diff --git a/doc/Makefile b/doc/Makefile index 7abd1c5a..d0c3cbf1 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -1,83 +1,20 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = - -# Internal variables. -PAPEROPT_a4 = -D latex_paper_size=a4 -PAPEROPT_letter = -D latex_paper_size=letter -ALLSPHINXOPTS = -d build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source - -.PHONY: help clean html web pickle htmlhelp latex changes linkcheck - -help: - @echo "Please use \`make ' where is one of" - @echo " html to make standalone HTML files" - @echo " apidoc to run epydoc" - @echo " pickle to make pickle files" - @echo " json to make JSON files" - @echo " htmlhelp to make HTML files and a HTML help project" - @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" - @echo " changes to make an overview over all changed/added/deprecated items" - @echo " linkcheck to check all external links for integrity" - -clean: - -rm -rf docbuild/* - -html: - mkdir -p build/html build/doctrees - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) docbuild/html - @echo - @echo "Build finished. The HTML pages are in docbuild/html." - -apidoc: - mkdir -p build/html/apidoc - epydoc-2.6 --docformat restructuredtext ../lib/bx -o docbuild/html/apidoc - @echo - @echo "Epydoc finished. The pages are in docbuild/html/apidoc." - - -pickle: - mkdir -p build/pickle build/doctrees - $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) docbuild/pickle - @echo - @echo "Build finished; now you can process the pickle files." - -web: pickle - -json: - mkdir -p build/json build/doctrees - $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) docbuild/json - @echo - @echo "Build finished; now you can process the JSON files." - -htmlhelp: - mkdir -p build/htmlhelp build/doctrees - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) docbuild/htmlhelp - @echo - @echo "Build finished; now you can run HTML Help Workshop with the" \ - ".hhp project file in build/htmlhelp." - -latex: - mkdir -p build/latex build/doctrees - $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) docbuild/latex - @echo - @echo "Build finished; the LaTeX files are in build/latex." - @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ - "run these through (pdf)latex." - -changes: - mkdir -p build/changes build/doctrees - $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) docbuild/changes - @echo - @echo "The overview file is in build/changes." - -linkcheck: - mkdir -p build/linkcheck build/doctrees - $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) docbuild/linkcheck - @echo - @echo "Link check complete; look for any errors in the above output " \ - "or in build/linkcheck/output.txt." +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(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/doc/make.bat b/doc/make.bat new file mode 100644 index 00000000..dc1312ab --- /dev/null +++ b/doc/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/doc/requirements.txt b/doc/requirements.txt index 24ce15ab..d090a2ea 100644 --- a/doc/requirements.txt +++ b/doc/requirements.txt @@ -1 +1,3 @@ numpy +sphinx +sphinx-rtd-theme diff --git a/doc/source/conf.py b/doc/source/conf.py index 43935eff..b16bb3e9 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -1,194 +1,42 @@ +# Configuration file for the Sphinx documentation builder. # -# BxPython documentation build configuration file, created by -# sphinx-quickstart on Fri May 08 10:18:22 2009. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# The contents of this file are pickled, so don't put values in the namespace -# that aren't pickleable (module imports are okay, they're removed automatically). -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If your extensions are in another directory, add it here. If the directory -# is relative to the documentation root, use os.path.abspath to make it -# absolute, like shown here. -import bx +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html -# General configuration -# --------------------- +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ["sphinx.ext.autodoc", "sphinx.ext.doctest", "sphinx.ext.intersphinx"] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ["templates"] - -# The suffix of source filenames. -source_suffix = ".rst" - -# The encoding of source files. -# source_encoding = 'utf-8' - -# The master toctree document. -master_doc = "index" +import bx -# General information about the project. project = "bx-python" -copyright = "2017, James Taylor" - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. +copyright = "2005-2019, James Taylor; 2019-2023, Nicola Soranzo" +author = "James Taylor" version = bx.__version__ - -# The full version, including alpha/beta/rc tags. release = version -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -# today = '' -# Else, today_fmt is used as the format for a strftime call. -# today_fmt = '%B %d, %Y' - -# List of documents that shouldn't be included in the build. -# unused_docs = [] - -# List of directories, relative to source directory, that shouldn't be searched -# for source files. -exclude_trees = [] - -# The reST default role (used for this markup: `text`) to use for all documents. -# default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -# add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -# add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -# show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -# Options for HTML output -# ----------------------- - -# The style sheet to use for HTML and HTML Help pages. A file of that name -# must exist either in Sphinx' static/ path, or in one of the custom paths -# given in html_static_path. -html_style = "base.css" - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -# html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -# html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -# html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -# html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ["static"] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -# html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -# html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -html_index = "index.html" -html_sidebars = {"index": "indexsidebar.html"} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -##html_additional_pages = { -## 'index': 'index.html', -##} - -# If false, no module index is generated. -# html_use_modindex = True - -# If false, no index is generated. -# html_use_index = True - -# If true, the index is split into individual pages for each letter. -# html_split_index = False - -# If true, the reST sources are included in the HTML build as _sources/. -# html_copy_source = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -# html_use_opensearch = '' - -# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). -# html_file_suffix = '' - -# Output file base name for HTML help builder. -htmlhelp_basename = "bx-doc" - - -# Options for LaTeX output -# ------------------------ - -# The paper size ('letter' or 'a4'). -# latex_paper_size = 'letter' - -# The font size ('10pt', '11pt' or '12pt'). -# latex_font_size = '10pt' - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, document class [howto/manual]). -latex_documents = [ - ("index", "bx-python.tex", "bx-python Documentation", "James Taylor", "manual"), +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.doctest", + "sphinx.ext.intersphinx", + "sphinx_rtd_theme", ] -# The name of an image file (relative to this directory) to place at the top of -# the title page. -# latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -# latex_use_parts = False +templates_path = ["_templates"] +exclude_patterns = [] -# Additional stuff for the LaTeX preamble. -# latex_preamble = '' -# Documents to append as an appendix to all manuals. -# latex_appendices = [] +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output -# If false, no module index is generated. -# latex_use_modindex = True +html_theme = "sphinx_rtd_theme" +html_static_path = ["_static"] +# -- Options for intersphinx extension --------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#configuration -# Example configuration for intersphinx: refer to the Python standard library. -# intersphinx_mapping = {'http://docs.python.org/dev': None} +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), +} diff --git a/doc/source/contents.rst b/doc/source/contents.rst deleted file mode 100644 index c0d48d2f..00000000 --- a/doc/source/contents.rst +++ /dev/null @@ -1,18 +0,0 @@ - - -bx-python documentation contents -================================ - -Browse the Python API `class documentation `_ - -Contents: - -.. toctree:: - :maxdepth: 2 - - modules/index.rst - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/doc/source/index.rst b/doc/source/index.rst index 69ed3dfb..e257d4e3 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -1,28 +1,25 @@ -About bx-python -=============== - -The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: - - * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats) - * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems) - * Data structures for working with intervals on sequences - * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly - * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation - -These tools have been used in a variety of published research, and are a fundamental part of the ongoing Galaxy and ESPERR projects. - -Contents -======== - -.. toctree:: - :maxdepth: 5 - - Application Documentation - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - +Welcome to bx-python's documentation! +===================================== + +The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: + + * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats) + * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems) + * Data structures for working with intervals on sequences + * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly + * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation + +These tools have been used in a variety of published research, and are a fundamental part of the ongoing Galaxy and ESPERR projects. + +.. toctree:: + :maxdepth: 4 + :caption: Contents: + + Application Documentation + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/doc/source/lib/bx.align.axt.rst b/doc/source/lib/bx.align.axt.rst index 807863a2..3eb45e26 100644 --- a/doc/source/lib/bx.align.axt.rst +++ b/doc/source/lib/bx.align.axt.rst @@ -2,6 +2,6 @@ bx.align.axt module =================== .. automodule:: bx.align.axt - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.core.rst b/doc/source/lib/bx.align.core.rst index d3337551..4ff436cc 100644 --- a/doc/source/lib/bx.align.core.rst +++ b/doc/source/lib/bx.align.core.rst @@ -2,6 +2,6 @@ bx.align.core module ==================== .. automodule:: bx.align.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.epo.rst b/doc/source/lib/bx.align.epo.rst index e0ed150d..8088515b 100644 --- a/doc/source/lib/bx.align.epo.rst +++ b/doc/source/lib/bx.align.epo.rst @@ -2,6 +2,6 @@ bx.align.epo module =================== .. automodule:: bx.align.epo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.epo_tests.rst b/doc/source/lib/bx.align.epo_tests.rst index 14a8fee4..8a794c8d 100644 --- a/doc/source/lib/bx.align.epo_tests.rst +++ b/doc/source/lib/bx.align.epo_tests.rst @@ -1,7 +1,7 @@ -bx.align.epo_tests module -========================= +bx.align.epo\_tests module +========================== .. automodule:: bx.align.epo_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.lav.rst b/doc/source/lib/bx.align.lav.rst index 85a17d68..a2827a21 100644 --- a/doc/source/lib/bx.align.lav.rst +++ b/doc/source/lib/bx.align.lav.rst @@ -2,6 +2,6 @@ bx.align.lav module =================== .. automodule:: bx.align.lav - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.lav_tests.rst b/doc/source/lib/bx.align.lav_tests.rst index 1d465213..044aaa5b 100644 --- a/doc/source/lib/bx.align.lav_tests.rst +++ b/doc/source/lib/bx.align.lav_tests.rst @@ -1,7 +1,7 @@ -bx.align.lav_tests module -========================= +bx.align.lav\_tests module +========================== .. automodule:: bx.align.lav_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.maf.rst b/doc/source/lib/bx.align.maf.rst index b4d00c68..e5e62332 100644 --- a/doc/source/lib/bx.align.maf.rst +++ b/doc/source/lib/bx.align.maf.rst @@ -2,6 +2,6 @@ bx.align.maf module =================== .. automodule:: bx.align.maf - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.maf_tests.rst b/doc/source/lib/bx.align.maf_tests.rst index 6fda3ce8..1af3fd27 100644 --- a/doc/source/lib/bx.align.maf_tests.rst +++ b/doc/source/lib/bx.align.maf_tests.rst @@ -1,7 +1,7 @@ -bx.align.maf_tests module -========================= +bx.align.maf\_tests module +========================== .. automodule:: bx.align.maf_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.rst b/doc/source/lib/bx.align.rst index e8924e20..e742e310 100644 --- a/doc/source/lib/bx.align.rst +++ b/doc/source/lib/bx.align.rst @@ -5,14 +5,16 @@ Subpackages ----------- .. toctree:: + :maxdepth: 3 - bx.align.sitemask - bx.align.tools + bx.align.sitemask + bx.align.tools Submodules ---------- .. toctree:: + :maxdepth: 3 bx.align.axt bx.align.core @@ -29,6 +31,6 @@ Module contents --------------- .. automodule:: bx.align - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.score.rst b/doc/source/lib/bx.align.score.rst index 9a87e1f8..f425857c 100644 --- a/doc/source/lib/bx.align.score.rst +++ b/doc/source/lib/bx.align.score.rst @@ -2,6 +2,6 @@ bx.align.score module ===================== .. automodule:: bx.align.score - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.score_tests.rst b/doc/source/lib/bx.align.score_tests.rst index d8c758a0..bac70c36 100644 --- a/doc/source/lib/bx.align.score_tests.rst +++ b/doc/source/lib/bx.align.score_tests.rst @@ -1,7 +1,7 @@ -bx.align.score_tests module -=========================== +bx.align.score\_tests module +============================ .. automodule:: bx.align.score_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.sitemask.core.rst b/doc/source/lib/bx.align.sitemask.core.rst index 548052ce..8f9320ef 100644 --- a/doc/source/lib/bx.align.sitemask.core.rst +++ b/doc/source/lib/bx.align.sitemask.core.rst @@ -2,6 +2,6 @@ bx.align.sitemask.core module ============================= .. automodule:: bx.align.sitemask.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.sitemask.cpg.rst b/doc/source/lib/bx.align.sitemask.cpg.rst index 5a1454ff..e2ef3014 100644 --- a/doc/source/lib/bx.align.sitemask.cpg.rst +++ b/doc/source/lib/bx.align.sitemask.cpg.rst @@ -2,6 +2,6 @@ bx.align.sitemask.cpg module ============================ .. automodule:: bx.align.sitemask.cpg - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.sitemask.quality.rst b/doc/source/lib/bx.align.sitemask.quality.rst index 5061690d..660f2700 100644 --- a/doc/source/lib/bx.align.sitemask.quality.rst +++ b/doc/source/lib/bx.align.sitemask.quality.rst @@ -2,6 +2,6 @@ bx.align.sitemask.quality module ================================ .. automodule:: bx.align.sitemask.quality - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.sitemask.rst b/doc/source/lib/bx.align.sitemask.rst index 2c0d9ad5..85c4437c 100644 --- a/doc/source/lib/bx.align.sitemask.rst +++ b/doc/source/lib/bx.align.sitemask.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.align.sitemask.core bx.align.sitemask.cpg @@ -15,6 +16,6 @@ Module contents --------------- .. automodule:: bx.align.sitemask - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.sitemask.sitemask_tests.rst b/doc/source/lib/bx.align.sitemask.sitemask_tests.rst index 3d0593f5..a95798ec 100644 --- a/doc/source/lib/bx.align.sitemask.sitemask_tests.rst +++ b/doc/source/lib/bx.align.sitemask.sitemask_tests.rst @@ -1,7 +1,7 @@ -bx.align.sitemask.sitemask_tests module -======================================= +bx.align.sitemask.sitemask\_tests module +======================================== .. automodule:: bx.align.sitemask.sitemask_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.tools.chop.rst b/doc/source/lib/bx.align.tools.chop.rst index c1153cee..82b921cb 100644 --- a/doc/source/lib/bx.align.tools.chop.rst +++ b/doc/source/lib/bx.align.tools.chop.rst @@ -2,6 +2,6 @@ bx.align.tools.chop module ========================== .. automodule:: bx.align.tools.chop - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.tools.fuse.rst b/doc/source/lib/bx.align.tools.fuse.rst index 6fd51ab8..9f3acde0 100644 --- a/doc/source/lib/bx.align.tools.fuse.rst +++ b/doc/source/lib/bx.align.tools.fuse.rst @@ -2,6 +2,6 @@ bx.align.tools.fuse module ========================== .. automodule:: bx.align.tools.fuse - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.tools.rst b/doc/source/lib/bx.align.tools.rst index 63baf336..e8d318bd 100644 --- a/doc/source/lib/bx.align.tools.rst +++ b/doc/source/lib/bx.align.tools.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.align.tools.chop bx.align.tools.fuse @@ -15,6 +16,6 @@ Module contents --------------- .. automodule:: bx.align.tools - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.tools.thread.rst b/doc/source/lib/bx.align.tools.thread.rst index d7e36d7b..8b6bcee9 100644 --- a/doc/source/lib/bx.align.tools.thread.rst +++ b/doc/source/lib/bx.align.tools.thread.rst @@ -2,6 +2,6 @@ bx.align.tools.thread module ============================ .. automodule:: bx.align.tools.thread - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.align.tools.tile.rst b/doc/source/lib/bx.align.tools.tile.rst index acb45163..ff53de53 100644 --- a/doc/source/lib/bx.align.tools.tile.rst +++ b/doc/source/lib/bx.align.tools.tile.rst @@ -2,6 +2,6 @@ bx.align.tools.tile module ========================== .. automodule:: bx.align.tools.tile - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.arrays.array_tree.rst b/doc/source/lib/bx.arrays.array_tree.rst index 2b689227..e5fc65b9 100644 --- a/doc/source/lib/bx.arrays.array_tree.rst +++ b/doc/source/lib/bx.arrays.array_tree.rst @@ -1,7 +1,7 @@ -bx.arrays.array_tree module -=========================== +bx.arrays.array\_tree module +============================ .. automodule:: bx.arrays.array_tree - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.arrays.array_tree_tests.rst b/doc/source/lib/bx.arrays.array_tree_tests.rst index 9f04d019..169f8a5c 100644 --- a/doc/source/lib/bx.arrays.array_tree_tests.rst +++ b/doc/source/lib/bx.arrays.array_tree_tests.rst @@ -1,7 +1,7 @@ -bx.arrays.array_tree_tests module -================================= +bx.arrays.array\_tree\_tests module +=================================== .. automodule:: bx.arrays.array_tree_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.arrays.bed.rst b/doc/source/lib/bx.arrays.bed.rst index fcb5d36c..1ee1dd53 100644 --- a/doc/source/lib/bx.arrays.bed.rst +++ b/doc/source/lib/bx.arrays.bed.rst @@ -2,6 +2,6 @@ bx.arrays.bed module ==================== .. automodule:: bx.arrays.bed - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.arrays.rst b/doc/source/lib/bx.arrays.rst index a6417ec1..f4bbbff2 100644 --- a/doc/source/lib/bx.arrays.rst +++ b/doc/source/lib/bx.arrays.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.arrays.array_tree bx.arrays.array_tree_tests @@ -15,6 +16,6 @@ Module contents --------------- .. automodule:: bx.arrays - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.arrays.wiggle.rst b/doc/source/lib/bx.arrays.wiggle.rst index 560d4051..1f65fe23 100644 --- a/doc/source/lib/bx.arrays.wiggle.rst +++ b/doc/source/lib/bx.arrays.wiggle.rst @@ -2,6 +2,6 @@ bx.arrays.wiggle module ======================= .. automodule:: bx.arrays.wiggle - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.bbi_file.rst b/doc/source/lib/bx.bbi.bbi_file.rst index f4ddad43..066c598a 100644 --- a/doc/source/lib/bx.bbi.bbi_file.rst +++ b/doc/source/lib/bx.bbi.bbi_file.rst @@ -1,7 +1,7 @@ -bx.bbi.bbi_file module -====================== +bx.bbi.bbi\_file module +======================= .. automodule:: bx.bbi.bbi_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.bigbed_file.rst b/doc/source/lib/bx.bbi.bigbed_file.rst index 7219d4b8..5aba2c3d 100644 --- a/doc/source/lib/bx.bbi.bigbed_file.rst +++ b/doc/source/lib/bx.bbi.bigbed_file.rst @@ -1,7 +1,7 @@ -bx.bbi.bigbed_file module -========================= +bx.bbi.bigbed\_file module +========================== .. automodule:: bx.bbi.bigbed_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.bigwig_file.rst b/doc/source/lib/bx.bbi.bigwig_file.rst index badeec64..f0994758 100644 --- a/doc/source/lib/bx.bbi.bigwig_file.rst +++ b/doc/source/lib/bx.bbi.bigwig_file.rst @@ -1,7 +1,7 @@ -bx.bbi.bigwig_file module -========================= +bx.bbi.bigwig\_file module +========================== .. automodule:: bx.bbi.bigwig_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.bigwig_tests.rst b/doc/source/lib/bx.bbi.bigwig_tests.rst index a267a388..3cf8b803 100644 --- a/doc/source/lib/bx.bbi.bigwig_tests.rst +++ b/doc/source/lib/bx.bbi.bigwig_tests.rst @@ -1,7 +1,7 @@ -bx.bbi.bigwig_tests module -========================== +bx.bbi.bigwig\_tests module +=========================== .. automodule:: bx.bbi.bigwig_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.bpt_file.rst b/doc/source/lib/bx.bbi.bpt_file.rst index 8af609fc..c6acd733 100644 --- a/doc/source/lib/bx.bbi.bpt_file.rst +++ b/doc/source/lib/bx.bbi.bpt_file.rst @@ -1,7 +1,7 @@ -bx.bbi.bpt_file module -====================== +bx.bbi.bpt\_file module +======================= .. automodule:: bx.bbi.bpt_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.cirtree_file.rst b/doc/source/lib/bx.bbi.cirtree_file.rst index 5c9878b8..8e3035b0 100644 --- a/doc/source/lib/bx.bbi.cirtree_file.rst +++ b/doc/source/lib/bx.bbi.cirtree_file.rst @@ -1,7 +1,7 @@ -bx.bbi.cirtree_file module -========================== +bx.bbi.cirtree\_file module +=========================== .. automodule:: bx.bbi.cirtree_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bbi.rst b/doc/source/lib/bx.bbi.rst index 24b6d607..455c2e01 100644 --- a/doc/source/lib/bx.bbi.rst +++ b/doc/source/lib/bx.bbi.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.bbi.bbi_file bx.bbi.bigbed_file @@ -17,6 +18,6 @@ Module contents --------------- .. automodule:: bx.bbi - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.binned_array.rst b/doc/source/lib/bx.binned_array.rst index 918ea824..578b8563 100644 --- a/doc/source/lib/bx.binned_array.rst +++ b/doc/source/lib/bx.binned_array.rst @@ -1,7 +1,7 @@ -bx.binned_array module -====================== +bx.binned\_array module +======================= .. automodule:: bx.binned_array - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.binned_array_tests.rst b/doc/source/lib/bx.binned_array_tests.rst index a1c5ac9e..81e4f4f3 100644 --- a/doc/source/lib/bx.binned_array_tests.rst +++ b/doc/source/lib/bx.binned_array_tests.rst @@ -1,7 +1,7 @@ -bx.binned_array_tests module -============================ +bx.binned\_array\_tests module +============================== .. automodule:: bx.binned_array_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bitset.rst b/doc/source/lib/bx.bitset.rst index 3c5634b5..9c9c08aa 100644 --- a/doc/source/lib/bx.bitset.rst +++ b/doc/source/lib/bx.bitset.rst @@ -2,6 +2,6 @@ bx.bitset module ================ .. automodule:: bx.bitset - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bitset_builders.rst b/doc/source/lib/bx.bitset_builders.rst index 9c3e4b8f..baed34f8 100644 --- a/doc/source/lib/bx.bitset_builders.rst +++ b/doc/source/lib/bx.bitset_builders.rst @@ -1,7 +1,7 @@ -bx.bitset_builders module -========================= +bx.bitset\_builders module +========================== .. automodule:: bx.bitset_builders - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bitset_tests.rst b/doc/source/lib/bx.bitset_tests.rst index ebd3da70..a07676b8 100644 --- a/doc/source/lib/bx.bitset_tests.rst +++ b/doc/source/lib/bx.bitset_tests.rst @@ -1,7 +1,7 @@ -bx.bitset_tests module -====================== +bx.bitset\_tests module +======================= .. automodule:: bx.bitset_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.bitset_utils.rst b/doc/source/lib/bx.bitset_utils.rst index 6bfcd83d..a106355c 100644 --- a/doc/source/lib/bx.bitset_utils.rst +++ b/doc/source/lib/bx.bitset_utils.rst @@ -1,7 +1,7 @@ -bx.bitset_utils module -====================== +bx.bitset\_utils module +======================= .. automodule:: bx.bitset_utils - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.cookbook.argparse.rst b/doc/source/lib/bx.cookbook.argparse.rst index d1a79599..e5ca0126 100644 --- a/doc/source/lib/bx.cookbook.argparse.rst +++ b/doc/source/lib/bx.cookbook.argparse.rst @@ -2,6 +2,6 @@ bx.cookbook.argparse module =========================== .. automodule:: bx.cookbook.argparse - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.cookbook.attribute.rst b/doc/source/lib/bx.cookbook.attribute.rst index e3c5d657..8f58e7e9 100644 --- a/doc/source/lib/bx.cookbook.attribute.rst +++ b/doc/source/lib/bx.cookbook.attribute.rst @@ -2,6 +2,6 @@ bx.cookbook.attribute module ============================ .. automodule:: bx.cookbook.attribute - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.cookbook.doc_optparse.rst b/doc/source/lib/bx.cookbook.doc_optparse.rst index 7091c7c1..099ea9b3 100644 --- a/doc/source/lib/bx.cookbook.doc_optparse.rst +++ b/doc/source/lib/bx.cookbook.doc_optparse.rst @@ -1,7 +1,7 @@ -bx.cookbook.doc_optparse module -=============================== +bx.cookbook.doc\_optparse module +================================ .. automodule:: bx.cookbook.doc_optparse - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.cookbook.progress_bar.rst b/doc/source/lib/bx.cookbook.progress_bar.rst index 5d828a1b..2b050950 100644 --- a/doc/source/lib/bx.cookbook.progress_bar.rst +++ b/doc/source/lib/bx.cookbook.progress_bar.rst @@ -1,7 +1,7 @@ -bx.cookbook.progress_bar module -=============================== +bx.cookbook.progress\_bar module +================================ .. automodule:: bx.cookbook.progress_bar - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.cookbook.rst b/doc/source/lib/bx.cookbook.rst index 215de67d..a35bb144 100644 --- a/doc/source/lib/bx.cookbook.rst +++ b/doc/source/lib/bx.cookbook.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.cookbook.argparse bx.cookbook.attribute @@ -15,6 +16,6 @@ Module contents --------------- .. automodule:: bx.cookbook - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.filter.rst b/doc/source/lib/bx.filter.rst index 2e1cf1d9..5b3693ff 100644 --- a/doc/source/lib/bx.filter.rst +++ b/doc/source/lib/bx.filter.rst @@ -2,6 +2,6 @@ bx.filter module ================ .. automodule:: bx.filter - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.gene_reader.rst b/doc/source/lib/bx.gene_reader.rst index a99b1a70..d43a4e06 100644 --- a/doc/source/lib/bx.gene_reader.rst +++ b/doc/source/lib/bx.gene_reader.rst @@ -1,7 +1,7 @@ -bx.gene_reader module -===================== +bx.gene\_reader module +====================== .. automodule:: bx.gene_reader - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.interval_index_file.rst b/doc/source/lib/bx.interval_index_file.rst index 59428ba2..494429b6 100644 --- a/doc/source/lib/bx.interval_index_file.rst +++ b/doc/source/lib/bx.interval_index_file.rst @@ -1,7 +1,7 @@ -bx.interval_index_file module -============================= +bx.interval\_index\_file module +=============================== .. automodule:: bx.interval_index_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.interval_index_file_tests.rst b/doc/source/lib/bx.interval_index_file_tests.rst index b1d9a987..f56abc2f 100644 --- a/doc/source/lib/bx.interval_index_file_tests.rst +++ b/doc/source/lib/bx.interval_index_file_tests.rst @@ -1,7 +1,7 @@ -bx.interval_index_file_tests module -=================================== +bx.interval\_index\_file\_tests module +====================================== .. automodule:: bx.interval_index_file_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.cluster.rst b/doc/source/lib/bx.intervals.cluster.rst index ef3c8d47..4aff3138 100644 --- a/doc/source/lib/bx.intervals.cluster.rst +++ b/doc/source/lib/bx.intervals.cluster.rst @@ -2,6 +2,6 @@ bx.intervals.cluster module =========================== .. automodule:: bx.intervals.cluster - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.cluster_tests.rst b/doc/source/lib/bx.intervals.cluster_tests.rst index cb45a59c..cb974de3 100644 --- a/doc/source/lib/bx.intervals.cluster_tests.rst +++ b/doc/source/lib/bx.intervals.cluster_tests.rst @@ -1,7 +1,7 @@ -bx.intervals.cluster_tests module -================================= +bx.intervals.cluster\_tests module +================================== .. automodule:: bx.intervals.cluster_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.intersection.rst b/doc/source/lib/bx.intervals.intersection.rst index ce7febc2..6199303f 100644 --- a/doc/source/lib/bx.intervals.intersection.rst +++ b/doc/source/lib/bx.intervals.intersection.rst @@ -2,6 +2,6 @@ bx.intervals.intersection module ================================ .. automodule:: bx.intervals.intersection - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.intersection_tests.rst b/doc/source/lib/bx.intervals.intersection_tests.rst index c6ebb8df..d53a6aac 100644 --- a/doc/source/lib/bx.intervals.intersection_tests.rst +++ b/doc/source/lib/bx.intervals.intersection_tests.rst @@ -1,7 +1,7 @@ -bx.intervals.intersection_tests module -====================================== +bx.intervals.intersection\_tests module +======================================= .. automodule:: bx.intervals.intersection_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.io.rst b/doc/source/lib/bx.intervals.io.rst index 051c9575..1135f085 100644 --- a/doc/source/lib/bx.intervals.io.rst +++ b/doc/source/lib/bx.intervals.io.rst @@ -2,6 +2,6 @@ bx.intervals.io module ====================== .. automodule:: bx.intervals.io - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.base_coverage.rst b/doc/source/lib/bx.intervals.operations.base_coverage.rst index 5b6d01b1..b63c4392 100644 --- a/doc/source/lib/bx.intervals.operations.base_coverage.rst +++ b/doc/source/lib/bx.intervals.operations.base_coverage.rst @@ -1,7 +1,7 @@ -bx.intervals.operations.base_coverage module -============================================ +bx.intervals.operations.base\_coverage module +============================================= .. automodule:: bx.intervals.operations.base_coverage - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.complement.rst b/doc/source/lib/bx.intervals.operations.complement.rst index 434ddbcf..f37b3de0 100644 --- a/doc/source/lib/bx.intervals.operations.complement.rst +++ b/doc/source/lib/bx.intervals.operations.complement.rst @@ -2,6 +2,6 @@ bx.intervals.operations.complement module ========================================= .. automodule:: bx.intervals.operations.complement - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.concat.rst b/doc/source/lib/bx.intervals.operations.concat.rst index ad9ed441..332a7e2e 100644 --- a/doc/source/lib/bx.intervals.operations.concat.rst +++ b/doc/source/lib/bx.intervals.operations.concat.rst @@ -2,6 +2,6 @@ bx.intervals.operations.concat module ===================================== .. automodule:: bx.intervals.operations.concat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.coverage.rst b/doc/source/lib/bx.intervals.operations.coverage.rst index 80c67bac..bc124b46 100644 --- a/doc/source/lib/bx.intervals.operations.coverage.rst +++ b/doc/source/lib/bx.intervals.operations.coverage.rst @@ -2,6 +2,6 @@ bx.intervals.operations.coverage module ======================================= .. automodule:: bx.intervals.operations.coverage - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.find_clusters.rst b/doc/source/lib/bx.intervals.operations.find_clusters.rst index 96c49929..81a66ead 100644 --- a/doc/source/lib/bx.intervals.operations.find_clusters.rst +++ b/doc/source/lib/bx.intervals.operations.find_clusters.rst @@ -1,7 +1,7 @@ -bx.intervals.operations.find_clusters module -============================================ +bx.intervals.operations.find\_clusters module +============================================= .. automodule:: bx.intervals.operations.find_clusters - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.intersect.rst b/doc/source/lib/bx.intervals.operations.intersect.rst index 46851427..4b2c97b5 100644 --- a/doc/source/lib/bx.intervals.operations.intersect.rst +++ b/doc/source/lib/bx.intervals.operations.intersect.rst @@ -2,6 +2,6 @@ bx.intervals.operations.intersect module ======================================== .. automodule:: bx.intervals.operations.intersect - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.join.rst b/doc/source/lib/bx.intervals.operations.join.rst index 608cc5de..82a1bdc3 100644 --- a/doc/source/lib/bx.intervals.operations.join.rst +++ b/doc/source/lib/bx.intervals.operations.join.rst @@ -2,6 +2,6 @@ bx.intervals.operations.join module =================================== .. automodule:: bx.intervals.operations.join - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.merge.rst b/doc/source/lib/bx.intervals.operations.merge.rst index bc2dc543..f41055c6 100644 --- a/doc/source/lib/bx.intervals.operations.merge.rst +++ b/doc/source/lib/bx.intervals.operations.merge.rst @@ -2,6 +2,6 @@ bx.intervals.operations.merge module ==================================== .. automodule:: bx.intervals.operations.merge - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.quicksect.rst b/doc/source/lib/bx.intervals.operations.quicksect.rst index dbeaaf22..7149a5d0 100644 --- a/doc/source/lib/bx.intervals.operations.quicksect.rst +++ b/doc/source/lib/bx.intervals.operations.quicksect.rst @@ -2,6 +2,6 @@ bx.intervals.operations.quicksect module ======================================== .. automodule:: bx.intervals.operations.quicksect - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.rst b/doc/source/lib/bx.intervals.operations.rst index d4c52278..936e2eff 100644 --- a/doc/source/lib/bx.intervals.operations.rst +++ b/doc/source/lib/bx.intervals.operations.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.intervals.operations.base_coverage bx.intervals.operations.complement @@ -21,6 +22,6 @@ Module contents --------------- .. automodule:: bx.intervals.operations - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.operations.subtract.rst b/doc/source/lib/bx.intervals.operations.subtract.rst index 2430b94c..cd5078df 100644 --- a/doc/source/lib/bx.intervals.operations.subtract.rst +++ b/doc/source/lib/bx.intervals.operations.subtract.rst @@ -2,6 +2,6 @@ bx.intervals.operations.subtract module ======================================= .. automodule:: bx.intervals.operations.subtract - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.random_intervals.rst b/doc/source/lib/bx.intervals.random_intervals.rst index 3970489e..e20e9f7a 100644 --- a/doc/source/lib/bx.intervals.random_intervals.rst +++ b/doc/source/lib/bx.intervals.random_intervals.rst @@ -1,7 +1,7 @@ -bx.intervals.random_intervals module -==================================== +bx.intervals.random\_intervals module +===================================== .. automodule:: bx.intervals.random_intervals - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intervals.rst b/doc/source/lib/bx.intervals.rst index e63d2feb..33a85db2 100644 --- a/doc/source/lib/bx.intervals.rst +++ b/doc/source/lib/bx.intervals.rst @@ -5,13 +5,15 @@ Subpackages ----------- .. toctree:: + :maxdepth: 3 - bx.intervals.operations + bx.intervals.operations Submodules ---------- .. toctree:: + :maxdepth: 3 bx.intervals.cluster bx.intervals.cluster_tests @@ -24,6 +26,6 @@ Module contents --------------- .. automodule:: bx.intervals - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intseq.ngramcount.rst b/doc/source/lib/bx.intseq.ngramcount.rst index 44665edb..dc33c2f4 100644 --- a/doc/source/lib/bx.intseq.ngramcount.rst +++ b/doc/source/lib/bx.intseq.ngramcount.rst @@ -2,6 +2,6 @@ bx.intseq.ngramcount module =========================== .. automodule:: bx.intseq.ngramcount - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.intseq.rst b/doc/source/lib/bx.intseq.rst index c1721503..9b7b809e 100644 --- a/doc/source/lib/bx.intseq.rst +++ b/doc/source/lib/bx.intseq.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.intseq.ngramcount @@ -12,6 +13,6 @@ Module contents --------------- .. automodule:: bx.intseq - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.bgzf.rst b/doc/source/lib/bx.misc.bgzf.rst index bf4c413d..25c9d46d 100644 --- a/doc/source/lib/bx.misc.bgzf.rst +++ b/doc/source/lib/bx.misc.bgzf.rst @@ -2,6 +2,6 @@ bx.misc.bgzf module =================== .. automodule:: bx.misc.bgzf - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.bgzf_tests.rst b/doc/source/lib/bx.misc.bgzf_tests.rst index c78fd0d6..fb0495d0 100644 --- a/doc/source/lib/bx.misc.bgzf_tests.rst +++ b/doc/source/lib/bx.misc.bgzf_tests.rst @@ -1,7 +1,7 @@ -bx.misc.bgzf_tests module -========================= +bx.misc.bgzf\_tests module +========================== .. automodule:: bx.misc.bgzf_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.binary_file.rst b/doc/source/lib/bx.misc.binary_file.rst index c87493c2..b0ccd630 100644 --- a/doc/source/lib/bx.misc.binary_file.rst +++ b/doc/source/lib/bx.misc.binary_file.rst @@ -1,7 +1,7 @@ -bx.misc.binary_file module -========================== +bx.misc.binary\_file module +=========================== .. automodule:: bx.misc.binary_file - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.cdb.rst b/doc/source/lib/bx.misc.cdb.rst index c414a9c7..4863429d 100644 --- a/doc/source/lib/bx.misc.cdb.rst +++ b/doc/source/lib/bx.misc.cdb.rst @@ -2,6 +2,6 @@ bx.misc.cdb module ================== .. automodule:: bx.misc.cdb - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.cdb_tests.rst b/doc/source/lib/bx.misc.cdb_tests.rst index 048d97ec..93ea5347 100644 --- a/doc/source/lib/bx.misc.cdb_tests.rst +++ b/doc/source/lib/bx.misc.cdb_tests.rst @@ -1,7 +1,7 @@ -bx.misc.cdb_tests module -======================== +bx.misc.cdb\_tests module +========================= .. automodule:: bx.misc.cdb_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.filecache.rst b/doc/source/lib/bx.misc.filecache.rst index 8d5bd01f..7c97463f 100644 --- a/doc/source/lib/bx.misc.filecache.rst +++ b/doc/source/lib/bx.misc.filecache.rst @@ -2,6 +2,6 @@ bx.misc.filecache module ======================== .. automodule:: bx.misc.filecache - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.filecache_tests.rst b/doc/source/lib/bx.misc.filecache_tests.rst index f4464bdd..8d5055d5 100644 --- a/doc/source/lib/bx.misc.filecache_tests.rst +++ b/doc/source/lib/bx.misc.filecache_tests.rst @@ -1,7 +1,7 @@ -bx.misc.filecache_tests module -============================== +bx.misc.filecache\_tests module +=============================== .. automodule:: bx.misc.filecache_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.readlengths.rst b/doc/source/lib/bx.misc.readlengths.rst index 89f34fb5..b5710844 100644 --- a/doc/source/lib/bx.misc.readlengths.rst +++ b/doc/source/lib/bx.misc.readlengths.rst @@ -2,6 +2,6 @@ bx.misc.readlengths module ========================== .. automodule:: bx.misc.readlengths - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.rst b/doc/source/lib/bx.misc.rst index 7f67d46a..4ee4257c 100644 --- a/doc/source/lib/bx.misc.rst +++ b/doc/source/lib/bx.misc.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.misc.bgzf bx.misc.bgzf_tests @@ -23,6 +24,6 @@ Module contents --------------- .. automodule:: bx.misc - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.seekbzip2.rst b/doc/source/lib/bx.misc.seekbzip2.rst index a6192d8b..94bd6a7b 100644 --- a/doc/source/lib/bx.misc.seekbzip2.rst +++ b/doc/source/lib/bx.misc.seekbzip2.rst @@ -2,6 +2,6 @@ bx.misc.seekbzip2 module ======================== .. automodule:: bx.misc.seekbzip2 - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.seekbzip2_tests.rst b/doc/source/lib/bx.misc.seekbzip2_tests.rst index 40de576e..dee56266 100644 --- a/doc/source/lib/bx.misc.seekbzip2_tests.rst +++ b/doc/source/lib/bx.misc.seekbzip2_tests.rst @@ -1,7 +1,7 @@ -bx.misc.seekbzip2_tests module -============================== +bx.misc.seekbzip2\_tests module +=============================== .. automodule:: bx.misc.seekbzip2_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.seeklzop.rst b/doc/source/lib/bx.misc.seeklzop.rst index 675ee92c..9659f343 100644 --- a/doc/source/lib/bx.misc.seeklzop.rst +++ b/doc/source/lib/bx.misc.seeklzop.rst @@ -2,6 +2,6 @@ bx.misc.seeklzop module ======================= .. automodule:: bx.misc.seeklzop - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.misc.seeklzop_tests.rst b/doc/source/lib/bx.misc.seeklzop_tests.rst index 41e48500..5a99c75a 100644 --- a/doc/source/lib/bx.misc.seeklzop_tests.rst +++ b/doc/source/lib/bx.misc.seeklzop_tests.rst @@ -1,7 +1,7 @@ -bx.misc.seeklzop_tests module -============================= +bx.misc.seeklzop\_tests module +============================== .. automodule:: bx.misc.seeklzop_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.io.rst b/doc/source/lib/bx.motif.io.rst index 58004a0b..4f40ae53 100644 --- a/doc/source/lib/bx.motif.io.rst +++ b/doc/source/lib/bx.motif.io.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.motif.io.transfac bx.motif.io.transfac_tests @@ -13,6 +14,6 @@ Module contents --------------- .. automodule:: bx.motif.io - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.io.transfac.rst b/doc/source/lib/bx.motif.io.transfac.rst index 009b0f73..4d80891d 100644 --- a/doc/source/lib/bx.motif.io.transfac.rst +++ b/doc/source/lib/bx.motif.io.transfac.rst @@ -2,6 +2,6 @@ bx.motif.io.transfac module =========================== .. automodule:: bx.motif.io.transfac - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.io.transfac_tests.rst b/doc/source/lib/bx.motif.io.transfac_tests.rst index e0dbba97..a2c6f646 100644 --- a/doc/source/lib/bx.motif.io.transfac_tests.rst +++ b/doc/source/lib/bx.motif.io.transfac_tests.rst @@ -1,7 +1,7 @@ -bx.motif.io.transfac_tests module -================================= +bx.motif.io.transfac\_tests module +================================== .. automodule:: bx.motif.io.transfac_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.logo.rst b/doc/source/lib/bx.motif.logo.rst index 1fc74480..dd6530e1 100644 --- a/doc/source/lib/bx.motif.logo.rst +++ b/doc/source/lib/bx.motif.logo.rst @@ -5,6 +5,6 @@ Module contents --------------- .. automodule:: bx.motif.logo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.pwm.rst b/doc/source/lib/bx.motif.pwm.rst index 9411e941..411c271a 100644 --- a/doc/source/lib/bx.motif.pwm.rst +++ b/doc/source/lib/bx.motif.pwm.rst @@ -2,6 +2,6 @@ bx.motif.pwm module =================== .. automodule:: bx.motif.pwm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.pwm_tests.rst b/doc/source/lib/bx.motif.pwm_tests.rst index 0310f55f..64966447 100644 --- a/doc/source/lib/bx.motif.pwm_tests.rst +++ b/doc/source/lib/bx.motif.pwm_tests.rst @@ -1,7 +1,7 @@ -bx.motif.pwm_tests module -========================= +bx.motif.pwm\_tests module +========================== .. automodule:: bx.motif.pwm_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.motif.rst b/doc/source/lib/bx.motif.rst index dc2608cc..2d731726 100644 --- a/doc/source/lib/bx.motif.rst +++ b/doc/source/lib/bx.motif.rst @@ -5,14 +5,16 @@ Subpackages ----------- .. toctree:: + :maxdepth: 3 - bx.motif.io - bx.motif.logo + bx.motif.io + bx.motif.logo Submodules ---------- .. toctree:: + :maxdepth: 3 bx.motif.pwm bx.motif.pwm_tests @@ -21,6 +23,6 @@ Module contents --------------- .. automodule:: bx.motif - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.phylo.newick.rst b/doc/source/lib/bx.phylo.newick.rst index 9f4c8b23..cc5d84c8 100644 --- a/doc/source/lib/bx.phylo.newick.rst +++ b/doc/source/lib/bx.phylo.newick.rst @@ -2,6 +2,6 @@ bx.phylo.newick module ====================== .. automodule:: bx.phylo.newick - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.phylo.newick_tests.rst b/doc/source/lib/bx.phylo.newick_tests.rst index f2712dfe..bdebc6c0 100644 --- a/doc/source/lib/bx.phylo.newick_tests.rst +++ b/doc/source/lib/bx.phylo.newick_tests.rst @@ -1,7 +1,7 @@ -bx.phylo.newick_tests module -============================ +bx.phylo.newick\_tests module +============================= .. automodule:: bx.phylo.newick_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.phylo.phast.rst b/doc/source/lib/bx.phylo.phast.rst index 5ee8255c..d243a1cb 100644 --- a/doc/source/lib/bx.phylo.phast.rst +++ b/doc/source/lib/bx.phylo.phast.rst @@ -2,6 +2,6 @@ bx.phylo.phast module ===================== .. automodule:: bx.phylo.phast - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.phylo.phast_tests.rst b/doc/source/lib/bx.phylo.phast_tests.rst index 7925f217..37cb2ecf 100644 --- a/doc/source/lib/bx.phylo.phast_tests.rst +++ b/doc/source/lib/bx.phylo.phast_tests.rst @@ -1,7 +1,7 @@ -bx.phylo.phast_tests module -=========================== +bx.phylo.phast\_tests module +============================ .. automodule:: bx.phylo.phast_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.phylo.rst b/doc/source/lib/bx.phylo.rst index 13f6223a..d9439742 100644 --- a/doc/source/lib/bx.phylo.rst +++ b/doc/source/lib/bx.phylo.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.phylo.newick bx.phylo.newick_tests @@ -15,6 +16,6 @@ Module contents --------------- .. automodule:: bx.phylo - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.bed_score_aligned_pwm.rst b/doc/source/lib/bx.pwm.bed_score_aligned_pwm.rst index 43ed464d..e86703ba 100644 --- a/doc/source/lib/bx.pwm.bed_score_aligned_pwm.rst +++ b/doc/source/lib/bx.pwm.bed_score_aligned_pwm.rst @@ -1,7 +1,7 @@ -bx.pwm.bed_score_aligned_pwm module -=================================== +bx.pwm.bed\_score\_aligned\_pwm module +====================================== .. automodule:: bx.pwm.bed_score_aligned_pwm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.bed_score_aligned_string.rst b/doc/source/lib/bx.pwm.bed_score_aligned_string.rst index 80c72c31..1c5cb315 100644 --- a/doc/source/lib/bx.pwm.bed_score_aligned_string.rst +++ b/doc/source/lib/bx.pwm.bed_score_aligned_string.rst @@ -1,7 +1,7 @@ -bx.pwm.bed_score_aligned_string module -====================================== +bx.pwm.bed\_score\_aligned\_string module +========================================= .. automodule:: bx.pwm.bed_score_aligned_string - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.maf_select_motifs.rst b/doc/source/lib/bx.pwm.maf_select_motifs.rst index 0c475f56..1bcc31aa 100644 --- a/doc/source/lib/bx.pwm.maf_select_motifs.rst +++ b/doc/source/lib/bx.pwm.maf_select_motifs.rst @@ -1,7 +1,7 @@ -bx.pwm.maf_select_motifs module -=============================== +bx.pwm.maf\_select\_motifs module +================================= .. automodule:: bx.pwm.maf_select_motifs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.position_weight_matrix.rst b/doc/source/lib/bx.pwm.position_weight_matrix.rst index ff486904..dfb42fee 100644 --- a/doc/source/lib/bx.pwm.position_weight_matrix.rst +++ b/doc/source/lib/bx.pwm.position_weight_matrix.rst @@ -1,7 +1,7 @@ -bx.pwm.position_weight_matrix module -==================================== +bx.pwm.position\_weight\_matrix module +====================================== .. automodule:: bx.pwm.position_weight_matrix - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.pwm_score_maf.rst b/doc/source/lib/bx.pwm.pwm_score_maf.rst index d597544a..f19b5a49 100644 --- a/doc/source/lib/bx.pwm.pwm_score_maf.rst +++ b/doc/source/lib/bx.pwm.pwm_score_maf.rst @@ -1,7 +1,7 @@ -bx.pwm.pwm_score_maf module -=========================== +bx.pwm.pwm\_score\_maf module +============================= .. automodule:: bx.pwm.pwm_score_maf - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.pwm_score_motifs.rst b/doc/source/lib/bx.pwm.pwm_score_motifs.rst index 192a665a..84a8afb0 100644 --- a/doc/source/lib/bx.pwm.pwm_score_motifs.rst +++ b/doc/source/lib/bx.pwm.pwm_score_motifs.rst @@ -1,7 +1,7 @@ -bx.pwm.pwm_score_motifs module -============================== +bx.pwm.pwm\_score\_motifs module +================================ .. automodule:: bx.pwm.pwm_score_motifs - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.pwm_score_positions.rst b/doc/source/lib/bx.pwm.pwm_score_positions.rst index cba956b8..d0caa749 100644 --- a/doc/source/lib/bx.pwm.pwm_score_positions.rst +++ b/doc/source/lib/bx.pwm.pwm_score_positions.rst @@ -1,7 +1,7 @@ -bx.pwm.pwm_score_positions module -================================= +bx.pwm.pwm\_score\_positions module +=================================== .. automodule:: bx.pwm.pwm_score_positions - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.pwm_tests.rst b/doc/source/lib/bx.pwm.pwm_tests.rst index 1b65c126..7f47610a 100644 --- a/doc/source/lib/bx.pwm.pwm_tests.rst +++ b/doc/source/lib/bx.pwm.pwm_tests.rst @@ -1,7 +1,7 @@ -bx.pwm.pwm_tests module -======================= +bx.pwm.pwm\_tests module +======================== .. automodule:: bx.pwm.pwm_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.pwm.rst b/doc/source/lib/bx.pwm.rst index c00f09f0..7026146c 100644 --- a/doc/source/lib/bx.pwm.rst +++ b/doc/source/lib/bx.pwm.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.pwm.bed_score_aligned_pwm bx.pwm.bed_score_aligned_string @@ -19,6 +20,6 @@ Module contents --------------- .. automodule:: bx.pwm - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.rst b/doc/source/lib/bx.rst index b667d663..14d4fda6 100644 --- a/doc/source/lib/bx.rst +++ b/doc/source/lib/bx.rst @@ -5,24 +5,26 @@ Subpackages ----------- .. toctree:: - - bx.align - bx.arrays - bx.bbi - bx.cookbook - bx.intervals - bx.intseq - bx.misc - bx.motif - bx.phylo - bx.pwm - bx.seq - bx.tabular + :maxdepth: 3 + + bx.align + bx.arrays + bx.bbi + bx.cookbook + bx.intervals + bx.intseq + bx.misc + bx.motif + bx.phylo + bx.pwm + bx.seq + bx.tabular Submodules ---------- .. toctree:: + :maxdepth: 3 bx.binned_array bx.binned_array_tests @@ -43,6 +45,6 @@ Module contents --------------- .. automodule:: bx - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.core.rst b/doc/source/lib/bx.seq.core.rst index 00cfcce5..f8919b17 100644 --- a/doc/source/lib/bx.seq.core.rst +++ b/doc/source/lib/bx.seq.core.rst @@ -2,6 +2,6 @@ bx.seq.core module ================== .. automodule:: bx.seq.core - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.fasta.rst b/doc/source/lib/bx.seq.fasta.rst index 3918d5b9..81217e9d 100644 --- a/doc/source/lib/bx.seq.fasta.rst +++ b/doc/source/lib/bx.seq.fasta.rst @@ -2,6 +2,6 @@ bx.seq.fasta module =================== .. automodule:: bx.seq.fasta - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.fasta_tests.rst b/doc/source/lib/bx.seq.fasta_tests.rst index f5bf7948..e6880de8 100644 --- a/doc/source/lib/bx.seq.fasta_tests.rst +++ b/doc/source/lib/bx.seq.fasta_tests.rst @@ -1,7 +1,7 @@ -bx.seq.fasta_tests module -========================= +bx.seq.fasta\_tests module +========================== .. automodule:: bx.seq.fasta_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.nib.rst b/doc/source/lib/bx.seq.nib.rst index 03f9c67a..84c7458d 100644 --- a/doc/source/lib/bx.seq.nib.rst +++ b/doc/source/lib/bx.seq.nib.rst @@ -2,6 +2,6 @@ bx.seq.nib module ================= .. automodule:: bx.seq.nib - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.nib_tests.rst b/doc/source/lib/bx.seq.nib_tests.rst index c701dd1e..b73fc129 100644 --- a/doc/source/lib/bx.seq.nib_tests.rst +++ b/doc/source/lib/bx.seq.nib_tests.rst @@ -1,7 +1,7 @@ -bx.seq.nib_tests module -======================= +bx.seq.nib\_tests module +======================== .. automodule:: bx.seq.nib_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.qdna.rst b/doc/source/lib/bx.seq.qdna.rst index 32055d4b..6a181e69 100644 --- a/doc/source/lib/bx.seq.qdna.rst +++ b/doc/source/lib/bx.seq.qdna.rst @@ -2,6 +2,6 @@ bx.seq.qdna module ================== .. automodule:: bx.seq.qdna - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.qdna_tests.rst b/doc/source/lib/bx.seq.qdna_tests.rst index ad33feca..23632143 100644 --- a/doc/source/lib/bx.seq.qdna_tests.rst +++ b/doc/source/lib/bx.seq.qdna_tests.rst @@ -1,7 +1,7 @@ -bx.seq.qdna_tests module -======================== +bx.seq.qdna\_tests module +========================= .. automodule:: bx.seq.qdna_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.rst b/doc/source/lib/bx.seq.rst index 4d781254..2475452b 100644 --- a/doc/source/lib/bx.seq.rst +++ b/doc/source/lib/bx.seq.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.seq.core bx.seq.fasta @@ -22,6 +23,6 @@ Module contents --------------- .. automodule:: bx.seq - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.seq.rst b/doc/source/lib/bx.seq.seq.rst index f483cdc7..d14d1891 100644 --- a/doc/source/lib/bx.seq.seq.rst +++ b/doc/source/lib/bx.seq.seq.rst @@ -2,6 +2,6 @@ bx.seq.seq module ================= .. automodule:: bx.seq.seq - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.seq_tests.rst b/doc/source/lib/bx.seq.seq_tests.rst index 98cc278f..257ad48a 100644 --- a/doc/source/lib/bx.seq.seq_tests.rst +++ b/doc/source/lib/bx.seq.seq_tests.rst @@ -1,7 +1,7 @@ -bx.seq.seq_tests module -======================= +bx.seq.seq\_tests module +======================== .. automodule:: bx.seq.seq_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.twobit.rst b/doc/source/lib/bx.seq.twobit.rst index 958cb2b0..b3bfd698 100644 --- a/doc/source/lib/bx.seq.twobit.rst +++ b/doc/source/lib/bx.seq.twobit.rst @@ -2,6 +2,6 @@ bx.seq.twobit module ==================== .. automodule:: bx.seq.twobit - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seq.twobit_tests.rst b/doc/source/lib/bx.seq.twobit_tests.rst index 7cbe2300..9bf1ca79 100644 --- a/doc/source/lib/bx.seq.twobit_tests.rst +++ b/doc/source/lib/bx.seq.twobit_tests.rst @@ -1,7 +1,7 @@ -bx.seq.twobit_tests module -========================== +bx.seq.twobit\_tests module +=========================== .. automodule:: bx.seq.twobit_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seqmapping.rst b/doc/source/lib/bx.seqmapping.rst index 6b5f1e14..ea2bb79a 100644 --- a/doc/source/lib/bx.seqmapping.rst +++ b/doc/source/lib/bx.seqmapping.rst @@ -2,6 +2,6 @@ bx.seqmapping module ==================== .. automodule:: bx.seqmapping - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.seqmapping_tests.rst b/doc/source/lib/bx.seqmapping_tests.rst index 6539435e..75512fdf 100644 --- a/doc/source/lib/bx.seqmapping_tests.rst +++ b/doc/source/lib/bx.seqmapping_tests.rst @@ -1,7 +1,7 @@ -bx.seqmapping_tests module -========================== +bx.seqmapping\_tests module +=========================== .. automodule:: bx.seqmapping_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.tabular.io.rst b/doc/source/lib/bx.tabular.io.rst index 213b3df0..330497fd 100644 --- a/doc/source/lib/bx.tabular.io.rst +++ b/doc/source/lib/bx.tabular.io.rst @@ -2,6 +2,6 @@ bx.tabular.io module ==================== .. automodule:: bx.tabular.io - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.tabular.rst b/doc/source/lib/bx.tabular.rst index 4b06698b..5da0affa 100644 --- a/doc/source/lib/bx.tabular.rst +++ b/doc/source/lib/bx.tabular.rst @@ -5,6 +5,7 @@ Submodules ---------- .. toctree:: + :maxdepth: 3 bx.tabular.io @@ -12,6 +13,6 @@ Module contents --------------- .. automodule:: bx.tabular - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.wiggle.rst b/doc/source/lib/bx.wiggle.rst index 50e6e43e..8f6e61bb 100644 --- a/doc/source/lib/bx.wiggle.rst +++ b/doc/source/lib/bx.wiggle.rst @@ -2,6 +2,6 @@ bx.wiggle module ================ .. automodule:: bx.wiggle - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx.wiggle_tests.rst b/doc/source/lib/bx.wiggle_tests.rst index 8c4408f6..f1f373c5 100644 --- a/doc/source/lib/bx.wiggle_tests.rst +++ b/doc/source/lib/bx.wiggle_tests.rst @@ -1,7 +1,7 @@ -bx.wiggle_tests module -====================== +bx.wiggle\_tests module +======================= .. automodule:: bx.wiggle_tests - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.fpconst.rst b/doc/source/lib/bx_extras.fpconst.rst index e193071d..208c54f0 100644 --- a/doc/source/lib/bx_extras.fpconst.rst +++ b/doc/source/lib/bx_extras.fpconst.rst @@ -1,7 +1,7 @@ -bx_extras.fpconst module -======================== +bx\_extras.fpconst module +========================= .. automodule:: bx_extras.fpconst - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.lrucache.rst b/doc/source/lib/bx_extras.lrucache.rst index e403ad6a..c717330c 100644 --- a/doc/source/lib/bx_extras.lrucache.rst +++ b/doc/source/lib/bx_extras.lrucache.rst @@ -1,7 +1,7 @@ -bx_extras.lrucache module -========================= +bx\_extras.lrucache module +========================== .. automodule:: bx_extras.lrucache - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.pstat.rst b/doc/source/lib/bx_extras.pstat.rst index 6aea33a6..c0a6a7ac 100644 --- a/doc/source/lib/bx_extras.pstat.rst +++ b/doc/source/lib/bx_extras.pstat.rst @@ -1,7 +1,7 @@ -bx_extras.pstat module -====================== +bx\_extras.pstat module +======================= .. automodule:: bx_extras.pstat - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.pyparsing.rst b/doc/source/lib/bx_extras.pyparsing.rst index 83f54313..7eab3e11 100644 --- a/doc/source/lib/bx_extras.pyparsing.rst +++ b/doc/source/lib/bx_extras.pyparsing.rst @@ -1,7 +1,7 @@ -bx_extras.pyparsing module -========================== +bx\_extras.pyparsing module +=========================== .. automodule:: bx_extras.pyparsing - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.rst b/doc/source/lib/bx_extras.rst index 239579f9..7e106af1 100644 --- a/doc/source/lib/bx_extras.rst +++ b/doc/source/lib/bx_extras.rst @@ -1,12 +1,14 @@ -bx_extras package -================= +bx\_extras package +================== Submodules ---------- .. toctree:: + :maxdepth: 3 bx_extras.fpconst + bx_extras.fpconst_tests bx_extras.lrucache bx_extras.pstat bx_extras.pyparsing @@ -16,6 +18,6 @@ Module contents --------------- .. automodule:: bx_extras - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/bx_extras.stats.rst b/doc/source/lib/bx_extras.stats.rst index 097eaed1..c13aa071 100644 --- a/doc/source/lib/bx_extras.stats.rst +++ b/doc/source/lib/bx_extras.stats.rst @@ -1,7 +1,7 @@ -bx_extras.stats module -====================== +bx\_extras.stats module +======================= .. automodule:: bx_extras.stats - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/lib/modules.rst b/doc/source/lib/modules.rst index a0bba841..7672e969 100644 --- a/doc/source/lib/modules.rst +++ b/doc/source/lib/modules.rst @@ -2,7 +2,7 @@ lib === .. toctree:: - :maxdepth: 4 + :maxdepth: 3 bx bx_extras diff --git a/doc/source/lib/psyco_full.rst b/doc/source/lib/psyco_full.rst index 370be057..6a398fe7 100644 --- a/doc/source/lib/psyco_full.rst +++ b/doc/source/lib/psyco_full.rst @@ -1,7 +1,7 @@ -psyco_full module -================= +psyco\_full module +================== .. automodule:: psyco_full - :members: - :undoc-members: - :show-inheritance: + :members: + :undoc-members: + :show-inheritance: diff --git a/doc/source/static/base.css b/doc/source/static/base.css deleted file mode 100644 index e8dbe6a6..00000000 --- a/doc/source/static/base.css +++ /dev/null @@ -1,152 +0,0 @@ -@import url(tripoli.base.css); - -html { - font-family: 'Verdana', sans-serif; - color: #333333; -} -body { - padding: 3em 3em; -} - -h1.pageheader { - font-variant: small-caps; - margin-top: 0; - border-top: solid 1px; - padding-top: 2px; - border-bottom: solid 1px; - border-color: #CCCCCC; - margin-bottom: 1em; -} - -h1.pageheader a { - color: inherit; - text-decoration: inherit; - border: none; -} - -.content h1, .content h2, .content h3, .content h4, .content h5, .content h6 { - font-family: 'Hoefler Text', 'Georgia', serif; - font-weight: normal; - color: #666666; - /* border-bottom: solid #666666 1px; */ -} - -.content h1.pagetitle { - color: #c33; -} - -#main { -} - -.colpad { - padding: 0 2em; -} - -#main > .inner { - min-width: 70em; - max-width: 90em; - margin: auto; - height: 100%; -} - -#left { - background: white; - margin-right: 36%; /* 31em; */ - padding-right: 3%; - height: 100%; -} - -#right { - float: right; - width: 33%; /* 28em; */ - padding-left: 3%; - border-left: solid #CCCCCC 1px; -} - -.sidebar { - font-size: 1em; -} - -.sidebar ul { - margin-left: 0; -} - -.sidebar ul li { - list-style-type: none; - margin-bottom: 0.6em; -} - -.sidebar ul.pages { - margin-left: 5px; - margin-top: 0.6em; -} - -.sidebar ul.pages li { - background: url(hbullet.png) 0 0.4em no-repeat; - padding-left: 25px; - list-style-type: none; -} - -.sidebar ul.pages li { -} - -.sidebar h1 { - clear: both; -} - -.sidebar .publications .info { - color: #666666; -} - -.postinfo { - color: #666666; - font-size: 92%; - margin-top: -1em; -} - -.postreadlink { - margin-top: -1em; -} - -.sidebar .posts .info { - color: #666666; -} - -.comments_title { - margin-top: 2em; -} - -label { - display: block; -} - -#footer { - clear: both; -} - -a, a:link, a:visited { - text-decoration: none; - border-bottom: dotted #666666 1px; - color: black; -} - -a:hover { - color: #CC3333; -} - -li { - list-style: square; -} - -table.layout td { - vertical-align: top; - padding-left: 2em; - padding-right: 2em; - border-left: solid #999999 1px -} - -hr { - border: none; - height: 1px; - background: #999999; -} diff --git a/doc/source/static/tripoli.base.css b/doc/source/static/tripoli.base.css deleted file mode 100644 index da578421..00000000 --- a/doc/source/static/tripoli.base.css +++ /dev/null @@ -1,509 +0,0 @@ -/* - * Tripoli is a generic CSS standard for HTML rendering. - * Copyright (C) 2007 David Hellsing - * - * http://devkick.com/lab/tripoli/ - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . -**/ - -/* -_______________________________ -RESET */ - -* -{ - text-decoration:none; - font-size:1em; - outline:none; - margin:0; - padding:0; -} - -code,kbd,samp,pre,tt,var,textarea,input,select,isindex,listing,xmp,plaintext -{ - font:inherit; - white-space:normal; -} - -a,img,a img,iframe,form,abbr,acronym,object,applet,table,a abbr,a acronym -{ - border-width:0; -} - -dfn,i,cite,var,address,em -{ - font-style:normal; -} - -th,b,strong,h1,h2,h3,h4,h5,h6,dt -{ - font-weight:normal; -} - -caption,th,td -{ - text-align:left; -} - -html -{ - background:white; - color:black; - line-height:1; - font-family:arial, sans-serif; -} - -/* \*/ - -html -{ - font-family:sans-serif; -} - -/* */ - -q -{ - quotes:"\201C""\201D""\2018""\2019"; -} - -ul,ol,dir,menu -{ - list-style:none; -} - -sub,sup -{ - vertical-align:baseline; -} - -a -{ - color:inherit; -} - -/* -_______________________________ -DISABLE DEPRECATED HTML */ - -font,basefont -{ - color:inherit; - font:inherit; - font-size:100%; 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Welcome

- -

- - The bx-python project is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: - -

    -
  • Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats)
    • -
  • Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems) -
    • -
  • Data structures for working with intervals on sequences
    • -
  • "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
    • -
  • "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
    • - - These tools have been used in a variety of published research, and are a fundamental part of the ongoing Galaxy and ESPERR projects. - -
- -

- -

Documentation

- - - -{% endblock %} diff --git a/doc/source/templates/indexsidebar.html b/doc/source/templates/indexsidebar.html deleted file mode 100644 index 4247e03b..00000000 --- a/doc/source/templates/indexsidebar.html +++ /dev/null @@ -1,9 +0,0 @@ -

About bx-python

- -

Current version: {{ version }}

- -

Download

- -

- bx-python source -

diff --git a/doc/source/templates/layout.html b/doc/source/templates/layout.html deleted file mode 100644 index 48b10452..00000000 --- a/doc/source/templates/layout.html +++ /dev/null @@ -1,51 +0,0 @@ -{% extends "!layout.html" %} - -{%- block document %} -
-
-
-

- bx-python -

-
- -
-
- {%- if builder != 'htmlhelp' %} -
- {%- endif %} -
- {% block body %} {% endblock %} -
- {%- if builder != 'htmlhelp' %} -
- {%- endif %} -
-
-
-
-{%- endblock %} - -{% block doctype %} - -{% endblock %} - -{% block rootrellink %} -
  • bx-python home
    • -
  • Table of contents
    • -{% endblock %} - -{# Sidebar and already handled #} - -{% block relbar1 %}{% endblock %} -{% block relbar2 %}{% endblock %} - -{% block sidebar1 %}{% endblock %} -{% block sidebar2 %}{% endblock %} - -{% block footer %}{% endblock %} \ No newline at end of file