bump up azure and gh CI to py3.11 (MDAnalysis#3903)

Towards MDAnalysis#3878 * bump up gh CI to py311 * Add rdkit to azure pipelines * Fix cibuildwheels to add py311 * bump up windows minimum numpy version * Add 3.11 to testpypi checks
SampurnaM · Dec 9, 2022 · 10b0a91 · 10b0a91
1 parent a05a524
commit 10b0a91
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Showing 5 changed files with 29 additions and 16 deletions.
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -33,10 +33,10 @@ jobs:
       fail-fast: false
       matrix:
         buildplat:
-          - [ubuntu-18.04, manylinux_x86_64]
-          - [macos-10.15, macosx_*]
+          - [ubuntu-20.04, manylinux_x86_64]
+          - [macos-11, macosx_*]
           - [windows-2019, win_amd64]
-        python: ["cp38", "cp39", "cp310"]
+        python: ["cp38", "cp39", "cp310", "cp311"]
     defaults:
       run:
         working-directory: ./package
@@ -46,7 +46,7 @@ jobs:
           fetch-depth: 0
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.6.0
+        uses: pypa/cibuildwheel@v2.11.2
         with:
           package-dir: package
         env:
@@ -189,9 +189,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         type: ["FULL", "MIN"]
         exclude:
+          # Py311 doesn't support all optional deps yet
+          - python-version: "3.11"
+            type: "FULL"
           # Multiple deps don't like windows
           - os: windows-latest
             python-version: "3.8"

diff --git a/.github/workflows/gh-ci.yaml b/.github/workflows/gh-ci.yaml
@@ -28,11 +28,17 @@ jobs:
         fail-fast: false
         matrix:
           os: [ubuntu-latest, ]
-          python-version: [3.8, 3.9, "3.10"]
+          python-version: ["3.8", "3.9", "3.10"]
           full-deps: [true, ]
           install_hole: [true, ]
           codecov: [true, ]
           include:
+            - name: py311-ubuntu-min
+              os: ubuntu-latest
+              python-version: "3.11"
+              full-deps: false
+              install_hole: true
+              codecov: false
             - name: macOS_monterey_py39
               os: macOS-12
               python-version: 3.9

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -36,23 +36,23 @@ jobs:
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'normal'
           imageName: 'windows-2019'
-        Win-Python39-64bit-full-wheel:
-          PYTHON_VERSION: '3.9'
+        Win-Python310-64bit-full-wheel:
+          PYTHON_VERSION: '3.10'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.20.0'
+          NUMPY_MIN: '1.22.3'
           imageName: 'windows-2019'
         Win-Python38-64bit-full-wheel:
           PYTHON_VERSION: '3.8'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
           NUMPY_MIN: '1.20.0'
           imageName: 'windows-2019'
-        Linux-Python39-64bit-full-wheel:
-          PYTHON_VERSION: '3.9'
+        Linux-Python310-64bit-full-wheel:
+          PYTHON_VERSION: '3.10'
           PYTHON_ARCH: 'x64'
           BUILD_TYPE: 'wheel'
-          NUMPY_MIN: '1.20.0'
+          NUMPY_MIN: '1.21.6'
           imageName: 'ubuntu-latest'
         Linux-Python38-64bit-full-wheel:
           PYTHON_VERSION: '3.8'
@@ -74,7 +74,7 @@ jobs:
   # "manually"
   - powershell: |
       cd package
-      python -m pip install .
+      python -m pip -v install .
       cd ..
     displayName: 'Build MDAnalysis (wheel)'
     condition: and(succeeded(), eq(variables['BUILD_TYPE'], 'wheel'))
@@ -104,7 +104,6 @@ jobs:
       python -m pip install numpy==$(NUMPY_MIN)
     displayName: 'pin to older NumPy (wheel test)'
     condition: and(succeeded(), eq(variables['BUILD_TYPE'], 'wheel'))
-  # TODO: recent rdkit is not on PyPI
   - script: >-
       python -m pip install
       biopython
@@ -117,6 +116,7 @@ jobs:
       networkx
       parmed
       tidynamics>=1.0.0
+      rdkit>=2020.03.1
     displayName: 'Install additional dependencies for 64-bit tests'
     condition: and(succeeded(), eq(variables['PYTHON_ARCH'], 'x64'))
   - powershell: |

diff --git a/package/CHANGELOG b/package/CHANGELOG
@@ -70,6 +70,8 @@ Enhancements
   * Added isolayer selection method (Issue #3845)
 
 Changes
+ * Minimum numpy version for python 3.10 and Windows has been raised to 1.22.3
+   (PR #3903)
  * Replaced deprecated Bio.pairwise2 with Bio.align.PairwiseAligner in
    MDAnalysis.analysis.align.sequence_alignment (Issue #3950)
  * Increased minimal version of biopython to 1.80 (Issue #3950)

diff --git a/package/pyproject.toml b/package/pyproject.toml
@@ -13,9 +13,11 @@ requires = [
     # arm64 on darwin for py3.8+ requires numpy >=1.21.0
     "numpy==1.21.0; python_version=='3.8' and platform_machine=='arm64' and platform_system=='Darwin' and platform_python_implementation != 'PyPy'",
     "numpy==1.21.0; python_version=='3.9' and platform_machine=='arm64' and platform_system=='Darwin' and platform_python_implementation != 'PyPy'",
+    # Scipy: On windows avoid 1.21.6, 1.22.0, and 1.22.1 because they were built on vc142
+    "numpy==1.22.3; python_version=='3.10' and platform_system=='Windows' and platform_python_implementation != 'PyPy'",
     # As per https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
-    # safest to build at 1.21.6 for all platforms
-    "numpy==1.21.6; python_version=='3.10' and platform_python_implementation != 'PyPy'",
+    # safest to build at 1.21.6 for all other platforms
+    "numpy==1.21.6; python_version=='3.10' and platform_system !='Windows'and platform_python_implementation != 'PyPy'",
     "numpy==1.23.2; python_version=='3.11' and platform_python_implementation != 'PyPy'",
     # For unreleased versions of Python there is currently no known supported
     # NumPy version. In that case we just let it be a bare NumPy install