Update for the latest develop OpenMS from develop branch #45

Workflow file for this run

.github/workflows/build_executable_msi.yaml at 1db4be8

	name: Build windows executable (.msi)
	on:
	push:
	branches:
	- main
	pull_request:
	branches: [ "main" ]
	workflow_dispatch:

	env:
	PYTHON_VERSION: 3.10.0
	# Define unique GUID for UpgradeCode
	APP_UpgradeCode: "c1c7c11f-b063-4100-9854-af555d1b26d1"
	# Define needed TOPP tools need in NuXLApp
	TOPP_TOOLS: "OpenNuXL FileConverter PercolatorAdapter TextExporter FileInfo"
	# App name
	APP_NAME: OpenMS-NuXLApp

	jobs:
	build-executable:
	runs-on: windows-2022

	env:
	PYTHON_VERSION: 3.10.0
	APP_NAME: OpenMS-NuXLApp

	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Download OpenMS release asset
	env:
	GH_TOKEN: ${{ github.token }}
	shell: bash
	run: \|
	gh release download openms-package_develop_26_03_2026 \
	--repo Arslan-Siraj/nuxl_webapp_supporting_files \
	--pattern "*.zip"

	- name: Verify downloaded file
	shell: bash
	run: \|
	ls -lh
	file *.zip
	unzip -t *.zip

	- name: Extract OpenMS package
	shell: bash
	run: \|
	unzip *.zip -d openms-package
	ls -R openms-package

	- name: Extract inner OpenMS package
	shell: bash
	run: \|
	unzip \
	openms-package/openms-package/OpenMS/bld/openms-package.zip \
	-d openms-inner

	- name: Promote OpenMS bin and share to root
	shell: bash
	run: \|
	mkdir -p openms-bin openms-share
	cp -r openms-inner/openms-package/bin/* openms-bin/
	cp -r openms-inner/openms-package/share/* openms-share/

	- 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: Setup python embeddable version
	run: \|
	# Create a directory for the embeddable Python version
	mkdir python-${{ env.PYTHON_VERSION }}

	# Download and unzip the embeddable 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
	# Define paths for the regular Python distribution and the embeddable distribution
	$PYTHON_DIR="${{ runner.tool_cache }}/Python/${{ env.PYTHON_VERSION }}/x64" # Path from actions/setup-python
	$EMBED_DIR="python-${{ env.PYTHON_VERSION }}"

	mkdir -p $EMBED_DIR/Lib/site-packages/tkinter
	mkdir -p $EMBED_DIR/tcl
	# Copy necessary Tkinter files from the regular Python distribution
	cp -r $PYTHON_DIR/Lib/tkinter/* $EMBED_DIR/Lib/site-packages/tkinter/
	cp -r $PYTHON_DIR/tcl/* $EMBED_DIR/tcl/
	cp $PYTHON_DIR/DLLs/_tkinter.pyd $EMBED_DIR/
	cp $PYTHON_DIR/DLLs/tcl86t.dll $EMBED_DIR/
	cp $PYTHON_DIR/DLLs/tk86t.dll $EMBED_DIR/

	- name: Bundle MSVC runtime DLLs
	shell: powershell
	run: \|
	$embed = "python-${{ env.PYTHON_VERSION }}"
	$dlls = @(
	"vcomp140.dll",
	"vcruntime140.dll",
	"vcruntime140_1.dll",
	"msvcp140.dll"
	)

	foreach ($dll in $dlls) {
	Copy-Item "C:\Windows\System32\$dll" "$embed\$dll" -Force
	}

	- 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 python310._pth file
	run: \|
	sed -i 's/#import site/import site/' python-${{ env.PYTHON_VERSION }}/python310._pth

	#- name: Install Required Packages
	# run: .\python-${{ env.PYTHON_VERSION }}\python -m pip install --force-reinstall -r requirements_embd_py310_win.txt --no-warn-script-location

	- name: Set to offline deployment
	run: \|
	$content = Get-Content -Raw settings.json \| ConvertFrom-Json
	$content.online_deployment = $false
	$content \| ConvertTo-Json -Depth 100 \| Set-Content settings.json

	- name: Create launcher .bat file
	shell: pwsh
	run: \|
	$batContent = @"
	@echo off
	set PYTHON=.\python-${{ env.PYTHON_VERSION }}\python
	set REQ=.\requirements_embd_py310_win.txt
	set MARKER=.\python-${{ env.PYTHON_VERSION }}\.deps_installed

	REM If marker exists, skip installation
	if exist "%MARKER%" goto RUN_APP

	echo Preparing Python environment for launching App...

	REM Ensure pip exists
	"%PYTHON%" -m ensurepip >nul 2>&1

	REM Attempt installation
	"%PYTHON%" -m pip install -r "%REQ%" --no-warn-script-location
	if errorlevel 1 (
	echo Dependency installation failed or was interrupted.
	exit /b 1
	)

	REM Copy NuXL share folder to pyopenms share
	xcopy /E /I /Y ".\NuXL" ".\python-3.10.0\Lib\site-packages\pyopenms\share\OpenMS\NuXL"

	REM Rename folder
	ren "streamlit" ".streamlit"

	REM Create marker only after full success
	echo OK>"%MARKER%"

	:RUN_APP
	start /min "" "%PYTHON%" -m streamlit run app.py
	"@

	$batContent \| Set-Content -Encoding ASCII "${{ env.APP_NAME }}.bat"

	- name: Verify .streamlit folder exists
	shell: bash
	run: \|
	echo "PWD:"
	pwd
	echo "Listing repo root:"
	ls -la
	echo "Listing .streamlit:"
	ls -la .streamlit

	- name: Create All-in-one executable folder
	shell: bash
	run: \|
	if [ -d "streamlit_exe" ]; then
	rm -rf streamlit_exe
	fi

	mkdir -p streamlit_exe
	mv python-${{ env.PYTHON_VERSION }} streamlit_exe
	cp -r src streamlit_exe
	cp -r content streamlit_exe
	cp -r assets streamlit_exe
	#cp -r example-data streamlit_exe
	cp app.py streamlit_exe
	cp settings.json streamlit_exe
	cp ${{ env.APP_NAME }}.bat streamlit_exe
	cp requirements_embd_py310_win.txt streamlit_exe

	mkdir -p streamlit_exe streamlit_exe/share

	# Copy all DLLs from openms-bin
	cp -r openms-bin/*.dll streamlit_exe/

	# Copy share folder
	cp -r openms-share/* streamlit_exe/share/
	cp -r openms-share/OpenMS/NuXL streamlit_exe/NuXL/

	# copy chemistry outside
	cp -r openms-share/OpenMS/CHEMISTRY streamlit_exe/

	# Copy only selected .exe files from openms-bin
	for tool in $TOPP_TOOLS; do
	if [ -f "openms-bin/$tool.exe" ]; then
	cp "openms-bin/$tool.exe" streamlit_exe/
	else
	echo "Warning: $tool.exe not found in openms-bin"
	fi
	done

	# copy thirdparty folder
	cp -r openms-package/openms-package/_thirdparty streamlit_exe/

	- name: Create Streamlit config
	shell: bash
	run: \|
	mkdir -p streamlit_exe/streamlit

	cat <<'EOF' > streamlit_exe/streamlit/config.toml
	[global]
	developmentMode = false

	[server]
	maxUploadSize = 50000
	port = 8505

	[theme]
	primaryColor = "#29379b"
	EOF

	- name: Generate Readme.txt
	shell: bash
	run: \|
	cat <<EOF > streamlit_exe/Readme.txt
	Welcome to ${{ env.APP_NAME }} app!
	To launch the application:
	1. Navigate to the installation directory.
	2. Double-click on the file: ${{ env.APP_NAME }}.bat or ${{ env.APP_NAME }} shortcut.
	Additional Information:
	- If multiple Streamlit apps are running, you can change the port in the .streamlit/config.toml file.
	Example:
	[server]
	port = 8505
	Reach out to us:
	- Join our Discord server for support and community discussions: https://discord.com/invite/4TAGhqJ7s5
	- Contribute or stay updated with the latest OpenMS web app developments on GitHub: https://github.com/OpenMS/streamlit-template
	- Checkout the ${{ env.APP_NAME }} on Github: https://github.com/Arslan-Siraj/nuxl-app
	- Visit our website for more information: https://openms.de/

	Thanks for using ${{ env.APP_NAME }}!
	EOF

	- name: Install WiX Toolset
	run: \|
	curl -LO https://github.com/wixtoolset/wix3/releases/download/wix3111rtm/wix311-binaries.zip
	unzip wix311-binaries.zip -d wix
	rm wix311-binaries.zip

	- name: Build .wxs for streamlit_exe folder
	run: \|
	./wix/heat.exe dir streamlit_exe -gg -sfrag -sreg -srd -template component -cg StreamlitExeFiles -dr AppSubFolder -out streamlit_exe_files.wxs

	- name: Generate VBScript file
	shell: bash
	run: \|
	cat <<EOF > ShowSuccessMessage.vbs
	MsgBox "The ${{ env.APP_NAME }} application is successfully installed.", vbInformation, "Installation Complete"
	EOF

	- name: Prepare SourceDir
	run: \|
	if (Test-Path -Path "SourceDir") {
	Remove-Item -Recurse -Force "SourceDir"
	}

	mkdir SourceDir
	mv streamlit_exe/* SourceDir
	cp ShowSuccessMessage.vbs SourceDir
	cp assets/openms_license.rtf SourceDir
	# Logo of app : from https://www.xiconeditor.com/
	cp assets/openNuXL.ico SourceDir

	- name: Generate WiX XML file
	shell: bash
	run: \|
	cat <<EOF > streamlit_exe.wxs
	<?xml version="1.0"?>
	<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" />

	<!-- Folder structure -->
	<Property Id="WIXUI_INSTALLDIR" Value="INSTALLFOLDER" />
	<Directory Id="TARGETDIR" Name="SourceDir">
	<Directory Id="ProgramFilesFolder">
	<Directory Id="INSTALLFOLDER" Name="${{ env.APP_NAME }}">
	<Directory Id="AppSubFolder" Name="${{ env.APP_NAME }}" />
	<Component Id="CreateAppFolder" Guid="95dbfa06-d36a-427f-995c-e87769ac2e59">
	<CreateFolder>
	<Permission User="Everyone" GenericAll="yes" />
	</CreateFolder>
	</Component>
	</Directory>
	</Directory>
	<Directory Id="DesktopFolder" />
	</Directory>

	<!-- Add components -->
	<Feature Id="MainFeature" Title="Main Application" Level="1">
	<ComponentGroupRef Id="StreamlitExeFiles" />
	<ComponentRef Id="CreateAppFolder" />
	<ComponentRef Id="DesktopShortcutComponent" />
	<ComponentRef Id="InstallDirShortcutComponent" />
	</Feature>

	<!-- Create shortcut for running app on desktop -->
	<Component Id="DesktopShortcutComponent" Guid="3597b243-9180-4d0b-b105-30d8b0d1a334" Directory="DesktopFolder">
	<Shortcut Id="DesktopShortcut" Name="${{ env.APP_NAME }}" Description="Launch ${{ env.APP_NAME }}" Target="[AppSubFolder]${{ env.APP_NAME }}.bat" WorkingDirectory="AppSubFolder" Icon="AppIcon" />
	<RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="DesktopShortcut" Type="integer" Value="1" KeyPath="yes" />
	</Component>

	<!-- Create shortcut for running app in installer folder -->
	<Component Id="InstallDirShortcutComponent" Guid="c2df9472-3b45-4558-a56d-6034cf7c8b72" Directory="AppSubFolder">
	<Shortcut Id="InstallDirShortcut" Name="${{ env.APP_NAME }}" Description="Launch ${{ env.APP_NAME }}" Target="[AppSubFolder]${{ env.APP_NAME }}.bat" WorkingDirectory="AppSubFolder" Icon="AppIcon" />
	<RegistryValue Root="HKCU" Key="Software\\OpenMS\\${{ env.APP_NAME }}" Name="InstallFolderShortcut" Type="integer" Value="1" KeyPath="yes" />
	</Component>

	<!-- Provide icon here; it should exist in the SourceDir folder -->
	<Icon Id="AppIcon" SourceFile="SourceDir/openNuXL.ico" />

	<!-- Run app directly after installation -->
	<!-- <CustomAction Id="RunApp" Directory="AppSubFolder" Execute="deferred" Return="asyncNoWait" Impersonate="no"
	ExeCommand="cmd.exe /c "[AppSubFolder]${{ env.APP_NAME }}.bat"" /> -->

	<!-- Custom Action to Show Success Message -->
	<Binary Id="ShowMessageScript" SourceFile="SourceDir/ShowSuccessMessage.vbs" />
	<CustomAction Id="ShowSuccessMessage" BinaryKey="ShowMessageScript" VBScriptCall="" Execute="immediate" Return="check" />

	<!-- Add all Custom Actions -->
	<InstallExecuteSequence>
	<!-- Custom action display success message -->
	<Custom Action="ShowSuccessMessage" After="InstallFinalize">NOT Installed</Custom>
	<!-- Run app directly after installation -->
	<!-- <Custom Action="RunApp" Before="InstallFinalize">NOT REMOVE</Custom> -->
	</InstallExecuteSequence>

	<!-- Interface options -->
	<UI>
	<UIRef Id="WixUI_InstallDir" />
	<UIRef Id="WixUI_ErrorProgressText" />
	</UI>

	<!-- Provide license; it should exist in the SourceDir folder -->
	<WixVariable Id="WixUILicenseRtf" Value="SourceDir/openms_license.rtf" />
	</Product>
	</Wix>
	EOF

	- name: Build .wixobj file with candle.exe
	run: \|
	./wix/candle.exe streamlit_exe.wxs streamlit_exe_files.wxs

	- name: Link .wixobj file into .msi with light.exe
	run: \|
	./wix/light.exe -ext WixUIExtension -sice:ICE60 -o ${{ env.APP_NAME }}.msi streamlit_exe_files.wixobj streamlit_exe.wixobj

	#- name: Compress Installer
	# run: \|
	# 7z a ${{ env.APP_NAME }}.zip

	- name: Archive build artifacts
	uses: actions/upload-artifact@v4
	with:
	name: ${{ env.APP_NAME }}
	path: \|
	${{ env.APP_NAME }}.msi

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update for the latest develop OpenMS from develop branch #45

Workflow file

Update for the latest develop OpenMS from develop branch #45

Uh oh!

Workflow file for this run