Ak

README.md

@@ -32,7 +32,11 @@ MTpy is licensed under the GPL version 3
 The license agreement is contained in the repository and should be kept together with the code.
 
 
+<<<<<<< HEAD
 Copyright: Lars Krieger, Jared Peacock, Kent Inverarity, Alison Kirkby; Adelaide, 2013
+=======
+Copyright: Lars Krieger, Jared Peacock, Kent Inverarity, Alison Kirkby; Adelaide, 2015
+>>>>>>> beta
 
 
 

doc/Makefile

@@ -7,6 +7,11 @@ 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
@@ -29,17 +34,20 @@ help:
 	@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)/*
+	rm -rf $(BUILDDIR)/*
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@@ -108,6 +116,12 @@ latexpdf:
 	$(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
@@ -151,3 +165,13 @@ 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/analysis.rst

@@ -0,0 +1,31 @@
+***********
+Analysis 
+***********
+
+**Module Distortion**
+========================
+.. automodule:: mtpy.analysis.distortion
+	:members:
+
+**Module Geometry**
+========================
+.. automodule:: mtpy.analysis.geometry
+	:members:
+
+**Module Phase Tensor**
+========================
+.. automodule:: mtpy.analysis.pt
+	:members:
+
+**Module Static Shift**
+========================
+.. automodule:: mtpy.analysis.staticshift
+	:members:
+
+**Module Z Invariants**
+========================
+.. automodule:: mtpy.analysis.zinvariants
+	:members:
+
+
+

doc/conf.py

@@ -1,31 +1,53 @@
 # -*- coding: utf-8 -*-
 #
 # MTpy documentation build configuration file, created by
-# sphinx-quickstart on Tue Dec 17 11:03:33 2013.
+# sphinx-quickstart on Thu May 19 15:22:56 2016.
 #
-# This file is execfile()d with the current directory set to its containing dir.
+# 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, os
+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('.'))
+#sys.path.insert(0, os.path.abspath('.'))
 
-# -- General configuration -----------------------------------------------------
+# -- 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', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
+# 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',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+	'sphinx.ext.napoleon'
+]
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -37,20 +59,20 @@
 #source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = 'master_index'
 
 # General information about the project.
 project = u'MTpy'
-copyright = u'2013, Jared Peacock, Lars Krieger, Stephan Thiel, Kent Inverarity'
+copyright = u'2016, J. Peacock, L. Krieger'
 
 # 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 = '0.1'
+version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = '0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -66,7 +88,8 @@
 # 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.
+# 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.
@@ -86,8 +109,11 @@
 # 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 ---------------------------------------------------
+
+# -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
@@ -122,6 +148,11 @@
 # 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'
@@ -167,7 +198,7 @@
 htmlhelp_basename = 'MTpydoc'
 
 
-# -- Options for LaTeX output --------------------------------------------------
+# -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
 # The paper size ('letterpaper' or 'a4paper').
@@ -181,10 +212,11 @@
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'MTpy.tex', u'MTpy Documentation',
-   u'Jared Peacock, Lars Krieger, Stephan Thiel, Kent Inverarity', 'manual'),
+  ('master_index', 'MTpy.tex', u'MTpy Documentation',
+   u'J. Peacock, L. Krieger', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -208,27 +240,27 @@
 #latex_domain_indices = True
 
 
-# -- Options for manual page output --------------------------------------------
+# -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'mtpy', u'MTpy Documentation',
-     [u'Jared Peacock, Lars Krieger, Stephan Thiel, Kent Inverarity'], 1)
+    ('master_index', 'mtpy', u'MTpy Documentation',
+     [u'J. Peacock, L. Krieger'], 1)
 ]
 
 # If true, show URL addresses after external links.
 #man_show_urls = False
 
 
-# -- Options for Texinfo output ------------------------------------------------
+# -- 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', 'MTpy', u'MTpy Documentation',
-   u'Jared Peacock, Lars Krieger, Stephan Thiel, Kent Inverarity', 'MTpy', 'One line description of project.',
+  ('master_index', 'MTpy', u'MTpy Documentation',
+   u'J. Peacock, L. Krieger', 'MTpy', 'One line description of project.',
    'Miscellaneous'),
 ]
 
@@ -240,3 +272,76 @@
 
 # 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
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'MTpy'
+epub_author = u'J. Peacock, L. Krieger'
+epub_publisher = u'J. Peacock, L. Krieger'
+epub_copyright = u'2016, J. Peacock, L. Krieger'
+
+# The basename for the epub file. It defaults to the project name.
+#epub_basename = u'MTpy'
+
+# The HTML theme for the epub output. Since the default themes are not optimized
+# for small screen space, using the same theme for HTML and epub output is
+# usually not wise. This defaults to 'epub', a theme designed to save visual
+# space.
+#epub_theme = 'epub'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# A sequence of (type, uri, title) tuples for the guide element of content.opf.
+#epub_guide = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files shat should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+# Choose between 'default' and 'includehidden'.
+#epub_tocscope = 'default'
+
+# Fix unsupported image types using the PIL.
+#epub_fix_images = False
+
+# Scale large images.
+#epub_max_image_width = 0
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#epub_show_urls = 'inline'
+
+# If false, no index is generated.
+#epub_use_index = True