Major refactor of files organization (#15)

* add export to trackmate format

* add to_trackmate to __init__.py main

* made to_trackmate compatible with fiji trackmate reader

* added pytrackmate to tox testenv dependencies

* refactoring tracks aux function organization and function naming

* bumped version

* moved add flow field func

* fixed flow tests

* refactored overwriting and store utilities

* simplified labels to edges array creation

* created utils.array with array utilities that were spread

* added plantseg & microsam tests

* added cellpose tests

* removed from __init__ files that depend on torch

* torch is no longer optional

* fixing flow and cellpose tests

* updated zebrahub demo

* updated stardist demo

* updated neuromast and zebrahub examples

* added badges to reademe

* updated multi color example

* starting documentation

* updated cli and api docs

* added first faq, added template to quickstart and index

* updated code and example documentations

* added docs github workflow

* testing docs workflow pr

* added flow to 'track' main function

* fixed docs workflow install

* updated pyproject dependency

* added missings docs source and updatedependenceis

* added tracks length and update doc

* updated micro sam example

* fix widget import

* added link validation widget / function

* improved tribolium documentation

* updating segmentation engine connection frequency

* reducing test flow precision

* updating docs to only run on main

* added citation to quickstart guide

* making flow field tests looser

* uploaded multi-color-ensemble data

.github/workflows/docs.yml

@@ -0,0 +1,59 @@
+name: Build and deploy docs
+
+on:
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[docs]"
+      - name: Set environment
+        run: |
+          REPO_OWNER="${GITHUB_REPOSITORY%%/*}"
+          REPO_NAME="${GITHUB_REPOSITORY#*/}"
+          echo "GITHUB_PAGES_URL=https://$REPO_OWNER.github.io/$REPO_NAME" >> $GITHUB_ENV
+      - name: Build the docs
+        working-directory: ./docs
+        run: |
+          echo $GITHUB_PAGES_URL
+          make html
+          touch build/html/.nojekyll
+      - name: Upload build artifacts
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: './docs/build/html'
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1

README.md

@@ -1,7 +1,17 @@
-
 # ULTRACK
 
-Cell tracking and segmentation software.
+![tests](https://github.com/royerlab/ultrack/actions/workflows/test_pull_request.yml/badge.svg)
+[![codecov](https://codecov.io/gh/royerlab/ultrack/branch/main/graph/badge.svg?token=9FFo4zNtYP)](https://codecov.io/gh/royerlab/ultrack)
+[![PyPI version](https://badge.fury.io/py/ultrack.svg)](https://badge.fury.io/py/ultrack)
+[![Downloads](https://pepy.tech/badge/ultrack)](https://pepy.tech/project/ultrack)
+[![Downloads](https://pepy.tech/badge/ultrack/month)](https://pepy.tech/project/ultrack)
+[![Python version](https://img.shields.io/pypi/pyversions/ultrack)](https://pypistats.org/packages/ultrack)
+[![Licence: BSD-3](https://img.shields.io/github/license/royerlab/ultrack)](https://github.com/royerlab/ultrack/blob/main/LICENSE)
+[![Contributors](https://img.shields.io/github/contributors-anon/royerlab/ultrack)](https://github.com/royerlab/ultrack/graphs/contributors)
+[![GitHub stars](https://img.shields.io/github/stars/royerlab/ultrack?style=social)](https://github.com/royerlab/ultrack/)
+[![GitHub forks](https://img.shields.io/github/forks/royerlab/ultrack?style=social)](https://git:hub.com/royerlab/ultrack/)
+
+Large-scale cell tracking under segmentation uncertainty.
 
 https://github.com/royerlab/ultrack/assets/21022743/10aace9c-0e0e-4310-a103-f846683cfc77
 
@@ -39,15 +49,15 @@ Usage examples can be found [here](examples), including their environment files
 
 The `ultrack` library relies on a configuration schema, its description is [here](ultrack/config/README.md).
 
-The segmentation and tracking data are stored in a SQL database, described [here](ultrack/core/README.md).
+The segmentation and tracking data are stored in an SQL database, described [here](ultrack/core/README.md).
 
-Helper functions to export to the cell tracking challenge and napari formats are available, [reference](ultrack/core/export).
+Helper functions to export to the cell tracking challenge and napari formats are available [here](ultrack/core/export).
 
 ## Citing
 
 ```
 @misc{bragantini2023ultrack,
-      title={Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps}, 
+      title={Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps},
       author={Jordão Bragantini and Merlin Lange and Loïc Royer},
       year={2023},
       eprint={2308.04526},

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)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api.rst

@@ -0,0 +1,88 @@
+API
+---
+
+Core functionalities
+
+.. autosummary::
+
+    ultrack.track
+    ultrack.segment
+    ultrack.link
+    ultrack.solve
+    ultrack.add_flow
+    ultrack.load_config
+
+.. could not make it work for ultrack.utils.array
+
+Image processing utilities
+
+.. autosummary::
+
+    ultrack.imgproc.segmentation.Cellpose
+    ultrack.imgproc.plantseg.PlantSeg
+    ultrack.imgproc.sam
+    ultrack.imgproc.flow
+
+Exporting
+
+.. autosummary::
+
+   ultrack.core.export.to_ctc
+   ultrack.core.export.to_trackmate
+   ultrack.core.export.to_tracks_layer
+   ultrack.core.export.tracks_to_zarr
+
+====================
+Core functionalities
+====================
+
+.. automodule:: ultrack
+    :members:
+    :imported-members:
+
+===============
+Array utilities
+===============
+
+.. automodule:: ultrack.utils.array
+    :members:
+
+==========================
+Image processing utilities
+==========================
+
+-------------------
+DL models interface
+-------------------
+
+.. autoclass:: ultrack.imgproc.segmentation.Cellpose
+    :members:
+
+.. autoclass:: ultrack.imgproc.plantseg.PlantSeg
+    :members:
+
+.. automodule:: ultrack.imgproc.sam
+    :members:
+
+----
+Flow
+----
+
+.. automodule:: ultrack.imgproc.flow
+    :members:
+
+================
+Tracks utilities
+================
+
+.. automodule:: ultrack.tracks
+    :imported-members:
+    :members:
+
+=========
+Exporting
+=========
+
+.. automodule:: ultrack.core.export
+    :members:
+    :imported-members:

docs/source/cli.rst

@@ -0,0 +1,25 @@
+CLI
+---
+
+
+.. click:: ultrack.cli.config:config_cli
+    :prog: ultrack create_config
+
+.. click:: ultrack.cli.segment:segmentation_cli
+    :prog: ultrack segment
+
+.. click:: ultrack.cli.flow:add_flow_cli
+    :prog: ultrack flow
+
+.. click:: ultrack.cli.link:link_cli
+    :prog: ultrack link
+
+.. click:: ultrack.cli.solve:solve_cli
+    :prog: ultrack solve
+
+.. click:: ultrack.cli.export:export_cli
+    :prog: ultrack export
+    :nested: full
+
+.. click:: ultrack.cli.clear_database:clear_database_cli
+    :prog: ultrack clear_database

docs/source/conf.py

@@ -0,0 +1,62 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+from importlib.metadata import version as libversion
+
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- Project information -----------------------------------------------------
+
+project = "ultrack"
+copyright = "2023, Jordão Bragantini"
+author = "Jordão Bragantini"
+
+# The full version, including alpha/beta/rc tags
+release = libversion("ultrack")
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx.ext.autodoc", "sphinx_click.ext", "sphinx.ext.autosummary"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- AutoDoc configuration --------------------------------------------------
+
+# Automatically extract typehints when specified and place them in
+# descriptions of the relevant function/method.
+autodoc_typehints = "description"
+
+# Don't show class signature with the class' name.
+# autodoc_class_signature = "separated"

docs/source/faq.rst

@@ -0,0 +1,5 @@
+FAQ
+---
+
+**Q: What is each configuration parameters for?**
+    A: See the `configuration README <https://github.com/royerlab/ultrack/tree/main/ultrack/config>`_.

docs/source/index.rst

@@ -0,0 +1,29 @@
+.. ultrack documentation main file
+
+ultrack
+=======
+
+Large-scale cell tracking under segmentation uncertainty.
+
+.. raw:: html
+
+   <video width="480" autoplay muted>
+     <source src="https://github.com/royerlab/ultrack/assets/21022743/10aace9c-0e0e-4310-a103-f846683cfc77" type="video/mp4">
+     Your browser does not support the video tag.
+   </video>
+
+Zebrafish imaged using `DaXi <https://www.nature.com/articles/s41592-022-01417-2>`_ whole embryo tracking.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Basics:
+
+   quickstart
+   theory
+   faq
+
+.. toctree::
+   :caption: Reference:
+
+   api
+   cli