Clean up the main page, and remove useless SG logs (#92)

* Removes sg timings from the output

* Reorganized main page to make it clearer

Also removed unnecessary links to autogenerated rst files to further
clean up the sitemap.

Author: ceriottm

CONTRIBUTING.rst

@@ -132,8 +132,6 @@ Support
 If you still have problems adding your example to the repository, please feel
 free to contact one of the developers, e.g.
 
-`@agoscinski (Alexander Goscinski) <alexander.goscinski@epfl.ch>`_
-
 `@davidetisi (Davide Tisi) <davide.tisi@epfl.ch>`_
 
 Code of Conduct

INSTALLING.rst

@@ -0,0 +1,42 @@
+Installing a recipe
+===================
+
+The main repository contains the source files of all recipes, but you 
+should only fetch the entire repository if you plan on contributing 
+one (see also  <CONTRIBUTING.rst>`_). If you are interested in learning
+the techniques discussed in a specific recipe, this is not recommended,
+as you will also have to understand the build mechanism for the 
+website.
+
+.. marker-install-start
+
+Each recipe can be viewed online as an interactive HTML page, but 
+can also be downloaded as a stand-alone ``.py`` script, or a  
+``.ipynb`` Jupyter notebook. 
+To simplify setting up an environment that contains all the dependencies
+needed for each recipe, you can also download an ``environment.yml`` file 
+that you can use with conda to create a custom environment to run the example.
+If you have never used conda before, you may want to read this
+`beginners guide 
+<https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+
+.. 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>
+
+You can then execute the script from the command line, or open the
+notebook in Jupyter lab.  Additional data needed for each example is usually 
+either downloaded dynamically, or can be found in a ``data`` folder for each 
+example, or downloaded as a ``data.zip`` file at the end of each recipe in
+the website. In the latter case, don't forget to unzip the file in the 
+same folder as the ``.py`` or ``.ipynb`` files for the example. 
+
+.. marker-install-end
+
+
+
+

README.rst

@@ -1,13 +1,13 @@
 Atomistic Cookbook
 ==================
 
-The source code for the Atomistic Cookbook is maintained
-as a GitHub pages site.
-The home page is accessible at https://atomistic-cookbook.org
+This repository contains the source code for the Atomistic Cookbook,
+that is automatically compiled and deployed as a GitHub pages site,
+accessible at https://atomistic-cookbook.org
 
 .. marker-intro-start
 
-This cookbook contains recipes for atomic-scale modelling for materials and
+The 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
@@ -18,9 +18,17 @@ 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.
 
+You can view the recipes online, compiled as webpages containing explanations,
+code snippets, plots and interactive viewers based on
+`chemiscope <https://chemiscope.org>`_. However, it is also possible (and
+hopefully simple) to download scripts, and `conda environments
+<https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_,
+to run the recipe on your computer, and that you can use as a starting point to
+adapt them to your own use case.
+
 .. marker-intro-end
 
-Contributors
+Contributing
 ------------
 
 If you want contribute an example, recipe or tutorial that combines multiple software

docs/src/conf.py

@@ -45,6 +45,9 @@
 
 htmlhelp_basename = "The Atomistic Cookbook"
 html_theme = "furo"
+html_theme_options = {
+    "top_of_page_buttons": [],
+}
 html_static_path = ["_static"]
 html_favicon = "_static/cookbook-icon.png"
 html_logo = "_static/cookbook-icon.svg"

docs/src/downloading.rst

@@ -0,0 +1,6 @@
+Downloading and running the recipes
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. include:: ../../INSTALLING.rst
+   :start-after: marker-install-start
+   :end-before: marker-install-end

docs/src/index.rst

@@ -5,29 +5,6 @@ The Atomistic Cookbook
    :start-after: marker-intro-start
    :end-before: marker-intro-end
 
-Downloading and running the recipes
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Each recipe can be viewed online as an interactive HTML page, but 
-can also be downloaded as a stand-alone ``.py`` script of 
-``.ipynb`` Jupyter notebook. 
-To simplify setting up an environment that contains all the dependencies
-needed for each recipe, you can also download an ``environment.yml`` file 
-that you can use with conda to create a custom environment to run the 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>
-
-Additional data needed for each example is usually either downloaded
-dynamically, or can be found in a ``data`` folder for each example,
-or downloaded as a ``data.zip`` file at the end of each recipe in
-the website.
-
 Table of contents
 ~~~~~~~~~~~~~~~~~
 
@@ -37,6 +14,7 @@ Table of contents
    topics/index
    software/index
    all-examples
+   downloading
    contributing
 
 Recipe of the day

src/generate-gallery.py

@@ -40,7 +40,7 @@ def __init__(self, example):
             "filename_pattern": ".*",
             "examples_dirs": os.path.join(ROOT, example),
             "gallery_dirs": gallery_dir,
-            "min_reported_time": 60,
+            "write_computation_times": False,
             "copyfile_regex": r".*\.(sh|xyz|cp2k|yml|png|zip)",
             "matplotlib_animations": True,
             "within_subsection_order": "FileNameSortKey",