instance_id stringlengths 10 57 | file_changes listlengths 1 15 | repo stringlengths 7 53 | base_commit stringlengths 40 40 | problem_statement stringlengths 11 52.5k | patch stringlengths 251 7.06M |
|---|---|---|---|---|---|
openmc-dev__openmc-2622 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/plots.py:PlotBase.to_xml_element",
"openmc/plots.py:Plot.to_xml_element",
"openmc/plots.py:Plot.from_xml_element",
"openmc/plots.py:ProjectionPlot.to_xml_element",
... | openmc-dev/openmc | d47e9a10928d594dcf5e29acccdb65bc75950c4c | Documentation improvement section 15.2.1 mentions debug
[This section](
https://docs.openmc.org/en/latest/usersguide/troubleshoot.html#runtimeerror-openmc-aborted-unexpectedly) of the docs suggests ```cmake -Ddebug=on``` which produces a CMake Warning
```
CMake Warning:
Manually-specified variables were not use... | diff --git a/docs/source/usersguide/troubleshoot.rst b/docs/source/usersguide/troubleshoot.rst
index b1cd80f3e..f86ed7274 100644
--- a/docs/source/usersguide/troubleshoot.rst
+++ b/docs/source/usersguide/troubleshoot.rst
@@ -28,7 +28,7 @@ commands:
.. code-block:: sh
mkdir build-debug && cd build-debug
- cma... |
openmc-dev__openmc-2647 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/deplete/results.py:Results.get_step_where"
],
"edited_modules": [
"openmc/deplete/results.py:Results"
]
},
"file": "openmc/deplete/results.py"
},
{
"chan... | openmc-dev/openmc | 1d29adc0808a726fba93ad687fcce7b1b6632f66 | `Universe.plot` seed does not change color behavior.
## Bug Description
I noticed today that setting the `seed` parameter when calling `Universe.plot` doesn't affect the colors in a plot.
## Steps to Reproduce
Run the following in a notebook for the assembly model located at `examples/assembly` in the repo.
<im... | diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst
index 1016fbaa3..36027ef2f 100644
--- a/docs/source/io_formats/settings.rst
+++ b/docs/source/io_formats/settings.rst
@@ -345,6 +345,15 @@ either "false" or "true".
*Default*: false
+-----------------------
+``<plot_seed>`` El... |
openmc-dev__openmc-2713 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/mesh.py:CylindricalMesh.from_domain"
],
"edited_modules": [
"openmc/mesh.py:CylindricalMesh"
]
},
"file": "openmc/mesh.py"
}
] | openmc-dev/openmc | 972dd73ae9db8fbacd398c5483aa6326665b2f0a | <volume_calc> settings.xml element file format outdated
<!--Describe the issue with the documentation and include a URL to the corresponding page-->
https://docs.openmc.org/en/latest/io_formats/settings.html#volume-calc-element
A few elements read by the C++ code are undocumented online:
- `domain_type`
- `th... | diff --git a/README.md b/README.md
index 561bf4e1a..6539ec3c7 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# OpenMC Monte Carlo Particle Transport Code
[](https://docs.openmc.org/en/latest/license.html)
-[![GitHub Actions build status (Linux)](http... |
openmc-dev__openmc-2882 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/deplete/abc.py:Integrator._get_bos_data_from_restart",
"openmc/deplete/abc.py:Integrator.integrate",
"openmc/deplete/abc.py:SIIntegrator.integrate"
],
"edited_modules"... | openmc-dev/openmc | e8f68a0159302f69ad04f0ca56e062f88324a411 | Transport-corrected MGXS generation with merging broken
<!--
If you are a user of OpenMC and are running into trouble with the code or are
seeking general user support, we highly recommend posting on the OpenMC
discourse forum first. GitHub issues should be used specifically for bug reports
and feature requests.
... | diff --git a/openmc/deplete/abc.py b/openmc/deplete/abc.py
index 1dea8440c..a574d4855 100644
--- a/openmc/deplete/abc.py
+++ b/openmc/deplete/abc.py
@@ -769,7 +769,7 @@ class Integrator(ABC):
self.operator.write_bos_data(step_index + self._i_res)
return x, res
- def _get_bos_data_from_restart(sel... |
openmc-dev__openmc-2977 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/lattice.py:RectLattice.create_xml_subelement"
],
"edited_modules": [
"openmc/lattice.py:RectLattice"
]
},
"file": "openmc/lattice.py"
},
{
"changes": {
... | openmc-dev/openmc | 2a53aba1c171773e11305a841e8b714d81c5e186 | Extra error checking on mesh creation
## Description
Currently it is possible to build cylindricalmesh objects with phi_grid values that don't make sense. For example
```python
cylindrical_mesh = openmc.CylindricalMesh(
r_grid=[0, 1, 2],
phi_grid=[2],
z_grid=[0, 10, 20],
)
>>> CylindricalMesh
... | diff --git a/openmc/lattice.py b/openmc/lattice.py
index f7f9da8ea..518068560 100644
--- a/openmc/lattice.py
+++ b/openmc/lattice.py
@@ -884,6 +884,10 @@ class RectLattice(Lattice):
dimension = ET.SubElement(lattice_subelement, "dimension")
dimension.text = ' '.join(map(str, self.shape))
+ # ... |
openmc-dev__openmc-3018 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/cell.py:Cell.get_all_cells",
"openmc/cell.py:Cell.get_all_universes",
"openmc/cell.py:Cell.clone",
"openmc/cell.py:Cell.create_xml_subelement"
],
"edited_modul... | openmc-dev/openmc | 1702b4554bfb1a7f19cc2b9f1318edeb0f7ad0d2 | CylinderSector doesn't properly generate planes for off origin centers
## Bug Description
If you create an `openmc.model.CylinderSector` that is not located at the origin, the planes that define the sector do not appear to intersect the center.
Reading the code it seems like this issue is [this line and the next ... | diff --git a/openmc/cell.py b/openmc/cell.py
index 94fac8413..fe3939bbe 100644
--- a/openmc/cell.py
+++ b/openmc/cell.py
@@ -426,15 +426,13 @@ class Cell(IDManagerMixin):
instances
"""
+ if memo is None:
+ memo = set()
+ elif self in memo:
+ return {}
+ ... |
openmc-dev__openmc-3045 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openmc/model/surface_composite.py:IsogonalOctagon.__init__",
"openmc/model/surface_composite.py:IsogonalOctagon.__neg__",
"openmc/model/surface_composite.py:IsogonalOctagon.__pos__"
... | openmc-dev/openmc | e33e66aa888453efaf43afcc94e7d6b2c74b1e7c | Make `IsogonalOctagon` objects parallel to `y` axis use `xz` basis.
## Description
<!--What is the feature or enhancement?-->
Currently, `IsogonalOctagon` objects parallel to the `y` axis will assume a `zx` basis. This was done to make the implementation easier. In practice, it is confusing for users, so we should s... | diff --git a/openmc/model/surface_composite.py b/openmc/model/surface_composite.py
index 1fa4234fb..7c134e843 100644
--- a/openmc/model/surface_composite.py
+++ b/openmc/model/surface_composite.py
@@ -233,7 +233,7 @@ class IsogonalOctagon(CompositeSurface):
r"""Infinite isogonal octagon composite surface
An... |
openml__openml-python-1354 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openml/tasks/functions.py:get_tasks",
"openml/tasks/functions.py:get_task"
],
"edited_modules": [
"openml/tasks/functions.py:get_tasks",
"openml/tasks/functions.py:ge... | openml/openml-python | d37542bfbea024621bbca171358ac489a8919707 | Don't download (large) datasets by default
#### Description
In datasets.get_dataset(data_id) the default is currently to always download the dataset:
https://openml.github.io/openml-python/master/generated/openml.datasets.get_dataset.html#openml.datasets.get_dataset
This is problematic for large datasets - it take... | diff --git a/openml/tasks/functions.py b/openml/tasks/functions.py
index c763714b..9fd2e4be 100644
--- a/openml/tasks/functions.py
+++ b/openml/tasks/functions.py
@@ -347,8 +347,8 @@ def __list_tasks( # noqa: PLR0912, C901
# TODO(eddiebergman): Maybe since this isn't public api, we can make it keyword only?
def get_... |
openml__openml-python-1364 | [
{
"changes": {
"added_entities": null,
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},
"file": "examples/40_paper/2018_kdd_rijn_example.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | openml/openml-python | 26ae499c06927e7b9f6258bbed35cba903a58364 | Improve error message when API key is not provided
The error message for a missing API key looks very generic and is not very user friendly:
```
Traceback (most recent call last):
File "/home/feurerm/sync_dir/projects/openml/python/local/example.py", line 13, in <module>
run = openml.runs.run_model_on_task(cl... | diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index bc4a04bc..773dda6f 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -29,10 +29,7 @@ jobs:
python-version: 3.8
- name: Install dependencies
run: |
- pip install -e .[docs,examples,example... |
openml__openml-python-677 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/datasets_tutorial.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edit... | openml/openml-python | 813daebea2d0c4932641f013ef79ba0ca72a9f46 | openml.datasets.get_data() has unpredictable number of return values
MWE:
```
dataset = openml.datasets.get_dataset(40978)
res = dataset.get_data(target=dataset.default_target_attribute)
print(len(res))
dataset = openml.datasets.get_dataset(2)
res = dataset.get_data(target=dataset.default_target_attribute)
p... | diff --git a/examples/datasets_tutorial.py b/examples/datasets_tutorial.py
index dd24e349..4d340de7 100644
--- a/examples/datasets_tutorial.py
+++ b/examples/datasets_tutorial.py
@@ -60,10 +60,9 @@ print(dataset.description[:500])
# controlled with the parameter ``dataset_format`` which can be either 'array'
# (defau... |
openml__openml-python-755 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "openml/evaluations/__init__.py"
},
{
"changes": {
"added_entities": [
"openml/evaluations/functions.py:list_evaluations_setups"
],... | openml/openml-python | e6ee09d6af0c1aea7aa1a65b10638000338d55e6 | Python version requirements inconsistent
I noticed in your `setup.py` file that you have [a requirement for Python version >= 3.5](https://github.com/openml/openml-python/blob/56fcc00cb16b102e4778c1f1dadd7d9919e9eca4/setup.py#L16), but you do not have a [`python_requires` keyword](https://packaging.python.org/guides/di... | diff --git a/doc/progress.rst b/doc/progress.rst
index 5ce263fc..8381f3a9 100644
--- a/doc/progress.rst
+++ b/doc/progress.rst
@@ -8,6 +8,7 @@ Changelog
0.10.0
~~~~~~
+* ADD #737: Add list_evaluations_setups to return hyperparameters along with list of evaluations.
* FIX #261: Test server is cleared of all files u... |
openml__openml-python-823 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openml/datasets/dataset.py:OpenMLDataset.__init__",
"openml/datasets/dataset.py:OpenMLDataset._parse_data_from_arff"
],
"edited_modules": [
"openml/datasets/dataset.py:OpenML... | openml/openml-python | 4853d7cfa279e5fb348cc96471c4cf61fdaf8b23 | Cannot load sparse datasets with categorical variables any more
Can be reproduced with:
```
import openml
openml.datasets.get_dataset(395)
``` | diff --git a/openml/datasets/dataset.py b/openml/datasets/dataset.py
index fb760583..fde45cc5 100644
--- a/openml/datasets/dataset.py
+++ b/openml/datasets/dataset.py
@@ -109,17 +109,18 @@ class OpenMLDataset(object):
paper_url=None, update_comment=None,
md5_checksum=None, data_file=... |
openml__openml-python-931 | [
{
"changes": {
"added_entities": null,
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"edited_entities": null,
"edited_modules": null
},
"file": "examples/30_extended/fetch_evaluations_tutorial.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entitie... | openml/openml-python | 4256834c3f9a361f748c26bed925a3e6d6d08739 | The API docs should document the openml config options
#### Description
The API Docs: http://openml.github.io/openml-python/master/api.html
do not cover the API config options, such as 'server, api_key, verbosity,...'
Could this be added?
#### Steps/Code to Reproduce
Try to look up the OpenML-Python config opt... | diff --git a/doc/usage.rst b/doc/usage.rst
index 36c8584f..d7ad0d52 100644
--- a/doc/usage.rst
+++ b/doc/usage.rst
@@ -29,6 +29,35 @@ the OpenML Python connector, followed up by a simple example.
* `Introduction <examples/introduction_tutorial.html>`_
+~~~~~~~~~~~~~
+Configuration
+~~~~~~~~~~~~~
+
+The configurati... |
openml__openml-python-980 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
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},
"file": "examples/30_extended/run_setup_tutorial.py"
},
{
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"edited_entities": [
... | openml/openml-python | 07e87add438cd36008442a3aaecfbea25fc7e10b | Checking active datasets
https://github.com/openml/openml-python/blob/3dc6dee62c1835e9b4f2bc9b6f9208d902263606/openml/datasets/functions.py#L295-L296
Maybe we should `list_datasets(status='active')` and if a `dataset_id` from the iterable of `dataset_ids` that we want to check is in the results, we can mark it as Tr... | diff --git a/doc/progress.rst b/doc/progress.rst
index c3aaf8d1..7dc63334 100644
--- a/doc/progress.rst
+++ b/doc/progress.rst
@@ -8,6 +8,7 @@ Changelog
0.11.1
~~~~~~
+* MAINT #671: Improved the performance of ``check_datasets_active`` by only querying the given list of datasets in contrast to querying all datasets... |
openml__openml-python-983 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openml/datasets/dataset.py:OpenMLDataset._parse_data_from_arff"
],
"edited_modules": [
"openml/datasets/dataset.py:OpenMLDataset"
]
},
"file": "openml/datasets/dataset.... | openml/openml-python | 3132dac1fa33e1666cc85b3cb7d3b7ce1c3ace9d | pickle for SVHN bigger than arff file
For dataset 41081, I get:
```
1.1G dataset.arff
2.3G dataset.pkl.py3
```
Maybe we should be using joblib instead? My hard drive is getting full because I'm trying to run CC-18 stuff, which is a bit annoying. | diff --git a/doc/progress.rst b/doc/progress.rst
index 7dc63334..2e077484 100644
--- a/doc/progress.rst
+++ b/doc/progress.rst
@@ -8,6 +8,7 @@ Changelog
0.11.1
~~~~~~
+* MAINT #891: Changed the way that numerical features are stored. Numerical features that range from 0 to 255 are now stored as uint8, which reduces... |
openmm__openmmforcefields-120 | [
{
"changes": {
"added_entities": [
"openmmforcefields/generators/template_generators.py:ClassProperty.__get__",
"openmmforcefields/generators/template_generators.py:SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS"
],
"added_modules": [
"openmmforcefields/generators/temp... | openmm/openmmforcefields | 32f891396d32209d142b06fd0cd08855be3278c4 | Openforcefields versions
This table will be updated as a part of the openforcefields release process, per https://github.com/openforcefield/openforcefields/wiki/Release-Process
Close this issue once https://github.com/openforcefield/openforcefield/issues/477 is implemented
| Filename | DOI | FF line | Release Date ... | diff --git a/README.md b/README.md
index 20f3113..b31c687 100644
--- a/README.md
+++ b/README.md
@@ -157,7 +157,7 @@ Newly parameterized molecules will be written to the cache, saving time next tim
## Using the Open Force Field Initiative SMIRNOFF small molecule force fields
The `openmmforcefields` package includes... |
openmrslab__suspect-148 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"suspect/io/ge.py:prepare_pfile_svs"
],
"edited_modules": [
"suspect/io/ge.py:prepare_pfile_svs"
]
},
"file": "suspect/io/ge.py"
},
{
"changes": {
"added_e... | openmrslab/suspect | 97d7a167cb6f139d5311cb194759285277ef5493 | LCModel IO - "VOLUME = NaN"
For 20% Siemens TWIX data I was unable to run LCModel analysis with an error 1 FATAL ZEROVX 4. In CONTROL file there was "VOLUME = NaN" instead of a some numerical value.
B. | diff --git a/docs/changelog.rst b/docs/changelog.rst
index f4113ab..9e4d883 100644
--- a/docs/changelog.rst
+++ b/docs/changelog.rst
@@ -4,6 +4,7 @@
Changelog
=========
+* :bug:`145` fixed issue with calculating transform for sagittally planned twix voxels
* :feature:`146` substantial overhaul of the singlet fitti... |
openmrslab__suspect-40 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"suspect/processing/denoising.py:spline",
"suspect/processing/denoising.py:wavelet"
],
"edited_modules": [
"suspect/processing/denoising.py:spline",
"suspect/processin... | openmrslab/suspect | b03275c0dd645fd522cab182a2cfbe28dfc948ed | Spline denoising fails on numpy 1.12
In numpy 1.12 spline denoising fails because it passes floating point values to _pad and roll instead of integer values. | diff --git a/suspect/processing/denoising.py b/suspect/processing/denoising.py
index f55b7ae..46dfc04 100644
--- a/suspect/processing/denoising.py
+++ b/suspect/processing/denoising.py
@@ -85,8 +85,8 @@ def svd(input_signal, rank):
def spline(input_signal, num_splines, spline_order):
# input signal has to be a... |
openmrslab__suspect-43 | [
{
"changes": {
"added_entities": null,
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},
"file": "suspect/__init__.py"
},
{
"changes": {
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"edited_modules... | openmrslab/suspect | 522105c8852802054a8849405e74c8cb8fa2bc60 | Spectra should be first class data objects
Currently MRSData objects contain FID data and provide various convenience methods and properties, while spectra are bare ndarrays without any additional information. It would be better if the two classes inherited from (let's say) MRSBase giving some core methods, and then pr... | diff --git a/requirements.txt b/requirements.txt
index 5af82e3..76bf75c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,3 +4,4 @@ nbsphinx
ipykernel
numpy
lmfit
+pydicom
diff --git a/suspect/__init__.py b/suspect/__init__.py
index 53dcc1a..5a58e22 100644
--- a/suspect/__init__.py
+++ b/suspect/__init__.py... |
openmrslab__suspect-46 | [
{
"changes": {
"added_entities": [
"suspect/_transforms.py:rotation_matrix"
],
"added_modules": [
"suspect/_transforms.py:rotation_matrix"
],
"edited_entities": null,
"edited_modules": null
},
"file": "suspect/_transforms.py"
},
{
"changes": {
... | openmrslab/suspect | 964f2460e46378c29e78d280f999128f34e829df | Get spatial information out of twix files
At the moment, only rda files load a transform to enable them to be co-registered to structural MRI images. It should in theory be possible to read this information out of the twix file as well. | diff --git a/suspect/_transforms.py b/suspect/_transforms.py
index 78bc68a..caddbfe 100644
--- a/suspect/_transforms.py
+++ b/suspect/_transforms.py
@@ -38,3 +38,33 @@ def transformation_matrix(x_vector, y_vector, translation, spacing):
for j in range(4):
matrix[i, j] *= spacing[j]
return mat... |
openmrslab__suspect-57 | [
{
"changes": {
"added_entities": [
"suspect/mrsobjects.py:MRSSpectrum.slice_hz",
"suspect/mrsobjects.py:MRSSpectrum.slice_ppm"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"suspect/mrsobjects.py:MRSSpectrum"
]
},
"file... | openmrslab/suspect | f65efe543321e1d75d6ecbc7c22be73ab84d3d8a | Slice spectrum
It should be possible to generate a slice object for a specified frequency range from an MRSSpectrum object, which can be used to extract specific regions of a spectrum (or set of spectra). | diff --git a/suspect/mrsobjects.py b/suspect/mrsobjects.py
index 7fb4764..3785dc1 100644
--- a/suspect/mrsobjects.py
+++ b/suspect/mrsobjects.py
@@ -324,3 +324,46 @@ class MRSSpectrum(MRSBase):
suspect.adjust_frequency : equivalent function
"""
return self.fid().adjust_frequency(frequency_shi... |
openmrslab__suspect-64 | [
{
"changes": {
"added_entities": [
"suspect/_transforms.py:normalise_positions_for_transform"
],
"added_modules": [
"suspect/_transforms.py:normalise_positions_for_transform"
],
"edited_entities": null,
"edited_modules": null
},
"file": "suspect/_trans... | openmrslab/suspect | e63218387349081ee3d790ee96d1cb8e0ec74af2 | ENH: to/from_scanner() should accept arrays of coords
Currently the to_scanner() and from_scanner() functions take three arguments: x, y, z and return an numpy array. It would be convenient if the functions could handle a numpy array as an input for consistency, this would also allow passing in an array of coords to be... | diff --git a/suspect/_transforms.py b/suspect/_transforms.py
index caddbfe..ee2f9f2 100644
--- a/suspect/_transforms.py
+++ b/suspect/_transforms.py
@@ -68,3 +68,37 @@ def rotation_matrix(angle, axis):
matrix[2, 1] = axis[2] * axis[1] * (1 - c) + axis[0] * s
matrix[2, 2] = c + axis[2] ** 2 * (1 - c)
retu... |
openmrslab__suspect-81 | [
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"file": "suspect/_version.py"
},
{
"changes": {
"added_entities": [
"suspect/base.py:ImageBase.centre",
"suspect/base.py:ImageBase.resamp... | openmrslab/suspect | f5a6a8e7875a9114bab75aba928028cb69d9665e | ENH: Resample image volumes
It should be possible to derive a new ImageBase from an existing ImageBase object by supplying the coordinate system, size and shape. | diff --git a/suspect/_version.py b/suspect/_version.py
index e19434e..334b899 100644
--- a/suspect/_version.py
+++ b/suspect/_version.py
@@ -1,1 +1,1 @@
-__version__ = "0.3.3"
+__version__ = "0.3.4"
diff --git a/suspect/base.py b/suspect/base.py
index 3bdf704..6952aa2 100644
--- a/suspect/base.py
+++ b/suspect/base.py
... |
openmrslab__suspect-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"suspect/base.py:ImageBase.row_vector",
"suspect/base.py:ImageBase.col_vector",
"suspect/base.py:ImageBase.resample"
],
"edited_modules": [
"suspect/base.py:ImageBase"... | openmrslab/suspect | 758a6d0d41dd61617d6957ae400a7b0c366b477b | BUG: resampling of image volumes doesn't work properly for single slices
When transforming coordinates the arrays are squeezed which can remove singlet spatial dimensions, leading to issues in interpreting the coordinate arrays. | diff --git a/suspect/base.py b/suspect/base.py
index 6952aa2..8be873b 100644
--- a/suspect/base.py
+++ b/suspect/base.py
@@ -122,12 +122,12 @@ class ImageBase(np.ndarray):
@property
@requires_transform
def row_vector(self):
- return self.transform[:3, 1] / np.linalg.norm(self.transform[:3, 1])
+ ... |
openqasm__oqpy-20 | [
{
"changes": {
"added_entities": [
"oqpy/base.py:OQPyExpression._to_unary",
"oqpy/base.py:OQPyExpression.__pos__",
"oqpy/base.py:OQPyExpression.__neg__",
"oqpy/base.py:OQPyExpression.__sub__",
"oqpy/base.py:OQPyExpression.__rsub__",
"oqpy/base.py:OQPyExpress... | openqasm/oqpy | 32cb438a101700af6c2b5c9be7d86d5ee2314ee6 | Support classical arguments and return types for defcals | diff --git a/oqpy/base.py b/oqpy/base.py
index 4a45796..43dece9 100644
--- a/oqpy/base.py
+++ b/oqpy/base.py
@@ -60,12 +60,29 @@ class OQPyExpression:
"""Helper method to produce a binary expression."""
return OQPyBinaryExpression(ast.BinaryOperator[op_name], first, second)
+ @staticmethod
+ d... |
openqasm__oqpy-43 | [
{
"changes": {
"added_entities": [
"oqpy/base.py:_get_type",
"oqpy/base.py:compute_product_types",
"oqpy/base.py:compute_quotient_types"
],
"added_modules": [
"oqpy/base.py:_get_type",
"oqpy/base.py:compute_product_types",
"oqpy/base.py:compute_q... | openqasm/oqpy | ffcf0041e31f37399c9f78c76c5a52cd354d1fe1 | Help user by converting floats to durations and vice versa where appropriate
In python, the user will likely be representing durations as floats with some canonical unit, probably seconds. It is inconvenient for the user to need to remember where a float is allowed and where a duration is required. We can help this alo... | diff --git a/oqpy/base.py b/oqpy/base.py
index d69383b..c1d5ca2 100644
--- a/oqpy/base.py
+++ b/oqpy/base.py
@@ -58,10 +58,13 @@ class OQPyExpression:
@staticmethod
def _to_binary(
- op_name: str, first: AstConvertible, second: AstConvertible
+ op_name: str,
+ first: AstConvertible,
+ ... |
openradar__xradar-118 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/util.py:extract_angle_parameters"
],
"edited_modules": [
"xradar/util.py:extract_angle_parameters"
]
},
"file": "xradar/util.py"
}
] | openradar/xradar | e464ac7d8de09bd70c2c7b719175c4c93648feb7 | possible bug with angle reindexing (?)
* xradar version: 0.1.0
* Python version: 3.9
* Operating System: Ubuntu 22.04
Hi everyone,
I am trying to apply the angle reindexing function to my dataset as is explained [here](https://docs.openradarscience.org/projects/xradar/en/stable/notebooks/angle_reindexing.html)... | diff --git a/docs/history.md b/docs/history.md
index 1abd0ad..b0456f8 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -5,7 +5,8 @@
* FIX: Correct DB_DBTE8/DB_DBZE8 and DB_DBTE16/DB_DBZE16 decoding for iris-backend ({pull}`110`) by [@kmuehlbauer](https://github.com/kmuehlbauer)
* FIX: Cast boolean string to int ... |
openradar__xradar-162 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/nexrad_level2.py:NexradLevel2Store.open_store_coordinates"
],
"edited_modules": [
"xradar/io/backends/nexrad_level2.py:NexradLevel2Store"
]
},
"file"... | openradar/xradar | 56a9ca1f42ca23074dc0b1d2a86d51e1bd4eafa2 | BUG: Expand Sweep Fixed Mode Variables in NEXRAD Reader
### Description
As of now, the elevation angle, variable thresholds, etc. are condensed into an ordered dictionary in the `sweep_fixed_mode` data variable in the individual sweep dataset.
For example,
```python
import xradar as xd
from open_radar_data i... | diff --git a/docs/history.md b/docs/history.md
index c45f272..bff2bfd 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -7,6 +7,7 @@
* MNT: use CODECOV token ({pull}`155`) by [@kmuehlbauer](https://github.com/kmuehlbauer).
* MNT: fix path for notebook coverage ({pull}`157`) by [@kmuehlbauer](https://github.com/km... |
openradar__xradar-177 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/iris.py:decode_array",
"xradar/io/backends/iris.py:IrisRawFile.get_compression_code",
"xradar/io/backends/iris.py:_get_required_root_dataset",
"xradar/io/backe... | openradar/xradar | 5ed1f43e821fdd12095b2f65e7eac5529a3458ce | Deprecated ruff call in CI ?
* xradar version: 0.5.0
* Python version: -
* Operating System: -
### Description
CI of xradar uses ruff in the following way
ruff .
But this leads to error
error: `ruff <path>` has been removed. Use `ruff check <path>` instead.
Error: Process completed with... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d1a621e..f8c6dcc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -27,7 +27,7 @@ jobs:
black --check .
- name: Lint with ruff
run: |
- ruff .
+ ruff check .
build_0:
name:... |
openradar__xradar-181 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/nexrad_level2.py:NEXRADLevel2File.get_data_header",
"xradar/io/backends/nexrad_level2.py:NexradLevel2Store.open_store_coordinates",
"xradar/io/backends/nexrad_level2.p... | openradar/xradar | 44df4e437782ad2179ef3bc29209eeef454a174f | Bugs in NEXRAD L2 reader
* xradar version: 0.5.0
* Python version: 3.11
* Operating System: Linux
### Description
I identified two bugs affecting the NEXRAD L2 reader.
- The first bug cause the `time` coordinates and `time_coverage` variables to be shifted by 1 day compared to the actual time. **This impac... | diff --git a/docs/history.md b/docs/history.md
index 4d2de54..cce02e2 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -6,6 +6,8 @@
* ADD: Add Alfonso to citation doc ({pull}`169`) by [@mgrover1](https://github.com/mgrover1).
* ENH: Adding global variables and attributes to iris datatree ({pull}`166`) by [@aladi... |
openradar__xradar-202 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/export/cfradial1.py:to_cfradial1"
],
"edited_modules": [
"xradar/io/export/cfradial1.py:to_cfradial1"
]
},
"file": "xradar/io/export/cfradial1.py"
},
{
... | openradar/xradar | 7ff84a72d45db7e8662998e41bbe98497bc33246 | Issue with cfradial1 writer: ValueError: cannot rename 'sweep_fixed_angle' because it is not a variable or dimension in this dataset
* xradar version: 0.6.4
* Python version: 3.12.5
* Operating System: MacOS Sonoma 14.6.1
```python
import xradar as xd
import matplotlib.pyplot as plt
from open_radar_data import ... | diff --git a/docs/history.md b/docs/history.md
index aa9dcd5..daabab9 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -1,14 +1,18 @@
# History
+## Development Version
+
+* ADD: Added `apply_to_sweeps` function for applying custom operations to all sweeps in a `DataTree` radar volume Implemented by [@syedhamida... |
openradar__xradar-234 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/common.py:_attach_sweep_groups"
],
"edited_modules": [
"xradar/io/backends/common.py:_attach_sweep_groups"
]
},
"file": "xradar/io/backends/common.py... | openradar/xradar | 1dce43b43bc346e0621fc1322a6116312042097c | Bug in transformation
* xradar version:0.7.+
* Python version:3.12
* Operating System:MacOS
### Description
We have a bug in the `transform` method when converting to cfradial1 or writing cfradial1 file. This issue arises when sweeps are of different shape, and when we transform it to CF1, it acquires the shape o... | diff --git a/docs/history.md b/docs/history.md
index e4ff41c..de8481a 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -4,6 +4,7 @@
This is the first version which uses datatree directly from xarray. Thus, xarray is pinned to version >= 2024.10.0.
+* FIX: Convert volumes to_cfradial1 containing sweeps with di... |
openradar__xradar-250 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/hpl.py:HplFile.__init__",
"xradar/io/backends/hpl.py:HPLBackendEntrypoint.open_dataset"
],
"edited_modules": [
"xradar/io/backends/hpl.py:HplFile",
... | openradar/xradar | b4684faca3f9b91717571e230f47f38edcde12d9 | TypeError: only integer scalar arrays can be converted to a scalar index
I'm currently working on a project where I'm working with raw LiDAR data that comes in .hpl format and I'm struggling to get xradar to read in the file.
I used the following code adapted from the example here: https://docs.openradarscience.org... | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6223eb4..26d306a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -157,7 +157,7 @@ jobs:
h5py
lat_lon_parser
netCDF4
- open-radar-data>=0.3.0
+ open-radar-data>=0.4.... |
openradar__xradar-267 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/nexrad_level2.py:NEXRADLevel2File.get_metadata_header",
"xradar/io/backends/nexrad_level2.py:NEXRADLevel2File.get_msg_5_data",
"xradar/io/backends/nexrad_level2.py:NEX... | openradar/xradar | f5f1f6f713f6271f9de5007112ea1ba5dc406d67 | NEXRADLevel2 Reader Error for Older Files
* xradar version: 0.8.0
* Python version: 3.12.2
* Operating System: Windows 11
### Description
I was loading in some radar data from KLIX on 8/28/2005 at 1800z using the NEXRADLevel2 engine for xarray that xradar provides and ran into this error. Seems to only happen w... | diff --git a/docs/history.md b/docs/history.md
index 8f2a6ee..1946f0a 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -11,6 +11,7 @@
* FIX: DataTree reader now works with sweeps containing different variables ({pull}`252`) by [@egouden](https://github.com/egouden).
* FIX: Correct retrieval of intermediate recor... |
openradar__xradar-269 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/backends/iris.py:IrisArrayWrapper._getitem",
"xradar/io/backends/iris.py:IrisStore.__init__",
"xradar/io/backends/iris.py:IrisStore.open",
"xradar/io/backends/iris.py:I... | openradar/xradar | fc43e6051a3d483521482c667b30a435054bc3ea | NEXRAD issue - IndexError index out of bounds
* xradar version: 0.6.4
* xarray version: 2024.7.0
* Python version: 3.12.4
* Operating System: Linux
### Description
I have found a puzzling bug that only comes up in certain situations with Dask
### What I Did
```python
import xradar
import xarray as xr
... | diff --git a/docs/history.md b/docs/history.md
index 1946f0a..2999ec2 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -12,6 +12,7 @@
* FIX: Correct retrieval of intermediate records in nexrad level2 reader ({issue}`259`) ({pull}`261`) by [@kmuehlbauer](https://github.com/kmuehlbauer).
* FIX: Test for magic numb... |
openradar__xradar-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"xradar/io/export/cfradial2.py:to_cfradial2"
],
"edited_modules": [
"xradar/io/export/cfradial2.py:to_cfradial2"
]
},
"file": "xradar/io/export/cfradial2.py"
},
{
... | openradar/xradar | 010b104034c1ab14d9e4f4ca72ea15fe1014c0df | Tree can't be exported with to_cfradial2 if time is first dimension
* xradar version: 0.1.0
* Python version: 3.11
* Operating System: Linux
### Description
While trying to export a DataTree (opened with `open_odim_datatree`) with `to_cfradial2` an error is raised.
```python
ValueError: cannot swap from dim... | diff --git a/docs/history.md b/docs/history.md
index 763f277..ebc1a86 100644
--- a/docs/history.md
+++ b/docs/history.md
@@ -1,5 +1,9 @@
# History
+## Development Version
+
+* FIX: check for dim0 if not given, only swap_dims if needed ({issue}`92`), ({pull}`94`) by [@kmuehlbauer](https://github.com/kmuehlbauer)
+
#... |
openshift__openshift-client-python-113 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "ansible/roles/openshift_client_python/library/openshift_client_python.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,... | openshift/openshift-client-python | 841da482321b2bc2a02fc400badf41e02a26222a | APIObject doesn't respect context namespace
If you create `APIObject` with a model that is missing `namespace` it will default to the `default` namespace instead of whatever namespace context has. | diff --git a/ansible/rebuild_module.digest b/ansible/rebuild_module.digest
index 02baf09..5055665 100644
--- a/ansible/rebuild_module.digest
+++ b/ansible/rebuild_module.digest
@@ -1,1 +1,1 @@
-0f98b612b97ffcc98304fc9581a8727a -
+45e5927b24842946eaf6fab1a145810f -
diff --git a/ansible/roles/openshift_client_python/li... |
openshift__openshift-restclient-python-231 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"openshift/dynamic/client.py:ResourceContainer.get"
],
"edited_modules": [
"openshift/dynamic/client.py:ResourceContainer"
]
},
"file": "openshift/dynamic/client.py"
}... | openshift/openshift-restclient-python | b52fc4a023fa662457723d245e82bfaa87842ccb | openshift dynamic client is now case sensitive
Using `kind=namespace` (for example) used to work but no longer does
See https://github.com/ansible/ansible/issues/48137
This breaks backwards compatibility. | diff --git a/.tito/packages/python-openshift b/.tito/packages/python-openshift
index f18cd6f..3f8c461 100644
--- a/.tito/packages/python-openshift
+++ b/.tito/packages/python-openshift
@@ -1,1 +1,1 @@
-0.6.2-12 ./
+0.8.0-1 ./
diff --git a/.tito/releasers.conf b/.tito/releasers.conf
index 2b4c815..f140a70 100644
--- a/.... |
openstates__pyopenstates-15 | [
{
"changes": {
"added_entities": [
"pyopenstates.py:get_organizations",
"pyopenstates.py:_fix_id_string",
"pyopenstates.py:_jurisdiction_id"
],
"added_modules": [
"pyopenstates.py:get_organizations",
"pyopenstates.py:_fix_id_string",
"pyopenstate... | openstates/pyopenstates | a313da467429d7e3e500e57ee8deb8e46d7c4ef4 | update for API v3
A reminder to myself, should be a fairly light lift since the methods are very similar in function. | diff --git a/pyopenstates.py b/pyopenstates.py
index 2b3a4dc..8ff9c32 100644
--- a/pyopenstates.py
+++ b/pyopenstates.py
@@ -25,14 +25,18 @@ limitations under the License."""
__version__ = "1.2.0"
-API_ROOT = "https://openstates.org/api/v1/"
+API_ROOT = "https://v3.openstates.org"
DEFAULT_USER_AGENT = "pyopenstat... |
opentok__Opentok-Python-SDK-124 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opentok/archives.py:Archive.__init__"
],
"edited_modules": [
"opentok/archives.py:Archive"
]
},
"file": "opentok/archives.py"
},
{
"changes": {
"added_ent... | opentok/Opentok-Python-SDK | 68c696a40470d261f169d50dc7045a91e0868416 | OpenTok.start_archive() doesn't have parameter 'resolution'
OpenTok.start_archive() doesn't have parameter 'resolution'. Python SDK is simply through requests.post to use Opentok REST API and it doesn't pass the parameter 'resolution' in the payload json which is default of '640x480'. | diff --git a/README.rst b/README.rst
index 3c51420..3b9d05a 100644
--- a/README.rst
+++ b/README.rst
@@ -45,14 +45,14 @@ Creating Sessions
~~~~~~~~~~~~~~~~~
To create an OpenTok Session, use the ``opentok.create_session()`` method. There are three optional
-keyword parameters for this method:
+keyword parameters f... |
opentok__Opentok-Python-SDK-89 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opentok/opentok.py:OpenTok.headers",
"opentok/opentok.py:OpenTok._create_jwt_auth_header"
],
"edited_modules": [
"opentok/opentok.py:OpenTok"
]
},
"file": "open... | opentok/Opentok-Python-SDK | 613e5368748ec31a18c4f47c26683bb3bcdbbcf1 | add an "iat" claim to opentok-auth tokens
something we overlooked before, but we're now trying to add into the OpenTok-Auth JWTs: https://tools.ietf.org/html/rfc7519#section-4.1.6. | diff --git a/opentok/opentok.py b/opentok/opentok.py
index d3f855f..61899fd 100644
--- a/opentok/opentok.py
+++ b/opentok/opentok.py
@@ -275,7 +275,7 @@ class OpenTok(object):
"""For internal use."""
return {
'User-Agent': 'OpenTok-Python-SDK/' + __version__ + ' ' + platform.python_versio... |
operator-framework__operator-courier-103 | [
{
"changes": {
"added_entities": [
"operatorcourier/validate.py:ValidateCmd._csv_spec_install_validation"
],
"added_modules": null,
"edited_entities": [
"operatorcourier/validate.py:ValidateCmd._csv_spec_validation"
],
"edited_modules": [
"operatorcour... | operator-framework/operator-courier | 5a4852c22f5de4d664ca1cc7da285e3e4972387b | incorrect yaml for deployments not caught by linter
in the file below
```
spec:
install:
spec:
deployments:
name: robin-operator
....
....
....
```
should be
```
spec:
install:
spec:
deployments:
- name: robin-operator
....
... | diff --git a/operatorcourier/validate.py b/operatorcourier/validate.py
index 64b97bd..a140a27 100644
--- a/operatorcourier/validate.py
+++ b/operatorcourier/validate.py
@@ -176,7 +176,10 @@ class ValidateCmd():
self._log_error("csv spec.installModes not defined")
valid = False
- if "i... |
opsdroid__opsdroid-163 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "opsdroid/const.py"
},
{
"changes": {
"added_entities": [
"opsdroid/loader.py:Loader.setup_modules_directory"
],
"added_modul... | opsdroid/opsdroid | b6a6b803844b36e49146b468dc104be1e49235a5 | Change default modules directory
Currently the default modules directory location is `./modules`.
This makes a few assumptions:
* Current directory is in the python path
* There are no other python modules in the current directory
* There are no other modules named `modules`
* Current directory is writable
... | diff --git a/opsdroid/const.py b/opsdroid/const.py
index be722ef..c12d2ae 100644
--- a/opsdroid/const.py
+++ b/opsdroid/const.py
@@ -4,5 +4,6 @@ __version__ = "0.7.1"
LOG_FILENAME = 'output.log'
DEFAULT_GIT_URL = "https://github.com/opsdroid/"
-MODULES_DIRECTORY = "modules"
+MODULES_DIRECTORY = "opsdroid-modules"
+... |
opsdroid__opsdroid-165 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opsdroid/__main__.py:main"
],
"edited_modules": [
"opsdroid/__main__.py:main"
]
},
"file": "opsdroid/__main__.py"
},
{
"changes": {
"added_entities": null... | opsdroid/opsdroid | a3e93bda15e1debbc368f5c947a10ad5f1027fbe | Generate default config automatically
Instead of running `opsdroid --gen-config` and piping the output into a file opsdroid should simply check for the existence of a config file and if it can't find one it should create one in `~/.opsdroid` using the default config file. | diff --git a/README.md b/README.md
index 098e647..7b9ad7b 100644
--- a/README.md
+++ b/README.md
@@ -10,16 +10,14 @@ An open source python chat-ops bot framework.
```
pip3 install opsdroid
-mkdir ~/.opsdroid
-opsdroid --gen-config > ~/.opsdroid/configuration.yaml
opsdroid
```
## Configuration
-Configuration ... |
opsdroid__opsdroid-225 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opsdroid/loader.py:Loader.load_config_file"
],
"edited_modules": [
"opsdroid/loader.py:Loader"
]
},
"file": "opsdroid/loader.py"
}
] | opsdroid/opsdroid | b67d32310da842dddddb9b907f731a03d0562a2f | Allow usage of env vars in config
The configuration should be parsed for environment variables when loaded. This would allow for secrets like api keys to be kept outside of the opsdroid configuration.
#### Example
```yaml
connectors:
- name: slack
default-room: '#general'
bot-name: "opsdroid"
i... | diff --git a/docs/configuration-reference.md b/docs/configuration-reference.md
index 2370bf9..cefea9c 100644
--- a/docs/configuration-reference.md
+++ b/docs/configuration-reference.md
@@ -176,3 +176,15 @@ databases:
repo: https://github.com/username/mymongofork.git
no-cache: true
```
+
+## Environment varia... |
opsdroid__opsdroid-58 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"opsdroid/connector.py:Connector.__init__"
],
"edited_modules": [
"opsdroid/connector.py:Connector"
]
},
"file": "opsdroid/connector.py"
},
{
"changes": {
... | opsdroid/opsdroid | bef3ccfae2b581b0e01fa001334a6beef7a7df57 | Default connector and default room
When writing a skill which originates from something other than a message (e.g cron #26) the response may need to know which room to post into.
Most chat clients have a default room, like `#general` in Slack. This could be available as a property in the connector so that skills can ... | diff --git a/docs/extending/connectors.md b/docs/extending/connectors.md
index 620723f..1d45b7d 100644
--- a/docs/extending/connectors.md
+++ b/docs/extending/connectors.md
@@ -1,6 +1,6 @@
# Creating a connector
-Connectors are a class which extends the base opsdroid Connector. The class has three mandatory methods,... |
opsview__plugnpy-8 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/check_cpu.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modul... | opsview/plugnpy | 61b5839f6e6fcaa6121f84a73ee42f058e6e0551 | Encoding error on README.md
In certain environments, the build will fail with an encoding error on README.md:
```
$ pip install -e .[test]
# ...
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "<string>", line 1, in <module>
File ... | diff --git a/README.md b/README.md
index 365bd2c..1d24eaa 100644
--- a/README.md
+++ b/README.md
@@ -14,13 +14,19 @@
## Installing the Library
-For use with versions of Opsview below 6.1, Opsview Python's pip will need to be used to install this library, as they do not ship with it pre-installed.
+For Opsview vers... |
optuna__optuna-1209 | [
{
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"edited_entities": [
"optuna/multi_objective/study.py:MultiObjectiveStudy.optimize"
],
"edited_modules": [
"optuna/multi_objective/study.py:MultiObjectiveStudy"
]
},
"file": "optuna/multi_ob... | optuna/optuna | dbdba521a55dd71d7b4f158fc125a01859cdb843 | Bug when passing multiple callbacks to `MultiObjectiveStudy.optimize`
<!-- Please write a clear and concise description of what the bug is. -->
When passing multiple callbacks to `MultiObjectiveStudy.optimize`, it uses only the last callback.
```python
import optuna
n_objectives = 2
directions = ["minimize... | diff --git a/optuna/multi_objective/study.py b/optuna/multi_objective/study.py
index db1f70402..0d9755d25 100644
--- a/optuna/multi_objective/study.py
+++ b/optuna/multi_objective/study.py
@@ -16,6 +16,7 @@ from optuna import multi_objective
from optuna.storages import BaseStorage
from optuna.study import Study
from... |
optuna__optuna-1248 | [
{
"changes": {
"added_entities": [
"optuna/_experimental.py:_get_docstring_indent"
],
"added_modules": [
"optuna/_experimental.py:_get_docstring_indent"
],
"edited_entities": [
"optuna/_experimental.py:experimental"
],
"edited_modules": [
... | optuna/optuna | e23ef651206815601c0910203bd78ad5d1a01cbb | `experimental` decorator adds extra indents to docs
An extra indent appears in the docs when the [`experimental`](https://github.com/optuna/optuna/blob/2d5f24b06eed56ece72b8dfa878135bb4bb63779/optuna/_experimental.py#L60) decorator is added to a method of a class. This does not happen with a top level (i.e., not nested... | diff --git a/optuna/_experimental.py b/optuna/_experimental.py
index dae7c4887..955414935 100644
--- a/optuna/_experimental.py
+++ b/optuna/_experimental.py
@@ -1,5 +1,6 @@
import functools
import inspect
+import textwrap
from typing import Any
from typing import Callable
import warnings
@@ -7,14 +8,11 @@ import w... |
optuna__optuna-1285 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/allennlp/allennlp_jsonnet.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | optuna/optuna | 71b0d997038e5b25bea8abfe261706c1c3dc4274 | `experimental` decorator breaks class documentation.
The `experimental` decorator used on classes break documentation. This could be one manifestation but there is an issue with how the documentation including type hints are propagated to the decorated class. This does not apply for free functions.
See https://githu... | diff --git a/examples/allennlp/allennlp_jsonnet.py b/examples/allennlp/allennlp_jsonnet.py
index 33f5318fd..976e27f77 100644
--- a/examples/allennlp/allennlp_jsonnet.py
+++ b/examples/allennlp/allennlp_jsonnet.py
@@ -15,7 +15,7 @@ We have the following two ways to execute this example:
(2) Execute through CLI.
... |
optuna__optuna-2652 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/distributions.py:DiscreteUniformDistribution._contains",
"optuna/distributions.py:IntUniformDistribution._contains",
"optuna/distributions.py:IntLogUniformDistribution._contains"
... | optuna/optuna | be407fdde4533c1df3fe8ec9026e884bc9d4fb15 | trial.suggest_int() ignores step
I used `trial.suggest_int()` with step. But, `suggest_int()` ignores arguments when study has trials with different distributions.
## Environment
- Optuna version: 2.6.0
- Python version: 3.7.10
- OS: (I used Google Colab)
- (Optional) Other libraries and their versions:
##... | diff --git a/optuna/distributions.py b/optuna/distributions.py
index f458fa72f..74eeb6d7a 100644
--- a/optuna/distributions.py
+++ b/optuna/distributions.py
@@ -228,7 +228,8 @@ class DiscreteUniformDistribution(BaseDistribution):
def _contains(self, param_value_in_internal_repr: float) -> bool:
value = ... |
optuna__optuna-3319 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/_transform.py:_untransform_numerical_param"
],
"edited_modules": [
"optuna/_transform.py:_untransform_numerical_param"
]
},
"file": "optuna/_transform.py"
}
] | optuna/optuna | e71e0f468b33c65cc560ed978b394fceccafacda | CmaEsSampler uses independent sampler even for non-dynamic search spaces
### Expected behavior
I am using a clearly non-dynamic search space with the `CmaEsSampler` but still see warnings that the independent sampler is triggered very frequently.
I investigated this with a debugger and found that `CmaEsSampler` s... | diff --git a/optuna/_transform.py b/optuna/_transform.py
index d9cc1ab69..c4832059a 100644
--- a/optuna/_transform.py
+++ b/optuna/_transform.py
@@ -319,7 +319,7 @@ def _untransform_numerical_param(
elif isinstance(d, DiscreteUniformDistribution):
# Clip since result may slightly exceed range due to round... |
optuna__optuna-3544 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/samplers/_grid.py:GridSampler.__init__",
"optuna/samplers/_grid.py:GridSampler._same_search_space"
],
"edited_modules": [
"optuna/samplers/_grid.py:GridSampler"
... | optuna/optuna | 94c67ce2dc7be5002bcd52ed4a93d24c10cd83e8 | `GridSearchSampler` raises `TypeError` when `choices` of `CategoricalDistribution` are not comparable
### Expected behavior
The folliwing grid search based optimisation works without any error because default sampler works fine.
```python
import optuna
def objective(trial):
x = trial.suggest_float("x", -... | diff --git a/optuna/samplers/_grid.py b/optuna/samplers/_grid.py
index 4673185db..699d33d6a 100644
--- a/optuna/samplers/_grid.py
+++ b/optuna/samplers/_grid.py
@@ -2,7 +2,6 @@ import collections
import itertools
import random
from typing import Any
-from typing import cast
from typing import Dict
from typing impo... |
optuna__optuna-3545 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/samplers/_grid.py:GridSampler._check_value"
],
"edited_modules": [
"optuna/samplers/_grid.py:GridSampler"
]
},
"file": "optuna/samplers/_grid.py"
}
] | optuna/optuna | f00abac7d53bb29e53e7c8bd13e9b4be9e0f9d44 | Show warning message by `GridSearchSampler` whose `CategoricalDistribution` contains unsupported typed values, not raising `ValueError`
### Motivation
The grid search sampler has a strict type rule for its search space for `CategoricalDistribution`, which is not consistent with the other samplers as reported in #3534.... | diff --git a/optuna/samplers/_grid.py b/optuna/samplers/_grid.py
index 4673185db..8ca3738cf 100644
--- a/optuna/samplers/_grid.py
+++ b/optuna/samplers/_grid.py
@@ -211,11 +211,12 @@ class GridSampler(BaseSampler):
if param_value is None or isinstance(param_value, (str, int, float, bool)):
return
... |
optuna__optuna-3742 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/samplers/_tpe/parzen_estimator.py:_ParzenEstimator._calculate_weights"
],
"edited_modules": [
"optuna/samplers/_tpe/parzen_estimator.py:_ParzenEstimator"
]
},
"f... | optuna/optuna | f0c4f380d9b7c3a86a1b15b952ee6e09b1451904 | An invalid `weights` argument of `TPESamper` does not raise any error
### Expected behavior
If we pass an invalid `weights` to `TPESamper`, it does not raise any error. We should raise an `ValueError` for those ivalid `weight`s. Examples of invalid `weight`s are as follows.
```python
lambda x: np.zeros(x),
lambda... | diff --git a/optuna/samplers/_tpe/parzen_estimator.py b/optuna/samplers/_tpe/parzen_estimator.py
index f74bab8ad..5c2d87ee8 100644
--- a/optuna/samplers/_tpe/parzen_estimator.py
+++ b/optuna/samplers/_tpe/parzen_estimator.py
@@ -216,6 +216,22 @@ class _ParzenEstimator:
if predetermined_weights is None:
... |
optuna__optuna-4479 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"optuna/samplers/_tpe/sampler.py:TPESampler._sample_relative"
],
"edited_modules": [
"optuna/samplers/_tpe/sampler.py:TPESampler"
]
},
"file": "optuna/samplers/_tpe/samp... | optuna/optuna | 9ac2f8f468f5fc6062e3c712cbb791918d24b190 | Use Sphinx 6 after `sphinx_rtd_theme` supports it
### What is an issue?
This is a reminder issue. TODO: Revert #4341.
At least, the following two problems should be fixed.
- The upper left logo does not appear. https://github.com/readthedocs/sphinx_rtd_theme/issues/1404
- The version selector does not work. | diff --git a/optuna/samplers/_tpe/sampler.py b/optuna/samplers/_tpe/sampler.py
index 4770e328d..ee023a929 100644
--- a/optuna/samplers/_tpe/sampler.py
+++ b/optuna/samplers/_tpe/sampler.py
@@ -392,10 +392,9 @@ class TPESampler(BaseSampler):
indices_below, indices_above = _split_observation_pairs(scores, self._... |
orangain__scrapy-s3pipeline-10 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"s3pipeline/pipelines.py:S3Pipeline.__init__",
"s3pipeline/pipelines.py:S3Pipeline._make_fileobj"
],
"edited_modules": [
"s3pipeline/pipelines.py:S3Pipeline"
]
},
... | orangain/scrapy-s3pipeline | 5243d8752724e66cca5e080fb0139585c9ea3398 | Json object are not delimited and not within array using JsonLinesItemExporter
Using scrapy-s3pipeline, a but json items are not delimited or within array
see https://github.com/scrapy/scrapy/issues/4960 | diff --git a/README.md b/README.md
index 6b03cd5..629e810 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,10 @@
[](https://badge.fury.io/py/scrapy-s3pipeline) 
-Scrapy pipelin... |
orcasgit__python-nokia-28 | [
{
"changes": {
"added_entities": [
"nokia/__init__.py:NokiaApi.get_sleep_summary",
"nokia/__init__.py:NokiaSleepSummarySeries.__init__",
"nokia/__init__.py:NokiaSleepSummary.__init__"
],
"added_modules": [
"nokia/__init__.py:NokiaSleepSummarySeries",
"no... | orcasgit/python-nokia | fd4951da6bb51d2e2893339032207b96070c4c79 | Add sleep summary API
We use this API in work, PR to follow. | diff --git a/nokia/__init__.py b/nokia/__init__.py
index 007910a..9fcbf45 100644
--- a/nokia/__init__.py
+++ b/nokia/__init__.py
@@ -221,6 +221,10 @@ class NokiaApi(object):
r = self.request('sleep', 'get', params=kwargs, version='v2')
return NokiaSleep(r)
+ def get_sleep_summary(self, **kwargs):... |
osantana__dicteval-13 | [
{
"changes": {
"added_entities": [
"dicteval/__init__.py:BuiltinLanguage.function_all"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"dicteval/__init__.py:BuiltinLanguage"
]
},
"file": "dicteval/__init__.py"
}
] | osantana/dicteval | 5e1970132fd7a6ac55785648a89cf2e3e2131965 | Implement and document builtin function: =all
Equivalent to the Python's builtin. | diff --git a/README.rst b/README.rst
index 2b11f85..878c709 100644
--- a/README.rst
+++ b/README.rst
@@ -109,6 +109,16 @@ Returns a number with the product of arguments:
>>> dicteval({"=mul": [3, 5]})
15
+Function ``=all``
+'''''''''''''''''
+
+Return True if all elements of the iterable are true (or if the i... |
osbuild__osbuild-107 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"osbuild/__main__.py:main"
],
"edited_modules": [
"osbuild/__main__.py:main"
]
},
"file": "osbuild/__main__.py"
},
{
"changes": {
"added_entities": [
... | osbuild/osbuild | 56a25adf7f02060f86735be1c6e1652be916493b | Proposal: cache assembler output
osbuild caches trees, but not output from assemblers. This is inconsistent, because trees are cached, but outputs are not. People (or programs like Composer) that use osbuild need to manage where they store the outputs themselves, using `--output`. That argument is a bit awkward to use... | diff --git a/.travis.yml b/.travis.yml
index 7aac0cc3..0dd5c85c 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,8 +21,8 @@ jobs:
- name: pipeline-noop
before_install: sudo apt-get install -y systemd-container
script:
- - sudo env "PATH=$PATH" python3 -m osbuild --libdir . --output . samples/... |
osbuild__osbuild-1643 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"osbuild/util/containers.py:containers_storage_source"
],
"edited_modules": [
"osbuild/util/containers.py:containers_storage_source"
]
},
"file": "osbuild/util/container... | osbuild/osbuild | 144b0563d63034c086ed375a821b1831cd04b5e7 | util/mount: allow `rw` mode
Currently the `MountGuard` has an option to set the `ro` option for mounts. However, with bind-mounting `containers-storage` to the store we need explicit an `rw`. The naive approach below is not great since it allows for `ro` and `rw` options to both be set at the same time:
https://git... | diff --git a/osbuild/util/containers.py b/osbuild/util/containers.py
index 0e0f801b..9b9f6a70 100644
--- a/osbuild/util/containers.py
+++ b/osbuild/util/containers.py
@@ -4,7 +4,7 @@ import subprocess
import tempfile
from contextlib import contextmanager
-from osbuild.util.mnt import MountGuard
+from osbuild.util.m... |
osbuild__osbuild-1968 | [
{
"changes": {
"added_entities": [
"osbuild/util/path.py:join_abs"
],
"added_modules": [
"osbuild/util/path.py:join_abs"
],
"edited_entities": null,
"edited_modules": null
},
"file": "osbuild/util/path.py"
}
] | osbuild/osbuild | fcb93bde01d4a027c67b5747c8f976ceb4fc8d80 | `org.osbuild.tuned`: use `os.path.join()` and add a unit tests to verify the behavior with different profile paths
<snip> ... we could do a followup that moves to either pathlib (my preferred choice) or os.path.join() but then it should be consistent for the entire file and ideally we would add tests for that too (i.e.... | diff --git a/Schutzfile b/Schutzfile
index 8c3c6338..9451d875 100644
--- a/Schutzfile
+++ b/Schutzfile
@@ -19,7 +19,7 @@
{
"title": "fedora-updates",
"name": "fedora-updates",
- "baseurl": "https://rpmrepo.osbuild.org/v2/mirror/public/f39/f39-x86_64-updates-released-20241... |
osmlab__maproulette-python-client-64 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/challenge_examples.py"
},
{
"changes": {
"added_entities": [
"maproulette/api/challenge.py:Challenge.get_challenges_by_tags"
... | osmlab/maproulette-python-client | 1bac9c8a2f80eee2cc69710f5abd29a03cb707f8 | [Feature Request] Add endpoint for searching for challenges based on keywords
**Is your feature request related to a problem? Please describe.**
Users should be able to search for challenges based on keywords or "tags" as they are referred to in the API docs. Namely, [this](https://maproulette2.geo.apple.com/docs/swag... | diff --git a/examples/challenge_examples.py b/examples/challenge_examples.py
index 0a809fe..54f8d04 100644
--- a/examples/challenge_examples.py
+++ b/examples/challenge_examples.py
@@ -19,6 +19,10 @@ project_id = '2491'
print(json.dumps(api.get_challenge_by_name(project_id=project_id,
... |
osmlab__maproulette-python-client-84 | [
{
"changes": {
"added_entities": [
"maproulette/api/challenge.py:Challenge.add_file_tasks_to_challenge"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"maproulette/api/challenge.py:Challenge"
]
},
"file": "maproulette/api/challe... | osmlab/maproulette-python-client | a10b1f3063e0cf3dd1e4247179d9ce8d288097ca | [Feature Request] Add support for the endpoint /challenge/{id}/addFileTasks
**Is your feature request related to a problem? Please describe.**
The endpoint [/challenge/{id}/addFileTasks](https://maproulette.org/docs/swagger-ui/index.html?url=/assets/swagger.json&docExpansion=none#/Challenge/addTasksToChallengeFromFile... | diff --git a/maproulette/api/challenge.py b/maproulette/api/challenge.py
index 18c6257..ca7f063 100644
--- a/maproulette/api/challenge.py
+++ b/maproulette/api/challenge.py
@@ -278,6 +278,32 @@ class Challenge(MapRouletteServer):
body=data)
return response
+ def add_file_tasks_to_challenge(se... |
osrf__rocker-83 | [
{
"changes": {
"added_entities": [
"src/rocker/extensions.py:Environment.check_args_for_activation"
],
"added_modules": null,
"edited_entities": [
"src/rocker/extensions.py:Environment.get_docker_args",
"src/rocker/extensions.py:Environment.register_arguments"
... | osrf/rocker | 413d25a7e578d4eab410eda99042cabb8dc8026b | Ubuntu 20.04 support for `--nvidia`
Currently testing some stuff with ROS2 Foxy on Ubutu 20.04. Looks like `--nvidia` isn't supported yet:
```
WARNING distro version 20.04 not in supported list by Nvidia supported versions ['16.04', '18.04']
```
Related: https://gitlab.com/nvidia/container-images/opengl/-/issues/... | diff --git a/src/rocker/extensions.py b/src/rocker/extensions.py
index a7894af..9d32843 100644
--- a/src/rocker/extensions.py
+++ b/src/rocker/extensions.py
@@ -215,9 +215,15 @@ class Environment(RockerExtension):
def get_docker_args(self, cli_args):
args = ['']
- envs = [ x for sublist in cli_ar... |
ovasquez__mkdocs-merge-18 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mkdocsmerge/merge.py:update_navs"
],
"edited_modules": [
"mkdocsmerge/merge.py:update_navs"
]
},
"file": "mkdocsmerge/merge.py"
}
] | ovasquez/mkdocs-merge | 06a63fc6580cd2056442dcb1fcb33d5a78cb70a5 | Add support for section index pages
Hey there!
Firstly, thank you so much for this amazing tool!
In our company, we use it in combo with [MkDocs Material](https://squidfunk.github.io/mkdocs-material/). Not sure about original MkDocs, but in this version, there is an option to set index pages for sections. To get ... | diff --git a/mkdocsmerge/merge.py b/mkdocsmerge/merge.py
index 5ed4499..279b9d4 100644
--- a/mkdocsmerge/merge.py
+++ b/mkdocsmerge/merge.py
@@ -147,7 +147,10 @@ def update_navs(navs, site_root, print_func):
"""
if isinstance(navs, list):
for page in navs:
- update_navs(page, site_root, pr... |
ovh__python-ovh-33 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"ovh/client.py:Client._canonicalize_kwargs"
],
"edited_modules": [
"ovh/client.py:Client"
]
},
"file": "ovh/client.py"
}
] | ovh/python-ovh | ae2981b26fce2641a9bae5af68a3d5043fdd8b46 | API raises BadParameterError for boolean arguments
Hello,
When an API call requires a boolean argument, we send it as `True` or `False` (valid Python booleans) but the API raises `BadParametersError` because it waits for a string (`'true'` or `'false'`) :
```python
In [1]: import ovh
In [2]: client = ovh.Clie... | diff --git a/ovh/client.py b/ovh/client.py
index fe989cf..82db162 100644
--- a/ovh/client.py
+++ b/ovh/client.py
@@ -289,14 +289,24 @@ class Client(object):
can be prefixed with an underscore. For example, ``from`` argument of
``POST /email/domain/{domain}/redirection`` may be replaced by ``_from``
... |
owkin__PyDESeq2-123 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet.vst"
],
"edited_modules": [
"pydeseq2/dds.py:DeseqDataSet"
]
},
"file": "pydeseq2/dds.py"
},
{
"changes": {
"added_entities":... | owkin/PyDESeq2 | e1d1752012cf8dcb01cba4c2984ace5697e880b0 | Implement fitType="mean" for vst
DESeq2 has a fit type "mean" for the vst which is used as the fallback when the parametric fit fails. It would be nice to have an equivalent in the python implementation.
Here's my attempt based on https://github.com/mikelove/DESeq2/blob/devel/R/vst.R#L188 and https://github.com/mike... | diff --git a/README.md b/README.md
index 8c70d6f..825f61b 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,9 @@ In case there is a feature you would particularly like to be implemented, feel f
## Installation
-`PyDESeq2` can be installed from PyPI:
+### PyPI
+
+`PyDESeq2` can be installed from PyPI using `pip`:... |
owkin__PyDESeq2-127 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/preprocessing.py:deseq2_norm"
],
"edited_modules": [
"pydeseq2/preprocessing.py:deseq2_norm"
]
},
"file": "pydeseq2/preprocessing.py"
}
] | owkin/PyDESeq2 | e8398354b45211d3ce75331ec8b1498c5884cf9f | [BUG] deseq2_norm throws KeyError when called on a pandas DataFrame
**Describe the bug**
We are trying to use deseq2_norm to normalized your example data set and our own rna_seq experiment, in both cases the function does not work.
**To Reproduce**
python version = 3.11.3
code :
counts_df = load_example_data(
... | diff --git a/pydeseq2/preprocessing.py b/pydeseq2/preprocessing.py
index 397f28c..2fa95ca 100644
--- a/pydeseq2/preprocessing.py
+++ b/pydeseq2/preprocessing.py
@@ -1,10 +1,13 @@
from typing import Tuple
+from typing import Union
import numpy as np
import pandas as pd
-def deseq2_norm(counts: pd.DataFrame) -> ... |
owkin__PyDESeq2-131 | [
{
"changes": {
"added_entities": [
"pydeseq2/dds.py:DeseqDataSet._check_full_rank_design"
],
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet.__init__",
"pydeseq2/dds.py:DeseqDataSet.vst"
],
"edited_modules": [
"pydeseq... | owkin/PyDESeq2 | 0133a5622730d59be25c0c3f41bf380158e2b3c1 | [BUG] `pydeseq2.ds.DeseqStats.lfc_shrink` gives wrong log2FoldChange signs
**Describe the bug**
When performing LFC shrinkage, the new version seems to flip the reference it uses. I've observed that the obtained `log2FoldChange` have opposite signs as the original contrast, which creates an inconsistency with the sign... | diff --git a/README.md b/README.md
index c521e40..825f61b 100644
--- a/README.md
+++ b/README.md
@@ -105,7 +105,7 @@ documentation to see how you can contribute to PyDESeq2.
### 2 - Create a conda environment
-Run `conda env create -n pydeseq2 python=3.8` (or higher python version) to create the `pydeseq2` environ... |
owkin__PyDESeq2-133 | [
{
"changes": {
"added_entities": [
"pydeseq2/dds.py:DeseqDataSet._check_full_rank_design"
],
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet.__init__"
],
"edited_modules": [
"pydeseq2/dds.py:DeseqDataSet"
]
},
"f... | owkin/PyDESeq2 | 3250158583094959df03fa1ecaa3a34b0d6557af | [BUG]` beta` referenced before assignment
**Describe the bug**
```
lib/python3.10/site-packages/pydeseq2/utils.py", line 471, in irls_solver
mu = np.maximum(size_factors * np.exp(X @ beta), min_mu)
UnboundLocalError: local variable 'beta' referenced before assignment
```
:
intercept=True,
)
+ # Check that the design matrix has full rank
+ self._check_full_rank_design()
+
... |
owkin__PyDESeq2-139 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet._check_full_rank_design"
],
"edited_modules": [
"pydeseq2/dds.py:DeseqDataSet"
]
},
"file": "pydeseq2/dds.py"
},
{
"changes": {
... | owkin/PyDESeq2 | 54b03ac57492866d0d78d36e22ab01213216754b | [BUG] Design matrix check prevents use of VST without design matrix
**Describe the bug**
When creating a DDS, the latest version now checks that the design matrix is full rank; however, I only wish to use it to run VST without a design matrix.
**To Reproduce**
```
import pydeseq2.dds
import numpy as np
import ... | diff --git a/pydeseq2/dds.py b/pydeseq2/dds.py
index 9b8b733..7789e5e 100644
--- a/pydeseq2/dds.py
+++ b/pydeseq2/dds.py
@@ -1041,8 +1041,11 @@ class DeseqDataSet(ad.AnnData):
num_vars = self.obsm["design_matrix"].shape[1]
if rank < num_vars:
- raise ValueError(
+ warnings.warn... |
owkin__PyDESeq2-172 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/plot_minimal_pydeseq2_pipeline.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
... | owkin/PyDESeq2 | 251b949ecb28d0b348134f0b393c6efe9e991ecb | [Feature request] Threshold-based Wald test
I think currently the Wald test is testing based on the null hypothesis of FC = 0. While in a lot of experiments we care more about a banded null hypothesis (FC > smth like 1.5).
In DESeq2 theres an option of passing the parameter lfcThreshold into the Wald test. Would b... | diff --git a/examples/plot_minimal_pydeseq2_pipeline.py b/examples/plot_minimal_pydeseq2_pipeline.py
index 5f95354..28b27aa 100644
--- a/examples/plot_minimal_pydeseq2_pipeline.py
+++ b/examples/plot_minimal_pydeseq2_pipeline.py
@@ -12,6 +12,7 @@ RNAseq data, using PyDESeq2.
We start by importing required packages and... |
owkin__PyDESeq2-175 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/utils.py:fit_rough_dispersions"
],
"edited_modules": [
"pydeseq2/utils.py:fit_rough_dispersions"
]
},
"file": "pydeseq2/utils.py"
}
] | owkin/PyDESeq2 | 07aa6b00459e2cfb74791a074b9d9ca477901726 | ValueError: The first guess on the deviance function returned a nan. This could be a boundary problem and should be reported.
Hello, thank you for the great tool!
**Describe the bug**
When trying to run the deseq2 method, the following error arises:
`
ValueError: The first guess on the deviance function return... | diff --git a/pydeseq2/utils.py b/pydeseq2/utils.py
index f456316..5b18559 100644
--- a/pydeseq2/utils.py
+++ b/pydeseq2/utils.py
@@ -1003,6 +1003,15 @@ def fit_rough_dispersions(
"""
num_samples, num_vars = design_matrix.shape
+ # This method is only possible when num_samples > num_vars.
+ # If this i... |
owkin__PyDESeq2-268 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet.__init__",
"pydeseq2/dds.py:DeseqDataSet.vst",
"pydeseq2/dds.py:DeseqDataSet.vst_fit",
"pydeseq2/dds.py:DeseqDataSet.vst_transform",
"pydeseq... | owkin/PyDESeq2 | 594691feece74719c82332918b162d287cbc033e | [BUG] The vst() function does not work when the algorithm switches to a mean-based dispersion trend.
**Describe the bug**
Calling the vst() leads to the fit_type variable being hard-coded to the chosen fit_type. Consequently when the vst_transform is called it breaks with:
`
File ".venv/lib/python3.10/site-packages/... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 69d6dea..aafd3db 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
args: # arguments to configure black
- --line-length=89
- repo: https://github.com/astral-sh/ruff-pre-commit
- rev: v0.4.4
... |
owkin__PyDESeq2-349 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/utils.py:nbinomGLM"
],
"edited_modules": [
"pydeseq2/utils.py:nbinomGLM"
]
},
"file": "pydeseq2/utils.py"
}
] | owkin/PyDESeq2 | 9355b55e6c7c10c759db674d9a26d067be50b827 | [BUG] lfc_shrink() generates wrong results
**Describe the bug**
lfc_shrink() generates wrong results. In most cases it acts as expected. For some genes it increases absolute value of fold change. For one differentially expressed gene with high expression (base_mean = 407277.128029) it even changes the sign (
log2Fold... | diff --git a/pydeseq2/utils.py b/pydeseq2/utils.py
index 4a686dd..db09e90 100644
--- a/pydeseq2/utils.py
+++ b/pydeseq2/utils.py
@@ -1083,7 +1083,7 @@ def nbinomGLM(
xbeta = design_matrix @ beta
d_neg_prior = (
beta * no_shrink_mask / prior_no_shrink_scale**2
- + 2 * beta * shr... |
owkin__PyDESeq2-356 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pydeseq2/dds.py:DeseqDataSet.__init__",
"pydeseq2/dds.py:DeseqDataSet.deseq2",
"pydeseq2/dds.py:DeseqDataSet.fit_size_factors"
],
"edited_modules": [
"pydeseq2/dds.py... | owkin/PyDESeq2 | 5a44961789b96edb8012c3b62ba650d9e14ed05a | Option to specify control genes for fitting size factors
The original DESeq2 package enables one to specify "control genes" that are used to fit the size factors. These are genes that are not expected to be changing between samples. See: https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/estimateSize... | diff --git a/pydeseq2/dds.py b/pydeseq2/dds.py
index 573efca..ff91a2e 100644
--- a/pydeseq2/dds.py
+++ b/pydeseq2/dds.py
@@ -87,6 +87,13 @@ class DeseqDataSet(ad.AnnData):
may be few or no genes which have no zero values.
``"iterative"``: fit size factors iteratively. (default: ``"ratio"``).
+ co... |
ownaginatious__mixpanel-jql-18 | [
{
"changes": {
"added_entities": [
"mixpanel_jql/query.py:JQL._group_by"
],
"added_modules": null,
"edited_entities": [
"mixpanel_jql/query.py:JQL.group_by",
"mixpanel_jql/query.py:JQL.group_by_user"
],
"edited_modules": [
"mixpanel_jql/query.p... | ownaginatious/mixpanel-jql | cad22fecf6220e3857dec5de122c8df8810c9737 | mixpanel_jql.exceptions.InvalidJavaScriptText
Hi, first of all thanks for this project!
I'm trying to run the first example and I'm getting:
`mixpanel_jql.exceptions.InvalidJavaScriptText: Must be a text type (str, unicode) or wrapped as raw(str||unicode)`
I'm runnning Python 3.6.5 on Ubuntu 18.04 | diff --git a/mixpanel_jql/query.py b/mixpanel_jql/query.py
index 919894f..768da83 100644
--- a/mixpanel_jql/query.py
+++ b/mixpanel_jql/query.py
@@ -394,19 +394,19 @@ class JQL(object):
return jql
def group_by(self, keys, accumulator):
- if not isinstance(keys, (tuple, set, list)):
- k... |
oxan__djangorestframework-dataclasses-25 | [
{
"changes": {
"added_entities": [
"rest_framework_dataclasses/serializers.py:DataclassSerializer._strip_empty_sentinels"
],
"added_modules": null,
"edited_entities": [
"rest_framework_dataclasses/serializers.py:DataclassSerializer.create",
"rest_framework_datacla... | oxan/djangorestframework-dataclasses | 562c4c62f1cdde883f9158f0468e0b5419b1f454 | Cannot use with PATCH method
The update method will not work with the PATCH method and partially updating.
Error: `TypeError: __init__() missing 3 required positional arguments: 'id', 'port', and 'cipher'`
It lists all the missing attributes and says they're required to init the dataclass. | diff --git a/README.rst b/README.rst
index ae8ca85..fd0f3e8 100644
--- a/README.rst
+++ b/README.rst
@@ -4,8 +4,8 @@ Dataclasses serializer
A `dataclasses <https://docs.python.org/3/library/dataclasses.html>`__ serializer for the `Django REST Framework
<http://www.django-rest-framework.org/>`__.
-.. image:: https:/... |
oxan__djangorestframework-dataclasses-36 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rest_framework_dataclasses/serializers.py:DataclassSerializer.get_fields",
"rest_framework_dataclasses/serializers.py:DataclassSerializer.create_field"
],
"edited_modules": [
... | oxan/djangorestframework-dataclasses | 484a6f5e9740f846dfc3e2135f37b6a1b06342d0 | Allow specifying serializer field configuration using dataclass field metadata?
As @intgr mentioned in #30, it might be nice to support specifying the serializer field configuration using dataclass field metadata.
> I've thought about this a bit. It would be helpful and much cleaner if one could pass custom field kw... | diff --git a/README.rst b/README.rst
index 1f928dc..89e172b 100644
--- a/README.rst
+++ b/README.rst
@@ -111,6 +111,26 @@ to dataclass serializers as well.
Customize field generation
--------------------------
+Besides overriding fields by declaring them explicitly on the serializer, you can also override the gener... |
oxan__djangorestframework-dataclasses-53 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rest_framework_dataclasses/field_utils.py:get_dataclass_definition"
],
"edited_modules": [
"rest_framework_dataclasses/field_utils.py:get_dataclass_definition"
]
},
"fi... | oxan/djangorestframework-dataclasses | 2d808db306d76c7455f83bf82a6973ac1260f9ee | Nested dataclasses and using drf-spectacular.
Hey,
I am using this great lib and found problems with drf-spectacular. These are my issues:
If I have nested dataclass like:
```py
@dataclass
class A():
foo: str
class B():
a: A
# serializer
class BSerializer(DataclassSerializer):
class Meta:... | diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7e49293..21969f6 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -1,3 +1,7 @@
+1.1.1, TBD
+----------
+* Fix usage of PEP 585 generics with forward references (e.g. ``list["str"]``).
+
1.1.0, 9 January 2021
---------------------
Features & fixes:
diff --git a/rest_f... |
oxan__djangorestframework-dataclasses-80 | [
{
"changes": {
"added_entities": [
"rest_framework_dataclasses/serializers.py:_create_instance"
],
"added_modules": [
"rest_framework_dataclasses/serializers.py:_create_instance"
],
"edited_entities": [
"rest_framework_dataclasses/serializers.py:_strip_empty... | oxan/djangorestframework-dataclasses | 69e4a91c12e98349c6458511c648b256d4c4e745 | Serializer initializing dataclass with non init fields
Hi there!
I have a situation here, that I think might be a bug, or maybe I just haven't found a way to solve it since I'm still new with the package.
Example:
```python
from dataclasses import dataclass, field
@dataclass
class A:
foo: str
ba... | diff --git a/rest_framework_dataclasses/serializers.py b/rest_framework_dataclasses/serializers.py
index b046fd0..7e5c5fd 100644
--- a/rest_framework_dataclasses/serializers.py
+++ b/rest_framework_dataclasses/serializers.py
@@ -31,6 +31,18 @@ T = TypeVar('T', bound=Dataclass)
AnyT = TypeVar('AnyT')
+# Helper func... |
oxan__djangorestframework-dataclasses-84 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rest_framework_dataclasses/serializers.py:DataclassSerializer.to_internal_value"
],
"edited_modules": [
"rest_framework_dataclasses/serializers.py:DataclassSerializer"
]
},... | oxan/djangorestframework-dataclasses | d275d6ddde06abb1281a8e0c6b79ee59f7bf3575 | DataclassSerializer fails with `source="*"` embedded serialiser fields because it requires Meta.dataclass
According to https://www.django-rest-framework.org/api-guide/fields/#using-source, the serialisers should allow for use of `source="*"`.
The issue can be reproduced in the following way. Copy the following snipp... | diff --git a/rest_framework_dataclasses/serializers.py b/rest_framework_dataclasses/serializers.py
index d01d319..72a35e6 100644
--- a/rest_framework_dataclasses/serializers.py
+++ b/rest_framework_dataclasses/serializers.py
@@ -1,5 +1,6 @@
from __future__ import annotations
+import collections
import copy
import ... |
oxan__djangorestframework-dataclasses-90 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"rest_framework_dataclasses/field_utils.py:get_type_info"
],
"edited_modules": [
"rest_framework_dataclasses/field_utils.py:get_type_info"
]
},
"file": "rest_framework_d... | oxan/djangorestframework-dataclasses | c243be7be7a848b77493bbf128082e361cc24d39 | PEP 695 type alias support
[PEP 695](https://peps.python.org/pep-0695/)/Python 3.12 introduced support for type aliases, which needs to be supported. The abbreviated type parameter syntax included in the same PEP probably already works, but needs tests. | diff --git a/rest_framework_dataclasses/field_utils.py b/rest_framework_dataclasses/field_utils.py
index 1fa0e31..bbeeb8e 100644
--- a/rest_framework_dataclasses/field_utils.py
+++ b/rest_framework_dataclasses/field_utils.py
@@ -75,7 +75,7 @@ def get_type_info(tp: type) -> TypeInfo:
tp = typing_utils.get_itera... |
paambaati__mae-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "mae/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"mae/mae.py:MesosAppE... | paambaati/mae | ab1eadba7bec0c47199827dfae5bfa57a6ac94b1 | An app without any labels can crash mae's response
When the app definition does not have any labels, the response is empty. This can fixed by adding defaults to the `get()` calls here —
https://github.com/paambaati/mae/blob/ab1eadba7bec0c47199827dfae5bfa57a6ac94b1/mae/mae.py#L48 | diff --git a/CHANGELOG.md b/CHANGELOG.md
index b188730..a12be4c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,10 @@
`mae` follows [Semantic Versioning](http://semver.org/).
+## [1.0.7] - 2019-02-28
+### Fixed
+- 🐞 Fixed a bug ([#1](https://github.com/paambaati/mae/issues/1)) where an app without labels ... |
package-url__packageurl-python-178 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/packageurl/__init__.py:PackageURL.from_string"
],
"edited_modules": [
"src/packageurl/__init__.py:PackageURL"
]
},
"file": "src/packageurl/__init__.py"
}
] | package-url/packageurl-python | 6f38e3e2f90be99d634cf72d0c0755c8c9e62084 | Creation PackageURL objects for invalid PURLs / Possible improper encoding of colons (":") in PURL fields
It is possible to create PackageURL objects that contain invalid fields, specifically by using the `PackageURL` kwarg constructor and passing in values that contain colons.
Simple example:
```
>>> from package... | diff --git a/src/packageurl/__init__.py b/src/packageurl/__init__.py
index 8199e39..9677b73 100644
--- a/src/packageurl/__init__.py
+++ b/src/packageurl/__init__.py
@@ -459,12 +459,17 @@ class PackageURL(
url=remainder, scheme="", allow_fragments=True
)
- if scheme or authority:
- ... |
package-url__packageurl-python-29 | [
{
"changes": {
"added_entities": [
"src/packageurl/__init__.py:PackageURL.__hash__"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/packageurl/__init__.py:PackageURL"
]
},
"file": "src/packageurl/__init__.py"
}
] | package-url/packageurl-python | a762fbd361a253e3c12f7fff61c305b6a69d0ed8 | PackageURL type is not hashable
Storing `PackageURL` instances in a set can be useful. Currently attempting this fails with the following error:
```
Python 3.8.2 (default, Feb 26 2020, 22:21:03)
[GCC 9.2.1 20200130] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from package... | diff --git a/src/packageurl/__init__.py b/src/packageurl/__init__.py
index 71225e9..ae6e148 100644
--- a/src/packageurl/__init__.py
+++ b/src/packageurl/__init__.py
@@ -282,6 +282,9 @@ class PackageURL(namedtuple('PackageURL', _components)):
def __str__(self, *args, **kwargs):
return self.to_string()
+ ... |
package-url__packageurl-python-44 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/packageurl/contrib/url2purl.py:build_github_purl"
],
"edited_modules": [
"src/packageurl/contrib/url2purl.py:build_github_purl"
]
},
"file": "src/packageurl/contrib... | package-url/packageurl-python | 46116009b6815fc7c31bf4319bdb7d18f79fa066 | Incorrect PURL inferred from download URL
With https://github.com/pypa/get-virtualenv/raw/20.0.31/public/virtualenv.pyz this purl is inferred:
`pkg:github/pypa/get-virtualenv@raw#20.0.31/public/virtualenv.pyz` and this is not correct.
It should be instead:
`pkg:github/pypa/get-virtualenv@20.0.31#/public/virtua... | diff --git a/src/packageurl/contrib/url2purl.py b/src/packageurl/contrib/url2purl.py
index 8d5bde2..d10f4ed 100644
--- a/src/packageurl/contrib/url2purl.py
+++ b/src/packageurl/contrib/url2purl.py
@@ -343,7 +343,7 @@ def build_github_api_purl(url):
github_codeload_pattern = (
r"https?://codeload.github.com/"
- ... |
package-url__packageurl-python-46 | [
{
"changes": {
"added_entities": [
"src/packageurl/contrib/url2purl.py:build_npm_web_purl"
],
"added_modules": [
"src/packageurl/contrib/url2purl.py:build_npm_web_purl"
],
"edited_entities": [
"src/packageurl/contrib/url2purl.py:build_npm_purl"
],
... | package-url/packageurl-python | 47c5bf81d1b0257db1606e648cab773bc0366b10 | npm url2purl should handle more npm package url schemes
Current implementation: https://github.com/package-url/packageurl-python/blob/00b7df61173be3c19eb65ce166271aed0e9ae00c/src/packageurl/contrib/url2purl.py#L82
We need to support more npm package url schemes, such as:
* https://www.npmjs.com/package/foo-utils
*... | diff --git a/src/packageurl/contrib/url2purl.py b/src/packageurl/contrib/url2purl.py
index 02ee631..b027a89 100644
--- a/src/packageurl/contrib/url2purl.py
+++ b/src/packageurl/contrib/url2purl.py
@@ -95,12 +95,15 @@ def get_path_segments(url):
return segments
-
@purl_router.route('https?://registry.npmjs.*/.... |
packit__ogr-636 | [
{
"changes": {
"added_entities": [
"ogr/abstract.py:Reaction.__init__",
"ogr/abstract.py:Reaction.__str__",
"ogr/abstract.py:Reaction.delete",
"ogr/abstract.py:Comment.get_reactions",
"ogr/abstract.py:Comment.add_reaction"
],
"added_modules": [
"... | packit/ogr | 1e50bf078cabd7e517b77a022317f0f353517869 | Give reaction on comment commands in GitHub and GitLab
According to [packit-service/issues/1081](https://github.com/packit/packit-service/issues/1081) we need to implement `give reaction to the comment` methods for Github and Gitlab.
TODO:
- [ ] give reaction to the Gitlab comment
- [ ] give reaction to the Github... | diff --git a/COMPATIBILITY.md b/COMPATIBILITY.md
index e509f64..8235cf3 100644
--- a/COMPATIBILITY.md
+++ b/COMPATIBILITY.md
@@ -10,12 +10,16 @@ In case you find any error, please [create a new issue](https://github.com/packi
| | GitHub | GitLab | Pagure |
| ---------------- | :----: | :----: | :----... |
pact-foundation__pact-python-539 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pact/pact.py:Pact.__exit__"
],
"edited_modules": [
"pact/pact.py:Pact"
]
},
"file": "pact/pact.py"
}
] | pact-foundation/pact-python | 7d112f3ed34d780e495a5c02f7eb74010c3e474e | Interactions not cleared when error in test
### Have you read the Contributing Guidelines on issues?
- [ ] I have read the [Contributing Guidelines on issues](https://github.com/pact-foundation/pact-python/main/CONTRIBUTING.md#issues).
### Prerequisites
- [X] I'm using the latest version of `pact-python`.
- [ ] I ha... | diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 1eb9ad5..8ec20af 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -45,7 +45,7 @@ jobs:
hatch build --target sdist
- name: Upload sdist
- uses: actions/upload-artifact@26f96dfa697d77e81fd5... |
pahaz__sshtunnel-216 | [
{
"changes": {
"added_entities": [
"sshtunnel.py:_StreamForwardServer.__init__",
"sshtunnel.py:SSHTunnelForwarder._make_stream_ssh_forward_server_class"
],
"added_modules": [
"sshtunnel.py:_StreamForwardServer",
"sshtunnel.py:_ThreadingStreamForwardServer"
... | pahaz/sshtunnel | cd374d585c117a8f91c49c682f656b48b0b1682b | User private keys are not found in default directory
This line of code
https://github.com/pahaz/sshtunnel/blob/bd4ae32344a3a68ce27b1ad27c992687613b3182/sshtunnel.py#L1021
prevents the `or` at
https://github.com/pahaz/sshtunnel/blob/bd4ae32344a3a68ce27b1ad27c992687613b3182/sshtunnel.py#L1026
to kick in and a... | diff --git a/appveyor.yml b/appveyor.yml
index b48e044..ad75469 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -11,6 +11,14 @@ environment:
PYTHON_VERSION: "2.7.x"
PYTHON_ARCH: "64"
+ - PYTHON: "C:\\Python35"
+ PYTHON_VERSION: "3.5.x"
+ PYTHON_ARCH: "32"
+
+ - PYTHON: "C:\\Python35-x64"... |
palantir__python-jsonrpc-server-37 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls_jsonrpc/endpoint.py:Endpoint._handle_response"
],
"edited_modules": [
"pyls_jsonrpc/endpoint.py:Endpoint"
]
},
"file": "pyls_jsonrpc/endpoint.py"
}
] | palantir/python-jsonrpc-server | 12d1f5125a103852fc8a2048508227ff13b91210 | Tests failing with Python 3.8
```
[ 11s] =================================== FAILURES ===================================
[ 11s] ______________________________ test_request_error ______________________________
[ 11s]
[ 11s] endpoint = <pyls_jsonrpc.endpoint.Endpoint object at 0x7f8e1ab39ee0>
[ 11s] cons... | diff --git a/pyls_jsonrpc/endpoint.py b/pyls_jsonrpc/endpoint.py
index e8bfb5b..0caf612 100644
--- a/pyls_jsonrpc/endpoint.py
+++ b/pyls_jsonrpc/endpoint.py
@@ -236,6 +236,7 @@ class Endpoint(object):
if error is not None:
log.debug("Received error response to message %s: %s", msg_id, error)
... |
palantir__python-language-server-124 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/language_server.py:start_tcp_lang_server",
"pyls/language_server.py:LanguageServer.m_exit"
],
"edited_modules": [
"pyls/language_server.py:start_tcp_lang_server",
... | palantir/python-language-server | aa8e1b2c12759470c18910c61f55ab4c6b80d344 | Severity of linting erros
I currently really dislike the displayed errors of the linters.
If I use `pycodestyle` and `Pyflakes` I would prefer that `pycodestyle`s errors like `line too long`, `missing whitespace` could be *downgraded* to warnings or info. Obviously `Pyflakes` messages are more severe, but I still woul... | diff --git a/pyls/language_server.py b/pyls/language_server.py
index cfd187b..ce11da6 100644
--- a/pyls/language_server.py
+++ b/pyls/language_server.py
@@ -37,7 +37,7 @@ def start_tcp_lang_server(bind_addr, port, handler_class):
log.info("Serving %s on (%s, %s)", handler_class.__name__, bind_addr, port)
... |
palantir__python-language-server-146 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/plugins/pycodestyle_lint.py:pyls_lint"
],
"edited_modules": [
"pyls/plugins/pycodestyle_lint.py:pyls_lint"
]
},
"file": "pyls/plugins/pycodestyle_lint.py"
}
] | palantir/python-language-server | a1bbd401621f8fc3083f4341b7912b491e82bf68 | Custom pycodestyle configuration via xcode/Atom settings
It would be really great to configure the ignored error codes and the maximum line length of `pycodestyle` via the settings if no configuration file is found on the system.
This is the most requested issue on the Atom package for `pyls`: https://github.com/lge... | diff --git a/pyls/plugins/pycodestyle_lint.py b/pyls/plugins/pycodestyle_lint.py
index 668096d..2a5baab 100644
--- a/pyls/plugins/pycodestyle_lint.py
+++ b/pyls/plugins/pycodestyle_lint.py
@@ -21,12 +21,29 @@ def pyls_lint(config, document):
conf_to_use = pycodestyle_conf if pycodestyle_conf else pep8_conf
... |
palantir__python-language-server-211 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/plugins/pycodestyle_lint.py:pyls_lint"
],
"edited_modules": [
"pyls/plugins/pycodestyle_lint.py:pyls_lint"
]
},
"file": "pyls/plugins/pycodestyle_lint.py"
}
] | palantir/python-language-server | 897980b7e2bd71811311cb49b18cf89ed3aa9cbe | Fix ignored and select settings interface with pycodestyle
On https://github.com/PyCQA/pycodestyle/pull/722 they refused to fix their interface. When passing the list arguments as `ignore` and `select` settings to `pycodestyle`, it is required to pass a python list as `["E201", "E501"]`, instead of a string `"E201,E501... | diff --git a/pyls/plugins/pycodestyle_lint.py b/pyls/plugins/pycodestyle_lint.py
index 8441281..96efafd 100644
--- a/pyls/plugins/pycodestyle_lint.py
+++ b/pyls/plugins/pycodestyle_lint.py
@@ -12,12 +12,12 @@ def pyls_lint(config, document):
log.debug("Got pycodestyle settings: %s", settings)
opts = {
- ... |
palantir__python-language-server-220 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/language_server.py:LanguageServer.m_initialize"
],
"edited_modules": [
"pyls/language_server.py:LanguageServer"
]
},
"file": "pyls/language_server.py"
},
{
... | palantir/python-language-server | 85907d6f7af5aaf1d6fd13c543327319b0c02282 | pycodestyle config not being read, seeing runtime errors since 0.12.0
Since upgrading to 0.12.1 (from 0.11.1) I noticed that I was getting D100 and D103 docstring warnings in my code, even though I ignored them via `$HOME/.config/pycodestyle`. I tried adding a `setup.cfg` to the project directory but I still got the w... | diff --git a/pyls/language_server.py b/pyls/language_server.py
index b898ae1..f310182 100644
--- a/pyls/language_server.py
+++ b/pyls/language_server.py
@@ -65,7 +65,7 @@ class LanguageServer(dispatcher.JSONRPCMethodDispatcher, JSONRPCServer):
pass
def m_initialize(self, **kwargs):
- log.debug("L... |
palantir__python-language-server-275 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/_utils.py:clip_column"
],
"edited_modules": [
"pyls/_utils.py:clip_column"
]
},
"file": "pyls/_utils.py"
},
{
"changes": {
"added_entities": null,
... | palantir/python-language-server | 67811f275c8ce61dea78400e2b202bf7f5dc4707 | TCP mode is not working since v0.15.0
When I attempt to start the language server in TCP mode using the command
``` pyls --tcp --host 127.0.0.1 --port 7003 ```
it fails to start the language server with the error ```Handler class must be an instance of PythonLanguageServer``` | diff --git a/pyls/_utils.py b/pyls/_utils.py
index fb353c3..56a8630 100644
--- a/pyls/_utils.py
+++ b/pyls/_utils.py
@@ -104,5 +104,5 @@ def format_docstring(contents):
def clip_column(column, lines, line_number):
# Normalise the position as per the LSP that accepts character positions > line length
# https:... |
palantir__python-language-server-63 | [
{
"changes": {
"added_entities": [
"pyls/__main__.py:_binary_stdio"
],
"added_modules": [
"pyls/__main__.py:_binary_stdio"
],
"edited_entities": [
"pyls/__main__.py:main"
],
"edited_modules": [
"pyls/__main__.py:main"
]
},
"... | palantir/python-language-server | 8c038c38106bae4d04faf88fa53755e263cfd586 | Newline issues on Windows
Hi there,
Thanks for the excellent work you've done on the language server! Overall, it's working great on OSX and Linux - I'm working on incorporating it into Oni: https://github.com/extr0py/oni
There is one blocking issue on Windows, however:
**Issue:** The LSP protocol expects ther... | diff --git a/pyls/__main__.py b/pyls/__main__.py
index fe9f564..b88ae07 100644
--- a/pyls/__main__.py
+++ b/pyls/__main__.py
@@ -53,4 +53,29 @@ def main():
if args.tcp:
language_server.start_tcp_lang_server(args.host, args.port, PythonLanguageServer)
else:
- language_server.start_io_lang_serve... |
palantir__python-language-server-69 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyls/python_ls.py:PythonLanguageServer.capabilities",
"pyls/python_ls.py:PythonLanguageServer.m_text_document__did_change"
],
"edited_modules": [
"pyls/python_ls.py:PythonLan... | palantir/python-language-server | df7d399499b0a31fd03da72c84428c7f8957935b | Support incremental TextDocumentSyncKind
Right now we get full text files each time they change. This is obviously bad.
I wonder if we could then propagate these changes to only re-lint the changed parts of the file? | diff --git a/pyls/python_ls.py b/pyls/python_ls.py
index 0cc0e40..08d4fed 100644
--- a/pyls/python_ls.py
+++ b/pyls/python_ls.py
@@ -36,7 +36,7 @@ class PythonLanguageServer(LanguageServer):
'signatureHelpProvider': {
'triggerCharacters': ['(', ',']
},
- 'textDocume... |
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