diff --git a/.gitignore b/.gitignore index 90d6956..77c690b 100644 --- a/.gitignore +++ b/.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 \ No newline at end of file +output +!docs +docs/build \ No newline at end of file diff --git a/Jenkinsfile b/Jenkinsfile index 8e97804..fa5569a 100644 --- a/Jenkinsfile +++ b/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") { diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 0000000..d0c3cbf --- /dev/null +++ b/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) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 0000000..747ffb7 --- /dev/null +++ b/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 diff --git a/docs/source/bmlsa.rst b/docs/source/bmlsa.rst new file mode 100644 index 0000000..415748c --- /dev/null +++ b/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: diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 0000000..bba3af0 --- /dev/null +++ b/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"] diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 0000000..122e6df --- /dev/null +++ b/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` diff --git a/docs/source/modules.rst b/docs/source/modules.rst new file mode 100644 index 0000000..5b5c2ed --- /dev/null +++ b/docs/source/modules.rst @@ -0,0 +1,7 @@ +bmlsa +===== + +.. toctree:: + :maxdepth: 4 + + bmlsa diff --git a/src/bmlsa/aligner.py b/src/bmlsa/aligner.py index 70aadc0..060a085 100644 --- a/src/bmlsa/aligner.py +++ b/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 diff --git a/src/bmlsa/io.py b/src/bmlsa/io.py index 53b9c0d..4561b59 100644 --- a/src/bmlsa/io.py +++ b/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`