Publish Docs on RTD (#24)

* Add docs/requirements.txt 
* Add NeuroTS to dependencies
* Add badges

Co-authored-by: Stanislav Schmidt <stanislav.schmidt@epfl.ch>

Author: FrancescoCasalegno

.readthedocs.yaml

@@ -0,0 +1,20 @@
+version: 2
+
+formats: []
+
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+
+build:
+    image: latest
+
+python:
+  version: "3.8"
+  install:
+    - method: pip
+      path: .
+
+    # inspired by: https://github.com/pyg-team/pytorch_geometric/blob/master/docs/requirements.txt
+    - requirements: docs/requirements.txt
+  system_packages: true

README.md

@@ -2,6 +2,48 @@
 MorphoClass is a toolbox for neuronal morphologies processing and
 classification using machine learning.
 
+<table>
+    <tr>
+        <td>Documentation</td>
+        <td>
+            <a href="https://morphoclass.readthedocs.io/en/latest/">
+                <img src="https://readthedocs.org/projects/morphoclass/badge/?version=latest" alt="Docs">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>License</td>
+        <td>
+            <a href="https://github.com/BlueBrain/morphoclass/blob/master/LICENSE.txt">
+                <img src="https://img.shields.io/github/license/BlueBrain/morphoclass" alt="License" />
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Static Typing</td>
+        <td>
+            <a href="http://mypy-lang.org/">
+                <img src="http://www.mypy-lang.org/static/mypy_badge.svg" alt="Mypy">
+            </a>
+        </td>
+    </tr>
+    <tr>
+        <td>Code Style</td>
+        <td>
+            <a href="https://github.com/psf/black">
+                <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Black">
+            </a>
+            <a href="https://pycqa.github.io/isort/">
+                <img src="https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336" alt="Isort">
+            </a>
+            <a href="https://flake8.pycqa.org/">
+                <img src="https://img.shields.io/badge/PEP8-flake8-informational" alt="Pydocstyle">
+            </a>
+        </td>
+    </tr>
+</table>
+
+
 # Installation
 Clone the repository and set up the virtual environment
 ```sh

docs/requirements.txt

@@ -0,0 +1,9 @@
+https://download.pytorch.org/whl/cpu/torch-1.11.0%2Bcpu-cp38-cp38-linux_x86_64.whl
+https://data.pyg.org/whl/torch-1.11.0%2Bcpu/torch_scatter-2.0.9-cp38-cp38-linux_x86_64.whl
+https://data.pyg.org/whl/torch-1.11.0%2Bcpu/torch_sparse-0.6.13-cp38-cp38-linux_x86_64.whl
+https://data.pyg.org/whl/torch-1.11.0%2Bcpu/torch_cluster-1.6.0-cp38-cp38-linux_x86_64.whl
+https://data.pyg.org/whl/torch-1.11.0%2Bcpu/torch_spline_conv-1.2.1-cp38-cp38-linux_x86_64.whl
+torch-geometric==1.7.2
+Sphinx==3.5.4
+sphinx-rtd-theme==1.0.0
+sphinx-bluebrain-theme==0.2.9

docs/source/sections/using_gnn.rst

@@ -74,7 +74,7 @@ is ``mc.models.ManNet``. It can be trained on the data loaded above in a few lin
     import torch.optim
     from tqdm import tqdm
 
-    import morphoclass as dm
+    import morphoclass as mc
     import morphoclass.models
     import morphoclass.training
     import morphoclass.utils

requirements.txt

@@ -14,6 +14,7 @@ morphio==3.3.3
 morphology-workflows==0.2.0
 networkx==2.5
 neurom==3.1.0
+neurots==3.1.1
 numpy==1.20.3
 pandas==1.3.4
 plotly==5.4.0

setup.cfg

@@ -38,6 +38,7 @@ install_requires =
     morphology-workflows>=0.2.0
     networkx
     neurom>=3
+    neurots
     numpy
     pandas
     plotly