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Add py3.13 support w/ minimal deps #4732

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merged 7 commits into from
Oct 13, 2024
Merged

Add py3.13 support w/ minimal deps #4732

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e8323ad
Add py3.13 to minimal tests
IAlibay Oct 13, 2024
ecd6807
Update changelog
IAlibay Oct 13, 2024
6add21e
fix typo and azure
IAlibay Oct 13, 2024
dba9ffc
minimum version of numpy is 2.1.0 for python 3.13
IAlibay Oct 13, 2024
23d06e7
fix tests for py3.13 output changes
IAlibay Oct 13, 2024
ab6773e
revert azure change until new rdkit release
IAlibay Oct 13, 2024
c84eecb
revert order switch
IAlibay Oct 13, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/deploy.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ jobs:
- [macos-12, macosx_*, x86_64]
- [windows-2019, win_amd64, AMD64]
- [macos-14, macosx_*, arm64]
python: ["cp310", "cp311", "cp312"]
python: ["cp310", "cp311", "cp312", "cp313"]
defaults:
run:
working-directory: ./package
Expand Down Expand Up @@ -243,7 +243,7 @@ jobs:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest, windows-latest]
python-version: ["3.10", "3.11", "3.12"]
python-version: ["3.10", "3.11", "3.12", "3.13"]
type: ["FULL", "MIN"]
exclude:
# Multiple deps don't like windows
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4 changes: 1 addition & 3 deletions .github/workflows/gh-ci-cron.yaml
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Expand Up @@ -41,8 +41,6 @@ jobs:
os-type: "ubuntu"

- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

# minimally install nightly wheels & core deps
- name: nightly_wheels
Expand Down Expand Up @@ -197,7 +195,7 @@ jobs:
strategy:
fail-fast: false
matrix:
python-version: ["3.10", "3.11", "3.12"]
python-version: ["3.10", "3.11", "3.12", "3.13"]
steps:
- uses: actions/checkout@v4

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5 changes: 5 additions & 0 deletions .github/workflows/gh-ci.yaml
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Expand Up @@ -32,6 +32,11 @@ jobs:
full-deps: [true, ]
codecov: [true, ]
include:
- name: python_313
os: ubuntu-latest
python-version: "3.13"
full-deps: false
codecov: true
- name: macOS_monterey_py311
os: macOS-12
python-version: "3.12"
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2 changes: 1 addition & 1 deletion azure-pipelines.yml
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Expand Up @@ -47,7 +47,7 @@ jobs:
PYTHON_VERSION: '3.12'
PYTHON_ARCH: 'x64'
BUILD_TYPE: 'wheel'
NUMPY_MIN: '1.26.0'
NUMPY_MIN: '2.1.0'
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did you mean to change to 3.13 above? I don't think that's a blocker here though

imageName: 'ubuntu-latest'
Linux-Python310-64bit-full-wheel:
PYTHON_VERSION: '3.10'
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -56,6 +56,7 @@ Fixes
* Fix groups.py doctests using sphinx directives (Issue #3925, PR #4374)

Enhancements
* MDAnalysis now supports Python 3.13 (PR #4732)
* Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
(Issue #4158, PR #4304)
* Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
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3 changes: 2 additions & 1 deletion package/pyproject.toml
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Expand Up @@ -61,6 +61,7 @@ classifiers = [
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
'Programming Language :: Python :: 3.13',
'Programming Language :: C',
'Topic :: Scientific/Engineering',
'Topic :: Scientific/Engineering :: Bio-Informatics',
Expand Down Expand Up @@ -124,6 +125,6 @@ MDAnalysis = [

[tool.black]
line-length = 79
target-version = ['py310', 'py311', 'py312']
target-version = ['py310', 'py311', 'py312', 'py313']
extend-exclude = '.'
required-version = '24'
8 changes: 4 additions & 4 deletions testsuite/MDAnalysisTests/analysis/test_base.py
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Expand Up @@ -345,17 +345,17 @@ def test_verbose_progressbar(u, capsys):
def test_verbose_progressbar_run(u, capsys):
FrameAnalysis(u.trajectory).run(verbose=True)
_, err = capsys.readouterr()
expected = u'100%|██████████| 98/98 [00:00<00:00, 8799.49it/s]'
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I think the reason why the full output was there originally was to give devs an idea what it looks like even if other parts could not be reliably tested.

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Unfortunately the py3.13 behaviour changed here and I can't work out exactly why - I'm not sure if there's a better way to deal with this without having an explicit python version check :/

expected = u'100%|██████████'
actual = err.strip().split('\r')[-1]
assert actual[:24] == expected[:24]
assert expected == actual[:15]
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Why did you switch actual and expected?

Doesn't really matter except for consistency throughout because in testsuite/MDAnalysisTests/lib/test_log.py it's still actual == expected.

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I had originally switched it to a expected in actual check, but decided to revert back to an equality check.

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Reverted the order in the latest commit.


def test_verbose_progressbar_run_with_kwargs(u, capsys):
FrameAnalysis(u.trajectory).run(
verbose=True, progressbar_kwargs={'desc': 'custom'})
_, err = capsys.readouterr()
expected = u'custom: 100%|██████████| 98/98 [00:00<00:00, 8799.49it/s]'
expected = u'custom: 100%|██████████'
actual = err.strip().split('\r')[-1]
assert actual[:30] == expected[:30]
assert expected == actual[:23]


def test_progressbar_multiprocessing(u):
Expand Down
4 changes: 2 additions & 2 deletions testsuite/MDAnalysisTests/lib/test_log.py
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Expand Up @@ -32,9 +32,9 @@ def test_output(self, capsys):
for i in ProgressBar(list(range(10))):
pass
out, err = capsys.readouterr()
expected = u'100%|██████████| 10/10 [00:00<00:00, 583.67it/s]'
expected = u'100%|██████████'
actual = err.strip().split('\r')[-1]
assert actual[:24] == expected[:24]
assert actual[:15] == expected

def test_disable(self, capsys):
for i in ProgressBar(list(range(10)), disable=True):
Expand Down
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