motile-tracker 0.0.1.dev0__tar.gz

motile_tracker-0.0.1.dev0/.github/dependabot.yml

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

motile_tracker-0.0.1.dev0/.github/workflows/deploy.yml

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+name: Deploy
+
+on:
+  push:
+    tags: ["*"]
+  workflow_dispatch:
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+    if: contains(github.ref, 'tags')
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Build a binary wheel and a source tarball
+        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
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+      - uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

motile_tracker-0.0.1.dev0/.github/workflows/docs.yml

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+name: Docs build
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  # Build the documentation and upload the static HTML files as an artifact.
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install conda dependencies
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: '3.10'
+          environment-file: conda_config.yml
+          channel-priority: true
+      - name: Install pip dependencies
+        shell: bash -el {0}  # this is necessary to activate the conda env
+        run: |
+          pip install ".[docs]"
+      - name: Build docs
+        shell: bash -el {0}
+        run: |
+          cd docs/
+          make html
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html
+
+  # Deploy the artifact to GitHub pages.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

motile_tracker-0.0.1.dev0/.github/workflows/publish.yml

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+name: publish
+
+on:
+  push:
+    branches: [deploy]
+    tags: ["v*"] # Push events to matching v*, i.e. v1.0, v20.15.10
+    paths:
+      - '.github/workflows/publish.yml' # this file
+  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/')
+    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: 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.{dmg|exe|run}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          draft: false
+          prerelease: false
+        

motile_tracker-0.0.1.dev0/.github/workflows/test.yml

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+name: tests
+
+on:
+  push:
+    branches: [main]
+    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:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, macos-latest] # windows-latest, temporarily disabled until ilpy is fixed
+        python-version: ["3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # note: if you need dependencies from conda, considering using
+      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+      - name: Install conda dependencies
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: conda_config.yml
+          channel-priority: true
+
+      - name: Install pip dependencies
+        shell: bash -el {0} # this is necessary to activate the conda env
+        run: |
+          pip install ".[testing]"
+
+      - name: Test with pytest
+        shell: bash -el {0}
+        run: |
+          pytest --color=yes --cov=motile-tracker --cov-report=xml --cov-report=term-missing tests
+
+      - name: Coverage
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: funkelab/motile-tracker

motile_tracker-0.0.1.dev0/.gitignore

@@ -0,0 +1,89 @@
+scripts/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Backup files
+*~
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# Pycharm and VSCode
+.idea/
+venv/
+.vscode/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+**/_version.py

motile_tracker-0.0.1.dev0/.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+ci:
+  autofix_prs: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        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: v0.11.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  # https://mypy.readthedocs.io/en/stable/introduction.html
+  # you may wish to add this as well!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v0.910-1
+  #   hooks:
+  #     - id: mypy

motile_tracker-0.0.1.dev0/LICENSE

@@ -0,0 +1,28 @@
+
+Copyright (c) 2023, Howard Hughes Medical Institute
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

motile_tracker-0.0.1.dev0/PKG-INFO

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+Metadata-Version: 2.4
+Name: motile-tracker
+Version: 0.0.1.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
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+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<2.1,>=1.26
+Requires-Dist: magicgui
+Requires-Dist: qtpy
+Requires-Dist: scikit-image
+Requires-Dist: motile>=0.3
+Requires-Dist: motile_toolbox==0.4.0
+Requires-Dist: pydantic
+Requires-Dist: tifffile[all]
+Requires-Dist: tqdm
+Requires-Dist: dask[array]>=2021.10.0
+Requires-Dist: fonticon-fontawesome6
+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"
+Requires-Dist: pytest-qt; extra == "testing"
+Provides-Extra: docs
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-autoapi; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinxcontrib-video; extra == "docs"
+Provides-Extra: dev
+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
+
+[![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-0.0.1.dev0/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-0.0.1.dev0/conda_config.yml

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+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-0.0.1.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-0.0.1.dev0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)