Merge pull request #48 from AurelienBesnier/master

Guidelines update

CHANGELOG.md

@@ -0,0 +1,30 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+- A `pyproject.toml` file.
+- This CHANGELOG.md file.
+- Phenotrack citation in [README.md](./README.md) (#44). 
+- [OpenAlea svg](./doc/_static/openalea_web.svg) logo for documentation.
+- More test for the test suite.
+
+### Changed
+
+- The documentation configuration file `conf.py` with [OpenAlea Guidelines](https://openalea.readthedocs.io/en/latest/development/guidelines.html).
+- Modernized the test suite.
+- Compatibility with numpy 2.0.
+- Updated code to respect guidelines.
+- Formating source files with [ruff](https://docs.astral.sh/ruff/).
+
+### Fixed
+
+- Updating skan function to more recent versions.
+- Removed warning of test files saved with python 2 by saving them again with python 3.
+- Fixing location of data for notebook examples.

README.md

@@ -5,7 +5,7 @@
 [![Last version](https://anaconda.org/openalea3/openalea.phenomenal/badges/version.svg)](https://anaconda.org/OpenAlea3/openalea.phenomenal/files)
 [![GitHub CI](https://github.com/openalea/phenomenal/actions/workflows/conda-package-build.yml/badge.svg)](https://github.com/openalea/phenomenal/actions/workflows/conda-package-build.yml)
 [![Documentation Status](https://readthedocs.org/projects/phenomenal/badge/?version=latest)](https://phenomenal.readthedocs.io/en/latest/?badge=latest)
-[![aunch interactive phenomenal notebook with myBinder service](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/openalea/phenomenal/master?filepath=examples)
+[![Launch interactive phenomenal notebook with myBinder service](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/openalea/phenomenal/master?filepath=examples)
 
 
 ## Phenomenal: An automatic open source library for 3D shoot architecture reconstruction and analysis for image-based plant phenotyping
@@ -31,21 +31,42 @@ If you find our work useful in your research, please consider citing:
         journal = {bioRxiv}
     }
 
+If you use PhenoTrack3D in your research, cite:
+
+Daviet, B., Fernandez, R., Cabrera-Bosquet, L. et al. PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time. Plant Methods 18, 130 (2022). https://doi.org/10.1186/s13007-022-00961-4
+
+```latex
+@article {daviet22,
+	author = {Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c c} and Pradal, Christophe and Fournier, Christian},
+	title = {PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
+	elocation-id = @article{daviet2022phenotrack3d,
+	title={PhenoTrack3D: an automatic high-throughput phenotyping pipeline to track maize organs over time},
+	author={Daviet, Benoit and Fernandez, Romain and Cabrera-Bosquet, Lloren{\c{c}} and Pradal, Christophe and Fournier, Christian},
+	journal={Plant Methods},
+	volume={18},
+	number={1},
+	pages={1--14},
+	year={2022},
+	publisher={Springer}
+}
+
+```
+
 
 ### Installation
 
-Conda environement : https://docs.conda.io/en/latest/index.html
+Conda environment : https://docs.conda.io/en/latest/index.html
 
 #### User
 
 ##### Create a new environment with phenomenal installed in there :
 
-    mamba create -n phm -c conda-forge -c openalea openalea.phenomenal
+    mamba create -n phm -c conda-forge -c openalea3 openalea.phenomenal
     mamba activate phm
 
 ##### In a existing environment :
 
-    mamba install -c conda-forge -c openalea openalea.phenomenal
+    mamba install -c conda-forge -c openalea3 openalea.phenomenal
 
 ##### (Optional) Test your installation :
 
@@ -58,7 +79,7 @@ Conda environement : https://docs.conda.io/en/latest/index.html
     # Install dependency with conda
     mamba create -n phm -c conda-forge python
     mamba activate phm
-    mamba install -c conda-forge -c numba cython numpy numba scipy scikit-image scikit-learn networkx opencv matplotlib vtk pytest skan=0.10
+    mamba install -c conda-forge cython numpy numba scipy scikit-image scikit-learn networkx opencv matplotlib vtk pytest skan
 
     # Load phenomenal and install
     git clone https://github.com/openalea/phenomenal.git

conda/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: openalea.phenomenal
-  version: "1.9.3"
+  version: "1.9.4"
 
 source:
   path: ..
@@ -42,7 +42,7 @@ requirements:
     - opencv >4.1.2 [osx]
     - matplotlib
     - vtk
-    - skan>=0.10
+    - skan
     - pywin32 [win]
 
 test: