Merge branch 'main' into feat/clean

.github/workflows/lint.yml

@@ -18,7 +18,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.12"
+        python-version: "3.11"
 
     - name: install dependencies
       run: pip install nox

CONTRIBUTING.rst

@@ -34,13 +34,20 @@ following files inside:
 - as many Python files as you want, each one will be converted to a separate
   HTML page.
 
+Keep in mind that sphinx-gallery will make it easy to download a Python file and
+the notebook generated from it, but it won't give direct access to additional
+files. If your example needs such data files, there are a few options available:
+
+- (preferred) have the data file stored in a publicly accessible location, e.g.
+  a Zotero record, and download the data file from the script
+- if the data files are small (few 10s of Kb) you may also include them in a
+  ``data/`` folder within the example folder. A zip file will be generated that
+  can be downloaded from the example page.
+
 .. _sphinx-gallery: https://sphinx-gallery.github.io/
 .. _RestructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
 .. _conda: https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#create-env-file-manually
 
-Finally, you'll need to add your example to the list so it is automatically
-build on CI. The list is in the ``.github/workflows/docs.yml`` file, near the
-``example-name:`` section.
 
 Converting a Jupyter notebook to a sphinx-gallery compatible Python script
 --------------------------------------------------------------------------
@@ -106,6 +113,6 @@ free to contact one of the people
 Code of Conduct
 ---------------
 
-Please note that the COSMO cookbook project is released with a `Contributor Code
-of Conduct <CONDUCT.md>`_. By contributing to this project you agree to abide by
-its terms.
+Please note that this project is released with a
+`Contributor Code of Conduct <CONDUCT.md>`_.
+By contributing to this project you agree to abide by its terms.

README.rst

@@ -1,17 +1,22 @@
-COSMO Software Cookbook
-=======================
+Atomistic Cookbook
+==================
 
-The source code for the COSMO cookbook is maintained as a GitHub pages site. The home
-page is accessible at https://lab-cosmo.github.io/software-cookbook/latest.
+The source code for the Atomistic Cookbook is maintained
+as a GitHub pages site.
+The home page is accessible at https://lab-cosmo.github.io/atomistic-cookbook.
 
 .. marker-intro-start
 
-The COSMO cookbook contains recipes for atomic-scale modelling for materials and
-molecules, with a particular focus on machine learning and statistical sampling methods.
-Rather than focusing on the usage of a specific package (see the `COSMO github page
-<https://github.com/lab-cosmo>`_ for a list of available tools, and their
-documentations) this cookbook provides concrete examples of the solution of modeling
-problems using a combination of the various tools.
+This cookbook contains recipes for atomic-scale modelling for materials and
+molecules, with a particular focus on machine learning and statistical
+sampling methods.
+Most of the examples rely heavily on software developed by the laboratory of
+computational science and modeling (COSMO, see its `github page
+<https://github.com/lab-cosmo>`_) but the cookbook is open for recipes using
+all types of modeling tools and techniques.
+Rather than focusing on the usage of a specific package, this cookbook provides
+concrete examples of the solution of modeling problems, often using a combination
+of several tools.
 
 .. marker-intro-end
 

docs/src/.gitignore

@@ -1,2 +1 @@
 sg_execution_times.rst
-index.rst

docs/src/analysis.rst

@@ -0,0 +1,13 @@
+Analysis and post-processing
+============================
+
+This section contains recipes that analyze the output of a simulation,
+for analysis or visualization purposes.
+
+.. toctree::
+   :caption: Recipes
+   :maxdepth: 1
+
+   examples/gaas-map/gaas-map
+   examples/lpr/lpr
+   examples/roy-gch/roy-gch