbear
"D", # pydocstyle
"E", # pycodestyle
"F", # pyflakes
"I", # isort
"PLE", # pylint error
"PLW", # pylint warning
"Q", # flake8-quotes
+ "SIM", # flake8-simplify
"TID", # tidy imports
+ "UP", # pyupgrade
"W", # pycodestyle
"YTT", # flake8-2020
]
```
followed by
```sh
ruff check . --fix
```
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| 1,590,930,477
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I_kwDOACgets5e06wt
| 2,852
|
OPTIMADE client generates malformed queries
|
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[
"(same thing also applies to string queries within the `filter` query parameter)",
"@ml-evs Sorry! That was my fault. We can definitely make a release before week's end. Thanks for #2853! 🙏 ",
"No problem, and thanks! Also found another bug where `chemical_formula_hill` was being passed incorrectly in queries (instead duplicating `chemical_formula_anonymous`).\r\n\r\nMy own client at https://www.optimade.org/optimade-python-tools/latest/getting_started/client/ is getting pretty mature and could probably integrated here... (already supports pymatgen Structure output, obeys all the standardized metadata we have for delaying requests, async queries over providers, custom callbacks for e.g., saving/storing in databases) Extra deps would be `httpx` and `rich`, could split it into a namespace package of `optimade-python-tools` if there is any interest.",
"> My own client at https://www.optimade.org/optimade-python-tools/latest/getting_started/client/ is getting pretty mature and could probably integrated here... (already supports pymatgen Structure output, obeys all the standardized metadata we have for delaying requests, async queries over providers, custom callbacks for e.g., saving/storing in databases)\r\n\r\nThat sounds great! 👍 ",
"> Extra deps would be `httpx` and `rich`, could split it into a namespace package of `optimade-python-tools` if there is any interest.\r\n\r\nI recommend coordinating with @munrojm on that but I'd be happy to help/act as reviewer if we go ahead."
] | 2023-02-20T00:32:48
| 2023-02-20T03:04:55
|
2023-02-20T03:04:55Z
|
CONTRIBUTOR
|
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**Describe the bug**
At some point, the OPTIMADE client in this repo was linted (presumably) and `f'?response_fields="{response_fields}"...'` was replaced with `f'?response_fields={response_fields!r}'`, which generates query parameters with the wrong (according to the OPTIMADE spec, at least) kind of quotes:
https://github.com/materialsproject/pymatgen/blob/ebec8497c05055db3b78fec4c4bba75aaefb7839/pymatgen/ext/optimade.py#L316
This renders the client useless, as every request has such malformed queries.
I'm happy to fix this (will make a PR straightaway), but please let me know if this could be released before the end of the week --- if not I will have to adjust the pymatgen OPTIMADE tutorials that are being delivered at a conference on the 28th Feb.
|
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https://github.com/materialsproject/pymatgen/pull/2853
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PR_kwDOACgets5KTAQ1
| 2,853
|
Fix OPTIMADE client generated filters and URLs
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[
"Sorry, took a few attempts to get around the linter... this should be good to go."
] | 2023-02-20T00:50:16
| 2023-02-20T03:04:54
|
2023-02-20T03:04:54Z
|
CONTRIBUTOR
|
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Closes #2852 by properly quoting OPTIMADE query URLs without using f-strings.
Also fixes an issue where `chemical_formula_hill` was not queryable.
|
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PR_kwDOACgets5KZAEM
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Ruff c4+ruf rules
|
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[] | 2023-02-21T03:52:54
| 2023-02-21T22:47:09
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2023-02-21T22:47:08Z
|
MEMBER
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Enable [Ruff-specific](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) and [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) sets for `ruff`.
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I_kwDOACgets5e9Oyd
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AttributeError in LinearAssignment.__init__(), pymatgen v. 2022.11.7, python 3.11.0
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[
"Typically you will use the C version of linear assignment. This suggests that your pymatgen is not properly installed."
] | 2023-02-21T09:13:58
| 2023-02-21T23:33:18
|
2023-02-21T23:26:49Z
|
NONE
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Novice at pymatgen and using the matgenb notebooks [(http://matgenb.materialsvirtuallab.org/)](url) to get familiar with the workflow.
When trying to use the function pymatgen.core.surface.generate_all_slabs, the following AttributeError is raise:
I tried to find the bug in linear_assignment, the AttributeError refers to line 72:
```
# initialize solution vectors
self._x = np.zeros(self.n, dtype=int) - 1
self._y = self._x.copy()
```
However, I have not been able to resolve the bug.
Numpy is version 1.24.2
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PR_kwDOACgets5KdxfY
| 2,856
|
Fix typo in OPTIMADE client: remove quotes in response fields
|
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[] | 2023-02-21T22:14:15
| 2023-02-21T22:35:52
|
2023-02-21T22:35:52Z
|
CONTRIBUTOR
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## Summary
One more fix related to #2852 -- response fields also should not have quotes around the entire field. This was caught by a test that directly queries MP, which was (also incorrectly) returning data that didn't quite match rather than an error, e.g.:
https://optimade.materialsproject.org/v1/structures?filter=(elements%20HAS%20ALL%20%22Ga%22,%20%22N%22)%20AND%20(nelements=2)&response_fields=%22species_at_sites,cartesian_site_positions,species,lattice_vectors,nsites%22
vs what should happen if you incorrectly format the response fields:
[https://optimade.odbx.science/v1/structures?response_fields="id"](https://optimade.odbx.science/v1/structures?response_fields=%22id%22)
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PR_kwDOACgets5Kj_NR
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2023.2.22 release
|
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[] | 2023-02-23T00:15:49
| 2023-02-23T00:34:23
|
2023-02-23T00:34:22Z
|
MEMBER
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Prepare 2023.2.22 release of pymatgen. The 1st one with official python 3.11 support! 🎉
This PR also adds [`ubuntu-latest` back to the release job matrix strategy](https://github.com/materialsproject/pymatgen/blob/be80e438ac851eea7950313efb60bbdb78a66c99/.github/workflows/test.yml#L132) since it's unclear why it was dropped. Thanks @ml-evs for pointing this out in https://github.com/materialsproject/pymatgen/issues/2849#issuecomment-1440318202. 👍
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PR_kwDOACgets5KwnC8
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Merge setup.cfg into pyproject.toml
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[] | 2023-02-25T16:56:28
| 2023-02-25T19:50:22
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2023-02-25T19:50:21Z
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MEMBER
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Enable `codespell` in pre-commit.ci.
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I_kwDOACgets5fXSm4
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Return value for the method "periodic_table_heatmap" should change from "plt" to "fig, ax"
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[] | 2023-02-26T05:55:42
| 2023-02-26T05:55:42
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NONE
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https://github.com/materialsproject/pymatgen/blob/b5eda8d3c343a6cb06c5cc02a34dbd30158637d1/pymatgen/util/plotting.py#L186-L329
If "plt" is returned, there is no object in it, only a class (`matplotlib.pyplot`) will be returned.
If we change the return to "fig, ax", then the periodic_table can be export by `fig.savefig(filename, dpi..)`.
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PR_kwDOACgets5Kyx60
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del class AtomicFile, _maketemp(), ask_yesno()
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[] | 2023-02-27T04:29:24
| 2023-02-27T04:50:29
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2023-02-27T04:50:27Z
|
MEMBER
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Presumed unused. Atomic commit for easy revertability in case still needed.
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PR_kwDOACgets5K2yKy
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Remove module pymatgen/command_line/gulp_caller.py
|
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[
"Why is this considered dead code? Though I don't use it, I was under the impression that it is working and some people actually use it.",
"My line of inquiry was following [this docs sentence](https://github.com/materialsproject/pymatgen/blob/40cbf1d7c47bb2eb75509780e356c9877ae9c2f7/docs_rst/installation.rst#optional-non-python-programs) saying the pymatgen `gulp_caller` module is \"used extensively\" by `pymatgen-analysis-defects`. I found no mention of gulp or `GulpIO` or `TersoffPotential` anywhere in `pymatgen-analysis-defects`. Awaiting confirmation for not being used in https://github.com/materialsproject/pymatgen-analysis-defects/issues/108.\r\n\r\nAnd also because [interest in gulp has steadily dropped](https://trends.google.com/trends/explore?date=all&geo=US&q=%2Fg%2F11byyl8mbg) over the years.\r\n\r\n**Google Trends**\r\n\r\n<img width=\"1265\" alt=\"Screenshot 2023-02-27 at 10 32 23\" src=\"https://user-images.githubusercontent.com/30958850/221652190-3b6f524e-33be-427b-911e-551a031340eb.png\">\r\n",
"I agree that GULP interest has decreased. But I think it is useful to just leave this unless it bothers someone majorly. It is still useful if you want to do some benchmarks with GULP based simulations.",
"Ok, closing."
] | 2023-02-27T17:42:12
| 2023-02-27T18:55:16
|
2023-02-27T18:55:10Z
|
MEMBER
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Don't want to step on anyone's feet so I'll leave this PR open for a while but looks like this might be dead code (based on not knowing anyone who still uses `gulp`).
@shyuep Let me know if this is a mistake.
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PR_kwDOACgets5K3NoB
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Enable flake8-simplify via ruff in pre-commit.ci
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[] | 2023-02-27T18:57:35
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2023-03-05T04:35:24Z
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Still wip. Requires fixing more violations.
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I_kwDOACgets5ffcKP
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to_string(cart_coords=True) broken in GaussianInput
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[
"Seems to be fixed from commit https://github.com/materialsproject/pymatgen/commit/577b2cddf8d8cbad218d7285341ddf5869d2cdea\r\n\r\nWill be included in the next version.",
"@gVallverdu - great!\r\nSee also #2865 ",
"@ConradJohnston Yes, as you mentioned it is the same bug and I think the same commit fix both.\r\nLet me know if you want to do something more about this but for me you could close the issues.",
"Fixed in #2891."
] | 2023-02-27T22:55:52
| 2023-05-19T20:20:06
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2023-05-19T20:16:05Z
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NONE
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**Describe the bug**
For the input generator class for Gaussian:
[pymatgen/io/gaussian.py : GaussianInput
](https://github.com/materialsproject/pymatgen/blob/0d2062a01bf0ccb36cb736c9a5d139787c55e4c1/pymatgen/io/gaussian.py#LL87C14-L87C14)
the `to_string()` method should produce a string consisting of a Gaussian input.
The option "`cart_coords=True`" is supposed to write cartesian coordinates into the input, while the default value of false writes a Z-matrix.
Choosing cartesian coordinates leads to the error:
`TypeError: str.join() takes exactly one argument (2 given)`
The buggy line is here:
https://github.com/materialsproject/pymatgen/blob/40cbf1d7c47bb2eb75509780e356c9877ae9c2f7/pymatgen/io/gaussian.py#L423
It looks to have been broken recently on Jan 6 in commit 0d2062a .
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.core import Molecule
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
methane = Molecule(["C", "H", "H", "H", "H"], coords)
from pymatgen.io import gaussian
inp = gaussian.GaussianInput(mol=methane)
inp.to_string(cart_coords=True)
```
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PR_kwDOACgets5K4ijZ
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fix reduced formula in Ion
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[
"Thanks for catching this!"
] | 2023-02-28T00:22:46
| 2023-03-02T03:57:34
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2023-02-28T21:11:30Z
|
MEMBER
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Fixed the handling of O-H containing compositions, where the string 'HO' was replaced by 'OH' directly in the reduced formula. This will cause certain materials, e.g. HSbO2, to have the wrong reduced formula of SbOH2.
This fix then adds a condition that the composition must have an equal number of H and O to be handled that way.
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I_kwDOACgets5fiiek
| 2,865
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Crash in GaussianInput when using to_string(cart_coords=True)
|
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[
"Duplicate of #2863 , by only a handful of hours. 😊 ",
"Thanks for linking these related issues. I wasn't aware of them when merging https://github.com/materialsproject/pymatgen/pull/2891. Closing this and #2863 now.",
"Thanks @janosh !\r\n"
] | 2023-02-28T11:47:29
| 2023-05-19T20:49:54
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2023-05-19T20:15:34Z
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NONE
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**Describe the bug**
A clear and concise description of what the bug is.
When creating a GaussianInput object and calling `to_string(cart_coords=True)` method, it raises an error:
File "python3.10/site-packages/pymatgen/io/gaussian.py", line 423, in get_cart_coords
outs.append(" ".join(site.species_string, " ".join([to_s(j) for j in site.coords])))
TypeError: str.join() takes exactly one argument (2 given)
This bug was created in commit 0d2062a01bf0ccb36cb736c9a5d139787c55e4c1 on 6 January 2023:
Prefer generator over list comprehension where equivalent (#2793)
**To Reproduce**
Steps to reproduce the behavior:
Execute the following code with pymatgen 2023.1.9 and later
```
from pymatgen.core import Molecule
from pymatgen.io import gaussian
molfile = """
5
methane
C 0.0000000000 0.0000000000 0.0000000000
H 0.6364381313 -0.0720602423 -0.9058204889
H 0.6364393234 -0.0721551627 0.9058120847
H -0.5344626307 0.9721659422 0.0000000000
H -0.7384146452 -0.8279502988 0.0000000000
"""
mol = Molecule.from_str(molfile, fmt="xyz")
file = gaussian.GaussianInput(mol)
print(file.to_string(cart_coords=True))
```
**Fix**
The lines 421-423 in file pymatgen/io/gaussian.py now look like:
```
outs = []
for site in self._mol:
outs.append(" ".join(site.species_string, " ".join([to_s(j) for j in site.coords])))
```
This does not works since the first join function call has two arguments:
1) `site.species_string`
2) `" ".join([to_s(j) for j in site.coords])`
The code before the commit 0d2062a01bf0ccb36cb736c9a5d139787c55e4c1 contains `[]` for list comprehension like this:
```
outs = []
for site in self._mol:
outs.append(" ".join([site.species_string, " ".join([to_s(j) for j in site.coords])]))
```
The square braquet in the second join function call can be removed to use generator expression but not in the first join.
Another possibility would be to remove the nested join functions with something like this:
```
outs = []
for site in self._mol:
outs.append(" ".join([site.species_string] + [to_s(j) for j in site.coords]))
```
I do not think replacing list comprehension by generator expression is required for performance gain in this case
Regards
Vincent LIEGEOIS
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I_kwDOACgets5fixm4
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test_dos.py test_get_dos_fp_similarity uses equality to test floating point number
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[
"Thanks for reporting!"
] | 2023-02-28T12:13:22
| 2023-03-24T03:34:01
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2023-03-24T03:33:45Z
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CONTRIBUTOR
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test_get_dos_fp_similarity in test_dos.py at
https://github.com/materialsproject/pymatgen/blob/40cbf1d7c47bb2eb75509780e356c9877ae9c2f7/pymatgen/electronic_structure/tests/test_dos.py#L285
uses equality to test a floating point number (`similarity_index`)
Inevitably that causes a failure, e.g. https://buildd.debian.org/status/fetch.php?pkg=pymatgen&arch=all&ver=2023.2.22%2Bdfsg1-1&stamp=1677585041&raw=0
```
.pybuild/test_python3.11/pymatgen/electronic_structure/tests/test_dos.py . [ 54%]
..........F
=================================== FAILURES ===================================
__________________ CompleteDosTest.test_get_dos_fp_similarity __________________
self = <electronic_structure.tests.test_dos.CompleteDosTest testMethod=test_get_dos_fp_similarity>
def test_get_dos_fp_similarity(self):
dos_fp = self.dos.get_dos_fp(type="s", min_e=-10, max_e=0, n_bins=56, normalize=True)
dos_fp2 = self.dos.get_dos_fp(type="tdos", min_e=-10, max_e=0, n_bins=56, normalize=True)
similarity_index = self.dos.get_dos_fp_similarity(dos_fp, dos_fp2, col=1, tanimoto=True)
assert similarity_index == approx(0.3342481451042263)
dos_fp = self.dos.get_dos_fp(type="s", min_e=-10, max_e=0, n_bins=56, normalize=True)
dos_fp2 = self.dos.get_dos_fp(type="s", min_e=-10, max_e=0, n_bins=56, normalize=True)
similarity_index = self.dos.get_dos_fp_similarity(dos_fp, dos_fp2, col=1, tanimoto=True)
> assert similarity_index == 1
E assert 0.9999999999999997 == 1
.pybuild/test_python3.11/pymatgen/electronic_structure/tests/test_dos.py:285: AssertionError
```
It should use a floating point comparison instead. Other tests there use `approx(...)`.
**To Reproduce**
Steps to reproduce the behavior:
1. `pytest-3 -vv pymatgen/electronic_structure/tests/test_dos.py`
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PR_kwDOACgets5K-Lm1
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Prepare release 2023.2.28
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[] | 2023-02-28T21:21:57
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2023-02-28T21:50:51Z
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MEMBER
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PR_kwDOACgets5K-aHu
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Very small Q-Chem tweak
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[] | 2023-02-28T22:18:36
| 2023-02-28T22:34:22
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2023-02-28T22:34:21Z
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CONTRIBUTOR
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## Summary
- One small error parsing tweak and one change of @staticmethod to @classmethod
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Bump pypa/cibuildwheel from 2.11.4 to 2.12.0
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| 2023-03-03T19:49:51
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.12.0</h2>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.12.0</h3>
<p><em>16 Jan 2023</em></p>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
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<li><a href="https://github.com/pypa/cibuildwheel/commit/a808017c3962f4d678fe685239668aad8c150932"><code>a808017</code></a> Bump version: v2.12.0</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/4e1fcb8df69a5eef7d82b06b70253846342eb0a0"><code>4e1fcb8</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1394">#1394</a> from pypa/update-dependencies-pr</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/4afa12ed06e8462c24040a41ee170c8983001172"><code>4afa12e</code></a> Update dependencies</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/92cb1d8990e2418c0bd24c5e8d74406345216b58"><code>92cb1d8</code></a> feat: add PyPy macOS arm64 (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/06c4927798c6cc67792db86e6e133df4ac0a7139"><code>06c4927</code></a> [Bot] Update dependencies (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1381">#1381</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/9b0d63b2f43d06853cbc7eae711646d93983a4e4"><code>9b0d63b</code></a> ci: use normal AppVeyor macOS image (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1388">#1388</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/6df156807a9b029ed513c6b5c4f4fbe43f7a2c0c"><code>6df1568</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://github-redirect.dependabot.com/pypa/cibuildwheel/issues/1382">#1382</a>)</li>
<li>See full diff in <a href="https://github.com/pypa/cibuildwheel/compare/v2.11.4...v2.12.0">compare view</a></li>
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</details>
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You can trigger Dependabot actions by commenting on this PR:
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Bump matplotlib from 3.5.2 to 3.7.0
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] | 2023-03-01T12:59:54
| 2023-03-03T19:49:51
|
2023-03-03T19:49:41Z
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Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.5.2 to 3.7.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<h2>REL: v3.7.0</h2>
<p>Highlights of this release include:</p>
<ul>
<li>Plotting and Annotation improvements
<ul>
<li><code>hatch</code> parameter for pie</li>
<li>Polar plot errors drawn in polar coordinates</li>
<li>Additional format string options in <code>~matplotlib.axes.Axes.bar_label</code></li>
<li><code>ellipse</code> boxstyle option for annotations</li>
<li>The <em>extent</em> of <code>imshow</code> can now be expressed with units</li>
<li>Reversed order of legend entries</li>
<li><code>pcolormesh</code> accepts RGB(A) colors</li>
<li>View current appearance settings for ticks, tick labels, and gridlines</li>
<li>Style files can be imported from third-party packages</li>
</ul>
</li>
<li>Improvements to 3D Plotting
<ul>
<li>3D plot pan and zoom buttons</li>
<li><em>adjustable</em> keyword argument for setting equal aspect ratios in 3D</li>
<li><code>Poly3DCollection</code> supports shading</li>
<li>rcParam for 3D pane color</li>
</ul>
</li>
<li>Figure and Axes Layout
<ul>
<li><code>colorbar</code> now has a <em>location</em> keyword argument</li>
<li>Figure legends can be placed outside figures using constrained_layout</li>
<li>Per-subplot keyword arguments in <code>subplot_mosaic</code></li>
<li><code>subplot_mosaic</code> no longer provisional</li>
</ul>
</li>
<li>Widget Improvements
<ul>
<li>Custom styling of button widgets</li>
<li>Blitting in Button widgets</li>
</ul>
</li>
<li>Other Improvements
<ul>
<li>Source links can be shown or hidden for each Sphinx plot directive</li>
<li>Figure hooks</li>
</ul>
</li>
<li>New & Improved Narrative Documentation
<ul>
<li>Brand new :doc:<code>Animations </tutorials/introductory/animation_tutorial></code> tutorial.</li>
<li>New grouped and stacked <code>bar chart <../../gallery/index.html#lines_bars_and_markers></code>_ examples.</li>
<li>New section for new contributors and reorganized git instructions in the :ref:<code>contributing guide<contributing></code>.</li>
<li>Restructured :doc:<code>/tutorials/text/annotations</code> tutorial.</li>
</ul>
</li>
</ul>
<h2>REL: v3.7.0rc1</h2>
<p>First release candidate for 3.7.0</p>
<h2>REL: v3.6.3</h2>
<p>This is the third bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Fix Artist removal from <code>axes_grid1</code> Axes classes</li>
<li>Fix <code>inset_locator</code> in subfigures</li>
<li>Fix <code>scatter</code> on masked arrays with units</li>
<li>Fix colorbar ticks with log norm contours</li>
<li>Fix deprecation warnings in GTK4 backend</li>
<li>Fix using relative paths in <code>HTMLWriter</code></li>
<li>Improve failure message from rcParams string validation for tuple inputs</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/matplotlib/matplotlib/commit/d6dd1b79142e4e2483244c25ff1e3ddb664722d3"><code>d6dd1b7</code></a> REL: v3.7.0</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/14a221f5ab986cacf4bf8515d1122a33eb1d41cd"><code>14a221f</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25194">#25194</a> from tacaswell/370_final</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/ddef53603582c3ccc4a3130df25df5183d5d0e6c"><code>ddef536</code></a> DOC: update what's new date for final release date</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/1b5c3fb2d7cfb449434bb944c9b3ebe46f89f66e"><code>1b5c3fb</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24781">#24781</a> from tacaswell/mnt/restore_doc_sha</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/769865b35dcd2b4efa28d9198f8ab83161e8bfd0"><code>769865b</code></a> DOC: Prepare release notes for 3.7.0</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/f78e8eccfc96674be027019c1549c778fba96d44"><code>f78e8ec</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25196">#25196</a>: Add deprecation for setting data with non sequence type i...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/172ede34c7a71cd8eecf904d6c2003fc5c251888"><code>172ede3</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25197">#25197</a> from meeseeksmachine/auto-backport-of-pr-25193-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/3e0e0b3ef883b0ea1f5438445847dfee874fee39"><code>3e0e0b3</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25193">#25193</a>: Fix displacement of colorbar for eps with bbox_inches='ti...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/fc775b1d3d6b134cce5817238a940fdff9732072"><code>fc775b1</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25188">#25188</a> from meeseeksmachine/auto-backport-of-pr-25085-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/12b1dc2619ce1355c6edaeebbcfe544e742da91e"><code>12b1dc2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/25170">#25170</a> from meeseeksmachine/auto-backport-of-pr-25097-on-v...</li>
<li>Additional commits viewable in <a href="https://github.com/matplotlib/matplotlib/compare/v3.5.2...v3.7.0">compare view</a></li>
</ul>
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PR_kwDOACgets5LB52r
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Bump beautifulsoup4 from 4.11.1 to 4.11.2
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] | 2023-03-01T13:00:14
| 2023-03-03T19:49:52
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2023-03-03T19:49:42Z
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Bumps [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) from 4.11.1 to 4.11.2.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
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PR_kwDOACgets5LB54p
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Bump pandas from 1.4.4 to 1.5.3
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.4.4 to 1.5.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
<blockquote>
<h2>Pandas 1.5.3</h2>
<p>This is a patch release in the 1.5.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/1.5.3/whatsnew/v1.5.3.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
<h2>Pandas 1.5.2</h2>
<p>This is a patch release in the 1.5.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/1.5.2/whatsnew/v1.5.2.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
<h2>Pandas 1.5.1</h2>
<p>This is a patch release in the 1.5.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/1.5.1/whatsnew/v1.5.1.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pandas-dev/pandas/commit/2e218d10984e9919f0296931d92ea851c6a6faf5"><code>2e218d1</code></a> RLS: 1.5.3</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/659de5fea920f15e88bed4cf43dc13df8569abad"><code>659de5f</code></a> DOC: Fix whatsnew (<a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50821">#50821</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/5aff5c9f62893a863d003ee15ba216a71f1bb4f3"><code>5aff5c9</code></a> Manual backport fix github quota (<a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50827">#50827</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/c2ab9024379fd63b1a213e385726a4f2928b5c34"><code>c2ab902</code></a> Manually Backport PR <a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50809">#50809</a> (<a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50813">#50813</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/24316d0bfe530ccf2cd36d7457db1584c31198f1"><code>24316d0</code></a> Backport PR <a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50800">#50800</a> on branch 1.5.x (DOC: Clean up 1.5.x whatsnews) (<a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50807">#50807</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/4ea0840aa3d42a6d6176e979d0719884e26ec2e6"><code>4ea0840</code></a> BUG: Change FutureWarning to DeprecationWarning for inplace setitem with Data...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/d9dec94ece852eb25b7c37c6fb48be0ab44aa8d7"><code>d9dec94</code></a> Backport PR <a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50682">#50682</a> on branch 1.5.x (BUG: pivot_table with nested elements and...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/ce123cd0024029bb9138acdcc14382628a9310fc"><code>ce123cd</code></a> REGR: NumPy func warning when dropping nuisance in agg, apply, transform (<a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50">#50</a>...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/54b40379e3fe6825f676cf02767ee81adb6ffeb5"><code>54b4037</code></a> Backport PR on Branch 1.5.x (REV: revert deprecation of Series.<strong>getitem</strong> sl...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/71db310a328a0dfa194ef0fe2b95238817b4f419"><code>71db310</code></a> Backport PR <a href="https://github-redirect.dependabot.com/pandas-dev/pandas/issues/50396">#50396</a> on branch 1.5.x (BUG/COMPAT: fix assert_* functions for ne...</li>
<li>Additional commits viewable in <a href="https://github.com/pandas-dev/pandas/compare/v1.4.4...v1.5.3">compare view</a></li>
</ul>
</details>
<br />
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5LB597
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Bump plotly from 5.11.0 to 5.13.1
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-03-01T13:00:27
| 2023-03-03T19:49:54
|
2023-03-03T19:49:44Z
|
CONTRIBUTOR
|
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.13.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.13.1</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>v5.13.0</h2>
<p>See the full release announcement with graphical examples on the forum: <a href="https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205">https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205</a></p>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>v5.12.0</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
<li><code>marker.angle</code> attribute now accepts iterables where appropriate [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4013">#4013</a>]</li>
<li><code>selector=0</code> now correctly returns the first trace in <code>.select_traces()</code> and related methods [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3817">#3817</a>]</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.13.1] - 2023-02-24</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>[5.13.0] - 2023-01-23</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>[5.12.0] - 2023-01-12</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
<li><code>marker.angle</code> attribute now accepts iterables where appropriate [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4013">#4013</a>]</li>
<li><code>selector=0</code> now correctly returns the first trace in <code>.select_traces()</code> and related methods [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3817">#3817</a>]</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/2a8a9b7c27310d968a55edf44144c7eff9718ccb"><code>2a8a9b7</code></a> missed a version</li>
<li><a href="https://github.com/plotly/plotly.py/commit/943f0d20546d2298c53b3527bd9cedb0c94cc521"><code>943f0d2</code></a> version changes for v5.13.1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/fc15102b3687b89649a309b4a9666e2b57cb1056"><code>fc15102</code></a> Create SECURITY.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/563cd123bc99842b80f09f254b87db4997ad30f5"><code>563cd12</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4077">#4077</a> from plotly/pjs-2.18.2-audit-fix</li>
<li><a href="https://github.com/plotly/plotly.py/commit/9a4f8536e86053a6bc9afeab8b21efded13e708b"><code>9a4f853</code></a> run npm audit fix</li>
<li><a href="https://github.com/plotly/plotly.py/commit/bce0d260adc15ad8ae50057a3138ab8913c2e654"><code>bce0d26</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4075">#4075</a> from plotly/update-plotly-js-2-18-2</li>
<li><a href="https://github.com/plotly/plotly.py/commit/ee803269ccfc5f9aada312aa655952046e847383"><code>ee80326</code></a> plotlyjs bundle</li>
<li><a href="https://github.com/plotly/plotly.py/commit/75fcfb156d5ba1e03f9f53a447f2192757dfeb8a"><code>75fcfb1</code></a> pin parmed, to fix build of pages with dash-bio</li>
<li><a href="https://github.com/plotly/plotly.py/commit/8b4b81d2209b808877d6ddbfde0b0bbe4283f8fe"><code>8b4b81d</code></a> update plotlyjs version</li>
<li><a href="https://github.com/plotly/plotly.py/commit/efe633855dee89a43300d3277e083ecad02dc4d6"><code>efe6338</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4055">#4055</a> from plotly/update-codegen</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.13.1">compare view</a></li>
</ul>
</details>
<br />
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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Bump scipy from 1.9.0 to 1.10.1
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-03-01T13:00:47
| 2023-03-03T19:49:56
|
2023-03-03T19:49:45Z
|
CONTRIBUTOR
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Bumps [scipy](https://github.com/scipy/scipy) from 1.9.0 to 1.10.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
<blockquote>
<h1>SciPy 1.10.1 Release Notes</h1>
<p>SciPy <code>1.10.1</code> is a bug-fix release with no new features
compared to <code>1.10.0</code>.</p>
<h1>Authors</h1>
<ul>
<li>Name (commits)</li>
<li>alice (1) +</li>
<li>Matt Borland (2) +</li>
<li>Evgeni Burovski (2)</li>
<li>CJ Carey (1)</li>
<li>Ralf Gommers (9)</li>
<li>Brett Graham (1) +</li>
<li>Matt Haberland (5)</li>
<li>Alex Herbert (1) +</li>
<li>Ganesh Kathiresan (2) +</li>
<li>Rishi Kulkarni (1) +</li>
<li>Loïc Estève (1)</li>
<li>Michał Górny (1) +</li>
<li>Jarrod Millman (1)</li>
<li>Andrew Nelson (4)</li>
<li>Tyler Reddy (50)</li>
<li>Pamphile Roy (2)</li>
<li>Eli Schwartz (2)</li>
<li>Tomer Sery (1) +</li>
<li>Kai Striega (1)</li>
<li>Jacopo Tissino (1) +</li>
<li>windows-server-2003 (1)</li>
</ul>
<p>A total of 21 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.</p>
<h1>SciPy 1.10.0 Release Notes</h1>
<p>SciPy <code>1.10.0</code> is the culmination of <code>6</code> months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with <code>python -Wd</code> and check for <code>DeprecationWarning</code> s).
Our development attention will now shift to bug-fix releases on the
1.10.x branch, and on adding new features on the main branch.</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/scipy/scipy/commit/c1ed5ece8ffbf05356a22a8106affcd11bd3aee0"><code>c1ed5ec</code></a> REL: 1.10.1 release commit [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/5f022bdff87a23b911cb23e78049319b439bb069"><code>5f022bd</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/scipy/scipy/issues/18001">#18001</a> from tylerjereddy/treddy_scipy_1_10_1_rd2</li>
<li><a href="https://github.com/scipy/scipy/commit/5789a76941463338cea7c3824bbe2424cb1b3bd2"><code>5789a76</code></a> MAINT: test wheel builds [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/79bc9c3a0efedee65e17b4a4df917a47150b9af2"><code>79bc9c3</code></a> DOC: update relnotes/mailmap</li>
<li><a href="https://github.com/scipy/scipy/commit/6abc551721757b197b5465fc2e639098a8fc9e2c"><code>6abc551</code></a> BUG: diffev exponential crossover</li>
<li><a href="https://github.com/scipy/scipy/commit/9bb12cd08786a323f5b3dbd57061047d971eae58"><code>9bb12cd</code></a> DOC: update link of the logo in the readme</li>
<li><a href="https://github.com/scipy/scipy/commit/c33c67926faa54f925c2a89e74549c3327787c83"><code>c33c679</code></a> BUG: Use raw strings for paths</li>
<li><a href="https://github.com/scipy/scipy/commit/78e790cf763e62014a9605ac31eeea19deccece7"><code>78e790c</code></a> Fix powm1 overflow handling</li>
<li><a href="https://github.com/scipy/scipy/commit/a225f2ba526570d3dd6fb096417174c4e9f40787"><code>a225f2b</code></a> BUG: fix Johnson's algorithm.</li>
<li><a href="https://github.com/scipy/scipy/commit/04e26b6ca442373af664c3a84864c68db9902478"><code>04e26b6</code></a> BUG: special: Fix handling of <code>powm1</code> overflow errors (<a href="https://github-redirect.dependabot.com/scipy/scipy/issues/17855">#17855</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/scipy/scipy/compare/v1.9.0...v1.10.1">compare view</a></li>
</ul>
</details>
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PR_kwDOACgets5LMTMq
| 2,875
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Add .circleci/config.yml
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[] | 2023-03-03T06:02:13
| 2023-03-03T06:04:53
|
2023-03-03T06:04:40Z
|
NONE
|
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## Summary
Include a summary of major changes in bullet points:
- Feature 1
- Feature 2
- Fix 1
- Fix 2
## Todo (if any)
If this is a work-in-progress, write something about what else needs to be done
- Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, but please put \[WIP\] in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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PR_kwDOACgets5LT_3h
| 2,876
|
IO: add passthrough kwargs to write / from_file
|
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[] | null |
[
"Nevermind; still impossible to do this properly and satisfy `mypy`."
] | 2023-03-05T20:29:28
| 2024-10-10T01:54:53
|
2023-03-05T21:09:55Z
|
CONTRIBUTOR
|
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Adds passthrough keyword arguments in `write_file` and `from_file`. This allows developers to add keyword arguments to `get_string` and `from_string` methods when implementing `InputFile` classes and still rely on the base `write_file` and `from_file`.
Prompted by my review of https://github.com/materialsproject/pymatgen/pull/2692
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PR_kwDOACgets5LUZ50
| 2,877
|
Fix ruff E741 ambiguous variable names
|
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[] | 2023-03-06T01:06:08
| 2023-03-08T02:35:55
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2023-03-08T02:35:54Z
|
MEMBER
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PR_kwDOACgets5LZNtG
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New class to handle `NcICOBILIST.lobster` files
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[
"I think the errors here should (mostly) disappear if you pull in `master` again.",
"Hi @janosh thx for looking into this :)\r\nMight be that people cannot use it right away because in the meantime we (+ @JaGeo ) found several problems in how LOBSTER outputs the NcICOBILIST.lobster file (but my test files are not affected as I created them mostly manually). ",
"> Hi @janosh thx for looking into this :) Might be that people cannot use it right away because in the meantime we (+ @JaGeo ) found several problems in how LOBSTER outputs the NcICOBILIST.lobster file (but my test files are not affected as I created them mostly manually).\r\n\r\nThe failing checks are caused by my implementation of the wrong format for the pytests. I will correct that within the next weeks and then I hope this can be merged, even though for now certain NcICOBILIST.lobster outputs should be handled with some caution.",
"Hi @janosh :D \r\ncould you help me to figure out what is making the tests fail and how we can make this PR successful?\r\n\r\n",
"Could you do an empty commit to get another run of the tests, @QuantumChemist ?\r\n\r\n`git commit --allow-empty -m \"Empty-Commit\"`",
"> Could you do an empty commit to get another run of the tests, @QuantumChemist ?\r\n> \r\n> `git commit --allow-empty -m \"Empty-Commit\"`\r\n\r\nI had to commit some changes anyways :)",
"Hi @janosh :D\r\nI think I addressed all issues. ",
"yay 🎉 thank you very much for your help @janosh!"
] | 2023-03-06T17:26:17
| 2023-10-04T19:23:16
|
2023-10-04T19:22:01Z
|
CONTRIBUTOR
|
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## Summary
Implemented a class to handle multi-center ICOBIs via NcICBILIST.lobster files with pymatgen in `pymatgen/io/lobster/outputs.py` and updated some comments. `Ncicobilist` is similar to `Icohplist` but not identical because of the different format styles of NcICOBILIST.lobster and ICO**LIST.lobster output files.
Added the respective NcICOBI test files to `test/files/cohp` for non-spinpolarized, non-orbitalwise case etc.
## Todo (if any)
Checking LOBSTER version (done)
Adapt for orbitalwise case. (will leave that out for now)
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<!--pre-commit.ci start-->
updates:
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- [github.com/MarcoGorelli/cython-lint: v0.12.4 → v0.12.5](https://github.com/MarcoGorelli/cython-lint/compare/v0.12.4...v0.12.5)
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PR_kwDOACgets5LdJEZ
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Handle serial version of VASP when reading the OUTCAR
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[] | null |
[
"Thanks! Even if it's an edge case, always good to handle things correctly.\r\n\r\nCould you compress `test_files/OUTCAR.serial` and then load the zipped file in your test? Important to minimize file sizes for people cloning the repo.",
"Sure! Done now.",
"Thanks! 👍 "
] | 2023-03-07T09:43:20
| 2023-03-08T17:07:35
|
2023-03-08T17:07:35Z
|
CONTRIBUTOR
|
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## Summary
When compiling VASP without MPI support, the OUTCAR has a few differences in some places compared to a compilation including MPI.
- In the preamble, the number of cores is not indicated with `running on 16 total cores` but `serial version`
- When reporting the number of plane waves for each k-point, in the serial version, only the `maximum number of plane-waves` is reported while in the parallel version, the `maximum and minimum number of plane-waves per node` is reported before and used as a footer_pattern to read the table-like data.
Of course, compiling the serial version of VASP must be a pretty rare thing to do, and I did it for testing only.
In this small PR, I simply accounts for these changes and add a small test.
I did not check whether other output files were affected by this.
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Optimizations for SubstrateAnalyzer
|
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[] | 2023-03-07T22:30:19
| 2023-03-07T22:55:53
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2023-03-07T22:55:52Z
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MEMBER
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## Summary
I noticed SubstrateAnalyzer was perhaps a bit on the slow side. There are a few optimizations here: for a test set of 100 structures, these took the evaluation time down from ~43 minutes down to 193 seconds.
Optimizations include some caching, particularly of calls to spglib, since these are expensive and often repeated multiple times for the same structure (e.g., in tensor operations for IEEE conversion). I also optionally allow the use of `numba` here, which provides an additional ~3x improvement.
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Add skip_checks pull request need approval
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[
"[I left a comment](https://github.com/materialsproject/pymatgen/pull/2836#issuecomment-1474312688) asking for a few changes."
] | 2023-03-08T16:43:43
| 2023-03-24T00:41:42
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2023-03-24T00:41:00Z
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CONTRIBUTOR
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A pull request I submitted is not going through any checks. it says "This workflow requires approval from a maintainer."
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Add structure_property attribute to `Structure`
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[
"I don't see a big issue with it, but what is the difference with `structure.hello = \"world\"`? Unlike sites and Elements which are designed to be immutable for the most part, there are no restrictions with structure.",
"The only issue with setting properties like that is they won't be serialised through `structure.as_dict()`. I'd like the information to be serialised so that it could be stored in a database along side the structure and then used in future MD jobs.",
"I was also considering proposing this feature. The ability to store metadata on structures like DFT params used is one thing I like about `AseAtoms` that `pymatgen` is currently lacking. It would also help with provenance.",
"@utf/@janosh, I would also really love this if it could be added eventually. I'm expecting something like `Structure.structure_properties` with a type `dict`. It should also be added to `Molecule`.",
"Big open question is serialization. I think it would be straightforward to read and write `structure_properties` from/to JSON. Don't know enough about other formats like CIF, POSCAR, etc. whether they support this.",
"I don't think it really has any relevance to the CIF or POSCAR. It should only be read/written out to JSON (or perhaps, pandas Dataframe as well but nobody really uses that I imagine).\r\n\r\nNote that if the user stores an `Atoms` object in `structure_properties`, there is a way to serialize/deserialize it even though it's not `MSONable`. You would do:\r\n\r\n```python\r\nfrom ase.io.jsonio import decode, encode\r\n\r\nencode(atoms) # serialize\r\ndecode(atoms) # deserialize\r\n```",
"I would say this:\r\n1. There are already structure properties (e.g., charge).\r\n2. In effect, the Structure.properties dict would essentially be for \"second class\" properties that are deemed not important enough to be a first class Structure.charge like property.\r\n3. I also think that using inspection, there would be a way to serialize a structure.hello = \"world\" property. Might be hard to do in a super robust way, but might solve all these problems once and for all.\r\n\r\nIn any case, I have no real objection to adding properties to Structure. (But pls do not call it `Structure.structure_properties`).",
"> But pls do not call it Structure.structure_properties).\r\n\r\nAgreed. 😄 "
] | 2023-03-09T11:12:34
| 2023-08-24T18:41:49
|
2023-08-24T18:41:49Z
|
MEMBER
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I'd like to add a `structure_property` attribute to the `Structure` class. Sometimes it is useful to have structure-wide properties that can be stored alongside the structure. One example is the `Poscar.predictor_corrector_preamble` which is necessary to write structures to continue MD simulations. Currently, only site-specific properties can be stored (e.g., the velocities and predictor-corrector coordinates).
With the present `Structure` class, it is not possible to store structures that can be used to continue MD simulations without storing this data separately which is quite unwieldy. I'm sure there are other instances where I've wanted to do this.
@shyuep would you support me adding this feature? The API would be the same as for adding site properties. E.g.,
```python
structure.add_structure_property("property_name", property_value)
```
This is related to https://github.com/materialsproject/atomate2/issues/185
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I_kwDOACgets5gc9Ya
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PDPlotter fails when there is no unstable entry
|
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[
"What is the error message?",
"This is definitely a bug. I noticed it recently as well, and I am sorry -- I think it might be related to Plotly code I wrote a few years back. \r\n\r\nI have been meaning to fix and will try to address soon!",
"@mattmcdermott There's a strange swapping in the order of keys and values in the plot_data dicts here:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/c8f99910ce7dec0d1a47d4678becd7f942d0c6f7/pymatgen/analysis/phase_diagram.py#L3026-L3027\r\n\r\nCoords as keys, entries as values, followed by entries as keys, coords as values. Is this by accident?"
] | 2023-03-10T01:08:12
| 2023-03-24T01:28:27
|
2023-03-24T01:28:27Z
|
NONE
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**Describe the bug**
PDPlotter fails when there is no unstable entry.
This issue only occurs when using "plotly" as the backend. 'matplotlib' backend would work.
**To Reproduce**
Steps to reproduce the behavior:
```
from pymatgen.core import Composition
from pymatgen.analysis.phase_diagram import PhaseDiagram,PDEntry,PDPlotter
pd_entries = []
for name in ['Li','Co','O']:
pde = PDEntry(Composition(name),0)
pd_entries.append(pde)
pd = PhaseDiagram(pd_entries)
plotter = PDPlotter(pd,backend='plotly',show_unstable=False)
plotter.get_plot().show()
```
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PR_kwDOACgets5Lulbq
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MPAqueousCompatiblity: compute hydrate correction using reduced rather than full composition
|
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[
"Since no concerns / comments have been raised, I'm going to move this out of WIP status.",
"@janosh soubds like this is ready to go. ",
"@arosen93 Thanks for the ping!\r\n\r\n@rkingsbury Thanks for adding tests! 👍 Merging now. "
] | 2023-03-10T01:25:15
| 2024-10-10T01:54:57
|
2023-06-02T14:08:36Z
|
CONTRIBUTOR
|
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## Summary
Small change to the way `MaterialsProjectAqueousCompatibility` corrects energies for materials containing `H2O`.
As [described by a user on MatSci](https://matsci.org/t/mpaqueouscompatibility-applies-hydrate-correction-to-non-hydrate-materials/47360/2), the current way of detecting whether a material contains 'H2O' can lead to false positives for formulas like `Li2O2H2`, causing this material to be corrected as if it were a hydrate when in fact it is not.
Here, I change the detection of hydrates to be based on `reduced_composition` instead of `composition` to avoid such false positives.
Tests appear to pass, but flagging @montoyjh and @as2362 in case there are concerns about how this will impact Pourbaix Diagrams. This should cause the energies of some -OH phases to change a bit because they won't receive the hydrate correction.
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find_points_in_sphere() throws error regarding data type
|
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[
"Issue is resolved when defining pbc like:\r\npbc = np.array([1, 1, 1], dtype=int)\r\n\r\nRecommend revising docstring to specify this required typing",
"I'm no Cython expert but I think #2907 should fix this error."
] | 2023-03-10T20:59:10
| 2023-03-24T00:25:44
|
2023-03-24T00:19:31Z
|
NONE
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## Describe the bug
"TypeError: a bytes-like object is required, not 'list'" is thrown when passing the appropriate types.
The doc string reads: "pbc: (list of bool) whether to set periodic boundaries" and I am passing a list of bools.
All other dtypes align with the requested types.
## To Reproduce
Steps to reproduce the behavior:
1. Call `pymatgen.core.neighbors.find_points_in_sphere()` with the correct types ('pbc' as a list of bools).
_Provide any example files that are needed to reproduce the error, especially if the bug pertains to parsing of a file._
## Expected behavior
The function should return:
- index1 (n, )
- index2 (n, )
- offset_vectors (n, 3)
- distances (n, )
index1 of center_coords, and index2 of all_coords that form the neighbor pair. Offset_vectors are the periodic image offsets for the all_coords.
## Screenshots
**Environment (please supply relevant versions and platform info):**
- OS: Mac
- Version: tested with (2022.3.7) and (2023.2.28)
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| 1,620,369,900
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I_kwDOACgets5glOHs
| 2,888
|
Lots of false energy messages in the entries returned through the new Materials project API
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[] | null |
[
"@munrojm I think this is for you.",
"@zifengdexiatian which version of `mp-api` are you running with? I don't see this issue on my end with the most up to date client. Try updating with `pip install mp-api --upgrade` and see if the problem persists.",
"> @zifengdexiatian which version of `mp-api` are you running with? I don't see this issue on my end with the most up to date client. Try updating with `pip install mp-api --upgrade` and see if the problem persists.\r\n\r\nIt worked, I upgraded mp-api from 0.29.8 to 0.30.1, thanks a lot !"
] | 2023-03-12T13:39:42
| 2023-03-13T01:49:00
|
2023-03-13T01:49:00Z
|
NONE
|
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**Describe the bug**
When I use
from pymatgen.ext.matproj import MPRester
with MPRester('new_API_KEY') as mpr:
entries=mpr.get_entries_in_chemsys('Cs-Pb-I')
to return all the entries, it contains obviously incorrect energy information, e.g. mp-540839-R2SCAN ComputedStructureEntry - Cs4 Pb4 I12 (CsPbI3) Energy (Uncorrected) = -644.3128 eV (-32.2156 eV/atom), which does not match the search results directly on the MP website by a huge margin. This leads to a huge error in the calculation of e above hull. When I use the API_KEY of the old version of Materials project, the returned entries are accurate and the error disappears.
**screenshots**
<img width="1131" alt="image" src="https://user-images.githubusercontent.com/83349433/224548778-0c72728c-6ebf-41ac-a48a-cf06ca95b0a8.png">
<img width="1122" alt="image" src="https://user-images.githubusercontent.com/83349433/224548805-4bd61b85-fab0-4625-ab43-5000aa86f310.png">
**Environment (please supply relevant versions and platform info):**
- OS: both Mac M1 and windows11
- Version (Latest 2023.3.10)
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| 1,620,515,414
|
PR_kwDOACgets5L1-V7
| 2,889
|
Replace `codecs.open` with `io.open` for reading `PotcarSingle`
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[] | 2023-03-12T21:17:28
| 2023-03-13T20:36:51
|
2023-03-13T20:36:50Z
|
MEMBER
|
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Following private discussion about unicode issues when reading POTCARs and @mkhorton mentioning `codecs.open` is potentially.
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| 1,621,327,086
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PR_kwDOACgets5L4rUU
| 2,891
|
Read input parameters for both internal and cartesian coordinates
|
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[] | null |
[
"This is causing some test failures. Could you take a look?\r\n\r\n```py\r\n ind = toks.pop(0)\r\n data = toks.pop(0)\r\n try:\r\n nn.append(int(ind))\r\n except ValueError:\r\n nn.append(species.index(ind) + 1)\r\n try:\r\n> val = float(data)\r\nE ValueError: could not convert string to float: 'B1'\r\n\r\npymatgen/io/gaussian.py:228: ValueError\r\n\r\nDuring handling of the above exception, another exception occurred:\r\n\r\nself = <tests.test_gaussian.GaussianInputTest testMethod=test_from_file>\r\n\r\n def test_from_file(self):\r\n filepath = os.path.join(test_dir, \"MethylPyrrolidine_drawn.gjf\")\r\n> gau = GaussianInput.from_file(filepath)\r\n\r\npymatgen/io/tests/test_gaussian.py:[79]\r\n```",
"The reason is `spaces` need be different for internal coordinates and cartesian coordinates, so the two types of coordinates should be treated differently. Now, I have fixed these failures.",
"Thanks! 👍 "
] | 2023-03-13T11:50:13
| 2023-05-19T20:13:53
|
2023-03-15T14:29:23Z
|
CONTRIBUTOR
|
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Closes #2863, closes #2865.
If there is only one blank line between `coord_lines` and `input_lines`, `input_params` will be ignored. So set `spaces` as 1 to avoid this case.
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PR_kwDOACgets5L7ns0
| 2,892
|
Minor Q-Chem fix
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[] | null |
[
"Test failure here is unrelated. Let me know if this is ready to go.",
"@janosh good to go"
] | 2023-03-13T20:24:38
| 2023-03-14T02:41:40
|
2023-03-14T02:41:40Z
|
CONTRIBUTOR
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## Summary
- Switch multiple_outputs_from_file to staticmethod to play nicely with Atomate
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I_kwDOACgets5gyLHM
| 2,893
|
str.join() error
|
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[
"I believe this was already fixed in https://github.com/materialsproject/pymatgen/pull/2891.\r\n\r\nBut the code could still be improved. There's no reason to use join in the first place if it's just 2 items.\r\n\r\n",
"@janosh yes , it could be just a string concatenation."
] | 2023-03-14T15:49:07
| 2023-03-23T15:06:34
|
2023-03-23T13:52:38Z
|
NONE
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Error that occurs:
```py
TypeError: str.join() takes eactly one argument (2 given)
```
I am gettting this error while trying to run "Gaussian_input.write_file(paramset=paramset, mol=mol)" where both the paramset and mol are correct inputs. Paramset includes the route parameters, and none otherwise, and the mol is an xyz string.
I believe there may be an issue where in `pymatgen.io.gaussian.py` on line 423,
```py
" ".join(site.species_string, " ".join([to_s(j) for j in site.coords]))
```
everything within the external `join` function needs to be in brackets.
|
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PR_kwDOACgets5MHMki
| 2,894
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Breaking: Rename `gen_sl_transform_matricies->gen_sl_transform_matrices`
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[] | 2023-03-15T14:28:38
| 2023-03-16T02:22:47
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2023-03-16T02:22:46Z
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MEMBER
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Also, fix variable name clash `shell == shell` in `pymatgen/analysis/xps.py` and fix CI failure following e4bde8e400.
|
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I_kwDOACgets5g6lEv
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Mulit element POTCAR loading broken.
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[
"This is not fixed yet (2023.9.25).\r\n\r\n```\r\n~/.local/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1806: UnknownPotcarWarning: POTCAR data with symbol O does not match any VASP POTCAR known to pymatgen. There is a possibility your POTCAR is corrupted or that the pymatgen database is incomplete.\r\n warnings.warn(\r\n~/.local/lib/python3.11/site-packages/pymatgen/io/vasp/inputs.py:1813: UserWarning: POTCAR with symbol Fe_pv and functional\r\nPBE has a SHA256 hash defined,\r\nbut the computed hash differs.\r\nYOUR POTCAR FILE HAS BEEN CORRUPTED AND SHOULD NOT BE USED!\r\n warnings.warn(\r\n```\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/4bff21d33625bc9f7077c7b4eb06098d1f50277c/pymatgen/io/vasp/inputs.py#L1970\r\n\r\nThe hashes of POTCAR_test.gz in the OP are `5d22e414b1f82158bf2c7ecb8b97b28fd0923e48cadc1c3bf74d524558f5dd32` and `52459ef0a41f1e32977d35179f8b492c701fda3d7e2f9b778c5c2267c5f2dbc0`.\r\nThe former is correct:\r\n\r\n```console\r\n$ grep SHA256 Fe_pv/POTCAR\r\n SHA256 = 5d22e414b1f82158bf2c7ecb8b97b28fd0923e48cadc1c3bf74d524558f5dd32 Fe_pv/POTCAR\r\n$ sed -e /COPYR/d -e /SHA256/d Fe_pv/POTCAR | sha256sum -\r\n5d22e414b1f82158bf2c7ecb8b97b28fd0923e48cadc1c3bf74d524558f5dd32 -\r\n```\r\n\r\nThe latter is however strangely computed, which can be reproduced by\r\n\r\n```console\r\n$ { sed -e /COPYR/d -e /SHA256/d -e '/^ *PAW_PBE/s/^ *//' -e '/^ *End of/s/^ *//' Fe_pv/POTCAR; printf ''; } | sha256sum -\r\n52459ef0a41f1e32977d35179f8b492c701fda3d7e2f9b778c5c2267c5f2dbc0 -\r\n```\r\n",
"Hi @e-kwsm !\r\n\r\nAFAIK there were some more changes to this since March. There is a pending PR that should fix this along another thing: #3204.\r\n\r\nHowever, POTCAR validation will likely be changed completely anyhow, making this a mute problem. See PR #3351.",
"I am not sure #3351 intends to address this, or checksum will be dropped in future, but anyway SHA256 computation is still (7cc629df501045d53857f26b59348f08a9da3fba) broken (https://github.com/materialsproject/pymatgen/issues/2895#issuecomment-1738275801)."
] | 2023-03-15T17:33:42
| 2023-10-03T02:03:43
|
2023-03-15T17:40:58Z
|
CONTRIBUTOR
|
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**Describe the bug**
Since commit e4bde8e400d28095425d0b1e7f0b1c8923ddc13a it seems that loading is broken if any but the first POTCAR in the file has a sha256 hash.
I really appreciate the effort by @shyuep to clean up the code and get rid of the regex stuff and unicode handling. However, a small mistake appears to have slipped in in line 2277 of `pymatgen/io/vasp/inputs.py`. There should be a unicode end of line character still:
~~~
potcar_strings = fdata.split("End of Dataset\n")
~~~
instead of
~~~
potcar_strings = fdata.split("End of Dataset")
~~~
If that is included, also the test that got modified in the commit can be changed back it seems.
However, since this all seems a bit fragile, I suggest to actually also downgrade the ValueError that is raised in line 1829 in `pymatgen/io/vasp/inputs.py` to a warning.
**To Reproduce**
load the attached POTCAR (containing O and Fe_pv_with_hash from `pymatgen/test_files/POT_GGA_PAW_PBE_54` with the Fe Potcar following the O) into a Potcar object:
[POTCAR_test.gz](https://github.com/materialsproject/pymatgen/files/10982996/POTCAR_test.gz)
~~~
from pymatgen.io.vasp.inputs import Potcar
pot = Potcar.from_file('POTCAR_test.gz')
~~~
results in:
~~~
ValueError: POTCAR with symbol Fe_pv and functional
PBE has a SHA256 hash defined,
but the computed hash differs.
YOUR POTCAR FILE HAS BEEN CORRUPTED AND SHOULD NOT BE USED!
~~~
**Expected behavior**
There should be no error for the SHA256, since the POTCAR is good.
**Environment (please supply relevant versions and platform info):**
- OS: Linux
- Version 2023.3.10
**Additional context**
I am happy to make a pull request if this is wanted.
|
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Enable Structure relaxations with TrajectoryObserver
|
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[
"FYI @janosh, there was no need to use m3gnet's custom `TrajectoryObserver`. ASE's native `Trajectory` object stores all the desired properties (e.g. positions, energies, forces, cells, stresses). I'm going to use ASE's `Trajectory` object in #3044 so that the user doesn't have to install `m3gnet` just to have a trajectory returned.",
"@arosen93 That's interesting. Are the two fully compatible? I think I checked back then that [`TrajectoryObserver` doesn't inherit](https://github.com/materialsvirtuallab/m3gnet/blob/d4ea965150bbbf2edb5239ee9dffe90635cffc5c/m3gnet/models/_dynamics.py#L182-L186) from ASE's `Trajectory` class. Of course, could be that they share enough API anyway. Didn't test that.\r\n\r\nThis might also interest @matthewkuner in the context of https://github.com/materialsproject/atomate2/pull/322. I think we discussed on Slack how best to record and expose the frames of an ML relaxation to `atomate2`.",
"EDIT: I now understand why the `TrajectoryObserver` was used. It was so you don't have any file I/O since m3gnet doesn't write out anything to the filesystem in contrast with most ASE calculators. Either way, they aren't interoperable because the schema is slightly different even though they share the same properties.\r\n\r\n-----\r\nAs far as I was able to tell, they share the same properties. However, they\r\nare formatted slightly differently, so that's worth noting.\r\n\r\nI wonder if TrajectoryObserver exists so ASE doesn't write out a trajectory\r\nfile every step, which may lead to large file I/O times for large\r\nstructures. That said, keeping it all in memory could be problematic too.\r\nProbably worth figuring it out in my linked PR.\r\n\r\nOn Tue, Jun 6, 2023, 7:02 AM Janosh Riebesell ***@***.***>\r\nwrote:\r\n\r\n> @arosen93 <https://github.com/arosen93> That's interesting. Are the two\r\n> fully compatible? I think I checked back then that TrajectoryObserver\r\n> doesn't inherit\r\n> <https://github.com/materialsvirtuallab/m3gnet/blob/d4ea965150bbbf2edb5239ee9dffe90635cffc5c/m3gnet/models/_dynamics.py#L182-L186>\r\n> from ASE's Trajectory class. Of course, could be that they share enough\r\n> API anyway. Didn't test that.\r\n>\r\n> This might also interest @matthewkuner <https://github.com/matthewkuner>\r\n> in the context of materialsproject/atomate2#322\r\n> <https://github.com/materialsproject/atomate2/pull/322>. I think we\r\n> discussed on Slack how best to record and expose the frames of an ML\r\n> relaxation to atomate2.\r\n>\r\n> —\r\n> Reply to this email directly, view it on GitHub\r\n> <https://github.com/materialsproject/pymatgen/pull/2896#issuecomment-1578828273>,\r\n> or unsubscribe\r\n> <https://github.com/notifications/unsubscribe-auth/ACCFWGHQVKH6JDXUDLNRPMDXJ4Z67ANCNFSM6AAAAAAV7G2YIQ>\r\n> .\r\n> You are receiving this because you were mentioned.Message ID:\r\n> ***@***.***>\r\n>",
"@arosen93 @janosh In case it is relevant, the [matgl repository](https://github.com/materialsvirtuallab/matgl) just pushed a pretrained m3gnet model. Moreover, that new matgl repo is meant to eventually replace the old [m3gnet repo](https://github.com/materialsvirtuallab/m3gnet)",
"Thanks! I opened an issue for it.",
"Apologies if missing something obvious, but why not use/adapt pymatgen’s Trajectory?\r\n\r\nIf one wants to use ASE’s Trajectory, it would be better to just use ASE. Mixing and matching data types doesn’t seem ideal.",
"I want to make the distinction between internal use of another library’s data type (within the body of a function) and the function return type too.",
"I agree that it would probably be better to return a Pymatgen Trajectory since the user presumably wants to predominantly stay in the Pymatgen ecosystem if they are calling `Structure.relax()`.\r\n\r\nHopefully someone will open a PR to address it because that one won't be me :)",
"Actually, what should perhaps really be done here is add an ASE `Trajectory`/m3gnet `TrajectoryObserver` to Pymatgen `Trajectory` (and vice versa) option to the `pymatgen.io.ASEAtomsAdaptor`. Then it would be extra trivial to simply return the transformed trajectory object in `Structure.relax()`.",
"> Hopefully someone will open a PR to address it because that one won't be me :)\r\n\r\nI'd be happy to do that at some point. No firm commitment though.\r\n\r\n\r\n\r\n> Actually, what should perhaps really be done here is add an ASE `Trajectory`/m3gnet `TrajectoryObserver` to Pymatgen `Trajectory` (and vice versa) option to the `pymatgen.io.ASEAtomsAdaptor`. Then it would be extra trivial to simply return the transformed trajectory object in `Structure.relax()`.\r\n\r\nGood idea! Considering @shyuep is a significant stakeholder in this, I'd be interested in his take. Either way, should probably become a new issue instead of closed PR discussion. 😄 ",
"I would say I support the suggestion but it will probably take some while before someone spends the effort doing it. "
] | 2023-03-18T03:34:23
| 2023-06-07T21:23:56
|
2023-03-18T04:13:10Z
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MEMBER
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813019427e add `return_trajectory` option to `Structure.relax()`
64dee2a8ba test new option in `test_relax_with_observer()`
db0871a327 convert vars to snake case
|
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PR_kwDOACgets5MXENM
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Fix D417 in `pymatgen/core`
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[] | 2023-03-18T15:18:13
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2023-03-18T15:39:11Z
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A lot of functions have undocumented arguments. This PR adds doc strings description for some of them.
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check vasp ionic convergence based on EDIFFG besides NSW
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[
"Maybe our resident VASP expert @arosen93 can chime in?",
"@janosh: This looks fine to me. The `len(final_esteps) < self.parameters[\"NELM\"]` check is the check for the SCF convergence and is unrelated to the \"ionic loop\" (i.e. relaxation trajectory). The line highlighted is indeed correct for checking that the SCF is converged.\r\n\r\nThe text below is the relevant data for the ionic convergence.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/89fc2d6f37dd4677e8f861f3227985daf6d3f812/pymatgen/io/vasp/outputs.py#L629-L636\r\n\r\nThat said, it is not clear to me what scenario would exist where convergence is achieved but this condition is not met. @mdforti suggests that it's possible to stop the ionic loop based on the walltime, but by this very definition that implies that the ionic loop has not yet converged (since the user has stopped it manually). I think Pymatgen has to rely on what VASP says is converged and not the user.\r\n\r\nA potential middle ground might be to add an optional kwarg that the user can set to check convergence by EDIFFG instead, regardless of the number of steps, but I think this is a somewhat niche use case barring any further justification.",
"@arosen93 Thanks for clarifying!\r\n\r\n@mdforti I'll close this for now. Feel free re-open with additional details if we missed something.",
"you are right,\r\n\r\n- I must have made a typo on the first comment, I am referring on cases where ionic relaxation convergence should be tested. \r\n- I just now see the converged_ionic method, thanks for pointing tho this. \r\n\r\nthat said, here is one scenario where converged_ionic wont work. I myself run in HPCs with max walltime (i.e. 24 hours), and some structures hard to converge. There should be smarter ways to do this, but I typically run a script which writes a STOPCAR if the run time is close to max walltime, so I get the CHGCAR and the calculation can be restarted easily. then I run another script which relaunches calculations if necessary. This implies checking weather the forces are converged or not, because the number of ionic steps will always be smaller than NSW.\r\n\r\nI understand now this might not be general enough, and actually this is already solved for me on my side. \r\n\r\nThank you all to look at this. "
] | 2023-03-18T15:39:33
| 2023-05-15T07:06:05
|
2023-05-14T22:54:12Z
|
NONE
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currently convergence of ionic loop of VASP calculation is checked on the number of ionic steps:
https://github.com/materialsproject/pymatgen/blob/89fc2d6f37dd4677e8f861f3227985daf6d3f812/pymatgen/io/vasp/outputs.py#L626
but this is wrong. many times it is possible to stop the ionic loop based i.e. on walltime using STOPCAR and the checker would fail to recognize the convergence at restarting the calculation.
The convergence should be checked also against EDIFFG. I understand this might get complicated due to EDIFFG might be positive or negative etc.
It is also possible to search parsing for the string "reached required accuracy" but that is also incomplete, as it is sometimes desirable to change the EDIFF (the string would be present from previous step)
Thank you for considering this feature request!
|
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fix AbinitHeader functionality broken during linting
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[
"Good catch and thanks for the new test! 👍 "
] | 2023-03-19T22:48:17
| 2023-03-21T03:43:14
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2023-03-21T03:43:02Z
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CONTRIBUTOR
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I_kwDOACgets5hSd3M
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Wulff plot not working
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[
"Bug confirmed.\r\n\r\n@CifLord Are you familiar with this code? If you have time, maybe you could take look?",
"Yeah I can take a look, thanks for letting me know!",
"Made a pull request to fix this. @cedenoruel do you know what version of matplotlib you're using? If its 3.6.0 or higher, its not compatible with the Wulffshape plotter. In any case, the pull request should fix the compatibility issue now",
"> Made a pull request to fix this. @cedenoruel do you know what version of matplotlib you're using? If its 3.6.0 or higher, its not compatible with the Wulffshape plotter. In any case, the pull request should fix the compatibility issue now\r\n\r\n@CifLord @janosh Now, it's working again. Thank you very much. "
] | 2023-03-20T14:28:08
| 2023-04-26T12:33:15
|
2023-04-22T02:02:48Z
|
NONE
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**The Bug**
The wulff.show() function which normally gives a static plot no longer works.
Instead, it returns `<Figure size 576x576 with 0 Axes> `
However, wulff.get_plotly() works (which gives an interactive plot).
**To Reproduce**
```
!pip install pymatgen
# Import the neccesary tools to generate surfaces
from pymatgen.core.surface import SlabGenerator, generate_all_slabs, Structure, Lattice
# Import the neccesary tools for making a Wulff shape
from pymatgen.analysis.wulff import WulffShape
lattice = Lattice.cubic(3.508)
Ni = Structure(
lattice,
["Ni", "Ni", "Ni", "Ni"],
[[0, 0, 0], [0, 0.5, 0], [0.5, 0, 0], [0, 0, 0.5]],)
surface_energies_Ni = {
(3, 2, 0): 2.3869,
(1, 1, 0): 2.2862,
(3, 1, 0): 2.3964,
(2, 1, 0): 2.3969,
(3, 3, 2): 2.0944,
(1, 0, 0): 2.2084,
(2, 1, 1): 2.2353,
(3, 2, 2): 2.1242,
(3, 2, 1): 2.3183,
(2, 2, 1): 2.1732,
(3, 3, 1): 2.2288,
(3, 1, 1): 2.3039,
(1, 1, 1): 1.9235,
}
miller_list = surface_energies_Ni.keys()
e_surf_list = surface_energies_Ni.values()
# We can now construct a Wulff shape with an accuracy up to a max Miller index of 3
wulffshape = WulffShape(Ni.lattice, miller_list, e_surf_list)
# Let's get some useful information from our wulffshape object
print(
"shape factor: %.3f, anisotropy: \
%.3f, weighted surface energy: %.3f J/m^2"
% (
wulffshape.shape_factor,
wulffshape.anisotropy,
wulffshape.weighted_surface_energy,
)
)
# If we want to see what our Wulff shape looks like
wulffshape.show()
```
- OS: (Windows 10)
- Platform: Google Colab
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PR_kwDOACgets5MfFLw
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Cp2k patch
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[
"Thanks! 👍 ",
"Why protect only `ELEMENT` and not `KIND`? When defining basis sets and pseudopotentials per element, wouldn't `SUBSYS` include something like this?\r\n\r\n```\r\n &KIND F\r\n BASIS_SET some_basis_set\r\n POTENTIAL some_ecp\r\n &END KIND\r\n```",
"@svandenhaute It never came up because the input sets generate kind names with numerical suffixes, so the set will produce \r\n\r\n```\r\n &KIND F_1\r\n BASIS_SET some_basis_set\r\n POTENTIAL some_ecp\r\n &END KIND\r\n```\r\n\r\nHowever, if the input was generated in some other way, then you are right that there will be an issue. I don't have write access to the master branch, so it would be best if you could open a PR for a fix."
] | 2023-03-20T19:57:21
| 2023-12-08T19:22:40
|
2023-03-21T03:41:19Z
|
CONTRIBUTOR
|
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## Summary
Patch for cp2k module.
- Fix 1: Postprocessor typecasts Element "F" to "False". Add a workaround.
- Fix 2: Site properties are set to "None" by default, which can cause problems if user doesn't set magnetization or ghost properly. Add a check for this. Long term it might be nice to have a pydantic (or equivalent) typecasting system.
- Fix 3: Add "." for os.path.join as default. If environment isn't set right, this can cause an argument error, making debug difficult.
|
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PR_kwDOACgets5Mga9C
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Drop explicit defaults and repeated copyright notice
|
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[] | 2023-03-21T03:35:04
| 2023-03-21T03:54:02
|
2023-03-21T03:54:01Z
|
MEMBER
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8c2fda6646 os.environ.get() -> os.getenv()
a82d23326d dict.get(key, None) -> dict.get(key)
de4b02a36e remove repeated copyright notice in every source file (not needed, license applies to whole code base)
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PR_kwDOACgets5Mke8p
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|
New oxygen_edge_extender
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[
"@janosh This should be good to go"
] | 2023-03-21T17:06:55
| 2023-03-21T19:19:11
|
2023-03-21T19:19:11Z
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CONTRIBUTOR
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## Summary
OpenBabelNN() will miss molecular O-C or O-H bonds if oxygen is forming three bonds, e.g. in H3O+ or XOH2+. In order to remedy this, I have implemented pymatgen.analysis.local_env.oxygen_edge_extender in a similar vein as pymatgen.analysis.local_env.metal_edge_extender, but simpler. I have also written a test.
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I_kwDOACgets5hcp3l
| 2,904
|
Key error of io.CifParser.parse_magmoms
|
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[
"Yes, this was intentional, but I'm adding a note here to explain: the magCIF standard was a working standard, with many magCIF files \"in the wild\" prior to the standard being finalised. During this process, some of the keys changed, so there are two supported notations for this field, and the current pymatgen parser looks like it uses the older standard.\r\n\r\nThe canonical field names are defined by the IUCr, see here: https://www.iucr.org/__data/iucr/cifdic_html/3/MAGNETIC_CIF/index.html\r\n\r\nThe action here will probably be to update pymatgen to support both."
] | 2023-03-22T01:07:27
| 2023-08-15T16:26:58
|
2023-08-15T16:26:58Z
|
NONE
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I notice the static method `parse_magmoms` in class `CifParser` use the keys such as
- `_atom_site_moment_label`
- `_atom_site_moment_crystalaxis_x`
to parse atomic magnetic moments.
But the mcif files in MAGNDATA(<http://webbdcrista1.ehu.es/magndata/>), a large database with more than 2000 published magnetic structures, use the keys such as
- `_atom_site_moment.label`
- `_atom_site_moment.crystalaxis_x`.
It is a dot, not an underline, after the string '_atom_site_moment'. So `parse_magmoms` is not compatible with this mcif format.
|
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I_kwDOACgets5heID1
| 2,905
|
refined/conventional structure retaining properties not working as expected
|
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[
"I recently ran into the same issue, with magnetic moments this time. After querying FeNi (mp-2213) and calling `SpaceGroupAnalyzer(struct).get_conventional_standard_structure(keep_site_properties=True)` on it, the magnetic moments on Ni sites are incorrect. Taking a closer look, the culprit seems to be the `get_refined_structure()`, more specifically how the `site_properties` are transferred at https://github.com/materialsproject/pymatgen/blob/e2b0801ea6bf5aa30b57d922395dadd729e8f122/pymatgen/symmetry/analyzer.py#L340\r\n\r\nI won't attempt a PR at this moment but for the time being transferring the site properties some other way is probably safer.\r\n\r\nThis is a minimal repro with magnetic moments;\r\n\r\n```\r\nfrom mp_api.client import MPRester\r\nfrom pymatgen.symmetry.analyzer import SpacegroupAnalyzer\r\n\r\nwith MPRester() as mpr:\r\n struct = mpr.get_structure_by_material_id(\"mp-2213\")\r\n\r\nsga = SpacegroupAnalyzer(struct)\r\n\r\nrefined_bulk = sga.get_refined_structure(keep_site_properties=True)\r\n```\r\n\r\nwhere in the original structure the magnetic moments on Fe and Ni sites are 2.941 and 0.767, respectively, while in the refined structure they are both set to 2.941."
] | 2023-03-22T08:35:26
| 2023-06-07T10:14:11
|
NONE
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When converting a primitive cell to a conventional one with `keep_site_properties=True` (https://github.com/materialsproject/pymatgen/pull/2349), the resulting properties are incorrect.
**To Reproduce**
In this example I mark each site with a different label to find where the corresponding cite is in the resulting cell.
(this is based on mp-35591)
```python
import numpy as np
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
matrix = [[7.5866, 0.0, 0.0], [7.5866, 6.7002, 0.0], [3.7932, 4.5096, 3.1886]]
species = ["Li", "Li", "Er", "Er"] + ["S"] * 4
frac_coords = np.array([
[0.00, 0.00, 0.00],
[0.75, 0.50, 0.00],
[0.25, 0.50, 0.00],
[0.50, 0.00, 0.00],
[0.25, 0.00, 0.50],
[0.75, 0.00, 0.50],
[0.50, 0.50, 0.50],
[0.00, 0.50, 0.50],
])
structure = Structure(matrix, species, frac_coords, site_properties={"site_id" : "abcdefgh"})
structure_refined = SpacegroupAnalyzer(structure).get_refined_structure(keep_site_properties=True)
structure_conventional = SpacegroupAnalyzer(structure).get_conventional_standard_structure(keep_site_properties=True)
print(structure.site_properties["site_id"])
print(structure_refined.site_properties["site_id"])
print(structure_conventional.site_properties["site_id"])
```
Output:
```bash
['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h']
['a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c']
['a', 'a', 'a', 'a', 'b', 'b', 'b', 'b', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c']
```
**Expected behavior**
Ideally, I'd expect the sites with different properties to be treated as different ones and therefore I expect the output structures to have all the labels from `a` to `h`. Note that the result is incorrect even if the same-element sites are treated as equivalent ones. E.g., Er got a label that belonged to Li, and S got a label from Er.
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|
New release?
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[] | null |
[
"Done. v2023.3.23.",
"Thanks."
] | 2023-03-23T11:55:04
| 2023-03-23T14:42:56
|
2023-03-23T14:38:18Z
|
CONTRIBUTOR
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Dear developers,
I wonder if it's possible to release a new version of pymatgen that contains the bug fix merged in #2899.
so that I can release a new version of abipy that is required for the implementation of the ABINIT workflows in atomate2.
Best regards,
Matteo
|
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PR_kwDOACgets5MyX8I
| 2,907
|
Fix TypeError: a bytes-like object is required, not 'list' when passing triplet of bools to `find_points_in_spheres()` `pbc` kwarg
|
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[] | 2023-03-24T00:00:23
| 2023-03-24T00:19:31
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2023-03-24T00:19:30Z
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MEMBER
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Closes #2887.
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PR_kwDOACgets5MyeO6
| 2,908
|
Fix ValueError: not enough values to unpack in PDPlotter if no unstable entries in PD
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[] | 2023-03-24T00:37:10
| 2023-03-24T01:28:27
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2023-03-24T01:28:26Z
|
MEMBER
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Closes #2885.
933d3eb2e4 fix ValueError: not enough values to unpack (expected 2, got 0)
f654d9f32c add test to prevent regression
|
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PR_kwDOACgets5My9DH
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|
Fix `VolumetricData.to_cube()` not preserving structure dimensions
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[] | 2023-03-24T04:03:22
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2023-03-24T04:49:16Z
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Closes #2817.
697e73ad61 VolumetricData.to_cube() doesn't preserve structure dimensions
f2d89233e1 create pymatgen/io/tests/test_common.py with test_cube_io_faithful() to prevent future regression
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bug fix for potcar parsing
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[
"@janosh @shyuep, I think I have tests are failing due to some hash mismatches.\r\nI'm not familiar with the hashing setup but since I'm only removing blank lines I think it should have been OK.\r\n",
"> I'm not familiar with the hashing setup but since I'm only removing blank lines I think it should have been OK.\r\n\r\nAgreed.",
"So this is still failing, I really hope this is somewhat connected to the massive amount of warnings I always get during POTCAR reading so w/e fixes this will fix that as well. Maybe we have to redo the hashes and be more consistent about trimming? Again I'm not too familiar with that part of the code.",
"I have merged this first. But I really really dislike the whole hash system. Unless someone gives me a good reason why we are spending so much effort on this, I am disabling the tests and in future, I will disable the hash checks for good as well.\r\n",
"> Unless someone gives me a good reason why we are spending so much effort on this, I am disabling the tests and in future, I will disable the hash checks for good as well.\r\n\r\nI don't see a reason. Just to be clear, you mean keep all the Potcar tests and just disable those that relate to the hashes? I think that would be good.",
"@shyuep I think 99% of people only rely on the headers. I recall there were \"secret\" custom PAWs with the same headers as standard ones that people used (which later got released under a different header). But I feel like if you are using those then it's on the user to sort that out. \r\n\r\nHowever, I assume the hashing was added to get to make sure the build process is a bit more careful (and might be used by the builders) so you might need to ping @munrojm before any major changes.\r\n",
"I agree. So why don't you comment out the offending tests in the PR to let it pass. We will then merge. I think the hash checks can throw warnings like they do currently, but I am really tired of these tests failing because of some minor missing new line or space somewhere.",
"As long as the hashing functionality remains in the code, we should be okay. We currently use hash checking as part of the calculation validation pipeline. ",
"@munrojm I will leave the hash generation in. But if we are disabling the tests, I make no guarantees that future hashes generated will be valid. In other words, the hash is just being generated and we do not test for correctness. As I said, this is far too much effort to maintain for a functionality that very few people care about.",
"@shyuep, that is fair.",
"Can this get merged, please? I think the failing tests are from an unrelated issue.",
"> I agree. So why don't you comment out the offending tests in the PR to let it pass.\r\n\r\nI think this is waiting on commenting out the failing POTCAR hash tests as @shyuep suggested.",
"@janosh I modified to test and now it just attempts parsing withouth any checks. I actually wasn't sure if it was proper etiquette for someon other than the maintainers to delete tests which is why I didn't do it originally.",
"@jmmshn Thanks! The remaining errors here come from breaking changes in `pandas` v2 should be fixed by #2935. Merging now."
] | 2023-03-25T21:39:26
| 2023-04-04T02:48:43
|
2023-04-04T01:33:41Z
|
CONTRIBUTOR
|
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## bug fix for potcar parsing
2023.3.10 rewrote the `PotcarSingle.from_file` function slightly.
This caused a parsing error in the tests for `pymatgen-analysis-defects`.
I think this small change gives the intended behavior.
Otherwise, the POTCAR in this folder cannot be parsed.
https://github.com/materialsproject/pymatgen-analysis-defects/tree/main/tests/test_files/v_Ga/ccd_0_-1/optics
Without the fix:
```python
pc = Potcar.from_file("./POTCAR")
{d.header for d in pc}
```
Gives:
```
{'PAW_PBE Ga_d 06Jul2010', ''}
```
with the fix, you get:
```
{'PAW_PBE Ga_d 06Jul2010', 'PAW_PBE N 08Apr2002'}
```
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I_kwDOACgets5hy3Vx
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FileNotFoundError: [Errno 2] No such file or directory: 'vasprun.xml'
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[
"I think the error message is quite clear that you do not have vasprun.xml file?",
"But if I have it, what happens is that I don't know where to put it. A Now that file is in a subfolder of pymatgen, test_files",
"> I think the error message is quite clear that you do not have vasprun.xml file?\r\nBut if I have it, what happens is that I don't know where to put it. A Now that file is in a subfolder of pymatgen, test_files\r\n",
"> I think the error message is quite clear that you do not have vasprun.xml file?\r\n\r\nOk, thanks i think that was a problem of installation."
] | 2023-03-26T01:25:37
| 2023-03-28T21:25:19
|
2023-03-28T21:25:19Z
|
NONE
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I can't get past the line:
run = BSVasprun("vasprun.xml", parse_projected_eigen=True)
of notebook 2013-01-01-Bandstructure of NiO
|
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PR_kwDOACgets5M7iMO
| 2,912
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Update team.rst
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[] | 2023-03-27T03:32:48
| 2023-03-30T21:48:17
|
2023-03-27T17:08:55Z
|
CONTRIBUTOR
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## Matched my name to github
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PR_kwDOACgets5M7kWM
| 2,913
|
BUG FIX: BSDOSPlotter.get_plot
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[] | 2023-03-27T03:49:21
| 2024-06-18T14:28:29
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2024-06-18T14:28:29Z
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NONE
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Line 2288
```py
if dos:
```
change to
```py
if isinstance(dos, CompleteDos): # Dos obj has no structure
```
The DOS object has no structure property, which causes error if parsing DOS data without projection.
This modification allows user to plot BS and TDOS at the same time, while keeping the BS+PDOS plotting not affected.
Cheers.
|
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I_kwDOACgets5h6UM0
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Pandas v2 tracking issue
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[] | 2023-03-27T19:18:45
| 2023-04-04T01:50:46
|
2023-04-04T01:50:46Z
|
MEMBER
|
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[`pandas` v2](https://pandas.pydata.org/docs/dev/whatsnew/v2.0.0.html) is [about to be](https://twitter.com/pandas_dev/status/1636497983578447872?s=20) released [which removes several deprecated dataframe](https://pandas.pydata.org/docs/dev/whatsnew/v2.0.0.html#removal-of-prior-version-deprecations-changes) methods like `df.append` used by `pymatgen`.
This issue is just a heads-up that our CI will break soon and to track the required fixes.
|
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Faff
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[] | 2023-03-28T02:16:49
| 2023-03-28T02:41:39
|
2023-03-28T02:41:38Z
|
MEMBER
|
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3f353862e3 de-duplicate `docs/_static/(examples|phase_diagram).png`
1d0a89d85e add link to personal homepage in `docs_rst/team.rst`
4d0947eb12 absolufy imports in `pymatgen/core/__init__.py`
7566e92138 rename var `nndata` -> `nn_data`
|
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|
Add `formal_chempots` option to `ChemicalPotentialDiagram` to plot the formal chemical potentials rather than the DFT energies
|
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[
"Thanks @kavanase for the clear explanation and screenshots. Very helpful!",
"No problem @janosh, thanks for the speedy merge!",
"Just wanted to second, this was a great change. Thanks @kavanase!",
"No problem @mkhorton! 😃 \r\nJust curious, do you know if/when this will be reflected in the `Phase Diagram Explorer` app on the MP website? I guess it's (currently) fixed to a specific `pymatgen` version, but can't find this anywhere in the docs. ",
"@kavanase The `web` client is currently set to `pymatgen==2023.3.23`. This fix came just after that release and the next release wasn't until 2 days ago. We'll probably make a another web deployment next week (maybe even this Fri).",
"Ok cool! Thanks very much for the info @janosh! 🙌 ",
"Just pinging @tschaume and @yang-ruoxi to make sure we bump pymatgen for the next web deployment to publish this fix.",
"@janosh had a browse through, looks great! 😃 \r\nThanks very much all for the speedy update and deployment! 🙌 \r\n\r\nThe elemental forms now arise when `μ_X = 0` as expected, and the chemical potential values are physically meaningful (relative rather than absolute DFT energies):\r\n\r\n\r\n\r\n",
"Looks good to me as well. Thanks for making this change @kavanase. I should have fixed this a long time ago ;) ",
"Thanks for confirming the fix @kavanase @mattmcdermott."
] | 2023-03-28T11:00:16
| 2023-05-15T18:59:57
|
2023-03-28T21:13:37Z
|
CONTRIBUTOR
|
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The `ChemicalPotentialDiagram` object for which the (very useful! 🙌) `pymatgen.analysis.chempot_diagram` module is written, plots the chemical potential diagram using the absolute DFT energies, rather than the actual (formal) chemical potentials (aka. reference potentials) of the elements, which are the meaningful values that can be compared to experiment.
This is essentially the difference between absolute DFT energies (which on their own are essentially meaningless and differ substantially between different functional choices, input parameter/grid settings, vdW corrections, DFT codes etc) and _formation energies_ (i.e. energies relative to the elemental energies) which are meaningful, and far more robust with respect to input parameter choice.
Moreover, the axis labels for these plots in the output of `ChemicalPotentialDiagram.get_plot()` (which is also used on the Materials Project website for the chemical potential diagram plots) are given as `μ_X - μ_X^0`, which means it _should_ refer to the formal chemical potentials, but in fact it's the absolute DFT energies that are shown (i.e. μ_X(DFT)).
This PR adds an optional parameter `formal_chempots = True` to `ChemicalPotentialDiagram` which renormalises the entry energies and plots the formal chemical potentials.
```
formal_chempots (bool): Whether to plot the formal ('reference') chemical potentials
(i.e. μ_X - μ_X^0) or the absolute DFT reference energies (i.e. μ_X(DFT)).
Default is True (i.e. plot formal chemical potentials).
```
## Example changes:
The chemical potential diagram of the Y-Ti-O-S phase space on the Materials Project (using the old code):
You can see the energies of the elemental reference states are not zero as they should be (i.e. not corresponding to their `μ_X - μ_X^0` axis labels). – Might need to click into the image to see this clearly.
With the updated code we get the expected/desired behaviour:
<img width="705" alt="image" src="https://user-images.githubusercontent.com/51478689/228214689-1b9d69e9-3b53-4d64-b8e8-f3eda4981727.png">
Further examples can be generated using the test data in `test_chempot_diagram.py`.
I've added docstrings for these additions and also added a full set of tests to `test_chempot_diagram.py` for this option.
|
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I_kwDOACgets5iApDo
| 2,917
|
Molecule.from_file cannot read .xyz file from stk
|
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[
"Hey! The xyz file you attached seems more complex than the simple format the Molecule.from_file() can read.\r\nI see two extra columns containing M,V30,index. There are also some extra lines, sections.\r\n\r\nYou could remove that extra info if not needed either manually or with some sort of converter.\r\n\r\nThough, I let some other fellows more expert in molecules comment on this.",
"here you can see an example of what the Molecule.from_file() can read\r\nhttps://github.com/materialsproject/pymatgen/blob/master/test_files/multiple_frame_xyz.xyz",
"It works now thanks!"
] | 2023-03-28T16:53:57
| 2023-04-21T15:39:39
|
2023-04-21T15:39:39Z
|
NONE
|
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I have a .xyz file generated by stk and when I try and create a molecule from it I get the following error:
IndexError: list index out of range
Maybe stk writes .xyz files in a format that isn't quite standard?
Input code:
test_mof=Molecule.from_file("test.xyz")
Full error messages:
File "test.py", line 54, in <module>
test_mof=Molecule.from_file("test.xyz")
File ".../pymatgen/core/structure.py", line 3314, in from_file
return cls.from_str(contents, fmt="xyz")
File ".../pymatgen/core/structure.py", line 3276, in from_str
m = XYZ.from_string(input_string).molecule
File ".../site-packages/pymatgen/io/xyz.py", line 46, in molecule
return self._mols[-1]
IndexError: list index out of range
The .xyz file is as follows (I renamed it as test.txt rather than test.xyz so I could attach it):
[test.txt](https://github.com/materialsproject/pymatgen/files/11092277/test.txt)
Thanks
|
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ImportError: cannot import name 'MPRester' from 'pymatgen' (unknown location), how to solve this problem?
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[] | 2023-03-30T16:33:54
| 2023-03-30T17:02:53
|
2023-03-30T17:02:53Z
|
NONE
|
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I am new to this pymatgen, but this first challenge suppress me. Please give me some help.
|
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I_kwDOACgets5iOlD3
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|
how to solve such a problem about object has no attribute phase _type?
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[] | 2023-03-30T17:01:38
| 2023-03-30T18:35:19
|
2023-03-30T18:35:19Z
|
NONE
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Create a Pourbaix diagram object:
```py
pd = PourbaixDiagram(entries)
>>> Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_18612\515482332.py in <module>
1 # Create the Pourbaix diagram object
----> 2 pd = PourbaixDiagram(entries)
D:\Install\anaconda\lib\site-packages\pymatgen\analysis\pourbaix_diagram.py in __init__(self, entries, comp_dict, conc_dict, filter_solids, nproc)
510 self.pourbaix_elements = self.pbx_elts
511
--> 512 solid_entries = [entry for entry in entries if entry.phase_type == "Solid"]
513 ion_entries = [entry for entry in entries if entry.phase_type == "Ion"]
514
D:\Install\anaconda\lib\site-packages\pymatgen\analysis\pourbaix_diagram.py in <listcomp>(.0)
510 self.pourbaix_elements = self.pbx_elts
511
--> 512 solid_entries = [entry for entry in entries if entry.phase_type == "Solid"]
513 ion_entries = [entry for entry in entries if entry.phase_type == "Ion"]
514
AttributeError: 'ComputedStructureEntry' object has no attribute 'phase_type'
```
|
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I_kwDOACgets5iPFSL
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'MPRester' object has no attribute 'search'
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[] | 2023-03-30T18:34:12
| 2023-03-30T18:44:45
|
2023-03-30T18:44:45Z
|
NONE
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I am getting the below error while running MPrester from pymatgen. I have updated pymatgen as well. Help me.
```py
from pymatgen.ext.matproj import MPRester
import numpy as np
import pandas as pd
# Load SAXS data
data = load_data('SCOOH_Au10_1to4_NH2_Au5_HCl_1mM_20.0C_00133.avg') # replace with your own data file name and path
# Extract scattering vector and intensity data
q = data['q'] # scattering vector in 1/Angstroms
I = data['Intensity'] # intensity
def load_data(filename):
"""Load the original data into a dataframe"""
df=pd.read_csv(filename, skiprows=9, sep='\t',
names=['q', 'Intensity', 'Error'])
return df
# Calculate interplanar spacing from peak positions
lambda_ = 1.5418 # X-ray wavelength in Angstroms (replace with your own wavelength)
theta = 2*np.arcsin(q*lambda_/(4*np.pi))
d = lambda_/(2*np.sin(theta/2))
# Set up Materials Project API key
api_key = 'WJykuMzHXfCduDr3pp7ol7O5Y6EZBPe9' # replace with your own Materials Project API key
# Search the Materials Project for potential matches
with MPRester(api_key) as mpr:
results = mpr.search({'d_hkl': {'$in': [d]}}, ['material_id'])
# Display results
print('Potential matches found in the Materials Project:')
for result in results:
print('- {}'.format(result['material_id']))
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_18132/291635017.py in <module>
9 # Search the Materials Project for potential matches
10 with MPRester(api_key) as mpr:
---> 11 results = mpr.search({'d_hkl': {'$in': [d]}}, ['material_id'])
12
13 # Display results
~\Anaconda3\lib\site-packages\mp_api\client\mprester.py in __getattr__(self, attr)
204 )
205 else:
--> 206 raise AttributeError(f"{self.__class__.__name__!r} object has no attribute {attr!r}")
207
208 def get_task_ids_associated_with_material_id(
AttributeError: 'MPRester' object has no attribute 'search'
```
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I_kwDOACgets5iPaN5
| 2,924
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frac_tolerance argument in Structure.from_file() function fails when input file is POSCAR
|
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[] | null |
[
"That's because `Poscar.from_string()` doesn't have a `frac_tolerance` kwarg. \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/713740f5b8bf27990d9d0c92ca154fae4164ec59/pymatgen/io/vasp/inputs.py#L247-L280\r\n\r\nThat functionality currently only exists in `CifParser`:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/713740f5b8bf27990d9d0c92ca154fae4164ec59/pymatgen/io/cif.py#L288\r\n\r\nHappy to take a PR that adds this! :shipit: "
] | 2023-03-30T19:41:56
| 2023-08-15T16:26:17
|
2023-08-15T16:26:16Z
|
NONE
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**Describe the bug**
`frac_tolerance` argument in `Structure.from_file()` function fails when input file is `POSCAR`. Error message is:
```py
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_20036\3595116257.py in <module>
1 from pymatgen.core.structure import Structure
----> 2 s = Structure.from_file(r"input_files\POSCAR_25K_distorted_ts_1000.POSCAR",frac_tolerance=0)
C:\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_file(cls, filename, primitive, sort, merge_tol, **kwargs)
2686 return cls.from_str(contents, fmt="cif", primitive=primitive, sort=sort, merge_tol=merge_tol, **kwargs)
2687 if fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
-> 2688 s = cls.from_str(contents, fmt="poscar", primitive=primitive, sort=sort, merge_tol=merge_tol, **kwargs)
2689
2690 elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
C:\Anaconda3\lib\site-packages\pymatgen\core\structure.py in from_str(cls, input_string, fmt, primitive, sort, merge_tol, **kwargs)
2604 from pymatgen.io.vasp import Poscar
2605
-> 2606 s = Poscar.from_string(input_string, False, read_velocities=False, **kwargs).structure
2607 elif fmt_low == "cssr":
2608 from pymatgen.io.cssr import Cssr
TypeError: from_string() got an unexpected keyword argument 'frac_tolerance'
```
**To Reproduce**
Attempt to use function to load a POSCAR file, and set frac_tolerance. I.e.:
```py
s = Structure.from_file(r"input_files\POSCAR_25K_distorted_ts_1000.POSCAR",frac_tolerance=0)
```
**Expected behavior**
It should load the structure with `frac_tolerance` set to zero, i.e. no rounding of sites to high-symmetry positions.
**Additional context**
I imagine this will be very easy to fix.
|
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PR_kwDOACgets5NTScj
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auto version
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[
"I think forks just need to merge from the main master branch for versioning to be correct? The versions are updated when the release happens.",
"So merging from the upstream master did no work.\r\nThe following setting in the `pyproject.toml` breaks because the setuptools thinks the `pymatgen` version is too old despite merging from upstream. \r\n \r\n```toml\r\ndependencies = [\r\n 'pymatgen@git+https://github.com/jmmshn/pymatgen#egg=master',\r\n 'jobflow@git+https://github.com/jmmshn/jobflow@main#egg=main',\r\n 'atomate2@git+https://github.com/jmmshn/atomate2@main#egg=main'\r\n]\r\n```\r\n\r\nWithout `pymatgen`, the other two codes required the tag to be pushed up to the forked repo to resolve dependencies properly. \r\n\r\n",
"I am not sure how the pyproject fixes this problem? You need to pull from origin/master for the version to be updated.",
"So the problem was that if I forked `master` in 2022, and keep pulling from `materialsproject/master`, I still get a version name `2022...post370+gff40e46 ` even when I have the most up-to-date code. This is usually not a problem if you just clone all the repos and install the newest code in edit mode.\r\n\r\nHowever, if you have that branch as a dependency, it will cause pip resolve issues since the version number/name is wrong despite the code being correct.\r\nSo if I have the following three dependencies in a repo and would like to install them on some system, I could not do that\r\n```\r\ndependencies = [\r\n 'pymatgen@git+https://github.com/jmmshn/pymatgen#egg=master',\r\n 'jobflow@git+https://github.com/jmmshn/jobflow@main#egg=main',\r\n 'atomate2@git+https://github.com/jmmshn/atomate2@main#egg=main'\r\n]\r\n```\r\n \r\nThis morning all three branches were up-to-date in code but not in tags. For `jobflow` and `atomate2` simply pushing the new tags to `origin` fixed the problem because they had this stanza in their respective `pyproject.toml` but `pymatgen` did not, so I still cannot install these three branches. After putting this stanza in and pushing the recently released tag to `origin`, it looks like the versioning is permanently changed for all commits past the release tag and now I'm able to install all three packages.\r\n\r\n",
"This is a pretty niche issue since most people aren't doing production runs while changing multiple packages. \r\nHowever, I think the setup of automatically pulling from the git tags for version information is generally useful and takes care of edge cases like mine."
] | 2023-03-30T21:52:20
| 2023-03-31T03:02:05
|
2023-03-31T03:02:05Z
|
CONTRIBUTOR
|
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## Allow proper versioning for forked repos
I'm not 100% sure how the current version numbering is updated for `pymatgen` but it's not able to update the number properly for forks. The forks seem to keep a much older version number (from before the forking)
This creates problems if you have the forked repo as a dependency in a requirement.txt file.
This should fix that issue.
|
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PR_kwDOACgets5NY8qJ
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Plotting of Multicenter COBIs
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[
"Just as a warning that this might sit here for a longer time. I discovered an issue for the multi-center COBI computations in Lobster for the spin-polarized case during the plotting implementation. I will wait until there is a new Lobster version that can generate useful test data.",
"Will try to finalize a first implementation soon. I have not forgotten about this pull request.",
"Will work on this one here again tonight and hopefully finish it! I still have to resolve a few merge conflict or issues due to changes in the pymatgen code base.",
"@janosh if you have some time to review this, this would be awesome. If we don't merge it soon, this will never get merged as tons of merge conflicts show up very fast here in pymatgen and it would be sad as it was a lot of work ...",
"@janosh , The renaming is fine as it is not used yet anywhere."
] | 2023-03-31T21:47:02
| 2024-03-16T13:44:32
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2024-03-16T13:44:31Z
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MEMBER
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## Summary
Lobster now also has options to compute multi-center interactions. This leads to a different format of the COBICAR.lobster (e.g., no average COBI is included) and the labels of the bonds are different. At this stage, I can already plot this different format but no tests are included so far. Bond lengths are missing in this output. I might add a computation of those based on the site index and cell number of the interacting atoms.
TODO:
- [x] Tests for input/output modules
- [x] Tests for from_ and as_dict options of CompleteCohp
- [x] Tests for from_file of CompleteCohp
- [x] Bond length computation from cell information (cannot be done without structure. Will therefore not be done)
- [x] Code simplification (e.g., many if clauses at the moment, probably simplifications are possible)
- [x] check recomputed average cobi in detail
- [x] test spin polarization in detail
- [x] Extend from three to really any multicenter bond
|
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PR_kwDOACgets5NZb-W
| 2,927
|
add kwarg to MoleculeGraph method and fix PackmolSet bug
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[
"Thanks @orionarcher! 👍 ",
"Thank you @janosh!"
] | 2023-04-01T01:36:43
| 2023-04-04T15:13:19
|
2023-04-04T15:13:19Z
|
CONTRIBUTOR
|
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## Summary
The get_disconnected_fragments method returns a new graph with reordered indices but provides no way to get the mapping from new to original indices. This PR reconstructs that map and adds an optional keyword argument to return it. This will not affect current functionality.
Additionally, I found an error in the `pymatgen.io.packmol` code where a non-abstract class had an abstract method, preventing it from being instantiated. This slipped under the radar because the tests are skipped due to a difficult dependency (`packmol`). The tests are now passing locally for me.
A downstream code I am working on requires this addition.
- a new `return_index_map` kwarg for MoleculeGraph.get_disconnected_fragments
- remove `abc.abstractmethod` decorator from `PackmolBoxGen.get_input_set()`
## Checklist
- [x] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
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PR_kwDOACgets5NaJQP
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Bump pypa/cibuildwheel from 2.11.4 to 2.12.1
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[
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-04-01T12:57:41
| 2023-04-04T16:31:30
|
2023-04-04T16:31:18Z
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CONTRIBUTOR
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.12.1</h2>
<ul>
<li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
</ul>
<h2>v2.12.0</h2>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.12.1</h3>
<p><em>11 March 2023</em></p>
<ul>
<li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
</ul>
<h3>v2.12.0</h3>
<p><em>16 Jan 2023</em></p>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
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<summary>Commits</summary>
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<li><a href="https://github.com/pypa/cibuildwheel/commit/02ad79a31bf7aa0eee07f690509048d2fb9fd445"><code>02ad79a</code></a> Bump version: v2.12.1</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/1d6ee75d21e2d39eeff59a101efbdff3f926060d"><code>1d6ee75</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a> from henryiii/henryiii/fix/pipconfigopts</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/0b1b539450d86f7be21182225467c24303b687f7"><code>0b1b539</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1425">#1425</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/2e48667e29fa128d96738dd6bb585aaab232b580"><code>2e48667</code></a> refactor: use frontend instead of plural</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/c6818608d23a2f54b26e48b22c28fceb40ce2c57"><code>c681860</code></a> fix: pip config options were broken</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/7190b1a6a7be78508bc9a75badd370ec33018880"><code>7190b1a</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1428">#1428</a> from henryiii/henryiii/ci/appveyor</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/16380b855562429b51e9ac36f6dd57094121c4b4"><code>16380b8</code></a> Update CI table</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/94efa61f7667e9451d24b5ce8265b0afaaead76a"><code>94efa61</code></a> ci: fix appveyor (Python 3.8+ needed for macOS)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/acdbe87e3d002598b10435bb6f17bae758418ba8"><code>acdbe87</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1427">#1427</a> from pypa/pre-commit-ci-update-config</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/49b736d1c725bda880a31df86e46a3d1a09d92b8"><code>49b736d</code></a> [pre-commit.ci] pre-commit autoupdate</li>
<li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.11.4...v2.12.1">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5NaJal
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Bump networkx from 2.8.8 to 3.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-04-01T12:58:39
| 2023-04-04T16:31:30
|
2023-04-04T16:31:19Z
|
CONTRIBUTOR
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Bumps [networkx](https://github.com/networkx/networkx) from 2.8.8 to 3.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/networkx/networkx/releases">networkx's releases</a>.</em></p>
<blockquote>
<h2>NetworkX 3.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Tests added in test_centrality.py by <a href="https://github.com/Mjh9122"><code>@Mjh9122</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6200">networkx/networkx#6200</a></li>
<li>add laplacian_spectrum example by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6169">networkx/networkx#6169</a></li>
<li>PR for issue <a href="https://redirect.github.com/networkx/networkx/issues/6033">#6033</a> Improve test coverage for algorithms in betweenness_subset.py <a href="https://redirect.github.com/networkx/networkx/issues/6033">#6033</a> by <a href="https://github.com/ladykkk"><code>@ladykkk</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6083">networkx/networkx#6083</a></li>
<li>Di graph edges doc fix by <a href="https://github.com/nsengiyumva-wilberforce"><code>@nsengiyumva-wilberforce</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6108">networkx/networkx#6108</a></li>
<li>Improve coverage for core.py by <a href="https://github.com/Mjh9122"><code>@Mjh9122</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6116">networkx/networkx#6116</a></li>
<li>Add clear edges method as a method to be frozen by nx.freeze by <a href="https://github.com/AdamWRichardson"><code>@AdamWRichardson</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6190">networkx/networkx#6190</a></li>
<li>Adds LCA test case for self-ancestors from <a href="https://redirect.github.com/networkx/networkx/issues/4458">gh-4458</a>. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6218">networkx/networkx#6218</a></li>
<li>Minor Python 2 cleanup by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6219">networkx/networkx#6219</a></li>
<li>Add example laplacian matrix by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6168">networkx/networkx#6168</a></li>
<li>Revert 6219 and delete comment. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6222">networkx/networkx#6222</a></li>
<li>fix wording in error message by <a href="https://github.com/ikethefifth"><code>@ikethefifth</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6228">networkx/networkx#6228</a></li>
<li>Rm incorrect test case for connected edge swap by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6223">networkx/networkx#6223</a></li>
<li>add missing <code>seed</code> to function called by <code>connected_double_edge_swap</code> by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6231">networkx/networkx#6231</a></li>
<li>Hide edges with a weight of None in A*. by <a href="https://github.com/brianhou"><code>@brianhou</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/5945">networkx/networkx#5945</a></li>
<li>Add dfs_labeled_edges reporting of reverse edges due to depth_limit. by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6240">networkx/networkx#6240</a></li>
<li>Warn users about duplicate nodes in generator function input by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6237">networkx/networkx#6237</a></li>
<li>Reenable geospatial examples by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6252">networkx/networkx#6252</a></li>
<li>Draft 3.0 release notes by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6232">networkx/networkx#6232</a></li>
<li>Add 2.8.x release notes by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6255">networkx/networkx#6255</a></li>
<li>doc: clarify allowed <code>alpha</code> when using nx.draw_networkx_edges by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6254">networkx/networkx#6254</a></li>
<li>Add a contributor by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6256">networkx/networkx#6256</a></li>
<li>Allow MultiDiGraphs for LCA by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6234">networkx/networkx#6234</a></li>
<li>Update simple_paths.py to improve readability of the BFS. by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6273">networkx/networkx#6273</a></li>
<li>doc: update documentation when providing an iterator over current graph to add/remove_edges_from. by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6268">networkx/networkx#6268</a></li>
<li>Fix bug vf2pp is isomorphic issue 6257 by <a href="https://github.com/reneechebbo"><code>@reneechebbo</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6270">networkx/networkx#6270</a></li>
<li>Improve test coverage for Eigenvector centrality by <a href="https://github.com/Qudirah"><code>@Qudirah</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6227">networkx/networkx#6227</a></li>
<li>Bug fix in swap: directed_edge_swap and double_edge_swap by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6149">networkx/networkx#6149</a></li>
<li>Adding a test to verify that a NetworkXError is raised when calling n… by <a href="https://github.com/reneechebbo"><code>@reneechebbo</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6265">networkx/networkx#6265</a></li>
<li>Pin to sphinx 5.2.3 by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6277">networkx/networkx#6277</a></li>
<li>Update pre-commit hooks by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6278">networkx/networkx#6278</a></li>
<li>Update GH actions by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6280">networkx/networkx#6280</a></li>
<li>Fix links in release notes by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6281">networkx/networkx#6281</a></li>
<li>bug fix in smallworld.py: random_reference and lattice_reference by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6151">networkx/networkx#6151</a></li>
<li>[DOC] Follow numpydoc standard in barbell_graph documentation by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6286">networkx/networkx#6286</a></li>
<li>Update simple_paths.py: consistent behaviour for <code>is_simple_path</code> when path contains nodes not in the graph. by <a href="https://github.com/SultanOrazbayev"><code>@SultanOrazbayev</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6272">networkx/networkx#6272</a></li>
<li>Correctly point towards 2.8.8 in release notes by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6298">networkx/networkx#6298</a></li>
<li>Isomorphism improve documentation by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6295">networkx/networkx#6295</a></li>
<li>Improvements and test coverage for <code>line.py</code> by <a href="https://github.com/Aufinal"><code>@Aufinal</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6215">networkx/networkx#6215</a></li>
<li>Fix typo in Katz.py by <a href="https://github.com/faze-geek"><code>@faze-geek</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6310">networkx/networkx#6310</a></li>
<li>Broken link in isomorphism documentation by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6296">networkx/networkx#6296</a></li>
<li>Update copyright years to 2023 by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6322">networkx/networkx#6322</a></li>
<li>fix warnings for make doctest by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6323">networkx/networkx#6323</a></li>
<li>fix whitespace issue in test_internet_as_graphs by <a href="https://github.com/danieleades"><code>@danieleades</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6324">networkx/networkx#6324</a></li>
<li>Create a Tikz latex drawing feature for networkx by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6238">networkx/networkx#6238</a></li>
<li>Fix docstrings by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6329">networkx/networkx#6329</a></li>
<li>Fix documentation deployment by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6330">networkx/networkx#6330</a></li>
<li>Fix links to migration guide by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6331">networkx/networkx#6331</a></li>
<li>Fix typo in readme file by <a href="https://github.com/tinaoberoi"><code>@tinaoberoi</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6312">networkx/networkx#6312</a></li>
</ul>
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</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/networkx/networkx/commit/58994819583fddf3fea813daec520946c550bcd8"><code>5899481</code></a> Designate 3.0 release</li>
<li><a href="https://github.com/networkx/networkx/commit/2522f1d03b0d0115fcdcd3ab852d38444bec2848"><code>2522f1d</code></a> Update release notes (<a href="https://redirect.github.com/networkx/networkx/issues/6341">#6341</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/8334e96bd794e56940e5b554c6773d62617141e3"><code>8334e96</code></a> Refactor vf2pp modules and test files (<a href="https://redirect.github.com/networkx/networkx/issues/6334">#6334</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/83948b6dc61f507adb4cd1a71561eac9ed3b72ec"><code>83948b6</code></a> Fix typos in the networkx codebase (<a href="https://redirect.github.com/networkx/networkx/issues/6335">#6335</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/851aab2dad6dda73995b06d1ef01b95c3aa79891"><code>851aab2</code></a> Fix typo in readme file (<a href="https://redirect.github.com/networkx/networkx/issues/6312">#6312</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/f4ae9173f4e6dadd6245d8efe34008a0ccf9e4b6"><code>f4ae917</code></a> Fix links to migration guide (<a href="https://redirect.github.com/networkx/networkx/issues/6331">#6331</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/1efafc5a949c3cb9ffc0f9126a1e50dc26fe3d39"><code>1efafc5</code></a> Fix documentation deployment (<a href="https://redirect.github.com/networkx/networkx/issues/6330">#6330</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/a7d50d2c40be1261ecd7372c08ce6ec0a0106c55"><code>a7d50d2</code></a> Fix docstrings (<a href="https://redirect.github.com/networkx/networkx/issues/6329">#6329</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/59ed0cfdc5262219da5aa120a11c9df3d6fab879"><code>59ed0cf</code></a> Create a Tikz latex drawing feature for networkx (<a href="https://redirect.github.com/networkx/networkx/issues/6238">#6238</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/814b295eddcad7374d494fa5f5b7fe08ee765ad7"><code>814b295</code></a> fix whitespace issue in 'networkx.generators.tests.test_internet_as_g… (<a href="https://redirect.github.com/networkx/networkx/issues/6324">#6324</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/networkx/networkx/compare/networkx-2.8.8...networkx-3.0">compare view</a></li>
</ul>
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Bump tqdm from 4.64.1 to 4.65.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
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2023-04-04T16:31:20Z
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.64.1 to 4.65.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/tqdm/tqdm/releases">tqdm's releases</a>.</em></p>
<blockquote>
<h2>tqdm v4.65.0 stable</h2>
<ul>
<li>add Python 3.11 and drop Python 3.6 support (<a href="https://redirect.github.com/tqdm/tqdm/issues/1439">#1439</a>, <a href="https://redirect.github.com/tqdm/tqdm/issues/1419">#1419</a>, <a href="https://redirect.github.com/tqdm/tqdm/issues/502">#502</a> <- <a href="https://redirect.github.com/tqdm/tqdm/issues/720">#720</a>, <a href="https://redirect.github.com/tqdm/tqdm/issues/620">#620</a>)</li>
<li>misc code & docs tidy</li>
<li>fix & update CI workflows & tests</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/tqdm/tqdm/commit/0bb91857eca0d4aea08f66cf1c8949abe0cd6b7a"><code>0bb9185</code></a> bump version, merge pull request <a href="https://redirect.github.com/tqdm/tqdm/issues/1439">#1439</a> from tqdm/devel</li>
<li><a href="https://github.com/tqdm/tqdm/commit/687f5e4ccf473980a373d7e17208c53dcd9ec60d"><code>687f5e4</code></a> tech-debt: drop more legacy code</li>
<li><a href="https://github.com/tqdm/tqdm/commit/c0a893b9e4501a872e8768b7f82d89f505b10d42"><code>c0a893b</code></a> docs: update badge</li>
<li><a href="https://github.com/tqdm/tqdm/commit/32da44f3404f50708c181ec871302334eb92c0a0"><code>32da44f</code></a> build: drop disco-py from snap</li>
<li><a href="https://github.com/tqdm/tqdm/commit/4a442b462a8ce62c749278e77c822d0d49961d48"><code>4a442b4</code></a> misc linting</li>
<li><a href="https://github.com/tqdm/tqdm/commit/7cb795d7ee7a96b4fdea74e38727b0c2c861373e"><code>7cb795d</code></a> tests: skip tensorflow on py3.11</li>
<li><a href="https://github.com/tqdm/tqdm/commit/8785c52025959b5e093e3b40d63be3a408b3d609"><code>8785c52</code></a> build: bump snap to core22 <= core18</li>
<li><a href="https://github.com/tqdm/tqdm/commit/05bb4ffa1ba8ff72eb8a8d499045003263a2d3a7"><code>05bb4ff</code></a> tests: tidy tox</li>
<li><a href="https://github.com/tqdm/tqdm/commit/8f8560c9450488fc4c1aad37f2042ce4888e3005"><code>8f8560c</code></a> drop redundant <strong>future</strong> imports</li>
<li><a href="https://github.com/tqdm/tqdm/commit/a587f3037eb6822573ffe36eda79105569a5a8b4"><code>a587f30</code></a> drop py<=3.6</li>
<li>Additional commits viewable in <a href="https://github.com/tqdm/tqdm/compare/v4.64.1...v4.65.0">compare view</a></li>
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Bump mp-api from 0.27.3 to 0.30.11
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] | 2023-04-01T12:59:08
| 2023-04-04T16:31:30
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2023-04-04T16:31:20Z
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Bumps [mp-api](https://github.com/materialsproject/api) from 0.27.3 to 0.30.11.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/materialsproject/api/releases">mp-api's releases</a>.</em></p>
<blockquote>
<h2>v0.30.11</h2>
<p>Pin <code>emmet-core</code> to fix <code>TaskDoc</code> validation</p>
<h2>v0.30.10</h2>
<p>Set default value of <code>api_key</code> to <code>None</code> in <code>MPRester</code> and <code>BaseRester</code> classes.</p>
<h2>v0.30.9</h2>
<p>Allow <code>thermo_type</code> to be passed a string in <code>get_phase_diagram_from_chemsys</code>.</p>
<h2>v0.30.8</h2>
<p>Ensures <code>qhull_data</code> returned with <code>PhaseDiagram</code> objects is formatted as a numpy array to allow for plotting with <code>PDPlotter</code>.</p>
<h2>v0.30.7</h2>
<p>Ensures <code>PhaseDiagram</code> objects returned from the client can be plotted with <code>PDPlotter</code>.</p>
<h2>v0.30.6</h2>
<p>Version 0.30.6</p>
<h3>Commits</h3>
<ul>
<li>[98eb3605] Set default thermo_type in thermo search method (<a href="https://redirect.github.com/materialsproject/api/issues/726">#726</a>)</li>
<li>[15c378bc] use query_contributions for ion ref data</li>
<li>[bebe77bd] formatting; 32 apikey length</li>
<li>[02e322f7] Fix session typo</li>
<li>[5ef93138] FIx order of input chemsys for pd search (<a href="https://redirect.github.com/materialsproject/api/issues/719">#719</a>)</li>
<li>[8f21dbbb] Fix passing session and headers in base rester (<a href="https://redirect.github.com/materialsproject/api/issues/717">#717</a>)</li>
<li>[ac4bb36a] Custom sessions (<a href="https://redirect.github.com/materialsproject/api/issues/716">#716</a>)</li>
<li>[6bf17910] Header dictionary pass through and <code>BaseRester</code> nesting fix (<a href="https://redirect.github.com/materialsproject/api/issues/715">#715</a>)</li>
<li>[49fc74a0] Update thermo rester methods (<a href="https://redirect.github.com/materialsproject/api/issues/714">#714</a>)</li>
<li>[fecf7fda] Fix robocrys search pagination (<a href="https://redirect.github.com/materialsproject/api/issues/712">#712</a>)</li>
<li>[bc5a9fb7] Add task_id list and elements to task <code>search</code> method (<a href="https://redirect.github.com/materialsproject/api/issues/709">#709</a>)</li>
<li>[80f46865] Allow the pmgrc file to be read for the MPREster settings (<a href="https://redirect.github.com/materialsproject/api/issues/708">#708</a>)</li>
<li>[574cda52] Fix charge density <code>task_ids</code> list query (<a href="https://redirect.github.com/materialsproject/api/issues/707">#707</a>)</li>
<li>[17dd2cca] Implement method to get NOMAD download URL (<a href="https://redirect.github.com/materialsproject/api/issues/702">#702</a>)</li>
<li>[ebe7c43b] Insert missing comma in setup.py (<a href="https://redirect.github.com/materialsproject/api/issues/697">#697</a>)</li>
<li>[d3f76872] Smart chunk with max URL length consideration (<a href="https://redirect.github.com/materialsproject/api/issues/695">#695</a>)</li>
<li>[72eafaa4] Add back <code>additional_criteria</code> as an input to <code>get_entries</code> and <code>get_entries_in_chemsys</code> (<a href="https://redirect.github.com/materialsproject/api/issues/693">#693</a>)</li>
<li>[2292fc1a] Ensure parity with top level legacy methods (<a href="https://redirect.github.com/materialsproject/api/issues/691">#691</a>)</li>
<li>[25b21d81] Use six API keys in testing workflow instead of one (<a href="https://redirect.github.com/materialsproject/api/issues/687">#687</a>)</li>
<li>[9f821a12] Remove manual dispatch from release wflow (<a href="https://redirect.github.com/materialsproject/api/issues/686">#686</a>)</li>
<li>[f94a4fbc] Fix wflow dispatch</li>
<li>[045f94e8] Fix release wflow</li>
<li>[99132393] Add sphinx docs (<a href="https://redirect.github.com/materialsproject/api/issues/684">#684</a>)</li>
<li>[89b37a60] Bump emmet (<a href="https://redirect.github.com/materialsproject/api/issues/679">#679</a>)</li>
<li>[0b4520f7] Remove <code>pytest.mark.xfail</code> decorator, test expected to pass</li>
<li>[2849726d] use latest actions/setup-python and actions/checkout (<a href="https://redirect.github.com/materialsproject/api/issues/678">#678</a>)</li>
<li>[f29b2e03] support single values as search filters (<a href="https://redirect.github.com/materialsproject/api/issues/672">#672</a>)</li>
<li>[3f97decb] Adding <code>msgpack</code> to requirements</li>
<li>[6b9ebdf1] Add msgpack to reqs (<a href="https://redirect.github.com/materialsproject/api/issues/671">#671</a>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/materialsproject/api/commit/f5055d0bf06052aa61b1cac077b295ac68874244"><code>f5055d0</code></a> Pin emmet core to fix task doc validation</li>
<li><a href="https://github.com/materialsproject/api/commit/7aceb53cc37012ba2224665b1cf8663cfcba534b"><code>7aceb53</code></a> Fix material rester tests (<a href="https://redirect.github.com/materialsproject/api/issues/760">#760</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/dd9c5db9c6e9001d35f644244dacea712b8876ac"><code>dd9c5db</code></a> Small edit to add <code>backoff_factor</code> to client (<a href="https://redirect.github.com/materialsproject/api/issues/759">#759</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/858409f522b165f7581fcb949313569742ce3e87"><code>858409f</code></a> Default API key value to None in MPRester (<a href="https://redirect.github.com/materialsproject/api/issues/743">#743</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/2ec98bd0861902c70f683adc7b87367e3a41f4f0"><code>2ec98bd</code></a> Allow <code>thermo_type</code> string passing for phase diagram method (<a href="https://redirect.github.com/materialsproject/api/issues/742">#742</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/9dc27dcb2fd528e985bd99aa512d382bd5babccc"><code>9dc27dc</code></a> add duplicate element checking in MPRester.get_entries_in_chemsys (<a href="https://redirect.github.com/materialsproject/api/issues/736">#736</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/0713f8c6a3b53f71ba00c6408fe573103716bb81"><code>0713f8c</code></a> Accept <code>list[str]</code> for <code>thermo_types</code> in <code>ThermoRester.search()</code> (<a href="https://redirect.github.com/materialsproject/api/issues/729">#729</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/1e83e2b99323bcda760301a1f96c8dd0418d7d23"><code>1e83e2b</code></a> Ensure PhaseDiagram qhull_data is a numpy array (<a href="https://redirect.github.com/materialsproject/api/issues/731">#731</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/ece1b3effeebae208a16d98776a3bb555ec8e459"><code>ece1b3e</code></a> Fix <code>el_refs</code> dict keys in <code>PhaseDiagram</code> objects (<a href="https://redirect.github.com/materialsproject/api/issues/730">#730</a>)</li>
<li><a href="https://github.com/materialsproject/api/commit/98eb360521bb27de380620a02580e05a250a7070"><code>98eb360</code></a> Set default thermo_type in thermo search method (<a href="https://redirect.github.com/materialsproject/api/issues/726">#726</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/materialsproject/api/compare/v0.27.3...v0.30.11">compare view</a></li>
</ul>
</details>
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