Merge remote-tracking branch 'origin/main'

Author: t0mdavid-m

.github/workflows/build-windows-executable-app.yaml

@@ -235,18 +235,30 @@ jobs:
         cp $PYTHON_DIR/DLLs/tcl86t.dll $EMBED_DIR/
         cp $PYTHON_DIR/DLLs/tk86t.dll $EMBED_DIR/
 
-    - name: Install pip
-      run: |
-        curl -O https://bootstrap.pypa.io/get-pip.py
-        ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
-        rm get-pip.py
-
     - name: Uncomment 'import site' in python311._pth file
       run: |
         sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
 
     - name: Install Required Packages
-      run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements.txt --no-warn-script-location
+      # Use system Python (which has development headers) to compile packages,
+      # installing into the embeddable Python's site-packages directory.
+      # The embeddable Python lacks Python.h headers needed for native extensions.
+      run: python -m pip install -r requirements.txt --target python-${{ env.PYTHON_VERSION }}/Lib/site-packages --upgrade --no-warn-script-location
+
+    - name: Clean up unnecessary Python files
+      shell: pwsh
+      run: |
+        $sitePkgs = "py/Lib/site-packages"
+
+        # Remove __pycache__ directories
+        Get-ChildItem -Path $sitePkgs -Recurse -Directory -Filter "__pycache__" | Remove-Item -Recurse -Force
+
+        # Remove test directories
+        Get-ChildItem -Path $sitePkgs -Recurse -Directory | Where-Object { $_.Name -match "^tests?$" } | Remove-Item -Recurse -Force
+
+        # Count remaining files
+        $count = (Get-ChildItem -Path $sitePkgs -Recurse -File).Count
+        Write-Host "Remaining files in site-packages: $count"
 
     - name: Set to offline deployment
       run: |
@@ -357,7 +369,7 @@ jobs:
         <Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">
           <Product Id="*" Name="${{ env.APP_NAME }}" Language="1033" Version="1.0.0.0" Codepage="1252" Manufacturer="OpenMS Developer Team" UpgradeCode="${{ env.APP_UpgradeCode }}">
             <Package Id="*" InstallerVersion="300" Compressed="yes" InstallPrivileges="elevated" Platform="x64" />
-            <Media Id="1" Cabinet="streamlit.cab" EmbedCab="yes" />
+            <MediaTemplate EmbedCab="yes" MaximumUncompressedMediaSize="200" CabinetTemplate="data{0}.cab" />
         
             <!-- Folder structure -->
             <Property Id="WIXUI_INSTALLDIR" Value="INSTALLFOLDER" />

.github/workflows/test-win-exe-w-embed-py.yaml

@@ -17,29 +17,31 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Set up Python (regular distribution)
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }} # Use the same version as the embeddable version
+
       - name: Download python embeddable version
         run: |
           mkdir python-${{ env.PYTHON_VERSION }}
           curl -O https://www.python.org/ftp/python/${{ env.PYTHON_VERSION }}/python-${{ env.PYTHON_VERSION }}-embed-amd64.zip
           unzip python-${{ env.PYTHON_VERSION }}-embed-amd64.zip -d python-${{ env.PYTHON_VERSION }}
           rm python-${{ env.PYTHON_VERSION }}-embed-amd64.zip
 
-      - name: Install pip
-        run: |
-          curl -O https://bootstrap.pypa.io/get-pip.py
-          ./python-${{ env.PYTHON_VERSION }}/python get-pip.py --no-warn-script-location
-          rm get-pip.py
-          
       - name: Uncomment 'import site' in python311._pth file
         run: |
           sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python311._pth
-          
+
       - name: Print content of python311._pth file
         run: |
           cat python-${{ env.PYTHON_VERSION }}/python311._pth
 
       - name: Install Required Packages
-        run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install -r requirements.txt --no-warn-script-location
+        # Use system Python (which has development headers) to compile packages,
+        # installing into the embeddable Python's site-packages directory.
+        # The embeddable Python lacks Python.h headers needed for native extensions.
+        run: python -m pip install -r requirements.txt --target python-${{ env.PYTHON_VERSION }}/Lib/site-packages --upgrade --no-warn-script-location
 
       - name: Create .bat file
         run: |

.github/workflows/test-win-exe-w-pyinstaller.yaml

@@ -68,13 +68,14 @@ jobs:
 
     - name: Copy everything to dist directory
       shell: bash
-      run: | 
+      run: |
         cp -r .streamlit dist/.streamlit
         cp -r content dist/content
         cp -r src dist/src
         cp -r example-data dist/example-data
         cp -r assets dist/assets
         cp app.py dist/
+        cp presets.json dist/
 
     - name: Modify .spec file
       shell: bash

.gitignore

@@ -11,3 +11,4 @@ python*
 **/__pycache__/
 gdpr_consent/node_modules/
 *~
+.streamlit/secrets.toml

.streamlit/config.toml

@@ -5,8 +5,13 @@ gatherUsageStats = false
 developmentMode = false
 
 [server]
+address = "0.0.0.0"
 maxUploadSize =  200 #MB
 port = 8501 # should be same as configured in deployment repo
+address = "0.0.0.0"
+enableCORS = false
+enableXsrfProtection = false
+
 
 [theme]
 # The preset Streamlit theme that your custom theme inherits from. One of "light" or "dark".

.streamlit/secrets.toml.example

@@ -0,0 +1,8 @@
+# Streamlit Secrets Configuration
+# Copy this file to secrets.toml and fill in your values.
+# IMPORTANT: Never commit secrets.toml to version control!
+
+[admin]
+# Password required to save workspaces as demo workspaces (online mode only)
+# Set a strong, unique password here
+password = "your-secure-admin-password-here"

Dockerfile

@@ -73,10 +73,10 @@ COPY utils/ /app/utils
 COPY app.py /app/app.py
 COPY settings.json /app/settings.json
 COPY default-parameters.json /app/default-parameters.json
+COPY presets.json /app/presets.json
 
 # For streamlit configuration
-COPY .streamlit/config.toml /app/.streamlit/config.toml
-
+COPY .streamlit/ /app/.streamlit/
 COPY clean-up-workspaces.py /app/clean-up-workspaces.py
 
 # add cron job to the crontab
@@ -114,13 +114,13 @@ if [ "$SERVER_COUNT" -gt 1 ]; then\n\
 \n\
     # Write nginx config\n\
     mkdir -p /etc/nginx\n\
-    echo -e "worker_processes auto;\\npid /run/nginx.pid;\\n\\nevents {\\n    worker_connections 1024;\\n}\\n\\nhttp {\\n    client_max_body_size 0;\\n\\n    map \\$cookie_stroute \\$route_key {\\n        \\x22\\x22      \\$request_id;\\n        default \\$cookie_stroute;\\n    }\\n\\n    upstream streamlit_backend {\\n        hash \\$route_key consistent;\\n${UPSTREAM_SERVERS}    }\\n\\n    map \\$http_upgrade \\$connection_upgrade {\\n        default upgrade;\\n        \\x27\\x27 close;\\n    }\\n\\n    server {\\n        listen 8501;\\n\\n        location / {\\n            proxy_pass http://streamlit_backend;\\n            proxy_http_version 1.1;\\n            proxy_set_header Upgrade \\$http_upgrade;\\n            proxy_set_header Connection \\$connection_upgrade;\\n            proxy_set_header Host \\$host;\\n            proxy_set_header X-Real-IP \\$remote_addr;\\n            proxy_set_header X-Forwarded-For \\$proxy_add_x_forwarded_for;\\n            proxy_set_header X-Forwarded-Proto \\$scheme;\\n            proxy_read_timeout 86400;\\n            proxy_send_timeout 86400;\\n            proxy_buffering off;\\n            add_header Set-Cookie \\x22stroute=\\$route_key; Path=/; HttpOnly; SameSite=Lax\\x22 always;\\n        }\\n    }\\n}" > /etc/nginx/nginx.conf\n\
+    echo -e "worker_processes auto;\\npid /run/nginx.pid;\\n\\nevents {\\n    worker_connections 1024;\\n}\\n\\nhttp {\\n    client_max_body_size 0;\\n\\n    map \\$cookie_stroute \\$route_key {\\n        \\x22\\x22      \\$request_id;\\n        default \\$cookie_stroute;\\n    }\\n\\n    upstream streamlit_backend {\\n        hash \\$route_key consistent;\\n${UPSTREAM_SERVERS}    }\\n\\n    map \\$http_upgrade \\$connection_upgrade {\\n        default upgrade;\\n        \\x27\\x27 close;\\n    }\\n\\n    server {\\n        listen 0.0.0.0:8501;\\n\\n        location / {\\n            proxy_pass http://streamlit_backend;\\n            proxy_http_version 1.1;\\n            proxy_set_header Upgrade \\$http_upgrade;\\n            proxy_set_header Connection \\$connection_upgrade;\\n            proxy_set_header Host \\$host;\\n            proxy_set_header X-Real-IP \\$remote_addr;\\n            proxy_set_header X-Forwarded-For \\$proxy_add_x_forwarded_for;\\n            proxy_set_header X-Forwarded-Proto \\$scheme;\\n            proxy_read_timeout 86400;\\n            proxy_send_timeout 86400;\\n            proxy_buffering off;\\n            add_header Set-Cookie \\x22stroute=\\$route_key; Path=/; HttpOnly; SameSite=Lax\\x22 always;\\n        }\\n    }\\n}" > /etc/nginx/nginx.conf\n\
 \n\
-    # Start Streamlit instances on internal ports (localhost only)\n\
+    # Start Streamlit instances on internal ports\n\
     for i in $(seq 0 $((SERVER_COUNT - 1))); do\n\
         PORT=$((BASE_PORT + i))\n\
         echo "Starting Streamlit instance on port $PORT..."\n\
-        streamlit run app.py --server.port $PORT --server.address 127.0.0.1 &\n\
+        streamlit run app.py --server.port $PORT --server.address 0.0.0.0 &\n\
     done\n\
 \n\
     sleep 2\n\
@@ -129,7 +129,7 @@ if [ "$SERVER_COUNT" -gt 1 ]; then\n\
 else\n\
     # Single instance mode (default) - run Streamlit directly on port 8501\n\
     echo "Starting Streamlit app..."\n\
-    exec streamlit run app.py\n\
+    exec streamlit run app.py --server.address 0.0.0.0\n\
 fi\n\
 ' > /app/entrypoint.sh
 # make the script executable