Updates to documentation.

.readthedocs.yaml

@@ -17,7 +17,7 @@ build:
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
   builder: html
-  configuration: docs/conf.py
+  configuration: docs/source/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"

TODO.org

@@ -6,6 +6,26 @@
 # .kdb files should be debrujin graph databases
 # The final prototype would be .bgzf format from biopython
 
+* 8/8/24 Taking Notes on Xuejiang Xiong Mouse model IBD study
+
+** SRA Accession id
+
+*** SRA051354
+SRA051354
+*** 
+** What is the purpose of this study?
+
+The goal of this study is to recreate a mouse model of the disease called "Irritable Bowel Disease", using agents that induce responses and irritation to the point where the induced condition and the condition known as "irritable bowel disorder" are functionally similar.
+
+The mice are NOD (non-obese diabetic) and suceptible to germs. They are colonized with 8 symbiotic bowel microbes, known as Altered Schaedler flora (ASF).
+
+Samples taken from the bowels of these mice reveal the effect of the irritant/inducer agent on the gut microflora as measurable by Illumina High-throughput sequencing (HTS). Specifically, transcriptional libraries are prepared following RiboMinus treatment, to enrich for mRNAs and other non-rRNAs.
+
+The mRNA libraries were processed on a Genome Analyzer IIx in this study. The SRA accession id for the single-end fastq datasets, bulk RNA for metatranscriptomics and assembly, is SRA051354.
+
+The study used 
+
+
 * 8/3/24 Kolmogorov complexity and Generalized Suffix Arrays
 
 ** Suffix array

docs/conf.py.old

@@ -0,0 +1,38 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'kmerdb'
+copyright = '2024, Matt Ralston'
+author = 'Matt Ralston'
+release = '0.8.6'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    #'sphinx.ext.duration',
+    #'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+#    'sphinx_rtd_theme',
+]
+
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+html_static_path = ['_static']

docs/index.rst.old

@@ -1,5 +1,4 @@
 
-
 kmerdb
 ===================
 
@@ -70,17 +69,18 @@ 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
 
 Created by Matthew Ralston - [Scientist, Programmer, Musician](http://matthewralston.github.io) - [Email](mailto:[email protected])
 
 Distributed under the Apache license. See `LICENSE.txt` for the copy distributed with this project. Open source software is not for everyone, and im the author and maintainer. cheers, on me. You may use and distribute this software, gratis, so long as the original LICENSE.txt is distributed along with the software. This software is distributed AS IS and provides no warranties of any kind.
 
-```
+::
    Copyright 2020 Matthew Ralston
 
    Licensed under the Apache License, Version 2.0 (the "License");
@@ -94,7 +94,7 @@ Distributed under the Apache license. See `LICENSE.txt` for the copy distributed
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
-```
+
 
 ## Contributing
 
@@ -113,3 +113,114 @@ Thank you to the authors of kPAL and Jellyfish for the inspiration and bit shift
 The intention is that more developers would want to add functionality to the codebase or even just utilize things downstream, but to build out directly with numpy and scipy/scikit as needed to suggest the basic infrastructure for the ML problems and modeling approaches that could be applied to such datasets. This project began under GPL v3.0 and was relicensed with Apache v2. Hopefully this project could gain some interest. I have so much fun working on this project. There's more to it than meets the eye. I'm working on a preprint, and the draft is included in some of the latest versions of the codebase, specifically .Rmd files.
 
 More on the flip-side. It's so complex with technology these days...
+
+.. kmerdb documentation master file, created by
+   sphinx-quickstart on Thu Aug  8 00:32:04 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+kmerdb documentation
+====================
+
+Add your content using 'reStructuredText' syntax. See the
+`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
+documentation for details.
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+.. automodule:: kmerdb.fileutil
+   :members:
+
+.. automodule:: kmerdb.graph
+   :members:
+
+.. automodule:: kmerdb.parse
+   :members:
+
+.. automodule:: kmerdb.kmer
+   :members:
+
+.. automodule:: kmerdb.util
+   :members:
+
+.. automodule:: kmerdb.index
+   :members:
+
+.. automodule:: kmerdb.logger
+   :members:
+
+.. automodule:: kmerdb.distance
+   :members:
+
+.. automodule:: kmerdb.python_distances
+   :members:
+
+.. automodule:: kmerdb.probability
+   :members:
+
+.. autoclass:: kmerdb.fileutil
+   :members:
+
+.. autoclass:: kmerdb.graph
+   :members:
+
+.. autoclass:: kmerdb.parse
+   :members:
+
+.. autoclass:: kmerdb.kmer
+   :members:
+
+.. autoclass:: kmerdb.util
+   :members:
+
+.. autoclass:: kmerdb.index
+   :members:
+
+.. autoclass:: kmerdb.logger
+   :members:
+
+.. autoclass:: kmerdb.distance
+   :members:
+
+.. autoclass:: kmerdb.python_distances
+   :members:
+
+.. autoclass:: kmerdb.probability
+   :members:
+
+.. autoexception:: kmerdb.fileutil
+   :members:
+
+.. autoexception:: kmerdb.graph
+   :members:
+
+.. autoexception:: kmerdb.parse
+   :members:
+
+.. autoexception:: kmerdb.kmer
+   :members:
+
+.. autoexception:: kmerdb.util
+   :members:
+
+.. autoexception:: kmerdb.index
+   :members:
+
+.. autoexception:: kmerdb.logger
+   :members:
+
+.. autoexception:: kmerdb.distance
+   :members:
+
+.. autoexception:: kmerdb.python_distances
+   :members:
+
+.. autoexception:: kmerdb.probability
+   :members:
+
+
+
+

docs/conf.py → docs/source/conf.py

@@ -1,8 +1,3 @@
-#!/bin/env python3
-
-import sys
-import os
-
 # Configuration file for the Sphinx documentation builder.
 #
 # For the full list of built-in configuration values, see the documentation:
@@ -12,31 +7,13 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'kmerdb'
-
+copyright = '2024, Matt Ralston'
+author = 'Matt Ralston'
 release = '0.8.6'
-author = 'Matt Ralston <[email protected]>, and the kmerdb project contributors'
-copyright = '2020, Matt Ralston <[email protected]>'
-language = 'en'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-
-
-# -- Options for HTML output -------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
-
-html_theme = 'alabaster'
-html_static_path = ['_static']
-
-
-#html_theme = 'sphinx_rtd_theme'
-#html_context = {}
-
-
-
-
-
 extensions = [
     #'sphinx.ext.duration',
     #'sphinx.ext.doctest',
@@ -48,25 +25,14 @@
 #    'sphinx_rtd_theme',
 ]
 
+
 templates_path = ['_templates']
-source_suffix = '.rst'
 exclude_patterns = []
-locale_dirs = ['locale/']
-gettext_compact = False
 
-master_doc = 'index'
-suppress_warnings = ['image.nonlocal_uri']
-pygments_style = 'default'
 
-if sys.version_info < (3, 0):
-    tags.add("python2")
-else:
-    tags.add("python3")
-
-intersphinx_mapping = {
-    'numpy': ('https://numpy.readthedocs.io/en/latest', None),
-    'rtd': ('https://docs.readthedocs.io/en/stable/', None),
-    'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
-}
 
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
+html_theme = 'alabaster'
+html_static_path = ['_static']