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add GHA to test all components #4885

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add GHA to test all components #4885

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d024b25
add GHA to test all components
mirpedrol Feb 8, 2024
5972590
parallelize pytest
mashehu Feb 8, 2024
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260 changes: 260 additions & 0 deletions .github/workflows/test_all.yml
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name: Run all tests
on:
workflow_dispatch:

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Suggested change

push:
branches: [master]
pull_request:
branches: [master]

# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true

env:
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

jobs:
nf-core-lint:
runs-on: ubuntu-latest
name: nf-core-lint-all
strategy:
fail-fast: false
steps:
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11"

- uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-

- name: Install pip
run: python -m pip install --upgrade pip

- uses: actions/setup-java@v3
with:
distribution: "temurin"
java-version: "17"
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v1

- name: Install nf-core tools development version
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev

- name: Lint all modules
run: nf-core modules lint --all

- name: Lint all subworkflows
run: nf-core subworkflows lint --all

pytest:
runs-on: ubuntu-latest
name: pytest-all
strategy:
fail-fast: false
env:
NXF_ANSI_LOG: false
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

steps:
- uses: actions/checkout@v4

- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11"

- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow cryptography

- uses: actions/setup-java@v3
with:
distribution: "temurin"
java-version: "17"
- name: Setup Nextflow ${{ matrix.NXF_VER }}
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Setup apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main

- name: Set up Singularity
if: matrix.profile == 'singularity'
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR

- name: Set up miniconda
uses: conda-incubator/setup-miniconda@v2
with:
miniconda-version: "latest"
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}

- name: Conda setup
run: |
conda clean -a
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH

# Set up secrets
- name: Set up nextflow secrets
if: env.SENTIEON_LICENSE_BASE64 != null
run: |
nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
SENTIEON_AUTH_DATA=$(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64

# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest tests/ --symlink --kwdof --git-aware --color=yes

- name: Output log on failure
if: failure()
run: |
sudo apt-get update > /dev/null
sudo apt-get install bat > /dev/null
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err}

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v3
with:
name: logs-${{ matrix.profile }}
path: |
/home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work
!/home/runner/pytest_workflow_*/*/work/conda
!/home/runner/pytest_workflow_*/*/work/singularity
!${{ github.workspace }}/.singularity

nf-test:
runs-on: ubuntu-latest
name: nf-test-all
strategy:
fail-fast: false
env:
NXF_ANSI_LOG: false
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
NFTEST_VER: "0.8.4"

steps:
- uses: actions/checkout@v4

- uses: actions/setup-java@v3
with:
distribution: "temurin"
java-version: "17"
- name: Setup Nextflow
uses: nf-core/setup-nextflow@v1

- name: Cache nf-test installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest

- name: Install nf-test
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash
sudo mv nf-test /usr/local/bin/

- name: Setup apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main

- name: Set up Singularity
if: matrix.profile == 'singularity'
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR

- name: Set up miniconda
uses: conda-incubator/setup-miniconda@v2
with:
miniconda-version: "latest"
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}

- name: Conda setup
run: |
conda clean -a
conda install -n base conda-libmamba-solver
conda config --set solver libmamba
pip install pdiff
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH

# Set up secrets
- name: Set up nextflow secrets
if: env.SENTIEON_LICENSE_BASE64 != null
run: |
nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
SENTIEON_AUTH_DATA=$(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64

# Test the module
- name: Run nf-test
env:
NFT_DIFF: "pdiff"
NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
run: |
NFT_WORKDIR=~ \
nf-test test \
--profile=${{ matrix.profile }} \
--tap=test.tap \
--verbose

- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap

confirm-pass:
runs-on: ubuntu-latest
needs: [nf-core-lint, pytest, nf-test]
name: confirm-pass-all-tests
if: always()
steps:
- name: All tests ok
if: ${{ success() || !contains(needs.*.result, 'failure') }}
run: exit 0
- name: One or more tests failed
if: ${{ contains(needs.*.result, 'failure') }}
run: exit 1

- name: debug-print
if: always()
run: |
echo "toJSON(needs) = ${{ toJSON(needs) }}"
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
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