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Joss review edits

Joss review edits #188

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: CI
# define when this workflow is triggered
on:
workflow_dispatch:
pull_request:
push:
branches:
- main
# cancel any currently running workflows in this same PR
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
# Use bash by default in all jobs
defaults:
run:
shell: bash -el {0}
jobs:
# run pre-commit which includes many formatting and linting tools
pre-commit:
name: Format
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: actions/setup-python@v5
with:
python-version: "3.x"
- uses: pre-commit/[email protected]
with:
extra_args: --hook-stage manual --all-files
- name: Run PyLint
run: pipx run nox -s pylint -- --output-format=github
# Run tests and upload to codecov
test:
name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
runs-on: ${{ matrix.runs-on }}
if: |
${{!startsWith(github.event.head_commit.message, 'docs:') }} ||
${{!startsWith(github.event.head_commit.message, 'style:') }}
needs: [pre-commit]
strategy:
# Otherwise, the workflow would stop if a single job fails. We want to
# run all of them to catch failures in different combinations.
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12"]
runs-on: [ubuntu-latest, macos-latest, windows-latest]
env:
FORCE_COLOR: 3
NUMBA_DISABLE_JIT: "1"
steps:
# Checkout current git repository
- name: Checkout
uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Switch to Current Branch
run: git checkout ${{ env.BRANCH }}
# Install Mambaforge with conda-forge dependencies
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
activate-environment: polartoolkit
environment-file: env/testing_env.yml
python-version: ${{ matrix.python-version }}
channels: conda-forge,nodefaults
channel-priority: strict
miniforge-version: latest
miniforge-variant: Mambaforge
mamba-version: "*"
use-mamba: true
auto-activate-base: false
# Install the package in editable mode
- name: Install local package
run: pip install -e .
# Show installed pkg information for postmortem diagnostic
- name: List installed packages
run: mamba list
- name: Run the tests
run: >-
pytest -m "not earthdata and not issue" -ra --cov --cov-report=xml
--cov-report=term --durations=20
- name: Upload coverage report
uses: codecov/[email protected]
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}