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name: Tests | ||
on: | ||
push: | ||
branches: [ master ] | ||
pull_request: | ||
branches: [ master ] | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.ref }} | ||
cancel-in-progress: true | ||
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env: | ||
FORCE_COLOR: 3 | ||
CONDA_ENV: ./environment.yml | ||
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jobs: | ||
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lint: | ||
name: Run Linters | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
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- name: Run black | ||
uses: psf/black@stable | ||
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- name: Run flake8 | ||
uses: py-actions/flake8@v2 | ||
with: | ||
path: "tjpcov tests" | ||
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tests: | ||
needs: lint | ||
name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} | ||
runs-on: ${{ matrix.runs-on }} | ||
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defaults: | ||
run: | ||
# IMPORTANT: this is needed to make sure that the conda environment is auto activated | ||
shell: bash -el {0} | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
python-version: ["3.8", "3.11"] | ||
runs-on: [ubuntu-latest, macos-latest] | ||
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steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
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- name: Set up mamba | ||
uses: conda-incubator/setup-miniconda@v2 | ||
with: | ||
channels: conda-forge | ||
python-version: ${{ matrix.python-version }} | ||
channel-priority: strict | ||
show-channel-urls: true | ||
auto-update-conda: true | ||
use-mamba: true | ||
activate-environment: tjpcov | ||
miniforge-version: latest | ||
miniforge-variant: Mambaforge | ||
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- name: Cache Date | ||
id: get-date | ||
run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | ||
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- name: Check for cached environment | ||
uses: actions/cache@v3 | ||
id: cache | ||
env: | ||
# Increase this value to reset cache if etc/example-environment.yml has not changed | ||
CACHE_NUMBER: 0 | ||
with: | ||
path: ${{env.CONDA}}/envs | ||
key: | ||
${{runner.os}}.${{runner.arch}}.mamba-py.${{matrix.python-version}}.${{hashFiles('pyproject.toml')}}.${{hashFiles('environment.yml')}}.${{steps.get-date.outputs.today}}.${{env.CACHE_NUMBER}} | ||
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- name: Install environment packages | ||
if: steps.cache.outputs.cache-hit != 'true' | ||
run: | | ||
export MAMBA_NO_BANNER=1 | ||
mamba env update --file ${{ env.CONDA_ENV }} | ||
- name: Install TJPCov | ||
run: pip install .[nmt] --no-deps | ||
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- name: Run Tests | ||
run: pytest --cov-report lcov -vv tests/test_covariance_clusters.py --cov=tjpcov | ||
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- name: Collect coverage report | ||
uses: coverallsapp/github-action@v2 | ||
with: | ||
flag-name: run-${{matrix.python-version}}-${{matrix.runs-on}} | ||
parallel: true | ||
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# - name: Run MPI Tests (OpenMPI) | ||
# run: | | ||
# mamba install -y openmpi | ||
# pip install .[mpi] --no-deps | ||
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# mpiexec -n 2 pytest -vv tests/test_mpi.py | ||
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# mamba remove -y openmpi | ||
# pip uninstall -y mpi4py | ||
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# - name: Run MPI Tests (mpich) | ||
# run: | | ||
# mamba install -y mpich | ||
# pip install -U mpi4py --no-cache-dir --no-deps | ||
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# mpiexec -n 2 pytest -vv tests/test_mpi.py | ||
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- name: Collect coverage report | ||
uses: coverallsapp/github-action@v2 | ||
with: | ||
flag-name: run-${{matrix.python-version}}-${{matrix.runs-on}} | ||
parallel: true | ||
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finish: | ||
needs: tests | ||
name: Collect and publish coverage report | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Publish code coverage report | ||
uses: coverallsapp/github-action@v2 | ||
with: | ||
parallel-finished: true | ||
carryforward: "run-3.8-ubuntu-latest,run-3.11-ubuntu-latest,run-3.8-macos-latest,run-3.11-macos-latest," |
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name: tjpcov # minimum environment for tjpcov development | ||
name: tjpcov | ||
channels: | ||
- conda-forge | ||
- defaults | ||
dependencies: | ||
- python>=3.8 | ||
- mpi4py | ||
- pip | ||
- numpy | ||
- wheel | ||
- black | ||
- flake8 | ||
- pytest | ||
- pytest-cov | ||
- pytest-rerunfailures | ||
- coveralls | ||
- nox | ||
- numpy | ||
- scipy | ||
- pyyaml | ||
- pyccl >= 2.5.0, < 2.8.0 | ||
- sacc>=0.8 | ||
- namaster | ||
# tjpcov is only available at the moment through PyPi | ||
- pip: | ||
# Installing TJPcov in two steps to avoid making NaMaster installation to | ||
# fail due to (https://github.com/LSSTDESC/NaMaster/issues/138) | ||
- tjpcov[full] | ||
- camb | ||
- Jinja2 | ||
- healpy | ||
- h5py | ||
- mpi4py | ||
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