Added basic automatic documentation generation

.gitignore

@@ -212,4 +212,6 @@ pyrightconfig.json
 
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
-output
+output
+!docs
+docs/build

Jenkinsfile

@@ -21,13 +21,16 @@ pipeline {
         stage("build") {
             steps {
                 sh "python -m build"
+                sh 'sphinx-apidoc -o docs/source/ src/bmlsa'
+                sh 'make -C docs html'
+                publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html', reportFiles: 'index.html', reportName: 'BMLSA Docs', reportTitles: ''])
             }
         }
         stage("test installation") {
             steps {
                 sh "pip install dist/*.whl --force-reinstall"
                 sh "bmlsa -h"
-                sh "bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta /output/"
+                sh "bmlsa -I id -S sequence -B BLASTp tests/resources/SARS_CoV-2_genes.csv tests/resources/NC_045512_coding.fasta ./output/"
             }
         }
         stage("archive") {

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/bmlsa.rst

@@ -0,0 +1,53 @@
+bmlsa package
+=============
+
+Submodules
+----------
+
+bmlsa.aligner module
+--------------------
+
+.. automodule:: bmlsa.aligner
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bmlsa.cli module
+----------------
+
+.. automodule:: bmlsa.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bmlsa.datatypes module
+----------------------
+
+.. automodule:: bmlsa.datatypes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bmlsa.exceptions module
+-----------------------
+
+.. automodule:: bmlsa.exceptions
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+bmlsa.io module
+---------------
+
+.. automodule:: bmlsa.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: bmlsa
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/conf.py

@@ -0,0 +1,33 @@
+import os
+import sys
+
+# Configure system path
+
+sys.path.insert(0, os.path.abspath("../src/"))
+
+# 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 = "BMLSA"
+copyright = "2023, Harrison"
+author = "Harrison"
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["sphinx.ext.autodoc"]
+
+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/source/index.rst

@@ -0,0 +1,21 @@
+.. BMLSA documentation master file, created by
+   sphinx-quickstart on Fri Apr 28 13:04:16 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to BMLSA's documentation!
+=================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+   
+   modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/modules.rst

@@ -0,0 +1,7 @@
+bmlsa
+=====
+
+.. toctree::
+   :maxdepth: 4
+
+   bmlsa

src/bmlsa/aligner.py

@@ -27,10 +27,10 @@ def align_many_to_one_ssw(
     :param alignment_mode: The alignment mode to use. Either "local" or "global".
     :type alignment_mode: str
     :param substitution_matrix: The name of the substitution matrix available
-    in :module:`Bio.Align`, defaults to "BLOSUM62"
+        in :mod:`Bio.Align`, defaults to "BLOSUM62"
     :type substitution_matrix: str, optional
     :yield: Pairs of :obj:`bmlsa.datatypes.QuerySequence` objects where the first is
-    the original, and the second is the aligned version
+        the original, and the second is the aligned version
     :rtype: a generator of :obj:`bmlsa.datatypes.QuerySequence` objects
     """
     # TODO Consider using the built in "scoring" parameter

src/bmlsa/io.py

@@ -24,13 +24,13 @@ def queries_from_csv(
     :param name_header: The column title for the name of the sequence, defaults to None
     :type name_header: str, optional
     :param desc_header: The column title for the description of the sequence,
-    defaults to None
+        defaults to None
     :type desc_header: str, optional
     :param start_header: The column title for the start position of the sequence,
-    defaults to None
+        defaults to None
     :type start_header: str, optional
     :param end_header: The column title for the end position of the sequence,
-    defaults to None
+        defaults to None
     :type end_header: str, optional
     :yield: One :obj:`bmlsa.datatypes.QuerySequence` for each row
     :rtype: A generator that yields objects of :class:`bmlsa.datatypes.QuerySequence`