rectanglepy 0.5.4__tar.gz → 1.0.0__tar.gz

{rectanglepy-0.5.4 → rectanglepy-1.0.0}/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.4
+current_version = 1.0.0
 tag = True
 commit = True
 

{rectanglepy-0.5.4 → rectanglepy-1.0.0}/.gitignore

@@ -26,3 +26,4 @@ __pycache__/
 # IDEs
 /.idea/
 /.vscode/
+/docs/visium.zarr/

rectanglepy-1.0.0/CHANGELOG.md

@@ -0,0 +1,23 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog][],
+and this project adheres to [Semantic Versioning][].
+
+[keep a changelog]: https://keepachangelog.com/en/1.0.0/
+[semantic versioning]: https://semver.org/spec/v2.0.0.html
+
+## [Unreleased]
+
+## [1.0.0] - 2025-08-14
+
+### Added
+
+-   Public release of Rectangle with full core functionalities and documentation for cell-type deconvolution.
+
+## [0.1.0] - 2024-04-25
+
+### Added
+
+-   Initial public release of Rectangle.

{rectanglepy-0.5.4 → rectanglepy-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rectanglepy
-Version: 0.5.4
+Version: 1.0.0
 Summary: Hierarchical deconvolution of bulk  transcriptomics
 Project-URL: Documentation, https://rectanglepy.readthedocs.io/
 Project-URL: Source, https://github.com/ComputationalBiomedicineGroup/Rectangle
@@ -718,24 +718,23 @@ Description-Content-Type: text/markdown
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle is an open-source Python package developed for computational deconvolution.
+Rectangle is an open-source Python package for single-cell-informed cell-type deconvolution of bulk and spatial transcriptomic data, which is part of the [scverse ecosystem](https://scverse.org/packages/).
 
-Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
-an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical signature building for fine-grained cell-type deconvolution, estimation and correction of unknown cellular content, and efficient handling of large-scale single-cell data during signature matrix computation.
 
-Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
-improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
+Rectangle was developed to overcome the current challenges in cell-type deconvolution, providing a robust and accurate methodology while ensuring a low computational profile.
 
 ## Getting started
 
 Please refer to the [documentation][link-docs]. In particular, the
 
+-   [Tutorials][link-docs/tutorials] for a step-by-step guide on how to use Rectangle, and the
+
 -   [API documentation][link-api].
 
 ## Installation
 
-You need to have Python 3.10 or higher installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+You need to have Python 3.10 or higher installed on your system.
 
 How to install Rectangle:
 
@@ -755,10 +754,11 @@ If you found a bug, please use the [issue tracker][issue-tracker].
 
 ## Citation
 
-> t.b.a
+> If you use Rectangle in your project, please cite: (TBA)
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/ComputationalBiomedicineGroup/Rectangle/issues
 [changelog]: https://rectanglepy.readthedocs.io/changelog.html
 [link-docs]: https://Rectanglepy.readthedocs.io
 [link-api]: https://rectanglepy.readthedocs.io/api.html
+[link-docs/tutorials]: https://rectanglepy.readthedocs.io/notebooks/example.html

{rectanglepy-0.5.4 → rectanglepy-1.0.0}/README.md

@@ -7,24 +7,23 @@
 [link-tests]: https://github.com/ComputationalBiomedicineGroup/Rectangle/actions/workflows/build.yaml
 [badge-docs]: https://img.shields.io/readthedocs/rectanglepy
 
-Rectangle is an open-source Python package developed for computational deconvolution.
+Rectangle is an open-source Python package for single-cell-informed cell-type deconvolution of bulk and spatial transcriptomic data, which is part of the [scverse ecosystem](https://scverse.org/packages/).
 
-Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical processing,
-an estimation of unknown cellular content and a significant reduction in data volume during signature matrix computation.
+Rectangle presents a novel approach to second-generation deconvolution, characterized by hierarchical signature building for fine-grained cell-type deconvolution, estimation and correction of unknown cellular content, and efficient handling of large-scale single-cell data during signature matrix computation.
 
-Rectangle was developed to outperform existing deconvolution solutions by introducing methods that promise
-improvements in cell-type fraction estimation accuracy while keeping a low computational profile.
+Rectangle was developed to overcome the current challenges in cell-type deconvolution, providing a robust and accurate methodology while ensuring a low computational profile.
 
 ## Getting started
 
 Please refer to the [documentation][link-docs]. In particular, the
 
+-   [Tutorials][link-docs/tutorials] for a step-by-step guide on how to use Rectangle, and the
+
 -   [API documentation][link-api].
 
 ## Installation
 
-You need to have Python 3.10 or higher installed on your system. If you don't have
-Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+You need to have Python 3.10 or higher installed on your system.
 
 How to install Rectangle:
 
@@ -44,10 +43,11 @@ If you found a bug, please use the [issue tracker][issue-tracker].
 
 ## Citation
 
-> t.b.a
+> If you use Rectangle in your project, please cite: (TBA)
 
 [scverse-discourse]: https://discourse.scverse.org/
 [issue-tracker]: https://github.com/ComputationalBiomedicineGroup/Rectangle/issues
 [changelog]: https://rectanglepy.readthedocs.io/changelog.html
 [link-docs]: https://Rectanglepy.readthedocs.io
 [link-api]: https://rectanglepy.readthedocs.io/api.html
+[link-docs/tutorials]: https://rectanglepy.readthedocs.io/notebooks/example.html

rectanglepy-1.0.0/docs/contributing.md

@@ -0,0 +1,14 @@
+# Contributing Guide
+
+We welcome contributions! The best way to contribute is by opening a pull request on GitHub.
+
+## How to Contribute
+
+1. Fork the repository and create a new branch for your changes.
+2. Make your changes (bug fixes, new features, documentation, etc.).
+3. Open a pull request describing your changes.
+
+Please ensure your code is clear and well-documented. If you add new features or fix bugs, tests are appreciated.
+If you have questions or need help, feel free to open an issue.
+
+Thank you for helping improve Rectangle!

{rectanglepy-0.5.4 → rectanglepy-1.0.0}/docs/index.md

@@ -7,7 +7,8 @@
 :maxdepth: 1
 
 api.md
-notebooks/example
+installation.md
+tutorials.md
 changelog.md
 contributing.md
 references.md

rectanglepy-1.0.0/docs/installation.md

@@ -0,0 +1,11 @@
+# Installation
+
+You need to have Python 3.10 or higher installed on your system.
+
+To install the latest release of `Rectangle` from PyPI:
+
+```bash
+pip install rectanglepy
+```
+
+For more details, see the [documentation](https://Rectanglepy.readthedocs.io).