Add py3.13 support w/ minimal deps (#4732)

* Add Python 3.13 to minimal CI testing, and include some minor test shims to accommodate.

.github/workflows/deploy.yaml

@@ -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
@@ -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

.github/workflows/gh-ci-cron.yaml

@@ -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
@@ -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
 

.github/workflows/gh-ci.yaml

@@ -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"

azure-pipelines.yml

@@ -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'
           imageName: 'ubuntu-latest'
         Linux-Python310-64bit-full-wheel:
           PYTHON_VERSION: '3.10'

package/CHANGELOG

@@ -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)

package/pyproject.toml

@@ -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',
@@ -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'

testsuite/MDAnalysisTests/analysis/test_base.py

@@ -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]'
+    expected = u'100%|██████████'
     actual = err.strip().split('\r')[-1]
-    assert actual[:24] == expected[:24]
+    assert actual[:15] == expected
 
 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 actual[:23] == expected
 
 
 def test_progressbar_multiprocessing(u):

testsuite/MDAnalysisTests/lib/test_log.py

@@ -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):