cellects 0.2.2__tar.gz → 0.3.2__tar.gz

{cellects-0.2.2 → cellects-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: cellects
-Version: 0.2.2
+Version: 0.3.2
 Summary: Cell Expansion Computer Tracking Software.
 Author: Aurèle Boussard
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -714,17 +714,24 @@ Requires-Dist: mkdocstrings[python]; extra == "doc"
 Requires-Dist: mkdocs-gen-files; extra == "doc"
 Requires-Dist: mkdocs-autorefs; extra == "doc"
 Requires-Dist: pymdown-extensions; extra == "doc"
+Requires-Dist: mkdocs-literate-nav; extra == "doc"
+Requires-Dist: mkdocs-section-index; extra == "doc"
+Requires-Dist: mkdocs-jupyter; extra == "doc"
 
-Cellects: Cell Expansion Computer Tracking Software
-===================================================
+<h1>
+  <img src="https://raw.githubusercontent.com/Aurele-B/cellects/main/.github/icon.png"
+       width="42"
+       style="vertical-align: middle; margin-right: 12px;">
+  Cellects: Cell Expansion Computer Tracking Software
+</h1>
 
 [![PyPI version](https://img.shields.io/pypi/v/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
 ![PyPI - Downloads](https://img.shields.io/pypi/dm/cellects)
 [![Python versions](https://img.shields.io/pypi/pyversions/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
 [![License](https://img.shields.io/pypi/l/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/blob/main/LICENSE)
 [![Stars](https://img.shields.io/github/stars/Aurele-B/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/stargazers)
-![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Fci.yml)
-![Coverage](https://Aurele-B.github.io/cellects/badges/coverage.svg)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Frelease.yml)
+![Coverage](https://raw.githubusercontent.com/Aurele-B/cellects/gh-pages/badges/coverage.svg)
 
 Description
 -----------
@@ -734,7 +741,8 @@ Cellects’ main strengths are its broad scope of action, automated computation
 easy installation and user-friendly interface.
 
 <figure>
-  <img src="doc/static/UserManualFigure1.png" alt="Cellects first window" class="center" width="600">
+  <img src="doc/static/UserManualFigure1.png" alt="Cellects first window"
+       style="display:block;float:none;margin-left:auto;margin-right:auto;width:100%">
   <figcaption><strong>Figure 1:</strong> Cellects first window</figcaption>
 </figure>
 
@@ -761,9 +769,12 @@ Cellects
 
 ## 📚 Documentation
 
-Full documentation is available in the [docs](https://aurele-b.github.io/Cellects/) folder and includes:
-- [**User Manual**](https://aurele-b.github.io/Cellects/first-analysis/): Step-by-step workflows for data localization, image analysis and video tracking 
-- [**Advanced Features**](https://aurele-b.github.io/Cellects/advanced/): Customization options, batch processing, parameter tuning.
+Cellects' workflow is described in a [complete documentation](https://aurele-b.github.io/Cellects/). It includes:
+- [**What is Cellects**](https://aurele-b.github.io/Cellects/what-is-cellects/): Purpose of the software, usable data and introduction of its user manual
+- [**Setting up a first analysis**](https://aurele-b.github.io/Cellects/first-analysis/): Step-by-step workflows for data localization, image analysis and video tracking 
+- [**Improving the analysis**](https://aurele-b.github.io/Cellects/advanced/): Customization options, batch processing, parameter tuning.
+- [**Use cases**](https://aurele-b.github.io/Cellects/use-cases/): Real-world cases using the GUI (interface) and the API (scripts).
+- [**Contributing**](https://aurele-b.github.io/Cellects/contributing/): Report bugs and feature requests; contribute; testing and documentation processes.
 - [**API Reference**](https://aurele-b.github.io/Cellects/api/): Auto-generated from source code docstrings (see [Build Documentation]).
 
 ---

{cellects-0.2.2 → cellects-0.3.2}/README.md

@@ -1,101 +1,109 @@
-Cellects: Cell Expansion Computer Tracking Software
-===================================================
-
-[![PyPI version](https://img.shields.io/pypi/v/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
-![PyPI - Downloads](https://img.shields.io/pypi/dm/cellects)
-[![Python versions](https://img.shields.io/pypi/pyversions/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
-[![License](https://img.shields.io/pypi/l/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/blob/main/LICENSE)
-[![Stars](https://img.shields.io/github/stars/Aurele-B/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/stargazers)
-![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Fci.yml)
-![Coverage](https://Aurele-B.github.io/cellects/badges/coverage.svg)
-
-Description
------------
-
-Cellects is a tracking software for organisms whose shape and size change over time. 
-Cellects’ main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, 
-easy installation and user-friendly interface.
-
-<figure>
-  <img src="doc/static/UserManualFigure1.png" alt="Cellects first window" class="center" width="600">
-  <figcaption><strong>Figure 1:</strong> Cellects first window</figcaption>
-</figure>
-
----
-
-## 🚀 Installation (Short version)
-Install using our Windows installer: [Cellects_installer.exe](https://github.com/Aurele-B/Cellects/releases/)
-
-Or, install via pip:
-```bash
-pip install cellects
-```
-Any difficulties? follow our [complete installation tutorial](https://aurele-b.github.io/Cellects/installation/)
-
----
-
-## 🎯 Quick Start
-Run in terminal:
-```bash
-Cellects
-```
-
----
-
-## 📚 Documentation
-
-Full documentation is available in the [docs](https://aurele-b.github.io/Cellects/) folder and includes:
-- [**User Manual**](https://aurele-b.github.io/Cellects/first-analysis/): Step-by-step workflows for data localization, image analysis and video tracking 
-- [**Advanced Features**](https://aurele-b.github.io/Cellects/advanced/): Customization options, batch processing, parameter tuning.
-- [**API Reference**](https://aurele-b.github.io/Cellects/api/): Auto-generated from source code docstrings (see [Build Documentation]).
-
----
-
-## 🧪 Use Cases
-
-See [use cases](https://aurele-b.github.io/Cellects/use-cases/) for real-world examples:
-- Automated Physarum polycephalum tracking using GUI
-- Automated Physarum polycephalum tracking using API
-- Colony growth tracking
-
----
-
-## 🛠 Contributing
-
-We welcome contributions!  
-1. Fork the repository and create a new branch.
-2. Submit issues/PRs via [GitHub](https://github.com/Aurele-B/cellects/issues).
-
-For developer workflows, see [**Contributing**](https://aurele-b.github.io/Cellects/contributing/).
-
----
-
-## 📌 License & Citation
-
-GNU GPL3 License (see [LICENSE](https://github.com/Aurele-B/cellects/blob/main/LICENSE)).
-
-To cite Cellects, use:
-```bibtex
-@article{boussard2024cellects,
-  title={Cellects, a software to quantify cell expansion and motion},
-  author={Boussard, Aur{\`e}le and Arrufat, Patrick and Dussutour, Audrey and P{\'e}rez-Escudero, Alfonso},
-  journal={bioRxiv},
-  pages={2024--03},
-  year={2024},
-  publisher={Cold Spring Harbor Laboratory}
-}
-```
-
----
-
-## 🧪 Testing
-
-Run unit tests with:
-```bash
-pytest
-```
-
----
-
-## Resources
-- [Usage example (video)](https://www.youtube.com/watch?v=N-k4p_aSPC0)
+<h1>
+  <img src="https://raw.githubusercontent.com/Aurele-B/cellects/main/.github/icon.png"
+       width="42"
+       style="vertical-align: middle; margin-right: 12px;">
+  Cellects: Cell Expansion Computer Tracking Software
+</h1>
+
+[![PyPI version](https://img.shields.io/pypi/v/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/cellects)
+[![Python versions](https://img.shields.io/pypi/pyversions/cellects.svg?style=flat-square)](https://pypi.org/project/cellects/)
+[![License](https://img.shields.io/pypi/l/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/blob/main/LICENSE)
+[![Stars](https://img.shields.io/github/stars/Aurele-B/cellects.svg?style=flat-square)](https://github.com/Aurele-B/cellects/stargazers)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/Aurele-B/Cellects/.github%2Fworkflows%2Frelease.yml)
+![Coverage](https://raw.githubusercontent.com/Aurele-B/cellects/gh-pages/badges/coverage.svg)
+
+Description
+-----------
+
+Cellects is a tracking software for organisms whose shape and size change over time. 
+Cellects’ main strengths are its broad scope of action, automated computation of a variety of geometrical descriptors, 
+easy installation and user-friendly interface.
+
+<figure>
+  <img src="doc/static/UserManualFigure1.png" alt="Cellects first window"
+       style="display:block;float:none;margin-left:auto;margin-right:auto;width:100%">
+  <figcaption><strong>Figure 1:</strong> Cellects first window</figcaption>
+</figure>
+
+---
+
+## 🚀 Installation (Short version)
+Install using our Windows installer: [Cellects_installer.exe](https://github.com/Aurele-B/Cellects/releases/)
+
+Or, install via pip:
+```bash
+pip install cellects
+```
+Any difficulties? follow our [complete installation tutorial](https://aurele-b.github.io/Cellects/installation/)
+
+---
+
+## 🎯 Quick Start
+Run in terminal:
+```bash
+Cellects
+```
+
+---
+
+## 📚 Documentation
+
+Cellects' workflow is described in a [complete documentation](https://aurele-b.github.io/Cellects/). It includes:
+- [**What is Cellects**](https://aurele-b.github.io/Cellects/what-is-cellects/): Purpose of the software, usable data and introduction of its user manual
+- [**Setting up a first analysis**](https://aurele-b.github.io/Cellects/first-analysis/): Step-by-step workflows for data localization, image analysis and video tracking 
+- [**Improving the analysis**](https://aurele-b.github.io/Cellects/advanced/): Customization options, batch processing, parameter tuning.
+- [**Use cases**](https://aurele-b.github.io/Cellects/use-cases/): Real-world cases using the GUI (interface) and the API (scripts).
+- [**Contributing**](https://aurele-b.github.io/Cellects/contributing/): Report bugs and feature requests; contribute; testing and documentation processes.
+- [**API Reference**](https://aurele-b.github.io/Cellects/api/): Auto-generated from source code docstrings (see [Build Documentation]).
+
+---
+
+## 🧪 Use Cases
+
+See [use cases](https://aurele-b.github.io/Cellects/use-cases/) for real-world examples:
+- Automated Physarum polycephalum tracking using GUI
+- Automated Physarum polycephalum tracking using API
+- Colony growth tracking
+
+---
+
+## 🛠 Contributing
+
+We welcome contributions!  
+1. Fork the repository and create a new branch.
+2. Submit issues/PRs via [GitHub](https://github.com/Aurele-B/cellects/issues).
+
+For developer workflows, see [**Contributing**](https://aurele-b.github.io/Cellects/contributing/).
+
+---
+
+## 📌 License & Citation
+
+GNU GPL3 License (see [LICENSE](https://github.com/Aurele-B/cellects/blob/main/LICENSE)).
+
+To cite Cellects, use:
+```bibtex
+@article{boussard2024cellects,
+  title={Cellects, a software to quantify cell expansion and motion},
+  author={Boussard, Aur{\`e}le and Arrufat, Patrick and Dussutour, Audrey and P{\'e}rez-Escudero, Alfonso},
+  journal={bioRxiv},
+  pages={2024--03},
+  year={2024},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```
+
+---
+
+## 🧪 Testing
+
+Run unit tests with:
+```bash
+pytest
+```
+
+---
+
+## Resources
+- [Usage example (video)](https://www.youtube.com/watch?v=N-k4p_aSPC0)

{cellects-0.2.2 → cellects-0.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cellects"
-version = "0.2.2"
+version = "0.3.2"
 description = "Cell Expansion Computer Tracking Software."
 readme = "README.md"
 license = { file = "LICENSE" }
@@ -51,6 +51,9 @@ doc = [
   "mkdocs-gen-files",
   "mkdocs-autorefs",
   "pymdown-extensions",
+  "mkdocs-literate-nav",
+  "mkdocs-section-index",
+  "mkdocs-jupyter",
 ]
 
 [project.urls]