Merge pull request #3 from PlasmoGenEpi/update_pmo_app

Update pmo app

Author: kathrynmurie

.github/workflows/deploy.yml

@@ -0,0 +1,44 @@
+name: Build and Deploy
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:  # Allow manual triggering
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        submodules: recursive
+        token: ${{ secrets.GITHUB_TOKEN }}
+    
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install jinja2
+    
+    - name: Build site
+      run: |
+        python build_site.py
+    
+    - name: Commit and push built files
+      if: github.ref == 'refs/heads/main'
+      run: |
+        git config --local user.email "action@github.com"
+        git config --local user.name "GitHub Action"
+        git add docs/
+        git diff --staged --quiet || git commit -m "Build site from submodule [skip ci]"
+        git push
+

.gitignore

@@ -0,0 +1,34 @@
+# Build artifacts - these are generated from source files during build
+# These will be regenerated by GitHub Actions on each deployment
+docs/app/
+docs/site-packages/
+docs/_setup_pmotools.py
+docs/index.html
+
+# Keep docs/assets/ committed (contains wheel file needed for build)
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+ENV/
+.venv
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Local test files
+*.log
+

build_site.py

@@ -1,15 +1,16 @@
 import jinja2
 import os
 import shutil
+import zipfile
 
 requirements = [
     "pandas",
     "fuzzywuzzy",
     "openpyxl",
-    # TODO: remove this once the package is published
-    "https://plasmogenepi.github.io/pmotool-app-web/assets/pmotools_python-0.1.0-py3-none-any.whl"
+    # pmotools is extracted from wheel and included directly in filesystem
 ]
 
+
 entrypoint = "PMO_Builder.py"
 build_dir = "docs"
 
@@ -19,34 +20,97 @@ def build_site():
     with open(template_path, "r") as f:
         template = jinja2.Template(f.read())
 
-    # Load the python files in all subdirectories
+    # Copy Python and JSON files from submodule to docs/app/ directory
+    app_dir = os.path.join(build_dir, "app")
     parsed_files = []
+    
+    # Copy Python files
     for root, dirs, files in os.walk("pmotools-app"):
         for file in files:
             if file.endswith(".py"):
-                with open(os.path.join(root, file), "r") as f:
-                    file_name = os.path.join(root, file).replace("pmotools-app/", "")
-                    parsed_files.append({"name": file_name, "content": f"`{f.read()}`"})
+                src_path = os.path.join(root, file)
+                # Preserve directory structure relative to pmotools-app
+                rel_path = os.path.relpath(src_path, "pmotools-app")
+                dst_path = os.path.join(app_dir, rel_path)
+                
+                # Create destination directory
+                os.makedirs(os.path.dirname(dst_path), exist_ok=True)
+                shutil.copy(src_path, dst_path)
+                
+                # Store file path for template
+                file_name = rel_path.replace("\\", "/")  # Normalize path separators
+                parsed_files.append({"name": file_name, "url": f"app/{file_name}"})
 
-    # Add the images to the parsed files
-    for root, dirs, files in os.walk("pmotools-app"):
-        for file in files:
-            if file.endswith(".png"):
-                file_name = os.path.join(root, file).replace("pmotools-app/", "")
-                # copy the file to the build directory
-                os.makedirs(os.path.join(build_dir, "images"), exist_ok=True)
-                shutil.copy(os.path.join(root, file), os.path.join(build_dir, "images", file))
-                build_url = f"images/{file}"
-                parsed_files.append({"name": file_name, "content": {"url": build_url}})
-
-    # Add conf files to the parsed files
+    # Copy JSON config files
     for root, dirs, files in os.walk("pmotools-app"):
         for file in files:
             if file.endswith(".json"):
-                with open(os.path.join(root, file), "r") as f:
-                    file_name = os.path.join(root, file).replace("pmotools-app/", "")
-                    parsed_files.append({"name": file_name, "content": f"`{f.read()}`"})
+                src_path = os.path.join(root, file)
+                # Preserve directory structure relative to pmotools-app
+                rel_path = os.path.relpath(src_path, "pmotools-app")
+                dst_path = os.path.join(app_dir, rel_path)
+                
+                # Create destination directory
+                os.makedirs(os.path.dirname(dst_path), exist_ok=True)
+                shutil.copy(src_path, dst_path)
+                
+                # Store file path for template
+                file_name = rel_path.replace("\\", "/")  # Normalize path separators
+                parsed_files.append({"name": file_name, "url": f"app/{file_name}"})
 
+    # Extract pmotools package from wheel and add to filesystem
+    # This avoids installing dependencies that are already in requirements
+    wheel_path = os.path.join(build_dir, "assets", "pmotools-0.1.0-py3-none-any.whl")
+    if os.path.exists(wheel_path):
+        with zipfile.ZipFile(wheel_path, 'r') as wheel:
+            # Extract only pmotools package files (not dist-info)
+            for member in wheel.namelist():
+                if member.startswith('pmotools/') and not member.endswith('/'):
+                    # Extract to app directory (which is in Python path in stlite)
+                    # Store as site-packages/pmotools/... for proper Python import
+                    relative_path = member  # This is already pmotools/...
+                    dst_path = os.path.join(app_dir, "site-packages", relative_path)
+                    os.makedirs(os.path.dirname(dst_path), exist_ok=True)
+                    
+                    # Extract and write the file
+                    with wheel.open(member) as source:
+                        with open(dst_path, 'wb') as target:
+                            target.write(source.read())
+                    
+                    # Add to parsed files for template
+                    file_name = relative_path.replace("\\", "/")
+                    parsed_files.append({"name": file_name, "url": f"app/site-packages/{file_name}"})
+        
+        # Create __init__.py for site-packages if needed
+        site_packages_init = os.path.join(app_dir, "site-packages", "__init__.py")
+        if not os.path.exists(site_packages_init):
+            os.makedirs(os.path.dirname(site_packages_init), exist_ok=True)
+            with open(site_packages_init, 'w') as f:
+                f.write("")
+        
+        # Create a setup file to add site-packages to sys.path
+        setup_file = os.path.join(app_dir, "_setup_pmotools.py")
+        with open(setup_file, 'w') as f:
+            f.write("""import sys
+import os
+# Add site-packages to Python path so pmotools can be imported
+site_packages = os.path.join(os.path.dirname(__file__), 'site-packages')
+if site_packages not in sys.path:
+    sys.path.insert(0, site_packages)
+""")
+        # Add setup file to parsed files
+        parsed_files.append({"name": "_setup_pmotools.py", "url": "app/_setup_pmotools.py"})
+        
+        # Modify PMO_Builder.py to import setup first
+        pmo_builder_path = os.path.join(app_dir, "PMO_Builder.py")
+        if os.path.exists(pmo_builder_path):
+            with open(pmo_builder_path, 'r') as f:
+                content = f.read()
+            # Add import at the very beginning if not already present
+            if "import _setup_pmotools" not in content:
+                content = "import _setup_pmotools\n" + content
+                with open(pmo_builder_path, 'w') as f:
+                    f.write(content)
 
     # Render the template
     rendered = template.render(files=parsed_files, requirements=requirements, entrypoint=entrypoint)