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Fix nonlinear iterative inversion removing modeled data from the entire map instead of locally #514

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Fix nonlinear iterative inversion removing modeled data from the entire map instead of locally

Fix nonlinear iterative inversion removing modeled data from the entire map instead of locally #514

Workflow file for this run

.github/workflows/test.yml at cf9c36d
# Configuration for running tests with GitHub Actions
#
# NOTE: Pin actions to a specific commit to avoid having the authentication
# token stolen if the Action is compromised. See the comments and links here:
# https://github.com/pypa/gh-action-pypi-publish/issues/27
#
name: test
# Only build PRs, the main branch, and releases. Pushes to branches will only
# be built when a PR is opened. This avoids duplicated buids in PRs comming
# from branches in the origin repository (1 for PR and 1 for push).
on:
pull_request:
push:
branches:
- main
release:
types:
- published
permissions: {}
# Use bash by default in all jobs
defaults:
run:
# -e makes sure builds fail if any command fails
shell: bash -o pipefail -e {0}
jobs:
#############################################################################
# Run tests
test:
name: ${{ matrix.os }} python=${{ matrix.python }} dependencies=${{ matrix.dependencies }}
runs-on: ${{ matrix.os }}
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:
os: [ubuntu-latest, macos-latest, windows-latest]
python: ["3.9", "3.12"]
include:
- python: "3.9"
dependencies: oldest
- python: "3.12"
dependencies: latest
env:
REQUIREMENTS: env/requirements-build.txt env/requirements-test.txt
# Used to tag codecov submissions
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
# Checks-out your repository under $GITHUB_WORKSPACE
- name: Checkout
uses: actions/checkout@v5
with:
# Need to fetch more than the last commit so that setuptools_scm can
# create the correct version string. If the number of commits since
# the last release is greater than this, the version still be wrong.
# Increase if necessary.
fetch-depth: 100
# The GitHub token is preserved by default but this job doesn't need
# to be able to push to GitHub.
persist-credentials: false
# Need the tags so that setuptools_scm can form a valid version number
- name: Fetch git tags
run: git fetch origin 'refs/tags/*:refs/tags/*'
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version: ${{ matrix.python }}
- name: Collect requirements
run: |
echo "Install Dependente to capture dependencies:"
python -m pip install dependente==0.3.0
echo ""
echo "Capturing run-time dependencies:"
if [[ "${{ matrix.dependencies }}" == "oldest" ]]; then
dependente --source install --oldest > requirements-full.txt
else
dependente --source install > requirements-full.txt
fi
echo ""
echo "Capturing dependencies from:"
for requirement in $REQUIREMENTS
do
echo " $requirement"
cat $requirement >> requirements-full.txt
done
echo ""
echo "Collected dependencies:"
cat requirements-full.txt
- name: Get the pip cache folder
id: pip-cache
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- name: Setup caching for pip packages
uses: actions/cache@v4
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-${{ hashFiles('requirements-full.txt') }}
- name: Check Python and pip version
run: |
python --version; python -m pip --version
- name: Install requirements
run: |
python -m pip install --requirement requirements-full.txt
- name: List installed packages
run: python -m pip freeze
# Needs to be editable for coverage reporting to work
- name: Install the package in editable mode
run: python -m pip install --no-deps --editable .
- name: Get the version of ensaio
id: ensaio-version
run: echo "v=$(grep ensaio env/requirements-docs.txt)" >> $GITHUB_OUTPUT
- name: Setup caching of Ensaio datasets
uses: actions/cache@v4
with:
path: ${{ runner.temp }}/cache/ensaio
key: ensaio-data-${{ steps.ensaio-version.outputs.v }}
- name: Run the tests
run: make test
env:
# Define directory where sample data will be stored
ENSAIO_DATA_DIR: ${{ runner.temp }}/cache/ensaio/
# Don't spam Zenodo from CI
ENSAIO_DATA_FROM_GITHUB: true
- name: Rename the coverage artifact
run: mv .coverage .coverage.${{ matrix.os }}_${{ matrix.python }}_${{ matrix.dependencies }}
- name: Upload coverage as artifact
uses: actions/upload-artifact@v4
with:
path: .coverage.*
name: coverage_${{ matrix.os }}_${{ matrix.python }}_${{ matrix.dependencies }}
if-no-files-found: ignore
include-hidden-files: true
#############################################################################
# Check coverage and upload a report
# Inspired by: https://hynek.me/articles/ditch-codecov-python/
coverage:
name: test coverage is 100%
if: always()
needs: test
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v5
with:
# The GitHub token is preserved by default but this job doesn't need
# to be able to push to GitHub.
persist-credentials: false
- uses: actions/setup-python@v6
with:
# Use latest Python, so it understands all syntax.
python-version: "3.13"
- name: Get the pip cache folder
id: pip-cache
run: echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- name: Setup caching for pip packages
uses: actions/cache@v4
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-coverage
- uses: actions/download-artifact@v5
with:
pattern: coverage_*
# If true, the downloaded artifacts will be in the same directory
# specified by path.
merge-multiple: true
- name: Install coverage.py
run: python -m pip install --upgrade coverage[toml]
- name: Combine coverage
run: python -m coverage combine
- name: Make an HTML report
run: python -m coverage html --skip-empty
- name: Report coverage on the job summary
run: python -m coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
- name: Fail if coverage is not 100%
run: python -m coverage report --fail-under=100
- name: Upload HTML report if check failed
uses: actions/upload-artifact@v4
with:
name: html-report
path: htmlcov
if: ${{ failure() }}