Revisiting sphinx-autodoc extensions.

.readthedocs.yml

@@ -0,0 +1,39 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: requirements-dev.txt
+
+

docs/index.rst

@@ -69,9 +69,10 @@ IUPAC residues (ATCG+RYSWKM+BDHV) are kept throughout the k-mer counting. But no
 ## Development
 
 
-```bash
-python setup.py test
-```
+::
+
+  python setup.py test
+
 
 ## License
 
@@ -121,14 +122,116 @@ More on the flip-side. It's so complex with technology these days...
 kmerdb documentation
 ====================
 
-Add your content using ``reStructuredText`` syntax. See the
+Add your content using 'reStructuredText' syntax. See the
 `reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
 documentation for details.
 
 
 .. toctree::
-
-   api
    :maxdepth: 2
    :caption: Contents:
 
+.. automodule:: fileutil
+   :members:
+
+.. automodule:: graph
+   :members:
+
+.. automodule:: parse
+   :members:
+
+.. automodule:: seqparser
+   :members:
+
+.. automodule:: kmer
+   :members:
+
+.. automodule:: util
+   :members:
+
+.. automodule:: index
+   :members:
+
+.. automodule:: logger
+   :members:
+
+.. automodule:: distance
+   :members:
+
+.. automodule:: python_distances
+   :members:
+
+.. automodule:: probability
+   :members:
+
+.. autoclass:: fileutil
+   :members:
+
+.. autoclass:: graph
+   :members:
+
+.. autoclass:: parse
+   :members:
+
+.. autoclass:: seqparser
+   :members:
+
+.. autoclass:: kmer
+   :members:
+
+.. autoclass:: util
+   :members:
+
+.. autoclass:: index
+   :members:
+
+.. autoclass:: logger
+   :members:
+
+.. autoclass:: distance
+   :members:
+
+.. autoclass:: python_distances
+   :members:
+
+.. autoclass:: probability
+   :members:
+
+.. autoexception:: kmerdb
+   :members:
+
+.. autoexception:: fileutil
+   :members:
+
+.. autoexception:: graph
+   :members:
+
+.. autoexception:: parse
+   :members:
+
+.. autoexception:: seqparser
+   :members:
+
+.. autoexception:: kmer
+   :members:
+
+.. autoexception:: util
+   :members:
+
+.. autoexception:: index
+   :members:
+
+.. autoexception:: logger
+   :members:
+
+.. autoexception:: distance
+   :members:
+
+.. autoexception:: python_distances
+   :members:
+
+.. autoexception:: probability
+   :members:
+
+
+