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/*
* sphinxdoc.css_t
* ~~~~~~~~~~~~~~~
*
* Sphinx stylesheet -- sphinxdoc theme. Originally created by
* Armin Ronacher for Werkzeug.
*
* :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
'Verdana', sans-serif;
font-size: 14px;
letter-spacing: -0.01em;
line-height: 150%;
text-align: center;
background-color: #BFD1D4;
color: black;
padding: 0;
border: 1px solid #aaa;
margin: 0px 80px 0px 80px;
min-width: 740px;
}
div.document {
background-color: white;
text-align: left;
background-image: url(contents.png);
background-repeat: repeat-x;
}
div.bodywrapper {
margin: 0 240px 0 0;
border-right: 1px solid #ccc;
}
div.body {
margin: 0;
padding: 0.5em 20px 20px 20px;
}
div.related {
font-size: 1em;
}
div.related ul {
background-image: url(navigation.png);
height: 2em;
border-top: 1px solid #ddd;
border-bottom: 1px solid #ddd;
}
div.related ul li {
margin: 0;
padding: 0;
height: 2em;
float: left;
}
div.related ul li.right {
float: right;
margin-right: 5px;
}
div.related ul li a {
margin: 0;
padding: 0 5px 0 5px;
line-height: 1.75em;
color: #EE9816;
}
div.related ul li a:hover {
color: #3CA8E7;
}
div.sphinxsidebarwrapper {
padding: 0;
}
div.sphinxsidebar {
margin: 0;
padding: 0.5em 15px 15px 0;
width: 210px;
float: right;
font-size: 1em;
text-align: left;
}
div.sphinxsidebar h3, div.sphinxsidebar h4 {
margin: 1em 0 0.5em 0;
font-size: 1em;
padding: 0.1em 0 0.1em 0.5em;
color: white;
border: 1px solid #86989B;
background-color: #AFC1C4;
}
div.sphinxsidebar h3 a {
color: white;
}
div.sphinxsidebar ul {
padding-left: 1.5em;
margin-top: 7px;
padding: 0;
line-height: 130%;
}
div.sphinxsidebar ul ul {
margin-left: 20px;
}
div.footer {
background-color: #E3EFF1;
color: #86989B;
padding: 3px 8px 3px 0;
clear: both;
font-size: 0.8em;
text-align: right;
}
div.footer a {
color: #86989B;
text-decoration: underline;
}
/* -- body styles ----------------------------------------------------------- */
p {
margin: 0.8em 0 0.5em 0;
}
a {
color: #000000; /*!!! MAKE LINKS ORANGE AGAIN: #CA7900;*/
text-decoration: none;
}
a:hover {
color: #2491CF;
}
div.body a {
text-decoration: none; /*!!! UNDERLINE LINKS AGAIN: underline;*/
}
h1 {
margin: 0;
padding: 0.7em 0 0.3em 0;
font-size: 1.5em;
color: #11557C;
background-color: #ccd8ff;
}
h2 {
margin: 1.3em 0 0.2em 0;
font-size: 1.35em;
padding: 0;
background-color: #ccd8ff;
}
h3 {
margin: 1em 0 -0.3em 0;
font-size: 1.2em;
background-color: #ccd8ff;
}
h4 {
background-color: #ccd8ff
}
h5 {
background-color: #ccd8ff
}
div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a {
color: black!important;
}
h1 a.anchor, h2 a.anchor, h3 a.anchor, h4 a.anchor, h5 a.anchor, h6 a.anchor {
display: none;
margin: 0 0 0 0.3em;
padding: 0 0.2em 0 0.2em;
color: #aaa!important;
}
h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor,
h5:hover a.anchor, h6:hover a.anchor {
display: inline;
}
h1 a.anchor:hover, h2 a.anchor:hover, h3 a.anchor:hover, h4 a.anchor:hover,
h5 a.anchor:hover, h6 a.anchor:hover {
color: #777;
background-color: #eee;
}
a.headerlink {
color: #c60f0f!important;
font-size: 1em;
margin-left: 6px;
padding: 0 4px 0 4px;
text-decoration: none!important;
}
a.headerlink:hover {
background-color: #ccc;
color: white!important;
}
cite, code, tt {
font-family: 'Consolas', 'Deja Vu Sans Mono',
'Bitstream Vera Sans Mono', monospace;
font-size: 1.17em;
letter-spacing: 0.01em;
}
tt {
background-color: #f2f2f2;
border-bottom: 1px solid #ddd;
color: #333;
}
tt.descname, tt.descclassname, tt.xref {
border: 0;
}
hr {
border: 1px solid #abc;
margin: 2em;
}
a tt {
border: 0;
color: #CA7900;
}
a tt:hover {
color: #2491CF;
}
th {
background-color: #fff3cc;
}
pre {
font-family: 'Consolas', 'Deja Vu Sans Mono',
'Bitstream Vera Sans Mono', monospace;
font-size: 0.95em;
letter-spacing: 0.015em;
line-height: 120%;
padding: 0.5em;
border: 1px solid #ccc;
background-color: #f8f8f8;
}
pre a {
color: inherit;
text-decoration: underline;
}
td.linenos pre {
padding: 0.5em 0;
}
div.quotebar {
background-color: #f8f8f8;
max-width: 250px;
float: right;
padding: 2px 7px;
border: 1px solid #ccc;
}
div.topic {
background-color: #f8f8f8;
}
table {
border-collapse: collapse;
margin: 0 -0.5em 0 -0.5em;
}
table td, table th {
padding: 0.2em 0.5em 0.2em 0.5em;
}
div.admonition, div.warning {
font-size: 0.9em;
margin: 1em 0 1em 0;
border: 1px solid #86989B;
background-color: #f7f7f7;
padding: 0;
}
div.admonition p, div.warning p {
margin: 0.5em 1em 0.5em 1em;
padding: 0;
}
div.admonition pre, div.warning pre {
margin: 0.4em 1em 0.4em 1em;
}
div.admonition p.admonition-title,
div.warning p.admonition-title {
margin: 0;
padding: 0.1em 0 0.1em 0.5em;
color: white;
border-bottom: 1px solid #86989B;
font-weight: bold;
background-color: #AFC1C4;
}
div.warning {
border: 1px solid #940000;
}
div.warning p.admonition-title {
background-color: #CF0000;
border-bottom-color: #940000;
}
div.admonition ul, div.admonition ol,
div.warning ul, div.warning ol {
margin: 0.1em 0.5em 0.5em 3em;
padding: 0;
}
div.versioninfo {
margin: 1em 0 0 0;
border: 1px solid #ccc;
background-color: #DDEAF0;
padding: 8px;
line-height: 1.3em;
font-size: 0.9em;
}
.viewcode-back {
font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
'Verdana', sans-serif;
}
div.viewcode-block:target {
background-color: #f4debf;
border-top: 1px solid #ac9;
border-bottom: 1px solid #ac9;
}
\ No newline at end of file
docs/Pyramid Logo.png → docs/EMPyRe Logo.png
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docs/Makefile
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# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
PAPER =
BUILDDIR = .build
# You can set these variables from the command line, and also
# from the environment for the first two.
SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
SOURCEDIR = .
BUILDDIR = _build
# 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
# Put it first so that "make" without argument is like "make help".
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 " applehelp to make an Apple Help Book"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " epub3 to make an epub3"
@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)"
@echo " coverage to run coverage check of the documentation (if enabled)"
@echo " dummy to check syntax errors of document sources"
.PHONY: clean
clean:
rm -rf $(BUILDDIR)/*
.PHONY: html
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
.PHONY: dirhtml
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
.PHONY: singlehtml
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
.PHONY: pickle
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
.PHONY: json
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
.PHONY: htmlhelp
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."
.PHONY: qthelp
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/Pyramid.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Pyramid.qhc"
.PHONY: applehelp
applehelp:
$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
@echo
@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
@echo "N.B. You won't be able to view it unless you put it in" \
"~/Library/Documentation/Help or install it in your application" \
"bundle."
.PHONY: devhelp
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/Pyramid"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Pyramid"
@echo "# devhelp"
.PHONY: epub
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
.PHONY: epub3
epub3:
$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
@echo
@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
.PHONY: latex
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)."
.PHONY: latexpdf
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."
.PHONY: latexpdfja
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."
.PHONY: text
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
.PHONY: man
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
.PHONY: texinfo
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)."
.PHONY: info
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."
.PHONY: gettext
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
.PHONY: changes
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
.PHONY: linkcheck
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."
.PHONY: doctest
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."
.PHONY: coverage
coverage:
$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
@echo "Testing of coverage in the sources finished, look at the " \
"results in $(BUILDDIR)/coverage/python.txt."
.PHONY: xml
xml:
$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
@echo
@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: pseudoxml
pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
.PHONY: help Makefile
.PHONY: dummy
dummy:
$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
@echo
@echo "Build finished. Dummy builder generates no files."
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
docs/conf.py
View file @ 6e3128b8
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Configuration file for the Sphinx documentation builder.
#
# Pyramid documentation build configuration file, created by
# sphinx-quickstart on Mon Feb 6 10:57:49 2017.
#
# 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.
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# Use command in docs to generate stubs and make html afterwards:
# > sphinx-apidoc -o api ../src/empyre
# > make html
# -- Path setup --------------------------------------------------------------
# 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('.'))
import os
import sys
sys.path.insert(0, os.path.abspath(os.path.join('..', 'src')))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# -- Project information -----------------------------------------------------
project = 'EMPyRe'
copyright = '2020, Jan Caron'
author = 'Jan Caron'
# -- General configuration ---------------------------------------------------
# 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.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.autosummary',
'numpydoc'
]
extensions = ['sphinx.ext.autodoc',
'sphinx.ext.viewcode',
'numpydoc',
'nbsphinx',
'nbsphinx_link']
numpydoc_show_class_members = False
add_module_names = False
# 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 = 'Pyramid'
copyright = '2017, Jan Caron'
author = 'Jan Caron'
# 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'
# The full version, including alpha/beta/rc tags.
release = '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'
templates_path = ['_templates']
# 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 = ['.build', 'Thumbs.db', '.DS_Store']
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
# 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
# -- Options for HTML output -------------------------------------------------
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'sphinx_rtd_theme'
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False
# 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']
# 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 = 'sphinxdoc'
# 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 = 'Pyramid v0.1'
# A shorter title for the navigation bar. Default is the same as html_title.
#
# html_short_title = None
todo_include_todos = True
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
html_logo = 'Pyramid Logo.png'
html_logo = 'EMPyRe Logo.png'
# The name of an image file (relative to this directory) to use as a favicon of
# the doc. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
html_favicon = 'icon.ico'
# 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', 'h', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'r', '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 = 'Pyramiddoc'
# -- 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, 'Pyramid.tex', 'Pyramid Documentation',
'Jan Caron', '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 = []
# It false, will not define \strong, \code, itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True
# 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, 'pyramid', 'Pyramid 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, 'Pyramid', 'Pyramid Documentation',
author, 'Pyramid', '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
# -- Options for Epub output ----------------------------------------------
# Bibliographic Dublin Core info.
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
# The basename for the epub file. It defaults to the project name.
# epub_basename = project
# 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 that 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 Pillow.
#
# 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
# -- Options for PDF output --------------------------------------------------
# Grouping the document tree into PDF files. List of tuples
# (source start file, target name, title, author, options).
#
# If there is more than one author, separate them with \\.
# For example: r'Guido van Rossum\\Fred L. Drake, Jr., editor'
#
# The options element is a dictionary that lets you override
# this config per-document.
# For example,
# ('index', u'MyProject', u'My Project', u'Author Name',
# dict(pdf_compressed = True))
# would mean that specific document would be compressed
# regardless of the global pdf_compressed setting.
pdf_documents = [
('index', u'Pyramid', u'Pyramid', u'Jan Caron'),
]
# A comma-separated list of custom stylesheets. Example:
pdf_stylesheets = ['sphinx','kerning','a4']
# A list of folders to search for stylesheets. Example:
pdf_style_path = ['.', '_styles']
# Create a compressed PDF
# Use True/False or 1/0
# Example: compressed=True
#pdf_compressed = False
# A colon-separated list of folders to search for fonts. Example:
# pdf_font_path = ['/usr/share/fonts', '/usr/share/texmf-dist/fonts/']
# Language to be used for hyphenation support
#pdf_language = "en_US"
# Mode for literal blocks wider than the frame. Can be
# overflow, shrink or truncate
#pdf_fit_mode = "shrink"
# Section level that forces a break page.
# For example: 1 means top-level sections start in a new page
# 0 means disabled
#pdf_break_level = 0
# When a section starts in a new page, force it to be 'even', 'odd',
# or just use 'any'
#pdf_breakside = 'any'
# Insert footnotes where they are defined instead of
# at the end.
#pdf_inline_footnotes = True
# verbosity level. 0 1 or 2
#pdf_verbosity = 0
# If false, no index is generated.
#pdf_use_index = True
# If false, no modindex is generated.
#pdf_use_modindex = True
# If false, no coverpage is generated.
#pdf_use_coverpage = True
# Name of the cover page template to use
#pdf_cover_template = 'sphinxcover.tmpl'
# Documents to append as an appendix to all manuals.
#pdf_appendices = []
# Enable experimental feature to split table cells. Use it
# if you get "DelayedTable too big" errors
#pdf_splittables = False
# Set the default DPI for images
#pdf_default_dpi = 72
# Enable rst2pdf extension modules (default is only vectorpdf)
# you need vectorpdf if you want to use sphinx's graphviz support
#pdf_extensions = ['vectorpdf']
# Page template name for "regular" pages
#pdf_page_template = 'cutePage'
# Show Table Of Contents at the beginning?
#pdf_use_toc = True
# How many levels deep should the table of contents be?
pdf_toc_depth = 9999
# Add section number to section references
pdf_use_numbered_links = False
# Background images fitting mode
pdf_fit_background_mode = 'scale'
# cannot cache unpickable configuration value: 'nbsphinx_custom_formats
# See https://github.com/sphinx-doc/sphinx/issues/12300
suppress_warnings = ["config.cache"]
docs/demos.rst 0 → 100644
View file @ 6e3128b8
Demos
-----
.. toctree::
demos/demo1
demos/demo2
demos/demo3
docs/demos/demo1.nblink 0 → 100644
View file @ 6e3128b8
{
"path": "../../demos/demo1_first_steps.ipynb"
}
\ No newline at end of file
docs/demos/demo2.nblink 0 → 100644
View file @ 6e3128b8
{
"path": "../../demos/demo2_handling_3d_fields.ipynb"
}
\ No newline at end of file
docs/demos/demo3.nblink 0 → 100644
View file @ 6e3128b8
{
"path": "../../demos/demo3_io_and_field_manipulation.ipynb"
}
\ No newline at end of file
docs/fields.rst 0 → 100644
View file @ 6e3128b8
The Field container class
=========================
General empyre.fields docu here!
All functions implemented in the subpackages can be accessed directly in the ``empyre.fields`` namespace.
The field module
----------------
.. automodule:: empyre.fields.field
:members:
:show-inheritance:
The shapes module
-----------------
.. automodule:: empyre.fields.shapes
:members:
:show-inheritance:
The vectors module
------------------
.. automodule:: empyre.fields.vectors
:members:
:show-inheritance:
docs/index.rst
View file @ 6e3128b8
.. Pyramid documentation master file, created by
sphinx-quickstart on Thu Feb 25 19:34:18 2016.
.. EMPyRe documentation master file, created by
sphinx-quickstart on Mon Feb 17 14:19:01 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to Pyramid's documentation!
===================================
EMPyRe - Electron Microscopy Reconstruction
===========================================
Contents:
.. include:: ../README.rst
.. toctree::
:maxdepth: 4
:maxdepth: 2
:caption: Contents:
pyramid.rst
fields
vis
io
demos
Indices and tables
......@@ -20,4 +24,3 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
docs/io.rst 0 → 100644
View file @ 6e3128b8
The io visualization submodule
===============================
General empyre.io docu here!
The io_field module
-------------------
.. automodule:: empyre.io.io_field
:members:
:show-inheritance:
The field_plugins module
------------------------
.. automodule:: empyre.io.field_plugins
:members:
:show-inheritance:
docs/make.bat
View file @ 6e3128b8
@ECHO OFF
pushd %~dp0
REM Command file for Sphinx documentation
if "%SPHINXBUILD%" == "" (
set SPHINXBUILD=sphinx-build
)
set BUILDDIR=.build
set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
set I18NSPHINXOPTS=%SPHINXOPTS% .
if NOT "%PAPER%" == "" (
set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
)
set SOURCEDIR=.
set BUILDDIR=_build
if "%1" == "" goto help
if "%1" == "help" (
: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. epub3 to make an epub3
echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
echo. text to make text files
echo. man to make manual pages
echo. texinfo to make Texinfo files
echo. gettext to make PO message catalogs
echo. changes to make an overview over 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
echo. coverage to run coverage check of the documentation if enabled
echo. dummy to check syntax errors of document sources
goto end
)
if "%1" == "clean" (
for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
del /q /s %BUILDDIR%\*
goto end
)
REM Check if sphinx-build is available and fallback to Python version if any
%SPHINXBUILD% 1>NUL 2>NUL
if errorlevel 9009 goto sphinx_python
goto sphinx_ok
:sphinx_python
set SPHINXBUILD=python -m sphinx.__init__
%SPHINXBUILD% 2> nul
%SPHINXBUILD% >NUL 2>NUL
if errorlevel 9009 (
echo.
echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
......@@ -71,211 +25,11 @@ if errorlevel 9009 (
exit /b 1
)
:sphinx_ok
%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
goto end
if "%1" == "html" (
%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/html.
goto end
)
if "%1" == "dirhtml" (
%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
goto end
)
if "%1" == "singlehtml" (
%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
goto end
)
if "%1" == "pickle" (
%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the pickle files.
goto end
)
if "%1" == "json" (
%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can process the JSON files.
goto end
)
if "%1" == "htmlhelp" (
%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run HTML Help Workshop with the ^
.hhp project file in %BUILDDIR%/htmlhelp.
goto end
)
if "%1" == "qthelp" (
%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished; now you can run "qcollectiongenerator" with the ^
.qhcp project file in %BUILDDIR%/qthelp, like this:
echo.^> qcollectiongenerator %BUILDDIR%\qthelp\Pyramid.qhcp
echo.To view the help file:
echo.^> assistant -collectionFile %BUILDDIR%\qthelp\Pyramid.ghc
goto end
)
if "%1" == "devhelp" (
%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
if errorlevel 1 exit /b 1
echo.
echo.Build finished.
goto end
)
if "%1" == "epub" (
%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub file is in %BUILDDIR%/epub.
goto end
)
if "%1" == "epub3" (
%SPHINXBUILD% -b epub3 %ALLSPHINXOPTS% %BUILDDIR%/epub3
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The epub3 file is in %BUILDDIR%/epub3.
goto end
)
if "%1" == "latex" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
if errorlevel 1 exit /b 1
echo.
echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdf" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "latexpdfja" (
%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
cd %BUILDDIR%/latex
make all-pdf-ja
cd %~dp0
echo.
echo.Build finished; the PDF files are in %BUILDDIR%/latex.
goto end
)
if "%1" == "text" (
%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The text files are in %BUILDDIR%/text.
goto end
)
if "%1" == "man" (
%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The manual pages are in %BUILDDIR%/man.
goto end
)
if "%1" == "texinfo" (
%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
goto end
)
if "%1" == "gettext" (
%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
goto end
)
if "%1" == "changes" (
%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
if errorlevel 1 exit /b 1
echo.
echo.The overview file is in %BUILDDIR%/changes.
goto end
)
if "%1" == "linkcheck" (
%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
if errorlevel 1 exit /b 1
echo.
echo.Link check complete; look for any errors in the above output ^
or in %BUILDDIR%/linkcheck/output.txt.
goto end
)
if "%1" == "doctest" (
%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
if errorlevel 1 exit /b 1
echo.
echo.Testing of doctests in the sources finished, look at the ^
results in %BUILDDIR%/doctest/output.txt.
goto end
)
if "%1" == "coverage" (
%SPHINXBUILD% -b coverage %ALLSPHINXOPTS% %BUILDDIR%/coverage
if errorlevel 1 exit /b 1
echo.
echo.Testing of coverage in the sources finished, look at the ^
results in %BUILDDIR%/coverage/python.txt.
goto end
)
if "%1" == "xml" (
%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The XML files are in %BUILDDIR%/xml.
goto end
)
if "%1" == "pseudoxml" (
%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
if errorlevel 1 exit /b 1
echo.
echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
goto end
)
if "%1" == "dummy" (
%SPHINXBUILD% -b dummy %ALLSPHINXOPTS% %BUILDDIR%/dummy
if errorlevel 1 exit /b 1
echo.
echo.Build finished. Dummy builder generates no files.
goto end
)
:help
%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
:end
popd
docs/pyramid.rst deleted 100644 → 0
View file @ 45d1150a
pyramid Package
===============
:mod:`analytic` Module
----------------------
.. automodule:: pyramid.analytic
:members:
:show-inheritance:
:special-members:
:mod:`colormap` Module
--------------------------
.. automodule:: pyramid.colormap
:members:
:show-inheritance:
:special-members:
:mod:`costfunction` Module
--------------------------
.. automodule:: pyramid.costfunction
:members:
:show-inheritance:
:special-members:
:mod:`dataset` Module
---------------------
.. automodule:: pyramid.dataset
:members:
:show-inheritance:
:special-members:
:mod:`diagnostics` Module
--------------------------
.. automodule:: pyramid.diagnostics
:members:
:show-inheritance:
:special-members:
:mod:`fft` Module
--------------------------
.. automodule:: pyramid.fft
:members:
:show-inheritance:
:special-members:
:mod:`forwardmodel` Module
--------------------------
.. automodule:: pyramid.forwardmodel
:members:
:show-inheritance:
:special-members:
:mod:`kernel` Module
--------------------
.. automodule:: pyramid.kernel
:members:
:show-inheritance:
:special-members:
:mod:`magcreator` Module
------------------------
.. automodule:: pyramid.magcreator
:members:
:show-inheritance:
:special-members:
:mod:`magdata` Module
---------------------
.. automodule:: pyramid.magdata
:members:
:show-inheritance:
:special-members:
:mod:`phasemap` Module
----------------------
.. automodule:: pyramid.phasemap
:members:
:show-inheritance:
:special-members:
:mod:`phasemapper` Module
-------------------------
.. automodule:: pyramid.phasemapper
:members:
:show-inheritance:
:special-members:
:mod:`projector` Module
-----------------------
.. automodule:: pyramid.projector
:members:
:show-inheritance:
:special-members:
:mod:`quaternion` Module
----------------------------
.. automodule:: pyramid.quaternion
:members:
:show-inheritance:
:special-members:
:mod:`ramp` Module
----------------------------
.. automodule:: pyramid.ramp
:members:
:show-inheritance:
:special-members:
:mod:`reconstruction` Module
----------------------------
.. automodule:: pyramid.reconstruction
:members:
:show-inheritance:
:special-members:
:mod:`regularisator` Module
----------------------------
.. automodule:: pyramid.regularisator
:members:
:show-inheritance:
:special-members:
Subpackages
-----------
.. toctree::
pyramid.numcore
docs/vis.rst 0 → 100644
View file @ 6e3128b8
The vis visualization submodule
===============================
General empyre.vis docu here!
All functions implemented in the subpackages can be accessed directly in the ``empyre.io`` namespace, with the exception
of the ``color`` module, whose methods are accessible via ``empyre.vis.colors``.
Note that the y-axis of all image plots is flipped in comparison to ``matplotlib.pyplot.imshow``, i.e. that the
origin is `'lower'` in this case instead of `'upper'`.
Please note that 3D plots only work in your Jupyter notebook after first installing and then enabling the corresponding
mayavi extension:
.. code-block:: bash
$ jupyter nbextension install --py mayavi --user
$ jupyter nbextension enable mayavi --user --py
If you'd like to utilize 3D plots in your Jupyter Notebook or in the Python Interactive Window
.. code-block:: Python
>>> from mayavi import mlab
>>> mlab.init_notebook('x3d')
The backend, chosen by the `init_notebook` function can be `ipy` (the default, produces static images in Juypter
Notebook and does not work in VSCode), `x3d` (produces interactive plots in Jupyter Noteboo, but seems to not work with
VSCode), or `png` (produces png-images, which work in both Jupyter Notebooks and VSCode).
For more information and a quick introduction visit the `mayavi tips & tricks section <https://docs.enthought.com/mayavi/mayavi/tips.html>`_.
The plot2d module
-----------------
.. automodule:: empyre.vis.plot2d
:members:
:show-inheritance:
The decorators module
---------------------
.. automodule:: empyre.vis.decorators
:members:
:show-inheritance:
The colors module
-----------------
.. automodule:: empyre.vis.colors
:members:
:show-inheritance:
The tools module
----------------
.. automodule:: empyre.vis.tools
:members:
:show-inheritance:
environment.yml deleted 100644 → 0
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# Create environment with "conda env create", update with "conda env update"!
# This file contains the top level dependencies of the pyramid project!
# requirements.txt also contains sub-dependencies, generated by "pip freeze > requirements.txt"!
# Add new dependencies here, then "conda env update", then "pip freeze > requirements.txt"!
# When packages are deprecated/deleted, it may be best to recreate the environment from scratch!
name: pyramid
channels:
- defaults # Default conda channels, on top to keep highest priority!
- conda-forge # Used for hyperspy, pyFFTW (linux-64/osx-64)!
- ccpi # Used for pyFFTW on win-64!
dependencies:
# Basic:
- python=3.5 # TODO: upgrade to 3.6!
- numpy=1.11
- scipy=0.19
- tqdm=4.14
- scikit-image=0.13
# Fast computation:
- pyFFTW=0.10
# File IO:
- hyperspy=1.3
- hyperspy-gui-ipywidgets=1.0
- hyperspy-gui-traitsui=1.0 # TODO: Optional! Delete when mayavi is gone!
- h5py=2.7
# Plotting and colors: # TODO: Shift to plotting package?
- matplotlib=2.0 # Only works with qt4 from conda-forge channel!
- Pillow=4.1
- cmocean=1.1
- qt=4.8 # Necessary because of traits in mayavi...
- mayavi=4.5 # TODO: Get rid of!
#- colorspacious # TODO: NOT USED?
#- visvis # TODO: NOT USED?
# Testing:
- pytest=3.1
- pytest-cov=2.3
- pytest-flake8=0.8
- pytest-runner=2.11
- pytest-mpl=0.7 # Needed for testing hyperspy! TODO: Use for pyramid or plotting library, too!
- coverage=4.4
# IPython and notebooks:
- ipython=5.3
- jupyter=1.0
# TODO: Add back GUI dependencies!
# TODO: Get Jutil from gitlab (currently doesn't work, git and cygwin don't play nice,...
# TODO: ...because one is Unix, ond is Windows).
# - pip=9.0
# - pip:
# # ALSO NEEDS JUTIL!
# - "git+ssh://gitlab@iffgit.fz-juelich.de/unger/jutil.git"
#
# # FOLLOWING NOT USED ANYMORE, CONDA WORKS, TOO (with appropriate channels):
# # Install pyFFTW=0.10 from wheel:
# - http://www.lfd.uci.edu/~gohlke/pythonlibs/pyFFTW‑0.10.4‑cp35‑cp35m‑win_amd64.whl
# # Install mayavi=4.5 and VTK from wheel:
# - http://www.lfd.uci.edu/~gohlke/pythonlibs/mayavi‑4.5.0+vtk71‑cp35‑cp35m‑win_amd64.whl
pyproject.toml 0 → 100644
View file @ 6e3128b8
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "empyre"
dynamic = ["version"]
description = "Electron Microscopy Python Reconstruction"
readme = "README.rst"
license = "GPL-3.0-or-later"
requires-python = ">=3.6"
authors = [
{ name = "Jan Caron", email = "j.caron@fz-juelich.de" },
]
keywords = [
"Electron Microscopy",
"Inverse Problem Solving",
"Model-based Reconstrution",
]
classifiers = [
"Development Status :: 3 - Alpha",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Topic :: Scientific/Engineering",
]
dependencies = [
"matplotlib >= 3.2",
"numpy >= 1.17",
"Pillow",
"scikit-image",
"scipy",
"tqdm",
]
[project.optional-dependencies]
3d = [
"mayavi >= 4.7",
]
all = [
"cmocean",
"pyfftw",
]
colors = [
"cmocean",
]
docs = [
"nbsphinx",
"nbsphinx_link",
"numpydoc",
"pandoc",
"sphinx",
"sphinx_rtd_theme",
]
fftw = [
"pyfftw",
]
io = [
"hyperspy",
"tvtk",
]
tests = [
"coverage",
"pyroma",
"pytest",
"pytest-cov",
"pytest-flake8",
"pytest-runner",
]
[project.urls]
Homepage = "https://iffgit.fz-juelich.de/empyre/empyre"
[tool.hatch.version]
path = "src/empyre/__init__.py"
[tool.hatch.build.targets.sdist]
include = [
"/src",
"/tests",
]
pyramid/.DS_Store deleted 100644 → 0
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