Parallelize pytest

.devcontainer/devcontainer.json

@@ -3,6 +3,7 @@
     "image": "nfcore/gitpod:latest",
     "postCreateCommand": "python -m pip install --upgrade -r ../requirements-dev.txt -e ../ && pre-commit install --install-hooks",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/workflows/create-lint-wf.yml

@@ -27,14 +27,14 @@ jobs:
           - "latest-everything"
     steps:
       # Get the repo code
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
       # Set up nf-core/tools
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -48,7 +48,9 @@ jobs:
           version: ${{ matrix.NXF_VER }}
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

.github/workflows/create-test-lint-wf-template.yml

@@ -16,6 +16,7 @@ concurrency:
 
 env:
   NXF_ANSI_LOG: false
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   RunTestWorkflow:
@@ -32,13 +33,13 @@ jobs:
           - "template_skip_nf_core_configs.yml"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |
@@ -51,7 +52,9 @@ jobs:
           version: latest-everything
 
       # Install the Prettier linting tools
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier

.github/workflows/create-test-wf.yml

@@ -26,13 +26,13 @@ jobs:
           - "23.04.0"
           - "latest-everything"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/deploy-pypi.yml

@@ -13,13 +13,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Check out source-code repository
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
 
       - name: Install python dependencies
         run: |

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,9 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -38,10 +40,10 @@ jobs:
           # Override to remove the default --check flag so that we make changes
           options: "--color"
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
       - name: python-isort
         uses: isort/[email protected]
         with:

.github/workflows/lint-code.yml

@@ -14,11 +14,13 @@ concurrency:
 
 jobs:
   EditorConfig:
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -28,11 +30,13 @@ jobs:
         run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
 
   Prettier:
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: "20"
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -41,9 +45,9 @@ jobs:
         run: prettier --check ${GITHUB_WORKSPACE}
 
   PythonBlack:
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,17 +75,57 @@ jobs:
           allow-repeats: false
 
   isort:
-    runs-on: ubuntu-latest
+    runs-on: ["ubuntu-latest"]
     steps:
       - name: Check out source-code repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
+      - name: Set up Python 3.12
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.12
       - name: python-isort
         uses: isort/[email protected]
         with:
           isortVersion: "latest"
           requirementsFiles: "requirements.txt requirements-dev.txt"
+
+  static-type-check:
+    runs-on: ["ubuntu-latest"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        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: 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: Get Python changed files
+        id: changed-py-files
+        uses: tj-actions/changed-files@v23
+        with:
+          files: |
+            *.py
+            **/*.py
+      - name: Run if any of the listed files above is changed
+        if: steps.changed-py-files.outputs.any_changed == 'true'
+        run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }}

.github/workflows/push_dockerhub_dev.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:dev docker image
         run: docker build --no-cache . -t nfcore/tools:dev

.github/workflows/push_dockerhub_release.yml

@@ -23,7 +23,7 @@ jobs:
       fail-fast: false
     steps:
       - name: Check out code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Build nfcore/tools:latest docker image
         run: docker build --no-cache . -t nfcore/tools:latest