From 546b57005ef16aff1d7e319aa184881ad266d6d2 Mon Sep 17 00:00:00 2001
From: Pau Andrio <andriopau@gmail.com>
Date: Mon, 4 Nov 2024 10:35:28 +0100
Subject: [PATCH] [CI/CD](linting_and_testing.yml): Update set-up micromamba.

---
 .github/workflows/linting_and_testing.yml | 127 ++++++++++++++++++++++
 1 file changed, 127 insertions(+)
 create mode 100644 .github/workflows/linting_and_testing.yml

diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
new file mode 100644
index 0000000..1980ea3
--- /dev/null
+++ b/.github/workflows/linting_and_testing.yml
@@ -0,0 +1,127 @@
+name: tests
+
+on:
+  # workflow_dispatch
+  push:
+    branches: [ master ]
+    paths-ignore:
+      - '.gitignore'
+      - '.readthedocs.yaml'
+      - 'LICENSE'
+      - 'setup.py'
+      - 'README.md'
+      - 'CITATION.cff'
+      - 'references.jsonld'
+      - '**/docs/**'
+      - '**/json_schemas/**'
+
+jobs:
+  # Name of the Job
+  lint_and_test:
+    strategy:
+      matrix:
+        os: [self-hosted]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v4
+
+      - run: echo "Repository -> ${{ github.repository }}"
+      - run: echo "Branch -> ${{ github.ref }}"
+      - run: echo "Trigger event -> ${{ github.event_name }}"
+      - run: echo "Runner OS -> ${{ runner.os }}"
+
+
+      - name: List files in the repository
+        run: |
+          ls ${{ github.workspace }}
+
+      - name: Remove all micromamba installations
+        run: |
+          rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
+          touch /home/user/.bash_profile
+
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v2.0.0
+        with:
+          generate-run-shell: true
+          micromamba-version: '2.0.2-2'
+          post-cleanup: 'all'
+          init-shell: bash
+          environment-file: .github/env.yaml
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pytest
+            pytest-cov
+            pytest-html
+            flake8
+            pip
+
+      - name: Install genbadge from pip
+        shell: bash -l {0}
+        run: pip install genbadge[all]
+
+      - name: List installed package versions
+        shell: bash -l {0}
+        run: micromamba list
+
+
+      - name: Lint with flake8
+        shell: bash -l {0}
+        run: |
+          # F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
+          # E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
+
+          # Workflow fails: Stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+
+          # Create directory for flake8 reports
+          mkdir -p ./reports/flake8
+
+          # Exit-zero treats all errors as warnings, workflow will not fail:
+          flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
+
+      - name: Generate Flake8 badge
+        shell: bash -l {0}
+        run: |
+          genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt  --output-file ./reports/flake8/flake8badge.svg
+
+      - name: Checkout biobb_common
+        uses: actions/checkout@v4
+        with:
+          repository: bioexcel/biobb_common
+          path: './biobb_common'
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: |
+          # Ignoring docker and singularity tests
+          export PYTHONPATH=.:./biobb_common:$PYTHONPATH
+
+          # Create directory for tests reports
+          mkdir -p ./reports/junit
+
+          # Producction one
+          pytest biobb_pmx/test/unitests/ --cov=biobb_pmx/ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
+
+      - name: Generate Tests badge
+        shell: bash -l {0}
+        run: |
+          genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml  --output-file ./reports/junit/testsbadge.svg
+
+      - name: Generate Coverage badge
+        shell: bash -l {0}
+        run: |
+          # Create directory for flake8 reports
+          mkdir -p ./reports/coverage
+
+          coverage xml -o ./reports/coverage/coverage.xml
+          coverage html -d ./reports/coverage/
+
+          genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml  --output-file ./reports/coverage/coveragebadge.svg
+
+      - name: Publish coverage report to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: ./reports
\ No newline at end of file