From 716a5371ff4f211cdfb1398bf167e19562fd17d0 Mon Sep 17 00:00:00 2001
From: mirpedrol <mirp.julia@gmail.com>
Date: Fri, 23 Aug 2024 09:21:08 +0200
Subject: [PATCH] add github actions to lint and run tests and run test
 coverage

---
 .github/.coveragerc             |   4 +
 .github/workflows/lint-code.yml |  33 ++++++
 .github/workflows/pytest.yml    | 180 ++++++++++++++++++++++++++++++++
 3 files changed, 217 insertions(+)
 create mode 100644 .github/.coveragerc
 create mode 100644 .github/workflows/lint-code.yml
 create mode 100644 .github/workflows/pytest.yml

diff --git a/.github/.coveragerc b/.github/.coveragerc
new file mode 100644
index 0000000..8ea7c7c
--- /dev/null
+++ b/.github/.coveragerc
@@ -0,0 +1,4 @@
+[run]
+omit = nf_class/*-template/*
+source = nf_class
+relative_files = True
\ No newline at end of file
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
new file mode 100644
index 0000000..4e730a7
--- /dev/null
+++ b/.github/workflows/lint-code.yml
@@ -0,0 +1,33 @@
+name: Lint code formatting
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
new file mode 100644
index 0000000..ea097bf
--- /dev/null
+++ b/.github/workflows/pytest.yml
@@ -0,0 +1,180 @@
+name: Python tests
+# This workflow is triggered on pushes and PRs to the repository.
+# Only run if we changed a Python file
+on:
+  push:
+    branches:
+      - dev
+    paths-ignore:
+      - "CHANGELOG.md"
+  pull_request:
+    paths-ignore:
+      - "CHANGELOG.md"
+      # ignore github workflows except for the current one
+      - ".github/**"
+      - "!.github/workflows/pytest.yml"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run with the same workflow name is queued
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  setup:
+    runs-on: "ubuntu-latest"
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.12"]
+        runner: ["ubuntu-latest"]
+        include:
+          - python-version: "3.8"
+            runner: "ubuntu-20.04"
+
+    steps:
+      - name: Check conditions
+        id: conditions
+        run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT"
+
+    outputs:
+      python-version: ${{ matrix.python-version }}
+      runner: ${{ matrix.runner }}
+      run-tests: ${{ steps.conditions.outputs.run-tests }}
+
+  # create a test matrix based on all python files in /tests
+  list_tests:
+    name: Get test file matrix
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        name: Check out source-code repository
+
+      - name: List tests
+        id: list_tests
+        run: |
+          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+    outputs:
+      tests: ${{ steps.list_tests.outputs.tests }}
+
+  test:
+    name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
+    needs: [setup, list_tests]
+    if: ${{ needs.setup.outputs.run-tests }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
+      fail-fast: false # run all tests even if one fails
+    steps:
+      - name: go to subdirectory and change nextflow workdir
+        run: |
+          mkdir -p pytest
+          cd pytest
+          export NXF_WORK=$(pwd)
+
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        name: Check out source-code repository
+
+      - name: Set up Python ${{ needs.setup.outputs.python-version }}
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: ${{ needs.setup.outputs.python-version }}
+          cache: "pip"
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: Install dev version of nf-core
+        # reinstall the dev version of nf-core until v3.0.0 is released
+        run: |
+          pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
+
+      - name: Downgrade git to the Ubuntu official repository's version
+        if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }}
+        run: |
+          sudo apt update
+          sudo apt remove -y git git-man
+          sudo add-apt-repository --remove ppa:git-core/ppa
+          sudo apt install -y git
+
+      - name: Set up Singularity
+        if: ${{ matrix.test == 'test_download.py'}}
+        uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+        with:
+          singularity-version: 3.8.3
+
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
+      - name: Test with pytest
+        run: |
+          python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$?
+
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
+      - name: Upload coverage
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        with:
+          name: coverage_${{ env.test }}
+          path: .coverage
+
+  coverage:
+    needs: test
+    # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default
+    runs-on: ubuntu-latest
+    steps:
+      - name: go to subdirectory
+        run: |
+          mkdir -p pytest
+          cd pytest
+
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip -r requirements-dev.txt
+          pip install -e .
+
+      - name: move coveragerc file up
+        run: |
+          mv .github/.coveragerc .
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4
+      - name: Run coverage
+        run: |
+          coverage combine --keep coverage*/.coverage*
+          coverage report
+          coverage xml
+
+      - uses: codecov/codecov-action@5ecb98a3c6b747ed38dc09f787459979aebb39be # v4
+        with:
+          files: coverage.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}