Merge pull request #40 from hydra-genetics/develop

chore: dev to master

.github/CODEOWNERS

@@ -2,4 +2,4 @@
 # the repo. Unless a later match takes precedence,
 # @global-owner1 and @global-owner2 will be requested for
 # review when someone opens a pull request.
-* @jonca79
+* @Smeds @jonca79 @marrip @elleira @cl2014git @zezzipa

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,20 @@
+### This PR:
+
+(If this is a release PR, no need to add following. Leave this part empty)
+(Use the following lines to create a PR text body. Make sure to remove all non-relevant one after you're done)
+(Repeat each field as many times as necessary)
+
+Added: for new features.
+Changed: for changes in existing functionality.
+Deprecated: for soon-to-be removed features.
+Removed: for now removed features.
+Fixed: for any bug fixes.
+Security: in case of vulnerabilities.
+
+### Review and tests:
+- [ ] Tests pass
+- [ ] If you've fixed a bug or added code that should be tested, add tests!
+- [ ] Code review
+- [ ] `CHANGELOG.md` is updated
+- [ ] New code is executed and covered by tests, and test approve
+- [ ] Module compatibility section in `README.md` is up to date

.github/workflows/compatibility.yaml

@@ -0,0 +1,39 @@
+name: Compatibility test
+
+on:
+  push:
+    branches:
+     - develop
+     - master
+  pull_request:
+    branches:
+     - develop
+     - master
+  workflow_dispatch:
+
+jobs:
+  compatibility-test:
+    name: Run compatibility test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Get branch names
+        id: branch-name
+        uses: tj-actions/[email protected]
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Add conda to system path
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+      - name: snakemake dry run
+        working-directory: .tests/compatibility
+        run: |
+          snakemake -n -s Snakefile --configfile config.yaml

.github/workflows/conventional-prs.yml

@@ -0,0 +1,18 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/integration.yaml

@@ -0,0 +1,51 @@
+name: small integration test
+
+# Controls when the action will run.
+on:
+   # Triggers the workflow on push or pull request events but only for the master and develop branch
+  push:
+    # do not run the integration test as this is not set up for this module
+    branches:
+     # - develop
+     # - master
+     - dummy
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  integration-small-singularity:
+    name: integration small data set singularity
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+            miniforge-variant: Mambaforge
+            miniforge-version: latest
+            activate-environment: my-env
+            use-mamba: true
+      - name: Set strict channel
+        run: |
+          conda config --set channel_priority strict
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+      - name: Add conda to system path
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
+      - name: Install singularity
+        run: |
+          mamba install -c conda-forge -c bioconda singularity=3.8.6
+      - name: Integration test - small dataset
+        working-directory: .tests/integration
+        run: |
+          snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs --configfile config.yaml --use-singularity --singularity-args  " --cleanenv --bind /home/runner "

.github/workflows/lint.yaml

@@ -1,8 +1,6 @@
 name: Lint
 
-# Controls when the action will run.
 on:
-   # Triggers the workflow on push or pull request events but only for the master and develop branch
   push:
     branches:
      - develop
@@ -11,21 +9,22 @@ on:
     branches:
      - develop
      - master
-
-  # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 jobs:
   lint:
     name: Lint workflow
     runs-on: ubuntu-latest
     steps:
-      - name: Check out the repo
-        uses: actions/checkout@v2
-      - name: Linting
-        uses: snakemake/[email protected]
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
         with:
-          directory: ".tests/integration"
-          snakefile: "workflow/Snakefile"
-          args: "--lint"
-          stagein: "pip install -r requirements.txt"
+          python-version: 3.8
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Linting
+        working-directory: .tests/integration
+        run: |
+          snakemake --lint -n -s ../../workflow/Snakefile --configfile config.yaml

.github/workflows/pycodestyl.yaml → .github/workflows/pycodestyle.yaml

@@ -24,13 +24,7 @@ jobs:
       - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
+          python-version: 3.8      
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/pytest.yaml

@@ -25,12 +25,6 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt

.github/workflows/snakefmt.yaml

@@ -25,7 +25,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Lint Code Base
-        uses: github/super-linter@v3
+        uses: github/super-linter@v4
         env:
           VALIDATE_ALL_CODEBASE: false
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/snakemake-dry-run.yaml

@@ -25,12 +25,6 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Add conda to system path
-        run: |
-          echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install dependencies
-        run: |
-          conda install -c conda-forge mamba
       - name: Install requirements.txt
         run: |
           pip install -r requirements.txt
@@ -40,5 +34,4 @@ jobs:
       - name: snakemake dry run
         working-directory: .tests/integration
         run: |
-          mamba install -c conda-forge -c bioconda snakemake singularity
-          snakemake -n -s ../../workflow/Snakefile
+          snakemake -n -s ../../workflow/Snakefile --configfile config.yaml

.github/workflows/test-build-mkdocs.yaml

@@ -0,0 +1,33 @@
+name: build mkdocs
+
+on:
+  push:
+    branches:
+     - develop
+     - master
+  pull_request:
+    branches:
+     - develop
+     - master
+  workflow_dispatch:
+
+jobs:
+  build-mkdocs:
+    name: build mkdocs
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+          pip install -r docs/requirements.txt
+      - name: build mkdocs
+        run: |
+          mkdocs build

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt