Major docs update

README.rst

-========
-Overview
-========
-
-Goal
-----
-
-* Read in data for many channels and sources
-* Plot data for each channel in an interactive format
-* Easily see and keep track of combs
-* Organize plots by channel and time/date
-
-Status
-------
-
-Testing; likely to be buggy and constantly updated.
-
-=======
-Contact
-=======
-
-neunzert (at) umich (dot) edu
-
-============
-Dependencies
-============
-
-These scripts depend on a number of non-standard python libraries, namely:
-
-* gwpy (for loading data from detector channels)
-* bokeh (for interactive plotting)
-* pandas (for handling tables of data)
-* jinja2 (for creating web pages from a template)
-
-To avoid installing all of these things independently, work on the LHO cluster and source the following virtualenv::
-
-    $ source /home/aneunzert/gwypybokeh/bin/activate
-
-If you would like to work on a different cluster, email me and I will happily clone the virtualenv where necessary.
-
-======
-Basics
-======
-
-.. image:: finetooth_workflow.png
-
-* Modular workflow
-* All options are documented in their respective scripts; run ``python scriptname.py --help`` to see what is available (where scriptname is whatever python script you're trying to learn about).
-* See `the tutorial <tutorial.rst>`_ (in progress) to get started.
-* Comb finding is documented in `a separate file <combfinding.rst>`_ as it is currently a standalone task. This will also be addressed in the expanded version of the tutorial.
+Documentation for this project has recently been overhauled. Rendered docs can be found on my public_html page `here <https://ldas-jobs.ligo-wa.caltech.edu/~aneunzert/FineToothDocs/build/html/>`_ . All source files are also available in the repository under docs/source.

chdata.py

 from __future__ import division
 import argparse
 
+def makeparser():
+
 	parser = argparse.ArgumentParser(description="Calculate and save spectra using GWpy.")
 	parser.register('type', 'bool', (lambda x: x.lower() in ("yes", "true", "t", "1")))
 	parser.add_argument("--chlist",help="Channel list source (path to a newline-delimited text file)")
@@ -13,8 +15,11 @@ parser.add_argument("--ffttime",help="FFT time (s) (default 20)",default=20,type
 	parser.add_argument("--fftoverlap",help="FFT overlap (default 0.5)",default=0.5,type=float)
 	parser.add_argument("--verbose",help="Verbose output (default false)",default=False)
 	parser.add_argument("--overwrite",help="Overwrite existing files (default false)",default=False)
-args=parser.parse_args()
 
+	return parser
+
+def main():
+	''' '''
 
 	import os
 	import sys
@@ -25,6 +30,8 @@ from gwpy import time
 	import numpy as np
 	import hdf5io as h5
 
+	args=makeparser().parse_args()
+
 	# Get list of channels from the supplied txt file
 	f=open(args.chlist,'r')
 	chlist = [line[:-1] for line in f]
@@ -70,3 +77,6 @@ for ch in chlist:
 				continue
 
 	print("Program complete.")
+
+if __name__ == '__main__':
+	main()

chdataFscan.py

@@ -2,6 +2,7 @@ from __future__ import division
 import argparse
 import datetime
 
+def makeparser():
 	parser=argparse.ArgumentParser()
 	parser.register('type', 'bool', (lambda x: x.lower() in ("yes", "true", "t", "1")))
 	parser.add_argument("-d", "--date",help="Date in format \"YYYY-MM-DD\" (Default is today).",default=datetime.date.today().strftime('%Y-%m-%d'))
@@ -15,7 +16,12 @@ parser.add_argument("-s","--start",help="Start date for plots",default="")
 	parser.add_argument("-c","--cumulative",help="Compute cumulative plots (default=False)",default=False)
 	parser.add_argument("-w","--overwrite",help="Overwrite existing files.",type='bool',default=False)
 	parser.add_argument("-x","--checkOnly",help="Don't compute anything, just print which days have data.",type='bool',default=False)
-args=parser.parse_args()
+
+	return parser
+
+def main():
+	''' '''
+	args=makeparser().parse_args()
 
 	import sys
 	import os
@@ -211,3 +217,6 @@ for ch in chlist:
 					else:
 						print("Could not time-averaged spectrum files either.")
 						continue
+
+if __name__ == '__main__':
+	main()

chplot.py

@@ -2,6 +2,7 @@ from __future__ import division
 import argparse
 import glob
 
+def makeparser():
 	parser = argparse.ArgumentParser(description="Plot comb spectra using Bokeh. To run this script, first: $source /home/aneunzert/gwpybokeh/bin/activate")
 	parser.register('type', 'bool', (lambda x: x.lower() in ("yes", "true", "t", "1")))
 	parser.add_argument("--foldername",nargs="+",type=str,help="Name of folder to process (should point to a folder containing gz files generated by chdata.py)")
@@ -16,7 +17,13 @@ parser.add_argument("--verbose",help="Verbose output for errors (default=False)"
 	parser.add_argument("--truefcutoff",help="Truncate the frequency range (not just limiting the x-axis of initial plotting). Good for high resolution. (default=False)",type='bool',default=False)
 	parser.add_argument("--knownLinesFile",help="A file containing known lines and their descriptions, which should be added to the plot",default=None)
 	parser.add_argument("--zeroKnownLines",help="Zero out the known lines (requires knownLinesFile)",type='bool',default=False)
-args=parser.parse_args()
+
+	return parser
+
+def main():
+	''' '''
+
+	args=makeparser().parse_args()
 
 	import os
 	import sys
@@ -108,3 +115,7 @@ for folderpattern in args.foldername:
 						if args.verbose==True:
 							print(traceback.format_exc())
 						continue
+
+
+if __name__ == '__main__':
+	main()

docs/source/_static/custom.css

+.literal {
+font-weight: bold!important;
+}
+
+p {
+padding-bottom:10px!important;
+}

combfinding.rst → docs/source/combfinding.rst

-Introduction
-============
++++++++++++++++++++++++++
+Comb finding introduction
++++++++++++++++++++++++++
+
+Notes
+-----
 
 This document is an overview of the function *auto_find_comb()* in combfinder.py .
 
-NOTICE: this is in an early stage of development, is likely to be buggy, and will be constantly updated!
+NOTICE: this is in an early stage of development, is likely to be buggy, and will be constantly updated. Trust nothing!
 
 Quick start
 -----------
@@ -18,30 +22,27 @@ This will return a structured array containing frequency spacings ('sp'), offset
         comb[2]['str']
 
 
-Detailed explanation of optional parameters
--------------------------------------------
-
-Complete syntax::
-
-        auto_find_comb(vFreq,vData,scaleRange=5,nCheckAdj=2,nConsecReq=5,nTopPeaks=600,nNearestAmpNeighbors=30,nMostCommonCombs=300,spacingmin=None,spacingmax=None,verbose=False,showBeforeZeroing=False):
+Algorithm and parameter details
+-------------------------------
 
-This kind of requires a full explanation of the code. Optional parameter names are *emphasized*  so that its clear where they appear.
+.. autofunction:: combfinder.auto_find_comb
+   :noindex:
 
 This algorithm proceeds as follows:
 
-* Flatten the data, to avoid getting thrown off by changes in the overall noise level across the spectrum. For each bin, the sum of the nearest *scaleRange* bins is calculated, and the bin values is divided by that total.
+* Flatten the data, to avoid getting thrown off by changes in the overall noise level across the spectrum. For each bin, the sum of the nearest ``scaleRange`` bins is calculated, and the bin values is divided by that total.
 
-* Determine which points on the spectrum are peaks. Peaks are defined as bins with values higher than the *nCheckAdj* adjacent bins.
+* Determine which points on the spectrum are peaks. Peaks are defined as bins with values higher than the ``nCheckAdj`` adjacent bins.
 
-* Get a sorted list of the *nTopPeaks* highest-amplitude peaks.
+* Get a sorted list of the ``nTopPeaks`` highest-amplitude peaks.
 
-* For each peak in the list, consider its *nNearestAmpNeighbors* nearest neighbors in amplitude. For each (peak, neighbor) pair, calculate the spacing and offset of the simplest comb on which both members of the pair would fall. (Spacing = frequency difference, offset = frequency of either, modulo spacing.) Append this spacing and offset to a list of comb candidates.
+* For each peak in the list, consider its ``nNearestAmpNeighbors`` nearest neighbors in amplitude. For each (peak, neighbor) pair, calculate the spacing and offset of the simplest comb on which both members of the pair would fall. (Spacing = frequency difference, offset = frequency of either, modulo spacing.) Append this spacing and offset to a list of comb candidates.
 
-* If the user has supplied *spacingmin* or *spacingmax*, reject any combs with spacings that fall outside this range. Otherwise, skip this step.
+* If the user has supplied ``spacingmin`` or ``spacingmax``, reject any combs with spacings that fall outside this range. Otherwise, skip this step.
 
-* Count how many times each comb candidate appears in the list. Retain the *nMostCommonCombs* most common candidates.
+* Count how many times each comb candidate appears in the list. Retain the ``nMostCommonCombs`` most common candidates.
 
-* Calculate an improved strength statistic for each comb candidate retained. This uses *nCheckAdj* (again) and *nConsecReq*. More detail is given in the following section.
+* Calculate an improved strength statistic for each comb candidate retained. This uses ``nCheckAdj`` (again) and ``nConsecReq``. More detail is given in the following section.
 
 * Organize the combs by strength statistic.
 
@@ -51,10 +52,10 @@ This algorithm proceeds as follows:
 
 * Return all the combs found.
 
-* If *verbose* is specified, print detailed information. If *showBeforeZeroing* is specified, show all the combs prior to the iterative zeroing process.
+* If ``verbose`` is specified, print detailed information. If ``showBeforeZeroing`` is specified, show all the combs prior to the iterative zeroing process.
 
-Strength statistic details
---------------------------
+Comb "likelihood" statistic
+---------------------------
 
 At present, the strength of a comb is given by this formula (which was found by some vague logic + trial and error) (pseudocode).
 
@@ -62,9 +63,9 @@ Note that this is a very ad-hoc method and I'm working on improving it.
 
 * Predict bins where the comb should lie.
 
-* Determine if each predicted bin contains a peak, using the requirement that it be higher than *nCheckAdj* of its neighbors.
+* Determine if each predicted bin contains a peak, using the requirement that it be higher than ``nCheckAdj`` of its neighbors.
 
-* If the bin contains a peak, and is also part of a row of more than *nConsecReq* consecutive peaks, consider it to be a 'real' part of the comb.
+* If the bin contains a peak, and is also part of a row of more than ``nConsecReq`` consecutive peaks, consider it to be a 'real' part of the comb.
 
 * Multiply the following quantities together:
 

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# FineTooth documentation build configuration file, created by
+# sphinx-quickstart on Thu Sep  8 13:52:19 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# 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 extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../..'))
+
+def setup(app):
+    app.add_stylesheet('custom.css')
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# 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.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinxarg.ext'
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The encoding of source files.
+#
+# source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'FineTooth'
+copyright = u'2016, Ansel Neunzert'
+author = u'Ansel Neunzert'
+
+# 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.
+version = u'0.1'
+# The full version, including alpha/beta/rc tags.
+release = u'0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+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 patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = []
+
+# 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'
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'nature'
+
+# 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
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+html_title = u'FineTooth v0.1'
+
+# 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 (relative to this directory) to use as a 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']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#
+# html_extra_path = []
+
+# If not None, a 'Last updated on:' timestamp is inserted at every page
+# bottom, using the given strftime format.
+# The empty string is equivalent to '%b %d, %Y'.
+#
+# html_last_updated_fmt = None
+
+# 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_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#
+# html_additional_pages = {}
+
+# If false, no module index is generated.
+#
+# html_domain_indices = 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, links to the reST sources are added to the pages.
+#
+# html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+# html_file_suffix = None
+
+# Language to be used for generating the HTML full-text search index.
+# Sphinx supports the following languages:
+#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
+#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
+#
+# html_search_language = 'en'
+
+# A dictionary with options for the search language support, empty by default.
+# 'ja' uses this config value.
+# 'zh' user can custom change `jieba` dictionary path.
+#
+# html_search_options = {'type': 'default'}
+
+# The name of a javascript file (relative to the configuration directory) that
+# implements a search results scorer. If empty, the default will be used.
+#
+# html_search_scorer = 'scorer.js'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'FineTooth'
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+     # The paper size ('letterpaper' or 'a4paper').
+     #
+     # 'papersize': 'letterpaper',
+
+     # The font size ('10pt', '11pt' or '12pt').
+     #
+     # 'pointsize': '10pt',
+
+     # Additional stuff for the LaTeX preamble.
+     #
+     # 'preamble': '',
+
+     # Latex figure (float) alignment
+     #
+     # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'FineTooth.tex', u'FineTooth Documentation',
+     u'Ansel Neunzert', 'manual'),
+]
+
+# 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
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'finetoothdocs', u'FineTooth Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'FineTooth', u'FineTooth Documentation',
+     author, 'FineTooth', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False

docs/source/funcdocs.rst

+========================
+Module and function docs
+========================
+
+chdata.py (script)
+------------------
+
+Source
+~~~~~~
+.. automodule:: chdata
+   :members:
+
+Options
+~~~~~~~
+.. argparse::
+   :ref: chdata.makeparser
+   :prog: chdata
+
+chdataFscan.py (script)
+-----------------------
+
+Source
+~~~~~~
+.. automodule:: chdataFscan
+   :members:
+
+Options
+~~~~~~~
+.. argparse::
+   :ref: chdataFscan.makeparser
+   :prog: chdataFscan
+
+chplot.py (script)
+------------------
+
+Source
+~~~~~~
+.. automodule:: chplot
+   :members:
+
+Options
+~~~~~~~
+.. argparse::
+   :ref: chplot.makeparser
+   :prog: chplot
+
+combfinder.py (module only)
+---------------------------
+
+.. automodule:: combfinder
+   :members:
+
+hdf5io.py (module only)
+-----------------------
+
+(This module has yet to be documented/expanded)
+
+.. automodule:: hdf5io
+   :members:
+   :undoc-members:

docs/source/index.rst

+.. FineTooth documentation master file, created by
+   sphinx-quickstart on Thu Sep  8 13:52:19 2016.
+
+FineTooth documentation
+=======================
+
+[`Gitlab repository <https://gitlab.aei.uni-hannover.de/aneunzert/FineTooth/>`_]
+
+.. toctree::
+   :maxdepth: 2
+
+   overview
+   tutorial
+   funcdocs
+   combfinding
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/source/overview.rst

+++++++++
+Overview
+++++++++
+
+Goals
+=====
+
+* Read in data for many channels and sources
+* Plot data for each channel in an interactive format
+* Easily see and keep track of combs
+* Organize plots by channel and time/date
+
+Status
+======
+
+Testing; likely to be buggy and constantly updated.
+
+Contact
+=======
+
+neunzert (at) umich (dot) edu
+
+Dependencies
+============
+
+These scripts depend on a number of non-standard python libraries, namely:
+
+* gwpy (for loading data from detector channels)
+* bokeh (for interactive plotting)
+* pandas (for handling tables of data)
+* jinja2 (for creating web pages from a template)
+
+To avoid installing all of these things independently, work on the LHO cluster and source the following virtualenv::
+
+    $ source /home/aneunzert/gwypybokeh/bin/activate
+
+If you would like to work on a different cluster, email me and I will happily clone the virtualenv where necessary.
+
+Structure
+=========
+
+.. image:: _static/finetooth_workflow.png
+

tutorial.rst → docs/source/tutorial.rst

-[WORK IN PROGRESS]
+++++++++
+Tutorial
+++++++++
 
-This is a tutorial for getting started with FineTooth. If you can run through this tutorial, everything should be in working order.
 
 Loading and plotting data
 -------------------------