add pixi and contribution instructions to repo

Author: gletort

.gitignore

@@ -5,7 +5,7 @@ target/
 
 # IPython Notebook
 .ipynb_checkpoints
-o# OS
+# OS
 .DS_Store
 
 .github/
@@ -14,6 +14,8 @@ __pycache__/
 src/epicure/resources/__pycache__/
 src/epicure/__pycache__/
 
+.pixi/
+pixi.lock
 env/
 build/
 develop-eggs/

README.md

@@ -67,6 +67,16 @@ To suggest the addition of a new feature, you can also contact us by filing an i
 If you encounter a code related issue using EpiCure, please [file an issue](https://github.com/Image-Analysis-Hub/epicure/issues) in this repository.
 
 
+To facilitate contributions, we added a pixi file in the repository.
+Developers can run:
+* `pixi run build` to install locally the plugin and test it manually
+* `pixi run test` to run locally the tests from the `src/tests` directory
+* `pixi run build-doc` to locally build the documentation pages. The documentation will be build in the `site` folder in the repository. The file `site\index.html` can be open in a browser to see the generated documentation. 
+
+The code API can be found [here](https://image-analysis-hub.github.io/Epicure/api/epicure.html) in the online documentation.
+Examples of using EpiCure without opening the interface can be found in the test files and the repository notebooks.
+
+
 [napari]: https://github.com/napari/napari
 [file an issue]: https://github.com/Image-Analysis-Hub/epicure/issues
 [pip]: https://pypi.org/project/pip/

docs/index.md

@@ -41,7 +41,7 @@ When you have selected the two files, you can start editing by clicking on the `
 
 * [Edit](.//Edit.md): clean the segmentation or correct manually errors through EpiCure options :wrench: 
 * [Inspect](./Inspect.md): determine cells suspicious of having an error, based on a few morphological or track features, or handle cellular events as divisions :mag: 
-* [Track](./Track/md): links the labels from one frame to another to reconstruct the whole cell track. 
+* [Track](./Track.md): links the labels from one frame to another to reconstruct the whole cell track. 
 * [Output](./Output.md): measure/display cell or track features, export results to other plugins/softwares :outbox_tray: 
 * [Display](./Display.md): display additional informations (segmentation skeleton, general informations...) or a spatial grid :window:  
 * [Preferences](./Preferences.md): to set-up user-specific preferences as keyboard shortcuts :capital_abcd: 

pixi.toml

@@ -0,0 +1,30 @@
+[workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64", "win-64", "osx-64", "osx-arm64"]
+
+[dependencies]
+python = ">=3.10,<3.14"
+pip = ">=26.0.1,<27"
+wheel = ">=0.46.3,<0.47"
+hatchling = ">=1.29.0,<2"
+cmake = ">=4.3.0,<5"
+
+[feature.dev.dependencies]
+pytest = ">=9.0.2,<10"
+pytest-cov = ">=7.0.0,<8"
+pytest-qt = "*"
+tox = "*"
+mkdocs-material = "*"
+pdoc = "*"
+
+[feature.dev.pypi-dependencies]
+napari = { version = ">=0.6.0, <0.7", extras = ["all"] }
+
+[tasks]
+build = "pip install -e ."
+test = "pytest -v"
+build-doc = "pip install -e . & pdoc epicure -o docs/api & mkdocs build"
+go = "pip install -e . & napari"
+
+[environments]
+default = { features = ["dev"], solve-group = "default" }