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 |
|---|---|---|---|---|---|
GenericMappingTools__pygmt-574 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/modules.py:info"
],
"edited_modules": [
"pygmt/modules.py:info"
]
},
"file": "pygmt/modules.py"
}
] | GenericMappingTools/pygmt | 4856d64e441434e395c5b8e7874022052c76f9af | Let pygmt.info support pandas.DataFrame or 2D numpy.array inputs
**Description of the desired feature**
The [pygmt.info](https://www.pygmt.org/v0.1.2/api/generated/pygmt.info.html) function should accept pandas.DataFrame or 2D numpy.array matrices as input. This was mentioned in passing when `pygmt.info` was origina... | diff --git a/pygmt/modules.py b/pygmt/modules.py
index 73392410..94512ec3 100644
--- a/pygmt/modules.py
+++ b/pygmt/modules.py
@@ -1,6 +1,7 @@
"""
Non-plot GMT modules.
"""
+import numpy as np
import xarray as xr
from .clib import Session
@@ -55,7 +56,7 @@ def grdinfo(grid, **kwargs):
@fmt_docstring
@use_ali... |
GenericMappingTools__pygmt-575 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/modules.py:info"
],
"edited_modules": [
"pygmt/modules.py:info"
]
},
"file": "pygmt/modules.py"
}
] | GenericMappingTools/pygmt | 89857c32c7e61c57fb1f03993cfb090c76366783 | Return values of gmt.info
This issue is opened to further discuss the https://github.com/GenericMappingTools/gmt-python/pull/106#issuecomment-363649758 about `gmt.info`.
> Do you think we should print the output instead of returning it? There could be a flag to trigger a return instead of printing.
IMHO, returnin... | diff --git a/pygmt/modules.py b/pygmt/modules.py
index 94512ec3..1cacf67d 100644
--- a/pygmt/modules.py
+++ b/pygmt/modules.py
@@ -60,14 +60,17 @@ def info(table, **kwargs):
"""
Get information about data tables.
- Reads from files and finds the extreme values in each of the columns.
- It recognizes N... |
GenericMappingTools__pygmt-619 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/modules.py:info"
],
"edited_modules": [
"pygmt/modules.py:info"
]
},
"file": "pygmt/modules.py"
}
] | GenericMappingTools/pygmt | 9e0a8688afafefff970a2c5901322ddf3c5a2c6a | Running info on pandas.DataFrame with time column doesn't work
**Description of the problem**
Just noticed that datetime columns being passed into `pygmt.info` doesn't work. This follows on from the `pandas.DataFrame` inputs into `pygmt.info` functionality added in #574, see also #464 and #562 where the datetime mac... | diff --git a/pygmt/modules.py b/pygmt/modules.py
index 1cacf67d..477bc992 100644
--- a/pygmt/modules.py
+++ b/pygmt/modules.py
@@ -78,9 +78,10 @@ def info(table, **kwargs):
Parameters
----------
- table : pandas.DataFrame or np.ndarray or str
- Either a pandas dataframe, a 1D/2D numpy.ndarray or a... |
GenericMappingTools__pygmt-702 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/loading.py:load_libgmt",
"pygmt/clib/loading.py:clib_names",
"pygmt/clib/loading.py:clib_full_names",
"pygmt/clib/loading.py:check_libgmt"
],
"edited_modul... | GenericMappingTools/pygmt | b8385bfd21faa3d282be5482d0cc056e7abe70ca | Find the GMT library by calling "gmt --show-library"
**Description of the desired feature**
Currently, PyGMT first checks if the environmental variable **GMT_LIBRARY_PATH** is defined. If yes, it tries to find the GMT library in the specified path. Otherwise, it will search for the GMT library in standard library pa... | diff --git a/doc/install.rst b/doc/install.rst
index 0b8c32f3..86bc5208 100644
--- a/doc/install.rst
+++ b/doc/install.rst
@@ -14,15 +14,44 @@ Installing
<https://forum.generic-mapping-tools.org/c/questions/pygmt-q-a>`__.
+Quickstart
+----------
+
+The fastest way to install PyGMT is with the
+`conda <https://... |
GenericMappingTools__pygmt-716 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/base_plotting.py:BasePlotting.text"
],
"edited_modules": [
"pygmt/base_plotting.py:BasePlotting"
]
},
"file": "pygmt/base_plotting.py"
}
] | GenericMappingTools/pygmt | ce8ecf8c324a37e044bad802385ca0b99058a569 | Varying transparency levels for plot, plot3d and text
**Description of the desired feature**
#614 added the `transparency` argument to all plotting functions. In most functions, `transparency` can be an int/float value in 0-100. For a few functions (plot, plot3d and text), transparency can be a list to have varying ... | diff --git a/pygmt/base_plotting.py b/pygmt/base_plotting.py
index 2a908b18..a203def4 100644
--- a/pygmt/base_plotting.py
+++ b/pygmt/base_plotting.py
@@ -1481,6 +1481,10 @@ class BasePlotting:
{p}
{t}
"""
+
+ # pylint: disable=too-many-locals
+ # pylint: disable=too-many-branch... |
GenericMappingTools__pygmt-724 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/base_plotting.py:BasePlotting.text"
],
"edited_modules": [
"pygmt/base_plotting.py:BasePlotting"
]
},
"file": "pygmt/base_plotting.py"
}
] | GenericMappingTools/pygmt | 2a88f73bda4d54a4f8dbe53e3e8a30f34915e3f9 | fig.text() doesn't work if "text" is integer or float
**Description of the problem**
<!-- Please be as detailed as you can when describing an issue. The more information we have, the easier it will be for us to track this down. -->
**Full code that generated the error**
```python
import pygmt
fig = pygmt.Fig... | diff --git a/pygmt/base_plotting.py b/pygmt/base_plotting.py
index a203def4..5b1f4076 100644
--- a/pygmt/base_plotting.py
+++ b/pygmt/base_plotting.py
@@ -1536,7 +1536,8 @@ class BasePlotting:
np.atleast_1d(x),
np.atleast_1d(y),
*extra_arrays,
-... |
GenericMappingTools__pygmt-975 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session._check_dtype_and_dim",
"pygmt/clib/session.py:Session.put_vector"
],
"edited_modules": [
"pygmt/clib/session.py:Session"
]
},
"fil... | GenericMappingTools/pygmt | 6f3650a0d6db63cd1a164c00d192ef0c3dc24b22 | Support passing in degrees, minutes, seconds (DMS) geographical coordinates
**Description of the desired feature**
In GMT, geographical coordinates can be given in floating points or many [different geographical formats](https://docs.generic-mapping-tools.org/latest/cookbook/features.html#input-data-formats) (e.g.,... | diff --git a/doc/api/index.rst b/doc/api/index.rst
index 6460eb53..0c07c18a 100644
--- a/doc/api/index.rst
+++ b/doc/api/index.rst
@@ -224,6 +224,7 @@ Low level access (these are mostly used by the :mod:`pygmt.clib` package):
clib.Session.get_default
clib.Session.create_data
clib.Session.put_matrix
+ ... |
GenericMappingTools__pygmt-976 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/datasets/earth_relief.py:load_earth_relief"
],
"edited_modules": [
"pygmt/datasets/earth_relief.py:load_earth_relief"
]
},
"file": "pygmt/datasets/earth_relief.py... | GenericMappingTools/pygmt | d99204b49909865fe37720c830067a80082a96ff | Allow load_earth_relief() to load the original land-only SRTM tiles
**Description of the desired feature**
Refer to https://docs.generic-mapping-tools.org/latest/datasets/remote-data.html#technical-information for details.
> The 3 and 1 arc second data are the SRTM 1x1 degree tiles from NASA. Note: The 3 and 1 ar... | diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.github/ISSUE_TEMPLATE/release_checklist.md
index f3479658..60c16647 100644
--- a/.github/ISSUE_TEMPLATE/release_checklist.md
+++ b/.github/ISSUE_TEMPLATE/release_checklist.md
@@ -38,7 +38,7 @@ assignees: ''
- [ ] GMT [forum](https://forum.generic-mapping-to... |
GenericMappingTools__pygmt-990 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pygmt/clib/session.py:Session.virtualfile_from_data"
],
"edited_modules": [
"pygmt/clib/session.py:Session"
]
},
"file": "pygmt/clib/session.py"
},
{
"changes":... | GenericMappingTools/pygmt | 5385fa5468cc9f12f3169218369dfd2d9915bb52 | Support 2D list as input
**Description of the problem**
PyGMT doesn't allow 2D list as input.
**Full code that generated the error**
The script below doesn't work:
```python
import pygmt
fig = pygmt.Figure()
fig.plot(data=[[0, 0]], region=[-2, 2, -2, 2], frame=True, style="c0.5c", pen="1p")
fig.show()
... | diff --git a/pygmt/clib/session.py b/pygmt/clib/session.py
index 64bcd55c..3e79f558 100644
--- a/pygmt/clib/session.py
+++ b/pygmt/clib/session.py
@@ -1360,7 +1360,9 @@ class Session:
with self.open_virtual_file(*args) as vfile:
yield vfile
- def virtualfile_from_data(self, check_kind=None, d... |
GeoscienceAustralia__GeodePy-101 | [
{
"changes": {
"added_entities": [
"geodepy/convert.py:rect_radius",
"geodepy/convert.py:alpha_coeff",
"geodepy/convert.py:beta_coeff",
"geodepy/convert.py:psfandgridconv",
"geodepy/convert.py:geo2grid",
"geodepy/convert.py:grid2geo",
"geodepy/conver... | GeoscienceAustralia/GeodePy | a5bb77e79eb670c776f998a54c7f29a862f67716 | Shift llh2xyz, xyz2llh, grid2geo, and geo2grid from transform module to convert module
These four functions are coordinate conversions within the same datum and are better placed in the convert module | diff --git a/geodepy/convert.py b/geodepy/convert.py
index efd3e18..c9b3cb1 100644
--- a/geodepy/convert.py
+++ b/geodepy/convert.py
@@ -5,8 +5,13 @@ Geoscience Australia - Python Geodesy Package
Convert Module
"""
-from math import sin, cos, atan2, radians, degrees, sqrt
+from math import sin, cos, atan2, radians,... |
GeoscienceAustralia__GeodePy-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"geodepy/convert.py:DMSAngle.__init__",
"geodepy/convert.py:DMSAngle.__repr__",
"geodepy/convert.py:DMSAngle.__truediv__",
"geodepy/convert.py:DMSAngle.__abs__",
"geodepy/... | GeoscienceAustralia/GeodePy | 3c1531ecbca268ea1cf720854685917726670b63 | Integer Negative Zero issue in DMSAngle and DDMAngle classes
When entering the degree component of a DMSAngle(degree, minute, second) or DDMAngle(degree, minute) object, if the degree component is between -1 and 0 (i.e. DMSAngle(-0,12,14)) this will incorrectly convert this to a positive value. This is because python i... | diff --git a/geodepy/convert.py b/geodepy/convert.py
index ed91357..988581a 100755
--- a/geodepy/convert.py
+++ b/geodepy/convert.py
@@ -23,13 +23,33 @@ def hp2dec(hp):
class DMSAngle(object):
- def __init__(self, degree=0, minute=0, second=0):
- self.degree = int(degree)
+ def __init__(self, degree=0... |
Geosyntec__cloudside-63 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "cloudside/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"cloudside/stor... | Geosyntec/cloudside | 4ad1f23964c2dc44d770fbdcae0a3586c99ff470 | Storms that conclude near end of record extend too far
When the time between the last observed rainfall and the end of the record is less than the interevent dry duration, the current implementation of the storm parser (wrongly, IMO) extends the last storm to the end of the record.
You can see this in the "expected"... | diff --git a/cloudside/__init__.py b/cloudside/__init__.py
index a7559cf..21e1ce2 100644
--- a/cloudside/__init__.py
+++ b/cloudside/__init__.py
@@ -7,4 +7,4 @@ from . import asos # noqa
__author__ = "Paul Hobson"
__email__ = "pmhobson@gmail.com"
-__version__ = "0.2.1"
+__version__ = "0.3.0"
diff --git a/cloudside... |
GibbsConsulting__django-plotly-dash-307 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"demo/demo/dash_apps.py:callback_test2",
"demo/demo/dash_apps.py:callback_test"
],
"edited_modules": [
"demo/demo/dash_apps.py:callback_test2",
"demo/demo/dash_apps.py... | GibbsConsulting/django-plotly-dash | 03f8554f1fd8773271938cad0f78ec5876b0c7fc | Add support for wildcard callbacks
Dash now permits the use of wildcards in callbacks. This issue is a placeholder for investigating the work needed to extend support to cover this feature and for any resultant implementation.
If you are interested in sponsoring this work please reach out [here](https://gibbsconsult... | diff --git a/check_code_dpd b/check_code_dpd
index a6483f9..09d12c8 100755
--- a/check_code_dpd
+++ b/check_code_dpd
@@ -2,4 +2,4 @@
#
source env/bin/activate
#
-pylint django_plotly_dash
+pylint django_plotly_dash --rcfile=pylintrc
diff --git a/demo/demo/dash_apps.py b/demo/demo/dash_apps.py
index e8a5a55..f85c763 ... |
GibbsConsulting__django-plotly-dash-309 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"demo/demo/dash_apps.py:callback_test2",
"demo/demo/dash_apps.py:callback_test"
],
"edited_modules": [
"demo/demo/dash_apps.py:callback_test2",
"demo/demo/dash_apps.py... | GibbsConsulting/django-plotly-dash | 03f8554f1fd8773271938cad0f78ec5876b0c7fc | Remove multiple return value check for clientside_callbacks
As reported in #301 there is a check to prevent use of multiple server-side callback values as this is not handled at present.
However, the check appears to also prevent the use of client-side callbacks with multiple return values, and should be relaxed to ... | diff --git a/CONTRIBUTIONS.md b/CONTRIBUTIONS.md
index c45c689..20eefa6 100644
--- a/CONTRIBUTIONS.md
+++ b/CONTRIBUTIONS.md
@@ -39,3 +39,6 @@ Thanks to the following people:
[CaseGuide](https://github.com/CaseGuide)
[manish-podugu](https://github.com/manish-podugu)
+
+[sdementen](https://github.com/sdementen)
+
di... |
GibbsConsulting__django-plotly-dash-313 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"demo/demo/dash_apps.py:callback_test2"
],
"edited_modules": [
"demo/demo/dash_apps.py:callback_test2"
]
},
"file": "demo/demo/dash_apps.py"
},
{
"changes": {
... | GibbsConsulting/django-plotly-dash | f410c48c025cc470138e5d5ee9569709b8cc28d4 | Move to newer urls function to avoid Django 4.0 deprecation warning
When running the test suite there are a number of warnings of the form
```
demo/tests/test_dpd_demo.py::test_template_tag_use
/home/mark/local/django-plotly-dash/demo/demo/urls.py:38: RemovedInDjango40Warning:
```
These can be removed by modif... | diff --git a/CONTRIBUTIONS.md b/CONTRIBUTIONS.md
index c45c689..20eefa6 100644
--- a/CONTRIBUTIONS.md
+++ b/CONTRIBUTIONS.md
@@ -39,3 +39,6 @@ Thanks to the following people:
[CaseGuide](https://github.com/CaseGuide)
[manish-podugu](https://github.com/manish-podugu)
+
+[sdementen](https://github.com/sdementen)
+
di... |
GjjvdBurg__paper2remarkable-43 | [
{
"changes": {
"added_entities": [
"paper2remarkable/log.py:Logger.append"
],
"added_modules": null,
"edited_entities": [
"paper2remarkable/log.py:Logger._log",
"paper2remarkable/log.py:Logger.info",
"paper2remarkable/log.py:Logger.warning"
],
... | GjjvdBurg/paper2remarkable | 90e97824287c192d3d99cae2981cbd35905cb91d | p2r asking for pdftk instead of using qpdf on ubuntu
I have kubuntu 18.04. When I run the example command
`p2r -v https://arxiv.org/abs/1811.11242 `. It gives the error
`[Errno 2] No such file or directory: 'pdftk': 'pdftk'` | diff --git a/paper2remarkable/log.py b/paper2remarkable/log.py
index bae1cbf..3a2fcc5 100644
--- a/paper2remarkable/log.py
+++ b/paper2remarkable/log.py
@@ -38,19 +38,27 @@ class Logger(metaclass=Singleton):
def disable(self):
self.enabled = False
- def _log(self, msg, mode):
+ def _log(self, msg,... |
GoogleCloudPlatform__cloud-sql-python-connector-1221 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"google/cloud/sql/connector/connector.py:Connector.__init__"
],
"edited_modules": [
"google/cloud/sql/connector/connector.py:Connector"
]
},
"file": "google/cloud/sql/co... | GoogleCloudPlatform/cloud-sql-python-connector | dde235b0207b861e2a262964f35e7141885384ed | Add support for `GOOGLE_CLOUD_UNIVERSE_DOMAIN` env variable
Google Client libraries should check the env variable `GOOGLE_CLOUD_UNIVERSE_DOMAIN` as a secondary way of setting the TPC universe.
Priority should be as follows:
1. Use `universe_domain` param of `Connector` if set
2. Use `GOOGLE_CLOUD_UNIVERSE_DOMAIN... | diff --git a/google/cloud/sql/connector/connector.py b/google/cloud/sql/connector/connector.py
index ada14cb..5160513 100755
--- a/google/cloud/sql/connector/connector.py
+++ b/google/cloud/sql/connector/connector.py
@@ -19,6 +19,7 @@ from __future__ import annotations
import asyncio
from functools import partial
im... |
GoogleCloudPlatform__django-cloud-deploy-242 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"django_cloud_deploy/cloudlib/database.py:DatabaseClient.with_cloud_sql_proxy"
],
"edited_modules": [
"django_cloud_deploy/cloudlib/database.py:DatabaseClient"
]
},
"fil... | GoogleCloudPlatform/django-cloud-deploy | 7d61adf2dbd3f319165da69e4c6f9353f1eef12d | Add a label for Github Issues generated crash handling | diff --git a/django_cloud_deploy/cloudlib/database.py b/django_cloud_deploy/cloudlib/database.py
index cb5ed34..63c4980 100644
--- a/django_cloud_deploy/cloudlib/database.py
+++ b/django_cloud_deploy/cloudlib/database.py
@@ -18,13 +18,16 @@ See https://cloud.google.com/sql/docs/
import contextlib
import signal
+imp... |
GoogleCloudPlatform__django-cloud-deploy-349 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"django_cloud_deploy/cli/cloudify.py:add_arguments"
],
"edited_modules": [
"django_cloud_deploy/cli/cloudify.py:add_arguments"
]
},
"file": "django_cloud_deploy/cli/clou... | GoogleCloudPlatform/django-cloud-deploy | 088ec94961e1b0881df15f950cea6187a7b46764 | Update GCS bucket Cross-Origin Resource Sharing Policy after creation
Webbrowser deny to access font files in GCS bucket. Error message:
```
Access to font at 'https://storage.googleapis.com/django-447998/static/webfonts/fa-solid-900.woff2' from origin 'https://django-447998.appspot.com' has been blocked by CORS poli... | diff --git a/django_cloud_deploy/.yapfignore b/django_cloud_deploy/.yapfignore
index fe867f6..db9c862 100644
--- a/django_cloud_deploy/.yapfignore
+++ b/django_cloud_deploy/.yapfignore
@@ -3,3 +3,6 @@
# Django project source files used in test
**/data
+
+# Automatically generated nox files
+.nox
\ No newline at end... |
GoogleCloudPlatform__django-cloud-deploy-358 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"django_cloud_deploy/skeleton/source_generator.py:_YAMLFileGenerator.generate_new"
],
"edited_modules": [
"django_cloud_deploy/skeleton/source_generator.py:_YAMLFileGenerator"
]... | GoogleCloudPlatform/django-cloud-deploy | d8a5c1a8312898648589ab9e42005dec99ca5923 | Unable to deploy to GKE when the Django project name has uppercase letters
## Issue running command
django-cloud-deploy cloudify
## Please describe what is wrong
## Environment information
Django Cloud Deploy: [0.2.1]
Platform: [Linux-4.19.20-1rodete1-amd64-x86_64-with-Debian-rodete-rodete]
Gcloud... | diff --git a/django_cloud_deploy/skeleton/source_generator.py b/django_cloud_deploy/skeleton/source_generator.py
index d74be49..70ea8cb 100644
--- a/django_cloud_deploy/skeleton/source_generator.py
+++ b/django_cloud_deploy/skeleton/source_generator.py
@@ -647,7 +647,7 @@ class _YAMLFileGenerator(_Jinja2FileGenerator):... |
GoogleCloudPlatform__flask-talisman-18 | [
{
"changes": {
"added_entities": [
"flask_talisman/talisman.py:Talisman._make_nonce",
"flask_talisman/talisman.py:get_random_string"
],
"added_modules": [
"flask_talisman/talisman.py:get_random_string"
],
"edited_entities": [
"flask_talisman/talisman... | GoogleCloudPlatform/flask-talisman | d9f97215035b6e5e2425243e9e2dc6cb0184a313 | Add support for CSP nonce values
This is to allow support for inline script values. Use of nonce endorsed by https://csp.withgoogle.com/docs/strict-csp.html | diff --git a/README.rst b/README.rst
index 47dcb92..68b0902 100644
--- a/README.rst
+++ b/README.rst
@@ -91,6 +91,9 @@ Options
whether subdomains should also use HSTS.
- ``content_security_policy``, default ``default-src: 'self'``, see the
`Content Security Policy`_ section.
+- ``content_security_policy_nonc... |
GoogleCloudPlatform__flask-talisman-26 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "example_app/main.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules... | GoogleCloudPlatform/flask-talisman | eb5bd5a241ef59e508a2e6f8076a12a49099855d | Support Feature Policy
The Feature-Policy is a relatively new header which is supported in Chrome which would be nice to have supported as well.
https://scotthelme.co.uk/a-new-security-header-feature-policy/ | diff --git a/README.rst b/README.rst
index 0a7258d..9198b94 100644
--- a/README.rst
+++ b/README.rst
@@ -70,6 +70,7 @@ There is also a full `Example App <https://github.com/GoogleCloudPlatform/flask-
Options
-------
+- ``feature_policy``, default ``{}``, see the `Feature Policy` section.
- ``force_https``, defau... |
GoogleCloudPlatform__httplib2shim-9 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"httplib2shim/__init__.py:_default_make_pool",
"httplib2shim/__init__.py:Http.__init__"
],
"edited_modules": [
"httplib2shim/__init__.py:_default_make_pool",
"httplib2... | GoogleCloudPlatform/httplib2shim | 128d229807577809a437cd20161c3c496080991f | proxy_info cannot be None for the ver. 0.0.2
After upgrade to ver. 0.0.2 I cannot call `httplib2shim.Http(proxy_info=None)`, it results in:
```
File "/usr/local/lib/python3.5/dist-packages/httplib2shim/__init__.py", line 114, in __init__
pool = self._make_pool(proxy_info=proxy_info())
TypeError: 'NoneType' obj... | diff --git a/httplib2shim/__init__.py b/httplib2shim/__init__.py
index bdc9a8c..42b3aa6 100644
--- a/httplib2shim/__init__.py
+++ b/httplib2shim/__init__.py
@@ -20,6 +20,7 @@
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
+import collections
import errno
import socket
import ssl
@... |
GothenburgBitFactory__holidata-115 | [
{
"changes": {
"added_entities": [
"src/holidata/holidays/US.py:US.date_is_not_saturday",
"src/holidata/holidays/US.py:US.date_is_friday",
"src/holidata/holidays/US.py:US.date_is_saturday",
"src/holidata/holidays/US.py:US.date_is_sunday"
],
"added_modules": null... | GothenburgBitFactory/holidata | 37b41c76c6f6a3f21a8ceb72f1e7bea016c87355 | Add Juneteenth to en-US
Add 19 June annually for en-US as a holiday for `Juneteenth National Independence Day` ([details](https://www.nps.gov/subjects/npscelebrates/juneteenth.htm)). | diff --git a/ChangeLog b/ChangeLog
index 75be09f..56ce49d 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,6 @@
+- #115 US: Implement federal holidays
+ (thanks to J. David Stark)
+
2024.11.0
- hu-HU: Add non-working days for 2025 in Hungary
diff --git a/src/holidata/holidays/US.py b/src/holidata/holida... |
GreenBuildingRegistry__usaddress-scourgify-12 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"scourgify/normalize.py:normalize_occupancy_type"
],
"edited_modules": [
"scourgify/normalize.py:normalize_occupancy_type"
]
},
"file": "scourgify/normalize.py"
}
] | GreenBuildingRegistry/usaddress-scourgify | 29912c8c00bbb3d5c899fb64772ecf07d9020b1e | Valid occupancy types replaced by 'UNIT'
HI there, I appreciate your work on normalizing the US Address library!
I notice the following issue:
```
>>> from scourgify import normalize_address_record
>>> normalize_address_record('12345 Somewhere Street Apt 1, Town, MA 12345')
{'address_line_1': '12345 SOMEWHERE... | diff --git a/scourgify/normalize.py b/scourgify/normalize.py
index 4270b68..8827088 100644
--- a/scourgify/normalize.py
+++ b/scourgify/normalize.py
@@ -535,7 +535,8 @@ def normalize_occupancy_type(parsed_addr, default=None):
default = default if default is not None else 'UNIT'
occupancy_type_label = 'Occupan... |
HBClab__NiBetaSeries-289 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"src/nibetaseries/interfaces/nistats.py:LSSBetaSeriesInputSpec",
"src/nibetaseries/interfaces/nistats.py:LSABetaSeriesInputSpec"
]
},
"file": "src/nibe... | HBClab/NiBetaSeries | e8e367021a63fad37db43f95045c6d7ea6894d5b | allow users to pass nibabel objects to nistats interfaces
**Is your feature request related to a problem? Please describe.**
I'm running a [butt-ton of simulations using the lss/lsa interfaces](https://github.com/jdkent/betaSeriesSimulations/blob/31230b13a79d245eb36dae42b941095300ac293f/beta_sim/workflow.py#L165-L180)... | diff --git a/src/nibetaseries/interfaces/nistats.py b/src/nibetaseries/interfaces/nistats.py
index 88e8c6d..44818fd 100644
--- a/src/nibetaseries/interfaces/nistats.py
+++ b/src/nibetaseries/interfaces/nistats.py
@@ -7,6 +7,7 @@ from nipype.interfaces.base import (
OutputMultiPath, File, LibraryBaseInterface,
... |
HBClab__NiBetaSeries-298 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run.py:main"
],
"edited_modules": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run... | HBClab/NiBetaSeries | e9d8c2a9607a65cfcfbc910444b5ae41224912be | Option to not scale voxel timeseries
**Is your feature request related to a problem? Please describe.**
I'm trying to measure how the BOLD amplitude relates to noise amplitude/standard deviation, and I want the time series to not be transformed so the units are in the original units of the voxels (not a percentage).
... | diff --git a/docs/workflows.rst b/docs/workflows.rst
index b244d3a..da8a1c2 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -26,6 +26,7 @@ Participant Workflow
output_dir='.',
preproc_img_list=[''],
selected_confounds=[''],
+ signal_scaling=0,
smoothing_kernel=None... |
HBClab__NiBetaSeries-299 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run.py:main"
],
"edited_modules": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run... | HBClab/NiBetaSeries | 245575d89682ed810e6979018486a7e191e9d0d6 | Output normalized betaseries
**Is your feature request related to a problem? Please describe.**
Estimating betaseries can result in poor fits and bizarre parameter estimates. These outlier estimates can then influence subsequent analyses.
**Describe the solution you'd like**
One approach to dealing with this issu... | diff --git a/docs/workflows.rst b/docs/workflows.rst
index da8a1c2..37e7da5 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -23,6 +23,7 @@ Participant Workflow
hrf_model='glover',
high_pass=0.008,
name='subtest',
+ norm_betas=False,
output_dir='.',
preproc... |
HBClab__NiBetaSeries-304 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run.py:main"
],
"edited_modules": [
"src/nibetaseries/cli/run.py:get_parser",
"src/nibetaseries/cli/run... | HBClab/NiBetaSeries | 45e16203adcd6e6fdb7d7c88e1ee920d7b5a846b | connect residuals to output
**Is your feature request related to a problem? Please describe.**
While residuals were added to the interfaces (#294), these are not connected to the main workflow for users.
**Describe the solution you'd like**
Pass residual to the output directory.
**Describe alternatives you've con... | diff --git a/docs/FAQ.rst b/docs/FAQ.rst
index ce538a4..1ed0e95 100644
--- a/docs/FAQ.rst
+++ b/docs/FAQ.rst
@@ -7,8 +7,7 @@ Frequently Asked Questions
Does NiBetaSeries work with output from old fMRIPrep (< v1.2.0)?
----------------------------------------------------------------
-Yes, NiBetaSeries will currently ... |
HDFGroup__hsds-366 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "hsds/app.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hsds/util/globparser.py:... | HDFGroup/hsds | 268bd655768fe6755ea2bc1a9a7bcb5145defbfb | typo, should be password_file
https://github.com/HDFGroup/hsds/blob/268bd655768fe6755ea2bc1a9a7bcb5145defbfb/hsds/app.py#L32 | diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
index 0e72a00..583dff9 100644
--- a/.github/workflows/dependency-review.yml
+++ b/.github/workflows/dependency-review.yml
@@ -18,3 +18,6 @@ jobs:
uses: actions/checkout@v3
- name: 'Dependency Review'
... |
HDembinski__jacobi-16 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "src/jacobi/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/jacobi/co... | HDembinski/jacobi | 9b3811bb96b43f2a28f0d2c05ef570214ce50bf1 | propagate: support functions with multiple independent arguments
Often, one has a function that takes independent arguments. Propagating this currently is a bit cumbersome, one has to combine the arguments into a vector and the covariances into joint block covariance matrix. `propagate` could be made more flexible to m... | diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d7ba3ca..d787190 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -47,5 +47,12 @@ repos:
rev: 'v0.971'
hooks:
- id: mypy
- args: [--allow-redefinition, --ignore-missing-imports, src]
+ args: [src]
pass_filename... |
HECBioSim__Longbow-106 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/applications.py:checkapp",
"longbow/applications.py:processjobs"
],
"edited_modules": [
"longbow/applications.py:checkapp",
"longbow/applications.py:processjo... | HECBioSim/Longbow | 7e8d4e78e2e0590083c8a5630c24d175ba49ce48 | Implement update mode for disconnected sessions
When using the disconnect mode with --disconnect, currently the only way to reconnect is via the --recover option, but this reconnects permanently without then disconnecting again. A new mode should be implemented to reconnect to update the status of the jobs, transfer fi... | diff --git a/longbow/applications.py b/longbow/applications.py
index 8f99c1e..b2ee695 100644
--- a/longbow/applications.py
+++ b/longbow/applications.py
@@ -82,7 +82,7 @@ def checkapp(jobs):
LOG.info("Testing the executables defined for each job.")
- for job in jobs:
+ for job in [a for a in jobs if "lbo... |
HECBioSim__Longbow-107 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/schedulers/lsf.py:prepare"
],
"edited_modules": [
"longbow/schedulers/lsf.py:prepare"
]
},
"file": "longbow/schedulers/lsf.py"
},
{
"changes": {
"... | HECBioSim/Longbow | 585dc2198b0f3817e4822da13725489585efcf15 | memory parameter only used in PBS
Either rename this to pbs-memory to denote that it is pbs only or add support in the other schedulers. | diff --git a/longbow/schedulers/lsf.py b/longbow/schedulers/lsf.py
index ab20689..8992636 100644
--- a/longbow/schedulers/lsf.py
+++ b/longbow/schedulers/lsf.py
@@ -98,6 +98,10 @@ def prepare(job):
jobfile.write("#BSUB -m " + job["lsf-cluster"] + "\n")
+ if job["memory"] is not "":
+
+ jobfile.wr... |
HECBioSim__Longbow-110 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/schedulers/lsf.py:prepare"
],
"edited_modules": [
"longbow/schedulers/lsf.py:prepare"
]
},
"file": "longbow/schedulers/lsf.py"
},
{
"changes": {
"... | HECBioSim/Longbow | 70d129033143ef63b307cedce05b1ddfd8c41e8c | redirects for stdout and stderr from schedulers
Self explanatory | diff --git a/longbow/schedulers/lsf.py b/longbow/schedulers/lsf.py
index eca4234..51dd4a2 100644
--- a/longbow/schedulers/lsf.py
+++ b/longbow/schedulers/lsf.py
@@ -129,22 +129,22 @@ def prepare(job):
jobfile.write("#BSUB -n " + job["cores"] + "\n")
# Redirect stdout
- if job["stdout"] == "":
+ if job... |
HECBioSim__Longbow-111 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "longbow/configuration.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/sch... | HECBioSim/Longbow | c81fcaccfa7fb2dc147e40970ef806dc6d6b22a4 | PBS and NAMD SMP
On ARCHER, NAMD jobs with SMP have intermittent difficulties with the ncpus and/or mpiprocs directive to "-l". This should be investigated, further. It appears to stem from the corespernode needing to be set at 1 which also sets ncpus to 1.There are several possibilities here:
1. A return to default... | diff --git a/longbow/configuration.py b/longbow/configuration.py
index bd12c87..2426df1 100644
--- a/longbow/configuration.py
+++ b/longbow/configuration.py
@@ -93,29 +93,30 @@ JOBTEMPLATE = {
"host": "",
"localworkdir": "",
"lsf-cluster": "",
- "modules": "",
"maxtime": "24:00",
"memory": "... |
HECBioSim__Longbow-123 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/entrypoints.py:_setuplogger"
],
"edited_modules": [
"longbow/entrypoints.py:_setuplogger"
]
},
"file": "longbow/entrypoints.py"
}
] | HECBioSim/Longbow | 063049d26872ea4056202ab22bc1ea4a18ff4585 | rename default log file name
Shouldn't simply be "log", lots of other software have the same naming and it interferes. Maybe longbow.log would be best. | diff --git a/longbow/entrypoints.py b/longbow/entrypoints.py
index 3911a83..f413500 100644
--- a/longbow/entrypoints.py
+++ b/longbow/entrypoints.py
@@ -800,7 +800,7 @@ def _setuplogger(parameters):
# If no log file name was given then default to "log".
if parameters["log"] is "":
- parameters["log"]... |
HECBioSim__Longbow-134 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/entrypoints.py:launcher"
],
"edited_modules": [
"longbow/entrypoints.py:launcher"
]
},
"file": "longbow/entrypoints.py"
}
] | HECBioSim/Longbow | 51288dd52da6e2223d019fc1b91f5670c15b734f | Longbow should exit with non zero when error occurs
Friendly error logging has lead to Longbow exiting with non zero error code. This should not be the case.
Raised by @drewsilcock | diff --git a/longbow/entrypoints.py b/longbow/entrypoints.py
index f413500..741d850 100644
--- a/longbow/entrypoints.py
+++ b/longbow/entrypoints.py
@@ -317,6 +317,8 @@ def launcher():
LOG.error(err)
+ exit(1)
+
# Show nice exit message.
finally:
|
HECBioSim__Longbow-135 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/entrypoints.py:launcher"
],
"edited_modules": [
"longbow/entrypoints.py:launcher"
]
},
"file": "longbow/entrypoints.py"
},
{
"changes": {
"added_e... | HECBioSim/Longbow | 800f49ba14b0ba5c423b35c7e7d52aff25b7f2e1 | spelling in docs
--verbose is spelled wrong in the dis-connectable session docs | diff --git a/docs/usr-running-jobs.rst b/docs/usr-running-jobs.rst
index 847ae49..41f3784 100644
--- a/docs/usr-running-jobs.rst
+++ b/docs/usr-running-jobs.rst
@@ -300,7 +300,7 @@ A useful feature is the ability for Longbow to disconnect itself shortly after s
Longbow will simply submit your jobs and then write out... |
HECBioSim__Longbow-138 | [
{
"changes": {
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},
"file": "longbow/apps/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/con... | HECBioSim/Longbow | 168f629c04128751902eed35ca04dac9fbefc51f | module override parameter has gone missing
In older versions of Longbow there used to be a MODULEOVERRIDE parameter that could be optionally provided in application plugin files to alter the default naming of modules from the name of the plugin file to something else. This could be used by users to set the module name ... | diff --git a/longbow/apps/__init__.py b/longbow/apps/__init__.py
index 662c5a6..7ad59fb 100644
--- a/longbow/apps/__init__.py
+++ b/longbow/apps/__init__.py
@@ -45,6 +45,7 @@ MODULES = pkgutil.iter_modules(path=[PATH])
EXECLIST = []
PLUGINEXECS = {}
+MODNAMEOVERRIDES = {}
# Loop through all the modules in the pl... |
HECBioSim__Longbow-140 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/applications.py:processjobs"
],
"edited_modules": [
"longbow/applications.py:processjobs"
]
},
"file": "longbow/applications.py"
},
{
"changes": {
... | HECBioSim/Longbow | 56e89f021949f6ccde03d5495e529b7b004bce18 | Longbow still breaks with generic executables
This is evident when trialling a link with chemshell and longbow. Initial goes at launching chemshell with Longbow using a hard path triggers a python traceback
```
Traceback (most recent call last):
File "/home/jimboid/.local/lib/python2.7/site-packages/longbow/core... | diff --git a/longbow/applications.py b/longbow/applications.py
index 0046592..c89cd77 100644
--- a/longbow/applications.py
+++ b/longbow/applications.py
@@ -146,8 +146,6 @@ def processjobs(jobs):
for job in [a for a in jobs if "lbowconf" not in a]:
filelist = []
- appplugins = getattr(apps, "PLUG... |
HECBioSim__Longbow-93 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/applications.py:_procfiles",
"longbow/applications.py:_procfilesreplicatejobs"
],
"edited_modules": [
"longbow/applications.py:_procfiles",
"longbow/applicati... | HECBioSim/Longbow | 145a985cb0b3eb18fc3dd1f0dc74a9ee4e9c236c | Allow replicate directory naming schemes
At the moment users have to have a specific fixed structure for replicates where the directory consists of rep[x] where the rep part is fixed and the number is incremented. Users have requested that the rep part is flexible so Longbow can be better chained with other tools. | diff --git a/longbow/applications.py b/longbow/applications.py
index c693b42..8f99c1e 100755
--- a/longbow/applications.py
+++ b/longbow/applications.py
@@ -353,13 +353,15 @@ def _procfiles(job, arg, filelist, foundflags, substitution):
# Otherwise we have a replicate job so check these.
else:
- ... |
HECBioSim__Longbow-94 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"longbow/applications.py:_procfiles",
"longbow/applications.py:_procfilesreplicatejobs"
],
"edited_modules": [
"longbow/applications.py:_procfiles",
"longbow/applicati... | HECBioSim/Longbow | 99ce093c8b3daab24c4cb4f64b3f7e3f22690073 | Using pre-existing queue scripts
Hi James,
I was wondering if it would be possible to include the option of longbow using an already existing queue script instead of creating one on the fly. That way I would no need to struggle with longbow if I want to write non-standard commands in the queue script and I could sti... | diff --git a/longbow/applications.py b/longbow/applications.py
index 8f99c1e..c693b42 100755
--- a/longbow/applications.py
+++ b/longbow/applications.py
@@ -353,15 +353,13 @@ def _procfiles(job, arg, filelist, foundflags, substitution):
# Otherwise we have a replicate job so check these.
else:
- ... |
HEPData__hepdata_lib-259 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "hepdata_lib/c_file_reader.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edite... | HEPData/hepdata_lib | db53815f4963bd11cc62f88c9111f45134ccac67 | Add flag to disable features requiring ROOT
There are use cases where the tool is used but no ROOT installation is available. We should add an option that disables all features that use ROOT to make the other features work independently (e.g. reading in a text file). For ROOT TTrees, we could fall back to uproot. | diff --git a/README.md b/README.md
index 6f9ba74..4b716ce 100644
--- a/README.md
+++ b/README.md
@@ -72,8 +72,8 @@ There are a few more examples available that can directly be run using the [bind
- [Reading TGraph and TGraphError from '.C' files](https://github.com/HEPData/hepdata_lib/blob/main/examples/read_c_file.ip... |
HEPData__hepdata_lib-265 | [
{
"changes": {
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"added_modules": null,
"edited_entities": [
"hepdata_lib/__init__.py:Variable.make_dict"
],
"edited_modules": [
"hepdata_lib/__init__.py:Variable"
]
},
"file": "hepdata_lib/__init__.py"
},
{
"changes": {
... | HEPData/hepdata_lib | dcc23bd4dbbabcf0bf69914bc56bb0c1f817d9d0 | Support inhomogeneous uncertainties
> I'm currently struggling to use the `hepdata_lib` for cases with inhomogeneous error breakdowns across bins. For instance, I have a distribution with three bins where the first two bins have two error components 'A' and 'B' (but not 'C') and the third bin has error component 'C' (b... | diff --git a/docs/usage.rst b/docs/usage.rst
index 410f000..31a183d 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -370,5 +370,7 @@ multiple dependent variables and a (different) subset of the bins has missing co
In this case the uncertainties should be set to zero for the missing bins with a non-numeric central ... |
HK3-Lab-Team__pytrousse-62 | [
{
"changes": {
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},
"file": "scripts/use_anonymize_database.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"... | HK3-Lab-Team/pytrousse | d958265f3abda0fa07566c086a51f07d4eae873a | DataFrameWithInfo features columns could be a subset of metadata columns
At the moment `DataFrameWithInfo` takes as parameters `metadata_cols` (tuple, i.e. the columns of the dataframe to be used as metadata) and `metadata_as_features` (bool, i.e. whether to consider all the metadata columns as features). It could be u... | diff --git a/scripts/use_anonymize_database.py b/scripts/use_anonymize_database.py
index 2a105d5..a49de15 100644
--- a/scripts/use_anonymize_database.py
+++ b/scripts/use_anonymize_database.py
@@ -12,5 +12,9 @@ output_data_dir = os.path.join(os.getcwd(), "data")
df_sani = pd.read_csv(df_sani_dir)
anonymize_data(
- ... |
HK3-Lab-Team__pytrousse-66 | [
{
"changes": {
"added_entities": [
"src/trousse/dataset.py:Dataset.nan_columns"
],
"added_modules": null,
"edited_entities": [
"src/trousse/dataset.py:Dataset.__init__",
"src/trousse/dataset.py:Dataset.many_nan_columns",
"src/trousse/dataset.py:Dataset.tri... | HK3-Lab-Team/pytrousse | 28ae6abc5c1c743050789c0e2be66161e8ee3073 | Dataset method: nan_columns
nan_columns(tolerance) [2c]
Tolerance is a (optional, default=1) float number (0 to 1) representing the ratio “nan samples”/”total samples” for the column to be considered a “nan column”.
| diff --git a/src/trousse/dataset.py b/src/trousse/dataset.py
index 450f923..ce949a1 100644
--- a/src/trousse/dataset.py
+++ b/src/trousse/dataset.py
@@ -141,7 +141,6 @@ class Dataset:
feature_cols: Tuple = None,
data_file: str = None,
df_object: pd.DataFrame = None,
- nan_percentage_th... |
HK3-Lab-Team__pytrousse-93 | [
{
"changes": {
"added_entities": [
"src/trousse/feature_operations.py:FillNA.__repr__",
"src/trousse/feature_operations.py:FillNA.__str__",
"src/trousse/feature_operations.py:ReplaceSubstrings.__repr__",
"src/trousse/feature_operations.py:ReplaceSubstrings.__str__",
... | HK3-Lab-Team/pytrousse | f878ec1693098e212c652896274ec08756e31a46 | Add __str__ method for FillNA | diff --git a/README.md b/README.md
index 01f5eb7..3c181e0 100644
--- a/README.md
+++ b/README.md
@@ -37,18 +37,15 @@ The traced data path can be inspected through `operation_history` attribute.
>>> dataset.operations_history
```
```bash
-[
- FillNA(
- columns=["column_with_nan"],
- derived_columns=[... |
HK3-Lab-Team__pytrousse-95 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"src/trousse/feature_fix.py:split_continuous_column_into_bins",
"src/trousse/feature_fix.py:combine_categorical_columns_to_one",
"src/trousse/feature_fix.py:_one_hot_encode_column",
... | HK3-Lab-Team/pytrousse | dcbcdc592790178f40630aeb908d7dc8da4f20df | FeatureOperation: OrdinalEncoder
[3c iii] | diff --git a/src/trousse/feature_fix.py b/src/trousse/feature_fix.py
index 34980f2..7512603 100644
--- a/src/trousse/feature_fix.py
+++ b/src/trousse/feature_fix.py
@@ -1,13 +1,13 @@
import itertools
import logging
-from typing import Tuple
+from typing import Any, Tuple
import numpy as np
import pandas as pd
-fr... |
HTTP-APIs__hydra-python-core-28 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra_python_core/doc_maker.py:create_doc",
"hydra_python_core/doc_maker.py:create_property",
"hydra_python_core/doc_maker.py:create_operation"
],
"edited_modules": [
... | HTTP-APIs/hydra-python-core | 099b3d33466a60519fbb3a660d2ed455197c41a4 | Update the core repo with the latest spec changes
We need to have a detailed analysis about what changes have been made to the spec in the last two years and how do we include them here. We might need a report on current attributes of the spec and what core is missing.
As far as I can see, now that we have separated... | diff --git a/hydra_python_core/doc_maker.py b/hydra_python_core/doc_maker.py
index 38afa4f..83f02b1 100644
--- a/hydra_python_core/doc_maker.py
+++ b/hydra_python_core/doc_maker.py
@@ -104,8 +104,13 @@ def create_doc(doc: Dict[str, Any], HYDRUS_SERVER_URL: str = None,
class_obj, collection, collection_path = c... |
HTTP-APIs__hydra-python-core-91 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hydra_python_core/doc_maker.py:create_property"
],
"edited_modules": [
"hydra_python_core/doc_maker.py:create_property"
]
},
"file": "hydra_python_core/doc_maker.py"
... | HTTP-APIs/hydra-python-core | f191e9e58a7ab81552814303031aaa3bf90ff514 | Implement copying of data types properties
### I'm submitting a
- [x ] feature request.
If the declaration of a type for a field is present in the original ontology, it should be copied in the ApiDoc to allow `hydrus` to read it and genreate the right column type.
Necessary for https://github.com/HTTP-APIs/hydr... | diff --git a/hydra_python_core/doc_maker.py b/hydra_python_core/doc_maker.py
index 31996c4..aa80d4a 100644
--- a/hydra_python_core/doc_maker.py
+++ b/hydra_python_core/doc_maker.py
@@ -332,6 +332,17 @@ def create_property(supported_property: Dict[str, Any]) -> Union[HydraLink, Hydr
prop_require = supported_propert... |
HTenkanen__pyrosm-98 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyrosm/graphs.py:to_networkx"
],
"edited_modules": [
"pyrosm/graphs.py:to_networkx"
]
},
"file": "pyrosm/graphs.py"
}
] | HTenkanen/pyrosm | 01a62587f7fef26e955a6a1d3514353c8d523a87 | BUG: creating network creates ghost copies of each node
I've discovered what looks to be a bug in the `to_graph` algorithm.
The number of nodes in the graph resulting from `to_graph` is double the number of nodes pulled by `get_network`. Furthermore, exactly half the nodes in the graph have no `geometry` attribute ... | diff --git a/pyrosm/graphs.py b/pyrosm/graphs.py
index 9d010fc..b4e46d5 100644
--- a/pyrosm/graphs.py
+++ b/pyrosm/graphs.py
@@ -162,9 +162,9 @@ def to_networkx(nodes,
edges = edges.rename(columns={edge_id_col: 'osmid'})
node_id_col = "osmid"
- # Add 'osmid' as index
- nodes = nodes.se... |
HXLStandard__libhxl-python-174 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hxl/validation.py:make_rule_hash",
"hxl/validation.py:make_json_report",
"hxl/validation.py:make_json_issue"
],
"edited_modules": [
"hxl/validation.py:make_rule_hash"... | HXLStandard/libhxl-python | 1bc7e92a3844dd443f9e31f478357ea7b599c831 | Double counting of errors p-code adm name combination consistency errors
When I put the below into data check, I get 2 of every cell eg. F3,F3,F4,F4,F5,F5...
https://data.humdata.org/dataset/77c97850-4004-4285-94db-0b390a962d6e/resource/d6c0dbac-683d-42d7-82b4-a6379bd4f48e/download/mrt_population_statistics_ons_rgph_2... | diff --git a/hxl/validation.py b/hxl/validation.py
index 3eb1eba..922bfaf 100644
--- a/hxl/validation.py
+++ b/hxl/validation.py
@@ -1508,11 +1508,6 @@ def validate(data, schema=None):
issue_map = dict()
- def make_rule_hash(rule):
- """Make a good-enough hash for a rule."""
- s = "\r".join([s... |
Hanaasagi__pymem-2 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pymem/debugger/lldb.py:LLDBDebugger._format_command"
],
"edited_modules": [
"pymem/debugger/lldb.py:LLDBDebugger"
]
},
"file": "pymem/debugger/lldb.py"
}
] | Hanaasagi/pymem | 530ccd096d0b2af0c704daec2b0e8e09c6e68852 | Not work with LLDB 8.0
### Environment
- Linux archlinux 5.1.16-arch1-1-ARCH
- Python 3.7.3
- lldb version 8.0.0
### How To Reproduce
Run
```Bash
pymem [pid] -d lldb
```
Full Trackback
```
Traceback (most recent call last):
File "/root/py37/bin/pymem", line 11, in <module>
load_entry_point(... | diff --git a/pymem/debugger/lldb.py b/pymem/debugger/lldb.py
index 8583c92..b669726 100644
--- a/pymem/debugger/lldb.py
+++ b/pymem/debugger/lldb.py
@@ -17,5 +17,6 @@ class LLDBDebugger(BaseDebugger):
r"expr (void) PyGILState_Release($gil)",
]
arguments = ["-p", str(self.target_pid), "--b... |
HdrHistogram__HdrHistogram_py-26 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"hdrh/codec.py:PayloadHeader"
]
},
"file": "hdrh/codec.py"
},
{
"changes": {
"added_entities": [
"hdrh/histogram.py:HdrHistogram.get_int_... | HdrHistogram/HdrHistogram_py | d566355a8f055d6ae78679f8f92e63be92c24470 | PayloadHeader conversion_ratio_bits type should be c_double
Based on the [Encoded Histogram format wiki](https://github.com/HdrHistogram/HdrHistogram.NET/wiki/Encoded-Histogram-format), the header element `Integer to double conversion ratio` is a double precision float. Currently the python version is using a long data... | diff --git a/hdrh/codec.py b/hdrh/codec.py
index a3f38f8..e6f2e3b 100644
--- a/hdrh/codec.py
+++ b/hdrh/codec.py
@@ -35,6 +35,7 @@ from ctypes import c_byte
from ctypes import c_ushort
from ctypes import c_uint
from ctypes import c_ulonglong
+from ctypes import c_double
import zlib
@@ -98,7 +99,7 @@ class Paylo... |
HewlettPackard__oneview-python-63 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "examples/restores.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpOneView/onevi... | HewlettPackard/oneview-python | 2a07ab1ce11a0513e2a1d52605a71665d8dcc618 | MISSING_JSON_TYPE error code is thrown when attempting to restore the appliance
For OneView's X-API-VERSION: **1200** the DTO type for restore is `RESTOREV1000`. I believe this is causing the below error message when attempting to restore a 5.00 OneView appliance with the default X-API-VERSION.
```hpOneView.exceptio... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index cc1d1195..2bf3ad10 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,14 @@
# 5.2.1 (unreleased)
+#### Notes
+Extends support of the SDK to OneView REST API version 800, 1000, 1200 and 1600.
Added code to handle login acknowledgement.
+#### Features supported
+- R... |
HewlettPackard__oneview-python-65 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpOneView/resources/settings/backups.py:Backups.upload"
],
"edited_modules": [
"hpOneView/resources/settings/backups.py:Backups"
]
},
"file": "hpOneView/resources/setti... | HewlettPackard/oneview-python | 5449634aad2edee13ec7b66c4a1df298280b750f | In correct endpoint passed when uploading a downloaded appliance backup
The library uses the URI `/rest/backups` instead of `/rest/backups/archive` resulting in **HPOneViewExection** being raised. This is expected due to an internal error. | diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0c6e05b..cc1d1195 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
Added code to handle login acknowledgement.
#### Bug fixes & Enhancements
+- #21 In correct endpoint passed when uploading a downloaded appliance backup
- #58 loginMsgAck is not handled in... |
HewlettPackard__oneview-python-68 | [
{
"changes": {
"added_entities": [
"hpOneView/oneview_client.py:OneViewClient.__validate_host"
],
"added_modules": null,
"edited_entities": [
"hpOneView/oneview_client.py:OneViewClient.__init__",
"hpOneView/oneview_client.py:OneViewClient.create_image_streamer_cli... | HewlettPackard/oneview-python | bbf361692bb8e09a2d0d63635f79c55e5e0affeb | raise exception with proper error message when ip is not provided in config
Currently, while running i3s examples without providing i3s ip in config, oneview_client doesn't raise any exception and throws improper error messages which becomes quite difficult for user to understand the root cause of error.
Expected re... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2bf3ad10..2581312f 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ Added code to handle login acknowledgement.
- #23 MISSING_JSON_TYPE error code is thrown when attempting to restore the appliance
- #58 loginMsgAck is not handled in python code
- #60 SPT ... |
HewlettPackard__python-hpOneView-310 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"hpOneView/connection.py:connection.login"
],
"edited_modules": [
"hpOneView/connection.py:connection"
]
},
"file": "hpOneView/connection.py"
},
{
"changes": {
... | HewlettPackard/python-hpOneView | 294a2d9f6510d39865b9bc638a2f08459a7374e2 | HPOneViewException not raised when connection with paused VM fails
Hi guys,
When I try to create the OneView client but my VM is paused, an **OSError** exception is raised instead of a HPOneViewException. The HPOneViewException should not cover this type of exception in this scenario? For treat this exception is on... | diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1c4a8175..04f9040a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,8 +1,11 @@
-# v4.1.0 (Unreleased)
+# v4.1.0
#### New Resources:
- Appliance node information
+#### Bug fixes & Enhancements
+- [#309](https://github.com/HewlettPackard/python-hpOneView/issues/30... |
Hrabal__TemPy-30 | [
{
"changes": {
"added_entities": [
"tempy/tempy.py:DOMElement.wrap_many"
],
"added_modules": null,
"edited_entities": [
"tempy/tempy.py:DOMElement.__imul__",
"tempy/tempy.py:DOMElement._insert"
],
"edited_modules": [
"tempy/tempy.py:DOMElement"... | Hrabal/TemPy | 7995be8f846c0aa8338fa0f3bc01aa3e3a21a6b8 | TODO: Wrapping into multiple containers
`DOMElement.wrap` now accepts a single `DOMElement` instance and wraps `self` into this other instance.
Method signature should change to accept a iterable as first argument or multiple (single or iterable) arguments. `self` (copies of) will be wrapped inside each given elemen... | diff --git a/tempy/tempy.py b/tempy/tempy.py
index 3385be4..83ec459 100755
--- a/tempy/tempy.py
+++ b/tempy/tempy.py
@@ -2,19 +2,20 @@
# @author: Federico Cerchiari <federicocerchiari@gmail.com>
"""Main Tempy classes"""
import html
+from collections import deque, Iterable
from copy import copy
-from uuid import uui... |
HumanCompatibleAI__overcooked_ai-104 | [
{
"changes": {
"added_entities": [
"src/overcooked_ai_py/mdp/overcooked_env.py:Overcooked.__init__"
],
"added_modules": null,
"edited_entities": [
"src/overcooked_ai_py/mdp/overcooked_env.py:Overcooked.custom_init",
"src/overcooked_ai_py/mdp/overcooked_env.py:Over... | HumanCompatibleAI/overcooked_ai | 0571eb0172ac983428faedfcb6a2b5206074db0d | Compliance with standard gym API
Hi, it seems that the current repo does not fully comply with the standard gym API? E.g., if I create an env using `gym.make('Overcooked-v0')`, its action space will be None. Am I doing something wrong here? | diff --git a/src/overcooked_ai_py/mdp/overcooked_env.py b/src/overcooked_ai_py/mdp/overcooked_env.py
index b803db4..294192a 100644
--- a/src/overcooked_ai_py/mdp/overcooked_env.py
+++ b/src/overcooked_ai_py/mdp/overcooked_env.py
@@ -686,12 +686,19 @@ class Overcooked(gym.Env):
env_name = "Overcooked-v0"
- d... |
IAMconsortium__nomenclature-279 | [
{
"changes": {
"added_entities": [
"nomenclature/processor/region.py:RegionAggregationMapping.reverse_rename_mapping",
"nomenclature/processor/region.py:RegionProcessor.revert"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nomenclat... | IAMconsortium/nomenclature | 638fe79939c20b9fe3b0f1665eccd629062a3d7e | Implement processor to "undo" region processing
It can be useful/required to "undo" or reverse the renaming done as part of the region-processing, so taking the model-native-in-ensemble-region-names and rename to model-native-as-used-originally-region-names.
My hunch is that this would be better implemented as a new... | diff --git a/nomenclature/processor/region.py b/nomenclature/processor/region.py
index 918e6d7..3c6e1b6 100644
--- a/nomenclature/processor/region.py
+++ b/nomenclature/processor/region.py
@@ -292,6 +292,10 @@ class RegionAggregationMapping(BaseModel):
def rename_mapping(self) -> Dict[str, str]:
return {r... |
IAMconsortium__nomenclature-284 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/processor/region.py:RegionProcessor.apply"
],
"edited_modules": [
"nomenclature/processor/region.py:RegionProcessor"
]
},
"file": "nomenclature/processor/r... | IAMconsortium/nomenclature | c2769559263617c6b0a066e958ca1f1627080b55 | Invalid regions do not raise an error as part of RegionProcessor
The method `RegionProcessor.apply()` does not raise an error when the IamDataFrame includes (or aggregates to) a region that is not listed in the region definitions.
This is because the `validate_items()` method only returns the invalid items but does ... | diff --git a/nomenclature/processor/region.py b/nomenclature/processor/region.py
index 3c6e1b6..2da9d07 100644
--- a/nomenclature/processor/region.py
+++ b/nomenclature/processor/region.py
@@ -26,6 +26,7 @@ from nomenclature.error.region import (
)
from nomenclature.processor import Processor
from nomenclature.proce... |
IAMconsortium__nomenclature-314 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/codelist.py:CodeList.from_directory",
"nomenclature/codelist.py:RegionCodeList.from_directory"
],
"edited_modules": [
"nomenclature/codelist.py:CodeList",
... | IAMconsortium/nomenclature | 87311de5a6bcab2d0f64c6682c5b4c8c4e039634 | Raise all duplicate-errors during initialization
Currently, only a unique duplicate-code error is raised during initialization (e.g., from `validate-project`). It would be great to collect all duplicates and raise one pydantic-error-collection. | diff --git a/nomenclature/codelist.py b/nomenclature/codelist.py
index 7cb3994..9c8e158 100644
--- a/nomenclature/codelist.py
+++ b/nomenclature/codelist.py
@@ -13,7 +13,7 @@ from pydantic_core import PydanticCustomError
import nomenclature
from nomenclature.code import Code, MetaCode, RegionCode, VariableCode
from ... |
IAMconsortium__nomenclature-324 | [
{
"changes": {
"added_entities": [
"nomenclature/config.py:Repository.check_external_repo_double_stacking"
],
"added_modules": null,
"edited_entities": [
"nomenclature/config.py:Repository.fetch_repo"
],
"edited_modules": [
"nomenclature/config.py:Repo... | IAMconsortium/nomenclature | 8f39de170ffe6f3ef00a6962e87c632df2ce99a4 | Double stacking external repos does not work as expected
I just ran into this potential issue when trying to create a DataStructure definition based of off legacy definitions.
What I did is:
1. Create a new (local) repository with an empty definitions folder and a `nomenclature.yaml` file with the following entry:
`... | diff --git a/nomenclature/config.py b/nomenclature/config.py
index 0bfb112..c037274 100644
--- a/nomenclature/config.py
+++ b/nomenclature/config.py
@@ -82,6 +82,20 @@ class Repository(BaseModel):
repo.git.clean("-xdf")
if self.revision == "main":
repo.remotes.origin.pull()
+ self.... |
IAMconsortium__nomenclature-384 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/processor/required_data.py:RequiredDataValidator.apply",
"nomenclature/processor/required_data.py:RequiredDataValidator.check_required_data_per_model"
],
"edited_modules... | IAMconsortium/nomenclature | 6a6e7deb76877c2086f74b660a54126771a7dea0 | Improve required data output
Currently the output of the `RequiredDataValidator` in the case of missing variables is not useful in understanding what exactly is missing. For example:
```console
2023-06-29 13:49:37 ERROR Required data [{'region': ['ABW', 'AFG', 'AGO', 'ALB', 'ARE', 'ARG', 'ARM', 'ASM', 'ATG', 'AU... | diff --git a/nomenclature/processor/required_data.py b/nomenclature/processor/required_data.py
index 3d229e8..65643bd 100644
--- a/nomenclature/processor/required_data.py
+++ b/nomenclature/processor/required_data.py
@@ -178,7 +178,13 @@ class RequiredDataValidator(Processor):
for model, data_list in missi... |
IAMconsortium__nomenclature-390 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/code.py:RegionCode.check_iso3_codes"
],
"edited_modules": [
"nomenclature/code.py:RegionCode"
]
},
"file": "nomenclature/code.py"
}
] | IAMconsortium/nomenclature | 367e10cf9656ba4ac630f25aaac5c95acc9c8a5e | ErrorCollection for countries-validation
The validation of countries-elements in the RegionCode class raises a ValueError directly. It would be better to use the error-collection utility (rather than only raising the first problem in a region-yaml-file.
To be specific: this error https://github.com/IAMconsortium/nom... | diff --git a/nomenclature/code.py b/nomenclature/code.py
index 097b644..0d7e536 100644
--- a/nomenclature/code.py
+++ b/nomenclature/code.py
@@ -12,6 +12,8 @@ from pydantic import (
ValidationInfo,
)
+from nomenclature.error import ErrorCollector
+
from pyam.utils import to_list
from .countries import count... |
IAMconsortium__nomenclature-391 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/code.py:RegionCode.check_iso3_codes"
],
"edited_modules": [
"nomenclature/code.py:RegionCode"
]
},
"file": "nomenclature/code.py"
},
{
"changes": {... | IAMconsortium/nomenclature | 367e10cf9656ba4ac630f25aaac5c95acc9c8a5e | Better formatting for error messages
Some error messages are currently somewhat hard to read, example:
```console
pydantic.error_wrappers.ValidationError: 1 validation error for RegionProcessor
mappings -> ['REMIND 3.0']
Region(s) ['REMIND 3.0|Canada, NZ, Australia', 'REMIND 3.0|China', 'REMIND 3.0|EU 28', 'REM... | diff --git a/nomenclature/code.py b/nomenclature/code.py
index 097b644..0d7e536 100644
--- a/nomenclature/code.py
+++ b/nomenclature/code.py
@@ -12,6 +12,8 @@ from pydantic import (
ValidationInfo,
)
+from nomenclature.error import ErrorCollector
+
from pyam.utils import to_list
from .countries import count... |
IAMconsortium__nomenclature-392 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/code.py:RegionCode.check_iso3_codes"
],
"edited_modules": [
"nomenclature/code.py:RegionCode"
]
},
"file": "nomenclature/code.py"
},
{
"changes": {... | IAMconsortium/nomenclature | 367e10cf9656ba4ac630f25aaac5c95acc9c8a5e | Remove the warning of missing model mapping
This causes more harm than good, should be removed. | diff --git a/nomenclature/code.py b/nomenclature/code.py
index 097b644..0d7e536 100644
--- a/nomenclature/code.py
+++ b/nomenclature/code.py
@@ -12,6 +12,8 @@ from pydantic import (
ValidationInfo,
)
+from nomenclature.error import ErrorCollector
+
from pyam.utils import to_list
from .countries import count... |
IAMconsortium__nomenclature-419 | [
{
"changes": {
"added_entities": [
"nomenclature/cli.py:cli_validate_scenarios"
],
"added_modules": [
"nomenclature/cli.py:cli_validate_scenarios"
],
"edited_entities": null,
"edited_modules": null
},
"file": "nomenclature/cli.py"
}
] | IAMconsortium/nomenclature | 7913ff11b22dc6af9a7fbff4d79f66e62d854378 | CLI to validate a scenario data file
To make it easier for non-expert users to check their data against a DataStructureDefinition, we need a simple CLI that takes an input file (IAMC scenario data) and validates it against a the definitions.
Basically, this should be a reduced version of `cli_run_workflow`, but only... | diff --git a/nomenclature/cli.py b/nomenclature/cli.py
index 33cdafc..18ef895 100644
--- a/nomenclature/cli.py
+++ b/nomenclature/cli.py
@@ -277,3 +277,29 @@ def cli_run_workflow(
df = getattr(workflow, workflow_function)(IamDataFrame(input_file))
if output_file is not None:
df.to_excel(output_file)
... |
IAMconsortium__nomenclature-420 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/code.py:Code.replace_tag"
],
"edited_modules": [
"nomenclature/code.py:Code",
"nomenclature/code.py:VariableCode"
]
},
"file": "nomenclature/code.p... | IAMconsortium/nomenclature | cf930aa4fc3782f53bfa7a1c20d3f045d810cd56 | Make "tier" a known attribute as integer
We often use `tier` as a variable-attribute to indicate importance of a variable - tier 1 is mandatory to be reported in a scenario-comparison project, tier 2 and 3 are optional.
This could be added as a standard attribute (as integer) to the VariableCode, but with a tag-list... | diff --git a/nomenclature/code.py b/nomenclature/code.py
index 47762ce..f983edc 100644
--- a/nomenclature/code.py
+++ b/nomenclature/code.py
@@ -125,12 +125,26 @@ class Code(BaseModel):
def _replace_or_recurse(_attr, _value):
# if the attribute is a string and contains "{tag}" replace
... |
IAMconsortium__nomenclature-431 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/codelist.py:RegionCodeList.from_directory"
],
"edited_modules": [
"nomenclature/codelist.py:RegionCodeList"
]
},
"file": "nomenclature/codelist.py"
},
... | IAMconsortium/nomenclature | a32eca924fa325db5664725e93b08f8aa77d13a3 | Add warning-feature to DataValidator
As a next step for scenario validation and vetting, we need to extend the **DataValidator** class to enable showing a warning instead of raising an error.
My proposed implementation is the following:
- Add a **warning-level** attribute to a validation-criteria item, which defaul... | diff --git a/docs/user_guide/config.rst b/docs/user_guide/config.rst
index f000d7b..57f3db8 100644
--- a/docs/user_guide/config.rst
+++ b/docs/user_guide/config.rst
@@ -126,12 +126,12 @@ By setting *definitions.region.nuts* (optional) in the configuration file:
nuts:
nuts-1: [ AT, BE, CZ ]
nuts... |
IAMconsortium__nomenclature-442 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/codelist.py:VariableCodeList.validate_units"
],
"edited_modules": [
"nomenclature/codelist.py:VariableCodeList"
]
},
"file": "nomenclature/codelist.py"
}... | IAMconsortium/nomenclature | 4e059f8350b51ac3593c8083feafee2b0223b763 | One of multiple allowed units not passing validation
As just reported by @EmiFej, nomenclature scenario-validation currently fails if multiple units are allowed.
Error message:
```
- 'Primary Energy|Coal' - expected: one of '['EJ/yr', 'GWh/yr']', found: 'GWh/yr'
```
FYI @phackstock @dc-almeida
| diff --git a/nomenclature/codelist.py b/nomenclature/codelist.py
index 685bb48..0283487 100644
--- a/nomenclature/codelist.py
+++ b/nomenclature/codelist.py
@@ -622,7 +622,7 @@ class VariableCodeList(CodeList):
(variable, unit, self.mapping[variable].unit)
for variable, unit in unit_mapping.it... |
IAMconsortium__nomenclature-456 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/codelist.py:CodeList.check_illegal_characters"
],
"edited_modules": [
"nomenclature/codelist.py:CodeList"
]
},
"file": "nomenclature/codelist.py"
}
] | IAMconsortium/nomenclature | 4456054624f856f9bad6cf9f501d6389d5f33be6 | Include which illegal character was found in a faulty variable and in which attribute
Currently, we only get the information that an illegal character was found, not which one which makes trouble shooting unnecessarily tedious.
As an example, I get this output for one of our old repositories:
```console
...
162... | diff --git a/nomenclature/codelist.py b/nomenclature/codelist.py
index 0b7f434..af4ff77 100644
--- a/nomenclature/codelist.py
+++ b/nomenclature/codelist.py
@@ -339,28 +339,27 @@ class CodeList(BaseModel):
illegal = ["{", "}"] + config.illegal_characters
errors = ErrorCollector()
- def _check... |
IAMconsortium__nomenclature-459 | [
{
"changes": {
"added_entities": [
"nomenclature/code.py:Code.from_external_repository"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nomenclature/code.py:Code"
]
},
"file": "nomenclature/code.py"
},
{
"changes": {
... | IAMconsortium/nomenclature | c62da7f6bf68628a386f6145f1d8d55a1deed844 | Rename `repository` attribute in `Code` for readability
Not part of this PR, but I'd suggest renaming this attribute to `from_external_repository`. This would make the code easier to read.
_Originally posted by @phackstock in https://github.com/IAMconsortium/nomenclature/pull/456#discussion_r1916221928_
... | diff --git a/docs/user_guide/config.rst b/docs/user_guide/config.rst
index 57f3db8..65ef063 100644
--- a/docs/user_guide/config.rst
+++ b/docs/user_guide/config.rst
@@ -152,3 +152,25 @@ validation:
- region
- variable
- scenario
+
+
+Filter model mappings from external repositories
+---------------------... |
IAMconsortium__nomenclature-460 | [
{
"changes": {
"added_entities": [
"nomenclature/config.py:MappingRepository.regex_include_patterns",
"nomenclature/config.py:MappingRepository.match_models"
],
"added_modules": null,
"edited_entities": null,
"edited_modules": [
"nomenclature/config.py:Mappi... | IAMconsortium/nomenclature | c62da7f6bf68628a386f6145f1d8d55a1deed844 | Allow filtering of model mappings from external repositories
Example:
```yaml
...
mappings:
repository:
name: common-definitions
include:
- MESSAGEix-GLOBIOM-GAINS 2.1-M-R12
``` | diff --git a/docs/user_guide/config.rst b/docs/user_guide/config.rst
index 57f3db8..65ef063 100644
--- a/docs/user_guide/config.rst
+++ b/docs/user_guide/config.rst
@@ -152,3 +152,25 @@ validation:
- region
- variable
- scenario
+
+
+Filter model mappings from external repositories
+---------------------... |
IAMconsortium__nomenclature-463 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/codelist.py:CodeList.check_illegal_characters"
],
"edited_modules": [
"nomenclature/codelist.py:CodeList"
]
},
"file": "nomenclature/codelist.py"
},
{
... | IAMconsortium/nomenclature | 4456054624f856f9bad6cf9f501d6389d5f33be6 | Check native regions belong to the same model in mappings
Following up on [this common-definitions PR](https://github.com/IAMconsortium/common-definitions/pull/247), check if the constituent regions used are the same native regions listed in the mappings file | diff --git a/nomenclature/codelist.py b/nomenclature/codelist.py
index 0b7f434..af4ff77 100644
--- a/nomenclature/codelist.py
+++ b/nomenclature/codelist.py
@@ -339,28 +339,27 @@ class CodeList(BaseModel):
illegal = ["{", "}"] + config.illegal_characters
errors = ErrorCollector()
- def _check... |
IAMconsortium__nomenclature-466 | [
{
"changes": {
"added_entities": [
"nomenclature/processor/region.py:RegionAggregationMapping.serialize_model",
"nomenclature/processor/region.py:RegionAggregationMapping.serialize_native_regions",
"nomenclature/processor/region.py:RegionAggregationMapping.serialize_common_regions"... | IAMconsortium/nomenclature | 941fc73b255347c79ef62afd559ca24b8dcad9c6 | Get rid of None as default where possible
Currently, we have `None` as the default value in a lot of places. This makes for code that is hard to read, write and maintain.
One example is class variables that are lists that can be empty. The default should be an empty list rather than None. This way, worst case, you iter... | diff --git a/nomenclature/processor/region.py b/nomenclature/processor/region.py
index e853e64..c325583 100644
--- a/nomenclature/processor/region.py
+++ b/nomenclature/processor/region.py
@@ -13,10 +13,12 @@ from pydantic import (
AfterValidator,
BaseModel,
ConfigDict,
+ Field,
ValidationInfo,
... |
IAMconsortium__nomenclature-9 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"nomenclature/core.py:Nomenclature.__init__"
],
"edited_modules": [
"nomenclature/core.py:Nomenclature"
]
},
"file": "nomenclature/core.py"
},
{
"changes": {
... | IAMconsortium/nomenclature | 979ce2aeb281396110ab2a08ed734cf075fca8b6 | Relative definition of path in Nomenclature
The relative definition of the `path` variable in the `__init__` of `Nomenclature` `def __init__(self, path="definitions")` can lead to problems when the workflow where it is used is not started from the parent directory of `definitions`.
One possible fix would be to remo... | diff --git a/nomenclature/core.py b/nomenclature/core.py
index 93180ed..cb40464 100644
--- a/nomenclature/core.py
+++ b/nomenclature/core.py
@@ -7,10 +7,13 @@ from nomenclature.validation import validate
class Nomenclature:
"""A nomenclature with codelists for all dimensions used in the IAMC data format"""
- ... |
IAMconsortium__pyam-261 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.filter"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | d5a3a9f46a087e92d28754ba91d9ae48c5db638a | `filter()` assumes non-starred `dict` as `keep` kwarg
# Observed (user) error
Just ran into a stupid error where I used `df.filter(dict(foo='bar')` instead of `df.filter(**dict(foo='bar')`, so rather than applying the expected `foo='bar'` rule, the function interprets the dict as the `keep` kwarg.
# Suggested sol... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 3cf842e..bbd0b84 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,6 +1,7 @@
# Next Release
+- [#261](https://github.com/IAMconsortium/pyam/pull/261) Add a check that `keep` in `filter()` is a boolean
- [#243](https://github.com/IAMconsortium/pyam/pu... |
IAMconsortium__pyam-297 | [
{
"changes": {
"added_entities": [
"pyam/core.py:IamDataFrame.empty"
],
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.timeseries"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
... | IAMconsortium/pyam | 16c0ea5714cbb85bbbfebda895b2a853cd1b7dc4 | `timeseries()` on empty `IamDataFrame` fails very loudly
# Description of the issue
When calling `timeseries()` on an empty `IamDataFrame`, the internally used `pandas.DataFrame.pivot_table()` fails with a long, non-intuitive error message (see below). This might be quite intimidating to non-expert users.
## Impr... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index c868d77..c43a18f 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,6 +1,7 @@
# Next Release
+- [#297](https://github.com/IAMconsortium/pyam/pull/297) Add `empty` attribute, better error for `timeseries()` on empty dataframe
- [#292](https://github.c... |
IAMconsortium__pyam-305 | [
{
"changes": {
"added_entities": [
"pyam/core.py:IamDataFrame._all_other_regions",
"pyam/core.py:_aggregate_weight",
"pyam/core.py:_get_method_func",
"pyam/core.py:_get_value_col"
],
"added_modules": [
"pyam/core.py:_aggregate_weight",
"pyam/core... | IAMconsortium/pyam | 61778d80403102abc8a852c5eb8b903de36f912a | Suggest to change default behaviour of `aggegate_region()` for components
## Introduction
The current implementation of [aggegate_region()](https://pyam-iamc.readthedocs.io/en/stable/api.html#pyam.IamDataFrame.aggregate_region) has an option to add `components` (other variables), which are only defined at the (aggre... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 9e6f437..4cda6f2 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,6 +1,14 @@
-
# Next Release
+## API changes
+
+PR [#305](https://github.com/IAMconsortium/pyam/pull/305) changed the default
+behaviour of `aggregate_region()` regarding the treatment of... |
IAMconsortium__pyam-413 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.downscale_region"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
},
{
"changes": {
"added_entiti... | IAMconsortium/pyam | 911dcd4bbc7a8e8d4a91d3cb8c77ffea389252d2 | Add better documentation and testing of objects returned IIASA-db connection
We need to add better documentation and more unit tests of the objects returned via the Rest API of the IIASA database infrastructure.
See https://github.com/iiasa/ipcc_sr15_scenario_analysis/issues/28 for an issue where this caused problem... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index e4f9a2e..b1a6edf 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -2,6 +2,16 @@
## API changes
+PR [#413](https://github.com/IAMconsortium/pyam/pull/413) changed the
+return type of `pyam.read_iiasa()` and `pyam.iiasa.Connection.query()`
+to an `IamData... |
IAMconsortium__pyam-429 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.validate"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 139d3e6a5695289dd8c92f71e2bc884f18c4fccd | Check output consistency of `.validate` and similar
Came across an issue with the newest version where an output of `.validate()`, which I think was previously a `pd.DataFrame` is now a `pd.Series`.
Not a problem in itself - but scripts that then take this output and perform operations that only work with DataFrame wi... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 6322dee..5ba5190 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -13,6 +13,7 @@ via getter and setter functions.
- [#437](https://github.com/IAMconsortium/pyam/pull/437) Improved test for appending mismatched timeseries
- [#436](https://github.com/IAMco... |
IAMconsortium__pyam-436 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.append"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 448425a819acd8a24d08da8077d65e24e08a5b75 | When appending inconsistent dfs in the new pyam, inplace=True suppresses errors
As the title indicates. the new pyam appears to produce a viable output when appending dfs with different numbers of meta columns. It will discover it is broken at a later point.
Example code:
import pyam
import pandas as pd
_mc = "... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 6044222..a0f58b8 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -11,6 +11,7 @@ via getter and setter functions.
## Individual updates
+- [#436](https://github.com/IAMconsortium/pyam/pull/436) Raise an error with appending mismatching timeseries index ... |
IAMconsortium__pyam-454 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.info"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
},
{
"changes": {
"added_entities": null,
... | IAMconsortium/pyam | faebaeb0c9ecf732b378277eae161300d7f83b65 | Allow undefined units?
Currently, pyam raises an error when initializing from a pandas.DataFrame with `nan` or when reading from xlsx/csv with empty cells in any index/coordinate dimension. This makes sense for model, scenario, variable and region, but there could be timeseries without a natural unit (e.g., population ... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 8226694..8324afc 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -2,6 +2,7 @@
## Individual updates
+- [#454](https://github.com/IAMconsortium/pyam/pull/454) Enable dimensionless units and fix `info()` if IamDataFrame is empty
- [#451](https://github.... |
IAMconsortium__pyam-456 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.interpolate"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 42da618f949611e13dfca1094f2b40239a9a34ea | `interpolate` does not follow other return conventions
We recently had a private communication regarding confusion with the `interpolate` function. The user was trying to do something like:
```
df_interp = df.filter().interpolate()
```
The returned object was *not* an interpolated dataframe. We advised the user... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 83bb415..ea75eca 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -5,6 +5,7 @@
- [#461](https://github.com/IAMconsortium/pyam/pull/461) Add list of authors to repo and docs pages
- [#459](https://github.com/IAMconsortium/pyam/pull/459) Add a `get_variable_... |
IAMconsortium__pyam-481 | [
{
"changes": {
"added_entities": [
"pyam/core.py:IamDataFrame._set_attributes",
"pyam/core.py:IamDataFrame._get_meta_index_levels"
],
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.__init__",
"pyam/core.py:IamDataFrame._init",
... | IAMconsortium/pyam | 9151156ab9064776aa84ada01a0e0c2843601665 | pyam.concat / pyam.append overwrites and not updates year parameter
the concat command has issues:
```
IAMC_IDX = ['model', 'scenario', 'region', 'variable', 'unit']
TEST_YEARS_PROJ = [2005, 2010]
TEST_YEARS_HIST = [2000]
proj = pd.DataFrame([
['model_a', 'scen_a', 'reg', 'PE', 'EJ/yr', 1, 6.],
],
... | diff --git a/.github/workflows/nightly.yml b/.github/workflows/nightly.yml
index 5157f8d..409a335 100644
--- a/.github/workflows/nightly.yml
+++ b/.github/workflows/nightly.yml
@@ -34,6 +34,9 @@ jobs:
with:
python-version: ${{ matrix.python-version }}
+ - name: Install Pandoc
+ uses: r-lib/act... |
IAMconsortium__pyam-488 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.export_meta",
"pyam/core.py:IamDataFrame.load_meta"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}... | IAMconsortium/pyam | c1346b63f13737ae207a77bb737ec56611c71ede | Proposal to read in multiple sheets (from Excel)
Planning to extend `pyam.IamDataFrame()` such that if the excel file has multiple sheets, they are each read in and concatenated.
Proposal would be to either:
- accept sheets if starting with "data", e.g. data1, data2, etc.. (could be automatically?)
- accept a`st... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 39c8af7..e797332 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,14 @@
# Next Release
+## API changes
+
+PR [#488](https://github.com/IAMconsortium/pyam/pull/488) changes the default
+behavior when initializing an IamDataFrame from xlsx: now, all... |
IAMconsortium__pyam-496 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.load_meta"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 76c33a51c57a62745af3cee30ea54ff89ea2e3d7 | Regression: `IamDataFrame.load_meta` with csv filename string broken
PR #491 removed the wrapping of the `path` variable into `pathlib.Path`:
https://github.com/IAMconsortium/pyam/commit/3d31fdd36f9b1ca6088eadbc01d23857b9fab4ae#diff-473e3e462e12aec320a41b983e95a130a194c4700b63a0a5f97f153b899129e7L1737-R1745
Which... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index b5f9472..b57d58a 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -8,6 +8,7 @@ starting with `data` will be parsed for timeseries data.
## Individual updates
+- [#496](https://github.com/IAMconsortium/pyam/pull/496) Enable loading meta from csv file
- ... |
IAMconsortium__pyam-510 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:concat"
],
"edited_modules": [
"pyam/core.py:concat"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | ebceba1078a665d57c3f673cacdde6877dc5c20e | concat uses pandas append instead of concat
The implementation of pyams concat method loops over pandas append instead of using pandas concat method. Especially for large dataframes with subannual data concat is much faster than append.
I already implemented pandas concat in pyams concat and will push it in a minute... | diff --git a/AUTHORS.rst b/AUTHORS.rst
index 106aae8..f49b3df 100644
--- a/AUTHORS.rst
+++ b/AUTHORS.rst
@@ -17,3 +17,4 @@ The following persons contributed to the development of the |pyam| framework:
- Maik Budzinski `@mabudz <https://github.com/mabudz>`_
- Jarmo Kikstra `@jkikstra <https://github.com/jkikstra>`_
-... |
IAMconsortium__pyam-695 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.set_meta",
"pyam/core.py:IamDataFrame.categorize"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | bd3aea4b062232f3f8ba225a346fdb6ef2c16f1b | Reading filtered dataframes from iiasa contain incorrect properties
When reading from the IIASA database, the returned database seems to always have .model, .scenario and .variable properties of the unfiltered database, even when we request only a subset of data.
`new_read = read_iiasa(
"iamc15", scenario=... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index a16b12d..1f98daf 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -2,6 +2,7 @@
## Individual updates
+- [#695](https://github.com/IAMconsortium/pyam/pull/695) Remove unused meta levels during initialization
- [#688](https://github.com/IAMconsortium/pya... |
IAMconsortium__pyam-697 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/iiasa.py:Connection.index",
"pyam/iiasa.py:Connection._query_index",
"pyam/iiasa.py:Connection.meta_columns",
"pyam/iiasa.py:Connection.meta",
"pyam/iiasa.py:Connect... | IAMconsortium/pyam | 7f00c7951f5aae42238461506572163adb0697e2 | Unexpected failures with incorrect permissions in the IIASA database system
When a user has access to a Scenario Explorer database instance but no permission to view any models (or no scenarios exist), querying data from the API fails with an error similar to
```
if nmissing == len(indexer):
if use_interva... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 1f98daf..757e2f8 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -2,6 +2,7 @@
## Individual updates
+- [#697](https://github.com/IAMconsortium/pyam/pull/697) Add warning if IIASA API returns empty result
- [#695](https://github.com/IAMconsortium/pyam/... |
IAMconsortium__pyam-739 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/figures.py:sankey"
],
"edited_modules": [
"pyam/figures.py:sankey"
]
},
"file": "pyam/figures.py"
},
{
"changes": {
"added_entities": null,
"ad... | IAMconsortium/pyam | a87e64e302c97ff71d1e284de5a64c51bb580cfc | Pandas 2.0 breaks some tests
As I was updating https://github.com/IAMconsortium/nomenclature to be pandas 2.0 compatible I checked if pandas 2.0 would break anything in pyam.
Turns out it does:
```console
================================================================ short test summary info ======================... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 0687aa4..75f077e 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,7 @@
# Next Release
+- [#738](https://github.com/IAMconsortium/pyam/pull/738) Ensure compatibility with **pandas v2.0**
+
# Release v1.8.0
## Highlights
diff --git a/docs/tutori... |
IAMconsortium__pyam-763 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/utils.py:format_data"
],
"edited_modules": [
"pyam/utils.py:format_data"
]
},
"file": "pyam/utils.py"
}
] | IAMconsortium/pyam | 4bfcec0ae0ae9815e67b283e88acf004e989cac2 | Helpful accessors confounded by pandas regression
The test below fails and I can't see why. This is the underlying cause of https://github.com/iiasa/climate-assessment/pull/36 I think.
In short: if you subset an `IamDataFrame` and then create new instances within some loop (probably a bad pattern, but let's ignore t... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 171057e..b5df329 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -14,6 +14,7 @@ When importing an xlsx file created with pyam < 2.0, which has an "exclude" colu
## Individual updates
+- [#763](https://github.com/IAMconsortium/pyam/pull/763) Implement a... |
IAMconsortium__pyam-772 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.require_data"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 9c947a8bb391f3939ac1e9f39f12adf44165eef4 | Support logical-and in `require_data()`
# Background
The method `reuqire_data()` applies a logical-or for each dimension, so a scenario is ok if any variable/region from a given list is present.
We should add a keyword argument "method" or "logical" that allow a user to select whether any or all elements should b... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index 6f7b2a2..768374a 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -19,6 +19,7 @@ instead of `pyam.to_list()`.
## Individual updates
+- [#772](https://github.com/IAMconsortium/pyam/pull/772) Show all missing rows for `require_data()`
- [#771](https://gi... |
IAMconsortium__pyam-792 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/aggregation.py:_aggregate_region",
"pyam/aggregation.py:_agg_weight"
],
"edited_modules": [
"pyam/aggregation.py:_aggregate_region",
"pyam/aggregation.py:_agg_we... | IAMconsortium/pyam | f023ec3444e0653408dbf95616b31fff745a2ca0 | df.aggregate_region() when inconsistent index (e.g. years)
There are instances when doing weighted aggregation of regions, when years between the variable and the weight variable may not be aligned or one variable has more years than the other. One gets error message:
```
File "c:\github\pyam\pyam\aggregation.py"... | diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
index e7d85bc..d373650 100644
--- a/RELEASE_NOTES.md
+++ b/RELEASE_NOTES.md
@@ -1,5 +1,7 @@
# Release v2.0.0
+- [#792](https://github.com/IAMconsortium/pyam/pull/792) Support region-aggregation with weights-index >> data-index
+
## Highlights
- Use **ixmp4** as de... |
IAMconsortium__pyam-816 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyam/core.py:IamDataFrame.rename"
],
"edited_modules": [
"pyam/core.py:IamDataFrame"
]
},
"file": "pyam/core.py"
}
] | IAMconsortium/pyam | 98cb3ed00132809e48dd7f7302eea070336690cd | Rename does not reorder
Currently running `IamDataFrame.rename()` does not reorder. | diff --git a/pyam/core.py b/pyam/core.py
index 7c61e41..b4f6096 100755
--- a/pyam/core.py
+++ b/pyam/core.py
@@ -1192,6 +1192,11 @@ class IamDataFrame(object):
if has_duplicates:
ret._data = ret._data.reset_index().groupby(ret.dimensions).sum().value
+ # quickfix for issue 811, to be remo... |
ICB-DCM__pyABC-121 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pyabc/visualization/__init__.py"
},
{
"changes": {
"added_entities": [
"pyabc/visualization/confidence.py:plot_credible_intervals",
... | ICB-DCM/pyABC | 23fd53b9f459ff807be474c15a8b829148a33f28 | Confidence intervals -> credible intervals
In visualization: Called it confidence intervals now, but in a Bayesian context should better call it credible intervals. | diff --git a/doc/examples/parameter_inference.ipynb b/doc/examples/parameter_inference.ipynb
index 72289d0..a038813 100644
--- a/doc/examples/parameter_inference.ipynb
+++ b/doc/examples/parameter_inference.ipynb
@@ -182,13 +182,13 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "INFO:H... |
ICB-DCM__pyABC-248 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules": null
},
"file": "pyabc/__init__.py"
},
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": null,
"edited_modules":... | ICB-DCM/pyABC | ee782cffb87a91223bec9fc7fdb78c580e7be358 | Implement ListTemperature
To allow a list of temperatures, similar to ListEpsilon. | diff --git a/pyabc/__init__.py b/pyabc/__init__.py
index 66155b8..688e949 100644
--- a/pyabc/__init__.py
+++ b/pyabc/__init__.py
@@ -46,6 +46,8 @@ from .epsilon import (
QuantileEpsilon,
MedianEpsilon,
ListEpsilon,
+ TemperatureBase,
+ ListTemperature,
Temperature,
TemperatureScheme,
... |
ICB-DCM__pyABC-279 | [
{
"changes": {
"added_entities": null,
"added_modules": null,
"edited_entities": [
"pyabc/distance/distance.py:AdaptivePNormDistance.__init__",
"pyabc/distance/distance.py:AdaptivePNormDistance.initialize",
"pyabc/distance/distance.py:AdaptiveAggregatedDistance.__init__... | ICB-DCM/pyABC | e3d4f3c73286fa44b092782d56cf517470fac33a | Allow for initial weights in AdaptiveAggregatedDistance
Use case is, if one has a reasonable set of first weights but would want to have them changed adaptively over the following populations.
Initializing with weights will also skip the prepopulation. | diff --git a/pyabc/distance/distance.py b/pyabc/distance/distance.py
index b9cb65f..245de38 100644
--- a/pyabc/distance/distance.py
+++ b/pyabc/distance/distance.py
@@ -143,6 +143,9 @@ class AdaptivePNormDistance(PNormDistance):
p: float, optional (default = 2)
p for p-norm. Required p >= 1, p = np.inf ... |
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