Update sphinx doc style

.gitignore

@@ -1,4 +1,4 @@
-.*
+.
 
 # Compiled python modules.
 *.pyc
@@ -19,5 +19,4 @@ docs/build*
 *.ipynb
 
 # python cache
-*/__pycache__/*
-
+*/__pycache__/*

docs/Makefile

@@ -1,10 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = funpipe
+# 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
 

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -39,6 +39,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'numpydoc',
     'sphinx.ext.autodoc',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
@@ -81,7 +82,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -167,4 +168,4 @@
 # -- Options for todo extension ----------------------------------------------
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
+todo_include_todos = True

docs/source/funpipe.rst

@@ -0,0 +1,109 @@
+funpipe package
+===============
+
+bam
+---
+
+.. automodule:: funpipe.bam
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fasta
+-----
+
+.. automodule:: funpipe.fasta
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+fastq
+-----
+
+.. automodule:: funpipe.fastq
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gatk
+----
+
+.. automodule:: funpipe.gatk
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+gt_pair
+-------
+
+.. automodule:: funpipe.gt_pair
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+microbiome
+----------
+
+.. automodule:: funpipe.microbiome
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+phylo
+-----
+
+.. automodule:: funpipe.phylo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+picard
+------
+
+.. automodule:: funpipe.picard
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+plink
+-----
+
+.. automodule:: funpipe.plink
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+utils
+-----
+
+.. automodule:: funpipe.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+vcf
+---
+
+.. automodule:: funpipe.vcf
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+vcfheader
+---------
+
+.. automodule:: funpipe.vcfheader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+vcfrecord
+---------
+
+.. automodule:: funpipe.vcfrecord
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+

docs/source/index.rst

@@ -1,24 +1,16 @@
 .. funpipe documentation master file, created by
-   sphinx-quickstart on Tue Apr  3 12:01:06 2018.
+   sphinx-quickstart on Sat Jul  3 23:56:18 2021.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
 Welcome to funpipe's documentation!
-===========================================
+===================================
 
 .. toctree::
- :maxdepth: 2
-
-    Installation <getting_started>
-    Tutorials <tutorials-landing>
-    Reference (Python API) <api>
-    Overview <overview/index>
-    Datasets <datasets>
-    How-To Guides <guides>
-    For Software Developers <getting_started_developing>
-    Other Resources <other_resources>
-    Change Log <change_log>
-
+   :maxdepth: 3
+   :caption: Contents:
+
+   funpipe
 
 
 Indices and tables

docs/source/modules.rst

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

docs/source/requirements.txt

@@ -0,0 +1,9 @@
+# crimson==1.1.0
+# matplotlib==3.7.1
+# numpy==1.24.2
+# pandas==1.5.3
+# scipy==1.10.1
+# seaborn==0.12.2
+# setuptools==65.6.3
+sphinx-rtd-theme==1.2.0
+numpydoc==1.5.0

readthedocs.yml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/source/requirements.txt

requirements.txt

@@ -1,2 +1,10 @@
-include README.md
-
+crimson==1.1.0
+matplotlib==3.7.1
+numpy==1.24.2
+pandas==1.5.3
+scipy==1.10.1
+seaborn==0.12.2
+setuptools==65.6.3
+# these are auto-doc packages and specify in /docs/source/requirements.txt
+# sphinx-rtd-theme==1.2.0
+# numpydoc==1.5.0

scripts/fastqc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 import argparse
 import os
-from funpipe import bam.fastqc, picard
+from funpipe.bam import fastqc, picard
 
 
 def bam_fast_qc(bam, ref_fa, out_dir, prefix):