First very draft version of the documentation

doc/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = .build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Routing-WS.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Routing-WS.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/Routing-WS"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Routing-WS"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

doc/conf.py

+# -*- coding: utf-8 -*-
+#
+# dasscripts documentation build configuration file, created by
+# sphinx-quickstart on Dec 19 21:39:29 2019.
+#
+# 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.
+
+import sys
+import os
+
+# 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.
+sys.path.insert(0, os.path.abspath('..'))
+
+# -- 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.todo',
+]
+
+# 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-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'dasscripts'
+copyright = u'2019-2020, Javier Quinteros - Deutsches GFZ Potsdam'
+author = u'Javier Quinteros'
+
+# 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 = '0.2'
+# The full version, including alpha/beta/rc tags.
+release = '0.2b1'
+
+# 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 patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['.build']
+
+# 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
+show_authors = True
+
+# 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
+
+
+# -- 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 = 'default'
+
+# 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 = {
+    'collapse_navigation': False,
+    'externalrefs': True,
+    'navigation_depth': 2,
+    'prev_next_buttons_location': 'both'
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+html_title = 'Dasscripts Documentation'
+
+# 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']
+
+# 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 '', 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_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
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Dasscripts-doc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
+    'papersize': 'a4paper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
+}
+
+# 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 = [
+  ('index', 'Dasscripts-Documentation.tex', u'Dasscripts Documentation',
+   u'Javier Quinteros', 'manual')
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = 'GFZ-logo.jpg'
+
+# 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 = [
+    ('index', 'dasscripts', u'Dasscripts Documentation',
+     [u'Javier Quinteros'], 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 = [
+  ('index', 'Dasscripts', u'Dasscripts Documentation',
+   u'Javier Quinteros', 'Dasscripts', 'Scripts to convert and manage data from DAS systems.',
+   '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

doc/dasconv.rst

+dasconv package
+===============
+
+.. automodule:: dasconv
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/index.rst

+Dasscripts documentation
+########################
+
+.. toctree::
+    :maxdepth: 2
+    :numbered:
+    :titlesonly:
+
+    userdoc.rst
+    modules.rst
+

doc/modules.rst

+Developer documentation
+=======================
+
+.. toctree::
+   :maxdepth: 4
+
+   dasconv

doc/userdoc.rst

+Dasscripts User documentation
+#############################
+
+Summary
+=======
+
+Dasscripts is basically a set of scripts to properly manage seismic
+waveforms from DAS systems.
+
+
+Installation
+============
+
+License
+-------
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Requirements
+------------
+
+ * Python 3.6+
+
+ * Obspy
+
+.. _installation:
+
+Installation
+------------
+
+This software can be easily installed by means of pip with the following command ::
+
+    $ sudo pip install dasscripts
+
+Optionally you could run it as a normal user (no sudo) and deploy it locally.
+
+.. _installation_from_code:
+
+Installation from source code
+-----------------------------
+
+You can always get the latest version of Dasscripts from its repository using git ::
+
+    $ git clone https://gitext.gfz-potsdam.de/javier/dasscripts.git
+
+This will create a folder called dasscripts from which you can install the software ::
+
+    $ cd dasscripts
+    $ sudo python3 setup.py install
+
+Running the code
+================
+
+To check if the software was properly installed you can run ::
+
+    $ dasconv -h
+    usage: dasconv [-h] [-l {CRITICAL,ERROR,WARNING,INFO,DEBUG}] [-d DIRECTORY]
+                   [--start START] [--end END] [--chstart CHSTART]
+                   [--chstop CHSTOP] [--chstep CHSTEP] [--decimate DECIMATE]
+                   [--version]
+                   filename
+
+    Read, manipulate and convert seismic waveforms generated by a DAS system.
+
+    positional arguments:
+      filename              Experiment to read and process. It is usually the
+                            first part of the filenames.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -l {CRITICAL,ERROR,WARNING,INFO,DEBUG}, --loglevel {CRITICAL,ERROR,WARNING,INFO,DEBUG}
+                            Verbosity in the output.
+      -d DIRECTORY, --directory DIRECTORY
+                            Directory where files are located.
+      --start START, --starttime START
+                            Start of the selected time window. Format:
+                            2019-02-01T00:01:02.123456Z
+      --end END, --endtime END
+                            End of the selected time window. Format:
+                            2019-02-01T00:01:02.123456Z
+      --chstart CHSTART     First channel to export
+      --chstop CHSTOP       Last channel to export
+      --chstep CHSTEP       Step between channels in the selection
+      --decimate {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16}
+                            Factor by which the sampling rate is lowered by
+                            decimation.
+      --metadata            Read and display the metadata from the TDMS files
+      --version             show program's version number and exit
+
+
+dasconv can be used to convert data from TDMS format into miniSEED. Below you will find some examples showing how to
+use it to select subsets of the original data and export it. A complete list of its parameters and default values can
+be found in the :ref:`Table of parameters<Table_Parameters>`
+
+.. _Table_Parameters:
+
+.. tabularcolumns:: |l|l|l|p{8cm}|c|
+.. table:: Input parameters description
+
+ =================== ======== ========================================= ==========
+ Parameter           Format   Description                               Default
+ =================== ======== ========================================= ==========
+ filename             str     Experiment to read and process. It is
+                              usually the first part of the filenames.
+                              It is mandatory to provide it
+ --directory (-d)     str     Directory where the data is saved          ``.``
+ --starttime (start) ISO 8601 Limit results to time series samples on
+                              or after the specified start time.         Any
+ --endtime (end)     ISO 8601 Limit results to time series samples on
+                              or before the specified end time.          Any
+ --chstart            int     First channel to be read and exported      ``0``
+ --chend              int     Last channel to be read and exported       last one
+ --chstep             int     Step to calculate the index of the next
+                              channel to export (1: next one; 2: skip
+                              one, etc)                                  ``1``
+ --decimate           int     Factor by which the sampling rate is
+                              lowered by decimation. Exactly the factor
+                              by which the number of samples will be
+                              reduced                                    ``5``
+ --metadata           bool    Read and display metadata information
+                              instead of exporting data                  Disable
+ --version            bool    Print version information                  Disable
+ =================== ======== ========================================= ==========
+
+
+
+
+Examples
+--------
+
+* Export waveforms from channels 800, 802 and 804 starting at 2019-05-08T09:37:35.409000 until 2019-05-08T09:38:05.400000.
+The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
+
+    dasconv -d /home/user/test/ --start "2019-05-08T09:37:35.409000" --end "2019-05-08T09:38:05.400000" default --chstart 800 --chstop 805 --chstep 2
+
+* Export waveforms from channels 0 and 1 from the beginning of the measurements until 2019-05-08T09:32:15.
+The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
+
+    dasconv -d /home/user/test/ --endtime "2019-05-08T09:32:15" default --chstart 0 --chstop 1
+
+* Export waveforms from channels 0 to 4 from the beginning of the measurements until 2019-05-08T09:32:15.
+The waveforms will be exported to MiniSEED format after being decimated by a factor of 5 (e.g. from 1000Hz to 200Hz). ::
+
+    dasconv -d /home/user/test/ --endtime "2019-05-08T09:32:15" default --chstart 0 --chstop 4 --decimate 2
+
+
+Testing the service
+-------------------
+
+.. todo:: Provide a ``test`` directory with a tdms file and its miniSEED version. Use dasconv to convert the data and
+check with the provided miniSEED file. The same for an ASCII format.
+
+Two scripts are provided to test the functionality of the service at different
+levels. These can be found in the ``test`` folder under the root directory of
+your installation.