Ci maintenance (#373)

* fix pypi upload
* lessons learned from morphio

Author: mgeplf

.github/workflows/clang_format_check.yaml

@@ -10,7 +10,7 @@ jobs:
 
     steps:
         - name: Fetch repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
           with:
             fetch-depth: 2
         - name: Install packages

.github/workflows/coverage_test.yaml

@@ -10,7 +10,7 @@ jobs:
 
         steps:
             - name: Checkout repository
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
             - name: Fetch repository
               run: git fetch --prune --unshallow
             - name: Get submodules

.github/workflows/docstring_check.yaml

@@ -10,7 +10,7 @@ jobs:
 
     steps:
         - name: Fetch repository
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
           with:
             submodules: recursive
 

.github/workflows/publish-sdist-wheels.yml

@@ -6,7 +6,7 @@ env:
 
   CIBW_BUILD_VERBOSITY: 3
   CIBW_BUILD: 'cp*'
-  CIBW_SKIP: 'cp35-* cp36-* cp37-* *-musllinux_* *-manylinux_i686'
+  CIBW_SKIP: 'cp35-* cp36-* cp37-* cp38-* *-musllinux_* *-manylinux_i686'
   CIBW_TEST_COMMAND: ( cd {project}/python/tests; python -m unittest -v )
   UNIXY_HDF5_VERSION: 1.14.3
 
@@ -19,14 +19,15 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-latest]
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-20.04, macos-13, macos-14]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'true'
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.11'
@@ -68,7 +69,7 @@ jobs:
         if: runner.os == 'macOS'
 
         env:
-          CIBW_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH CMAKE_OSX_ARCHITECTURES MACOSX_DEPLOYMENT_TARGET"
+          CIBW_ENVIRONMENT_PASS: "STATIC_HDF5 CMAKE_PREFIX_PATH"
           CIBW_BEFORE_BUILD: |
             # CMake complains if the dependencies come from within the same tree
             # as the source, so we'll just pretend they are elsewhere
@@ -79,19 +80,7 @@ jobs:
           # used by setup.py to decide if to set `FindHDF5` to use static hdf5 libraries
           export STATIC_HDF5=True
 
-          # x86_64 macOS allows for cross compilation; first we do arm64,
-          # only for the 11.0 target; and store in the cache the compiled code...
-          export CIBW_ARCHS_MACOS="arm64"
-          export CMAKE_OSX_ARCHITECTURES="arm64"
-          export MACOSX_DEPLOYMENT_TARGET="11.0"
-          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
-          python -m cibuildwheel --output-dir dist
-
-          # ...and now we do both targets for x86_64
-          export CIBW_ARCHS_MACOS="x86_64"
-          export CMAKE_OSX_ARCHITECTURES="x86_64"
-          unset MACOSX_DEPLOYMENT_TARGET
-          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-$CIBW_ARCHS_MACOS/install
+          export CMAKE_PREFIX_PATH=/Users/runner/work/src-cache/install-`uname -m`/install
           python -m cibuildwheel --output-dir dist
 
       - name: Store wheel as artifact
@@ -106,12 +95,12 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: 'true'
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -141,7 +130,7 @@ jobs:
       - name: Download artifacts produced during the build_wheels and build_sdist jobs
         uses: actions/download-artifact@v4
         with:
-          name: dist-*
+          pattern: dist-*
           path: dist/
           merge-multiple: true
 

.github/workflows/run-tests.yml

@@ -23,7 +23,7 @@ jobs:
             CXX: g++
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: 'true'
 
@@ -49,7 +49,7 @@ jobs:
             CXX: g++
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: 'true'
 
@@ -71,15 +71,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: 'true'
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: ${{ matrix.python-version }}
@@ -101,7 +101,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: 'true'
 

setup.py

@@ -126,7 +126,7 @@ def build_extension(self, ext):
     extras_require={
         'docs': ['sphinx-bluebrain-theme'],
     },
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     use_scm_version={"local_scheme": "no-local-version",
                      },
     package_dir={"": "python"},