Split (1)

train · 6.38k rows

instance_id stringlengths 10 57	patch stringlengths 261 37.7k	repo stringlengths 7 53	base_commit stringlengths 40 40	test_patch stringlengths 212 2.22M	problem_statement stringlengths 23 37.7k	environment_setup_commit stringlengths 40 40	FAIL_TO_PASS listlengths 1 4.94k	PASS_TO_PASS listlengths 0 7.82k	meta dict	created_at stringlengths 25 25	license stringclasses 8 values	__index_level_0__ int64 0 6.41k
Backblaze__b2-sdk-python-120	diff --git a/.travis.yml b/.travis.yml index 3e06cfe7..806c817e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,9 +37,9 @@ matrix: # Enable nightly without globally enabling sudo and xenial for other build jobs # disabled because nosetests is not supported on 3.9. We'll move to pytest. # disabled by co...	Backblaze/b2-sdk-python	6d35959ccfb06c3888702d91f3ce8d699f24f8e0	diff --git a/test/v0/test_exception.py b/test/v0/test_exception.py index 5bcb7fca..a90e5329 100644 --- a/test/v0/test_exception.py +++ b/test/v0/test_exception.py @@ -50,7 +50,7 @@ class TestExceptions(TestBase): try: raise BadUploadUrl('foo') except BadUploadUrl as e: - assert...	No public API for getting a list of file ids for a filename In order to delete a file you need to know the file id of the version to delete but unless I'm missing something there is no straightforward way to list the different versions of a file with a given filename. `bucket.ls` exists but since it enforces a trailing...	6d35959ccfb06c3888702d91f3ce8d699f24f8e0	[ "test/v1/test_exception.py::TestExceptions::test_command_error", "test/v1/test_exception.py::TestExceptions::test_bad_upload_url_exception", "test/v1/test_exception.py::TestExceptions::test_already_failed_exception", "test/v1/test_exception.py::TestInterpretError::test_unauthorized", "test/v1/test_exception...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-04-26 15:55:54+00:00	mit	100
Backblaze__b2-sdk-python-121	diff --git a/b2sdk/v1/exception.py b/b2sdk/v1/exception.py index cf149a68..7815a28f 100644 --- a/b2sdk/v1/exception.py +++ b/b2sdk/v1/exception.py @@ -18,6 +18,7 @@ from b2sdk.exception import B2HttpCallbackException from b2sdk.exception import B2HttpCallbackPostRequestException from b2sdk.exception import B2HttpCall...	Backblaze/b2-sdk-python	d1098c1d9d717a793872910edb314f0a26fa1f5d	diff --git a/test/v1/test_bucket.py b/test/v1/test_bucket.py index ec085c86..87c98d0f 100644 --- a/test/v1/test_bucket.py +++ b/test/v1/test_bucket.py @@ -21,6 +21,7 @@ from .test_base import TestBase from .deps_exception import ( AlreadyFailed, B2Error, + B2RequestTimeoutDuringUpload, InvalidAuthTok...	400 bad_request more than one upload using auth token I have a loop uploading files locally to B2 cloud. After a few thousand uploads over a few hours, I get this error: `b2sdk.exception.UnknownError: Unknown error: 400 bad_request more than one upload using auth token 4_0021a87abca5e6b0000000005_018fe4f8_97f3ec_uplg_...	d1098c1d9d717a793872910edb314f0a26fa1f5d	[ "test/v1/test_bucket.py::TestUpload::test_upload_bytes", "test/v1/test_bucket.py::TestUpload::test_upload_bytes_progress", "test/v1/test_bucket.py::TestUpload::test_upload_large", "test/v1/test_bucket.py::TestUpload::test_upload_file_one_fatal_error", "test/v1/test_bucket.py::TestUpload::test_upload_large_f...	[]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-04-30 12:17:14+00:00	mit	101
Backblaze__b2-sdk-python-163	diff --git a/.readthedocs.yml b/.readthedocs.yml index b4278123..7a1f282a 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -14,7 +14,7 @@ formats: all # Optionally set the version of Python and requirements required to build your docs python: - version: 3.9 + version: 3.8 install: - requirements: r...	Backblaze/b2-sdk-python	c510c73820774958ba1cc11153bc1fe7668d675e	diff --git a/test/unit/v0/test_raw_api.py b/test/unit/v0/test_raw_api.py index 222fae4d..b1a8e03b 100644 --- a/test/unit/v0/test_raw_api.py +++ b/test/unit/v0/test_raw_api.py @@ -7,6 +7,7 @@ # License https://www.backblaze.com/using_b2_code.html # #####################################################################...	should bucket.update() let me set my bucket_info to {}? Hi -- I'd like to set the bucket info on my bucket to not have any entries. To do that, I tried calling bucket.set_info() and got an assert. Here's a simple failing case: > b2_api = B2Api(InMemoryAccountInfo()) > b2_api.authorize_account(url, app_key_id...	c510c73820774958ba1cc11153bc1fe7668d675e	[ "test/unit/v0/test_raw_api.py::TestUpdateBucket::test_assertion_not_raises[None-bucket_info0]", "test/unit/v1/test_raw_api.py::TestUpdateBucket::test_assertion_not_raises[None-bucket_info0]" ]	[ "test/unit/v0/test_raw_api.py::TestRawAPIFilenames::test_b2_filename_checker", "test/unit/v0/test_raw_api.py::TestUpdateBucket::test_assertion_raises", "test/unit/v0/test_raw_api.py::TestUpdateBucket::test_assertion_not_raises[allPublic-None]", "test/unit/v1/test_raw_api.py::TestRawAPIFilenames::test_b2_filen...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-10-07 13:52:08+00:00	mit	102
Backblaze__b2-sdk-python-305	diff --git a/CHANGELOG.md b/CHANGELOG.md index e75521aa..6c6565f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Add pypy-3.8 to test matrix * Add support for unverified checksum upload mode * Add dedicated exception f...	Backblaze/b2-sdk-python	900df6b6921692cc8bc812c5d199b5989bdefcef	diff --git a/test/unit/sync/fixtures.py b/test/unit/sync/fixtures.py index 3ff871f0..a4861804 100644 --- a/test/unit/sync/fixtures.py +++ b/test/unit/sync/fixtures.py @@ -15,7 +15,7 @@ import pytest import apiver_deps from apiver_deps import AbstractFolder, B2Folder, LocalFolder, B2SyncPath, LocalSyncPath from apive...	Custom sync policy? Is there a way to create a custom sync policy? I want to keep some files in the bucket unchanged even though the local counterpart has these files with a newer timestamp. I've tried with exclude regexes but that will treat the excluded files as missing and deletes them in the bucket.	900df6b6921692cc8bc812c5d199b5989bdefcef	[ "test/unit/sync/test_sync.py::TestSynchronizer::test_illegal_args_up_v1_and_up[newer_file_mode]", "test/unit/sync/test_sync.py::TestSynchronizer::test_illegal_args_up_v1_and_up[keep_days_or_delete]", "test/unit/sync/test_sync.py::TestSynchronizer::test_illegal", "test/unit/sync/test_sync.py::TestSynchronizer:...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-03-03 22:21:19+00:00	mit	103
Backblaze__b2-sdk-python-433	diff --git a/CHANGELOG.md b/CHANGELOG.md index 03028df2..6b3a6531 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +### Fixed +* Fix ScanPoliciesManager support for compiled regexes + ### Infrastructure *...	Backblaze/b2-sdk-python	f04cca5b9cf0a95ea9d292325bf2ed0f1ec97b7a	diff --git a/test/unit/scan/test_scan_policies.py b/test/unit/scan/test_scan_policies.py index fe79c9a4..2c6cd2fc 100644 --- a/test/unit/scan/test_scan_policies.py +++ b/test/unit/scan/test_scan_policies.py @@ -70,3 +70,15 @@ class TestScanPoliciesManager: } with pytest.raises(exception): ...	passing compiled regex results in AttributeError I am using b2sdk-1.24.0. `b2sdk.v2.ScalPoliciesManager` accepts `Iterable[str \| re.Pattern]` for `exclude_dir_regexes`. However, if `exclude_dir_regexes` contains an `re.Pattern` instance, an Attribute error results at `b2sdk/scan/policies.py:70` because `re.Pattern h...	f04cca5b9cf0a95ea9d292325bf2ed0f1ec97b7a	[ "test/unit/scan/test_scan_policies.py::TestScanPoliciesManager::test_re_pattern_argument_support" ]	[ "test/unit/scan/test_scan_policies.py::TestScanPoliciesManager::test_include_file_regexes_without_exclude", "test/unit/scan/test_scan_policies.py::TestScanPoliciesManager::test_illegal_regex[exclude_dir_regexes-InvalidArgument]", "test/unit/scan/test_scan_policies.py::TestScanPoliciesManager::test_illegal_regex...	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2023-11-09 16:31:22+00:00	mit	104
BelgianBiodiversityPlatform__python-dwca-reader-101	diff --git a/dwca/files.py b/dwca/files.py index a1bcd9a..bada8fa 100644 --- a/dwca/files.py +++ b/dwca/files.py @@ -6,7 +6,7 @@ from array import array from typing import List, Union, IO, Dict, Optional from dwca.descriptors import DataFileDescriptor -from dwca.rows import CoreRow, ExtensionRow +from dwca.rows imp...	BelgianBiodiversityPlatform/python-dwca-reader	b5b2bea333527353c5fe05b22e01c347a890ac61	diff --git a/dwca/test/test_datafile.py b/dwca/test/test_datafile.py index d5d7841..3fc461b 100644 --- a/dwca/test/test_datafile.py +++ b/dwca/test/test_datafile.py @@ -31,9 +31,13 @@ class TestCSVDataFile(unittest.TestCase): with DwCAReader(sample_data_path("dwca-2extensions.zip")) as dwca: exten...	Extend CSVDataFile to support hash index on Core file ### Description It would be useful to be able to generalize iterators over the type of record. AFAIK, there's nothing particularly special about the Core Record data-format-wise, so it should be possible to create iterator methods that apply arbitrarily to Core ...	b5b2bea333527353c5fe05b22e01c347a890ac61	[ "dwca/test/test_datafile.py::TestCSVDataFile::test_close", "dwca/test/test_datafile.py::TestCSVDataFile::test_coreid_index", "dwca/test/test_datafile.py::TestCSVDataFile::test_file_descriptor_attribute", "dwca/test/test_datafile.py::TestCSVDataFile::test_get_line_at_position_raises_indexerror", "dwca/test/t...	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_added_files" ], "has_test_patch": true, "is_lite": false }	2023-11-08 16:12:20+00:00	bsd-3-clause	105
Benardi__touvlo-47	diff --git a/README.md b/README.md index 5c8227a..75e7723 100644 --- a/README.md +++ b/README.md @@ -6,8 +6,8 @@ <p align="center"> - <a href="https://travis-ci.org/Benardi/touvlo"> - <img src="https://api.travis-ci.org/Benardi/touvlo.svg?branch=master" + <a href="https://travis-ci.com/Benardi/touvlo"...	Benardi/touvlo	8eb6beaaf880527239a5a11524b10945e41175f8	diff --git a/tests/supv/test_lin_rg.py b/tests/supv/test_lin_rg.py index 001047e..4f452b3 100644 --- a/tests/supv/test_lin_rg.py +++ b/tests/supv/test_lin_rg.py @@ -3,9 +3,11 @@ import os import pytest from numpy.testing import assert_allclose from numpy import ones, zeros, float64, array, append, genfromtxt +from n...	Add classes for existing Linear Regression implementations #### Description Add classes to encapsulate existing Ridge and Unregularized Linear Regression implementations. #### Files * `touvlo/supv/lin_rg.py` - Existing linear regression module * `tests/supv/test_lin_rg.py` - Test suite for linear regression modul...	8eb6beaaf880527239a5a11524b10945e41175f8	[ "tests/supv/test_lin_rg.py::TestLinearRegression::test_normal_eqn_data1", "tests/supv/test_lin_rg.py::TestLinearRegression::test_normal_eqn_data2", "tests/supv/test_lin_rg.py::TestLinearRegression::test_reg_normal_eqn_data1_1", "tests/supv/test_lin_rg.py::TestLinearRegression::test_reg_normal_eqn_data1_2", ...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-10-26 20:41:20+00:00	mit	106
BlueBrain__NeuroM-1001	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index de024a1..4d0b572 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -3,6 +3,15 @@ Changelog Version 3.2.0 ------------- + +- Fix ``neurom.features.bifurcation.partition_asymmetry`` Uylings variant to not throw + for bifurcations with leaves. +- Fix ``neurom.features....	BlueBrain/NeuroM	127d6fd45167b3cf2ae6d41c51ad241846d082dc	diff --git a/tests/features/test_bifurcation.py b/tests/features/test_bifurcation.py index 530a4c4..f2eea4c 100644 --- a/tests/features/test_bifurcation.py +++ b/tests/features/test_bifurcation.py @@ -80,8 +80,7 @@ def test_partition_asymmetry(): assert bf.partition_asymmetry(root) == 0.5 assert bf.partition_...	Is `partition_asymmetry` with `Uylings` variant usable? I find peculiar the implementation of the Uylings variant of for the partition asymmetry: https://github.com/BlueBrain/NeuroM/blob/127d6fd45167b3cf2ae6d41c51ad241846d082dc/neurom/features/bifurcation.py#L102-L124 because all bifurcation points the childr...	127d6fd45167b3cf2ae6d41c51ad241846d082dc	[ "tests/features/test_bifurcation.py::test_partition_asymmetry" ]	[ "tests/features/test_bifurcation.py::test_local_bifurcation_angle", "tests/features/test_bifurcation.py::test_remote_bifurcation_angle", "tests/features/test_bifurcation.py::test_bifurcation_partition", "tests/features/test_bifurcation.py::test_sibling_ratio", "tests/features/test_bifurcation.py::test_diame...	{ "failed_lite_validators": [ "has_many_modified_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-03-10 15:36:02+00:00	bsd-3-clause	107
BlueBrain__NeuroM-1002	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 4d0b572..21e19fe 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,7 @@ Changelog Version 3.2.0 ------------- +- Fix warning system so that it doesn't change the pre-existing warnings configuration - Fix ``neurom.features.bifurcation.partition_asymmetry`` Uy...	BlueBrain/NeuroM	f57feb2f40c287f644b53da671f7b63cf7a8aef9	diff --git a/tests/test_utils.py b/tests/test_utils.py index f01a172..a8dd018 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -29,11 +29,20 @@ """Test neurom.utils.""" import json import warnings +from copy import deepcopy import numpy as np from neurom import utils as nu import pytest +from neu...	Inappropriate `warnings.simplefilter` in `neurom.utils.warn_deprecated` `warnings.simplefilter` is used to enforce that a deprecation warning is shown: https://github.com/BlueBrain/NeuroM/blob/c570a2faa18f4e417fcdb743f6487beee0c60c3e/neurom/utils.py#L40-L44 This is problematic for several reasons * It's not the bu...	f57feb2f40c287f644b53da671f7b63cf7a8aef9	[ "tests/test_utils.py::test_warn_deprecated", "tests/test_utils.py::test_NeuromJSON", "tests/test_utils.py::test_ordered_enum" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-03-11 10:23:29+00:00	bsd-3-clause	108
BlueBrain__NeuroM-1008	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 540b7e2..80313f9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,7 @@ Changelog Version 3.2.0 ------------- +- Fix ``neurom.morphmath.principal_direction_extent`` to calculate correctly the pca extent. - Fix ``neurom.features.neurite.segment_taper_rates`` ...	BlueBrain/NeuroM	fdf9f78be79508e34c0349936e233c184279c955	diff --git a/tests/features/test_get_features.py b/tests/features/test_get_features.py index 6661b89..a78efa7 100644 --- a/tests/features/test_get_features.py +++ b/tests/features/test_get_features.py @@ -793,18 +793,18 @@ def test_section_term_radial_distances(): def test_principal_direction_extents(): m = nm.lo...	Bug in principal direction extent There is a bug in the calculation of the principal direction extents: https://github.com/BlueBrain/NeuroM/blob/fdf9f78be79508e34c0349936e233c184279c955/neurom/morphmath.py#L462-L496 At the point where the most negative value is subtracted from the entire extent: ```python ...	fdf9f78be79508e34c0349936e233c184279c955	[ "tests/features/test_get_features.py::test_principal_direction_extents", "tests/test_morphmath.py::test_principal_direction_extent" ]	[ "tests/features/test_get_features.py::test_get_raises", "tests/features/test_get_features.py::test_register_existing_feature", "tests/features/test_get_features.py::test_number_of_sections", "tests/features/test_get_features.py::test_max_radial_distance", "tests/features/test_get_features.py::test_section_t...	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-03-21 07:49:17+00:00	bsd-3-clause	109
BlueBrain__NeuroM-1017	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 1a4feec..8606975 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,8 @@ Changelog Version 3.2.0 ------------- +- ``neurom.features.neurite.principal_direction_extents`` directions correspond to extents + ordered in a descending order. - Add features ``neuro...	BlueBrain/NeuroM	dc54aa8566d59ba08aefb3457412b23297903f49	diff --git a/tests/features/test_get_features.py b/tests/features/test_get_features.py index 6b480c8..20372b9 100644 --- a/tests/features/test_get_features.py +++ b/tests/features/test_get_features.py @@ -798,18 +798,46 @@ def test_principal_direction_extents(): # test with a realistic morphology m = nm.loa...	Maximal direction extent @lidakanari , asked for a maximal direction extent feature in https://github.com/BlueBrain/NeuroM/pull/1008#issuecomment-1073704148 There are two ways to achieve this: 1. Add a new feature that will return the maximum of the principal direction extents. 2. Order the existing principal_di...	dc54aa8566d59ba08aefb3457412b23297903f49	[ "tests/features/test_get_features.py::test_principal_direction_extents", "tests/test_morphmath.py::test_principal_direction_extent" ]	[ "tests/features/test_get_features.py::test_get_raises", "tests/features/test_get_features.py::test_register_existing_feature", "tests/features/test_get_features.py::test_number_of_sections", "tests/features/test_get_features.py::test_max_radial_distance", "tests/features/test_get_features.py::test_section_t...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-01 12:05:03+00:00	bsd-3-clause	110
BlueBrain__NeuroM-1064	diff --git a/neurom/features/__init__.py b/neurom/features/__init__.py index 1970d49..bf80af0 100644 --- a/neurom/features/__init__.py +++ b/neurom/features/__init__.py @@ -40,7 +40,9 @@ Examples: import inspect import operator from enum import Enum -from functools import partial, reduce +from functools import parti...	BlueBrain/NeuroM	8bddfc93ca6f4434e3db3ec124534fa8bde45bc9	diff --git a/tests/features/test_features.py b/tests/features/test_features.py new file mode 100644 index 0000000..42f3ec5 --- /dev/null +++ b/tests/features/test_features.py @@ -0,0 +1,98 @@ +"""Miscelaneous tests of features.""" +from pathlib import Path +from itertools import chain + +import numpy as np +import pyte...	Features should return consistent types The `NeuroM.features.*` functions return inconsistent types. For example, `segment_taper_rates` returns a list of `floats` while `section_taper_rates` returns a list of `numpy.float32`. This can be annoying to process results (e.g. it's harder to dump the results to JSON strings ...	8bddfc93ca6f4434e3db3ec124534fa8bde45bc9	[ "tests/features/test_neurite.py::test_section_partition_pairs", "tests/features/test_features.py::test_neurite_feature_types[Test", "tests/features/test_features.py::test_morphology_feature_types[Test" ]	[ "tests/features/test_neurite.py::test_terminal_path_length_per_neurite", "tests/features/test_neurite.py::test_local_bifurcation_angles", "tests/features/test_neurite.py::test_section_term_lengths", "tests/features/test_neurite.py::test_partition_asymmetry", "tests/features/test_neurite.py::test_section_ter...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2022-09-30 12:54:22+00:00	bsd-3-clause	111
BlueBrain__NeuroM-1073	diff --git a/neurom/features/morphology.py b/neurom/features/morphology.py index 69098cb..4b2c4de 100644 --- a/neurom/features/morphology.py +++ b/neurom/features/morphology.py @@ -63,6 +63,13 @@ from neurom.morphmath import convex_hull feature = partial(feature, namespace=NameSpace.NEURON) +def _assert_soma_cente...	BlueBrain/NeuroM	276c7b2bc925d6d61078018d0c3accf8fd59499f	diff --git a/tests/features/test_morphology.py b/tests/features/test_morphology.py index 2337c83..3bd49d5 100644 --- a/tests/features/test_morphology.py +++ b/tests/features/test_morphology.py @@ -33,6 +33,7 @@ import warnings from io import StringIO from pathlib import Path +import morphio import numpy as np imp...	Raise more informative error when a morph has no soma Some morphology files have no soma, which NeuroM is able to load. But when one compute features on such morphology, one may get obscure errors. For example: ```python nm.get("trunk_angles", neuron, neurite_type=nm.core.types.NeuriteType.basal_dendrite) ``` will ...	276c7b2bc925d6d61078018d0c3accf8fd59499f	[ "tests/features/test_morphology.py::test_missing_soma" ]	[ "tests/features/test_morphology.py::test_soma_volume", "tests/features/test_morphology.py::test_soma_radius", "tests/features/test_morphology.py::test_total_length_per_neurite", "tests/features/test_morphology.py::test_number_of_neurites", "tests/features/test_morphology.py::test_number_of_sections_per_neur...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-05-15 10:05:46+00:00	bsd-3-clause	112
BlueBrain__atlas-densities-25	diff --git a/atlas_densities/densities/fitting.py b/atlas_densities/densities/fitting.py index af117c5..775bdc4 100644 --- a/atlas_densities/densities/fitting.py +++ b/atlas_densities/densities/fitting.py @@ -177,7 +177,8 @@ def compute_average_intensity( Compute the average of `intensity` within the volume define...	BlueBrain/atlas-densities	9bfda2ba2827a9b8fc5e2201f91eeb63b528aa76	diff --git a/tests/densities/test_fitting.py b/tests/densities/test_fitting.py index 4338969..8d1e8b5 100644 --- a/tests/densities/test_fitting.py +++ b/tests/densities/test_fitting.py @@ -219,6 +219,10 @@ def test_compute_average_intensity(): assert np.allclose(actual, 0.3 / 2.0) actual = tested.compute_aver...	Check slices position during fitting For the fitting of the densities, the user can provide a list of coronal positions that corresponds to the original ISH slices in a separate file. There is no tests in atlas_densities/densities/fitting.py to check if these positions are in range of the annotation volume shape. S...	9bfda2ba2827a9b8fc5e2201f91eeb63b528aa76	[ "tests/densities/test_fitting.py::test_compute_average_intensity" ]	[ "tests/densities/test_fitting.py::test_create_dataframe_from_known_densities", "tests/densities/test_fitting.py::test_fill_in_homogenous_regions", "tests/densities/test_fitting.py::test_compute_average_intensities", "tests/densities/test_fitting.py::test_linear_fitting_xy", "tests/densities/test_fitting.py:...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2023-03-06 14:11:32+00:00	apache-2.0	114
BlueBrain__atlas-densities-61	diff --git a/README.rst b/README.rst index 8b8cc3b..8479266 100644 --- a/README.rst +++ b/README.rst @@ -10,8 +10,8 @@ The outcome of this project is a list of volumetric files that provides cell typ for each voxel of the mouse brain volume. The BBP Cell Atlas is the first model required to reconstruct BBP circuits o...	BlueBrain/atlas-densities	67d273c11bcb85dd7a5132dbaf879f88effba112	diff --git a/tests/app/test_cell_densities.py b/tests/app/test_cell_densities.py index ddc894d..df2d5dc 100644 --- a/tests/app/test_cell_densities.py +++ b/tests/app/test_cell_densities.py @@ -271,6 +271,8 @@ def _get_measurements_to_average_densities_result(runner, hierarchy_path, measur hierarchy_path, ...	Exception in fitting due to regions in json hierarchy but not in the annotations volume On master branch, when running the cell atlas pipeline with the CCFv3 annotation atlas, the following command: ``` atlas-densities cell-densities fit-average-densities \ --hierarchy-...	67d273c11bcb85dd7a5132dbaf879f88effba112	[ "tests/app/test_cell_densities.py::test_measurements_to_average_densities", "tests/densities/test_measurement_to_density.py::test_remove_unknown_regions" ]	[ "tests/app/test_cell_densities.py::test_cell_density", "tests/app/test_cell_densities.py::test_glia_cell_densities", "tests/app/test_cell_densities.py::test_inhibitory_and_excitatory_neuron_densities", "tests/app/test_cell_densities.py::test_compile_measurements", "tests/app/test_cell_densities.py::test_fit...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2024-02-06 18:19:39+00:00	apache-2.0	115
BlueBrain__atlas-splitter-12	diff --git a/atlas_splitter/utils.py b/atlas_splitter/utils.py index 66186d0..95407d8 100644 --- a/atlas_splitter/utils.py +++ b/atlas_splitter/utils.py @@ -9,6 +9,9 @@ from atlas_splitter.exceptions import AtlasSplitterError HierarchyDict = Dict[str, Any] +MIN_CUSTOM_ID = 1_000_000_000 +MAX_CUSTOM_ID = 4_000_000_...	BlueBrain/atlas-splitter	18932cbeb9dd4f0e38c0fae362a072e1d325d433	diff --git a/tests/barrel_splitter/test_somatosensory_barrels.py b/tests/barrel_splitter/test_somatosensory_barrels.py index 4f5ee74..e8d2a93 100644 --- a/tests/barrel_splitter/test_somatosensory_barrels.py +++ b/tests/barrel_splitter/test_somatosensory_barrels.py @@ -46,10 +46,11 @@ def test_layer_ids(): names = ...	`atlas-splitter split-isocortex-layer-23` outputs an annotation volume with region IDs not present in the output hierarchy Occurred with ``` cd /gpfs/bbp.cscs.ch/data/project/proj84/atlas_pipeline_runs/2024-03-12T15:01:39 atlas-splitter --version atlas-splitter, version 0.1.3 atlas-splitter split-isocortex-lay...	18932cbeb9dd4f0e38c0fae362a072e1d325d433	[ "tests/barrel_splitter/test_somatosensory_barrels.py::test_layer_ids", "tests/layer_splitter/test_isocortex_layer_23.py::test_edit_hierarchy", "tests/test_app_barrel_splitter.py::test_split_barrels", "tests/test_utils.py::test_id_from_acronym" ]	[ "tests/barrel_splitter/test_somatosensory_barrels.py::test_positions_to_mask", "tests/barrel_splitter/test_somatosensory_barrels.py::test_add_hierarchy_child", "tests/barrel_splitter/test_somatosensory_barrels.py::test_region_logical_and", "tests/barrel_splitter/test_somatosensory_barrels.py::test_get_hierarc...	{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2024-03-13 14:05:37+00:00	apache-2.0	116
Bogdanp__dramatiq_sqs-13	diff --git a/dramatiq_sqs/broker.py b/dramatiq_sqs/broker.py index 6ce094a..d9a2b8f 100644 --- a/dramatiq_sqs/broker.py +++ b/dramatiq_sqs/broker.py @@ -68,6 +68,7 @@ class SQSBroker(dramatiq.Broker): retention: int = MAX_MESSAGE_RETENTION, dead_letter: bool = False, max_receives:...	Bogdanp/dramatiq_sqs	69129e07c25be9aca5f5466c92ae7f6463926f65	diff --git a/tests/conftest.py b/tests/conftest.py index c961ed5..afd5441 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -26,6 +26,9 @@ def broker(): Pipelines(), Retries(min_backoff=1000, max_backoff=900000, max_retries=96), ], + tags={ + "owner": "dramat...	Allow tagging of queues on creation Tagging AWS resources is really useful to keep track of which resources belong to which application, and to track things like costs on a per-application basis. Currently the SQS broker doesn't allow tags to be set on the queue, but this would be useful functionality to have. I'm h...	69129e07c25be9aca5f5466c92ae7f6463926f65	[ "tests/test_broker.py::test_tags_queues_on_create" ]	[ "tests/test_broker.py::test_retention_period_is_validated", "tests/test_broker.py::test_creates_dead_letter_queue" ]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2021-01-15 11:54:40+00:00	apache-2.0	117
BraeWebb__allocate-10	diff --git a/README.md b/README.md index 551f73a..1fddaa2 100644 --- a/README.md +++ b/README.md @@ -50,7 +50,27 @@ The typical command run, assuming `tutors.csv`, `sessions.csv` and `availability allocate tutors.csv sessions.csv availability.csv ``` -## Examples +The `--stub` flag generates template `tutors.csv` a...	BraeWebb/allocate	f45769c8814ba399349f5feaa1f0a4511f32b4d4	diff --git a/tests/allocation_test.py b/tests/allocation_test.py index 8b0eb87..807fc57 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -3,7 +3,7 @@ import os from unittest import TestCase from contextlib import redirect_stdout -from allocate.allocation import run_allocation, stub_files +fro...	Compositional Allocations Allow for composition allocations by exporting an updated availability sheet based on an allocation run. This would allow for a regular allocation to be generated for normal weeks and then an additional 'overflow' allocation to be generated when more tutors are required. Example usage: ...	f45769c8814ba399349f5feaa1f0a4511f32b4d4	[ "tests/allocation_test.py::AllocationTest::test_stub_generation", "tests/allocation_test.py::AllocationTest::test_stub_generation_doodle" ]	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-02-07 05:22:30+00:00	mit	118
BraeWebb__allocate-7	diff --git a/README.md b/README.md index 5f97814..7d8a697 100644 --- a/README.md +++ b/README.md @@ -92,8 +92,8 @@ allocate tutors.csv sessions.csv availability.csv ``` ``` Henry,T01,P01,P02,P03,P05 -Brae,T04,P01,P03,P04,P05 -Emily,T02,T03,P02,P04 +Brae,T02,T04,P01,P03,P04,P05 +Emily,T03,P02,P04 ``` ## Support d...	BraeWebb/allocate	7194a80b506dead1a37482c8c0f36f94a1387ab0	diff --git a/tests/allocation_test.py b/tests/allocation_test.py index 56dfbec..ec34031 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -1,16 +1,39 @@ import io +import os from unittest import TestCase from contextlib import redirect_stdout -from allocate.allocation import run_allocation +f...	Stub Tutors and Sessions Ability to use an availability file to create empty files with the list of sessions and tutors filled out. ```bash allocate --stub tutors.csv sessions.csv availability.csv ```	7194a80b506dead1a37482c8c0f36f94a1387ab0	[ "tests/allocation_test.py::AllocationTest::test_stub_generation" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-02-07 01:53:09+00:00	mit	119
BraeWebb__allocate-8	diff --git a/README.md b/README.md index 7d8a697..551f73a 100644 --- a/README.md +++ b/README.md @@ -74,17 +74,17 @@ The following tables represent the 3 example CSV files that come with the projec \| P05 \| 2 \| 2 \| Thu \| 9 \| 2 \| ### availabilities.csv -\| "Poll ""Sample...	BraeWebb/allocate	b1af498fa349c77f77ac88ac6ec1b9c42aae3557	diff --git a/tests/allocation_test.py b/tests/allocation_test.py index ec34031..8b0eb87 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -32,12 +32,27 @@ Henry,,,,,,""" def test_sample_allocation(self): """Tests to ensure standard allocation works as expected - allocate sam...	Availabilities Format The only accepted format for availabilities at the moment is the output of a doodle poll. This format is kind of gross and it would be better to have a standard availability format with the ability to accept the doodle format being optional. With standard availability format: ```bash allocate...	b1af498fa349c77f77ac88ac6ec1b9c42aae3557	[ "tests/allocation_test.py::AllocationTest::test_stub_generation", "tests/allocation_test.py::AllocationTest::test_stub_generation_doodle" ]	[]	{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-02-07 04:39:39+00:00	mit	120
BurnzZ__scrapy-loader-upkeep-3	diff --git a/README.rst b/README.rst index 6fb0e87..3112d48 100644 --- a/README.rst +++ b/README.rst @@ -58,8 +58,8 @@ This only works for the following ``ItemLoader`` methods: - ``add_xpath()`` - ``replace_xpath()`` -Spider Example -~~~~~~~~~~~~~~ +Basic Spider Example +~~~~~~~~~~~~~~~~~~~~ This is taken fr...	BurnzZ/scrapy-loader-upkeep	0b36309d1c9ea814e097e06e9d7220cfef6e6f9e	diff --git a/examples/quotestoscrape/items.py b/examples/quotestoscrape/items.py index 360d6f0..2eac930 100644 --- a/examples/quotestoscrape/items.py +++ b/examples/quotestoscrape/items.py @@ -3,3 +3,4 @@ import scrapy class QuotesToScrapeItem(scrapy.Item): quote = scrapy.Field() author = scrapy.Field() + ...	Allow paths to be named When having several amounts of xpaths for each field, is really difficult to determine which one was added firsts, specially when there are different workflows on the code. To make easier the task to identify the paths on the stats, it would be great if we could name them. For example: ```...	0b36309d1c9ea814e097e06e9d7220cfef6e6f9e	[ "tests/test_loader.py::test_get_selector_values", "tests/test_loader.py::test_multiple_1_with_name", "tests/test_loader.py::test_multiple_2_with_name" ]	[ "tests/test_loader.py::test_get_selector_values_with_no_selector", "tests/test_loader.py::test_write_to_stats_with_uninjected_stat_dependency", "tests/test_loader.py::test_write_to_stats_with_no_parsed_data", "tests/test_loader.py::test_write_to_stats_with_no_field_name", "tests/test_loader.py::test_write_t...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-07-18 07:42:47+00:00	bsd-3-clause	121
ByteInternet__pip-install-privates-20	diff --git a/pip_install_privates/install.py b/pip_install_privates/install.py index db7eee3..acc62b1 100644 --- a/pip_install_privates/install.py +++ b/pip_install_privates/install.py @@ -100,7 +100,8 @@ are also stripped of the -e flag. If no token is given, private URLs will be kept, including the -e flag (otherwis...	ByteInternet/pip-install-privates	f92dabd7a3d4b2cca677ded7f2073162dd5349e2	diff --git a/tests/unit/test_commandline.py b/tests/unit/test_commandline.py index b694c25..eba89c5 100644 --- a/tests/unit/test_commandline.py +++ b/tests/unit/test_commandline.py @@ -40,6 +40,21 @@ class TestCommandLine(TestCase): self.mock_collect.assert_called_once_with('requirements.txt', ...	Environment variable GITHUB_TOKEN is ignored If `--token` isn't provided on invocation while environment variable `GITHUB_TOKEN` is defined, the environment variable's value should be used as the access token.	f92dabd7a3d4b2cca677ded7f2073162dd5349e2	[ "tests/unit/test_commandline.py::TestCommandLine::test_uses_github_token_environment_variable_if_no_token_supplied" ]	[ "tests/unit/test_commandline.py::TestCommandLine::test_calls_pip_with_install_and_collected_requirements", "tests/unit/test_commandline.py::TestCommandLine::test_raises_error_if_pip_fails", "tests/unit/test_commandline.py::TestCommandLine::test_commandline_passes_requirements_file_to_collect", "tests/unit/tes...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2019-04-05 09:51:03+00:00	mit	122
CMakePP__CMinx-57	diff --git a/.gitignore b/.gitignore index 79c016b..43ea2ec 100644 --- a/.gitignore +++ b/.gitignore @@ -27,6 +27,7 @@ examples/sphinx/build # Python virtual environment venv/ virt_env/ +Pipfile* # Python3 __pycache__ __pycache__/ diff --git a/cminx/parser/aggregator.py b/cminx/parser/aggregator.py index e9334a1...	CMakePP/CMinx	9bde06f9c97a278e14d4c8f438fd0ad538d28526	diff --git a/tests/examples/sphinx/source/example.rst b/tests/examples/sphinx/source/example.rst index acfa2e1..7a0ee3a 100644 --- a/tests/examples/sphinx/source/example.rst +++ b/tests/examples/sphinx/source/example.rst @@ -7,7 +7,7 @@ example.cmake .. function:: say_hi_to(person me) - + This function has ...	Toctree directive does not have necessary blank line between options and elements ## Describe the bug When running CMinx on a directory containing documented CMake functions, the `toctree` directives within the generated `index.rst` files generated are invalid, resulting in many `WARNING: Error in "toctree" directive:...	9bde06f9c97a278e14d4c8f438fd0ad538d28526	[ "tests/test_samples/test_samples.py::TestSamples::test_samples", "tests/unit_tests/test_init.py::TestInit::test_recursive", "tests/unit_tests/test_init.py::TestInit::test_recursive_prefix", "tests/unit_tests/test_rstwriter.py::TestRSTWriter::test_directive" ]	[ "tests/unit_tests/test_init.py::TestInit::test_document", "tests/unit_tests/test_init.py::TestInit::test_document_prefix", "tests/unit_tests/test_rstwriter.py::TestRSTWriter::test_admonition", "tests/unit_tests/test_rstwriter.py::TestRSTWriter::test_doctest", "tests/unit_tests/test_rstwriter.py::TestRSTWrit...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-30 05:03:54+00:00	apache-2.0	123
CODAIT__exchange-metadata-converter-38	diff --git a/setup.py b/setup.py index 1e62eb5..afb9bf4 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,7 @@ with open('README.md') as readme: setup( name='exchange-metadata-converter', packages=find_packages(), - version='0.0.8', + version='0.0.9', license='Apache-2.0', description='exchange metadata ...	CODAIT/exchange-metadata-converter	c306552b0a2fc25f868cfc7daee7b26a1c99f31b	diff --git a/tests/test_dlf.py b/tests/test_dlf.py index 9e37f60..e593f79 100644 --- a/tests/test_dlf.py +++ b/tests/test_dlf.py @@ -48,7 +48,7 @@ class TestDLF(unittest.TestCase): 'com.ie.ibm.hpsys/v1alpha1') self.assertEqual(out_dict['kind'], 'Dataset') self.ass...	Non-compliant metadata.name in the generated DLF YAML The `metadata.name` in the generated DLF YAML does not comply with the Kubernetes spec for DNS-1123 subdomain names. ```JSON { "kind": "Status", "apiVersion": "v1", "metadata": {}, "status": "Failure", "message": "Dataset.com.ie.ibm.hpsys \"Fina...	c306552b0a2fc25f868cfc7daee7b26a1c99f31b	[ "tests/test_dlf.py::TestDLF::test_dtest_dlf" ]	[ "tests/test_dlf.py::TestDLF::test_dax_dataset_descriptors" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2020-11-05 20:45:48+00:00	apache-2.0	124
CORE-GATECH-GROUP__serpent-tools-34	diff --git a/serpentTools/__init__.py b/serpentTools/__init__.py index 87c984c..bf0e5d3 100644 --- a/serpentTools/__init__.py +++ b/serpentTools/__init__.py @@ -5,13 +5,14 @@ ROOT_DIR = os.path.dirname(__file__) from serpentTools import settings # List TODOS/feature requests here for now -# Compatability +# Com...	CORE-GATECH-GROUP/serpent-tools	4db24e02a2491d3a6f0b7ffe1609d24175ebda7d	diff --git a/serpentTools/tests/test_settings.py b/serpentTools/tests/test_settings.py index e094205..f57fe77 100644 --- a/serpentTools/tests/test_settings.py +++ b/serpentTools/tests/test_settings.py @@ -2,6 +2,7 @@ import unittest from serpentTools import settings +from serpentTools.settings.messages import de...	Add more message types Add some future/depreciated warnings that can either piggy back off the [python builtin warnings](https://docs.python.org/2/library/warnings.html) but also conform to our messaging methodology	4db24e02a2491d3a6f0b7ffe1609d24175ebda7d	[ "serpentTools/tests/test_settings.py::DefaultSettingsTester::test_cannotChangeDefaults", "serpentTools/tests/test_settings.py::DefaultSettingsTester::test_getDefault", "serpentTools/tests/test_settings.py::RCTester::test_expandExtras", "serpentTools/tests/test_settings.py::RCTester::test_failAtBadSetting_opti...	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-10-13 20:00:47+00:00	mit	125
CORE-GATECH-GROUP__serpent-tools-35	diff --git a/serpentTools/objects/containers.py b/serpentTools/objects/containers.py new file mode 100644 index 0000000..ff8f941 --- /dev/null +++ b/serpentTools/objects/containers.py @@ -0,0 +1,144 @@ +""" +Supporting object that will be used by the branching reader and +results reader to store data for a single homog...	CORE-GATECH-GROUP/serpent-tools	0c0c57f55bd6632c7015406087b9cee12315ebed	diff --git a/serpentTools/tests/test_branching.py b/serpentTools/tests/test_branching.py index 0d4881d..6693d98 100644 --- a/serpentTools/tests/test_branching.py +++ b/serpentTools/tests/test_branching.py @@ -11,7 +11,7 @@ REF_FILE = os.path.join(TEST_ROOT, 'ref_branch.txt') class BranchTester(unittest.TestCase): ...	Support: Homogenized Universe Object Implement a supporting object that will be used by the branching reader and results reader that stores data for a single homogenized universe at a single instance in time. ## Requirements 1. Should store the universe number, and, optionally, day, burnup, and burnup step for this...	0c0c57f55bd6632c7015406087b9cee12315ebed	[ "serpentTools/tests/test_container.py::HomogenizedUniverseTester::test_getB1Exp", "serpentTools/tests/test_container.py::HomogenizedUniverseTester::test_getB1Unc", "serpentTools/tests/test_container.py::HomogenizedUniverseTester::test_getInfExp", "serpentTools/tests/test_container.py::HomogenizedUniverseTeste...	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_issue_reference", "has_added_files" ], "has_test_patch": true, "is_lite": false }	2017-10-17 13:59:19+00:00	mit	126
CORE-GATECH-GROUP__serpent-tools-4	diff --git a/serpentTools/__init__.py b/serpentTools/__init__.py index 8af8d0f..d38090d 100644 --- a/serpentTools/__init__.py +++ b/serpentTools/__init__.py @@ -1,7 +1,7 @@ from serpentTools import settings from serpentTools import parsers -__version__ = '0.1.1' +__version__ = '0.1.2' # List TODOS/feature ...	CORE-GATECH-GROUP/serpent-tools	606a90d665a15a16c437dd1fb72ef014aa480142	diff --git a/serpentTools/tests/test_depletion.py b/serpentTools/tests/test_depletion.py index 0574305..d7f6d52 100644 --- a/serpentTools/tests/test_depletion.py +++ b/serpentTools/tests/test_depletion.py @@ -156,6 +156,17 @@ class DepletedMaterialTester(_DepletionTestHelper): ...	`getXY` for `DepletedMaterial` raises unhelpful value error if days missing from object If a depleted material is asked to get some quantity for days that are not present, the following error is raised: ``` File "C:\Users\ajohnson400\AppData\Local\Continuum\Anaconda3\lib\site-packages\serpenttools-0.1.1rc0-py3.5.eg...	606a90d665a15a16c437dd1fb72ef014aa480142	[ "serpentTools/tests/test_depletion.py::DepletedMaterialTester::test_getXY_raisesError_badTime" ]	[ "serpentTools/tests/test_depletion.py::DepletionTester::test_ReadMaterials", "serpentTools/tests/test_depletion.py::DepletionTester::test_metadata", "serpentTools/tests/test_depletion.py::DepletedMaterialTester::test_fetchData", "serpentTools/tests/test_depletion.py::DepletedMaterialTester::test_getXY_adens",...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2017-09-19 15:34:09+00:00	mit	127
CS-SI__eodag-405	diff --git a/eodag/plugins/download/aws.py b/eodag/plugins/download/aws.py index 3202c76a..fe7d3573 100644 --- a/eodag/plugins/download/aws.py +++ b/eodag/plugins/download/aws.py @@ -253,11 +253,17 @@ class AwsDownload(Download): bucket_names_and_prefixes = [self.get_bucket_name_and_prefix(product)] ...	CS-SI/eodag	d9f16f411fdf5eb6ad752f984782dd06ed882dc8	diff --git a/tests/units/test_search_plugins.py b/tests/units/test_search_plugins.py index 405451a8..47ced2e6 100644 --- a/tests/units/test_search_plugins.py +++ b/tests/units/test_search_plugins.py @@ -297,3 +297,50 @@ class TestSearchPluginODataV4Search(BaseSearchPluginTest): self.assertEqual(estimate, self....	finalize_s2_safe_product: Fails when missing manifest.safe When downloading some products on `earth_search`, I have a problem when converting the product format to `.SAFE`: ![2022-02-22_14h47_27](https://user-images.githubusercontent.com/67311115/155145249-38c42542-b9bd-4888-9573-2f7d1cc24c6d.png) ![2022-02-22_14h48_...	d9f16f411fdf5eb6ad752f984782dd06ed882dc8	[ "tests/units/test_search_plugins.py::TestSearchPluginStacSearch::test_plugins_search_stacsearch_mapping_earthsearch" ]	[ "tests/units/test_search_plugins.py::TestSearchPluginQueryStringSearch::test_plugins_search_querystringseach_count_and_search_sobloo", "tests/units/test_search_plugins.py::TestSearchPluginQueryStringSearch::test_plugins_search_querystringseach_no_count_and_search_sobloo", "tests/units/test_search_plugins.py::Te...	{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-02-22 18:02:30+00:00	apache-2.0	128
CS-SI__eodag-586	diff --git a/eodag/api/product/_product.py b/eodag/api/product/_product.py index 777b3026..a0a3d78c 100644 --- a/eodag/api/product/_product.py +++ b/eodag/api/product/_product.py @@ -221,15 +221,30 @@ class EOProduct(object): """ self.downloader = downloader self.downloader_auth = authenticat...	CS-SI/eodag	3465afe00a492e73bfd517f19c409ba21196f85f	diff --git a/tests/units/test_eoproduct.py b/tests/units/test_eoproduct.py index ed716125..81bdd00f 100644 --- a/tests/units/test_eoproduct.py +++ b/tests/units/test_eoproduct.py @@ -453,3 +453,84 @@ class TestEOProduct(EODagTestCase): # progress bar finished self.assertEqual(progress_callback.n, prog...	percent variables parsing error in product location If product location contains some percent variables, it may conflict with `register_downloader()` internal parsing mechanism and raise: ``` Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/eodag/api/core.py", line 1474, in _do_searc...	3465afe00a492e73bfd517f19c409ba21196f85f	[ "tests/units/test_eoproduct.py::TestEOProduct::test_eoproduct_register_downloader_resolve_ignored" ]	[ "tests/units/test_eoproduct.py::TestEOProduct::test_eoproduct_default_driver_unsupported_product_type", "tests/units/test_eoproduct.py::TestEOProduct::test_eoproduct_download_http_default", "tests/units/test_eoproduct.py::TestEOProduct::test_eoproduct_download_http_delete_archive", "tests/units/test_eoproduct...	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2022-12-20 10:39:22+00:00	apache-2.0	129
CS-SI__eodag-592	diff --git a/eodag/api/product/metadata_mapping.py b/eodag/api/product/metadata_mapping.py index e449a643..3f014290 100644 --- a/eodag/api/product/metadata_mapping.py +++ b/eodag/api/product/metadata_mapping.py @@ -302,7 +302,10 @@ def format_metadata(search_param, args, *kwargs): @staticmethod de...	CS-SI/eodag	870580e4565e533838a1b3c1b2acd2edd335de11	diff --git a/tests/units/test_search_plugins.py b/tests/units/test_search_plugins.py index ca6c2456..b25b7ea7 100644 --- a/tests/units/test_search_plugins.py +++ b/tests/units/test_search_plugins.py @@ -187,6 +187,50 @@ class TestSearchPluginQueryStringSearch(BaseSearchPluginTest): "The FOO collection", ...	Add keywords to discovered product types Automatically add default keywords to discovered product types to help finding them using [guess_product_type()](https://eodag.readthedocs.io/en/stable/api_reference/core.html#eodag.api.core.EODataAccessGateway.guess_product_type). See also [Guess a product type documentation]...	870580e4565e533838a1b3c1b2acd2edd335de11	[ "tests/units/test_search_plugins.py::TestSearchPluginQueryStringSearch::test_plugins_search_querystringseach_discover_product_types_keywords" ]	[ "tests/units/test_search_plugins.py::TestSearchPluginQueryStringSearch::test_plugins_search_querystringseach_count_and_search_sobloo", "tests/units/test_search_plugins.py::TestSearchPluginQueryStringSearch::test_plugins_search_querystringseach_discover_product_types", "tests/units/test_search_plugins.py::TestSe...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-12-22 15:41:21+00:00	apache-2.0	130
CS-SI__eodag-927	diff --git a/docs/_static/product_types_information.csv b/docs/_static/product_types_information.csv index 21b10020..61464555 100644 --- a/docs/_static/product_types_information.csv +++ b/docs/_static/product_types_information.csv @@ -28,10 +28,10 @@ CLMS_GLO_GDMP_333M,"Gross dry matter Productivity (GDMP) is an indica...	CS-SI/eodag	72e7a48eba23f7debb89903f31d67555b53fcbce	diff --git a/tests/units/test_core.py b/tests/units/test_core.py index f5f118c4..46fc1bed 100644 --- a/tests/units/test_core.py +++ b/tests/units/test_core.py @@ -22,6 +22,7 @@ import json import logging import os import shutil +import tempfile import unittest import uuid from pathlib import Path @@ -1178,6 +1179...	EODataAccessGateway constructor fails on AWS Lambda Describe the bug `makedirs` [invocation](https://github.com/CS-SI/eodag/blob/develop/eodag/api/core.py#L98) within the EODataAccessGateway constructor causes `OSError: [Errno 30] Read-only file system` when run on AWS Lambda Code To Reproduce CLI comman...	72e7a48eba23f7debb89903f31d67555b53fcbce	[ "tests/units/test_core.py::TestCoreInvolvingConfDir::test_read_only_home_dir" ]	[ "tests/units/test_core.py::TestCore::test_build_index_ko", "tests/units/test_core.py::TestCore::test_core_object_locations_file_not_found", "tests/units/test_core.py::TestCore::test_core_object_open_index_if_exists", "tests/units/test_core.py::TestCore::test_core_object_set_default_locations_config", "tests...	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-11-16 13:22:12+00:00	apache-2.0	131
CSCfi__swift-browser-ui-41	diff --git a/docs/source/_static/api.yml b/docs/source/_static/api.yml index a46ecf9b..720d80bf 100644 --- a/docs/source/_static/api.yml +++ b/docs/source/_static/api.yml @@ -156,11 +156,34 @@ paths: get: tags: - API Endpoints - summary: Get container or object(s) metadata. + summary: Get...	CSCfi/swift-browser-ui	941a02a58da7335438f2cd91bb5765a84e8cf687	diff --git a/tests/unit/test_api.py b/tests/unit/test_api.py index e4888a19..ac566f9b 100644 --- a/tests/unit/test_api.py +++ b/tests/unit/test_api.py @@ -13,7 +13,8 @@ from swiftclient.service import SwiftError from swift_browser_ui.api import get_os_user, os_list_projects from swift_browser_ui.api import swift_list...	Split container and object metadata API request #### Description Container and object metadata would be more intuitive when queried from separate API endpoints. Proposal to split /bucket/meta -> /bucket/meta & /bucket/object/meta to make the API more intuitive. (inspired by PR #34) #### DoD (Definition of Done) Me...	941a02a58da7335438f2cd91bb5765a84e8cf687	[ "tests/unit/test_api.py::APITestClass::test_get_container_meta_swift", "tests/unit/test_api.py::APITestClass::test_get_object_meta_s3", "tests/unit/test_api.py::APITestClass::test_get_object_meta_swift", "tests/unit/test_api.py::APITestClass::test_get_object_meta_swift_whole", "tests/unit/test_api.py::APITe...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-10-20 18:35:23+00:00	mit	132
CTFd__CTFd-2269	diff --git a/CTFd/themes/admin/templates/config.html b/CTFd/themes/admin/templates/config.html index 3fae030e..1e097069 100644 --- a/CTFd/themes/admin/templates/config.html +++ b/CTFd/themes/admin/templates/config.html @@ -23,6 +23,9 @@ <li class="nav-item"> <a class="nav-link rounded-0" href="#accounts" rol...	CTFd/CTFd	68da00900a792fffae8e563198abe8045d33c0a9	diff --git a/tests/test_views.py b/tests/test_views.py index 3b814940..55da66bf 100644 --- a/tests/test_views.py +++ b/tests/test_views.py @@ -451,3 +451,19 @@ def test_user_can_access_files_if_view_after_ctf(): rmdir(directory) destroy_ctfd(app) + + +def test_robots_txt(): + """Does the robots.t...	Controlling static content like robots.txt Some users seem to wish to be able to control things like their robots.txt. Is this something that we could implement in CTFd? Perhaps as a type of Page with a custom reponse type?	68da00900a792fffae8e563198abe8045d33c0a9	[ "tests/test_views.py::test_robots_txt" ]	[ "tests/test_views.py::test_index", "tests/test_views.py::test_page", "tests/test_views.py::test_draft_pages", "tests/test_views.py::test_page_requiring_auth", "tests/test_views.py::test_hidden_pages", "tests/test_views.py::test_not_found", "tests/test_views.py::test_themes_handler", "tests/test_views....	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-03-12 20:26:01+00:00	apache-2.0	134
CTFd__CTFd-2333	diff --git a/CTFd/api/v1/hints.py b/CTFd/api/v1/hints.py index 0ee60fa3..8d347fd9 100644 --- a/CTFd/api/v1/hints.py +++ b/CTFd/api/v1/hints.py @@ -9,7 +9,8 @@ from CTFd.api.v1.schemas import APIDetailedSuccessResponse, APIListSuccessRespon from CTFd.constants import RawEnum from CTFd.models import Hints, HintUnlocks,...	CTFd/CTFd	7bae8360c83ad067c7f89d46bf57fd8e14f95d0d	diff --git a/tests/api/v1/user/test_hints.py b/tests/api/v1/user/test_hints.py index ad69882c..e7609135 100644 --- a/tests/api/v1/user/test_hints.py +++ b/tests/api/v1/user/test_hints.py @@ -3,6 +3,7 @@ from freezegun import freeze_time +from CTFd.models import Hints from CTFd.utils import set_config from tests....	Hints nonfunctional unless logged in <!-- If this is a bug report please fill out the template below. If this is a feature request please describe the behavior that you'd like to see. --> Environment: - CTFd Version/Commit: 3.5.0 - Operating System: any - Web Browser and Version: any **What happened...	7bae8360c83ad067c7f89d46bf57fd8e14f95d0d	[ "tests/api/v1/user/test_hints.py::test_api_hints_accessible_public" ]	[ "tests/api/v1/user/test_hints.py::test_api_hint_404", "tests/api/v1/user/test_hints.py::test_api_hint_visibility", "tests/api/v1/user/test_hints.py::test_api_hint_visibility_ctftime", "tests/api/v1/user/test_hints.py::test_api_hint_locked", "tests/api/v1/user/test_hints.py::test_api_hint_unlocked", "tests...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-06-16 20:31:25+00:00	apache-2.0	135
CTFd__ctfcli-148	diff --git a/ctfcli/cli/challenges.py b/ctfcli/cli/challenges.py index b56525c..51755e6 100644 --- a/ctfcli/cli/challenges.py +++ b/ctfcli/cli/challenges.py @@ -1,3 +1,4 @@ +import contextlib import logging import os import subprocess @@ -203,167 +204,253 @@ class ChallengeCommand: click.secho(f"Could not p...	CTFd/ctfcli	26bcec897fcc1f5f23c8117e2a225a130a8b0dea	diff --git a/tests/core/test_image.py b/tests/core/test_image.py index 2e773f4..8e6ab37 100644 --- a/tests/core/test_image.py +++ b/tests/core/test_image.py @@ -56,7 +56,9 @@ class TestImage(unittest.TestCase): self.assertTrue(image.built) self.assertEqual(image_name, "test-challenge") - mock...	Support Buildkit drivers for image builds [Buildkit drivers](https://docs.docker.com/build/drivers/) offer a lot of additional features over the default `docker` driver, like multi-arch images and remote builders. They could be supported by moving tag/push to `docker build --push`, depending on docker buildx which b...	26bcec897fcc1f5f23c8117e2a225a130a8b0dea	[ "tests/core/test_image.py::TestImage::test_build", "tests/core/test_image.py::TestImage::test_build_returns_none_if_failed", "tests/core/test_image.py::TestImage::test_builds_image_before_export", "tests/core/test_image.py::TestImage::test_builds_image_before_push" ]	[ "tests/core/test_image.py::TestImage::test_accepts_path_as_string_and_pathlike", "tests/core/test_image.py::TestImage::test_assigns_attributes", "tests/core/test_image.py::TestImage::test_export_built_image", "tests/core/test_image.py::TestImage::test_extracts_correct_basename", "tests/core/test_image.py::T...	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2024-03-07 11:52:44+00:00	apache-2.0	136
Cadair__parfive-16	diff --git a/README.rst b/README.rst index 8c8c05e..7014682 100644 --- a/README.rst +++ b/README.rst @@ -24,6 +24,28 @@ A simple example is:: files = dl.download() +Parfive also bundles a CLI. The following example will download the two files concurrently.:: + + $ parfive 'http://212.183.159.230/5MB.zip' 'http:...	Cadair/parfive	10fb4e49216c3cfd5a3c0dd0230e0917b3c0c27d	diff --git a/parfive/tests/test_main.py b/parfive/tests/test_main.py new file mode 100644 index 0000000..bfcaeab --- /dev/null +++ b/parfive/tests/test_main.py @@ -0,0 +1,38 @@ +from parfive.main import parse_args +import pytest + +REQUIRED_ARGUMENTS = ['test_url'] + +def test_no_url(): + with pytest.raises(SystemEx...	Command line interface? It might be useful to create a command line interface, so people can just fire off requests without having to write any code to use the library As a basic interface, just give it a file with one URL per line, or maybe a lot of URLs as arguments (although that could hit up against limits) I...	10fb4e49216c3cfd5a3c0dd0230e0917b3c0c27d	[ "parfive/tests/test_main.py::test_no_url", "parfive/tests/test_main.py::test_overwrite", "parfive/tests/test_main.py::test_max_conn", "parfive/tests/test_main.py::test_no_file_progress", "parfive/tests/test_main.py::test_print_filenames", "parfive/tests/test_main.py::test_directory" ]	[]	{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2019-07-19 07:01:34+00:00	mit	137
CharJon__GeCO-126	diff --git a/geco/graphs/__init__.py b/geco/graphs/__init__.py index 8bea5ee..e9aad98 100644 --- a/geco/graphs/__init__.py +++ b/geco/graphs/__init__.py @@ -1,3 +1,4 @@ import geco.graphs.chimera as chimera import geco.graphs.pegasus as pegasus import geco.graphs.utilities as utilities +import geco.graphs.lavrov_gra...	CharJon/GeCO	6db1a549b3145b3bc5d3025a9bccc03be6575564	diff --git a/geco/graphs/tests/test_lavrov_graph.py b/geco/graphs/tests/test_lavrov_graph.py new file mode 100644 index 0000000..efdcbdb --- /dev/null +++ b/geco/graphs/tests/test_lavrov_graph.py @@ -0,0 +1,20 @@ +from geco.graphs.lavrov_graph import lavrov_graph + +import pytest + + +def test_lavrov_graph_properties()...	Add Lavrov graphs [This comment](https://math.stackexchange.com/a/2811761/1039279) describes an interesting graph type. Add a generator for this class of graphs. I do not know if they have a name yet, so let's call them after the author of the comment (Lavrov).	6db1a549b3145b3bc5d3025a9bccc03be6575564	[ "geco/graphs/tests/test_lavrov_graph.py::test_lavrov_graph_properties", "geco/graphs/tests/test_lavrov_graph.py::test_lavrov_graph_edges" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_added_files" ], "has_test_patch": true, "is_lite": false }	2022-03-24 11:01:43+00:00	mit	138
Clarifai__clarifai-python-228	diff --git a/clarifai/utils/logging.py b/clarifai/utils/logging.py index 9fbc6e9..44373af 100644 --- a/clarifai/utils/logging.py +++ b/clarifai/utils/logging.py @@ -1,6 +1,6 @@ import logging from collections import defaultdict -from typing import Dict, List, Optional +from typing import Dict, List, Optional, Union ...	Clarifai/clarifai-python	445922866de2e88c75dbbae450568a311e7beaca	diff --git a/tests/test_misc.py b/tests/test_misc.py new file mode 100644 index 0000000..58f9658 --- /dev/null +++ b/tests/test_misc.py @@ -0,0 +1,19 @@ +import logging + +from rich.logging import RichHandler + +from clarifai.utils.logging import _get_library_name, get_logger + + +def test_get_logger(): + logger = get...	Handler added to root logger This library adds a `RichHandler` to the root logger through `logging.basicConfig` every time `get_logger` is called (which seems to be every time any common class/object is initialized): https://github.com/Clarifai/clarifai-python/blob/dbdcb493bdb9255244276086bd193a305e2cbcc0/clarifai/uti...	445922866de2e88c75dbbae450568a311e7beaca	[ "tests/test_misc.py::test_get_logger", "tests/test_misc.py::test_get_logger_defaults" ]	[]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2023-11-28 07:49:53+00:00	apache-2.0	139
ClarkSource__k8t-40	diff --git a/k8t/cli.py b/k8t/cli.py index f60d58e..b4429f3 100644 --- a/k8t/cli.py +++ b/k8t/cli.py @@ -180,7 +180,7 @@ def new_environment(cname, name, directory): @click.option("--environment", "-e", "ename", help="Deployment environment to use.") @click.option("--name", "-n", help="Template filename.") @click.op...	ClarkSource/k8t	7d577b6a3e1a6de8f59025d806df83b05fe56852	diff --git a/tests/secret_providers.py b/tests/secret_providers.py new file mode 100644 index 0000000..6e2f75c --- /dev/null +++ b/tests/secret_providers.py @@ -0,0 +1,20 @@ +# -- coding: utf-8 -- +# ISC License +# +# Copyright 2019 FL Fintech E GmbH +# +# Permission to use, copy, modify, and/or distribute this softw...	get_secret should offer a random provider to allow using the same templates for different environments we should add a random provider to the secrets function.	7d577b6a3e1a6de8f59025d806df83b05fe56852	[ "tests/secret_providers.py::test_random" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-02-06 17:04:01+00:00	isc	140
CleanCut__green-124	diff --git a/green/result.py b/green/result.py index f96019d..908bea4 100644 --- a/green/result.py +++ b/green/result.py @@ -417,7 +417,7 @@ class GreenTestResult(BaseTestResult): if obj_list: stats.append("{}={}".format(name, color_func(str(len(obj_list))))) if not stats: - ...	CleanCut/green	568e0240a41fe79af20bb520fef39062788aa09e	diff --git a/green/test/test_result.py b/green/test/test_result.py index 04f97f8..fdaa846 100644 --- a/green/test/test_result.py +++ b/green/test/test_result.py @@ -830,6 +830,8 @@ class TestGreenTestResultAdds(unittest.TestCase): """ self.args.verbose = 1 gtr = GreenTestResult(self.args, Gre...	Return a fail if no tests are found. # Summary: Currently (v2.4.1) `green` creates an empty test suite if no tests are found and then runs that empty suite, returning passing code. This can cause false-positives for CI and should be changed. ## Example: ``` $ python -m green -vvv -s 1 -W -t --run-coverage emap-co...	568e0240a41fe79af20bb520fef39062788aa09e	[ "green/test/test_result.py::TestGreenTestResultAdds::test_wasSuccessful", "green/test/test_runner.py::TestRun::test_noTestsFound" ]	[ "green/test/test_result.py::TestBaseTestResult::test_displayStderr", "green/test/test_result.py::TestBaseTestResult::test_displayStdout", "green/test/test_result.py::TestBaseTestResult::test_stderrErrput", "green/test/test_result.py::TestBaseTestResult::test_stderrNoErrput", "green/test/test_result.py::Test...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2016-05-24 23:12:35+00:00	mit	141
Clinical-Genomics__scout-593	diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py index 3a07b82d8..055963b99 100644 --- a/scout/adapter/mongo/query.py +++ b/scout/adapter/mongo/query.py @@ -114,15 +114,16 @@ class QueryHandler(object): cadd_query = {'cadd_score': {'$gt': float(cadd)}} logger.debug("Add...	Clinical-Genomics/scout	7b2419a20dd5dbae88f21b9a2afe2c2d4ad5277f	diff --git a/tests/adapter/test_query.py b/tests/adapter/test_query.py index e5aee3586..2d12aa555 100644 --- a/tests/adapter/test_query.py +++ b/tests/adapter/test_query.py @@ -57,7 +57,7 @@ def test_build_cadd_exclusive(adapter): def test_build_cadd_inclusive(adapter): case_id = 'cust000' cadd = 10.0 - c...	CADD score filter monday-issue! Thank you kindly for the quick inclusion of CADD score filtering! Will make a couple of our doctors very happy. One major caveat though: the current version seems to filter out unknown CADD scores as well (similar to the unknown frequency bug)! Not intended usage..	7b2419a20dd5dbae88f21b9a2afe2c2d4ad5277f	[ "tests/adapter/test_query.py::test_build_cadd_inclusive" ]	[ "tests/adapter/test_query.py::test_build_query", "tests/adapter/test_query.py::test_build_thousand_g_and_cadd", "tests/adapter/test_query.py::test_build_thousand_g_query", "tests/adapter/test_query.py::test_build_chrom", "tests/adapter/test_query.py::test_build_cadd_exclusive", "tests/adapter/test_query.p...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2017-09-05 12:38:59+00:00	bsd-3-clause	142
Clinical-Genomics__scout-656	diff --git a/scout/build/panel.py b/scout/build/panel.py index 1a4dfa0fd..85b02bfef 100644 --- a/scout/build/panel.py +++ b/scout/build/panel.py @@ -44,7 +44,7 @@ def build_gene(gene_info, adapter): hgnc_gene = adapter.hgnc_gene(hgnc_id) if hgnc_gene is None: - raise IntegrityError + raise...	Clinical-Genomics/scout	e41d7b94106581fa28da793e2ab19c466e2f2f5a	diff --git a/tests/parse/test_parse_coordinates.py b/tests/parse/test_parse_coordinates.py new file mode 100644 index 000000000..791148fb3 --- /dev/null +++ b/tests/parse/test_parse_coordinates.py @@ -0,0 +1,253 @@ +from scout.parse.variant.coordinates import (get_cytoband_coordinates, get_sub_category, + ...	CSV - length -1 for a deletion of 80 genes https://scout.scilifelab.se/cust003/17159/sv/variants?variant_type=clinical&gene_panels=EP&hgnc_symbols=&size=&chrom=&thousand_genomes_frequency= please have a look. Something doesn't fit here. A deletion of 1 bp can not contain 80 genes. thanks, Michela	e41d7b94106581fa28da793e2ab19c466e2f2f5a	[ "tests/parse/test_parse_coordinates.py::test_get_end_deletion", "tests/parse/test_parse_coordinates.py::test_parse_coordinates_snv", "tests/parse/test_parse_coordinates.py::test_get_sv_length_translocation", "tests/parse/test_parse_coordinates.py::test_get_sv_length_del_no_length", "tests/parse/test_parse_c...	[ "tests/parse/test_parse_coordinates.py::test_get_subcategory_indel", "tests/parse/test_parse_coordinates.py::test_get_length_snv", "tests/parse/test_parse_coordinates.py::test_get_length_indel", "tests/parse/test_parse_coordinates.py::test_get_subcategory_snv" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-11-10 12:04:32+00:00	bsd-3-clause	143
CodeForPhilly__chime-276	diff --git a/settings.cfg b/settings.cfg index 040d6e2..f8d1a3b 100644 --- a/settings.cfg +++ b/settings.cfg @@ -8,6 +8,6 @@ --icu-rate 0.0075 --market_share 0.15 --n-days 60 ---susceptible 4119405 +--population 4119405 --ventilated-los 10 --ventilated-rate 0.005 diff --git a/src/penn_chime/cli.py b/src/penn_chime...	CodeForPhilly/chime	0a0aece010073dd2facf67497efe649ff24a023a	diff --git a/tests/test_app.py b/tests/test_app.py index f5dc5dc..696663e 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -20,7 +20,7 @@ PARAM = Parameters( known_infected=5000, market_share=0.05, relative_contact_rate=0.15, - susceptible=500000, + population=500000, hospitalized=Rat...	Conflation of regional population with susceptible population is wrong with large infection count The raw data shows a total of S+I+R that is larger than the user-provided regional population. This is because the number presumed initially infected based on hospitalization rate isn't subtracted from the population to co...	0a0aece010073dd2facf67497efe649ff24a023a	[ "tests/test_app.py::test_sir", "tests/test_app.py::test_the_rest_of_header_shows_up", "tests/test_app.py::test_admitted_patients_chart", "tests/test_app.py::test_penn_logo_in_header", "tests/test_app.py::test_defaults_repr", "tests/test_app.py::test_new_admissions_chart", "tests/test_app.py::test_sim_si...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-03-27 00:10:56+00:00	mit	145
CodeForPhilly__chime-418	diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py index da7311f..6582b1c 100644 --- a/src/penn_chime/models.py +++ b/src/penn_chime/models.py @@ -9,7 +9,7 @@ from __future__ import annotations from datetime import date, datetime, timedelta from logging import INFO, basicConfig, getLogger from sys impo...	CodeForPhilly/chime	e6ff8aaa0be2be7c27ec9b98611147650d414270	diff --git a/tests/conftest.py b/tests/conftest.py index e822d91..b7cf01f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -51,6 +51,7 @@ def DEFAULTS(): doubling_time=4.0, n_days=60, market_share=0.15, + mitigation_date=datetime(year=2020, month=3, day=28), relative_...	["model"] social isolation started earlier than model assumes <!-- Please note: Any changes to the model have a huge impact on rapidly evolving hospital system & public health decisions. The current model has been in use for a while now, and it has been validated against other similar models, so any changes to the mod...	e6ff8aaa0be2be7c27ec9b98611147650d414270	[ "[", "[100%]", "tests/penn_chime/test_models.py::test_model_raw_end", "tests/penn_chime/test_models.py::test_model_conservation", "tests/penn_chime/test_models.py::test_sim_sir", "tests/penn_chime/test_models.py::test_model_cumulative_census", "tests/penn_chime/test_models.py::test_model", "tests/penn...	[ "tests/penn_chime/test_models.py::test_growth_rate", "tests/penn_chime/test_models.py::test_sir" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-04-01 20:18:49+00:00	mit	146
ContinualAI__avalanche-1216	diff --git a/avalanche/benchmarks/utils/data.py b/avalanche/benchmarks/utils/data.py index 533d79ee..9c11f60f 100644 --- a/avalanche/benchmarks/utils/data.py +++ b/avalanche/benchmarks/utils/data.py @@ -101,6 +101,10 @@ class AvalancheDataset(FlatData): DeprecationWarning, ) + if ...	ContinualAI/avalanche	f3abbc5500c928bb5fc5bcf4b31fcd0b504fdf26	diff --git a/tests/test_avalanche_dataset.py b/tests/test_avalanche_dataset.py index e7cf460b..67ccdecc 100644 --- a/tests/test_avalanche_dataset.py +++ b/tests/test_avalanche_dataset.py @@ -56,6 +56,17 @@ class FrozenTransformGroupsCenterCrop: class AvalancheDatasetTests(unittest.TestCase): + + def test_avalan...	bug for stream-level metrics in periodic eval periodic eval is broken in some subtle cases. Instead of calling `eval` on the entire stream, it calls it multiple times for each experience, breaking stream-level metrics. Reproduce: ``` from avalanche.benchmarks import SplitMNIST from avalanche.training import Naive...	f3abbc5500c928bb5fc5bcf4b31fcd0b504fdf26	[ "tests/test_avalanche_dataset.py::AvalancheDatasetTests::test_avalanche_dataset_tensor_task_labels", "tests/test_avalanche_dataset.py::AvalancheDatasetTests::test_disallowed_attribute_name", "tests/test_avalanche_dataset.py::AvalancheDatasetTests::test_subset_subset_merge", "tests/training/test_strategies.py:...	[]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-11-21 16:04:01+00:00	mit	147
ContinualAI__avalanche-1598	diff --git a/avalanche/benchmarks/scenarios/__init__.py b/avalanche/benchmarks/scenarios/__init__.py index f84a965c..83db8205 100644 --- a/avalanche/benchmarks/scenarios/__init__.py +++ b/avalanche/benchmarks/scenarios/__init__.py @@ -8,3 +8,4 @@ from .task_aware import * from .dataset_scenario import * from .exmodel...	ContinualAI/avalanche	524f70c50cb7090ac05aef87326300514e2d4d6f	diff --git a/tests/benchmarks/scenarios/test_dataset_scenario.py b/tests/benchmarks/scenarios/test_dataset_scenario.py index d5c11eab..dbb86ab7 100644 --- a/tests/benchmarks/scenarios/test_dataset_scenario.py +++ b/tests/benchmarks/scenarios/test_dataset_scenario.py @@ -6,12 +6,14 @@ from torch.utils.data import Tensor...	benchmark_with_validation stream removes or hides classes_in_experience attribute 🐛 Describe the bug When using benchmark_with_validation_stream, the classes_in_experience attribute is removed or hidden and cannot be caught during model adaptation. 🐜 To Reproduce ```{python} import torch import arg...	524f70c50cb7090ac05aef87326300514e2d4d6f	[ "tests/benchmarks/scenarios/test_dataset_scenario.py::TaskIncrementalScenarioTests::test_task_incremental_bm_basic", "tests/benchmarks/scenarios/test_dataset_scenario.py::DatasetScenarioTests::test_benchmark_from_dataset_heterogeneous_data", "tests/benchmarks/scenarios/test_dataset_scenario.py::DatasetSplitterT...	[]	{ "failed_lite_validators": [ "has_added_files", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2024-02-14 10:25:27+00:00	mit	148
CybOXProject__mixbox-35	diff --git a/mixbox/dates.py b/mixbox/dates.py index be279e1..794e0b0 100644 --- a/mixbox/dates.py +++ b/mixbox/dates.py @@ -73,10 +73,10 @@ def serialize_date(value): """ if not value: return None - elif isinstance(value, datetime.date): - return value.isoformat() elif isinstance(valu...	CybOXProject/mixbox	bab51cfd20757f9a64a61571631203dbbc3644f8	diff --git a/tests/dates_tests.py b/tests/dates_tests.py index f139939..d3be86b 100644 --- a/tests/dates_tests.py +++ b/tests/dates_tests.py @@ -15,6 +15,12 @@ class DatesTests(unittest.TestCase): dstr = "2015-04-01" parsed = dates.parse_date(dstr) self.assertEqual(dstr, parsed.isoformat()) +...	DateField does not properly serialize datetime objects When storing a Python `datetime` object in a property specified by a `DateField`, the value incorrectly serializes to an ISO timestamp (`YYYY-MM-DDThh:mm:ss`) instead of to a `xs:date` format (`YYYY-MM-DD`). class Foo(Entity): my_date = DateField("m...	bab51cfd20757f9a64a61571631203dbbc3644f8	[ "tests/dates_tests.py::DatesTests::test_serialize_datetime_as_date" ]	[ "tests/dates_tests.py::DatesTests::test_now", "tests/dates_tests.py::DatesTests::test_parse_date", "tests/dates_tests.py::DatesTests::test_parse_date_none", "tests/dates_tests.py::DatesTests::test_parse_datetime", "tests/dates_tests.py::DatesTests::test_parse_datetime_none", "tests/dates_tests.py::DatesTe...	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2017-01-06 16:30:59+00:00	bsd-3-clause	149
CycloneDX__cyclonedx-python-332	diff --git a/cyclonedx_py/utils/conda.py b/cyclonedx_py/utils/conda.py index 3cf2fc5..b5c26a0 100644 --- a/cyclonedx_py/utils/conda.py +++ b/cyclonedx_py/utils/conda.py @@ -20,15 +20,14 @@ import json import sys from json import JSONDecodeError -from typing import Optional +from typing import Optional, Tuple +from u...	CycloneDX/cyclonedx-python	c02d770cf18a57e118347a0a57db29ae65919c35	diff --git a/tests/fixtures/conda-list-broken.txt b/tests/fixtures/conda-list-broken.txt new file mode 100644 index 0000000..ed67b21 --- /dev/null +++ b/tests/fixtures/conda-list-broken.txt @@ -0,0 +1,2 @@ +# This package list id malformed. +https://repo.anaconda.com/pkgs/main/linux-64/malformed_source.conda diff --git...	bug: conda-parser raises error when unexpected build-number is detected ## Environment XUbuntu 20.04 Python 3.8.10 conda 4.12.0 #miniconda Name: cyclonedx-bom Version: 3.1.0 ## What I did * update conda base ``` ->$ conda update -n base -c defaults conda -y Collecting package metadata (current_repodata.json...	c02d770cf18a57e118347a0a57db29ae65919c35	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_build_number_text", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_malformed", "tests/test_utils_conda.py::TestUtilsConda::test_parse_conda_list_no_build_number" ]	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_explicit_md5", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_json", "tests/test_utils_conda.py::TestUtilsConda::test_parse_conda_json_no_hash", "tests/test_utils_conda.py::TestUtilsConda::test_parse_conda_list_build_number", "test...	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-03-19 09:34:08+00:00	apache-2.0	150
CycloneDX__cyclonedx-python-348	diff --git a/cyclonedx_py/parser/pipenv.py b/cyclonedx_py/parser/pipenv.py index 8e1676f..9339201 100644 --- a/cyclonedx_py/parser/pipenv.py +++ b/cyclonedx_py/parser/pipenv.py @@ -44,7 +44,7 @@ class PipEnvParser(BaseParser): type='pypi', name=package_name, version=str(package_data.get('version') ...	CycloneDX/cyclonedx-python	194d2878fe088f8f1a680cc4eb95504c046d34a2	diff --git a/tests/test_parser_pipenv.py b/tests/test_parser_pipenv.py index 9d19f1d..751d282 100644 --- a/tests/test_parser_pipenv.py +++ b/tests/test_parser_pipenv.py @@ -50,7 +50,8 @@ class TestPipEnvParser(TestCase): self.assertEqual('anyio', c_anyio.name) self.assertEqual('3.3.3', c_anyio.versi...	bug: hashes not always included in BOM when present in Pipfile.lock Hashes appear to only be included in BOM output if they were originally called in the Pipfile as direct dependencies. According to the usage document (docs/usage.rst) hashes should be included if they are present. Given the following Pipfile, only b...	194d2878fe088f8f1a680cc4eb95504c046d34a2	[ "tests/test_parser_pipenv.py::TestPipEnvParser::test_with_multiple_and_no_index" ]	[ "tests/test_parser_pipenv.py::TestPipEnvParser::test_simple" ]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2022-04-18 17:47:49+00:00	apache-2.0	151
CycloneDX__cyclonedx-python-366	diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py index 1c9197b..487ad08 100644 --- a/cyclonedx_py/parser/conda.py +++ b/cyclonedx_py/parser/conda.py @@ -25,10 +25,12 @@ from cyclonedx.model import ExternalReference, ExternalReferenceType, HashAlgori from cyclonedx.model.component import Compone...	CycloneDX/cyclonedx-python	b028c2b96fb2caea2d7f084b6ef88cba1bcade2b	diff --git a/tests/test_parser_conda.py b/tests/test_parser_conda.py index ece9aec..fcbd711 100644 --- a/tests/test_parser_conda.py +++ b/tests/test_parser_conda.py @@ -29,10 +29,10 @@ from cyclonedx_py.parser.conda import CondaListExplicitParser, CondaListJsonPars class TestCondaParser(TestCase): def test_cond...	[CONDA] Incorrect purl type in SBoM from Conda Explicit MD5 list * What I did ``` # Create Conda environment with openssl included $ conda create -y --name openssl openssl=1.1.1o # Create an explicit MD5 list $ conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt # Create a SBoM from ...	b028c2b96fb2caea2d7f084b6ef88cba1bcade2b	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_build_number_text", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_explicit_md5", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_json", "tests/test_utils_conda.py::TestUtilsConda::test_parse_conda_list_build_number", ...	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_malformed", "tests/test_utils_conda.py::TestUtilsConda::test_parse_conda_json_no_hash" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2022-06-07 15:08:00+00:00	apache-2.0	152
CycloneDX__cyclonedx-python-367	diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py index 59fc527..1c9197b 100644 --- a/cyclonedx_py/parser/conda.py +++ b/cyclonedx_py/parser/conda.py @@ -21,7 +21,7 @@ import json from abc import ABCMeta, abstractmethod from typing import List -from cyclonedx.model import ExternalReference, E...	CycloneDX/cyclonedx-python	e2be444b8db7dd12031f3e9b481dfdae23f3e59e	diff --git a/tests/test_parser_conda.py b/tests/test_parser_conda.py index cf6c6a5..ece9aec 100644 --- a/tests/test_parser_conda.py +++ b/tests/test_parser_conda.py @@ -21,6 +21,8 @@ import os import re from unittest import TestCase +from cyclonedx.model import HashAlgorithm, HashType + from cyclonedx_py.parser.co...	[CONDA] Include component hashes when generating SBoM from Conda Explicit MD5 List * What I did ``` # Create Conda environment with openssl included conda create -y --name openssl openssl=1.1.1o # Create an explicit MD5 list conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt # Create ...	e2be444b8db7dd12031f3e9b481dfdae23f3e59e	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_explicit_md5" ]	[ "tests/test_parser_conda.py::TestCondaParser::test_conda_list_build_number_text", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_json", "tests/test_parser_conda.py::TestCondaParser::test_conda_list_malformed" ]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2022-06-07 15:27:56+00:00	apache-2.0	153
DCC-Lab__RayTracing-133	diff --git a/raytracing/rays.py b/raytracing/rays.py index 7787434..11de6ad 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -29,6 +29,12 @@ class Rays: self._thetaHistogram = None self._directionBinEdges = None + self._countHistogramParameters = None + self._xValuesCountHis...	DCC-Lab/RayTracing	25d5ffdd500afc561b8ce7d25dded3b532fd44a1	diff --git a/raytracing/tests/testsRays.py b/raytracing/tests/testsRays.py new file mode 100644 index 0000000..9bb4c7c --- /dev/null +++ b/raytracing/tests/testsRays.py @@ -0,0 +1,34 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestRays(unittest.TestCa...	rayCountHistogram() and rayAnglesHistogram() of Rays raise exception when already computed When we compute `rayCountHistogram()` for a first time, it works perfectly. But when we run it a second time, it throws an exception because a variable is referenced before asignment.	25d5ffdd500afc561b8ce7d25dded3b532fd44a1	[ "raytracing/tests/testsRays.py::TestRays::testRayAnglesHist", "raytracing/tests/testsRays.py::TestRays::testRayCountHist" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-05-20 21:34:21+00:00	mit	154
DCC-Lab__RayTracing-135	diff --git a/raytracing/rays.py b/raytracing/rays.py index 11de6ad..283eb00 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -4,20 +4,36 @@ import matplotlib.pyplot as plt import pickle import time import os - -""" A group of rays kept as a list, to be used as a starting -point (i.e. an object) or as a cu...	DCC-Lab/RayTracing	203b3739d0804718664037706e2d43068fcd6ac5	diff --git a/raytracing/tests/testsComponents.py b/raytracing/tests/testsComponents.py new file mode 100644 index 0000000..a4aba5b --- /dev/null +++ b/raytracing/tests/testsComponents.py @@ -0,0 +1,60 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class Test4f...	Rays() accepts objects from every type This can cause further problems. In `__init__` itself it is not a big deal (except for coherence and logic) if `Rays` receive a string of nonsense or a list of numbers, but other methods will inevitably fail with exceptions of different types.	203b3739d0804718664037706e2d43068fcd6ac5	[ "raytracing/tests/testsRays.py::TestRays::testRaysInitDifferentInputs", "raytracing/tests/testsRaysSubclasses.py::TestRandomRays::testRandomRay" ]	[ "raytracing/tests/testsComponents.py::Test4fSystem::test2fSystem", "raytracing/tests/testsComponents.py::Test4fSystem::test4fIsTwo2f", "raytracing/tests/testsComponents.py::Test4fSystem::test4fSystem", "raytracing/tests/testsRays.py::TestRays::testRayAnglesHist", "raytracing/tests/testsRays.py::TestRays::te...	{ "failed_lite_validators": [ "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-05-21 13:56:03+00:00	mit	155
DCC-Lab__RayTracing-141	diff --git a/raytracing/rays.py b/raytracing/rays.py index aaf1971..83ffaf1 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -288,9 +288,9 @@ class RandomRays(Rays): def __getitem__(self, item): if self.rays is None: - raise NotImplemented("You cannot access RandomRays") + ...	DCC-Lab/RayTracing	3a1d740763e8a3138f7c2c025f0dce707249acd9	diff --git a/raytracing/tests/testsComponents.py b/raytracing/tests/testsComponents.py new file mode 100644 index 0000000..a4aba5b --- /dev/null +++ b/raytracing/tests/testsComponents.py @@ -0,0 +1,60 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class Test4f...	RandomRays raises a constant, not an exception In `RandomRays`, some methods have `raise NotImplemented("...")`, but `NotImplemented` is a constant used in some binary methods (see https://docs.python.org/3/library/constants.html). I suspect what we want is `raise NotImplementedError("...")`.	3a1d740763e8a3138f7c2c025f0dce707249acd9	[ "raytracing/tests/testsRaysSubclasses.py::TestRandomRays::testRandomRay" ]	[ "raytracing/tests/testsComponents.py::Test4fSystem::test2fSystem", "raytracing/tests/testsComponents.py::Test4fSystem::test4fIsTwo2f", "raytracing/tests/testsComponents.py::Test4fSystem::test4fSystem" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-05-21 19:36:50+00:00	mit	156
DCC-Lab__RayTracing-176	diff --git a/raytracing/rays.py b/raytracing/rays.py index 9129491..a424fad 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -207,6 +207,10 @@ class Rays: def load(self, filePath, append=False): with open(filePath, 'rb') as infile: loadedRays = pickle.Unpickler(infile).load() + ...	DCC-Lab/RayTracing	ce69bb2fc28ba9864f2631abd5e87819aad1de74	diff --git a/raytracing/tests/testsRays.py b/raytracing/tests/testsRays.py index 33ac2e3..833ade3 100644 --- a/raytracing/tests/testsRays.py +++ b/raytracing/tests/testsRays.py @@ -69,7 +69,6 @@ class TestRays(unittest.TestCase): r = Rays(listOfRays) self.assertEqual(len(r), len(listOfRays)) - ...	Rays can load any "pickled" file This can lead to unwanted behaviors. We should check if the content of the file is an iterable of `Ray` objects. `load` directly extends (or override) the inner list or rays in `Rays`. This can cause unexpected problems without proper guidance to what caused the issue.	ce69bb2fc28ba9864f2631abd5e87819aad1de74	[ "raytracing/tests/testsRays.py::TestRaysSaveAndLoad::testLoadWrongFileContent" ]	[ "raytracing/tests/testsRays.py::TestRays::testAppend", "raytracing/tests/testsRays.py::TestRays::testAppendInvalidInput", "raytracing/tests/testsRays.py::TestRays::testCountRays", "raytracing/tests/testsRays.py::TestRays::testDisplayProgress", "raytracing/tests/testsRays.py::TestRays::testDisplayProgressNot...	{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-05-26 20:24:10+00:00	mit	157
DCC-Lab__RayTracing-180	diff --git a/raytracing/laserpath.py b/raytracing/laserpath.py index 4f74727..edcf1b2 100644 --- a/raytracing/laserpath.py +++ b/raytracing/laserpath.py @@ -1,6 +1,7 @@ from .matrixgroup import * from .imagingpath import * + class LaserPath(MatrixGroup): """LaserPath: the main class of the module for coherent...	DCC-Lab/RayTracing	03535abea0f84ad4eeb61c8da671579d95d6217e	diff --git a/raytracing/tests/testsLaserPath.py b/raytracing/tests/testsLaserPath.py new file mode 100644 index 0000000..6b90b03 --- /dev/null +++ b/raytracing/tests/testsLaserPath.py @@ -0,0 +1,26 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestLaser...	EigenModes of LaserPath fails with exception when C = 0 When we create a `LaserPath` and its C component is 0, we have a division by 0, which raises an exception. We should check if the laser path has power (`self.hasPower`) before and return `(None, None)` (maybe?) if not. We then need to change other methods, like `...	03535abea0f84ad4eeb61c8da671579d95d6217e	[ "raytracing/tests/testsLaserPath.py::TestLaserPath::testEigenModes", "raytracing/tests/testsLaserPath.py::TestLaserPath::testLaserModes" ]	[]	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-05-27 15:06:04+00:00	mit	158
DCC-Lab__RayTracing-187	diff --git a/raytracing/laserpath.py b/raytracing/laserpath.py index edcf1b2..ec4fd0c 100644 --- a/raytracing/laserpath.py +++ b/raytracing/laserpath.py @@ -62,7 +62,7 @@ class LaserPath(MatrixGroup): return q - def display(self, inputBeam=None, inputBeams=None, comments=None): + def display(self, in...	DCC-Lab/RayTracing	fe768d07b48df2be9428da6dc3d7f738c652915e	diff --git a/raytracing/tests/testsLaserPath.py b/raytracing/tests/testsLaserPath.py index 6b90b03..38134af 100644 --- a/raytracing/tests/testsLaserPath.py +++ b/raytracing/tests/testsLaserPath.py @@ -7,20 +7,75 @@ inf = float("+inf") class TestLaserPath(unittest.TestCase): - def testEigenModes(self): + def ...	ImagingPath and LaserPath methods in MatrixGroup raise exception. They respectively return a ImagingPath instance and a LaserPath instance, but those classes are in other files not imported. It is also worth mentioning that they both inherit from MatrixGroup, so it is kind of incoherent to use them in MatrixGroup. Q...	fe768d07b48df2be9428da6dc3d7f738c652915e	[ "raytracing/tests/testsMatrixGroup.py::TestMatrixGroup::testInitWithAnotherMatrixGroup" ]	[ "raytracing/tests/testsLaserPath.py::TestLaserPath::testEigenModes", "raytracing/tests/testsLaserPath.py::TestLaserPath::testEigenModesNoPower", "raytracing/tests/testsLaserPath.py::TestLaserPath::testLaserModes", "raytracing/tests/testsLaserPath.py::TestLaserPath::testLaserModesNoPower", "raytracing/tests/...	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-05-27 21:10:46+00:00	mit	159
DCC-Lab__RayTracing-192	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 82765ea..6a7e46b 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -151,8 +151,12 @@ class ImagingPath(MatrixGroup): If the element B in the transfer matrix for the imaging path is zero, there is no value ...	DCC-Lab/RayTracing	8b8d8f660c634a5cee6b0e3f926e298824ffa4d7	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 4e9ed76..b543b8b 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -56,6 +56,10 @@ class TestImagingPath(unittest.TestCase): path = ImagingPath(elements) self.as...	ImagingPath: chiefRay not working with no aperture stop When we create an `ImagingPath` without any aperture stop, `chiefRay` raises a `TypeError`, because there is no aperture stop. For example: ```python path = ImagingPath(System2f(10)) # A 2f system with f = 10 and infinite diameter path.chiefRay() # Fails with...	8b8d8f660c634a5cee6b0e3f926e298824ffa4d7	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithFiniteLens", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithObjectHigherThanLens", "raytracing/tests/testsImagingPath...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-05-28 20:59:11+00:00	mit	160
DCC-Lab__RayTracing-196	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 9960d83..6c89bff 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -585,6 +585,9 @@ class ImagingPath(MatrixGroup): """ fieldOfView = self.fieldOfView() (distance, conjugateMatrix) = self.forwardC...	DCC-Lab/RayTracing	adc82c7e2d87b0d90f2a9790fe6f36c67a7d94d2	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index b543b8b..2e24ab7 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,5 +61,10 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.asse...	ImagingPath: imageSize fails when D is 0 When `D == 0`, there is no forward conjugate (nor backward), so we return `conjugateMatrix` as `None`. Because of that, `imageSize` raises an `AttributeError`. We should check if `conjugateMatrix` is `None`, but what should we return? Since there is no image, return `None`?	adc82c7e2d87b0d90f2a9790fe6f36c67a7d94d2	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testImageSizeDIs0" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithFiniteLens", "raytracing/tests/testsImagingPath.py::TestImagi...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-05-29 13:36:56+00:00	mit	161
DCC-Lab__RayTracing-199	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index aa348eb..5c3b21d 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -161,7 +161,7 @@ class ImagingPath(MatrixGroup): A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B - if B == ...	DCC-Lab/RayTracing	84522313da81dcea8cf30d398e63b5223c102976	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index a6b39da..4239a06 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,12 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.asse...	ImagingPath: chiefRay doesn't return None when B is very close but not 0 When `B == 0` in an `ImagingPath` instance, there is no chief ray. But because we use a computer, some calculations can lead to something close to 0 but not quite 0. For example: ```python path = ImagingPath(System4f(pi * 2, pi * 1.25)) # This i...	84522313da81dcea8cf30d398e63b5223c102976	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayBIs0" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayInfiniteFieldOfViewNoY", "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestI...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-05-29 14:36:25+00:00	mit	162
DCC-Lab__RayTracing-200	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index eaea927..aa348eb 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -166,6 +166,8 @@ class ImagingPath(MatrixGroup): if y is None: y = self.fieldOfView() + if abs(y) == float("+inf"): + ...	DCC-Lab/RayTracing	427fbe9fdcb21c452788b180ba683dff6a0c7321	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 6590fe8..a6b39da 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,12 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.asse...	ImagingPath: chiefRay returns y=inf and theta=-inf with really big (but not infinite) aperture and no specific y given When we create an `ImagingPath` with a really big aperture stop (but not infinite), the chief ray obtained has y = -theta = inf. This doesn't really make sense. This happens because the aperture is ...	427fbe9fdcb21c452788b180ba683dff6a0c7321	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayInfiniteFieldOfViewNoY" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithFiniteLens", "raytracing/tests/testsImagingPath.py::TestImagi...	{ "failed_lite_validators": [ "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-05-29 14:49:57+00:00	mit	163
DCC-Lab__RayTracing-202	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index b9ee7de..eaea927 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -188,7 +188,6 @@ class ImagingPath(MatrixGroup): """ return self.chiefRay(y=None) - def marginalRays(self, y=0): """This f...	DCC-Lab/RayTracing	2c3d3f64b5aa09fc0a45a2422fe8bef834972b0b	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index be8f0e1..6590fe8 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,10 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.asse...	ImagingPath: marginalRays raises exception when no apertureStop When we want the marginal rays of an `ImagingPath` that has no aperture stop, a `TypeError` is raised. Example: ```python path = ImagingPath(System4f(10, 10)) path.marginalRays() # Raises TypeError, no field stop ```	2c3d3f64b5aa09fc0a45a2422fe8bef834972b0b	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testMarginalRaysNoApertureStop" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithFiniteLens", "raytracing/tests/testsImagingPath.py::TestImagi...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-05-29 15:58:10+00:00	mit	164
DCC-Lab__RayTracing-204	diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 6c89bff..b9ee7de 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -260,6 +260,9 @@ class ImagingPath(MatrixGroup): A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B + if trans...	DCC-Lab/RayTracing	4e999c92bde9e68c018859054193bf4a00d560a3	diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 2e24ab7..be8f0e1 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,11 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.asse...	ImagingPath: division by 0 in marginalRays When we have an `ImagingPath` that has a transfer matrix to the aperture stop with `B == 0`, there is a division by 0 in the calculations of theta + and -. We should check when it's the case and return `None`.	4e999c92bde9e68c018859054193bf4a00d560a3	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testMarginalRaysIsImaging" ]	[ "raytracing/tests/testsImagingPath.py::TestImagingPath::testChiefRayNoApertureStop", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithEmptyPath", "raytracing/tests/testsImagingPath.py::TestImagingPath::testDisplayRangeWithFiniteLens", "raytracing/tests/testsImagingPath.py::TestImagi...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-05-29 16:14:37+00:00	mit	165
DCC-Lab__RayTracing-220	diff --git a/raytracing/gaussianbeam.py b/raytracing/gaussianbeam.py index 77dbfab..03bd73b 100644 --- a/raytracing/gaussianbeam.py +++ b/raytracing/gaussianbeam.py @@ -4,20 +4,46 @@ import cmath class GaussianBeam(object): """A gaussian laser beam using the ABCD formalism for propagation of complex radius of cur...	DCC-Lab/RayTracing	52e850c6260b476c4925eb543702195f73cc779b	diff --git a/raytracing/tests/testsGaussian.py b/raytracing/tests/testsGaussian.py index 8c26cff..be32f22 100644 --- a/raytracing/tests/testsGaussian.py +++ b/raytracing/tests/testsGaussian.py @@ -6,7 +6,6 @@ inf = float("+inf") class TestBeam(unittest.TestCase): def testBeam(self): - beam = GaussianBeam...	GaussianBeam: q or w should be specified (not both None) This can lead to some incoherence: we should check (if q and w are given) that q computed with w is relatively close to q given. Also, we should not be able to set both as `None`. Having w and q has `None` does nothing good, only lead to issues with methods, b...	52e850c6260b476c4925eb543702195f73cc779b	[ "raytracing/tests/testsGaussian.py::TestBeam::testInvalidParameters" ]	[ "raytracing/tests/testsGaussian.py::TestBeam::testBeam", "raytracing/tests/testsGaussian.py::TestBeam::testDielectricInterfaceBeam", "raytracing/tests/testsGaussian.py::TestBeam::testFocalSpot", "raytracing/tests/testsGaussian.py::TestBeam::testMultiplicationBeam", "raytracing/tests/testsGaussian.py::TestBe...	{ "failed_lite_validators": [ "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-06-02 14:09:43+00:00	mit	166
DCC-Lab__RayTracing-223	diff --git a/raytracing/matrix.py b/raytracing/matrix.py index 43f9790..c84cede 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -846,7 +846,8 @@ class Matrix(object): @property def hasPower(self): - """ If True, then there is a non-null focal length because C!=0 + """ If True, ...	DCC-Lab/RayTracing	ba11e628ea9be0cf8f45efc2013c49529bd2d801	diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index 9c75340..886a9b4 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -344,6 +344,15 @@ class TestMatrix(unittest.TestCase): m2 = Matrix(A=1, B=1, C=3, D=4) self.assertFalse(m2.isImagi...	Matrix: hasPower returns True when it should be False When we want to know if a `Matrix` has power, we check if `self.C != 0`. In some cases, computational errors occurs due to the fact that we are handling floats and `self.C` is really close to 0. Example: ```python d1 = 1.0000000000000017 # Some computation errors ...	ba11e628ea9be0cf8f45efc2013c49529bd2d801	[ "raytracing/tests/testsMatrix.py::TestMatrix::testHasNoPower" ]	[ "raytracing/tests/testsMatrix.py::TestMatrix::testApertureDiameter", "raytracing/tests/testsMatrix.py::TestMatrix::testAxesToDataScale", "raytracing/tests/testsMatrix.py::TestMatrix::testBackFocalLengthSupposedNone", "raytracing/tests/testsMatrix.py::TestMatrix::testDisplayHalfHeight", "raytracing/tests/tes...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-06-02 19:03:14+00:00	mit	167
DCC-Lab__RayTracing-258	diff --git a/raytracing/figure.py b/raytracing/figure.py index a0b9014..dee5eb4 100644 --- a/raytracing/figure.py +++ b/raytracing/figure.py @@ -180,6 +180,8 @@ class Figure: conjugates = self.path.intermediateConjugates() if len(conjugates) != 0: for (planePosition, magnification) in con...	DCC-Lab/RayTracing	12e2e1fe89e74637d25304b4e101c71103de480c	diff --git a/raytracing/tests/envtest.py b/raytracing/tests/envtest.py index c20889c..5a57a3b 100644 --- a/raytracing/tests/envtest.py +++ b/raytracing/tests/envtest.py @@ -5,7 +5,6 @@ import tempfile class RaytracingTestCase(unittest.TestCase): tempDir = os.path.join(tempfile.gettempdir(), "tempDir") - remo...	MatrixGroup: intermediateConjugates gives duplicates When we want the intermediate conjugates of some matrix groups, we have a list with duplicates. Is it normal? Example: ```python path = ImagingPath(System4f(10, 5)) print(path.intermediateConjugates()) ``` the output is: ```python [[30.0, -0.5], [30.0, -0.5...	12e2e1fe89e74637d25304b4e101c71103de480c	[ "raytracing/tests/testsFigure.py::TestFigure::testDisplayRangeImageOutOfView", "raytracing/tests/testsMatrixGroup.py::TestMatrixGroup::testIntermediateConjugatesDuplicates" ]	[ "raytracing/tests/testsEnvtest.py::TestUnittestSkipMethodsWrapper::testSkipIfWithFalseCondition", "raytracing/tests/testsEnvtest.py::TestUnittestSkipMethodsWrapper::testSkipUnlessTrueCondition", "raytracing/tests/testsEnvtest.py::TestEnvtestClass::testCreateTempDirectoryAlreadyExistsAndDelete", "raytracing/te...	{ "failed_lite_validators": [ "has_many_modified_files", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-06-11 13:42:58+00:00	mit	168
DCC-Lab__RayTracing-259	diff --git a/raytracing/figure.py b/raytracing/figure.py index a0b9014..dee5eb4 100644 --- a/raytracing/figure.py +++ b/raytracing/figure.py @@ -180,6 +180,8 @@ class Figure: conjugates = self.path.intermediateConjugates() if len(conjugates) != 0: for (planePosition, magnification) in con...	DCC-Lab/RayTracing	12e2e1fe89e74637d25304b4e101c71103de480c	diff --git a/raytracing/tests/envtest.py b/raytracing/tests/envtest.py index c20889c..5a57a3b 100644 --- a/raytracing/tests/envtest.py +++ b/raytracing/tests/envtest.py @@ -5,7 +5,6 @@ import tempfile class RaytracingTestCase(unittest.TestCase): tempDir = os.path.join(tempfile.gettempdir(), "tempDir") - remo...	Generating unnecessary images illumination = ImagingPath() illumination.append(Space(d=10)) illumination.append(Lens(f=10, diameter=100, label="Collector")) illumination.append(Space(d=10+30)) illumination.append(Lens(f=30, diameter=100, label="Condenser")) illumination.append(Space(d=30+7)) illumination.appen...	12e2e1fe89e74637d25304b4e101c71103de480c	[ "raytracing/tests/testsFigure.py::TestFigure::testDisplayRangeImageOutOfView" ]	[ "raytracing/tests/testsEnvtest.py::TestUnittestSkipMethodsWrapper::testSkipIfWithFalseCondition", "raytracing/tests/testsEnvtest.py::TestUnittestSkipMethodsWrapper::testSkipUnlessTrueCondition", "raytracing/tests/testsEnvtest.py::TestEnvtestClass::testCreateTempDirectoryAlreadyExistsAndDelete", "raytracing/te...	{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-06-11 13:46:04+00:00	mit	169
DCC-Lab__RayTracing-273	diff --git a/raytracing/matrix.py b/raytracing/matrix.py index ff6293f..5878f23 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -136,6 +136,10 @@ class Matrix(object): self.isFlipped = False super(Matrix, self).__init__() + @property + def isIdentity(self): + return self...	DCC-Lab/RayTracing	92c62c400ca31119d4896422f4fba2bd030d3739	diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index 58e8738..267ae0a 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -36,6 +36,42 @@ class TestMatrix(envtest.RaytracingTestCase): self.assertEqual(m3.C, 1 * 7 + 3 * 8) self.assertEqu...	Matrix multiplication returns a matrix with n1 = n2 = 1 I don't really know what we should do: in some cases, both matrices have the same n1 and n2, then the result should have n1 and n2. But sometimes they differ. I saw it happen in `MatrixGroup` when we append and build a transfer matrix: we create an identity matrix...	92c62c400ca31119d4896422f4fba2bd030d3739	[ "raytracing/tests/testsMatrix.py::TestMatrix::testIsIdentity", "raytracing/tests/testsMatrix.py::TestMatrix::testIsNotIdentity", "raytracing/tests/testsMatrix.py::TestMatrix::testMatrixProductIndicesLHSIsIdentity", "raytracing/tests/testsMatrix.py::TestMatrix::testMatrixProductIndicesRHSIsIdentity" ]	[ "raytracing/tests/testsMatrix.py::TestMatrix::testApertureDiameter", "raytracing/tests/testsMatrix.py::TestMatrix::testBackFocalLengthSupposedNone", "raytracing/tests/testsMatrix.py::TestMatrix::testDisplayHalfHeight", "raytracing/tests/testsMatrix.py::TestMatrix::testDisplayHalfHeightInfiniteDiameter", "ra...	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-06-15 18:27:04+00:00	mit	170
DCC-Lab__RayTracing-282	diff --git a/raytracing/matrix.py b/raytracing/matrix.py index 2f8ff11..7f32c1b 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -122,6 +122,8 @@ class Matrix(object): # Length of this element self.L = float(physicalLength) # Aperture + if apertureDiameter <= 0: + ...	DCC-Lab/RayTracing	0da4c11f47ae13a1db8272b8edc52387ad1863dd	diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index f36fe01..c160580 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -20,9 +20,17 @@ class TestMatrix(envtest.RaytracingTestCase): m = Matrix() self.assertIsNotNone(m) + def test...	Matrix accepts a negative aperture diameter This doesn't make any sense. Even the doc specifies that it must be positive.	0da4c11f47ae13a1db8272b8edc52387ad1863dd	[ "raytracing/tests/testsMatrix.py::TestMatrix::testNegativeApertureDiameter", "raytracing/tests/testsMatrix.py::TestMatrix::testNullApertureDiameter" ]	[ "raytracing/tests/testsMatrix.py::TestMatrix::testApertureDiameter", "raytracing/tests/testsMatrix.py::TestMatrix::testBackFocalLengthSupposedNone", "raytracing/tests/testsMatrix.py::TestMatrix::testDielectricInterfaceEffectiveFocalLengths", "raytracing/tests/testsMatrix.py::TestMatrix::testDisplayHalfHeight"...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-06-19 13:58:58+00:00	mit	171
DCC-Lab__RayTracing-293	diff --git a/raytracing/axicon.py b/raytracing/axicon.py index 4bf6013..680a686 100644 --- a/raytracing/axicon.py +++ b/raytracing/axicon.py @@ -2,130 +2,170 @@ from .matrix import * import matplotlib.pyplot as plt - class Axicon(Matrix): - """ - This class is an advanced module that describes an axicon lens, not...	DCC-Lab/RayTracing	0574559c65ccce3efb17d36176d0985c9c20a781	diff --git a/raytracing/tests/testsAxicon.py b/raytracing/tests/testsAxicon.py new file mode 100644 index 0000000..483cafa --- /dev/null +++ b/raytracing/tests/testsAxicon.py @@ -0,0 +1,108 @@ +import envtest + +from raytracing import * +from numpy import random +from numpy import * + +inf = float("+inf") +degrees = ma...	Axicon does not change the values of backIndex and frontIndex The `Axicon` class does not change the default values of `backIndex` and `frontIndex` with the input value `n`.	0574559c65ccce3efb17d36176d0985c9c20a781	[ "raytracing/tests/testsAxicon.py::TestAxicon::testDifferentMultiplications", "raytracing/tests/testsAxicon.py::TestAxicon::testFocalLineLengthSignOfY", "raytracing/tests/testsAxicon.py::TestAxicon::testMulMatrix" ]	[ "raytracing/tests/testsAxicon.py::TestAxicon::testAxicon", "raytracing/tests/testsAxicon.py::TestAxicon::testDeviationAngle", "raytracing/tests/testsAxicon.py::TestAxicon::testDeviationAngleIs0", "raytracing/tests/testsAxicon.py::TestAxicon::testDeviationAngleIs0Too", "raytracing/tests/testsAxicon.py::TestA...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2020-06-25 16:05:59+00:00	mit	172
DHI__mikeio-238	diff --git a/mikeio/dataset.py b/mikeio/dataset.py index b447f1c7..39255424 100644 --- a/mikeio/dataset.py +++ b/mikeio/dataset.py @@ -162,31 +162,44 @@ class Dataset(TimeSeries): def __len__(self): return len(self.items) - def __getitem__(self, x): + def __setitem__(self, key, value): - ...	DHI/mikeio	1805f86b1e3e2f6c9946759f99e9bdf957be9347	diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 1191c867..36b453b9 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -11,6 +11,7 @@ from mikeio.eum import EUMType, ItemInfo, EUMUnit def _get_time(nt): return list(rrule(freq=SECONDLY, count=nt, dtstart=datetime(2000, 1, 1))) + @...	Dataset item assignment ![image](https://user-images.githubusercontent.com/614215/132855983-021049d6-ad62-4bcf-8ff6-e137932fa4e8.png)	1805f86b1e3e2f6c9946759f99e9bdf957be9347	[ "tests/test_dataset.py::test_set_data_name" ]	[ "tests/test_dataset.py::test_get_names", "tests/test_dataset.py::test_select_subset_isel", "tests/test_dataset.py::test_select_temporal_subset_by_idx", "tests/test_dataset.py::test_temporal_subset_fancy", "tests/test_dataset.py::test_subset_with_datetime_is_not_supported", "tests/test_dataset.py::test_sel...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks", "has_media", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2021-09-10 15:41:27+00:00	bsd-3-clause	173
DHI__mikeio-442	diff --git a/mikeio/pfs.py b/mikeio/pfs.py index 10d80fce..e8812520 100644 --- a/mikeio/pfs.py +++ b/mikeio/pfs.py @@ -203,8 +203,11 @@ def parse_yaml_preserving_duplicates(src, unique_keywords=True): data[key] = [] data[key].append(val) else: - ...	DHI/mikeio	3f8bb643a6d4e0fefae07356fcf6a16ac2972035	diff --git a/tests/test_pfs.py b/tests/test_pfs.py index 1bf1e42e..6355799d 100644 --- a/tests/test_pfs.py +++ b/tests/test_pfs.py @@ -1,3 +1,4 @@ +from io import StringIO import sys import os import pytest @@ -375,8 +376,8 @@ def test_non_unique_keywords(): assert len(pfs.BoundaryExtractor.POINT_1) == 2 a...	PFS. read write of parameter list, which contains both boolean and string MIKE IO version 1.2.dev0 This is probably a rare case, but it seems that this line will fail: fill_list = false, 'TEST' if you read it from a pfs file and try to write it again you will get this: fill_list = 'false, 'TEST'' ...	3f8bb643a6d4e0fefae07356fcf6a16ac2972035	[ "tests/test_pfs.py::test_non_unique_keywords", "tests/test_pfs.py::test_read_in_memory_string", "tests/test_pfs.py::test_read_mixed_array", "tests/test_pfs.py::test_read_mixed_array2", "tests/test_pfs.py::test_read_mixed_array3", "tests/test_pfs.py::test_read_array", "tests/test_pfs.py::test_read_string...	[ "tests/test_pfs.py::test_pfssection", "tests/test_pfs.py::test_pfssection_keys_values_items", "tests/test_pfs.py::test_pfssection_from_dataframe", "tests/test_pfs.py::test_pfssection_to_dict", "tests/test_pfs.py::test_pfssection_get", "tests/test_pfs.py::test_pfssection_pop", "tests/test_pfs.py::test_pf...	{ "failed_lite_validators": [ "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-10-04 14:13:08+00:00	bsd-3-clause	174
DKISTDC__dkist-288	diff --git a/.readthedocs.yml b/.readthedocs.yml index a3619c6..13f5cf2 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,6 +7,7 @@ sphinx: # Optionally build your docs in additional formats such as PDF formats: - pdf + - htmlzip build: os: ubuntu-22.04 diff --git a/changelog/288.bugfix.rst b/cha...	DKISTDC/dkist	185c2490bd914ad3b12d9df2b845a3ffdbedd642	diff --git a/dkist/data/test/AGLKO-inv.ecsv b/dkist/data/test/AGLKO-inv.ecsv new file mode 100644 index 0000000..916821d --- /dev/null +++ b/dkist/data/test/AGLKO-inv.ecsv @@ -0,0 +1,114 @@ +# %ECSV 1.0 +# --- +# datatype: +# - {name: Start Time, datatype: string} +# - {name: End Time, datatype: string} +# - {name: Ins...	`transfer_complete_datasets` is being weird `transfer_complete_datasets("BKEWK", path="~/dkist_data")`	185c2490bd914ad3b12d9df2b845a3ffdbedd642	[ "dkist/utils/tests/test_inventory.py::test_cycle_single_row" ]	[ "dkist/utils/tests/test_inventory.py::test_humanize_loop", "dkist/utils/tests/test_inventory.py::test_path_format_table" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_added_files", "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2023-08-08 14:27:51+00:00	bsd-3-clause	175
DMTF__python-redfish-library-79	diff --git a/requirements.txt b/requirements.txt index 060d85f..fba487f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -jsonpatch +jsonpatch<=1.24 ; python_version == '3.4' +jsonpatch ; python_version >= '3.5' or python_version == '2.7' jsonpath_rw jsonpointer -urlparse2 \ No newline at end...	DMTF/python-redfish-library	58e4a2dfa58cbe51f4a8bef1fa20371d5197c8ed	diff --git a/tests/ris/test_rmc_helper.py b/tests/ris/test_rmc_helper.py new file mode 100644 index 0000000..dbf4a29 --- /dev/null +++ b/tests/ris/test_rmc_helper.py @@ -0,0 +1,29 @@ +# Copyright Notice: +# Copyright 2020 DMTF. All rights reserved. +# License: BSD 3-Clause License. For full text see link: +# https:...	Remove old library dependency - urlparse2 urlparse2 is an unmaintained library - last commit is 6 years old. The library is not python3 compatible (at least it's dependecy - recordtype library). HP's fork of python-redfish-library dropped urlparse2 last year... https://github.com/HewlettPackard/python-ilorest-libr...	58e4a2dfa58cbe51f4a8bef1fa20371d5197c8ed	[ "tests/ris/test_rmc_helper.py::RmcHelper::test_get_cache_dirname" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-01-29 23:24:24+00:00	bsd-3-clause	176
DOV-Vlaanderen__pydov-388	diff --git a/pydov/util/location.py b/pydov/util/location.py index d28fa33..f2b01aa 100644 --- a/pydov/util/location.py +++ b/pydov/util/location.py @@ -29,7 +29,16 @@ class AbstractLocation(object): """ + def _get_id_seed(self): + """Get the seed for generating a random but stable GML ID for this + ...	DOV-Vlaanderen/pydov	33c8b897494baba50aeea24b4421a407e40a057f	diff --git a/tests/test_util_location.py b/tests/test_util_location.py index bed8407..292dcc2 100644 --- a/tests/test_util_location.py +++ b/tests/test_util_location.py @@ -25,7 +25,8 @@ from tests.abstract import clean_xml class TestLocation(object): """Class grouping tests for the AbstractLocation subtypes.""" ...	Box and Point locations do not serialize into stable XML <!-- You can ask questions about the DOV webservices or about the `pydov` package. If you have a question about the `pydov` Python package, please use following template. --> * PyDOV version: master * Python version: 3.10.6 * Operating System: ubuntu ### ...	33c8b897494baba50aeea24b4421a407e40a057f	[ "tests/test_util_location.py::TestLocation::test_gml_id_stable", "tests/test_util_owsutil.py::TestWfsGetFeatureRequest::test_wfs_build_getfeature_request_gml_id_stable" ]	[ "tests/test_util_location.py::TestLocation::test_gml_id_unique", "tests/test_util_location.py::TestLocation::test_box", "tests/test_util_location.py::TestLocation::test_box_wgs84", "tests/test_util_location.py::TestLocation::test_box_invalid", "tests/test_util_location.py::TestLocation::test_box_invalid_wgs...	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-06-09 15:20:24+00:00	mit	177
DarkEnergySurvey__mkauthlist-16	diff --git a/.gitignore b/.gitignore index 5b6ffac..086cdcc 100644 --- a/.gitignore +++ b/.gitignore @@ -10,4 +10,5 @@ dist .out .aux .log -.spl \ No newline at end of file +.spl +.cls \ No newline at end of file diff --git a/data/author_order.csv b/data/author_order.csv index 3749293..de4b8f3 100644 --- a/dat...	DarkEnergySurvey/mkauthlist	15365e9ab90a623e3109739dd3f9c7d1fbb91fb7	diff --git a/tests/test_authlist.py b/tests/test_authlist.py index 958472e..cb57ba3 100644 --- a/tests/test_authlist.py +++ b/tests/test_authlist.py @@ -9,7 +9,7 @@ import logging import subprocess import unittest -class TestAuthlistFunc(unittest.TestCase): +class TestAuthlist(unittest.TestCase): def setUp(s...	Python 3 byte strings The Python 3 `str` object is based on Unicode, which means that `file.write(..., 'wb')` doesn't work anymore. We need to change this, but we should probably also understand why we were specifying `'wb'` in the first place. Some documentation on the Python 3 change: https://www.python.org/dev/p...	15365e9ab90a623e3109739dd3f9c7d1fbb91fb7	[ "tests/test_authlist.py::TestAuthlist::test_contribution", "tests/test_authlist.py::TestAuthlist::test_order", "tests/test_authlist.py::TestAuthlist::test_sort", "tests/test_authlist.py::TestAuthlist::test_sort_builder", "tests/test_authlist.py::TestAuthlist::test_sort_order" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-06-01 04:21:26+00:00	mit	178
DarkEnergySurvey__mkauthlist-29	diff --git a/data/author_order.csv b/data/author_order.csv index de4b8f3..e3bd9af 100644 --- a/data/author_order.csv +++ b/data/author_order.csv @@ -3,4 +3,5 @@ Sheldon, Erin #Commented, Name Drlica-Wagner Rykoff -Plazas Malagón \ No newline at end of file +Plazas Malagón +Sanchez, Carles diff --git a/data/example_a...	DarkEnergySurvey/mkauthlist	2644d26323e073616ccad45dea426bb9c485ee3a	diff --git a/tests/test_authlist.py b/tests/test_authlist.py index e879ff7..15ffb44 100644 --- a/tests/test_authlist.py +++ b/tests/test_authlist.py @@ -70,7 +70,7 @@ class TestAuthlist(unittest.TestCase): authors = [l for l in f.readlines() if l.startswith('\\author')] self.assertEqual(author...	Ordering with duplicate lastnames We currently throw an error when ordering on non-unique last names. We should be able to explicitly use author first names in ordering, but we currently don't require first names be included in the ordering file. This was causing issues for @joezuntz.	2644d26323e073616ccad45dea426bb9c485ee3a	[ "tests/test_authlist.py::TestAuthlist::test_order" ]	[ "tests/test_authlist.py::TestAuthlist::test_contribution", "tests/test_authlist.py::TestAuthlist::test_sort", "tests/test_authlist.py::TestAuthlist::test_sort_builder", "tests/test_authlist.py::TestAuthlist::test_sort_order" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2017-08-11 02:23:35+00:00	mit	179
DataBiosphere__newt-transformer-24	diff --git a/newt/transform/gen3old.py b/newt/transform/gen3old.py index 2c1ac2f..6c0c940 100644 --- a/newt/transform/gen3old.py +++ b/newt/transform/gen3old.py @@ -34,13 +34,17 @@ class Gen3Transformer(AbstractTransformer): @staticmethod def _build_metadata_dict(input_metadata): - def build_metadata...	DataBiosphere/newt-transformer	619bca38de35f68d12168d198892f1de3cfd40c3	diff --git a/tests/test_data/topmed-public.json b/tests/test_data/topmed-public.json index d2f5b41..61fce82 100644 --- a/tests/test_data/topmed-public.json +++ b/tests/test_data/topmed-public.json @@ -1,21833 +1,1 @@ -{ - "data_objects": [ - { - "checksums": [ - { - "checksum": "7af0014daca79bc...	Change data_bleach.py to retain sample.submitter_id The field `sample.submitter_id` is a useful value that should not be sanitized (cleared) by `data_bleach.py`	619bca38de35f68d12168d198892f1de3cfd40c3	[ "tests/test_all.py::TestSheepdogGen3Transforming::test_sheepdog_gen3_transforming", "tests/test_all.py::TestSheepdogGen3TransformingStandard::test_sheepdog_gen3_transforming" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-10-11 12:52:32+00:00	apache-2.0	180
DataBiosphere__newt-transformer-28	diff --git a/newt/main.py b/newt/main.py index f44243e..3910850 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,9 +16,9 @@ def open_json_file(json_path): return json.load(fp) -def write_output(bundles: typing.Iterator[Bundle], out_file): +def write_output(bundles: typing.Iterator[Bundle], out_file, pre...	DataBiosphere/newt-transformer	9ca346cb3dcdb18535e06c95fee10470f72d60cd	diff --git a/tests/schemas.py b/tests/schemas.py index 1acc954..8ac2944 100644 --- a/tests/schemas.py +++ b/tests/schemas.py @@ -124,7 +124,7 @@ data_object_schema = { data_bundle = { "type": "object", # TODO: required, but we don't have checksums for bundles - 'required': ['data_object_ids', 'created', '...	Add `program` metadata The Gen3 data model provides a `program` object, in addition to `project` and `study`. Currently the `newt` output includes `project` and `study` yet not `program`. The `program` object should be included in the `newt` output for indexing/display purposes. ┆Issue is synchronized with this [JIRA ...	9ca346cb3dcdb18535e06c95fee10470f72d60cd	[ "tests/test_all.py::TestSheepdogGen3TransformingStandard::test_sheepdog_gen3_transforming" ]	[ "tests/test_all.py::TestSheepdogGen3Transforming::test_sheepdog_gen3_transforming" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-10-12 17:47:34+00:00	apache-2.0	181
DataBiosphere__newt-transformer-32	diff --git a/newt/main.py b/newt/main.py index f44243e..3910850 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,9 +16,9 @@ def open_json_file(json_path): return json.load(fp) -def write_output(bundles: typing.Iterator[Bundle], out_file): +def write_output(bundles: typing.Iterator[Bundle], out_file, pre...	DataBiosphere/newt-transformer	9ca346cb3dcdb18535e06c95fee10470f72d60cd	diff --git a/tests/schemas.py b/tests/schemas.py index 1acc954..8ac2944 100644 --- a/tests/schemas.py +++ b/tests/schemas.py @@ -124,7 +124,7 @@ data_object_schema = { data_bundle = { "type": "object", # TODO: required, but we don't have checksums for bundles - 'required': ['data_object_ids', 'created', '...	Sanitize data using values of the same type Elasticsearch is very particular about the type of each JSON value. When sanitizing data with `data_bleach.py` the sanitized value must be of the same type as the original value. Currently, `data_bleach.py` sanitizes all values using an empty string value. ┆Issue is synchron...	9ca346cb3dcdb18535e06c95fee10470f72d60cd	[ "tests/test_all.py::TestSheepdogGen3TransformingStandard::test_sheepdog_gen3_transforming" ]	[ "tests/test_all.py::TestSheepdogGen3Transforming::test_sheepdog_gen3_transforming" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-10-25 16:42:25+00:00	apache-2.0	182
DataBiosphere__newt-transformer-36	diff --git a/newt/main.py b/newt/main.py index 3910850..aafa6f9 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,6 +16,39 @@ def open_json_file(json_path): return json.load(fp) +def _recursive_traversal(d, f): + """ + recursively apply function f to each value in a dictionary + + f takes in the...	DataBiosphere/newt-transformer	88473e29facefb7d8362e9956b5696091fe1c60f	diff --git a/tests/test_transform.py b/tests/test_transform.py index 6a46ee0..efe8bb1 100644 --- a/tests/test_transform.py +++ b/tests/test_transform.py @@ -7,7 +7,8 @@ import uuid import jsonschema from pathlib import Path -from newt.main import main +from newt.main import main, fix_empty_strings +from newt.transf...	Gen3 export/transform produces inconsistent JSON value types This is a duplication of a TLP ticket ┆Issue is synchronized with this [JIRA Task](https://ucsc-cgl.atlassian.net/browse/NEWT-28) ┆Project Name: CGP-Newt ┆Issue Number: NEWT-28	88473e29facefb7d8362e9956b5696091fe1c60f	[ "tests/test_transform.py::TestSheepdogGen3Transforming::test_sheepdog_gen3_transforming", "tests/test_transform.py::TestSheepdogGen3TransformingStandard::test_clearing_empty_strings", "tests/test_transform.py::TestSheepdogGen3TransformingStandard::test_sheepdog_gen3_transforming" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2018-11-01 23:57:53+00:00	apache-2.0	183
DataBiosphere__toil-4077	diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 89ac5dfe..901f7a19 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -97,9 +97,7 @@ py37_main: - virtualenv -p python3.7 venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[all] packages='htcondor awscli' - make t...	DataBiosphere/toil	b6b33030b165ac03a823f08b00f8fd8fa7590520	diff --git a/src/toil/test/lib/test_misc.py b/src/toil/test/lib/test_misc.py new file mode 100644 index 00000000..1924f7ae --- /dev/null +++ b/src/toil/test/lib/test_misc.py @@ -0,0 +1,83 @@ +# Copyright (C) 2015-2022 Regents of the University of California +# +# Licensed under the Apache License, Version 2.0 (the "Lic...	Toil can't start when the current user has no username As reported in https://github.com/ComparativeGenomicsToolkit/cactus/issues/677, the Kubernetes batch system calls `getpass.getuser()` when composing command line options, as Toil is starting up, but doesn't handle the `KeyError` it raises if you're running as a UID...	b6b33030b165ac03a823f08b00f8fd8fa7590520	[ "src/toil/test/lib/test_misc.py::UserNameAvailableTest::test_get_user_name", "src/toil/test/lib/test_misc.py::UserNameUnvailableTest::test_get_user_name", "src/toil/test/lib/test_misc.py::UserNameVeryBrokenTest::test_get_user_name" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-04-06 16:33:40+00:00	apache-2.0	184
DataBiosphere__toil-4445	diff --git a/src/toil/common.py b/src/toil/common.py index d0eb1bc8..d4a8c73c 100644 --- a/src/toil/common.py +++ b/src/toil/common.py @@ -198,7 +198,7 @@ class Config: self.writeLogs = None self.writeLogsGzip = None self.writeLogsFromAllJobs: bool = False - self.write_messages: str = ...	DataBiosphere/toil	2804edfc6128c2c9e66ff348696eda95cb63b400	diff --git a/src/toil/test/src/busTest.py b/src/toil/test/src/busTest.py index 6be0ab45..da6edb54 100644 --- a/src/toil/test/src/busTest.py +++ b/src/toil/test/src/busTest.py @@ -13,12 +13,19 @@ # limitations under the License. import logging +import os from threading import Thread, current_thread +from typing imp...	Toil relying on tmpfile directory structure during --restart This came up here: https://github.com/ComparativeGenomicsToolkit/cactus/issues/987 and, from the stack trace, doesn't look like it's coming from Cactus (?). The user reruns with `--restart` and Toil tries to write a temporary file into a temporary direct...	2804edfc6128c2c9e66ff348696eda95cb63b400	[ "src/toil/test/src/busTest.py::MessageBusTest::test_restart_without_bus_path" ]	[ "src/toil/test/src/busTest.py::MessageBusTest::test_cross_thread_messaging", "src/toil/test/src/busTest.py::MessageBusTest::test_enum_ints_in_file" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2023-04-20 17:36:28+00:00	apache-2.0	185
DataBiosphere__toil-4802	diff --git a/src/toil/batchSystems/abstractBatchSystem.py b/src/toil/batchSystems/abstractBatchSystem.py index 9da541de..fd0b30f9 100644 --- a/src/toil/batchSystems/abstractBatchSystem.py +++ b/src/toil/batchSystems/abstractBatchSystem.py @@ -59,13 +59,28 @@ class BatchJobExitReason(enum.IntEnum): MEMLIMIT: int = ...	DataBiosphere/toil	7166aa20554e02638d8afc638d2fadc30e23066d	diff --git a/src/toil/test/batchSystems/test_slurm.py b/src/toil/test/batchSystems/test_slurm.py index d8b3ac32..0e68391f 100644 --- a/src/toil/test/batchSystems/test_slurm.py +++ b/src/toil/test/batchSystems/test_slurm.py @@ -4,6 +4,7 @@ from queue import Queue import pytest import toil.batchSystems.slurm +from to...	Slurm job timeout doesn't seem to register as failure I just ran into the Slurm time limit for the first time. From the Toil logs, it looks like my job starts again, with no job failure or error message. Since there's nothing about deprecating `retryCount`, I suspect it may go on forever. It's only by looking in the...	7166aa20554e02638d8afc638d2fadc30e23066d	[ "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_exists", "src/...	[ "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_sacct_raises_job_not_exists", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_getJobDetailsFromSacct_many_all_exist", ...	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2024-02-16 19:05:57+00:00	apache-2.0	186
DataBiosphere__toil-4805	diff --git a/src/toil/options/common.py b/src/toil/options/common.py index 61086f3d..5c041f3b 100644 --- a/src/toil/options/common.py +++ b/src/toil/options/common.py @@ -733,4 +733,4 @@ def add_base_toil_options(parser: ArgumentParser, jobstore_as_flag: bool = False # dest is set to enableCaching to not conflic...	DataBiosphere/toil	6558c7f97fb37c6ef6f469c7ae614109050322f4	diff --git a/src/toil/test/options/__init__.py b/src/toil/test/options/__init__.py new file mode 100644 index 00000000..471fe7cd --- /dev/null +++ b/src/toil/test/options/__init__.py @@ -0,0 +1,13 @@ +# Copyright (C) 2015-2021 Regents of the University of California +# +# Licensed under the Apache License, Version 2.0 ...	FileJobStore's default_caching() result of False is not respected The `FileJobStore` is supposed to be able to set a default of no caching on the workflow: https://github.com/DataBiosphere/toil/blob/e45b27cb3086fc57f35653562357ab9537f45d4e/src/toil/jobStores/fileJobStore.py#L70-L78 But this no longer works. If I run a...	6558c7f97fb37c6ef6f469c7ae614109050322f4	[ "src/toil/test/options/options.py::OptionsTest::test_default_caching_slurm" ]	[ "src/toil/test/options/options.py::OptionsTest::test_caching_option_priority" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_issue_reference" ], "has_test_patch": true, "is_lite": false }	2024-02-22 04:30:15+00:00	apache-2.0	187
DataBiosphere__toil-4809	diff --git a/src/toil/worker.py b/src/toil/worker.py index 13d9a668..2f086c9f 100644 --- a/src/toil/worker.py +++ b/src/toil/worker.py @@ -118,6 +118,14 @@ def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, confi logger.debug("Next job is checkpoint, so finishing") return None ...	DataBiosphere/toil	c37f123ef2c67637f2aeec09ef2d6dddcfce90fd	diff --git a/src/toil/test/docs/scriptsTest.py b/src/toil/test/docs/scriptsTest.py index c1316a81..c1cd599b 100644 --- a/src/toil/test/docs/scriptsTest.py +++ b/src/toil/test/docs/scriptsTest.py @@ -5,6 +5,8 @@ import subprocess import sys import unittest +from typing import List + pkg_root = os.path.abspath(os.pa...	toil-wdl-runner can run task containers on the leader @jeizenga has a workflow where the first task doesn't ask for more than the default amount of resources. So we kick off the `WDLRootJob` locally on the leader, and it chains to a call-a-task job, which chains to the actual task job, which doesn't need to reschedule ...	c37f123ef2c67637f2aeec09ef2d6dddcfce90fd	[ "src/toil/test/src/workerTest.py::WorkerTests::testNextChainable" ]	[]	{ "failed_lite_validators": [ "has_hyperlinks" ], "has_test_patch": true, "is_lite": false }	2024-02-29 16:09:27+00:00	apache-2.0	188
DataBiosphere__toil-4873	diff --git a/src/toil/batchSystems/abstractGridEngineBatchSystem.py b/src/toil/batchSystems/abstractGridEngineBatchSystem.py index 98b48945..f41b3d0c 100644 --- a/src/toil/batchSystems/abstractGridEngineBatchSystem.py +++ b/src/toil/batchSystems/abstractGridEngineBatchSystem.py @@ -45,20 +45,21 @@ class AbstractGridEng...	DataBiosphere/toil	c566f315393f65804ead58e8f3878b010fff1cfe	diff --git a/src/toil/test/batchSystems/test_slurm.py b/src/toil/test/batchSystems/test_slurm.py index 0e68391f..483e8fb0 100644 --- a/src/toil/test/batchSystems/test_slurm.py +++ b/src/toil/test/batchSystems/test_slurm.py @@ -193,7 +193,7 @@ class SlurmTest(ToilTest): def setUp(self): self.monkeypatch ...	Failed `sbatch` may hang a workflow Mira noticed that a workflow she was running reported a failed `sbatch` command, and then reported a long run of `squeue` commands succeeding while apparently doing nothing. It may be that a failed `sbatch` can kill a job submission thread that we need to be alive for the workflow n...	c566f315393f65804ead58e8f3878b010fff1cfe	[ "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_many_all_exist", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_exists", "src/toil/test/batchSystems/test_slurm.py::SlurmTest::test_coalesce_job_exit_codes_one_not_exists", "src/toil/test...	[]	{ "failed_lite_validators": [ "has_hyperlinks", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2024-04-18 21:57:46+00:00	apache-2.0	189
DataDog__datadog-lambda-python-214	diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0d00bfc..7d7884d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -101,7 +101,7 @@ jobs: run: sudo yarn global add serverless@^2.72.2 --prefix /usr/local - name: Install Crossbuild Deps run...	DataDog/datadog-lambda-python	1f59f3a8821aef37a02e5099a5112d938e57e9c1	diff --git a/tests/test_tag_object.py b/tests/test_tag_object.py index 0936f0c..cdb2941 100644 --- a/tests/test_tag_object.py +++ b/tests/test_tag_object.py @@ -1,4 +1,5 @@ import unittest +from decimal import Decimal try: from unittest.mock import MagicMock, patch, call @@ -82,3 +83,14 @@ class TestTagObject(...	When the response of lambda contain data of type Decimal, datadog raise except TypeError: 'decimal.Decimal' object is not iterable ## Expected Behavior When return response from DynamoDB and DynamoDB contains data of type Decimal ## Actual Behavior Get data of DynamoDB that contains data of type Decimal and raise...	1f59f3a8821aef37a02e5099a5112d938e57e9c1	[ "tests/test_tag_object.py::TestTagObject::test_decimal_tag_object" ]	[ "tests/test_tag_object.py::TestTagObject::test_json_tag_object", "tests/test_tag_object.py::TestTagObject::test_redacted_tag_object", "tests/test_tag_object.py::TestTagObject::test_tag_object", "tests/test_tag_object.py::TestTagObject::test_unicode_tag_object" ]	{ "failed_lite_validators": [ "has_hyperlinks", "has_media", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-03-15 19:57:44+00:00	apache-2.0	190
DataDog__datadogpy-382	diff --git a/datadog/api/resources.py b/datadog/api/resources.py index ad53a50..23b3663 100644 --- a/datadog/api/resources.py +++ b/datadog/api/resources.py @@ -373,7 +373,9 @@ class ActionAPIResource(object): resource_id=id, action_name=name ) - + if method == "GET...	DataDog/datadogpy	500e96369108eee6eef6378a64efbe2dab898f3b	diff --git a/tests/unit/api/helper.py b/tests/unit/api/helper.py index 4ba6cc4..c72ee09 100644 --- a/tests/unit/api/helper.py +++ b/tests/unit/api/helper.py @@ -143,8 +143,8 @@ class DatadogAPITestCase(unittest.TestCase): def request_called_with(self, method, url, data=None, params=None): (req_method, r...	api.Monitor.search() returns "400 malformed request" html Any call to _api.Monitor.search()_ with parameters or without returns a 400 status code as response. For this call the request body is an empty JSON object('{}') rather than being _None_ (as for other 'GET' requests) and the headers accordingly contain _'Content...	500e96369108eee6eef6378a64efbe2dab898f3b	[ "tests/unit/api/test_api.py::TestResources::test_actionable", "tests/unit/api/test_api.py::TestInitialization::test_no_initialization_fails" ]	[ "tests/unit/api/test_api.py::TestResources::test_getable", "tests/unit/api/test_api.py::TestResources::test_listable", "tests/unit/api/test_api.py::TestResources::test_addable_sub_resources", "tests/unit/api/test_api.py::TestResources::test_updatable", "tests/unit/api/test_api.py::TestResources::test_creata...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2019-05-29 16:14:09+00:00	bsd-3-clause	191
DataDog__datadogpy-545	diff --git a/datadog/threadstats/base.py b/datadog/threadstats/base.py index ec89c3e..87421a0 100644 --- a/datadog/threadstats/base.py +++ b/datadog/threadstats/base.py @@ -7,20 +7,21 @@ performance. It collects metrics in the application thread with very little over and allows flushing metrics in process, in a thread...	DataDog/datadogpy	0ac41036382b9dc418afe367923ce14d7cdc4314	diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index 918a3b2..40c74a4 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -25,10 +25,6 @@ logger = logging.getLogger('dd.datadogpy') logger.setLevel(logging.ERRO...	Threadstatsd set metric There appears to be a disconnect between dogstatd and threadstatsd. the `set` method is not supported. What is the equivalent in the thread version? https://github.com/DataDog/datadogpy/blob/master/datadog/dogstatsd/base.py#L227	0ac41036382b9dc418afe367923ce14d7cdc4314	[ "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_set" ]	[ "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_tags", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_embedded_lambda_decorator", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_tags_from_environment", "tests/unit/threadstats/test_threadsta...	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2020-03-06 13:01:26+00:00	bsd-3-clause	192
DataDog__datadogpy-555	diff --git a/datadog/dogshell/wrap.py b/datadog/dogshell/wrap.py index 022b333..a454d33 100644 --- a/datadog/dogshell/wrap.py +++ b/datadog/dogshell/wrap.py @@ -211,8 +211,9 @@ def build_event_body(cmd, returncode, stdout, stderr, notifications): ) if notifications: + notifications = notification...	DataDog/datadogpy	6319ebde0e6bce51c5f6c21f253204c3a13f4d92	diff --git a/tests/unit/dogwrap/test_dogwrap.py b/tests/unit/dogwrap/test_dogwrap.py index e4cd2a3..02341ca 100644 --- a/tests/unit/dogwrap/test_dogwrap.py +++ b/tests/unit/dogwrap/test_dogwrap.py @@ -47,6 +47,11 @@ class TestDogwrap(unittest.TestCase): event_body = build_event_body(cmd, returncode, stdout, st...	String decode in dogwrap Describe the bug The parameters `notify_success`, `notify_warning` and `notify_error` cause the `AttributeError` shown below to be thrown when used. ``` Traceback (most recent call last): File "/usr/local/bin/dogwrap", line 8, in <module> sys.exit(main()) File "/usr/local/li...	6319ebde0e6bce51c5f6c21f253204c3a13f4d92	[ "tests/unit/dogwrap/test_dogwrap.py::TestDogwrap::test_build_event_body" ]	[ "tests/unit/dogwrap/test_dogwrap.py::TestDogwrap::test_poll_proc", "tests/unit/dogwrap/test_dogwrap.py::TestDogwrap::test_execute", "tests/unit/dogwrap/test_dogwrap.py::TestDogwrap::test_parse_options", "tests/unit/dogwrap/test_dogwrap.py::TestDogwrap::test_execute_oserror", "tests/unit/dogwrap/test_dogwrap...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-04-06 19:05:50+00:00	bsd-3-clause	193
DataDog__datadogpy-609	diff --git a/datadog/threadstats/aws_lambda.py b/datadog/threadstats/aws_lambda.py index fa24951..5a3c6de 100644 --- a/datadog/threadstats/aws_lambda.py +++ b/datadog/threadstats/aws_lambda.py @@ -44,6 +44,9 @@ class _LambdaDecorator(object): # This avoids adding execution time at the end of the lambda...	DataDog/datadogpy	1d796ec40d2e48b2059e9370b27bc1add4d5b1e1	diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index 40c74a4..bc1b9c1 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -17,7 +17,7 @@ from mock import patch # datadog from datadog import ThreadStats, lam...	"import datadog" executes statements Describe the bug `import datadog` executes statements. In particular, it runs `atexit.register(lambda: self.flush(float('inf')))` in `datadog/threadstats/base.py`. This results in errors in our unit tests because the exit handler, `datadog.threadstats.ThreadStats.flush`, calls ...	1d796ec40d2e48b2059e9370b27bc1add4d5b1e1	[ "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_tags_from_environment", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_event", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_metric_namespace", "tests/unit/threadstats/test_threadstats.py::T...	[]	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2020-10-06 08:05:40+00:00	bsd-3-clause	194
DataDog__datadogpy-625	diff --git a/datadog/threadstats/base.py b/datadog/threadstats/base.py index 5fc8a4e..84041bb 100644 --- a/datadog/threadstats/base.py +++ b/datadog/threadstats/base.py @@ -31,6 +31,12 @@ from datadog.threadstats.reporters import HttpReporter # Loggers log = logging.getLogger('datadog.threadstats') +DD_ENV_TAGS_MAP...	DataDog/datadogpy	b9449d6ae2a378ed6986b7977ed547f2c63beeef	diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index bc1b9c1..998633b 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -18,7 +18,7 @@ from mock import patch # datadog from datadog import ThreadStats, lambd...	DD_ENV (SERVICE, VERSION) are not used in ThreadStats https://github.com/DataDog/datadogpy/pull/548 added support for taking unified tags from env vars, but it doesn't works when using ThreadStats in the following way: ``` >>> from datadog import initialize, ThreadStats >>> initialize(api_key='my_api_key') >>> st...	b9449d6ae2a378ed6986b7977ed547f2c63beeef	[ "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_tags_from_environment_env_service_version" ]	[ "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_init", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_distribution", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats::test_counter", "tests/unit/threadstats/test_threadstats.py::TestUnitThreadStats:...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2021-01-21 13:47:51+00:00	bsd-3-clause	195
Deltares__pyflwdir-18	diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c0327c7..f240f71 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,16 @@ Change Log ########### +Unreleased +******************** + +Improved +--------- +* prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions, #17 + +B...	Deltares/pyflwdir	90be06f24c7d7ce9bbeeccf19b1452d5be8859d2	diff --git a/tests/test_dem.py b/tests/test_dem.py index 8d7449a..39ec1d4 100644 --- a/tests/test_dem.py +++ b/tests/test_dem.py @@ -24,12 +24,13 @@ def test_from_dem(): ) # NOTE: compared to paper same a_filled, but difference # in flowdir because row instead of col first .. + # and priority of non-b...	prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions	90be06f24c7d7ce9bbeeccf19b1452d5be8859d2	[ "tests/test_dem.py::test_from_dem" ]	[ "tests/test_dem.py::test_dem_adjust", "tests/test_dem.py::test_slope", "tests/test_dem.py::test_hand_fldpln" ]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2022-01-18 10:00:34+00:00	mit	196
Deric-W__ascii_progress-9	diff --git a/ascii_progress/__main__.py b/ascii_progress/__main__.py index f5d1e15..b550f91 100644 --- a/ascii_progress/__main__.py +++ b/ascii_progress/__main__.py @@ -16,7 +16,7 @@ for frames in ( (">))'>", " >))'>", " >))'>", " <'((<", " <'((<", "<'((<") ): sys.stdout.write("Working ")...	Deric-W/ascii_progress	a5f5f2815ba25cdfdcf57a0f02c025ef9dc2a3b0	diff --git a/tests/test_bar.py b/tests/test_bar.py index bfab94b..bc53278 100644 --- a/tests/test_bar.py +++ b/tests/test_bar.py @@ -5,8 +5,10 @@ import unittest import unittest.mock from io import StringIO +from typing import ContextManager from ascii_progress.bar import ( LAZY_FORMATTER, + BarContext, ...	improved context managers Problem: The messages displayed when using `Spinner` or `Bar` as context managers are hard coded. Solution: Add a `.handle_exceptions(message, error)` method to both classes which returns a context manager.	a5f5f2815ba25cdfdcf57a0f02c025ef9dc2a3b0	[ "tests/test_bar.py::TestBar::test_iter", "tests/test_bar.py::TestBar::test_handle_exceptions", "tests/test_bar.py::TestBar::test_eq", "tests/test_bar.py::TestBarFormat::test_generate_bar", "tests/test_bar.py::TestBarFormat::test_bar", "tests/test_bar.py::TestBarFormat::test_with_optimized_wrapper", "tes...	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks", "has_pytest_match_arg" ], "has_test_patch": true, "is_lite": false }	2021-10-30 12:16:54+00:00	mit	197
DevoInc__python-sdk-113	diff --git a/CHANGELOG.md b/CHANGELOG.md index 28e86d5..6686fd3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * `Lookup.send_headers` method not working as expected with key_index parameter * Add `type_of_key` parameter ...	DevoInc/python-sdk	3fa89f73be41307044fec587eb13b563201cd8f9	diff --git a/tests/sender/send_lookup.py b/tests/sender/send_lookup.py index 4e7e416..a0937a8 100644 --- a/tests/sender/send_lookup.py +++ b/tests/sender/send_lookup.py @@ -243,6 +243,96 @@ class TestLookup(unittest.TestCase): self.assertEqual(fields, ["a", "b", "c"]) self.assertEqual(processed_fields...	Lookup API is unable to send records with a double quote character in their content Right now, the `Lookup.clean_field` method wraps the field's content in double quotes, unless it is a number: https://github.com/DevoInc/python-sdk/blob/84a4e2c9da8d3013cd8f012e4399994d64817035/devo/sender/lookup.py#L400-L414 Howeve...	3fa89f73be41307044fec587eb13b563201cd8f9	[ "tests/sender/send_lookup.py::TestLookup::test_clean_field_parametrized" ]	[ "tests/sender/send_lookup.py::TestLookup::test_check_is_not_a_number", "tests/sender/send_lookup.py::TestLookup::test_process_fields_does_not_modify_arguments", "tests/sender/send_lookup.py::TestLookup::test_check_is_number" ]	{ "failed_lite_validators": [ "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2021-12-30 15:15:38+00:00	mit	198
DiCarloLab-Delft__PycQED_py3-284	diff --git a/examples/Setting up a basic measurement using the MC.ipynb b/examples/Setting up a basic measurement using the MC.ipynb index 95f8b96a..69639e6f 100644 --- a/examples/Setting up a basic measurement using the MC.ipynb +++ b/examples/Setting up a basic measurement using the MC.ipynb @@ -7,18 +7,12 @@ "c...	DiCarloLab-Delft/PycQED_py3	8c50aff24fc47d6fd986ee6925d7e274f5da4f9e	diff --git a/pycqed/tests/test_unit_conversions.py b/pycqed/tests/test_unit_conversions.py index b43958d4..0a8dd82d 100644 --- a/pycqed/tests/test_unit_conversions.py +++ b/pycqed/tests/test_unit_conversions.py @@ -3,6 +3,7 @@ import numpy as np import matplotlib.pyplot as plt from pycqed.analysis.tools.plotting impo...	Instrument monitor folds on update First reported by @fluthi , Makes it quite annoying to effectively use this in a real life scenario. Instrument monitor folds on every update.	8c50aff24fc47d6fd986ee6925d7e274f5da4f9e	[ "pycqed/tests/test_unit_conversions.py::Test_SI_prefix_scale_factor::test_SI_scale_factors", "pycqed/tests/test_unit_conversions.py::Test_SI_prefix_scale_factor::test_non_SI", "pycqed/tests/test_unit_conversions.py::test_SI_unit_aware_labels::test_label_scaling", "pycqed/tests/test_unit_conversions.py::test_S...	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2017-07-09 20:01:22+00:00	mit	199
DiamondLightSource__ispyb-api-46	diff --git a/conf/config.example.cfg b/conf/config.example.cfg index bd9d446..d1d5272 100644 --- a/conf/config.example.cfg +++ b/conf/config.example.cfg @@ -5,4 +5,3 @@ pw = host = localhost port = 3306 db = ispybtest -conn_inactivity = 360 diff --git a/ispyb/__init__.py b/ispyb/__init__.py index 3073240..377498b 10...	DiamondLightSource/ispyb-api	09dd224f8a861ab0019b223e1dfb7bcbbc5bfab2	diff --git a/ispyb/model/test_unitcell.py b/ispyb/model/test_unitcell.py new file mode 100644 index 0000000..e499ab4 --- /dev/null +++ b/ispyb/model/test_unitcell.py @@ -0,0 +1,12 @@ +from __future__ import absolute_import, division, print_function +import ispyb.model.integration + + +def test_value_in_equals_value_out...	Protection against DB connection loss Should handle database connection loss by catching the exception and attempt reconnecting. Should possibly 'ping' at set intervals to keep the connection alive.	09dd224f8a861ab0019b223e1dfb7bcbbc5bfab2	[ "ispyb/model/test_unitcell.py::test_value_in_equals_value_out" ]	[]	{ "failed_lite_validators": [ "has_short_problem_statement", "has_many_modified_files", "has_many_hunks" ], "has_test_patch": true, "is_lite": false }	2018-09-24 08:10:25+00:00	apache-2.0	200
DinoTools__python-overpy-64	diff --git a/overpy/__init__.py b/overpy/__init__.py index 13de583..377c28d 100644 --- a/overpy/__init__.py +++ b/overpy/__init__.py @@ -349,23 +349,39 @@ class Result(object): return result @classmethod - def from_xml(cls, data, api=None, parser=XML_PARSER_SAX): + def from_xml(cls, data, api=None...	DinoTools/python-overpy	d49ad8080ff9e9da3081a240380915b159172a87	diff --git a/tests/test_xml.py b/tests/test_xml.py index d81f003..e414ad4 100644 --- a/tests/test_xml.py +++ b/tests/test_xml.py @@ -171,6 +171,28 @@ class TestDataError(object): overpy.Way.from_xml(node) +class TestParser(BaseTestNodes): + def test_exception(self): + with pytest.raises(overp...	Result.from_xml data argument has a wrong type doc Passing Element as a data argument to Result.from_xml() as docstring suggests raises Exception. ``` >>> overpy.Result.from_xml(xml.etree.ElementTree.fromstring("<osm />")) Traceback (most recent call last): File "<input>", line 1, in <module> File "/home/w/osm...	d49ad8080ff9e9da3081a240380915b159172a87	[ "tests/test_xml.py::TestParser::test_exception", "tests/test_xml.py::TestParser::test_xml_element" ]	[ "tests/test_xml.py::TestAreas::test_node01", "tests/test_xml.py::TestNodes::test_node01", "tests/test_xml.py::TestRelation::test_relation01", "tests/test_xml.py::TestRelation::test_relation02", "tests/test_xml.py::TestRelation::test_relation03", "tests/test_xml.py::TestRelation::test_relation04", "tests...	{ "failed_lite_validators": [], "has_test_patch": true, "is_lite": true }	2017-04-07 12:09:15+00:00	mit	201
Dorthu__openapi3-76	diff --git a/openapi3/openapi.py b/openapi3/openapi.py index 5b79b14..0b2c753 100644 --- a/openapi3/openapi.py +++ b/openapi3/openapi.py @@ -101,16 +101,27 @@ class OpenAPI(ObjectBase): node = self for part in path: + part = part.replace('~1','/').replace('~0','~') if isinsta...	Dorthu/openapi3	0e02198948258b69e666f53aa2b22fcf4da62f97	diff --git a/tests/conftest.py b/tests/conftest.py index 5a10c1b..b4e83cf 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -178,3 +178,11 @@ def schema_without_properties(): Provides a spec that includes a schema with no properties defined """ yield _get_parsed_yaml("schema-without-properties.ya...	Testing doesn't work ``` $ PYTHONPATH=. python3 -mpytest -sxv tests/ Test session starts (platform: linux, Python 3.9.9, pytest 6.0.2, pytest-sugar 0.9.4) cachedir: .pytest_cache rootdir: /src/openapi3 plugins: asyncio-0.14.0, xdist-2.2.0, gc-0.0.1, sugar-0.9.4, cov-2.10.1, anyio-3.3.0.1, forked-1.3.0, mock-1.10...	0e02198948258b69e666f53aa2b22fcf4da62f97	[ "tests/ref_test.py::test_ref_6901_refs" ]	[ "tests/ref_test.py::test_ref_resolution", "tests/ref_test.py::test_allOf_resolution", "tests/ref_test.py::test_resolving_nested_allof_ref", "tests/ref_test.py::test_ref_allof_handling" ]	{ "failed_lite_validators": [ "has_many_modified_files" ], "has_test_patch": true, "is_lite": false }	2022-03-08 13:18:13+00:00	bsd-3-clause	202

Subsets and Splits

Long Problem Statements

Retrieves a subset of problem statements within a specific length range, ordered by length, which provides basic filtering but limited analytical value.