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DimitriPapadopoulosDimitriPapadopoulos
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use Conda Meson instead of system Meson
Otherwise, Meson insists on getting cython to include system Python headers which simply doesn't work: ----- Sanity check compile stderr: In file included from /usr/include/python3.10/Python.h:8, from sanity_check_for_cython.c:19: /usr/include/python3.10/pyconfig.h:9:12: fatal error: aarch64-linux-gnu/python3.10/pyconfig.h: No such file or directory 9 | # include <aarch64-linux-gnu/python3.10/pyconfig.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. ----- Also, avoid starting a new shell!
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Lines changed: 42 additions & 65 deletions

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‎.github/workflows/ci.yaml‎

Lines changed: 42 additions & 65 deletions
Original file line numberDiff line numberDiff line change
@@ -34,8 +34,9 @@ jobs:
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miniforge-version: latest
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python-version: ${{ matrix.python-version }}
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- name: Install compilers
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run: conda install -y c-compiler cxx-compiler
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- name: Install build dependencies and compilers
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run: |
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conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler
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- name: Install clang
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if: matrix.platform == 'macos-15-large'
@@ -47,43 +48,33 @@ jobs:
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conda config --show-sources
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conda list --show-channel-urls
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- name: Meson args - use active Python include/lib (Ubuntu)
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- name: Meson args - prefer Conda over system Python (Ubuntu)
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if: startsWith(matrix.platform, 'ubuntu')
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run: |
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PY_INC=$(python -c "import sysconfig; print(sysconfig.get_config_var('INCLUDEPY'))")
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echo "PY_INC=$PY_INC" >> $GITHUB_ENV
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echo "MESON_SETUP_ARGS=-Dc_args=-I${PY_INC} -Dc_link_args=-L${CONDA_PREFIX}/lib" >> $GITHUB_ENV
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echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
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PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
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echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
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echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
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echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV
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- name: Install numcodecs
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run: |
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if [[ "${{ startsWith(matrix.platform, 'ubuntu') }}" == "true" ]]; then
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# TODO: Remove this conditional when pcodec supports Python 3.14
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if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
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python -m pip install -v \
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--config-settings="setup-args=${MESON_SETUP_ARGS}" \
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".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]"
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else
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python -m pip install -v \
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--config-settings="setup-args=${MESON_SETUP_ARGS}" \
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".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]"
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fi
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# TODO: Remove this conditional when pcodec supports Python 3.14
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if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
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python -m pip install -v \
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".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]" \
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pytest
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else
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# TODO: Remove this conditional when pcodec supports Python 3.14
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if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
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python -m pip install -v \
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".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]"
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else
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python -m pip install -v \
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".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]"
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fi
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python -m pip install -v \
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".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]" \
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pytest
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fi
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- name: List installed packages
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run: python -m pip list
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- name: Run tests
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shell: "bash -l {0}"
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run: pytest -v
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run: python -m pytest -v
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- uses: codecov/codecov-action@v5
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with:
@@ -122,41 +113,31 @@ jobs:
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miniforge-version: latest
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python-version: "3.13"
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- name: Install compilers
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run: conda install -y c-compiler cxx-compiler
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- name: Install build dependencies and compilers
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run: |
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conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler
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- name: Meson args - use active Python include/lib (Ubuntu)
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if: startsWith(matrix.platform, 'ubuntu')
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- name: Meson args - prefer Conda over system Python (Ubuntu)
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run: |
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PY_INC=$(python -c "import sysconfig; print(sysconfig.get_config_var('INCLUDEPY'))")
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echo "PY_INC=$PY_INC" >> $GITHUB_ENV
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echo "MESON_SETUP_ARGS=-Dc_args=-I${PY_INC} -Dc_link_args=-L${CONDA_PREFIX}/lib" >> $GITHUB_ENV
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echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
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PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
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echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
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echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
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echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV
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- name: Install numcodecs
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run: |
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if [[ "${{ startsWith(matrix.platform, 'ubuntu') }}" == "true" ]]; then
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if [[ -n "${{ matrix.extras }}" ]]; then
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python -m pip install -v \
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--config-settings="setup-args=${MESON_SETUP_ARGS}" \
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".[${{ matrix.extras }},test]"
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else
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python -m pip install -v \
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--config-settings="setup-args=${MESON_SETUP_ARGS}" \
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".[test]"
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fi
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if [[ -n "${{ matrix.extras }}" ]]; then
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python -m pip install -v ".[${{ matrix.extras }},test]"
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else
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if [[ -n "${{ matrix.extras }}" ]]; then
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python -m pip install -v ".[${{ matrix.extras }},test]"
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else
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python -m pip install -v ".[test]"
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fi
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python -m pip install -v ".[test]"
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fi
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- name: List installed packages
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run: python -m pip list
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- name: Run checksum tests
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run: pytest -v tests/test_checksum32.py
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run: python -m pytest -v tests/test_checksum32.py
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- uses: codecov/codecov-action@v5
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with:
@@ -195,30 +176,26 @@ jobs:
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miniforge-version: latest
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python-version: "3.13"
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- name: Install compilers
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run: conda install -y c-compiler cxx-compiler
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- name: Install build dependencies and compilers
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run: |
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conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler
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- name: Meson args - use active Python include/lib (Ubuntu)
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if: startsWith(matrix.platform, 'ubuntu')
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- name: Meson args - prefer Conda over system Python (Ubuntu)
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run: |
204-
PY_INC=$(python -c "import sysconfig; print(sysconfig.get_config_var('INCLUDEPY'))")
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echo "PY_INC=$PY_INC" >> $GITHUB_ENV
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echo "MESON_SETUP_ARGS=-Dc_args=-I${PY_INC} -Dc_link_args=-L${CONDA_PREFIX}/lib" >> $GITHUB_ENV
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echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
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PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
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echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
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echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
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echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV
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- name: Install numcodecs and Zarr
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run: |
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if [[ "${{ startsWith(matrix.platform, 'ubuntu') }}" == "true" ]]; then
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python -m pip install -v \
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--config-settings="setup-args=${MESON_SETUP_ARGS}" \
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".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
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else
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python -m pip install -v ".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
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fi
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python -m pip install -v ".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
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- name: List installed packages
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run: python -m pip list
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- name: Run Zarr integration tests
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run: pytest tests/test_zarr3.py tests/test_zarr3_import.py
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run: python -m pytest tests/test_zarr3.py tests/test_zarr3_import.py
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- uses: codecov/codecov-action@v5
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with:

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