Merge pull request #2 from dmitrymyl/module_development

Module development

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/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: aacbdeae40c09c4f4a2033e0ffce02c6
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/index.rst.txt

@@ -0,0 +1,20 @@
+.. ortho2align documentation master file, created by
+   sphinx-quickstart on Wed Nov 20 18:27:31 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to ortho2align's documentation!
+=======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/build/html/_sources/modules.rst.txt

@@ -0,0 +1,7 @@
+ortho2align
+===========
+
+.. toctree::
+   :maxdepth: 4
+
+   ortho2align

docs/build/html/_sources/ortho2align.rst.txt

@@ -0,0 +1,62 @@
+ortho2align package
+===================
+
+Submodules
+----------
+
+ortho2align.alignment module
+----------------------------
+
+.. automodule:: ortho2align.alignment
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ortho2align.cli\_scripts module
+-------------------------------
+
+.. automodule:: ortho2align.cli_scripts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ortho2align.fitting module
+--------------------------
+
+.. automodule:: ortho2align.fitting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ortho2align.genomicranges module
+--------------------------------
+
+.. automodule:: ortho2align.genomicranges
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ortho2align.orthodb module
+--------------------------
+
+.. automodule:: ortho2align.orthodb
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ortho2align.parallel module
+---------------------------
+
+.. automodule:: ortho2align.parallel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: ortho2align
+   :members:
+   :undoc-members:
+   :show-inheritance: