Add GitHub workflows to lint code scripts and copyright

.github/check_license.py

@@ -0,0 +1,42 @@
+import os
+
+# Define the license header you are looking for
+license_header_first = [
+    "Copyright (c) MONAI Consortium",
+    "limitations under the License."
+]
+
+# List of file extensions to check
+file_extensions = ['.py', '.sh', '.ipynb', '.slurm']
+
+def check_license_in_file(file_path):
+    """Check if the file contains the license header"""
+    with open(file_path, 'r', encoding='utf-8') as file:
+        content = file.read()
+        for license_header in license_header_first:
+            if license_header not in content:
+                return False
+        return True
+
+def check_license_in_directory(directory):
+    """Check for missing license headers in all files in the directory"""
+    files_without_license = []
+
+    for root, dirs, files in os.walk(directory):
+        for file in files:
+            if any(file.endswith(ext) for ext in file_extensions):
+                file_path = os.path.join(root, file)
+                if not check_license_in_file(file_path):
+                    files_without_license.append(file_path)
+
+    return files_without_license
+
+
+if __name__ == '__main__':
+    # Change this to the directory you want to check
+    directory_to_check = '.'
+
+    missing_license_files = check_license_in_directory(directory_to_check)
+
+    if missing_license_files:
+        raise FileNotFoundError(f"Copyright is missing in the following files:\n {'\n'.join(missing_license_files)}")

.github/workflows/copyright.yml

@@ -0,0 +1,23 @@
+name: Copyright Check
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  copyright:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Run copyright check
+        run: |
+          python .github/check_license.py

.github/workflows/general-linting.yml

@@ -0,0 +1,37 @@
+name: General Linting
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements-ci.txt
+
+      - name: Run isort
+        run: |
+          isort --check-only --diff .
+
+      - name: Run black
+        run: |
+          black --diff .
+
+
+      - name: Run ruff
+        run: |
+          ruff check .

README.md

@@ -2,4 +2,26 @@
 
 # MONAI-VILA
 
-monai_vila2d
+monai_vila2d
+
+## Contributing
+
+To lint the code, please install these packages:
+
+```bash
+pip install -r requirements-ci.txt
+```
+
+Then run the following command:
+
+```bash
+isort --check-only --diff .  # using the configuration in pyproject.toml
+black . --check  # using the configuration in pyproject.toml
+ruff check .  # using the configuration in ruff.toml
+```
+
+To auto-format the code, run the following command:
+
+```bash
+isort . && black . && ruff format .
+```

pyproject.toml

@@ -0,0 +1,30 @@
+[tool.black]
+line-length = 122
+include = '\.pyi?$'
+exclude = '''
+/(
+    build
+  | docs
+  | setup\.py
+  | venv.*
+  | .*test_.*
+  | \.mypy_cache
+  | \.vscode
+)/
+'''
+
+[tool.isort]
+profile = "black"
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 122
+skip_glob = [
+  "build/*",
+  "docs/*",
+  "setup.py",
+  "venv*/",
+  "*test_*",
+  "./.vscode/*",
+]

requirements-ci.txt

@@ -0,0 +1,3 @@
+isort==5.13.2
+black==24.8.0
+ruff==0.6.3

ruff.toml

@@ -0,0 +1,13 @@
+line-length = 122
+
+exclude = [
+  "build/*",
+  "docs/*",
+  "setup.py",
+  "venv*/",
+  "*test_*",
+  "./.vscode/*",
+]
+
+[lint]
+select = ["D1"]