Add JAX 3D X-ray CT projector #488
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# Install scico requirements and run pytest | |
name: unit tests (ubuntu) | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
workflow_dispatch: | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
group: [1, 2, 3, 4, 5] | |
name: pytest split ${{ matrix.group }} (ubuntu) | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
# Check-out the repository under $GITHUB_WORKSPACE | |
- uses: actions/checkout@v4 | |
with: | |
submodules: recursive | |
# Set up conda/mamba environment | |
- name: Set up mambaforge | |
uses: conda-incubator/setup-miniconda@v3 | |
with: | |
miniforge-variant: Mambaforge | |
miniforge-version: latest | |
activate-environment: test-env | |
use-mamba: true | |
python-version: "3.10" | |
# Configure conda environment cache | |
- name: Set up conda environment cache | |
uses: actions/cache@v3 | |
with: | |
path: ${{ env.CONDA }}/envs | |
key: conda-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('requirements.txt') }}-${{ hashFiles('dev_requirements.txt') }}-${{ env.CACHE_NUMBER }} | |
env: | |
CACHE_NUMBER: 1 # Increase this value to force cache reset | |
id: cache | |
# Display environment details | |
- name: Display environment details | |
run: | | |
conda info | |
printenv | sort | |
# Install required system package | |
- name: Install required system package | |
run: sudo apt-get install -y libopenblas-dev | |
# Install dependencies in conda environment | |
- name: Install dependencies | |
if: steps.cache.outputs.cache-hit != 'true' | |
run: | | |
mamba install -c conda-forge pytest pytest-cov | |
python -m pip install --upgrade pip | |
pip install pytest-split | |
pip install -r requirements.txt | |
pip install -r dev_requirements.txt | |
mamba install -c conda-forge svmbir>=0.3.3 | |
mamba install -c conda-forge astra-toolbox | |
mamba install -c conda-forge pyyaml | |
pip install --upgrade --force-reinstall scipy>=1.6.0 # Temporary fix for GLIBCXX_3.4.30 not found in conda forge version | |
pip install bm3d>=4.0.0 | |
pip install bm4d>=4.2.2 | |
pip install "ray[tune]>=2.5.0" | |
pip install hyperopt | |
# Install package to be tested | |
- name: Install package to be tested | |
run: pip install -e . | |
# Run unit tests | |
- name: Run main unit tests | |
run: | | |
DURATIONS_FILE=$(mktemp) | |
bzcat data/pytest/durations_ubuntu.bz2 > $DURATIONS_FILE | |
pytest -x --cov --level=2 --durations-path=$DURATIONS_FILE --splits=5 --group=${{ matrix.group }} --pyargs scico | |
# Upload coverage data | |
- name: Upload coverage | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage${{ matrix.group }} | |
path: .coverage | |
# Run doc tests | |
- name: Run doc tests | |
if: matrix.group == 1 | |
run: | | |
pytest --ignore-glob="*test_*.py" --ignore=scico/linop/xray --doctest-modules scico | |
pytest --doctest-glob="*.rst" docs | |
coverage: | |
needs: test | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python 3.10 | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.10" | |
- name: Install deps | |
run: | | |
python -m pip install --upgrade pip | |
pip install coverage | |
- name: Download all artifacts | |
# Downloads coverage1, coverage2, etc. | |
uses: actions/download-artifact@v3 | |
- name: Run coverage | |
run: | | |
coverage combine coverage*/.coverage* | |
coverage report | |
coverage xml | |
- uses: codecov/codecov-action@v3 | |
with: | |
env_vars: OS,PYTHON | |
fail_ci_if_error: false | |
files: coverage.xml | |
flags: unittests | |
name: codecov-umbrella | |
verbose: true |