doctestplus fails with pytest==8.1.0 #239
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It looks like this was fixed in #236, but the fix hasn't been released. |
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Oh sorry, I just searched for a related issue, not related pull request ;) For a user it would be nice to have a release soon then. |
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I can make a release. |
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pytest-doctestplus 1.2.0 is released. But then again pytest 8.1 was also yanked. 🤷 |
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Oct 15, 2024
…ion 5.3.0
Brendan Moloney (12):
ENH: Add writer for Siemens CSA header
CLN: Cleanup whitespace and formatting
BF: Fix for 'split' (concatenated?) multiframe DICOM
BF+TST: Test and fix a bunch of multiframe fixes
BF: Trim unneeded trailing indices from _frame_indices
BF+TST: Fix 2D plus time case
BF+TST: Handle case with extra-spatial index that is unique per frame
TST: Expand test coverage for multiframe dicom shape determination
TST+CLN: More slice ordering testing, minor cleanup
DOC: Add some notes to the changelog
BF+ENH: Fixes to DICOM scaling, make frame filtering explicit
TST: Don't assume pydicom installed in test_dicomwrappers
Christopher J. Markiewicz (72):
ENH: Catch SVD failure and raise informative HeaderDataError
DOC: Fix references in changelog
MNT: Add tool for generating GitHub-friendly release notes
MNT: Avoid isort version with broken extras
DOC: Fix intersphinx mapping and reference type
MNT: Advertise Python 3.12 support
FIX: Tolerate missing git
MNT: Purge defunct nisext package
TEST: Accommodate pytest 8 changes
TYP: Update ignore comments
TEST: Prepare tests to fail at 6.0
DATA: Add dcm_qa_xa30 as submodule for test data
TEST: Add test for Siemens TRACE volume
FIX: Conditionally drop isotropic frames
RF: Consistently apply data type, shape and index order in GIFTI data blocks
TEST: Expect data arrays to be the advertised shapes
CI: Configure dependabot to update official actions in bulk
Update .github/workflows/test.yml
Update .github/workflows/test.yml
STY: blue/flake8
PIN: Temporarily pin pytest<8.1, pending scientific-python/pytest-doctestplus#239
FIX: Use np.asarray instead of np.array(..., copy=False)
Update doc/README.rst
TOX: Update dependencies for arm64
CI: Add/distinguish macos-13-x64 and macos-14-arm64 runs
TOX: Print durations to see slow tests
CI: Run pre-release tests only on SPEC-0 supported Python
MNT: Fix ruff arg in pre-commit config
ENH: Add Nifti2 capabilities to nib-nifti-dx
MNT: Update importlib_resources requirement to match 3.12 usage
FIX: Use legacy numpy printing during doc builds/tests
MNT: Update coverage config
MNT: Remove "pragma: no cover" from lines ignored by config
MNT: Require coverage>=7.2 for exclude_also
MNT: Stop excluding tests from coverage
CI: Add 3.13-nogil build
TOX: Add a Python 3.13 environment
TOX: Drop h5py and indexed_gzip dependencies for dev
CI: Run tox in debug to see what files are downloaded
TOX: Add PYTHON_GIL=0 to py313 environments
RF: Replace OneTimeProperty/auto_attr with cached_property
DOC: Use packaging.version.Version over LooseVersion
RF: nibabel.onetime.auto_attr -> functools.cached_property
fix: Update order of indices on mouseclick
test: Add regression test for rotated data
Revert "ENH: Add writer for Siemens CSA header"
TYP: Ignore overzealous warning for min/max with numpy scalars
Update pre-commit config
typ: Ignore Pointset.__rmatmul__/ndarray.__matmul__ inconsistency
MNT: Require typing_extensions for Python <3.13
RF: Add generic NiftiExtension base class
ENH: Add .text and .json() accessors for ease
TEST: Test content, text and json() access
ENH: Add from_bytes method for subclasses with known codes
TYP: Annotate Cifti2Extension
rf: Allow extensions to be constructed from objects without serialization
rf: Construct DicomExtensions more simply
TEST: Test NiftiJSONExtension
feat: Add current extension codes
Update nibabel/nifti1.py
fix: Import from typing in Python 3.13
Update nibabel/nifti1.py
sty: Remove unnecessary trailing whitespace in summary
sty: Apply UP007, UP012
DOC: Update changelog
DOC: Update Zenodo contributors
DOC: Update mailmap and contributor list
DOC: Remove end year from copyright
MNT: Update support matrix for Python and numpy
MNT: Remove workarounds used for Python 3.8 support
STY: ruff check --fix
MNT: Update release notes translator
Dimitri Papadopoulos Orfanos (93):
MNT: Apply Repo-Review suggestions
MNT: blue/isort/flake8 → ruff
MNT: run `ruff --fix` and `ruf format`
MNT: ruff 0.1.9 → 0.3.0
MNT: run `ruff check --fix` and `ruff format`
MNT: get rid of .flake8/.pep8speaks.yml
MNT: ignore F401 in __init__.py
MNT: ruff 0.3.0 → 0.3.4
Update doc/tools/apigen.py
Update nibabel/cifti2/tests/test_cifti2io_header.py
Update nibabel/gifti/tests/test_gifti.py
Update nibabel/tests/test_pkg_info.py
Update nibabel/gifti/tests/test_gifti.py
Update nibabel/tests/test_spatialimages.py
Update nibabel/tests/test_testing.py
Update tox.ini
Update nibabel/tests/test_testing.py
Update nibabel/gifti/tests/test_gifti.py
Update nibabel/gifti/tests/test_gifti.py
Update nibabel/gifti/tests/test_parse_gifti_fast.py
Update nibabel/gifti/tests/test_parse_gifti_fast.py
Update nibabel/nicom/tests/test_dicomwrappers.py
Update nibabel/streamlines/tests/test_tck.py
Update nibabel/streamlines/tests/test_trk.py
Update nibabel/tests/test_affines.py
Update nibabel/tests/test_arraywriters.py
Update nibabel/tests/test_arraywriters.py
Update nibabel/tests/test_image_load_save.py
Update nibabel/tests/test_imageclasses.py
Update nibabel/tests/test_minc2.py
Put back argument, used by @pytest.fixture
MNT: ignore F401 in doc/source/conf.py
MNT: Get rid of last `coding: utf-8`
STY: Apply ruff/flake8-implicit-str-concat rule ISC001
STY: Applty ruff/pyupgrade rule UP006
STY: Apply ruff/pyupgrade rule UP031
STY: Apply ruff/pyupgrade rule UP032
STY: Enforce ruff/pyupgrade rules (UP)
STY: Apply ruff/Pylint rule PLE0101
STY: Enforce ruff/Pylint rules, errors only (PLE)
STY: Apply ruff/flake8-raise rule RSE102
STY: Enforce ruff/flake8-raise rules (RSE)
STY: Apply ruff/flake8-bugbear rule B009
STY: Apply ruff/flake8-bugbear rule B015
STY: Enforce ruff/flake8-bugbear rules (B)
STY: Apply ruff/flake8-comprehensions rule C406
STY: Apply ruff/flake8-comprehensions rule C413
STY: Apply ruff/flake8-comprehensions rule C416
STY: Apply ruff/flake8-comprehensions rule C419
STY: Enforce ruff/flake8-comprehensions rules (C4)
STY: Apply ruff/flake8-type-checking rule TCH001
STY: Apply ruff/flake8-type-checking rule TCH002
STY: Apply ruff/flake8-type-checking rule TCH003
STY: Enforce ruff/flake8-type-checking rules (TCH)
STY: Apply ruff/flake8-pie rule PIE807
STY: Apply ruff/flake8-pie rule PIE808
STY: Enforce ruff/flake8-pie rules (PIE)
STY: Apply ruff/refurb rule FURB167
STY: Enforce ruff/refurb rules (FURB)
STY: Apply ruff/flake8-pyi rule PYI034
STY: Enforce ruff/flake8-pyi rules (PYI)
STY: Apply ruff/flynt rule FLY002
STY: Enforce ruff/flynt rules (FLY)
STY: Apply ruff/Perflint rule PERF102
STY: Apply ruff/Perflint rule PERF401
STY: Enforce ruff/Perflint rules (PERF)
STY: Consistency
STY: Prefix unused loop control variable with an underscore
STY: Apply ruff/flake8-pytest-style rule PT006
STY: Apply ruff/flake8-pytest-style rule PT014
STY: Apply ruff/flake8-pytest-style rule PT015
STY: Apply ruff/flake8-pytest-style rule PT017
STY: Apply ruff/flake8-pytest-style rule PT022
STY: Apply ruff/flake8-pytest-style rule PT027
STY: Enforce ruff/flake8-pytest-style rules (PT)
MNT: Drop test which verifies that TripWireError is an AttributeError
MNT: Simplify try/except/else block
STY: Apply ruff/pygrep-hooks rule PGH004
STY: Apply ruff/pygrep-hooks rule PGH004
STY: Enforce ruff/pygrep-hooks rules (PGH)
STY: Apply ruff rule RUF100
STY: Encorce ruff rules (RUF)
STY: Disable deprecated ruff rules
STY: Apply ruff/pyupgrade preview rule UP031
MNT: Python 3 string formatting: %i → %d
STY: Apply ruff/refurb preview rule FURB145
STY: Apply ruff/refurb preview rule FURB148
STY: Apply ruff/refurb preview rule FURB157
STY: Apply ruff/refurb preview rule FURB192
STY: Apply ruff/flake8-comprehensions preview rule C409
STY: Apply ruff/flake8-comprehensions preview rule C419
MNT: Fix misspellings found by codespell
MNT: better way to normalize sequences to lists and flatten
Guillaume Becq (5):
Update OrthoSlicer3D._set_position in viewers.py
Add files via upload
Add files via upload
BF for non RAS matrices
test for BF viwers non RSA matrices
Jon Haitz Legarreta (7):
DOC: Update affiliation of jhlegarreta
RF: Prefer using `getlocale()` instead of `getdefaultlocale()`
RF: Prefer using `np.vstack` instead of `np.row_stack`
RF: Fix `ast` library type and attribute deprecation warnings
RF: Remove unnecessary call to `asbytes` for `b`-prepended strings
RF: Fix for `abc` library `Traversable` class module
RF: Use `numpy.lib.scimath` to demonstrate warning context manager
Joshua Newton (3):
`casting.py`: Filter WSL1 + np.longdouble warning
`casting.py`: Remove `uname` check for WSL1
`.zenodo.json`: Add Joshua Newton
Matthew Brett (1):
DOC: fix typos for key
Paul McCarthy (2):
TEST: Unit test for loading ASCII-encoded "flat" GIFTI data array. Currently failing
RF: Make sure that ASCII-encoded DataArrays are returned with expected shape
Sandro (3):
Python 3.13: Account for dedented docstrings
Update instructions for building docs
Replace deprecated setup() and teardown()
Serge Koudoro (1):
allow inhomogeneous array
Yaroslav O. Halchenko (1):
Make "Calculated shape" more "correct" (do show shape) and informative
dependabot[bot] (3):
Build(deps): Bump the actions-infrastructure group with 3 updates
Build(deps): Bump codecov/codecov-action from 3 to 4
Bump deadsnakes/action from 3.1.0 to 3.2.0
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pytestv8.1.0 was released a few days ago, and with that new version our unit tests fail with:see https://github.com/audeering/audbackend/actions/runs/8138487619/job/22239475750?pr=190
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