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docs: add content to reproducibility page #444

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docs: add content to reproducibility page

docs: add content to reproducibility page #444

Workflow file for this run

.github/workflows/ci.yaml at faf5c7e
name: CI
# Enable Buildkit and let compose use it to speed up image building
env:
DOCKER_BUILDKIT: 1
COMPOSE_DOCKER_CLI_BUILD: 1
CONDA_ENV_NAME: clim-recal
# CONDA_ENV_PATH: conda-lock.yml
CONDA_ENV_PATH: .conda-linux-64.lock
MIN_PYTHON_VERSION: 3.12
PYTHON_MODULE_FOLDER: python/
COVERAGE_SVG_FOLDER: docs/assets/
COVERAGE_SVG_FILE_NAME: coverage.svg
# replace below with references to previous config lines
COVERAGE_SVG_PATH: docs/assets/coverage.svg
GH_PAGE_PATH: _gh-page
on:
pull_request:
branches: ['main', 'rm-cmethods', ]
paths-ignore: ['docs/**']
push:
branches: ['main', 'rm-cmethods', ]
paths-ignore: ['docs/**']
concurrency:
group: ${{ github.head_ref || github.run_id }}
cancel-in-progress: true
permissions:
contents: write
jobs:
linter:
runs-on: ubuntu-latest
steps:
- name: Checkout Code Repository
uses: actions/checkout@main
- name: Set up Python
uses: actions/setup-python@main
with:
python-version: ${{ env.MIN_PYTHON_VERSION }}
- name: Run pre-commit
uses: pre-commit/action@main
- name: Update pre-commit
uses: pre-commit-ci/lite-action@main
if: always()
pytest:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}
steps:
- name: Checkout Code Repository
uses: actions/checkout@main
- name: Build Conda Environment
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: ${{ env.CONDA_ENV_NAME }}
environment-file: ${{ env.CONDA_ENV_PATH }}
auto-activate-base: false
miniforge-version: latest
use-mamba: true
- name: Run Python Tests
# The first line below may be temporary,
# see this solution:
# https://github.com/pyenv/pyenv/issues/2625
run: |
mamba install libsqlite --force-reinstall
mamba run -n ${{ env.CONDA_ENV_NAME }} --cwd python pytest -m "not darwin and not mount"
shell: bash -el {0}
# - name: Copy test coverage results
# run: |
# cp ${{ env.PYTHON_MODULE_FOLDER }}${{ env.COVERAGE_SVG_PATH }} ${{ env.COVERAGE_SVG_FOLDER }}
- name: Archive coverage svg
uses: actions/upload-artifact@v3
with:
name: coverage-badge
path: ${{ env.COVERAGE_SVG_PATH }}
docs:
needs: [linter, pytest]
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v4
- name: Download coverage svg
uses: actions/download-artifact@v3
with:
name: coverage-badge
path: ${{ env.GH_PAGE_PATH }}${{ env.COVERAGE_SVG_PATH }}
- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
- name: Build Conda Environment
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: ${{ env.CONDA_ENV_NAME }}
environment-file: ${{ env.CONDA_ENV_PATH }}
auto-activate-base: false
miniforge-version: latest
- name: Run `quartodoc`
shell: bash -el {0}
run: |
mamba run -n ${{ env.CONDA_ENV_NAME }} quartodoc build
- name: Install Python and Dependencies
uses: actions/setup-python@v4
with:
python-version: '3.12'
cache: 'pip'
- name: Install gdal and local libraries
run: |
sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install gdal-bin libgdal-dev
pip install ./python
- name: Render and Publish
uses: quarto-dev/quarto-actions/publish@v2
with:
target: gh-pages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# The below raises a code 137 error on `GitHub` Actions
# docker:
# needs: [linter, pytest]
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@main
#
# - name: Build and Test with Root permission
# run: |
# docker compose build jupyter
# docker compose up jupyter --detach
# docker compose exec jupyter bash -c "conda run -n ${{ env.CONDA_ENV_NAME }} --cwd python pytest"
#
# - name: Clean-up
# run: docker compose down