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Add auto-built docs to pipeline
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‎.travis.yml‎

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language: python
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python:
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- 3.6
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install:
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- pip install -r requirements.txt
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- pip install codecov
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- pip install pytest pytest-cov
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script:
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- pytest --cov=./
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- pytest --cov=./
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after_success:
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- codecov
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- cd docs && make html
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deploy:
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provider: pages
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skip_cleanup: true
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github_token: $githubtoken
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local_dir: docs/build/html
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keep_history: true
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on:
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branch: master

‎docs/Makefile‎

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

‎docs/make.bat‎

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

‎docs/source/codonPython.rst‎

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codonPython package
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===================
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Submodules
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----------
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codonPython.age\_bands module
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-----------------------------
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.. automodule:: codonPython.age_bands
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.check\_consistent\_measures module
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----------------------------------------------
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.. automodule:: codonPython.check_consistent_measures
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.check\_consistent\_submissions module
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-------------------------------------------------
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.. automodule:: codonPython.check_consistent_submissions
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.check\_nat\_val module
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----------------------------------
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.. automodule:: codonPython.check_nat_val
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.check\_null module
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------------------------------
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.. automodule:: codonPython.check_null
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.dateValidator module
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--------------------------------
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.. automodule:: codonPython.dateValidator
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.file\_utils module
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------------------------------
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.. automodule:: codonPython.file_utils
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.nhsd\_colours module
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--------------------------------
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.. automodule:: codonPython.nhsd_colours
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.nhsNumber module
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----------------------------
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.. automodule:: codonPython.nhsNumber
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.suppression module
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------------------------------
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.. automodule:: codonPython.suppression
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.tableFromSql module
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-------------------------------
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.. automodule:: codonPython.tableFromSql
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:members:
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:undoc-members:
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:show-inheritance:
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codonPython.tolerance module
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----------------------------
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.. automodule:: codonPython.tolerance
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:members:
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:undoc-members:
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:show-inheritance:
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Module contents
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---------------
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.. automodule:: codonPython
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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#
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# This file only contains a selection of the most common options. For a full
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# list see the documentation:
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# https://www.sphinx-doc.org/en/master/usage/configuration.html
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# -- Path setup --------------------------------------------------------------
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# If extensions (or modules to document with autodoc) are in another directory,
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# add these directories to sys.path here. If the directory is relative to the
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# documentation root, use os.path.abspath to make it absolute, like shown here.
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#
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import os
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import sys
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sys.path.insert(0, os.path.abspath("../../"))
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sys.setrecursionlimit(1500)
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# -- Project information -----------------------------------------------------
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project = 'codon'
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copyright = 'under BSD-5 license'
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author = 'PH, PE, NC, GR, MM'
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# The full version, including alpha/beta/rc tags
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release = '0.0.21'
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# -- General configuration ---------------------------------------------------
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# Add any Sphinx extension module names here, as strings. They can be
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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autodoc',
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'sphinx.ext.napoleon',
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'sphinx.ext.githubpages',
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]
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ['_templates']
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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# This pattern also affects html_static_path and html_extra_path.
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exclude_patterns = []
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# -- Options for HTML output -------------------------------------------------
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# The theme to use for HTML and HTML Help pages. See the documentation for
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# a list of builtin themes.
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#
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html_theme = "sphinx_rtd_theme"
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# Add any paths that contain custom static files (such as style sheets) here,
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# relative to this directory. They are copied after the builtin static files,
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# so a file named "default.css" will overwrite the builtin "default.css".
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html_static_path = ['_static']

‎docs/source/index.rst‎

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Welcome to codonPython's documentation!
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=================================
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To find the documentation for the module you want, please search or click on `module index`.
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/source/modules.rst‎

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codonPython
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===========
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.. toctree::
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:maxdepth: 4
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codonPython
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setup

‎docs/source/setup.rst‎

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setup module
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============
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.. automodule:: setup
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:members:
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:undoc-members:
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:show-inheritance:

‎requirements.txt‎

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scikit-learn>=0.21.2
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statsmodels>=0.10.0
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seaborn>=0.9.0
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sphinx>=2.2.2
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sphinx-rtd-theme>=0.4.3

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