Updated installer hooks to use finn instead of napari

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      dependencies:
+        patterns:
+          - "*"

.github/workflows/deploy.yml

@@ -2,28 +2,146 @@ name: Deploy
 
 on:
   push:
-    tags: ["*"]
+    branches: [deploy] # Change this to run only for push events to main branch
+    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request: {}
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build-n-publish:
-    name: Build and publish Python 🐍 distributions 📦 to PyPI
+  prepare-matrix:
+    # See this SO answer for details on conditional matrices
+    # https://stackoverflow.com/a/65434401/3407590
+    name: Prepare matrix
     runs-on: ubuntu-latest
-    if: contains(github.ref, 'tags')
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
     steps:
-      - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.x"
-      - name: Build a binary wheel and a source tarball
+          python-version: "3.11"
+      - name: Prepare matrix
+        id: set-matrix
+        shell: python
+        # The Python versions chosen below will determine which
+        # Python versions the installers will bundle. The general
+        # principle is to follow the SPEC-0 recommendation:
+        # https://scientific-python.org/specs/spec-0000/
         run: |
-          python -m pip install -U pip
-          python -m pip install -U setuptools setuptools_scm build
-          python -m build --sdist --wheel --outdir dist/
-      - name: Publish to PyPI
+          import os
+          import json
+          elements = [
+            {
+              "os": "ubuntu-latest",
+              "target-platform": "linux-64",
+            },
+            {
+              "os": "macos-14",
+              "target-platform": "osx-arm64",
+            },
+            {
+              "os": "windows-latest",
+              "target-platform": "win-64",
+            },
+          ]
+          platforms_str = "${{ inputs.installer_platforms || 'linux-64,win-64,osx-arm64' }}"
+          platforms = {p.strip() for p in platforms_str.split(",")}
+          matrix = {"include": []}
+          for element in elements:
+            if element["target-platform"] in platforms:
+              matrix["include"].append(element)
+          with open(os.environ["GITHUB_OUTPUT"], "a") as f:
+            f.write(f"matrix={json.dumps(matrix)}\n")
+
+  create-app-bundle:
+    name: Create ${{ matrix.target-platform }} app bundle
+    runs-on: ${{ matrix.os }}
+    needs: prepare-matrix
+    if: startsWith(github.ref, 'refs/tags/') # Only run for tags
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJSON(needs.prepare-matrix.outputs.matrix) }}
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          path: motile-tracker
+
+      - name: Install pixi
+        uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.43.2
+          cache: false
+          run-install: false
+          manifest-path: motile-tracker/pixi.toml
+
+      - name: Install build tools (Windows only)
+        if: runner.os == 'Windows'
+        run: |
+          $installer = "vs_BuildTools.exe"
+
+          Invoke-WebRequest -Uri "https://aka.ms/vs/17/release/vs_BuildTools.exe" -OutFile $installer
+
+          Start-Process -Wait -FilePath .\$installer -ArgumentList `
+            "--quiet", `
+            "--wait", `
+            "--norestart", `
+            "--nocache", `
+            "--add Microsoft.VisualStudio.Workload.VCTools", `
+            "--add Microsoft.VisualStudio.Component.VC.Tools.x86.x64", `
+            "--add Microsoft.VisualStudio.Component.Windows10SDK.19041", `
+            "--includeRecommended"
+        shell: pwsh
+
+      - name: Install app dependencies
+        working-directory: motile-tracker
+        run: pixi run setup
+
+      - name: Build the PyPi package (Linux only)
+        working-directory: motile-tracker
+        if: runner.os == 'Linux'
+        run: pixi run build
+
+      - name: Publish to PyPi (Linux only)
         uses: pypa/gh-action-pypi-publish@release/v1
+        if: runner.os == 'Linux'
         with:
+          packages-dir: motile-tracker/dist
           password: ${{ secrets.PYPI_API_TOKEN }}
-      - uses: softprops/action-gh-release@v2
+
+      - name: Download installer app (Linux only)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y makeself
+
+      - name: Download installer app (macOS only)
+        if: runner.os == 'macOS'
+        run: |
+          brew install create-dmg
+
+      - name: Download installer app (Windows only)
+        if: runner.os == 'Windows'
+        run: |
+          choco install -y innosetup
+
+      - name: Package native app
+        working-directory: motile-tracker
+        run: pixi run create-installer
+
+      - name: Upload app
+        uses: softprops/action-gh-release@v2
+        if: startsWith(github.ref, 'refs/tags/')
         with:
+          files: |
+            motile-tracker/dist/MotileTrackerInstaller.*
           generate_release_notes: true
+          token: ${{ secrets.GITHUB_TOKEN }}
+          draft: ${{ contains(github.ref_name, '-dev') }}
+          prerelease: ${{ contains(github.ref_name, '-rc') }}

.gitignore

@@ -8,6 +8,9 @@ __pycache__/
 # C extensions
 *.so
 
+# Backup files
+*~
+
 # Distribution / packaging
 .Python
 env/

README.md

@@ -24,6 +24,13 @@ conda before installing the plugin with pip.
     conda install -c conda-forge -c funkelab -c gurobi ilpy
     pip install motile-tracker
 
+The conda environment can also be created from the provided conda_config.yml:
+
+    conda env create -f conda_config.yml
+    conda activate motile-tracker
+
+Alternatively one can use [pixi](https://pixi.sh/).
+
 ## Running Motile Tracker
 
 To run the application:
@@ -39,6 +46,27 @@ or
 
     motile_tracker
 
+If [pixi](https://pixi.sh/) is available, you can run motile-tracker using:
+
+    pixi run start
+
+## Package the application into an executable and create the installer
+
+To create the executab run
+
+    pixi run create-app
+
+This command will create an application (.app) on OSX, an EXE on Windows and an
+ELF executable on Linux.
+
+On Windows in order to be able to package the application the ilpy library must be
+properly installed and compiled. This will require [download](https://aka.ms/vs/17/release/vs_BuildTools.exe) and install [Visual Studio Build Tools](https://visualstudio.microsoft.com/downloads/). This comes with a script to set all required environment variables located typically at `"C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\Build\vcvars64.bat"` so before you setup the app you need to run this bat file. For powershell run `scripts\scripts/set-vs-buildTools-env.ps1 <fullpathto vcvars64>`.
+
+Further to create an installer for the app you will need:
+* InnoSetup on Windows (`scoop install inno-setup` or `winget install "Inno Setup"`)
+* create-dmg on OSX (`brew install create-dmg`)
+* makeself on Linux (`apt install makeself`)
+
 ## Issues
 
 If you encounter any problems, please

conda_config.yml

@@ -4,4 +4,9 @@ channels:
   - funkelab
   - gurobi
 dependencies:
-  - ilpy
+  - python=3.11.*
+  - ilpy=0.4.1
+  - scip=9.1.*
+  - pip
+  - pip:
+    - motile-tracker

construct.yaml

@@ -0,0 +1,12 @@
+name: motile-tracker
+version: 3.1.3
+extra_files:
+  - install-scripts/README.md: README.md
+environment_file: conda_config.yml
+keep_pkgs: false
+installer_type: all
+check_path_spaces: false
+register_envs: false
+post_install: ./install-scripts/postinstall.sh # [unix]
+post_install: ./install-scripts/postinstall.bat # [win]
+license_file: LICENSE

install-scripts/finalize-install.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+INSTALL_DIR=$PWD
+
+chmod go+rx ${INSTALL_DIR}
+
+echo "MotileTracker installed to ${INSTALL_DIR}"
+echo "Run it using: ${INSTALL_DIR}/MotileTracker"

install-scripts/wininstaller.iss

@@ -0,0 +1,26 @@
+#define AppName "MotileTracker"
+#define AppVersion GetFileVersion('dist\MotileTracker\MotileTracker.exe')
+#define AppURL "https://funkelab.github.io/motile_tracker"
+
+[Setup]
+AppName={#AppName}
+AppVersion="1.0"
+AppPublisherURL={#AppURL}
+DefaultDirName={commonpf}\{#AppName}
+LicenseFile="..\LICENSE"
+OutputDir="..\dist\"
+OutputBaseFilename={#AppName}Installer
+Compression=lzma
+SolidCompression=yes
+
+[Tasks]
+Name: "desktopicon"; Description: "{cm:CreateDesktopIcon}"; GroupDescription: "{cm:AdditionalIcons}"; Flags: unchecked
+
+[Files]
+Source: "..\dist\{#AppName}\{#AppName}.exe"; DestDir: "{app}"; Flags: ignoreversion
+Source: "..\dist\{#AppName}\*"; DestDir: "{app}"; Flags: ignoreversion recursesubdirs createallsubdirs
+
+[Icons]
+Name: "{group}\{#AppName}"; Filename: "{app}\{#AppName}.exe"
+Name: "{group}\{cm:UninstallProgram,{#AppName}}"; Filename: "{uninstallexe}"
+Name: "{commondesktop}\{#AppName}"; Filename: "{app}\{#AppName}.exe"; Tasks: desktopicon