added pages

Author: simongravelle

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "countoscope"]
 	path = countoscope
-	url = git@github.com:Countoscope/countoscope.git
+	url = https://github.com/Countoscope/countoscope.git

README.rst

@@ -1,20 +1,19 @@
 Countoscope documentation
 =========================
 
-
 How to
 ------
 
-Close the repository by typing in a terminal:
+Close the repository with its submodules by typing in a terminal:
 
 .. code-block:: bash
 
-    git clone https://github.com/Countoscope/countoscope.github.io.git
+    git clone https://github.com/Countoscope/countoscope.github.io.git --recurse-submodules
 
 To build the documentation localy, go to the docs/ folder and type:
 
 .. code-block:: bash
 
     make html
 
-The generated documentation can be accessed from the docs/build folder.
+The generated documentation can be accessed from the docs/build/ folder.

docs/source/conf.py

@@ -1,11 +1,21 @@
+#!/usr/bin/env python
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+#
+# Copyright (c) 2024 Authors and contributors
+# (see the AUTHORS.rst file for the full list of names)
+#
+# Released under MIT Licence
+#
 # Configuration file for the Sphinx documentation builder.
 
 project = 'Countoscope'
-copyright = '2024, Mackay et al.'
-author = 'Mackay et al.'
+copyright = 'MIT Licence'
+author = 'see the AUTHORS.rst fil'
 release = '0.0.1'
 
-extensions = []
+extensions = [
+    'sphinx.ext.autodoc',
+]
 
 templates_path = ['_templates']
 exclude_patterns = []

docs/source/index.rst

@@ -11,3 +11,13 @@ Indices and tables
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   modules/TRAJECTORY
+   modules/BOX
+   modules/SORTING
+   modules/COUNTOSCOPE
+   modules/UTILITIES

docs/source/modules/BOX.rst

@@ -0,0 +1,7 @@
+Box
+===
+
+.. automodule:: countoscope.Box
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/modules/COUNTOSCOPE.rst

@@ -0,0 +1,7 @@
+Countoscope
+===========
+
+.. automodule:: countoscope.Countoscope
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/modules/SORTING.rst

@@ -0,0 +1,7 @@
+Sorting
+=======
+
+.. automodule:: countoscope.Sorting
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/modules/TRAJECTORY.rst

@@ -0,0 +1,7 @@
+Trajectory
+==========
+
+.. automodule:: countoscope.Trajectory
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/source/modules/UTILITIES.rst

@@ -0,0 +1,7 @@
+Utilities
+=========
+
+.. automodule:: countoscope.util
+    :members:
+    :undoc-members:
+    :show-inheritance: