Infrastructure updates

docs/src/index.rst.in

@@ -6,6 +6,18 @@ COSMO Software Cookbook
    :end-before: marker-intro-end
 
 
+All the examples provide an ``environment.yml`` file that you can download and
+then use with conda to create a new environment with all the required
+dependencies for this example.
+
+.. code-block:: bash
+
+   # Pick a name for the environment and replace <environment-name> with it
+   conda env create --name <environment-name> --file environment.yml
+
+   # when you want to use the environment
+   conda env activate --name <environment-name>
+
 .. toctree::
    :caption: Table of Contents
    :maxdepth: 1

examples/batch-cp2k/reference-trajectory.py

@@ -2,7 +2,8 @@
 Batch run of CP2K calculations
 ==============================
 
-.. start-body
+:Authors: Matthias Kellner `@bananenpampe <https://github.com/bananenpampe/>`_,
+          Philip Loche `@PicoCentauri <https://github.com/PicoCentauri/>`_
 
 This is an example how to perform single point calculations based on list of structures
 using `CP2K <https://www.cp2k.org>`_ using its `reftraj functionality

examples/gaas-map/gaas-map.py

@@ -2,6 +2,9 @@
 PCA/PCovR Visualization for the rattled GaAs training dataset
 =============================================================
 
+:Authors: Michele Ceriotti `@ceriottm <https://github.com/ceriottm/>`_,
+          Giulio Imbalzano
+
 This example uses ``rascaline`` and ``metatensor`` to compute
 structural properties for the structures in a training for a ML model.
 These are then used with simple dimensionality reduction algorithms

examples/lode-linear/lode-linear.py

@@ -2,6 +2,9 @@
 LODE Tutorial
 =============
 
+:Authors: Philip Loche `@PicoCentauri <https://github.com/PicoCentauri/>`_,
+          Kevin Huguenin-Dumittan `@kvhuguenin <https://github.com/kvhuguenin>`_
+
 This tutorial explains how Long range equivariant descriptors can be constructed using
 rascaline and the resulting descriptors be used to construct a linear model with
 equisolve

examples/roy-gch/roy-gch.py

@@ -2,6 +2,8 @@
 Generalized Convex Hull construction for the polymorphs of ROY
 ==============================================================
 
+:Authors: Michele Ceriotti `@ceriottm <https://github.com/ceriottm/>`_
+
 This notebook analyzes the structures of 264 polymorphs of ROY, from
 `Beran et Al, Chemical Science
 (2022) <https://doi.org/10.1039/D1SC06074K>`__, comparing the

examples/sample-selection/sample-selection.py

@@ -2,7 +2,7 @@
 Sample and Feature Selection with FPS and CUR
 =============================================
 
-.. start-body
+:Authors: Davide Tisi `@DavideTisi <https://github.com/DavideTisi>`_
 
 In this tutorial we generate descriptors using rascaline, then select a subset
 of structures using both the farthest-point sampling (FPS) and CUR algorithms

generate-gallery.py

@@ -38,7 +38,7 @@ def __init__(self, example):
             "examples_dirs": os.path.join(HERE, example),
             "gallery_dirs": gallery_dir,
             "min_reported_time": 60,
-            "copyfile_regex": r".*\.(sh|xyz|cp2k)",
+            "copyfile_regex": r".*\.(sh|xyz|cp2k|yml)",
             "matplotlib_animations": True,
         }
 

noxfile.py

@@ -128,6 +128,30 @@ def build_docs(session):
 
                 output.write(f"   {path}\n")
 
+                # TODO: Explain
+                with open(file) as fd:
+                    content = fd.read()
+
+                if "Download Conda environment file" in content:
+                    # do not add the download link twice
+                    pass
+                else:
+                    lines = content.split("\n")
+                    with open(file, "w") as fd:
+                        for line in lines:
+                            if "sphx-glr-download-jupyter" in line:
+                                # add the new download link before
+                                fd.write(
+                                    """
+    .. container:: sphx-glr-download
+
+      :download:`Download Conda environment file: environment.yml <environment.yml>`
+"""
+                                )
+
+                            fd.write(line)
+                            fd.write("\n")
+
     session.run("sphinx-build", "-W", "-b", "html", "docs/src", "docs/build/html")