Brings latest work on VirtualFlyBrain/virtual-fly-brain branch into the Metacell/virtual-fly-brain branch

.github/workflows/docker_build.yml

@@ -0,0 +1,75 @@
+name: Build and Push VFB Containers
+
+on:
+  push:
+    branches: [ "main", "master", "development" ]
+  pull_request:
+    branches: [ "main", "master", "development" ]
+  # Allow manual trigger
+  workflow_dispatch:
+
+env:
+  REGISTRY: docker.io
+  BACKEND_IMAGE_NAME: virtualflybrain/vfb-backend
+  FRONTEND_IMAGE_NAME: virtualflybrain/vfb-frontend
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Log in to DockerHub
+        uses: docker/login-action@v3
+        with:
+          registry: docker.io
+          username: ${{ secrets.DOCKER_HUB_USER }}
+          password: ${{ secrets.DOCKER_HUB_PASSWORD }}
+          logout: true
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ${{ env.BACKEND_IMAGE_NAME }}
+            ${{ env.FRONTEND_IMAGE_NAME }}
+          tags: |
+            type=schedule
+            type=ref,event=branch
+            type=ref,event=tag
+            type=ref,event=pr
+            type=sha
+            type=raw,value=latest,enable={{is_default_branch}}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build and push Backend image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: Dockerfile.backend
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ env.BACKEND_IMAGE_NAME }}:latest,${{ env.BACKEND_IMAGE_NAME }}:${{ github.sha }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{ env.BACKEND_IMAGE_NAME }}:buildcache
+          cache-to: type=registry,ref=${{ env.BACKEND_IMAGE_NAME }}:buildcache,mode=max
+
+      - name: Build and push Frontend image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: Dockerfile.frontend
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ env.FRONTEND_IMAGE_NAME }}:latest,${{ env.FRONTEND_IMAGE_NAME }}:${{ github.sha }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=registry,ref=${{ env.FRONTEND_IMAGE_NAME }}:buildcache
+          cache-to: type=registry,ref=${{ env.FRONTEND_IMAGE_NAME }}:buildcache,mode=max

Dockerfile.backend

@@ -0,0 +1,55 @@
+# Use Python base image
+FROM python:3.9-slim
+
+# Set working directory
+WORKDIR /app
+
+# Install git, build tools, and OpenGL dependencies
+RUN apt-get update && apt-get install -y \
+    git \
+    build-essential \
+    libgl1-mesa-glx \
+    libgl1-mesa-dev \
+    xvfb \
+    libglu1-mesa \
+    libosmesa6 \
+    freeglut3-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up virtual display for OpenGL
+ENV DISPLAY=:99
+
+# Copy backend files first
+COPY applications/virtual-fly-brain/backend/virtual_fly_brain /app/virtual_fly_brain
+COPY applications/virtual-fly-brain/backend/setup.py /app/
+COPY applications/virtual-fly-brain/backend/requirements.txt /app/
+COPY applications/virtual-fly-brain/backend/test-requirements.txt /app/
+
+# Copy and install VFBquery
+COPY applications/virtual-fly-brain/backend/virtual_fly_brain/libs/VFBquery /app/VFBquery
+RUN cd /app/VFBquery && pip install -e .
+
+# Install Python dependencies
+RUN pip install --no-cache-dir -r requirements.txt -r test-requirements.txt
+
+# Add virtual_fly_brain to PYTHONPATH
+ENV PYTHONPATH=/app:/app/virtual_fly_brain:${PYTHONPATH} \
+    PYTHONUNBUFFERED=1
+
+# Create and set up volume directories
+RUN mkdir -p /app/data /app/cache
+VOLUME ["/app/data", "/app/cache"]
+
+# Expose port
+EXPOSE 8080
+
+# Create startup script
+RUN echo '#!/bin/bash\n\
+Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &\n\
+sleep 1\n\
+cd /app/virtual_fly_brain\n\
+python __main__.py' > /start.sh && \
+    chmod +x /start.sh
+
+# Command to run the application
+CMD ["/start.sh"]

Dockerfile.frontend

@@ -0,0 +1,54 @@
+# Use Node.js base image
+FROM node:16-bullseye-slim
+
+# Set working directory
+WORKDIR /app
+
+# Install required tools
+RUN apt-get update && \
+    apt-get install -y \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy package files
+COPY applications/virtual-fly-brain/client/package.json ./
+COPY applications/virtual-fly-brain/client/yarn.lock ./
+
+# Set up global dependencies
+RUN npm install -g eslint \
+    && yarn config set ignore-engines true
+
+# Set up basic eslint config to avoid build errors
+RUN echo '{"extends": ["react-app","eslint:recommended"],"rules":{"no-unused-vars":"warn"}}' > .eslintrc.json
+
+# Install dependencies with legacy peer deps to handle version conflicts
+RUN yarn install --legacy-peer-deps
+
+# Copy all configuration files
+COPY applications/virtual-fly-brain/client/.* ./
+COPY applications/virtual-fly-brain/client/tsconfig.json ./
+COPY applications/virtual-fly-brain/client/webpack.config*.js ./
+
+# Copy source files
+COPY applications/virtual-fly-brain/client/src ./src
+COPY applications/virtual-fly-brain/client/public ./public
+
+# Modify package.json scripts
+RUN sed -i 's/"start": ".*"/"start": "webpack serve --config webpack.config.dev.js --mode development"/' package.json
+
+# Build the application with NODE_ENV set to production
+RUN NODE_ENV=production yarn build
+
+# Create and set up volume directories
+RUN mkdir -p /app/build /app/node_modules
+VOLUME ["/app/build", "/app/node_modules"]
+
+# Expose port
+EXPOSE 3000
+
+# Set environment variable to disable eslint during runtime
+ENV DISABLE_ESLINT_PLUGIN=true \
+    NODE_ENV=production
+
+# Command to run the application
+CMD ["yarn", "start"]

applications/virtual-fly-brain/client/.babelrc

@@ -1,19 +1,26 @@
 {
     "presets": [
-      "@babel/preset-env",
-      "@babel/preset-react"
+        "@babel/preset-env",
+        "@babel/preset-react"
     ],
     "env": {
-        "production":{
-            "presets": ["minify"]
+        "production": {
+            // Remove the minify preset and add individual minification plugins
+            "plugins": [
+                "babel-plugin-transform-remove-console", // Remove console logs
+                "babel-plugin-minify-dead-code-elimination", // Remove dead code
+                "babel-plugin-minify-constant-folding", // Fold constants
+                "babel-plugin-transform-remove-debugger" // Remove debugger statements
+            ]
         }
     },
     "plugins": [
         "@babel/transform-regenerator",
         "@babel/plugin-proposal-class-properties",
         "@babel/transform-runtime",
         [
-            "module-resolver", {
+            "module-resolver",
+            {
                 "root": ["./src"]
             }
         ]

applications/virtual-fly-brain/client/package.json

@@ -69,11 +69,11 @@
     "@babel/preset-env": "^7.8.3",
     "@babel/preset-react": "^7.8.3",
     "@babel/runtime": "^7.8.3",
+    "babel-loader": "^8.2.3",
     "@typescript-eslint/eslint-plugin": "^5.57.0",
     "@typescript-eslint/parser": "^5.57.0",
     "awesome-typescript-loader": "^5.2.1",
     "babel-eslint": "^10.1.0",
-    "babel-loader": "^8.0.6",
     "babel-plugin-module-resolver": "^4.0.0",
     "babel-preset-minify": "^0.5.1",
     "clean-webpack-plugin": "^3.0.0",

applications/virtual-fly-brain/client/src/components/Layout.js

@@ -164,8 +164,6 @@ const MainLayout = ({ bottomNav, setBottomNav }) => {
     if ( openTemplate) {
       templateLoaded(id, openTemplate);
       templateRef = window.location.href.replace(id + ",", "")
-    }else {
-      getInstanceByID(id, false, true, false, false)
     }
     setModalOpen(false)
   }
@@ -230,8 +228,8 @@ const MainLayout = ({ bottomNav, setBottomNav }) => {
             The image you requested is aligned to another template. Click Okay
             to open in a new tab or Cancel to just view the image metadata.
           </Typography>
-          <Button variant="contained" color={primaryBg} onClick={() => handleModalClose(misalignedTemplate, true )} target="_blank" href={window.location.origin + "/?id=" + misalignedTemplate}>Okay</Button>
-          <Button variant="outlined" color={secondaryBtnColor} onClick={() => handleModalClose(misalignedTemplate, false )}>Cancel</Button>
+          <Button variant="contained" color={"primary"} onClick={() => handleModalClose(misalignedTemplate, true )} target="_blank" href={window.location.origin + "/?id=" + misalignedTemplate}>Okay</Button>
+          <Button variant="outlined" color={"secondary"} onClick={() => handleModalClose(misalignedTemplate, false )}>Cancel</Button>
         </Box>
       </Modal>
       <Box

requirements.txt

@@ -0,0 +1,3 @@
+requests>=2.31.0
+pandas>=2.1.0
+numpy>=1.24.0