Add initial python 3.14 support and bump up in line with SPEC0 (#5121)

IAlibay · web-flow · commit 58b872b8f91a · 2025-10-13T20:52:07.000+01:00
* Add support for python 3.14
* Bump up numpy and python versions in line with SPEC0, the minimum supported numpy is now 1.26.0 and the minimum python is 3.11.
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -41,7 +41,7 @@ jobs:
           - [macos-13, macosx_*, x86_64]
           - [windows-2022, win_amd64, AMD64]
           - [macos-14, macosx_*, arm64]
-        python: ["cp310", "cp311", "cp312", "cp313"]
+        python: ["cp311", "cp312", "cp313", "cp314"]
     defaults:
       run:
         working-directory: ./package
@@ -51,7 +51,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.0
+        uses: pypa/cibuildwheel@v3.2.0
         with:
           package-dir: package
         env:
@@ -246,14 +246,13 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         type: ["FULL", "MIN"]
         exclude:
           # Multiple deps don't like windows
           - os: windows-latest
             type: "FULL"
-          # Chemfiles won't install over py3.13
-          - python-version: "3.13"
+          - python-version: "3.14"
             type: "FULL"
     env:
       MPLBACKEND: agg
diff --git a/.github/workflows/gh-ci-cron.yaml b/.github/workflows/gh-ci-cron.yaml
@@ -6,8 +6,8 @@ on:
   workflow_dispatch:
   # Uncomment when you need to test on a PR
   # pull_request:
-  #  branches:
-  #    - develop
+  #   branches:
+  #     - develop
 
 
 concurrency:
@@ -107,7 +107,6 @@ jobs:
           pip
         condarc: |
           channels:
-            - jaimergp/label/unsupported-cudatoolkit-shim
             - conda-forge
             - bioconda
 
@@ -141,7 +140,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-13]
+        os: [ubuntu-22.04, macos-13]
 
     steps:
     - uses: actions/checkout@v4
@@ -156,11 +155,10 @@ jobs:
       with:
         environment-name: mda
         create-args: >-
-          python=3.10
+          python=3.11
           pip
         condarc: |
           channels:
-            - jaimergp/label/unsupported-cudatoolkit-shim
             - conda-forge
             - bioconda
 
@@ -190,7 +188,7 @@ jobs:
     strategy:
         fail-fast: false
         matrix:
-          python-version: ["3.10", "3.11", "3.12", "3.13"]
+          python-version: ["3.11", "3.12", "3.13", "3.14"]
     steps:
     - uses: actions/checkout@v4
 
@@ -233,10 +231,8 @@ jobs:
         matrix:
           # Stick to macos-13 because some of our
           # optional deps don't support arm64 (i.e. macos-14)
-          #
-          # add "3.13" once conda-forge packages are available (see #4805)
           os: [ubuntu-latest, macos-13]
-          python-version: ["3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
     - uses: actions/checkout@v4
 
@@ -252,10 +248,8 @@ jobs:
         create-args: >-
           python=${{ matrix.python-version }}
           pip
-        # using jaime's shim to avoid pulling down the cudatoolkit
         condarc: |
           channels:
-            - jaimergp/label/unsupported-cudatoolkit-shim
             - conda-forge
             - bioconda
 
@@ -298,15 +292,21 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: install_deps
+      shell: bash
+      run: |
+          pip install pytest-xdist pytest-timeout "numpy<2.3" "cython<3.1" wheel "setuptools>=40.9.0" packaging
+
     - name: install_mdanalysis
       shell: bash
       run: |
           # If wheels is False we build directly from source so we use the --no-binary flag
           # to avoid pulling down wheels for MDAnalysis (which are already precompiled)
+          # Also need to add `--no-build-isolation` until next release, see Issue #5125
           if [ "${{ matrix.wheels }}" == "false" ]; then
-            INSTALL_FLAGS="-vvv --no-binary"
+            INSTALL_FLAGS="--no-build-isolation --no-binary"
           fi
-          pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests pytest-xdist pytest-timeout
+          pip install ${INSTALL_FLAGS} mdanalysis mdanalysistests
 
     - name: run_tests
       shell: bash
diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -28,29 +28,43 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu-latest, ]
-          python-version: ["3.10", "3.11", "3.12"]
+          python-version: ["3.11", "3.12", "3.13"]
           full-deps: [true, ]
           codecov: [true, ]
+          cython: ["cython<3.1", ]
           include:
-            - name: python_313
+            # Including 3.14 and 3.11 without coverage
+            # and cython >=3.1 to deal temporarily with
+            # keeping on testing Cython whilst issue #5057
+            # is not fixed
+            - name: python_314_nocov
               os: ubuntu-latest
-              python-version: "3.13"
+              python-version: "3.14"
               full-deps: false
-              codecov: true
-            - name: macOS_14_arm64_py312
+              codecov: false
+              cython: "cython>=3.1"
+            - name: python_311_nocov
+              os: ubuntu-latest
+              python-version: "3.11"
+              full-deps: false
+              codecov: false
+              cython: "cython>=3.1"
+            - name: macOS_14_arm64_py313
               os: macOS-14
-              python-version: "3.12"
+              python-version: "3.13"
               full-deps: false
               codecov: true
+              cython: "cython<3.1"
             - name: numpy_min
               os: ubuntu-latest
-              python-version: "3.10"
+              python-version: "3.11"
               full-deps: false
               codecov: true
-              numpy: numpy=1.23.2
+              numpy: numpy=1.26.0
+              cython: "cython<3.1"
             - name: asv_check
               os: ubuntu-latest
-              python-version: "3.10"
+              python-version: "3.11"
               full-deps: true
               codecov: false
               extra-pip-deps: asv
@@ -88,7 +102,7 @@ jobs:
         # disable GSD because it occasionally introduce hanging in testing #4209
         gsd: ''
         # pin cython
-        cython: 'cython<3.1'
+        cython: ${{ matrix.cython }}
         # in most cases will just default to empty, i.e. pick up max version from other deps
         numpy: ${{ matrix.numpy }}
         extra-pip-deps: ${{ matrix.extra-pip-deps }}
@@ -151,12 +165,11 @@ jobs:
       with:
         environment-name: mda
         create-args: >-
-          python=3.10
+          python=3.11
           pip
         # using jaime's shim to avoid pulling down the cudatoolkit
         condarc: |
           channels:
-            - jaimergp/label/unsupported-cudatoolkit-shim
             - conda-forge
             - bioconda
 
diff --git a/.github/workflows/linters.yaml b/.github/workflows/linters.yaml
@@ -31,7 +31,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - uses: psf/black@stable
       with:
@@ -55,7 +55,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
 
     - name: install
       run: |
@@ -80,12 +80,10 @@ jobs:
         with:
           environment-name: mda
           create-args: >-
-            python=3.10
+            python=3.11
             pip
-          # using jaime's shim to avoid pulling down the cudatoolkit
           condarc: |
             channels:
-              - jaimergp/label/unsupported-cudatoolkit-shim
               - conda-forge
               - bioconda
 
@@ -94,7 +92,7 @@ jobs:
         with:
           micromamba: true
           full-deps: true
-          numpy: numpy=1.23.2
+          numpy: numpy=1.26.0
           rdkit: rdkit=2023.09.3
 
       - name: install
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -21,39 +21,39 @@ jobs:
     MPLBACKEND: agg
   strategy:
     matrix:
-        Win-Python310-64bit-full:
-          PYTHON_VERSION: '3.10'
+        Win-Python311-64bit-full:
+          PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'normal'
           imageName: 'windows-2019'
-        Win-Python312-64bit-full:
-          PYTHON_VERSION: '3.12'
+        Win-Python313-64bit-full:
+          PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'normal'
           imageName: 'windows-2019'
-        Win-Python312-64bit-full-wheel:
-          PYTHON_VERSION: '3.12'
+        Win-Python313-64bit-full-wheel:
+          PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.26.0'
+          NUMPY_MIN: '2.1.0'
           imageName: 'windows-2019'
-        Win-Python310-64bit-full-wheel:
-          PYTHON_VERSION: '3.10'
+        Win-Python311-64bit-full-wheel:
+          PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.23.2'
+          NUMPY_MIN: '1.26.0'
           imageName: 'windows-2019'
-        Linux-Python312-64bit-full-wheel:
-          PYTHON_VERSION: '3.12'
+        Linux-Python313-64bit-full-wheel:
+          PYTHON_VERSION: '3.13'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
           NUMPY_MIN: '2.1.0'
           imageName: 'ubuntu-latest'
-        Linux-Python310-64bit-full-wheel:
-          PYTHON_VERSION: '3.10'
+        Linux-Python311-64bit-full-wheel:
+          PYTHON_VERSION: '3.11'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.23.2'
+          NUMPY_MIN: '1.26.0'
           imageName: 'ubuntu-latest'
   pool:
     vmImage: $(imageName)
@@ -100,6 +100,8 @@ jobs:
       python -m pip install numpy==$(NUMPY_MIN)
     displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), ne(variables['NUMPY_MIN'], ''))
+  # Disabled PyTNG checking, see issue #5123
+  # TODO: add pytng>=0.2.3 back once resolved
   - script: >-
       python -m pip install -vvv
       biopython
@@ -110,7 +112,6 @@ jobs:
       mmtf-python
       networkx
       parmed
-      pytng>=0.2.3
       rdkit>=2024.03.4
       tidynamics>=1.0.0
       imdclient>=0.2.2
diff --git a/maintainer/conda/environment.yml b/maintainer/conda/environment.yml
@@ -17,9 +17,9 @@ dependencies:
   - mmtf-python
   - mock
   - networkx
-  - numpy>=1.23.2
+  - numpy>=1.26.0
   - pytest
-  - python==3.10
+  - python==3.11
   - pytng>=0.2.3
   - scikit-learn
   - scipy
diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -47,6 +47,7 @@ Fixes
     and does not result in an infinite loop (Issue #5112, PR #5113)
 
 Enhancements
+ * Support for Python 3.14 was added (PR #5121).
  * Added support for reading and processing streamed data in `coordinates.base`
    with new `StreamFrameIteratorSliced` and `StreamReaderBase` (Issue #4827, PR #4923)
  * New coordinate reader: Added `IMDReader` for reading real-time streamed
@@ -85,6 +86,7 @@ Enhancements
 
 
 Changes
+ * Support for Python 3.10 was removed, in line with SPEC0 (PR #5121).
  * Refactored the RDKit converter code to move the inferring code in a separate
    `RDKitInferring` module. The bond order and charges inferrer has been move to
    an `MDAnalysisInferrer` dataclass in there. (PR #4305)
diff --git a/package/pyproject.toml b/package/pyproject.toml
@@ -1,7 +1,7 @@
 [build-system]
 # Minimum requirements for the build system to execute
 requires = [
-    "Cython>=0.28,<3.1",
+    "Cython>=0.28",
     "packaging",
     # numpy requirement for wheel builds for distribution on PyPI - building
     # against 2.x yields wheels that are also compatible with numpy 1.x at
@@ -27,9 +27,9 @@ authors = [
 maintainers = [
     {name = 'MDAnalysis Core Developers', email = 'mdanalysis@numfocus.org'}
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
-    'numpy>=1.23.2',
+    'numpy>=1.26.0',
     'GridDataFormats>=0.4.0',
     'mmtf-python>=1.0.0',
     'joblib>=0.12',
@@ -55,10 +55,10 @@ classifiers = [
     'Operating System :: MacOS :: MacOS X',
     'Operating System :: Microsoft :: Windows',
     'Programming Language :: Python',
-    'Programming Language :: Python :: 3.10',
     'Programming Language :: Python :: 3.11',
     'Programming Language :: Python :: 3.12',
     'Programming Language :: Python :: 3.13',
+    'Programming Language :: Python :: 3.14',
     'Programming Language :: C',
     'Topic :: Scientific/Engineering',
     'Topic :: Scientific/Engineering :: Bio-Informatics',
@@ -126,7 +126,7 @@ MDAnalysis = [
 
 [tool.black]
 line-length = 79
-target-version = ['py310', 'py311', 'py312', 'py313']
+target-version = ['py311', 'py312', 'py313']
 extend-exclude = '''
 (
 __pycache__ 
diff --git a/testsuite/MDAnalysisTests/analysis/test_helix_analysis.py b/testsuite/MDAnalysisTests/analysis/test_helix_analysis.py
diff --git a/testsuite/pyproject.toml b/testsuite/pyproject.toml
