Skip to content

Fix CI: Use Conda Python headers #839

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
DimitriPapadopoulos wants to merge 2 commits into
base: main
Choose a base branch
from
+50 −13
Open

Fix CI: Use Conda Python headers #839

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ba35fc2
use Conda Meson instead of system Meson
DimitriPapadopoulos Apr 12, 2026
dc6cd1a
Create the `test` env
DimitriPapadopoulos Apr 18, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
63 changes: 50 additions & 13 deletions .github/workflows/ci.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,9 +33,12 @@ jobs:
channels: conda-forge
miniforge-version: latest
python-version: ${{ matrix.python-version }}
activate-environment: test
auto-activate-base: false

- name: Install compilers
run: conda install -y c-compiler cxx-compiler
- name: Install build dependencies and compilers
run: |
conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler

- name: Install clang
if: matrix.platform == 'macos-15-large'
Expand All @@ -47,21 +50,33 @@ jobs:
conda config --show-sources
conda list --show-channel-urls

- name: Meson args - prefer Conda over system Python (Ubuntu)
if: startsWith(matrix.platform, 'ubuntu')
run: |
echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV

- name: Install numcodecs
run: |
# TODO: Remove this conditional when pcodec supports Python 3.14
if [[ "${{ matrix.python-version }}" == "3.14" ]]; then
python -m pip install -v ".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]"
python -m pip install -v \
".[test,test_extras,msgpack,google_crc32c,crc32c,zfpy]" \
pytest
else
python -m pip install -v ".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]"
python -m pip install -v \
".[test,test_extras,msgpack,google_crc32c,crc32c,pcodec,zfpy]" \
pytest
fi

- name: List installed packages
run: python -m pip list

- name: Run tests
shell: "bash -l {0}"
run: pytest -v
run: python -m pytest -v

- uses: codecov/codecov-action@v5
with:
Expand Down Expand Up @@ -99,9 +114,20 @@ jobs:
channels: conda-forge
miniforge-version: latest
python-version: "3.13"
activate-environment: test
auto-activate-base: false

- name: Install compilers
run: conda install -y c-compiler cxx-compiler
- name: Install build dependencies and compilers
run: |
conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler

- name: Meson args - prefer Conda over system Python (Ubuntu)
run: |
echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV

- name: Install numcodecs
run: |
Expand All @@ -115,7 +141,7 @@ jobs:
run: python -m pip list

- name: Run checksum tests
run: pytest -v tests/test_checksum32.py
run: python -m pytest -v tests/test_checksum32.py

- uses: codecov/codecov-action@v5
with:
Expand Down Expand Up @@ -153,18 +179,29 @@ jobs:
channels: conda-forge
miniforge-version: latest
python-version: "3.13"
activate-environment: test
auto-activate-base: false

- name: Install build dependencies and compilers
run: |
conda install -y python numpy cython meson meson-python ninja c-compiler cxx-compiler

- name: Install compilers
run: conda install -y c-compiler cxx-compiler
- name: Meson args - prefer Conda over system Python (Ubuntu)
run: |
echo "MESONPY_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV
PY_INC="$(python -c 'import sysconfig; print(sysconfig.get_path("include"))')"
echo "CFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CFLAGS:-}" >> $GITHUB_ENV
echo "CPPFLAGS=-I${PY_INC} -I${CONDA_PREFIX}/include ${CPPFLAGS:-}" >> $GITHUB_ENV
echo "LDFLAGS=-L${CONDA_PREFIX}/lib ${LDFLAGS:-}" >> $GITHUB_ENV

- name: Install numcodecs and Zarr
run: |
python -m pip install -v ".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
python -m pip install -v ".[test,test_extras]" "${{ matrix.zarr-pkg }}" crc32c
- name: List installed packages
run: python -m pip list

- name: Run Zarr integration tests
run: pytest tests/test_zarr3.py tests/test_zarr3_import.py
run: python -m pytest tests/test_zarr3.py tests/test_zarr3_import.py

- uses: codecov/codecov-action@v5
with:
Expand Down
Loading