motile-tracker 3.1.3.dev0__tar.gz → 3.1.4.dev1__tar.gz

motile_tracker-3.1.4.dev1/.github/dependabot.yml

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

motile_tracker-3.1.4.dev1/.github/workflows/deploy.yml

@@ -0,0 +1,147 @@
+name: Deploy
+
+on:
+  push:
+    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:
+  prepare-matrix:
+    # See this SO answer for details on conditional matrices
+    # https://stackoverflow.com/a/65434401/3407590
+    name: Prepare matrix
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Prepare matrix
+        id: set-matrix
+        shell: python
+        # The Python versions chosen below will determine which
+        # Python versions the installers will bundle. The general
+        # principle is to follow the SPEC-0 recommendation:
+        # https://scientific-python.org/specs/spec-0000/
+        run: |
+          import os
+          import json
+          elements = [
+            {
+              "os": "ubuntu-latest",
+              "target-platform": "linux-64",
+            },
+            {
+              "os": "macos-14",
+              "target-platform": "osx-arm64",
+            },
+            {
+              "os": "windows-latest",
+              "target-platform": "win-64",
+            },
+          ]
+          platforms_str = "${{ 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/setup-pixi@v0.8.3
+        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 }}
+
+      - 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') }}

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev1}/.gitignore

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

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev1}/.pre-commit-config.yaml

@@ -1,6 +1,8 @@
+ci:
+  autofix_prs: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.2.0
+    rev: v5.0.0
     hooks:
       - id: check-docstring-first
       - id: end-of-file-fixer
@@ -8,7 +10,7 @@ repos:
         exclude: ^\.napari-hub/.*
       - id: check-yaml # checks for correct yaml syntax for github actions ex.
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.7
+    rev: v0.11.0
     hooks:
       - id: ruff
         args: [--fix]

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: motile-tracker
-Version: 3.1.3.dev0
+Version: 3.1.4.dev1
 Summary: Application for interactive tracking with global optimization
 Author-email: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>
 License: BSD 3-Clause License
@@ -23,7 +23,7 @@ Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: napari[all]
-Requires-Dist: numpy
+Requires-Dist: numpy<2.1,>=1.26
 Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
@@ -53,6 +53,7 @@ Requires-Dist: ruff; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Provides-Extra: all
 Requires-Dist: motile-tracker[dev,docs,testing]; extra == "all"
+Dynamic: license-file
 
 # Motile Tracker
 
@@ -81,6 +82,45 @@ 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:
+* activate the conda environment created in the [Installation Step](#installation)
+
+    conda activate motile-tracker
+
+* Run:
+
+    python -m motile_tracker.launcher
+
+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

motile_tracker-3.1.4.dev1/README.md

@@ -0,0 +1,71 @@
+# Motile Tracker
+
+[![tests](https://github.com/funkelab/motile_tracker/workflows/tests/badge.svg)](https://github.com/funkelab/motile_tracker/actions)
+[![codecov](https://codecov.io/gh/funkelab/motile_tracker/branch/main/graph/badge.svg)](https://codecov.io/gh/funkelab/motile_tracker)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/motile_tracker)](https://napari-hub.org/plugins/motile_tracker)
+
+The full documentation of the plugin can be found [here](https://funkelab.github.io/motile_tracker/).
+
+A plugin for tracking with [motile](https://github.com/funkelab/motile) in napari.
+Motile is a library that makes it easy to solve tracking problems using optimization
+by framing the task as an Integer Linear Program (ILP).
+See the motile [documentation](https://funkelab.github.io/motile)
+for more details on the concepts and method.
+
+----------------------------------
+
+## Installation
+
+This plugin depends on [motile](https://github.com/funkelab/motile), which in
+turn depends on gurobi and ilpy. These dependencies must be installed with
+conda before installing the plugin with pip.
+
+    conda create -n motile-tracker python=3.10
+    conda activate motile-tracker
+    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:
+* activate the conda environment created in the [Installation Step](#installation)
+
+    conda activate motile-tracker
+
+* Run:
+
+    python -m motile_tracker.launcher
+
+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
+[file an issue](https://github.com/funkelab/motile_tracker/issues)
+along with a detailed description.

motile_tracker-3.1.4.dev1/conda_config.yml

@@ -0,0 +1,12 @@
+name: motile-tracker
+channels:
+  - conda-forge
+  - funkelab
+  - gurobi
+dependencies:
+  - python=3.11.*
+  - ilpy=0.4.1
+  - scip=9.1.*
+  - pip
+  - pip:
+    - motile-tracker

motile_tracker-3.1.4.dev1/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

{motile_tracker-3.1.3.dev0 → motile_tracker-3.1.4.dev1}/docs/source/conf.py

@@ -1,5 +1,5 @@
 project = "Motile Tracker"
-copyright = "2024, Howard Hughes Medical Institute"
+copyright = "2024, Howard Hughes Medical Institute"  # noqa: A001
 author = "Caroline Malin-Mayor"
 
 extensions = [

motile_tracker-3.1.4.dev1/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"

motile_tracker-3.1.4.dev1/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

motile_tracker-3.1.4.dev1/motile-tracker.spec

@@ -0,0 +1,122 @@
+# -*- mode: python ; coding: utf-8 -*-
+import sys
+import napari
+from PyInstaller.building.build_main import Analysis, PYZ, EXE, COLLECT, BUNDLE
+
+
+sys.setrecursionlimit(sys.getrecursionlimit() * 5)
+
+sys.modules["FixTk"] = None
+
+NAME = "MotileTracker"
+WINDOWED = True if sys.platform == "darwin" else False
+DEBUG = False
+UPX = False
+BLOCK_CIPHER = None
+
+
+def get_icon():
+    logo_file = "motile_logo.ico" if sys.platform.startswith("win") else "motile_logo.icns"
+    return logo_file
+
+
+def get_version():
+    if sys.platform != "win32":
+        return None
+
+    from PyInstaller.utils.win32 import versioninfo as vi
+
+    ver_str = napari.__version__
+    version = ver_str.replace("+", ".").split(".")
+    version = [int(x) for x in version if x.isnumeric()]
+    version += [0] * (4 - len(version))
+    version = tuple(version)[:4]
+    return vi.VSVersionInfo(
+        ffi=vi.FixedFileInfo(filevers=version, prodvers=version),
+        kids=[
+            vi.StringFileInfo(
+                [
+                    vi.StringTable(
+                        "000004b0",
+                        [
+                            vi.StringStruct("CompanyName", NAME),
+                            vi.StringStruct("FileDescription", NAME),
+                            vi.StringStruct("FileVersion", ver_str),
+                            vi.StringStruct("LegalCopyright", ""),
+                            vi.StringStruct("OriginalFileName", NAME + ".exe"),
+                            vi.StringStruct("ProductName", NAME),
+                            vi.StringStruct("ProductVersion", ver_str),
+                        ],
+                    )
+                ]
+            ),
+            vi.VarFileInfo([vi.VarStruct("Translation", [0, 1200])]),
+        ],
+    )
+
+
+a = Analysis(
+    ["src/motile_tracker/launcher.py"],
+    hookspath=["src/installer_hooks"],
+    hiddenimports=[
+        "motile_tracker",
+    ],
+    runtime_hooks=[],
+    excludes=[
+        "FixTk",
+        "tcl",
+        "tk",
+        "_tkinter",
+        "tkinter",
+        "Tkinter",
+        "matplotlib",
+    ],
+    noarchive=False,
+    optimize=0,
+    cipher=BLOCK_CIPHER,
+)
+
+pyz = PYZ(a.pure, a.zipped_data, cipher=BLOCK_CIPHER)
+
+exe = EXE(
+    pyz,
+    a.scripts,
+    [],
+    exclude_binaries=True,
+    name=NAME,
+    debug=DEBUG,
+    bootloader_ignore_signals=False,
+    strip=False,
+    upx=UPX,
+    console=(not WINDOWED),
+    disable_windowed_traceback=False,
+    icon=get_icon(),
+    version=get_version(),
+    codesign_identity=None,
+    entitlements_file=None,
+)
+
+coll = COLLECT(
+    exe,
+    a.binaries,
+    a.zipfiles,
+    a.datas,
+    upx=UPX,
+    upx_exclude=[],
+    name=NAME,
+)
+
+if sys.platform == "darwin":
+    import motile_tracker
+
+    app = BUNDLE(
+        coll,
+        name=NAME + ".app",
+        icon=get_icon(),
+        bundle_identifier=f"com.{NAME}.{NAME}",
+        info_plist={
+            "CFBundleIdentifier": f"com.{NAME}.{NAME}",
+            "CFBundleShortVersionString": motile_tracker.__version__,
+            "NSHighResolutionCapable": "True",
+        },
+    )