Python 3.9 - 3.13: CI Updates

.appveyor.yml

@@ -1,14 +1,14 @@
 environment:
   matrix:
     - TARGET_ARCH: x64
-      CONDA_PY: 3.7
+      CONDA_PY: 3.9
       CONDA_INSTALL_LOCN: C:\\Miniconda37-x64
       APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
       platform: x64
       SHARED: OFF
 
     - TARGET_ARCH: x86
-      CONDA_PY: 3.7
+      CONDA_PY: 3.9
       CONDA_INSTALL_LOCN: C:\\Miniconda37
       APPVEYOR_BUILD_WORKER_IMAGE: Visual Studio 2017
       platform: x86

.github/workflows/linux.yml

@@ -213,7 +213,7 @@ jobs:
 #  gcc-4.8.5_py35_nompi_h5
 #  gcc-7.4.0_py_ompi_h5_ad2_coveralls
 
-  gcc7_py36_pd_dd_ompi_h5_ad2:
+  gcc7_py39_pd_dd_ompi_h5_ad2:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
@@ -224,19 +224,16 @@ jobs:
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install g++-7 gfortran libopenmpi-dev python3 python3-setuptools
+        sudo apt-get install g++-7 gfortran libopenmpi-dev python3.9 python3.9-dev python3.9-venv
         sudo .github/workflows/dependencies/install_spack
-        python3 -m pip install -U pip
-        python3 -m pip install -U numpy
-        python3 -m pip install -U mpi4py
-        python3 -m pip install -U pandas
-        python3 -m pip install -U dask
-        python3 -m pip install -U pyarrow
     - name: Build
       env: {CC: gcc-7, CXX: g++-7, CXXFLAGS: -Werror}
       run: |
         eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad2/)
         spack install
+        python3.9 -m venv env
+        source env/bin/activate
+        pip install numpy mpi4py pandas dask pyarrow
 
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
@@ -249,19 +246,22 @@ jobs:
         cd build
         ctest --output-on-failure
 
-  gcc9_py38_pd_nompi_h5_ad2_libcpp:
+  gcc9_py39_pd_nompi_h5_ad2_libcpp:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3 python3-numpy python3-mpi4py python3-pandas
+        sudo apt-get install g++ libopenmpi-dev libhdf5-openmpi-dev python3.9 python3.9-dev python3.9-venv
 #       TODO ADIOS2
     - name: Build
       env: {CXXFLAGS: -Werror, PKG_CONFIG_PATH: /usr/lib/x86_64-linux-gnu/pkgconfig}
       run: |
+        python3.9 -m venv env
+        source env/bin/activate
+        pip install numpy mpi4py pandas dask pyarrow
         share/openPMD/download_samples.sh build
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=ON \

.github/workflows/tooling.yml

@@ -47,9 +47,7 @@ jobs:
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install clang-10 libc++-dev libc++abi-dev python3 gfortran libopenmpi-dev
-        python3 -m pip install -U pip
-        python3 -m pip install -U numpy
+        sudo apt-get install clang-10 libc++-dev libc++abi-dev python3.9 python3.9-dev python3.9-venv gfortran libopenmpi-dev
         sudo .github/workflows/dependencies/install_spack
     - name: Build
       env: {CC: mpicc, CXX: mpic++, OMPI_CC: clang-10, OMPI_CXX: clang++-10, CXXFLAGS: -Werror, OPENPMD_HDF5_CHUNKS: none, OPENPMD_TEST_NFILES_MAX: 100}
@@ -58,6 +56,9 @@ jobs:
         spack install
         SOURCEPATH="$(pwd)"
         share/openPMD/download_samples.sh build
+        python3.9 -m venv env
+        source env/bin/activate
+        pip install numpy
         export LDFLAGS="${LDFLAGS} -fsanitize=address,undefined -shared-libsan"
         export CXXFLAGS="${CXXFLAGS} -fsanitize=address,undefined -shared-libsan"
         cmake -S . -B build               \
@@ -66,6 +67,7 @@ jobs:
           -DopenPMD_USE_HDF5=ON           \
           -DopenPMD_USE_ADIOS2=ON         \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
+          -DPython_EXECUTABLE="$(which python)" \
           -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build build --parallel 2
         export ASAN_OPTIONS=detect_stack_use_after_return=1:detect_leaks=1:check_initialization_order=true:strict_init_order=true:detect_stack_use_after_scope=1:fast_unwind_on_malloc=0

Dockerfile

@@ -112,21 +112,6 @@ RUN         for whl in /opt/src/dist/*.whl; do \
             && du -hs /opt/src/dist/* \
             && du -hs /wheelhouse/*
 
-# test in fresh env: Debian:Sid + Python 3.8
-FROM       debian:sid
-ENV        DEBIAN_FRONTEND noninteractive
-COPY --from=build-env /wheelhouse/openPMD_api-*-cp38-cp38-manylinux2010_x86_64.whl .
-RUN        apt-get update \
-           && apt-get install -y --no-install-recommends python3.8 python3-distutils ca-certificates curl \
-           && rm -rf /var/lib/apt/lists/*
-RUN        python3.8 --version \
-           && curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py \
-           && python3.8 get-pip.py \
-           && python3.8 -m pip install openPMD_api-*-cp38-cp38-manylinux2010_x86_64.whl
-RUN        python3.8 -c "import openpmd_api as io; print(io.__version__); print(io.variants)"
-RUN        python3.8 -m openpmd_api.ls --help
-RUN        openpmd-ls --help
-
 # test in fresh env: Debian:Bullseye + Python 3.9
 FROM       debian:bullseye
 ENV        DEBIAN_FRONTEND noninteractive

NEWS.rst

@@ -15,7 +15,7 @@ Note that ADIOS2 does not support compression in BP3 files.
 
 CMake 3.22.0 is now the minimally supported version for CMake.
 pybind11 2.13.0 is now the minimally supported version for Python support.
-Python 3.12 & 3.13 are now supported, Python 3.7 is removed.
+Python 3.12 & 3.13 are now supported, Python 3.7 & 3.8 are removed.
 
 The ``len(...)`` of many classes has been reworked for consistency and returns now the number of entries (iterations, record components, etc.).
 Previously, this sporadically returned the number of attributes, which is better queried via ``len(<object>.attributes)``.

README.md

@@ -115,7 +115,7 @@ while those can be built either with or without:
 
 Optional language bindings:
 * Python:
-  * Python 3.8 - 3.13
+  * Python 3.9 - 3.13
   * pybind11 2.13.0+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)

Singularity

@@ -42,7 +42,7 @@ Supported frontends are C++11 and Python3.
         -DopenPMD_USE_PYTHON=ON  \
         -DopenPMD_BUILD_TESTING=OFF       \
         -DCMAKE_INSTALL_PREFIX=/usr/local \
-        -DCMAKE_INSTALL_PYTHONDIR=lib/python3.6/dist-packages
+        -DCMAKE_INSTALL_PYTHONDIR=lib/python3.12/dist-packages
     make
     # make test
     make install

cmake/dependencies/pybind11.cmake

@@ -78,9 +78,9 @@ set(openPMD_pybind11_branch "v2.13.6"
     "Repository branch for openPMD_pybind11_repo if(openPMD_USE_INTERNAL_PYBIND11)")
 
 if(openPMD_USE_PYTHON STREQUAL AUTO)
-    find_package(Python 3.7.0 COMPONENTS Interpreter Development.Module)
+    find_package(Python 3.9.0 COMPONENTS Interpreter Development.Module)
 elseif(openPMD_USE_PYTHON)
-    find_package(Python 3.7.0 COMPONENTS Interpreter Development.Module REQUIRED)
+    find_package(Python 3.9.0 COMPONENTS Interpreter Development.Module REQUIRED)
 else()
     set(openPMD_HAVE_PYTHON FALSE)
 endif()

conda.yml

@@ -36,7 +36,7 @@ dependencies:
   - pre-commit
   - pyarrow  # for dask
 #  - pybind11  # shipped internally
-  - python>=3.8
+  - python>=3.9
 
 # just a note for later hackery, we could install pip packages inside the env, too:
 #  - pip:

docs/source/dev/dependencies.rst

@@ -38,7 +38,7 @@ Optional: language bindings
 
 * Python:
 
-  * Python 3.8 - 3.13
+  * Python 3.9 - 3.13
   * pybind11 2.13.0+
   * numpy 1.15+
   * mpi4py 2.1+ (optional, for MPI)

docs/source/install/install.rst

@@ -192,7 +192,7 @@ CMake will summarize the install paths for you before the build step.
    # Note that one some systems, /lib might need to be replaced with /lib64.
 
    #                change path to your python MAJOR.MINOR version
-   export PYTHONPATH=$HOME/somepath/lib/python3.8/site-packages:$PYTHONPATH
+   export PYTHONPATH=$HOME/somepath/lib/python3.12/site-packages:$PYTHONPATH
 
 Adding those lines to your ``$HOME/.bashrc`` and re-opening your terminal will set them permanently.
 

setup.py

@@ -196,7 +196,7 @@ def build_extension(self, ext):
     cmdclass=dict(build_ext=CMakeBuild),
     # scripts=['openpmd-ls'],
     zip_safe=False,
-    python_requires='>=3.8',
+    python_requires='>=3.9',
     # tests_require=['pytest'],
     install_requires=install_requires,
     # see: src/bindings/python/cli
@@ -225,7 +225,6 @@ def build_extension(self, ext):
         'Topic :: Database :: Front-Ends',
         'Programming Language :: C++',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',