Add Updated documentation notebook for running R CLI #536
Workflow file for this run
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name: ci | |
on: | |
push: | |
pull_request: | |
branches: | |
- develop | |
- main | |
env: | |
CACHE_NUMBER: 0 # increase to reset cache manually | |
jobs: | |
pre_job: | |
runs-on: ubuntu-latest | |
# Map a step output to a job output | |
outputs: | |
should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
steps: | |
- id: skip_check | |
uses: fkirc/skip-duplicate-actions@v5 | |
with: | |
# All of these options are optional, so you can remove them if you are happy with the defaults | |
concurrent_skipping: 'same_content_newer' | |
skip_after_successful_duplicate: 'true' | |
paths_ignore: '["**/README.md", "**/docs/**"]' | |
do_not_skip: '["workflow_dispatch", "schedule"]' | |
ci: | |
needs: pre_job | |
if: needs.pre_job.outputs.should_skip != 'true' | |
strategy: | |
fail-fast: false | |
matrix: | |
include: | |
- os: ubuntu | |
label: linux-64 | |
prefix: /usr/share/miniconda3/envs/boa | |
- os: macos | |
label: osx-64 | |
prefix: /Users/runner/miniconda3/envs/boa | |
- os: windows | |
label: win-64 | |
prefix: C:\Miniconda3\envs\boa | |
name: ${{ matrix.label }} | |
runs-on: ${{ matrix.os }}-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Setup Mambaforge | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniforge-variant: Mambaforge | |
miniforge-version: latest | |
python-version: 3.9 | |
activate-environment: boa | |
use-mamba: true | |
- name: Set cache date | |
run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
- uses: actions/cache@v3 | |
with: | |
path: ${{ matrix.prefix }} | |
key: ${{ matrix.label }}-conda-${{ hashFiles('environment_dev.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} | |
id: cache | |
- name: Update base environment | |
run: mamba env update -n boa -f environment_dev.yml --prune | |
if: steps.cache.outputs.cache-hit != 'true' | |
- name: export env to artifact | |
run: mamba env export -n boa > environment_ci_${{ matrix.os }}.yml | |
- uses: actions/upload-artifact@v3 | |
with: | |
name: environment_ci_${{ matrix.os }}.yml | |
path: environment_ci_${{ matrix.os }}.yml | |
- name: Lint | |
shell: bash -l {0} | |
run: | | |
invoke style --checkonly | |
- name: Run tests | |
shell: bash -l {0} | |
run: invoke tests --options '-s -v --cov=boa --cov-branch --cov-report=xml' | |
- name: Upload coverage to Codecov | |
if: startsWith(matrix.os, 'ubuntu') | |
uses: codecov/codecov-action@v3 | |
- name: Pytest coverage comment | |
if: startsWith(matrix.os, 'ubuntu') | |
uses: MishaKav/pytest-coverage-comment@main | |
with: | |
pytest-xml-coverage-path: ./coverage.xml | |
- name: Test package builds successfully | |
shell: bash -l {0} | |
run: | | |
python -m pip install build | |
python -m build | |
# Report final results of the matrix tests | |
result: | |
name: Result | |
if: needs.pre_job.outputs.should_skip != 'true' && always() | |
runs-on: ubuntu-latest | |
needs: | |
- pre_job | |
- ci | |
steps: | |
- name: Mark result as failed | |
if: needs.ci.result != 'success' | |
run: exit 1 |