motile-tracker 3.1.5.dev0__tar.gz → 3.2.1.dev0__tar.gz

motile_tracker-3.2.1.dev0/.github/dependabot.yml

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

motile_tracker-3.2.1.dev0/.github/workflows/deploy.yml

@@ -0,0 +1,16 @@
+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
+  workflow_dispatch:
+
+jobs:
+  packaging:
+    permissions:
+      contents: write
+    uses: funkelab/motile_tracker_bundled_app/.github/workflows/bundle_app.yml@main
+    secrets: inherit
+    with:
+      event_name: ${{ github.event_name }}

{motile_tracker-3.1.5.dev0 → motile_tracker-3.2.1.dev0}/.gitignore

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

{motile_tracker-3.1.5.dev0 → motile_tracker-3.2.1.dev0}/.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: v0.11.9
     hooks:
       - id: ruff
         args: [--fix]

{motile_tracker-3.1.5.dev0 → motile_tracker-3.2.1.dev0}/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: motile-tracker
-Version: 3.1.5.dev0
+Version: 3.2.1.dev0
 Summary: Application for interactive tracking with global optimization
 Author-email: Caroline Malin-Mayor <malinmayorc@janelia.hhmi.org>
 License: BSD 3-Clause License
 Project-URL: Bug Tracker, https://github.com/funkelab/motile_tracker/issues
 Project-URL: Documentation, https://funkelab.github.io/motile_tracker/
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: Framework :: napari
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: End Users/Desktop
 Classifier: Intended Audience :: Science/Research
@@ -22,8 +21,10 @@ Classifier: Topic :: Scientific/Engineering :: Image Processing
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: napari[all]
-Requires-Dist: numpy
+Requires-Dist: finn-viewer>=0.2
+Requires-Dist: funtracks
+Requires-Dist: appdirs
+Requires-Dist: numpy<2.1,>=1.26
 Requires-Dist: magicgui
 Requires-Dist: qtpy
 Requires-Dist: scikit-image
@@ -34,10 +35,9 @@ Requires-Dist: tifffile[all]
 Requires-Dist: tqdm
 Requires-Dist: dask[array]>=2021.10.0
 Requires-Dist: fonticon-fontawesome6
+Requires-Dist: PyQt5
 Requires-Dist: pyqtgraph
-Requires-Dist: lxml_html_clean
 Provides-Extra: testing
-Requires-Dist: napari; extra == "testing"
 Requires-Dist: pyqt5; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
@@ -59,11 +59,10 @@ Dynamic: license-file
 
 [![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.
+An application for interactive tracking with [motile](https://github.com/funkelab/motile)
 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)
@@ -73,7 +72,7 @@ for more details on the concepts and method.
 
 ## Installation
 
-This plugin depends on [motile](https://github.com/funkelab/motile), which in
+This application 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.
 
@@ -82,6 +81,49 @@ 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
+
+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

motile_tracker-3.2.1.dev0/README.md

@@ -0,0 +1,74 @@
+# 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)
+
+The full documentation of the plugin can be found [here](https://funkelab.github.io/motile_tracker/).
+
+An application for interactive tracking with [motile](https://github.com/funkelab/motile)
+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 application 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
+
+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
+[file an issue](https://github.com/funkelab/motile_tracker/issues)
+along with a detailed description.

motile_tracker-3.2.1.dev0/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-3.2.1.dev0/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-3.1.5.dev0 → motile_tracker-3.2.1.dev0}/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-3.2.1.dev0/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-3.2.1.dev0/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-3.2.1.dev0/motile-tracker.spec

@@ -0,0 +1,121 @@
+# -*- mode: python ; coding: utf-8 -*-
+import sys
+import motile_tracker
+
+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 = motile_tracker.__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":
+    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",
+        },
+    )