add logos, modify doc generation/aesthetics

.gitignore

@@ -9,3 +9,4 @@ __pycache__/
 .coverage
 junk/
 .*.swp
+.DS_Store

.zenodo.json

@@ -0,0 +1,13 @@
+{
+  "title": "Chmpy: A python library for computational chemistry",
+  "authors": [
+    {
+      "name": "Spackman, Peter R.",
+      "affiliation": "Curtin University"
+    },
+  ],
+  "description": "Molecules, crystals, promolecule and Hirshfeld surfaces using python.",
+  "license": "GPLv3",
+  "keywords": ["chemistry", "isosurface"]
+}
+

README.md

@@ -1,27 +1,43 @@
-# chmpy
-
 ![CI](https://github.com/peterspackman/chmpy/workflows/CI/badge.svg)
 [![DOI](https://zenodo.org/badge/211644812.svg)](https://zenodo.org/doi/10.5281/zenodo.10697512)
 
 
+<!-- PROJECT LOGO -->
+<br />
+<div align="center">
+  <a href="https://github.com/peterspackman/chmpy">
+    <img src="docs/assets/chmpy_logo.png" alt="Logo" height="80" width="80">
+  </a>
+
+  <h3 align="center">chmpy</h3>
+
+  <p align="center">
+    A library for computational chemistry in python.
+    <br />
+    <a href="https://peterspackman.github.io/chmpy"><strong>Documentation»</strong></a>
+    <br />
+    <a href="https://github.com/peterspackman/chmpy/issues">Report a bug</a>
+    ·
+    <a href="https://github.com/peterspackman/chmpy/issues">Request a new feature</a>
+  </p>
+</div>
 
-A library for computational chemistry in python. Featuring support for
-molecules, crystals, Hirshfeld & promolecule density isosurfaces,
-spherical harmonic shape descriptors and much more...
+chmpy supports handling molecules, crystals, Hirshfeld & promolecule 
+density isosurfaces, spherical harmonic shape descriptors and much more...
 
 ## Installation
 
 Basic installation can be done through the python package manager `pip`:
 
-```bash
+``` bash
 pip install chmpy
 # or to install directly from GitHub:
 pip install git+https://github.com/peterspackman/chmpy.git
 ```
 
 For development or modifications, install locally using pip:
 
-```bash
+``` bash
 pip install -e .
 ```
 
@@ -49,7 +65,7 @@ python.
 Loading a crystal structure from a CIF (`.cif`) or SHELX (`.res`)
 file, or a molecule from an XMOL (`.xyz`) file is straightforward:
 
-```python
+``` python
 from chmpy import Crystal, Molecule
 c = Crystal.load("tests/acetic_acid.cif")
 print(c)
@@ -70,7 +86,7 @@ Generation of surfaces with the default settings can be done with
 minimal hassle, simply by using the corresponding members of the Crystal
 class:
 
-```python
+``` python
 c = Crystal.load("tests/test_files/acetic_acid.cif")
 # This will generate a high resolution surface
 # for each symmetry unique molecule in the crystal
@@ -88,6 +104,11 @@ save_mesh(surfaces[0], "acetic_acid.ply")
 
 The resulting surface should look something like this when visualized:
 
-![acetic_acid.png](src/chmpy/tests/acetic_acid.png)
+<br />
+<div align="center">
+    <img src="src/chmpy/tests/acetic_acid.png" alt="Acetic acid" height=200>
+</div>
+
+
 
 

docs/index.md

@@ -21,51 +21,49 @@ how to represent crystal structures, molecules etc. and evaluate
 scientifically relevant information quickly and efficiently using
 python.
 
-## At a glance
-
-### Crystal structures and molecules
+## Crystal structures and molecules
 Loading a crystal structure from a CIF (`.cif`) or SHELX (``.res``)
 file, or a molecule from an XMOL (``.xyz``) file is straightforward:
 
-``` python
->>> from chmpy import Crystal, Molecule
->>> c = Crystal.load("tests/test_files/acetic_acid.cif")
->>> c
-<Crystal C2H4O2 Pna2_1>
+``` py title="chmpy_basics.py"
+from chmpy import Crystal, Molecule
+c = Crystal.load("tests/test_files/acetic_acid.cif")
+c
+# <Crystal C2H4O2 Pna2_1>
 
 # Calculate the unique molecules in this crystal
->>> c.symmetry_unique_molecules()
-[<Molecule: C2H4O2(2.12,1.15,0.97)>]
+c.symmetry_unique_molecules()
+# [<Molecule: C2H4O2(2.12,1.15,0.97)>]
 
->>> m = Molecule.load("tests/test_files/water.xyz")
->>> m
-<Molecule: H2O(-0.67,-0.00,0.01)>
+m = Molecule.load("tests/test_files/water.xyz")
+m
+# <Molecule: H2O(-0.67,-0.00,0.01)>
 ```
 
 
-### Hirshfeld and promolecule density isosurfaces
+## Hirshfeld and promolecule density isosurfaces
 
 Generation of surfaces with the default settings can be done with
 minimal hassle, simply by using the corresponding members of the ``Crystal``
 class:
 
 ``` python
->>> c = Crystal.load("tests/test_files/acetic_acid.cif")
+c = Crystal.load("tests/test_files/acetic_acid.cif")
 
 # This will generate a high resolution surface
 # for each symmetry unique molecule in the crystal
->>> surfaces = c.hirshfeld_surfaces()
->>> surfaces
-[<trimesh.Trimesh(vertices.shape=(3598, 3), faces.shape=(7192, 3))>]
+surfaces = c.hirshfeld_surfaces()
+surfaces
+# [<trimesh.Trimesh(vertices.shape=(3598, 3), faces.shape=(7192, 3))>]
 
 # We can generate lower resolution surfaces with the separation parameter
->>> surfaces = c.hirshfeld_surfaces(separation=0.5)
->>> surfaces
-[<trimesh.Trimesh(vertices.shape=(584, 3), faces.shape=(1164, 3))>]
+surfaces = c.hirshfeld_surfaces(separation=0.5)
+surfaces
+# [<trimesh.Trimesh(vertices.shape=(584, 3), faces.shape=(1164, 3))>]
 
 # Surfaces can be saved via trimesh
->>> surfaces[0].export("acetic_acid_trimesh.ply", "ply")
+surfaces[0].export("acetic_acid_trimesh.ply", "ply")
 # or a utility function provided in chmpy
->>> from chmpy.util.mesh import save_mesh
->>> save_mesh(surfaces[0], "acetic_acid.ply")
+from chmpy.util.mesh import save_mesh
+save_mesh(surfaces[0], "acetic_acid.ply")
 ```

mkdocs.yml

@@ -5,9 +5,16 @@ repo_name: peterspackman/chmpy
 
 theme:
     name: material
+    logo: assets/chmpy_logo_small_no_text_dark.png
+    features:
+        - content.code.copy
     palette:
-        primary: light blue
+        primary: blue grey
         scheme: preference
+    font:
+        text: Helvetica
+        code: Noto Sans Mono
+
 extra:
     social:
         - icon: fontawesome/brands/github
@@ -24,7 +31,13 @@ plugins:
 
 
 markdown_extensions:
-    - codehilite
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
 
 nav:
     - Home: index.md