Merge template

.github/dependabot.yml

@@ -0,0 +1,9 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"  # Location of your pyproject.toml or requirements.txt
+    schedule:
+      interval: "weekly"  # Checks for updates every week
+    commit-message:
+      prefix: "deps"  # Prefix for pull request titles
+    open-pull-requests-limit: 5  # Limit the number of open PRs at a time

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

@@ -14,7 +14,8 @@ env:
   OPENMS_VERSION: 3.2.0 
   PYTHON_VERSION: 3.11.0
   # Name of the installer
-  APP_NAME: FLASHApp-0.70
+  APP_NAME: FLASHApp-0.7.2
+  APP_UpgradeCode: "69ae44ad-d554-4e3c-8715-7c4daf60f8bb"
 
 jobs:
   build-vue-js-component:
@@ -58,6 +59,17 @@ jobs:
         repository: t0mdavid-m/OpenMS
         ref: FVdeploy
         path: 'OpenMS'
+
+    # Temporary fix - until seqan is back online or new OpenMS release (3.4)
+    - name: Get latest cibuild.cmake
+      working-directory: OpenMS
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "actions@github.com"
+        git fetch origin develop
+        git checkout origin/develop -- tools/ci/cibuild.cmake
+        git checkout origin/develop -- tools/ci/citest.cmake
+        git checkout origin/develop -- tools/ci/cipackage.cmake
 
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
@@ -213,6 +225,13 @@ jobs:
         name: vue-js-dist
         path: js-dist
 
+    - name: Set Version in settings.json
+      run: |
+        $VERSION="${{ github.event.release.tag_name }}"
+        $content = Get-Content -Raw settings.json | ConvertFrom-Json
+        $content.version = $VERSION
+        $content | ConvertTo-Json -Depth 100 | Set-Content settings.json
+
     - name: Download package as artifact
       uses: actions/download-artifact@v4
       with:
@@ -227,7 +246,7 @@ jobs:
         cp -r openms-package/share ../share
 
     - name: Set up Python (regular distribution)
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ env.PYTHON_VERSION }} # Use the same version as the embeddable version
 
@@ -276,7 +295,15 @@ jobs:
 
     - name: Create .bat file
       run: |
-          echo " start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local" > ${{ env.APP_NAME }}.bat
+        echo '@echo off' > ${{ env.APP_NAME }}.bat
+        echo '' >> ${{ env.APP_NAME }}.bat
+        echo 'REM Create .streamlit directory in user''s home if it doesn''t exist' >> ${{ env.APP_NAME }}.bat
+        echo 'if not exist "%USERPROFILE%\.streamlit" mkdir "%USERPROFILE%\.streamlit"' >> ${{ env.APP_NAME }}.bat
+        echo '' >> ${{ env.APP_NAME }}.bat
+        echo 'REM Create credentials.toml with empty email to disable email prompt' >> ${{ env.APP_NAME }}.bat
+        echo 'copy /Y ".streamlit\credentials.toml" "%USERPROFILE%\.streamlit\credentials.toml" > nul' >> ${{ env.APP_NAME }}.bat
+        echo '' >> ${{ env.APP_NAME }}.bat
+        echo 'start /min .\python-${{ env.PYTHON_VERSION }}\python -m streamlit run app.py local' >> ${{ env.APP_NAME }}.bat
 
     - name: Create All-in-one executable folder
       run: |
@@ -358,7 +385,7 @@ jobs:
         cat <<EOF > streamlit_exe.wxs
         <?xml version="1.0"?>
         <Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">
-          <Product Id="8434b940-a943-40f1-ab1f-4db3feedb4ba" Name="${{ env.APP_NAME }}" Language="1033" Version="1.0.0.0" Codepage="1252" Manufacturer="OpenMS Developer Team" UpgradeCode="8d28e8c7-45dc-446c-b889-99a6aea2f1a5">
+          <Product Id="*" Name="${{ 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" />
 

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

@@ -10,6 +10,7 @@ jobs:
 
     env:
       PYTHON_VERSION: 3.11.9
+      APP_UpgradeCode: 4abc2e23-3ba5-40e4-95c9-09e6cb8ecaeb
       APP_NAME: OpenMS-StreamlitTemplateApp-Test
 
     steps:
@@ -115,7 +116,7 @@ jobs:
           cat <<EOF > streamlit_exe.wxs
           <?xml version="1.0"?>
           <Wix xmlns="http://schemas.microsoft.com/wix/2006/wi">
-            <Product Id="8434b940-a943-40f1-ab1f-4db3feedb4ba" Name="${{ env.APP_NAME }}" Language="1033" Version="1.0.0.0" Codepage="1252" Manufacturer="OpenMS Developer Team" UpgradeCode="8d28e8c7-45dc-446c-b889-99a6aea2f1a5">
+            <Product Id="*" Name="${{ 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" />
 

.gitignore

@@ -5,6 +5,7 @@ myenv
 build.log
 run_app.spec
 clean-up-workspaces.log
+gdpr_consent/node_modules/
 
 # FLASHApp
 workspaces
@@ -23,4 +24,7 @@ workspaces-flashtaggerviewer
 # Temp files
 **/__pycache__
 .DS_Store
+*-embed-amd64
+*~
+
 

.streamlit/config.toml

@@ -1,12 +1,14 @@
+[browser]
+gatherUsageStats = false
+
 [global]
 developmentMode = false
 
 [server]
+maxUploadSize =  2000 #MB
 port = 8501 # should be same as configured in deployment repo
-maxUploadSize = 2000
 
 [theme]
-
 # The preset Streamlit theme that your custom theme inherits from. One of "light" or "dark".
 # base =
 
@@ -23,4 +25,4 @@ primaryColor = "#29379b"
 # textColor =
 
 # Font family for all text in the app, except code blocks. One of "sans serif", "serif", or "monospace".
-# font =
+# font =

.streamlit/credentials.toml

@@ -0,0 +1,2 @@
+[general]
+email = "" 

Dockerfile

@@ -73,8 +73,7 @@ RUN wget -q \
 RUN mamba --version
 
 # Setup mamba environment.
-COPY environment.yml ./environment.yml
-RUN mamba env create -f environment.yml
+RUN mamba create -n streamlit-env python=3.10
 RUN echo "mamba activate streamlit-env" >> ~/.bashrc
 SHELL ["/bin/bash", "--rcfile", "~/.bashrc"]
 SHELL ["mamba", "run", "-n", "streamlit-env", "/bin/bash", "-c"]
@@ -115,6 +114,10 @@ RUN make -j4 pyopenms
 WORKDIR /openms-build/pyOpenMS
 RUN pip install dist/*.whl
 
+# Install other dependencies (excluding pyopenms)
+COPY requirements.txt ./requirements.txt 
+RUN grep -v '^pyopenms' requirements.txt > requirements_cleaned.txt && mv requirements_cleaned.txt requirements.txt
+RUN pip install -r requirements.txt
 
 WORKDIR /
 RUN mkdir openms
@@ -172,14 +175,15 @@ RUN mamba run -n streamlit-env python hooks/hook-analytics.py
 # Set Online Deployment
 RUN jq '.online_deployment = true' settings.json > tmp.json && mv tmp.json settings.json
 
-# Download latest OpenMS App executable for Windows from Github actions workflow.
+# Download latest OpenMS App executable as a ZIP file
 RUN if [ -n "$GH_TOKEN" ]; then \
         echo "GH_TOKEN is set, proceeding to download the release asset..."; \
-        gh release download --repo ${GITHUB_USER}/${GITHUB_REPO} --pattern "${ASSET_NAME}" --dir /app; \
+        gh release download -R ${GITHUB_USER}/${GITHUB_REPO} -p "OpenMS-App.zip" -D /app; \
     else \
         echo "GH_TOKEN is not set, skipping the release asset download."; \
     fi
 
+
 # Run app as container entrypoint.
 EXPOSE $PORT
 ENTRYPOINT ["/app/entrypoint.sh"]

app.py

@@ -1,8 +1,13 @@
 import streamlit as st
 from pathlib import Path
+import json
 # For some reason the windows version only works if this is imported here
 import pyopenms
 
+if "settings" not in st.session_state:
+        with open("settings.json", "r") as f:
+            st.session_state.settings = json.load(f)
+
 if __name__ == '__main__':
     pages = {
         "FLASHApp" : [

docker-compose.yml

@@ -0,0 +1,19 @@
+version: '3.8'
+
+services:
+  openms-streamlit-template:
+    build:
+      context: .
+      dockerfile: Dockerfile
+      args:
+        GITHUB_TOKEN: $GITHUB_TOKEN
+    image: openms_streamlit_template
+    container_name: openms-streamlit-template
+    restart: always
+    ports:
+      - 8501:8501
+    volumes:
+      - workspaces-streamlit-template:/workspaces-streamlit-template
+    command: streamlit run openms-streamlit-template/app.py
+volumes:
+  workspaces-streamlit-template: