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Merge pull request #1648 from LOCEANlloydizard/fix-warnings #468

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Merge pull request #1648 from LOCEANlloydizard/fix-warnings

Merge pull request #1648 from LOCEANlloydizard/fix-warnings #468

Workflow file for this run

.github/workflows/build.yaml at 8062fbc
name: build
on:
push:
branches:
- main
paths-ignore: ["**/docker.yaml"]
workflow_dispatch:
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
env:
NUM_WORKERS: auto
USE_POOCH: "True"
ECHOPYPE_DATA_VERSION: v0.11.1a2
ECHOPYPE_DATA_BASEURL: https://github.com/OSOceanAcoustics/echopype/releases/download/{version}/
XDG_CACHE_HOME: ${{ github.workspace }}/.cache
jobs:
unit-tests:
name: unit--${{ matrix.python-version }}
runs-on: ubuntu-latest
if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
strategy:
fail-fast: false
matrix:
python-version: ["3.11", "3.12", "3.13"]
steps:
- name: Checkout repo
uses: actions/checkout@v6
with:
fetch-depth: 0
- name: Set up Python
uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
cache: pip
- name: Upgrade pip
run: python -m pip install --upgrade pip
- name: Remove docker-compose python
run: sed -i "/docker-compose/d" requirements-dev.txt
- name: Install dev tools
run: python -m pip install -r requirements-dev.txt
- name: Install echopype
run: python -m pip install -e ".[plot]"
- name: Install pooch (needed by conftest)
run: python -m pip install pooch
- name: Run unit tests
run: |
pytest -m unit -vvv -rx --numprocesses=auto \
--cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
- name: Upload code coverage to Codecov
uses: codecov/codecov-action@v6
with:
files: ./coverage.xml
flags: unit
env_vars: RUNNER_OS,PYTHON_VERSION
name: codecov-unit
fail_ci_if_error: false
integration-tests:
name: integration--${{ matrix.python-version }}
runs-on: ubuntu-latest
if: ${{ !contains(github.event.head_commit.message, '[skip ci]') }}
continue-on-error: ${{ matrix.experimental }}
strategy:
fail-fast: false
matrix:
python-version: ["3.11", "3.12", "3.13"]
runs-on: [ubuntu-latest]
experimental: [false]
services:
# TODO: figure out how to update tag when there's a new one
minio:
image: cormorack/minioci:latest
ports:
- 9000:9000
httpserver:
image: httpd:2.4
ports:
- 8080:80
steps:
- name: Checkout repo
uses: actions/checkout@v6
with:
fetch-depth: 0 # Fetch all history for all branches and tags.
- name: Free disk space
if: runner.os == 'Linux'
run: |
set -eux
echo "Before cleanup:"
df -h
for p in /usr/share/dotnet /opt/ghc /usr/local/lib/android /opt/hostedtoolcache/CodeQL; do
if [ -d "$p" ]; then
echo "Removing $p (size: $(du -sh "$p" | cut -f1))"
sudo rm -rf "$p"
else
echo "Not present: $p"
fi
done
sudo apt-get clean
sudo rm -rf /var/lib/apt/lists/*
echo "After cleanup:"
df -h
- name: Set up Python
uses: actions/setup-python@v6.2.0
with:
python-version: ${{ matrix.python-version }}
cache: pip
- name: System usage (baseline)
if: runner.os == 'Linux'
run: |
set -eux
echo "== Disk =="
df -h
echo "== Memory =="
free -h
echo "== Swap =="
swapon --show || true
echo "== Top memory processes =="
ps -eo pid,ppid,cmd,%mem,%cpu --sort=-%mem | head -n 20 || true
- name: Upgrade pip
run: python -m pip install --upgrade pip
- name: Set environment variables
run: |
echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
- name: Remove docker-compose python
run: sed -i "/docker-compose/d" requirements-dev.txt
- name: Install dev tools
run: python -m pip install -r requirements-dev.txt
- name: Cache echopype test data
uses: actions/cache@v5
with:
path: ${{ env.XDG_CACHE_HOME }}/echopype
key: ep-data-${{ env.ECHOPYPE_DATA_VERSION }}
- name: Ensure pooch (for GitHub assets)
run: python -m pip install "pooch>=1.8"
- name: Install error reporter
if: ${{ matrix.python-version == '3.13' }}
run: python -m pip install pytest-github-actions-annotate-failures
- name: Install echopype
run: python -m pip install -e ".[plot]"
- name: Print installed packages
run: python -m pip list
- name: System usage (after install)
if: runner.os == 'Linux'
run: |
set -eux
df -h
free -h
du -h -d 2 "${{ env.XDG_CACHE_HOME }}" || true
ps -eo pid,ppid,cmd,%mem,%cpu --sort=-%mem | head -n 20 || true
- name: Pre-fetch Pooch test data
run: |
pytest --collect-only -q
- name: Copy test data to MinIO and HTTP server
run: |
python .ci_helpers/docker/setup-services.py --deploy --data-only --http-server ${{ job.services.httpserver.id }}
# Check data endpoint
curl http://localhost:8080/data/
- name: System usage (after services)
if: runner.os == 'Linux'
run: |
set -eux
df -h
free -h
du -h -d 2 "${{ env.XDG_CACHE_HOME }}" || true
docker system df || true
ps -eo pid,ppid,cmd,%mem,%cpu --sort=-%mem | head -n 20 || true
- name: Running integration tests
shell: bash -l {0}
run: |
pytest -m integration -vvv -rx --numprocesses=${{ env.NUM_WORKERS }} --max-worker-restart=3 \
--cov=echopype --cov-report=xml --log-cli-level=WARNING --disable-warnings
- name: Upload code coverage to Codecov
uses: codecov/codecov-action@v6
with:
files: ./coverage.xml
flags: integration
env_vars: RUNNER_OS,PYTHON_VERSION
name: codecov-integration
fail_ci_if_error: false
- name: System usage (final)
if: always() && runner.os == 'Linux'
run: |
set -eux
echo "== Disk =="
df -h
echo "== Memory =="
free -h
echo "== Cache dir =="
du -h -d 2 "${{ env.XDG_CACHE_HOME }}" || true
echo "== Docker =="
docker system df || true
echo "== Top memory processes =="
ps -eo pid,ppid,cmd,%mem,%cpu --sort=-%mem | head -n 30 || true