Merge pull request #32 from SciLifeLab/master

Version sync

.devcontainer/devcontainer.json

@@ -1,31 +1,29 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
 {
-    "name": "TACA",
-    "build": {
-        // Sets the run context to one level up instead of the .devcontainer folder.
-        "context": "..",
-        // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-        "dockerfile": "../Dockerfile"
+  "name": "TACA",
+  "build": {
+    // Sets the run context to one level up instead of the .devcontainer folder.
+    "context": "..",
+    // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+    "dockerfile": "../Dockerfile",
+  },
+  "features": {},
+  "customizations": {
+    "vscode": {
+      "extensions": ["ms-python.python"],
     },
-    "features": {},
-    "customizations": {
-        "vscode": {
-            "extensions": [
-                "ms-python.python",
-            ]
-        }
-    },
-    // Features to add to the dev container. More info: https://containers.dev/features.
-    // "features": {},
-    // Use 'forwardPorts' to make a list of ports inside the container available locally.
-    // "forwardPorts": [],
-    "postCreateCommand": "cd ../flowcell_parser/ && pip3 install -e . && cd ../TACA && pip3 install -e .",
-    // Configure tool-specific properties.
-    // "customizations": {},
-    // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
-    // "remoteUser": "devcontainer"
-    "mounts": [
-        "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached"
-    ]
-}
+  },
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  // "features": {},
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+  "postCreateCommand": "cd ../flowcell_parser/ && pip3 install -e . && cd ../TACA && pip3 install -e .",
+  // Configure tool-specific properties.
+  // "customizations": {},
+  // Uncomment to connect as an existing user other than the container default. More info: https://aka.ms/dev-containers-non-root.
+  // "remoteUser": "devcontainer"
+  "mounts": [
+    "source=${localEnv:HOME}/repos/flowcell_parser,target=/workspaces/flowcell_parser,type=bind,consistency=cached",
+  ],
+}

.git-blame-ignore-revs

@@ -0,0 +1,9 @@
+# Start adding here
+
+# 2024-01-31, Non-invasive fixes after merge with master //AKe
+a676908bb32d60bcbc5e42ce710f889980845af4
+2ba0179015e380b3b7e0ce8b9b99666533a7443f
+8ea4523b1c9789d03410178d75aea93b6b2ffa77
+d5330f615b237beadcec22d5422dff3c02aa54ff
+b9ee704ad4da26790e539b8fe1d39aa71f831ef1
+6a3edf3710b6fdd8c233662ebf900e9bd24e6bd5

.github/pr_labels.yml

@@ -1,4 +1,4 @@
-version: '1'
+version: "1"
 invalidStatus: "pending"
 labelRule:
   values:

.github/workflows/check-log.yml

@@ -0,0 +1,26 @@
+name: Check VERSIONLOG.MD has been updated
+on: [pull_request]
+
+jobs:
+  check-versionlog:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout PR
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags
+
+      - name: Check for VERSIONLOG.MD changes
+        id: versionlog_check
+        # 1) Find the common ancestor between the current HEAD and the base branch
+        # 2) Then see if the versionlog has been updated in the PR since it diverged
+        #    from the common ancestor
+        run: |
+          PR_BASE_SHA=$(git merge-base HEAD ${{ github.event.pull_request.base.sha }})
+          FILE_CHANGED=$(git diff --name-only $PR_BASE_SHA HEAD | grep 'VERSIONLOG.md' || true)
+          if [ -n "$FILE_CHANGED" ]; then
+            echo "VERSIONLOG.MD has been changed."
+          else
+            echo "VERSIONLOG.MD has NOT been changed."
+            exit 1 # Fail the workflow if no changes in VERSIONLOG.MD
+          fi

.github/workflows/lint-code.yml

@@ -0,0 +1,124 @@
+name: Lint code
+on: [push, pull_request]
+
+jobs:
+  # Use ruff to check for code style violations
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check for style violations
+        # Configured in pyproject.toml
+        run: ruff check .
+
+  # Use ruff to check code formatting
+  ruff-format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check code formatting
+        run: ruff format --check .
+
+  # Use mypy for static type checking
+  mypy-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install mypy
+      # Start by installing type stubs
+      - name: mypy --> Install stubs
+        run: echo -e "y" | mypy --install-types **/*.py || exit 0
+      - name: mypy --> Static type checking
+        # Configured in pyprojet.toml
+        run: mypy **/*.py
+
+  # Use pipreqs to check for missing dependencies
+  pipreqs-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install pipreqs
+        run: pip install pipreqs
+
+      - name: Install requirements
+        run: pip install -r requirements.txt
+
+      - name: Run pipreqs
+        run: pipreqs --savepath pipreqs.txt
+
+      - name: Compare requirements
+        run: |
+          # Extract and sort package names
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | sort -u > requirements.compare
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | sort -u > pipreqs.compare
+
+          # Compare package lists
+          if cmp -s requirements.compare pipreqs.compare
+          then
+            echo "Requirements are the same"
+
+            exit 0
+          else
+            echo "Requirements are different"
+            echo ""
+
+            echo "=== current requirements.txt ==="
+            echo ""
+            cat requirements.compare
+            echo ""
+
+            echo "=== pipreqs requirements ==="
+            echo ""
+            cat pipreqs.compare
+
+            exit 1
+          fi
+
+  # Use Prettier to check various file formats
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .

.gitignore

@@ -9,3 +9,7 @@ _build
 .benchmarks
 .coverage
 __pycache__
+.pytest_cache
+.vscode
+.ruff_cache
+.mypy_cache

.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+# .pre-commit-config.yaml
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.7.1"
+    hooks:
+      - id: mypy
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier

CONTRIBUTING.md

@@ -2,13 +2,14 @@
 
 When contribution to this package please have the following things in mind:
 
-__NOTE__: _Please make sure that there are no exisiting [issues]((https://github.com/SciLifeLab/TACA/issues)) relating to whatever you want to report._
+**NOTE**: _Please make sure that there are no exisiting [issues](<(https://github.com/SciLifeLab/TACA/issues)>) relating to whatever you want to report._
 
 ####To contribute:
+
 1. Create an issue describing the bug / suggestion / improvement / ... [here](https://github.com/SciLifeLab/TACA/issues).
 2. Fork this repository to your GitHub account
 3. Make the necessary changes / additions to your forked TACA repository
-4. Please *make sure* that you've documented your code and changes using [sphinx](http://sphinx.readthedocs.org/en/latest/tutorial.html) syntax, as the documentation will be automatically generated using this engine, and published to [ReadTheDocs](http://project-management.readthedocs.org/)
+4. Please _make sure_ that you've documented your code and changes using [sphinx](http://sphinx.readthedocs.org/en/latest/tutorial.html) syntax, as the documentation will be automatically generated using this engine, and published to [ReadTheDocs](http://project-management.readthedocs.org/)
 5. Update the version number in `TACA/__init__.py`
 6. Pull Request and wait for the responsible reviewer to review and merge the code
 

Dockerfile

@@ -24,4 +24,4 @@ COPY requirements-dev.txt requirements-dev.txt
 RUN python -m pip install -r requirements-dev.txt
 
 RUN mkdir /root/.taca/
-COPY tests/data/taca_test_cfg.yaml /root/.taca/taca.yaml
+COPY tests/data/taca_test_cfg.yaml /root/.taca/taca.yaml