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Bump mamba-org/setup-micromamba from 1.8.1 to 1.9.0 (#268) #363

Bump mamba-org/setup-micromamba from 1.8.1 to 1.9.0 (#268)

Bump mamba-org/setup-micromamba from 1.8.1 to 1.9.0 (#268) #363

name: pytest-with-coverage
on:
push:
branches: ['*']
# Enable workflow to be triggered from GitHub CLI, browser, or via API
# primarily for testing conda env solution for new Python versions
workflow_dispatch:
jobs:
pytest-with-coverage:
permissions:
contents: read
pull-requests: write
strategy:
fail-fast: false
matrix:
python-version: [ '3.12' ]
runs-on: 'ubuntu-latest'
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Conda environment with Micromamba
uses: mamba-org/setup-micromamba@f8b8a1e23a26f60a44c853292711bacfd3eac822
with:
environment-file: envs/environment-test.yaml
environment-name: salishsea-nowcast-test
# environment caching does not play nicely with --editable installed packages
cache-environment: false
cache-downloads: true
# persist downloads cache for 1 day
cache-downloads-key: downloads-${{ steps.date.outputs.date }}
create-args: >-
python=${{ inputs.python-version }}
- name: Install editable-mode dependency packages
shell: bash -l {0}
run: |
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/43ravens/NEMO_Nowcast.git#egg=NEMO_Nowcast
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/moad_tools#egg=moad_tools
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/UBC-MOAD/Reshapr#egg=Reshapr
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/NEMO-Cmd.git#egg=NEMO-Cmd
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/SalishSeaCmd.git#egg=SalishSeaCmd
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable "git+https://github.com/SalishSeaCast/tools#egg=SalishSeaTools&subdirectory=SalishSeaTools"
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://github.com/SalishSeaCast/FVCOM-Cmd.git#egg=FVCOM-Cmd
# OPPTools is a private GitLab repo, so an access token is required
python3 -m pip install --src $GITHUB_WORKSPACE/../vcs_pkgs/ --editable git+https://oauth2:${{ secrets.GITLAB_ACCESS_TOKEN }}@gitlab.com/mdunphy/OPPTools.git@6c784a4dc44dd9030aafe9a8519e5ae0b6cc3183#egg=OPPTools
python3 -m pip install --editable $GITHUB_WORKSPACE
- name: pytest package with coverage
shell: bash -l {0}
run: |
pytest --cov=$GITHUB_WORKSPACE --cov-report=xml
- name: Upload coverage report to Codecov
uses: codecov/codecov-action@125fc84a9a348dbcf27191600683ec096ec9021c
with:
file: ./coverage.xml
flags: unittests
token: ${{ secrets.CODECOV_TOKEN }}