Provide a mechanism to download data files for an example

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
 --------------------------------------------------------------------------

docs/src/conf.py

@@ -20,10 +20,6 @@
     "Atomistic cookbook team"
 )
 
-htmlhelp_basename = "Atomistic cookbook"
-html_theme = "furo"
-
-
 intersphinx_mapping = {
     "ase": ("https://wiki.fysik.dtu.dk/ase/", None),
     "metatensor": ("https://lab-cosmo.github.io/metatensor/latest/", None),
@@ -35,11 +31,14 @@
 }
 
 html_js_files = [
-    (
+    (  # plausible.io tracking
         "https://plausible.io/js/script.js",
         {"data-domain": "lab-cosmo.github.io/atomistic-cookbook", "defer": "defer"},
     ),
 ]
 
+htmlhelp_basename = "Atomistic cookbook"
+html_theme = "furo"
 html_static_path = [os.path.join("..", "_static")]
 html_favicon = "../_static/cookbook-icon.png"
+html_logo = "../_static/cookbook-icon.svg"

examples/path-integrals/in.lmp → examples/path-integrals/data/in.lmp

@@ -6,7 +6,7 @@ bond_style      class2
 angle_style     harmonic
 kspace_style	pppm/tip4p 0.0001
 
-read_data	water_32_data.lmp
+read_data	data/water_32_data.lmp
 pair_coeff  * * 0 0
 pair_coeff  1  1  0.000295147 5.96946
 

examples/path-integrals/input_piglet.xml → examples/path-integrals/data/input_piglet.xml

@@ -14,7 +14,7 @@
   </ffsocket>
   <system>
     <initialize nbeads='8'>
-      <file mode='pdb'> water_32.pdb </file>
+      <file mode='pdb'> data/water_32.pdb </file>
       <velocities mode='thermal' units='kelvin'> 298 </velocities>
     </initialize>
     <forces>

examples/path-integrals/input_pimd.xml → examples/path-integrals/data/input_pimd.xml

@@ -14,7 +14,7 @@
   </ffsocket>
   <system>
     <initialize nbeads='8'>
-      <file mode='pdb' units='angstrom'> water_32.pdb </file>
+      <file mode='pdb' units='angstrom'> data/water_32.pdb </file>
       <velocities mode='thermal' units='kelvin'> 298 </velocities>
     </initialize>
     <forces>