Setup docs

CITATION.cff

@@ -1,13 +1,41 @@
 # YAML 1.2
 ---
 cff-version: "1.2.0"
-title: "diffwofost"
+title: "diffwofost: A differentiable implementation of the WOFOST crop growth model"
+type: software
 authors:
-  - family-names:
-    given-names:
-    orcid: ""
-date-released: 2025-07-11
-version: "0.1.0"
+  - given-names: Fakhereh (Sarah)
+    family-names: Alidoost
+    email: f.alidoost@esciencecenter.nl
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0001-8407-6472'
+  - given-names: Francesco
+    family-names: Nattino
+    email: f.nattino@esciencecenter.nl
+    affiliation: Netherlands eScience Center
+    orcid: 'https://orcid.org/0000-0003-3286-0139'
+  - given-names: Michiel
+    family-names: Kallenberg
+    email: michiel.kallenberg@wur.nl
+    affiliation: Wageningen University & Research
+    orcid: 'https://orcid.org/0000-0002-4661-6674'
+  - given-names: Ron
+    family-names: van Bree
+    email: ron.vanbree@wur.nl
+    affiliation: Wageningen University & Research
+    orcid: 'https://orcid.org/0009-0000-6365-6996'
+  - given-names: Ioannis
+    family-names: Athanasiadis
+    email: ioannis.athanasiadis@wur.nl
+    affiliation: Wageningen University & Research
+    orcid: 'https://orcid.org/0000-0003-2764-0078'
+  - given-names: Allard
+    family-names: de Wit
+    email: allard.dewit@wur.nl
+    affiliation: Wageningen University & Research
+    orcid: 'https://orcid.org/0000-0002-5517-6404'
+date-released: 2025-09-23
+version: "0.1.1"
 repository-code: "https://github.com/WUR-AI/diffwofost"
 keywords:
   - "pytorch"

LICENSE

@@ -1,16 +1,19 @@
-# Licensed under the EUPL, Version 1.1 or – as soon they
-# will be approved by the European Commission - subsequent
-# versions of the EUPL (the "Licence");
-# You may not use this work except in compliance with the
-# Licence.
-# You may obtain a copy of the Licence at:
+**EUPL, Version 1.1**
 
-# http://ec.europa.eu/idabc/eupl
+Licensed under the EUPL, Version 1.1 or as soon they
+will be approved by the European Commission - subsequent
+versions of the EUPL (the "Licence").
 
-# Unless required by applicable law or agreed to in
-# writing, software distributed under the Licence is
-# distributed on an "AS IS" basis,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
-# express or implied.
-# See the Licence for the specific language governing
-# permissions and limitations under the Licence.
+You may not use this work except in compliance with the
+Licence.
+You may obtain a copy of the Licence at:
+
+https://interoperable-europe.ec.europa.eu/licence/european-union-public-licence-version-11-eupl
+Unless required by applicable law or agreed to in
+writing, software distributed under the Licence is
+distributed on an "AS IS" basis,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
+express or implied.
+
+See the Licence for the specific language governing
+permissions and limitations under the Licence.

README.md

@@ -1,5 +1,15 @@
+<!-- (Customize these badges with your own links, and check https://shields.io/ or https://badgen.net/ to see which other badges are available.) -->
+
+[![github repo badge](https://img.shields.io/badge/github-repo-000.svg?logo=github&labelColor=gray&color=blue)](https://github.com/WUR-AI/diffWOFOST)
+[![PyPI - Version](https://badge.fury.io/py/diffwofost.svg)](https://img.shields.io/pypi/v/diffwofost)
+[![Python package built](https://github.com/WUR-AI/diffWOFOST/actions/workflows/build.yml/badge.svg)](https://github.com/WUR-AI/diffWOFOST/actions/workflows/build.yml)
+[![Documentation built](https://github.com/WUR-AI/diffWOFOST/actions/workflows/deploy-documentation.yml/badge.svg)](https://github.com/WUR-AI/diffWOFOST/actions/workflows/deploy-documentation.yml)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=WUR-AI_diffWOFOST&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=WUR-AI_diffWOFOST)
+
 # diffWOFOST
 
+<img align="right" width="90" alt="Logo" src="./docs/logo/diffwofost.png">
+
 The python package `diffWOFOST` is a differentiable implementation of WOFOST models using [`torch`](https://pytorch.org/),
 allowing gradients to flow through the simulations for optimization and data assimilation.
 
@@ -24,20 +34,14 @@ To work with notebooks, you need to install `jupyterlab`:
 pip install jupyterlab
 ```
 
-## Usage
-
-An example notebooks are provided in the `docs/notebooks` folder.
+## Documentation
 
-## PCSE
+The documentation for `diffWOFOST` is available at
+[https://WUR-AI.github.io/diffWOFOST](https://WUR-AI.github.io/diffWOFOST).
 
-The python implementation of WOFOST is available at
-[`PCSE`](https://pcse.readthedocs.io/en/stable/). For more information about the
-models, the functional components of PCSE, and documentation have a look at the
-following links:
+## Acknowledgements
 
-- [Models available in PCSE](https://pcse.readthedocs.io/en/stable/available_models.html#models-available-in-pcse)
-- [The Engine](https://pcse.readthedocs.io/en/stable/reference_guide.html#the-engine)
-- [PCSE source code](https://github.com/ajwdewit/pcse)
-- [PCSE test data](https://github.com/ajwdewit/pcse/tree/master/tests/test_data)
-- [PCSE example notebooks](https://github.com/ajwdewit/pcse_notebooks).
-- [WOFOST_crop_parameters](https://github.com/ajwdewit/WOFOST_crop_parameters): each branch contains the crop parameters for a specific crop model version
+The package `diffWOFOST` is developed in the
+[DeltaCrop](https://research-software-directory.org/projects/deltacrop) project, a
+collaboration between Wageningen University & Research and Netherlands eScience
+Center.

docs/CONTRIBUTING.md

@@ -1,6 +1,9 @@
-# Contributing guidelines
+#
 
-We welcome any kind of contribution to our software, from simple comment or question to a full fledged [pull request](https://help.github.com/articles/about-pull-requests/). Please read and follow our [Code of Conduct](CODE_OF_CONDUCT.md).
+We welcome any kind of contribution to our software, from simple comment or
+question to a full fledged [pull
+request](https://help.github.com/articles/about-pull-requests/). Please read and
+follow our [Code of Conduct](CODE_OF_CONDUCT.md).
 
 A contribution can be one of the following cases:
 
@@ -13,56 +16,50 @@ The sections below outline the steps in each case.
 
 ## You have a question
 
-1. use the search functionality [here](https://github.com/WUR-AI/diffwofost/issues) to see if someone already filed the same issue;
+1. use the search functionality [in
+   issues](https://github.com/WUR-AI/diffwofost/issues) to see if someone
+   already filed the same issue;
 2. if your issue search did not yield any relevant results, make a new issue;
 3. apply the "Question" label; apply other labels when relevant.
 
 ## You think you may have found a bug
 
-1. use the search functionality [here](https://github.com/WUR-AI/diffwofost/issues) to see if someone already filed the same issue;
-1. if your issue search did not yield any relevant results, make a new issue, making sure to provide enough information to the rest of the community to understand the cause and context of the problem. Depending on the issue, you may want to include:
-    - the [SHA hashcode](https://help.github.com/articles/autolinked-references-and-urls/#commit-shas) of the commit that is causing your problem;
-    - some identifying information (name and version number) for dependencies you're using;
-    - information about the operating system;
-1. apply relevant labels to the newly created issue.
+1. use the search functionality [in
+   issues](https://github.com/WUR-AI/diffwofost/issues) to see if someone
+   already filed the same issue;
+2. if your issue search did not yield any relevant results, make a new issue,
+   making sure to provide enough information to the rest of the community to
+   understand the cause and context of the problem.
 
 ## You want to make some kind of change to the code base
 
-1. (**important**) announce your plan to the rest of the community *before you start working*. This announcement should be in the form of a (new) issue;
-1. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
-1. if needed, fork the repository to your own Github profile and create your own feature branch off of the latest main commit. While working on your feature branch, make sure to stay up to date with the main branch by pulling in changes, possibly from the 'upstream' repository (follow the instructions [here](https://help.github.com/articles/configuring-a-remote-for-a-fork/) and [here](https://help.github.com/articles/syncing-a-fork/));
-1. install dependencies (see the [development documentation](README.dev.md#development_install));
-1. make sure the existing tests still work by running ``pytest``;
-1. add your own tests (if necessary);
-1. update or expand the documentation;
+1. (**important**) announce your plan to the rest of the community *before you
+   start working*. This announcement should be in the form of a (new) issue;
+2. (**important**) wait until some kind of consensus is reached about your idea being a good idea;
+3. follow the instruction in [developer_guide.md](developer_guide.md).
 
-1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the diffwofost repository on GitHub;
-1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
-
-In case you feel like you've made a valuable contribution, but you don't know how to write or run tests for it, or how to generate the documentation: don't let this discourage you from making the pull request; we can help you! Just go ahead and submit the pull request, but keep in mind that you might be asked to append additional commits to your pull request.
+In case you feel like you've made a valuable contribution, but you don't know
+how to write or run tests for it, or how to generate the documentation: don't
+let this discourage you from making the pull request; we can help you! Just go
+ahead and submit an issue and ask your questions.
 
 ## You want to make a new release of the code base
 
 To create a release you need write permission on the repository.
 
-1. Check the author list in [`CITATION.cff`](CITATION.cff)
-1. Bump the version using `bump-my-version bump <major|minor|patch>`. For example, `bump-my-version bump major` will increase major version numbers everywhere it's needed (code, meta, etc.) in the repo. Alternatively the version can be manually changed in diffwofost/__init__.py, pyproject.toml, CITATION.cffand docs/conf.py (and other places it was possibly added).
-
-1. Go to the [GitHub release page](https://github.com/WUR-AI/diffwofost/releases)
-1. Press draft a new release button
-1. Fill version, title and description field
-1. Press the Publish Release button
-<!--
-For projects that automatically publish to PyPI using a release or publish workflow, something like the following could be useful to add (make sure to replace the names and links):
-
-1. Wait until [PyPi publish workflow](https://github.com/WUR-AI/diffwofost/actions/workflows/publish.yml) has completed
-1. Verify new release is on [PyPi](https://pypi.org/project/matchms/#history)
--->
-<!--
-For projects that also build conda packages, e.g. on conda-forge or Bioconda, something like the following could be useful to add (example taken from matchms, make sure to replace the names and links):
-
-1. Wait until new release is also on Bioconda (https://anaconda.org/bioconda/diffwofost) via a automaticly created PR on [bioconda recipes repo](https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Apr+is%3Aopen+diffwofost)
-1. Test diffwofost from bioconda by manually running [Conda verify](https://github.com/WUR-AI/diffwofost/actions/workflows/conda_verify.yml) workflow
--->
-
-Also a Zenodo entry will be made for the release with its own DOI.
+1. Check the author list in `CITATION.cff`in
+   the root of the repository.
+2. Bump the version. The version can be manually changed in `pyproject.toml` in
+   the root of the repository. Follow [Semantic Versioning](https://semver.org/)
+   principles. Also, update `__version__` variable in `diffwofost/__init__.py` to the
+   same version.
+3. Go to the [GitHub release
+   page](https://github.com/WUR-AI/diffwofost/releases). Press draft a new
+   release button. Fill version, title and description field. Press the Publish
+   Release button. For this package, the zenodo integration is enabled, so a new
+   DOI will be created automatically.
+4. This software automatically publish to PyPI using a release or publish
+   workflow. Wait until [PyPi publish
+   workflow](https://github.com/WUR-AI/diffwofost/actions/workflows/python-publish.yml)
+   has completed and verify new release is on
+   [PyPi](https://pypi.org/project/matchms/#history)