From 07f5baa65c6a11e5d1b9f0258a92115f0927f7aa Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 13:41:00 -0600 Subject: [PATCH 01/70] inital version of .readthedocs.yaml --- .readthedocs.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 000000000..b17e3cab0 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,11 @@ +version: 2 + +conda: + environment: environment.yml + +build: + os: "ubuntu-20.04" + tool: + python: "3.8" + + From 17f11332ab5e33586b2e2013ac75e5b096688e86 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 13:41:54 -0600 Subject: [PATCH 02/70] update environent.yml --- environment.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/environment.yml b/environment.yml index 2b85c7459..795140449 100644 --- a/environment.yml +++ b/environment.yml @@ -1,5 +1,7 @@ +name: saltproc-env channels: - conda-forge + - defaults dependencies: - pyne>=0.5.11 - numpy>=1.14.0 @@ -7,3 +9,5 @@ dependencies: - networkx - pydotplus - pytest + - sphinx + - sphinx_rtd_theme From 1320f0b75732b7f1fc6dbc1b319a3fc4d9058090 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 13:43:24 -0600 Subject: [PATCH 03/70] add mambaforge --- .readthedocs.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index b17e3cab0..9a6e329da 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,11 +1,10 @@ version: 2 -conda: - environment: environment.yml - build: os: "ubuntu-20.04" tool: - python: "3.8" + python: "mambaforge-4.10" +conda: + environment: environment.yml From e95095a555b891edef12584eb85f8b9460aac5b4 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 14:00:26 -0600 Subject: [PATCH 04/70] add fail on warning for sphinx option --- .readthedocs.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 9a6e329da..c343c654e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,3 +8,5 @@ build: conda: environment: environment.yml +sphinx: + fail_on_warning: true From 100afd44eb3eec267944a6cb26d873e31ae0c94d Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 14:01:01 -0600 Subject: [PATCH 05/70] add pip deps to environment file --- environment.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/environment.yml b/environment.yml index 795140449..ba1607054 100644 --- a/environment.yml +++ b/environment.yml @@ -11,3 +11,5 @@ dependencies: - pytest - sphinx - sphinx_rtd_theme + - pip: + - argparse==1.4.0 From 361b0d602f56667e46578fde2cb39feadc6dc692 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:18:03 -0600 Subject: [PATCH 06/70] add correct version in sphinx config --- doc/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 8b92d6bdc..c119b3799 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -25,9 +25,9 @@ author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' # The short X.Y version -version = '' +version = '0.3' # The full version, including alpha/beta/rc tags -release = '' +release = '0.3.0-dev' # -- General configuration --------------------------------------------------- From c18e393d3aaa01228abba18e66b2f26a19a2a23b Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:20:26 -0600 Subject: [PATCH 07/70] make versions consistent --- doc/conf.py | 2 +- saltproc/version.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index c119b3799..b0382bb1a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -27,7 +27,7 @@ # The short X.Y version version = '0.3' # The full version, including alpha/beta/rc tags -release = '0.3.0-dev' +release = '0.3.1-dev' # -- General configuration --------------------------------------------------- diff --git a/saltproc/version.py b/saltproc/version.py index b4c09766e..d6647a702 100644 --- a/saltproc/version.py +++ b/saltproc/version.py @@ -4,9 +4,9 @@ # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z" _version_major = 0 _version_minor = 3 -_version_micro = '' # use '' for first of series, number for 1 and above -# _version_extra = 'dev' -_version_extra = '0' # Uncomment this for full releases +_version_micro = '1' # use '' for first of series, number for 1 and above +_version_extra = 'dev' +#_version_extra = '0' # Uncomment this for full releases # Construct full version string from these. _ver = [_version_major, _version_minor] From b9ae15baafae43aeb3bf921d2dd1943c5e4d0554 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:29:44 -0600 Subject: [PATCH 08/70] add new dependencies to installation page --- doc/installation.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/doc/installation.rst b/doc/installation.rst index cda9562c6..41a95b46e 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -18,13 +18,17 @@ SaltProc has the following dependencies: .. _PyTables: http://pytables.org .. _NetworkX: http://networkx.github.io .. _PyDotPlus: https://pydotplus.readthedocs.io/ +.. _pytest: https://docs.pytest.org +.. _sphinx: https://www.sphinx-doc.org +.. _sphinx-rtd-theme: https://sphinx-rtd-theme.readthedocs.io .. _matplotlib: http://matplotlib.org .. _ViTables: http://vitables.org .. _GitHub: http://github.com/arfc/saltproc Optional Depenendencies: - + #. `pytest`_ (for testing) + #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation) #. `matplotlib`_ #. `ViTables`_ From a4fbd6c417145dfca62c5d50edbbd316c8502100 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:31:16 -0600 Subject: [PATCH 09/70] update installation instructions --- doc/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/installation.rst b/doc/installation.rst index 41a95b46e..d6ebce79c 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -41,9 +41,9 @@ Then run the following commands from the directory above cloned repository: .. code-block:: bash - git clone https://github.com/arfc/saltproc.git + git clone git@github.com:arfc/saltproc.git cd saltproc/ - python setup.py install --user + pip install . Please let us know if you run into trouble. From 7bc7e88d72cfff4fc22818485d1296311b495a1a Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:42:51 -0600 Subject: [PATCH 10/70] typo fix in .readthedocs.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index c343c654e..8e48dea9c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -2,7 +2,7 @@ version: 2 build: os: "ubuntu-20.04" - tool: + tools: python: "mambaforge-4.10" conda: From e62483e3af47ddbe9ad6455054e149b766483a6a Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:50:24 -0600 Subject: [PATCH 11/70] try adding python --- .readthedocs.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 8e48dea9c..e4ee6e94e 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -8,5 +8,11 @@ build: conda: environment: environment.yml +python: + install: + - method: pip + path: . + sphinx: + configuration: docs/conf.py fail_on_warning: true From cea25adc281b262a444df85b60c4cc73c5e85976 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:58:26 -0600 Subject: [PATCH 12/70] doc->docs --- docs/Makefile | 177 +++++++++++++++++ docs/conf.py | 187 ++++++++++++++++++ docs/examples.rst | 29 +++ docs/index.rst | 80 ++++++++ docs/installation.rst | 86 ++++++++ docs/overview.rst | 87 ++++++++ docs/src/index.rst | 7 + docs/src/modules.rst | 7 + docs/src/saltproc.app.rst | 7 + docs/src/saltproc.depcode.rst | 7 + docs/src/saltproc.materialflow.rst | 7 + docs/src/saltproc.process.rst | 7 + docs/src/saltproc.reactor.rst | 7 + docs/src/saltproc.rst | 34 ++++ docs/src/saltproc.separator.rst | 7 + docs/src/saltproc.simulation.rst | 7 + docs/src/saltproc.sparger.rst | 7 + docs/src/saltproc.tests.rst | 24 +++ docs/src/saltproc.tests.test_app.rst | 7 + docs/src/saltproc.tests.test_depcode.rst | 7 + docs/src/saltproc.tests.test_materialflow.rst | 7 + docs/src/saltproc.tests.test_process.rst | 7 + docs/src/saltproc.tests.test_separator.rst | 7 + docs/src/saltproc.tests.test_simulation.rst | 7 + docs/src/saltproc.tests.test_sparger.rst | 7 + docs/src/saltproc.version.rst | 7 + 26 files changed, 830 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/conf.py create mode 100644 docs/examples.rst create mode 100644 docs/index.rst create mode 100644 docs/installation.rst create mode 100644 docs/overview.rst create mode 100644 docs/src/index.rst create mode 100644 docs/src/modules.rst create mode 100644 docs/src/saltproc.app.rst create mode 100644 docs/src/saltproc.depcode.rst create mode 100644 docs/src/saltproc.materialflow.rst create mode 100644 docs/src/saltproc.process.rst create mode 100644 docs/src/saltproc.reactor.rst create mode 100644 docs/src/saltproc.rst create mode 100644 docs/src/saltproc.separator.rst create mode 100644 docs/src/saltproc.simulation.rst create mode 100644 docs/src/saltproc.sparger.rst create mode 100644 docs/src/saltproc.tests.rst create mode 100644 docs/src/saltproc.tests.test_app.rst create mode 100644 docs/src/saltproc.tests.test_depcode.rst create mode 100644 docs/src/saltproc.tests.test_materialflow.rst create mode 100644 docs/src/saltproc.tests.test_process.rst create mode 100644 docs/src/saltproc.tests.test_separator.rst create mode 100644 docs/src/saltproc.tests.test_simulation.rst create mode 100644 docs/src/saltproc.tests.test_sparger.rst create mode 100644 docs/src/saltproc.version.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 000000000..f554f954e --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,177 @@ +# 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 ' where 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/pyrk.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyrk.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/pyrk" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyrk" + @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." diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 000000000..b0382bb1a --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,187 @@ +# -*- coding: utf-8 -*- +# +# Configuration file for the Sphinx documentation builder. +# +# This file does only contain a selection of the most common options. For a +# full list see the documentation: +# http://www.sphinx-doc.org/en/master/config + +# -- 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 +import sphinx_rtd_theme +sys.path.append(os.path.abspath('../')) +sys.path.append(os.path.abspath('../saltproc')) + +# -- Project information ----------------------------------------------------- + +project = u'Saltproc' +copyright = u'2018, Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' +author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' + +# The short X.Y version +version = '0.3' +# The full version, including alpha/beta/rc tags +release = '0.3.1-dev' + + +# -- 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.doctest', + 'sphinx.ext.intersphinx', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.napoleon', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', +] + +# Napoleon settings +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_include_init_with_doc = True +napoleon_include_private_with_doc = True +napoleon_include_special_with_doc = True +napoleon_use_admonition_for_examples = True +napoleon_use_admonition_for_notes = True +napoleon_use_admonition_for_references = True +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'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# 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 + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path . +exclude_patterns = ['_build'] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# 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 = "sphinx_rtd_theme" +html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] +html_show_copyright = False + +# 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 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'] + +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# The default sidebars (for documents that don't match any pattern) are +# defined by theme itself. Builtin themes are using these templates by +# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', +# 'searchbox.html']``. +# +# html_sidebars = {} + + +# -- Options for HTMLHelp output --------------------------------------------- + +# Output file base name for HTML help builder. +htmlhelp_basename = 'saltprocdoc' + + +# -- 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 = [ + ('index', 'saltproc.tex', u'SaltProc Documentation', + author, 'manual'), +] + + +# -- Options for manual page output ------------------------------------------ + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'saltproc', u'Saltproc Documentation', + [author], 1) +] + + +# -- 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, 'Saltproc', 'Saltproc Documentation', + author, 'Saltproc', + 'SaltProc is a tool for online reprocessing for Molten Salt Reactors.', + 'Miscellaneous'), +] + +# autodoc default options +autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance', + 'inherited-members', 'private-members'] diff --git a/docs/examples.rst b/docs/examples.rst new file mode 100644 index 000000000..4f1f2c98f --- /dev/null +++ b/docs/examples.rst @@ -0,0 +1,29 @@ +Examples +========= + +A number of examples are present in the `examples directory`_ provided with the source code. + +.. _examples directory: https://github.com/arfc/saltproc/tree/master/examples + +Transatomic Power Molten Salt Reactor example can be run with: + + +.. code-block:: bash + + cd /path/to/saltproc + python saltproc -i examples/tap/tap_main.json + + +In the example above, ``path/to/saltproc`` is, of course, the path to the main +saltproc directory, containing ``setup.py``. The ``tap_main.json`` is the main +Saltproc input file, which contains paths to Serpent input file +(``tap.serpent``), DOT-file with reprocessing scheme (``tap.dot``), and +reprocessing system components' detailed description (``tap_objects.json``). + + +Similarly, Molten Salt Breeder Reactor example can be run with: + + +.. code-block:: bash + + python saltproc -i examples/msbr/msbr_main.json diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 000000000..dd5ad5830 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,80 @@ +.. Saltproc documentation master file, created by + sphinx-quickstart on Tue Jul 3 14:26:54 2018. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +SaltProc +========= + +**SaltProc** is a python package for liquid-fueled nuclear reactor depletion +calculations. It couples directly with the Serpent 2 Monte Carlo depletion +software to enable online reprocessing system modeling in depletion +calculation. + +**SaltProc** welcomes your contributions. It already relies on many libraries +in the Scientific Python ecosystem including `pyne`_, `numpy`_, `matplotlib`_, +`networkx`_, and `pydotplus`_. + +.. _pyne: http://pyne.io/ +.. _numpy: http://numpy.org +.. _matplotlib: http://matplotlib.org +.. _networkx: http://networkx.github.io +.. _pydotplus: https://pydotplus.readthedocs.io/ + + +Documentation +------------- + +.. toctree:: + :maxdepth: 1 + + overview + installation + examples + src/index + How to cite + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + + + +Citation +-------- + +Up-to-date information about citing SaltProc can be found within the `citation`_ +file. + +.. _citation: https://github.com/arfc/saltproc/blob/master/CITATION.md + + +Get in touch +------------ + +- Please report bugs, suggest feature ideas, and browse the source code `on GitHub`_. +- There, new contributors can also find `a guide to contributing`_. +- Good start point for new contributors is `current open issues`_. + +.. _a guide to contributing: https://github.com/arfc/saltproc/blob/master/CONTRIBUTING.md +.. _current open issues: https://github.com/arfc/saltproc/issues?q=is%3Aopen+is%3Aissue +.. _on GitHub: http://github.com/arfc/saltproc + +Acknowledgment +-------------- + +SaltProc uses `Shablona`_ template which is universal solution for small +scientific python projects developed at University of Washington `eScience Insititute`_. + +.. _Shablona: https://github.com/uwescience/shablona +.. _eScience Insititute: https://escience.washington.edu + +License +------- + +SaltProc is available under the open source `BSD 3-clause License`__. + +__ https://raw.githubusercontent.com/arfc/saltproc/master/LICENSE diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 000000000..d6ebce79c --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,86 @@ +Installation +============ + +SaltProc has the following dependencies: + + #. `Python`_ (>=3.5) + #. `Serpent`_ (>=2.1.31) + #. `PyNE`_ (>=0.5.11) + #. `NumPy`_ (>=1.14.0) + #. `PyTables`_ + #. `NetworkX`_ + #. `PyDotPlus`_ + +.. _Serpent: http://montecarlo.vtt.fi +.. _PyNE: http://pyne.io +.. _Python: http://python.org +.. _NumPy: http://numpy.org +.. _PyTables: http://pytables.org +.. _NetworkX: http://networkx.github.io +.. _PyDotPlus: https://pydotplus.readthedocs.io/ +.. _pytest: https://docs.pytest.org +.. _sphinx: https://www.sphinx-doc.org +.. _sphinx-rtd-theme: https://sphinx-rtd-theme.readthedocs.io +.. _matplotlib: http://matplotlib.org +.. _ViTables: http://vitables.org +.. _GitHub: http://github.com/arfc/saltproc + + +Optional Depenendencies: + #. `pytest`_ (for testing) + #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation) + #. `matplotlib`_ + #. `ViTables`_ + + + +Most of the dependencies are readily available through package managers. +Once all the dependencies are installed, SaltProc can be installed. +Clone the source from the SaltProc repository from `GitHub`_. +Then run the following commands from the directory above cloned repository: + +.. code-block:: bash + + git clone git@github.com:arfc/saltproc.git + cd saltproc/ + pip install . + +Please let us know if you run into trouble. + +Cross Section Configuration +--------------------------- +SaltProc can use any cross section library that Serpent can. See `this page on the Serpent wiki`_ for information on how to configure the libraries. + +.. _this page on the Serpent wiki: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries + +Testing +------- +The SaltProc test suite has two types of tests: unit tests and regression tests. +The unit tests check that the individual functions and classes of the ``saltproc`` +module return the correct type of variables and correct values, where applicable. +The regression tests run a full SaltProc simulation and check the final result +with a precalculated result. +The integration tests require the `JEFF 3.1.2 cross section library`_ as well +as neutron induces and spontaneous fission product yield data from JEFF 3.3. +The publicly available versions of JEFF 3.1.2 cannot be used with Serpent right +out of the box due to `Serpent's notation for isomeric states`_. The scripts in +``scripts/xsdata`` download all necessary libraries and perform all the necessary processing on them for use in Serpent 2. +We recommend using them for your convenience. +See the `README`_ for more information. + +.. _Serpent's notation for isomeric states: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries +.. _JEFF 3.1.2 cross section library: https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_31/JEFF312/ +.. _README: https://github.com/arfc/saltproc/blob/master/scripts/README.md + +To run the tests, execute: + +.. code-block:: bash + + pytest saltproc/ + +from the root directory of SaltProc. If you just want to run the unit tests, execute + +.. code-block:: bash + + pytest --ignore saltproc/tests/integration_tests saltproc/ + diff --git a/docs/overview.rst b/docs/overview.rst new file mode 100644 index 000000000..82d263510 --- /dev/null +++ b/docs/overview.rst @@ -0,0 +1,87 @@ +Overview +========= + +SaltProc couples directly with the Monte Carlo neutron transport code Serpent 2 +and enables sophisticated, multi-component online fuel reprocessing system +modeling. SaltProc is the first open-source tool for liquid-fueled MSR +depletion simulation with the following capabilities: + +- neutron poison removal with user-defined efficiency, +- make-up mass loss by fresh fuel injection, +- reactivity control by adjusting fuel feed rate or geometry change, +- can model any reactor design, +- potentially, can couple with any depletion tool (i.e., MCNP, SCALE, OpenMC). + + +How SaltProc works +------------------- + +SaltProc is a driver for Serpent to simulate online fuel salt reprocessing for +Molten Salt Reactors. It performs following major functions: + + - runs SERPENT + - parses and stores Serpent output data in HDF5 + - modifies parsed material composition (`reprocesses`) + - creates Serpent input file + + +The code logic flow is the following: + + 1. Runs Serpent (`saltproc.depcode.run_depcode()`) + 2. Parses through the output `*_dep.m` file and creates PyNE Material object + for each burnable material. + 3. Processes Fuel (`saltproc.app.reprocessing()` and `saltproc.refill`): + + * Passes fuel composition throughout Processes objects (reprocessing system + components) to remove poisons with specific efficiency. + * Adds back fissile and/or fertile material to make-up loss of material. + + 4. Records data: + + - Depleted fuel composition (`materials/fuel/before_reproc` table in HDF5) + - Reprocessed fuel composition (`materials/fuel/after_reproc` table in + HDF5) + - Multiplication factor at the beginning and at the end of depletion step + (`simulation_parameters/keff_bds`, `simulation_parameters/keff_eds`) + - Effective Delayed Neutron Fraction (:math:`\beta_{eff}`) at the end of + the depletion step (`simulation_parameters/beta_eff_eds`) + - Waste and feed streams from each `Process` (`materials/in_out_streams/`) + + 5. Repeats 1-4. + +Updates +------- + +March 2021: + +Besides the existing flexibility like fixed removal efficiency definition for +each target isotope defined in the object input file, Saltproc code now +comprises `Sparging System package` that calculates removal efficiencies for +various target isotopes (i.e., Xe, Kr, and H). To enable this feature, use +the `"self"` command in the input file in the `"efficiency"` object names of +Sparger and Separator components. Each component can be employed separately. +An example is given below. In the example, capacity and mass flow rate are in +`g/s` unit while volume is in `cm`:math:`^3` unit. + +"sparger": { "capacity": 9920000, + "efficiency": "self", + "mass_flowrate": 9920000, + "volume": 10000000 }, +"entrainment_separator": { "capacity": 9920000, + "efficiency": "self", + "mass_flowrate": 9920000, + "volume": 11 } + +The Future +----------- + +A number of features will be implemented in SaltProc soon. Support of various +depletion codes (e.g., OpenMC) will be added. + + +.. warning:: + + SaltProc is a relatively new project and is still under heavy development. + Although we will make our best effort to maintain compatibility with the + current API, inevitably the API will change in future versions as SaltProc + matures. diff --git a/docs/src/index.rst b/docs/src/index.rst new file mode 100644 index 000000000..f09f9d4c0 --- /dev/null +++ b/docs/src/index.rst @@ -0,0 +1,7 @@ +SaltProc API +============= + +This is automatically generated API documentation from SaltProc source files. + +Click the "modules" (:ref:`modindex`) link to browse the modules. +Or, dive right into the autogenerated :doc:`saltproc` docs. diff --git a/docs/src/modules.rst b/docs/src/modules.rst new file mode 100644 index 000000000..1da7d5d98 --- /dev/null +++ b/docs/src/modules.rst @@ -0,0 +1,7 @@ +saltproc +======== + +.. toctree:: + :maxdepth: 4 + + saltproc diff --git a/docs/src/saltproc.app.rst b/docs/src/saltproc.app.rst new file mode 100644 index 000000000..a9b319fdd --- /dev/null +++ b/docs/src/saltproc.app.rst @@ -0,0 +1,7 @@ +saltproc.app module +=================== + +.. automodule:: saltproc.app + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.depcode.rst b/docs/src/saltproc.depcode.rst new file mode 100644 index 000000000..04ca7fc0b --- /dev/null +++ b/docs/src/saltproc.depcode.rst @@ -0,0 +1,7 @@ +saltproc.depcode module +======================= + +.. automodule:: saltproc.depcode + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.materialflow.rst b/docs/src/saltproc.materialflow.rst new file mode 100644 index 000000000..31a768303 --- /dev/null +++ b/docs/src/saltproc.materialflow.rst @@ -0,0 +1,7 @@ +saltproc.materialflow module +============================ + +.. automodule:: saltproc.materialflow + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.process.rst b/docs/src/saltproc.process.rst new file mode 100644 index 000000000..2ebcc3e14 --- /dev/null +++ b/docs/src/saltproc.process.rst @@ -0,0 +1,7 @@ +saltproc.process module +======================= + +.. automodule:: saltproc.process + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.reactor.rst b/docs/src/saltproc.reactor.rst new file mode 100644 index 000000000..07925c97a --- /dev/null +++ b/docs/src/saltproc.reactor.rst @@ -0,0 +1,7 @@ +saltproc.reactor module +======================= + +.. automodule:: saltproc.reactor + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.rst b/docs/src/saltproc.rst new file mode 100644 index 000000000..a7888ebbc --- /dev/null +++ b/docs/src/saltproc.rst @@ -0,0 +1,34 @@ +saltproc package +================ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + saltproc.tests + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + saltproc.app + saltproc.depcode + saltproc.materialflow + saltproc.process + saltproc.reactor + saltproc.separator + saltproc.simulation + saltproc.sparger + saltproc.version + +Module contents +--------------- + +.. automodule:: saltproc + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.separator.rst b/docs/src/saltproc.separator.rst new file mode 100644 index 000000000..2228b690c --- /dev/null +++ b/docs/src/saltproc.separator.rst @@ -0,0 +1,7 @@ +saltproc.separator module +========================= + +.. automodule:: saltproc.separator + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.simulation.rst b/docs/src/saltproc.simulation.rst new file mode 100644 index 000000000..7572435ea --- /dev/null +++ b/docs/src/saltproc.simulation.rst @@ -0,0 +1,7 @@ +saltproc.simulation module +========================== + +.. automodule:: saltproc.simulation + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.sparger.rst b/docs/src/saltproc.sparger.rst new file mode 100644 index 000000000..5460a476c --- /dev/null +++ b/docs/src/saltproc.sparger.rst @@ -0,0 +1,7 @@ +saltproc.sparger module +======================= + +.. automodule:: saltproc.sparger + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.rst b/docs/src/saltproc.tests.rst new file mode 100644 index 000000000..024331988 --- /dev/null +++ b/docs/src/saltproc.tests.rst @@ -0,0 +1,24 @@ +saltproc.tests package +====================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + saltproc.tests.test_app + saltproc.tests.test_depcode + saltproc.tests.test_materialflow + saltproc.tests.test_process + saltproc.tests.test_separator + saltproc.tests.test_simulation + saltproc.tests.test_sparger + +Module contents +--------------- + +.. automodule:: saltproc.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_app.rst b/docs/src/saltproc.tests.test_app.rst new file mode 100644 index 000000000..d7674c957 --- /dev/null +++ b/docs/src/saltproc.tests.test_app.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_app module +=============================== + +.. automodule:: saltproc.tests.test_app + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_depcode.rst b/docs/src/saltproc.tests.test_depcode.rst new file mode 100644 index 000000000..9f4918e71 --- /dev/null +++ b/docs/src/saltproc.tests.test_depcode.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_depcode module +=================================== + +.. automodule:: saltproc.tests.test_depcode + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_materialflow.rst b/docs/src/saltproc.tests.test_materialflow.rst new file mode 100644 index 000000000..14e2e41c9 --- /dev/null +++ b/docs/src/saltproc.tests.test_materialflow.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_materialflow module +======================================== + +.. automodule:: saltproc.tests.test_materialflow + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_process.rst b/docs/src/saltproc.tests.test_process.rst new file mode 100644 index 000000000..5b6813db0 --- /dev/null +++ b/docs/src/saltproc.tests.test_process.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_process module +=================================== + +.. automodule:: saltproc.tests.test_process + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_separator.rst b/docs/src/saltproc.tests.test_separator.rst new file mode 100644 index 000000000..9481465f2 --- /dev/null +++ b/docs/src/saltproc.tests.test_separator.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_separator module +===================================== + +.. automodule:: saltproc.tests.test_separator + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_simulation.rst b/docs/src/saltproc.tests.test_simulation.rst new file mode 100644 index 000000000..25aed9803 --- /dev/null +++ b/docs/src/saltproc.tests.test_simulation.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_simulation module +====================================== + +.. automodule:: saltproc.tests.test_simulation + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.tests.test_sparger.rst b/docs/src/saltproc.tests.test_sparger.rst new file mode 100644 index 000000000..b475f4cf9 --- /dev/null +++ b/docs/src/saltproc.tests.test_sparger.rst @@ -0,0 +1,7 @@ +saltproc.tests.test\_sparger module +=================================== + +.. automodule:: saltproc.tests.test_sparger + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/src/saltproc.version.rst b/docs/src/saltproc.version.rst new file mode 100644 index 000000000..9d7ecdbdf --- /dev/null +++ b/docs/src/saltproc.version.rst @@ -0,0 +1,7 @@ +saltproc.version module +======================= + +.. automodule:: saltproc.version + :members: + :undoc-members: + :show-inheritance: From 061c29f1a703ffbdaaa8f9a53114621caac68e53 Mon Sep 17 00:00:00 2001 From: yardasol Date: Wed, 19 Jan 2022 15:59:09 -0600 Subject: [PATCH 13/70] doc->docs --- doc/Makefile | 177 ---------------------------------------- doc/conf.py | 187 ------------------------------------------- doc/examples.rst | 29 ------- doc/index.rst | 80 ------------------ doc/installation.rst | 86 -------------------- doc/overview.rst | 87 -------------------- doc/src/index.rst | 7 -- 7 files changed, 653 deletions(-) delete mode 100644 doc/Makefile delete mode 100644 doc/conf.py delete mode 100644 doc/examples.rst delete mode 100644 doc/index.rst delete mode 100644 doc/installation.rst delete mode 100644 doc/overview.rst delete mode 100644 doc/src/index.rst diff --git a/doc/Makefile b/doc/Makefile deleted file mode 100644 index f554f954e..000000000 --- a/doc/Makefile +++ /dev/null @@ -1,177 +0,0 @@ -# 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 ' where 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/pyrk.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyrk.qhc" - -devhelp: - $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp - @echo - @echo "Build finished." - @echo "To view the help file:" - @echo "# mkdir -p $$HOME/.local/share/devhelp/pyrk" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyrk" - @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." diff --git a/doc/conf.py b/doc/conf.py deleted file mode 100644 index b0382bb1a..000000000 --- a/doc/conf.py +++ /dev/null @@ -1,187 +0,0 @@ -# -*- coding: utf-8 -*- -# -# Configuration file for the Sphinx documentation builder. -# -# This file does only contain a selection of the most common options. For a -# full list see the documentation: -# http://www.sphinx-doc.org/en/master/config - -# -- 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 -import sphinx_rtd_theme -sys.path.append(os.path.abspath('../')) -sys.path.append(os.path.abspath('../saltproc')) - -# -- Project information ----------------------------------------------------- - -project = u'Saltproc' -copyright = u'2018, Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' -author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' - -# The short X.Y version -version = '0.3' -# The full version, including alpha/beta/rc tags -release = '0.3.1-dev' - - -# -- 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.doctest', - 'sphinx.ext.intersphinx', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.napoleon', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'sphinx.ext.viewcode', -] - -# Napoleon settings -napoleon_google_docstring = False -napoleon_numpy_docstring = True -napoleon_include_init_with_doc = True -napoleon_include_private_with_doc = True -napoleon_include_special_with_doc = True -napoleon_use_admonition_for_examples = True -napoleon_use_admonition_for_notes = True -napoleon_use_admonition_for_references = True -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'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# 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 - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path . -exclude_patterns = ['_build'] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# 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 = "sphinx_rtd_theme" -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] -html_show_copyright = False - -# 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 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'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -# html_sidebars = {} - - -# -- Options for HTMLHelp output --------------------------------------------- - -# Output file base name for HTML help builder. -htmlhelp_basename = 'saltprocdoc' - - -# -- 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 = [ - ('index', 'saltproc.tex', u'SaltProc Documentation', - author, 'manual'), -] - - -# -- Options for manual page output ------------------------------------------ - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'saltproc', u'Saltproc Documentation', - [author], 1) -] - - -# -- 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, 'Saltproc', 'Saltproc Documentation', - author, 'Saltproc', - 'SaltProc is a tool for online reprocessing for Molten Salt Reactors.', - 'Miscellaneous'), -] - -# autodoc default options -autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance', - 'inherited-members', 'private-members'] diff --git a/doc/examples.rst b/doc/examples.rst deleted file mode 100644 index 4f1f2c98f..000000000 --- a/doc/examples.rst +++ /dev/null @@ -1,29 +0,0 @@ -Examples -========= - -A number of examples are present in the `examples directory`_ provided with the source code. - -.. _examples directory: https://github.com/arfc/saltproc/tree/master/examples - -Transatomic Power Molten Salt Reactor example can be run with: - - -.. code-block:: bash - - cd /path/to/saltproc - python saltproc -i examples/tap/tap_main.json - - -In the example above, ``path/to/saltproc`` is, of course, the path to the main -saltproc directory, containing ``setup.py``. The ``tap_main.json`` is the main -Saltproc input file, which contains paths to Serpent input file -(``tap.serpent``), DOT-file with reprocessing scheme (``tap.dot``), and -reprocessing system components' detailed description (``tap_objects.json``). - - -Similarly, Molten Salt Breeder Reactor example can be run with: - - -.. code-block:: bash - - python saltproc -i examples/msbr/msbr_main.json diff --git a/doc/index.rst b/doc/index.rst deleted file mode 100644 index dd5ad5830..000000000 --- a/doc/index.rst +++ /dev/null @@ -1,80 +0,0 @@ -.. Saltproc documentation master file, created by - sphinx-quickstart on Tue Jul 3 14:26:54 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -SaltProc -========= - -**SaltProc** is a python package for liquid-fueled nuclear reactor depletion -calculations. It couples directly with the Serpent 2 Monte Carlo depletion -software to enable online reprocessing system modeling in depletion -calculation. - -**SaltProc** welcomes your contributions. It already relies on many libraries -in the Scientific Python ecosystem including `pyne`_, `numpy`_, `matplotlib`_, -`networkx`_, and `pydotplus`_. - -.. _pyne: http://pyne.io/ -.. _numpy: http://numpy.org -.. _matplotlib: http://matplotlib.org -.. _networkx: http://networkx.github.io -.. _pydotplus: https://pydotplus.readthedocs.io/ - - -Documentation -------------- - -.. toctree:: - :maxdepth: 1 - - overview - installation - examples - src/index - How to cite - -Indices and tables ------------------- - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - - - -Citation --------- - -Up-to-date information about citing SaltProc can be found within the `citation`_ -file. - -.. _citation: https://github.com/arfc/saltproc/blob/master/CITATION.md - - -Get in touch ------------- - -- Please report bugs, suggest feature ideas, and browse the source code `on GitHub`_. -- There, new contributors can also find `a guide to contributing`_. -- Good start point for new contributors is `current open issues`_. - -.. _a guide to contributing: https://github.com/arfc/saltproc/blob/master/CONTRIBUTING.md -.. _current open issues: https://github.com/arfc/saltproc/issues?q=is%3Aopen+is%3Aissue -.. _on GitHub: http://github.com/arfc/saltproc - -Acknowledgment --------------- - -SaltProc uses `Shablona`_ template which is universal solution for small -scientific python projects developed at University of Washington `eScience Insititute`_. - -.. _Shablona: https://github.com/uwescience/shablona -.. _eScience Insititute: https://escience.washington.edu - -License -------- - -SaltProc is available under the open source `BSD 3-clause License`__. - -__ https://raw.githubusercontent.com/arfc/saltproc/master/LICENSE diff --git a/doc/installation.rst b/doc/installation.rst deleted file mode 100644 index d6ebce79c..000000000 --- a/doc/installation.rst +++ /dev/null @@ -1,86 +0,0 @@ -Installation -============ - -SaltProc has the following dependencies: - - #. `Python`_ (>=3.5) - #. `Serpent`_ (>=2.1.31) - #. `PyNE`_ (>=0.5.11) - #. `NumPy`_ (>=1.14.0) - #. `PyTables`_ - #. `NetworkX`_ - #. `PyDotPlus`_ - -.. _Serpent: http://montecarlo.vtt.fi -.. _PyNE: http://pyne.io -.. _Python: http://python.org -.. _NumPy: http://numpy.org -.. _PyTables: http://pytables.org -.. _NetworkX: http://networkx.github.io -.. _PyDotPlus: https://pydotplus.readthedocs.io/ -.. _pytest: https://docs.pytest.org -.. _sphinx: https://www.sphinx-doc.org -.. _sphinx-rtd-theme: https://sphinx-rtd-theme.readthedocs.io -.. _matplotlib: http://matplotlib.org -.. _ViTables: http://vitables.org -.. _GitHub: http://github.com/arfc/saltproc - - -Optional Depenendencies: - #. `pytest`_ (for testing) - #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation) - #. `matplotlib`_ - #. `ViTables`_ - - - -Most of the dependencies are readily available through package managers. -Once all the dependencies are installed, SaltProc can be installed. -Clone the source from the SaltProc repository from `GitHub`_. -Then run the following commands from the directory above cloned repository: - -.. code-block:: bash - - git clone git@github.com:arfc/saltproc.git - cd saltproc/ - pip install . - -Please let us know if you run into trouble. - -Cross Section Configuration ---------------------------- -SaltProc can use any cross section library that Serpent can. See `this page on the Serpent wiki`_ for information on how to configure the libraries. - -.. _this page on the Serpent wiki: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries - -Testing -------- -The SaltProc test suite has two types of tests: unit tests and regression tests. -The unit tests check that the individual functions and classes of the ``saltproc`` -module return the correct type of variables and correct values, where applicable. -The regression tests run a full SaltProc simulation and check the final result -with a precalculated result. -The integration tests require the `JEFF 3.1.2 cross section library`_ as well -as neutron induces and spontaneous fission product yield data from JEFF 3.3. -The publicly available versions of JEFF 3.1.2 cannot be used with Serpent right -out of the box due to `Serpent's notation for isomeric states`_. The scripts in -``scripts/xsdata`` download all necessary libraries and perform all the necessary processing on them for use in Serpent 2. -We recommend using them for your convenience. -See the `README`_ for more information. - -.. _Serpent's notation for isomeric states: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries -.. _JEFF 3.1.2 cross section library: https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_31/JEFF312/ -.. _README: https://github.com/arfc/saltproc/blob/master/scripts/README.md - -To run the tests, execute: - -.. code-block:: bash - - pytest saltproc/ - -from the root directory of SaltProc. If you just want to run the unit tests, execute - -.. code-block:: bash - - pytest --ignore saltproc/tests/integration_tests saltproc/ - diff --git a/doc/overview.rst b/doc/overview.rst deleted file mode 100644 index 82d263510..000000000 --- a/doc/overview.rst +++ /dev/null @@ -1,87 +0,0 @@ -Overview -========= - -SaltProc couples directly with the Monte Carlo neutron transport code Serpent 2 -and enables sophisticated, multi-component online fuel reprocessing system -modeling. SaltProc is the first open-source tool for liquid-fueled MSR -depletion simulation with the following capabilities: - -- neutron poison removal with user-defined efficiency, -- make-up mass loss by fresh fuel injection, -- reactivity control by adjusting fuel feed rate or geometry change, -- can model any reactor design, -- potentially, can couple with any depletion tool (i.e., MCNP, SCALE, OpenMC). - - -How SaltProc works -------------------- - -SaltProc is a driver for Serpent to simulate online fuel salt reprocessing for -Molten Salt Reactors. It performs following major functions: - - - runs SERPENT - - parses and stores Serpent output data in HDF5 - - modifies parsed material composition (`reprocesses`) - - creates Serpent input file - - -The code logic flow is the following: - - 1. Runs Serpent (`saltproc.depcode.run_depcode()`) - 2. Parses through the output `*_dep.m` file and creates PyNE Material object - for each burnable material. - 3. Processes Fuel (`saltproc.app.reprocessing()` and `saltproc.refill`): - - * Passes fuel composition throughout Processes objects (reprocessing system - components) to remove poisons with specific efficiency. - * Adds back fissile and/or fertile material to make-up loss of material. - - 4. Records data: - - - Depleted fuel composition (`materials/fuel/before_reproc` table in HDF5) - - Reprocessed fuel composition (`materials/fuel/after_reproc` table in - HDF5) - - Multiplication factor at the beginning and at the end of depletion step - (`simulation_parameters/keff_bds`, `simulation_parameters/keff_eds`) - - Effective Delayed Neutron Fraction (:math:`\beta_{eff}`) at the end of - the depletion step (`simulation_parameters/beta_eff_eds`) - - Waste and feed streams from each `Process` (`materials/in_out_streams/`) - - 5. Repeats 1-4. - -Updates -------- - -March 2021: - -Besides the existing flexibility like fixed removal efficiency definition for -each target isotope defined in the object input file, Saltproc code now -comprises `Sparging System package` that calculates removal efficiencies for -various target isotopes (i.e., Xe, Kr, and H). To enable this feature, use -the `"self"` command in the input file in the `"efficiency"` object names of -Sparger and Separator components. Each component can be employed separately. -An example is given below. In the example, capacity and mass flow rate are in -`g/s` unit while volume is in `cm`:math:`^3` unit. - -"sparger": { "capacity": 9920000, - "efficiency": "self", - "mass_flowrate": 9920000, - "volume": 10000000 }, -"entrainment_separator": { "capacity": 9920000, - "efficiency": "self", - "mass_flowrate": 9920000, - "volume": 11 } - -The Future ------------ - -A number of features will be implemented in SaltProc soon. Support of various -depletion codes (e.g., OpenMC) will be added. - - -.. warning:: - - SaltProc is a relatively new project and is still under heavy development. - Although we will make our best effort to maintain compatibility with the - current API, inevitably the API will change in future versions as SaltProc - matures. diff --git a/doc/src/index.rst b/doc/src/index.rst deleted file mode 100644 index f09f9d4c0..000000000 --- a/doc/src/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -SaltProc API -============= - -This is automatically generated API documentation from SaltProc source files. - -Click the "modules" (:ref:`modindex`) link to browse the modules. -Or, dive right into the autogenerated :doc:`saltproc` docs. From 480be718d92b76effd834941c7d4b7d2ab9a804d Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 20 Jan 2022 09:59:58 -0600 Subject: [PATCH 14/70] try disabling sphinx fail_on_error --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index e4ee6e94e..1ef94b015 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -15,4 +15,4 @@ python: sphinx: configuration: docs/conf.py - fail_on_warning: true + # fail_on_warning: true From e98049df2ac30c636c66e53690dba5e163ab3560 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 20 Jan 2022 10:34:36 -0600 Subject: [PATCH 15/70] remove cruft from docs/src --- docs/src/modules.rst | 7 ---- docs/src/saltproc.app.rst | 7 ---- docs/src/saltproc.depcode.rst | 7 ---- docs/src/saltproc.materialflow.rst | 7 ---- docs/src/saltproc.process.rst | 7 ---- docs/src/saltproc.reactor.rst | 7 ---- docs/src/saltproc.rst | 34 ------------------- docs/src/saltproc.separator.rst | 7 ---- docs/src/saltproc.simulation.rst | 7 ---- docs/src/saltproc.sparger.rst | 7 ---- docs/src/saltproc.tests.rst | 24 ------------- docs/src/saltproc.tests.test_app.rst | 7 ---- docs/src/saltproc.tests.test_depcode.rst | 7 ---- docs/src/saltproc.tests.test_materialflow.rst | 7 ---- docs/src/saltproc.tests.test_process.rst | 7 ---- docs/src/saltproc.tests.test_separator.rst | 7 ---- docs/src/saltproc.tests.test_simulation.rst | 7 ---- docs/src/saltproc.tests.test_sparger.rst | 7 ---- docs/src/saltproc.version.rst | 7 ---- 19 files changed, 177 deletions(-) delete mode 100644 docs/src/modules.rst delete mode 100644 docs/src/saltproc.app.rst delete mode 100644 docs/src/saltproc.depcode.rst delete mode 100644 docs/src/saltproc.materialflow.rst delete mode 100644 docs/src/saltproc.process.rst delete mode 100644 docs/src/saltproc.reactor.rst delete mode 100644 docs/src/saltproc.rst delete mode 100644 docs/src/saltproc.separator.rst delete mode 100644 docs/src/saltproc.simulation.rst delete mode 100644 docs/src/saltproc.sparger.rst delete mode 100644 docs/src/saltproc.tests.rst delete mode 100644 docs/src/saltproc.tests.test_app.rst delete mode 100644 docs/src/saltproc.tests.test_depcode.rst delete mode 100644 docs/src/saltproc.tests.test_materialflow.rst delete mode 100644 docs/src/saltproc.tests.test_process.rst delete mode 100644 docs/src/saltproc.tests.test_separator.rst delete mode 100644 docs/src/saltproc.tests.test_simulation.rst delete mode 100644 docs/src/saltproc.tests.test_sparger.rst delete mode 100644 docs/src/saltproc.version.rst diff --git a/docs/src/modules.rst b/docs/src/modules.rst deleted file mode 100644 index 1da7d5d98..000000000 --- a/docs/src/modules.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc -======== - -.. toctree:: - :maxdepth: 4 - - saltproc diff --git a/docs/src/saltproc.app.rst b/docs/src/saltproc.app.rst deleted file mode 100644 index a9b319fdd..000000000 --- a/docs/src/saltproc.app.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.app module -=================== - -.. automodule:: saltproc.app - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.depcode.rst b/docs/src/saltproc.depcode.rst deleted file mode 100644 index 04ca7fc0b..000000000 --- a/docs/src/saltproc.depcode.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.depcode module -======================= - -.. automodule:: saltproc.depcode - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.materialflow.rst b/docs/src/saltproc.materialflow.rst deleted file mode 100644 index 31a768303..000000000 --- a/docs/src/saltproc.materialflow.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.materialflow module -============================ - -.. automodule:: saltproc.materialflow - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.process.rst b/docs/src/saltproc.process.rst deleted file mode 100644 index 2ebcc3e14..000000000 --- a/docs/src/saltproc.process.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.process module -======================= - -.. automodule:: saltproc.process - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.reactor.rst b/docs/src/saltproc.reactor.rst deleted file mode 100644 index 07925c97a..000000000 --- a/docs/src/saltproc.reactor.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.reactor module -======================= - -.. automodule:: saltproc.reactor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.rst b/docs/src/saltproc.rst deleted file mode 100644 index a7888ebbc..000000000 --- a/docs/src/saltproc.rst +++ /dev/null @@ -1,34 +0,0 @@ -saltproc package -================ - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - saltproc.tests - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - saltproc.app - saltproc.depcode - saltproc.materialflow - saltproc.process - saltproc.reactor - saltproc.separator - saltproc.simulation - saltproc.sparger - saltproc.version - -Module contents ---------------- - -.. automodule:: saltproc - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.separator.rst b/docs/src/saltproc.separator.rst deleted file mode 100644 index 2228b690c..000000000 --- a/docs/src/saltproc.separator.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.separator module -========================= - -.. automodule:: saltproc.separator - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.simulation.rst b/docs/src/saltproc.simulation.rst deleted file mode 100644 index 7572435ea..000000000 --- a/docs/src/saltproc.simulation.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.simulation module -========================== - -.. automodule:: saltproc.simulation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.sparger.rst b/docs/src/saltproc.sparger.rst deleted file mode 100644 index 5460a476c..000000000 --- a/docs/src/saltproc.sparger.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.sparger module -======================= - -.. automodule:: saltproc.sparger - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.rst b/docs/src/saltproc.tests.rst deleted file mode 100644 index 024331988..000000000 --- a/docs/src/saltproc.tests.rst +++ /dev/null @@ -1,24 +0,0 @@ -saltproc.tests package -====================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - saltproc.tests.test_app - saltproc.tests.test_depcode - saltproc.tests.test_materialflow - saltproc.tests.test_process - saltproc.tests.test_separator - saltproc.tests.test_simulation - saltproc.tests.test_sparger - -Module contents ---------------- - -.. automodule:: saltproc.tests - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_app.rst b/docs/src/saltproc.tests.test_app.rst deleted file mode 100644 index d7674c957..000000000 --- a/docs/src/saltproc.tests.test_app.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_app module -=============================== - -.. automodule:: saltproc.tests.test_app - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_depcode.rst b/docs/src/saltproc.tests.test_depcode.rst deleted file mode 100644 index 9f4918e71..000000000 --- a/docs/src/saltproc.tests.test_depcode.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_depcode module -=================================== - -.. automodule:: saltproc.tests.test_depcode - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_materialflow.rst b/docs/src/saltproc.tests.test_materialflow.rst deleted file mode 100644 index 14e2e41c9..000000000 --- a/docs/src/saltproc.tests.test_materialflow.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_materialflow module -======================================== - -.. automodule:: saltproc.tests.test_materialflow - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_process.rst b/docs/src/saltproc.tests.test_process.rst deleted file mode 100644 index 5b6813db0..000000000 --- a/docs/src/saltproc.tests.test_process.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_process module -=================================== - -.. automodule:: saltproc.tests.test_process - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_separator.rst b/docs/src/saltproc.tests.test_separator.rst deleted file mode 100644 index 9481465f2..000000000 --- a/docs/src/saltproc.tests.test_separator.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_separator module -===================================== - -.. automodule:: saltproc.tests.test_separator - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_simulation.rst b/docs/src/saltproc.tests.test_simulation.rst deleted file mode 100644 index 25aed9803..000000000 --- a/docs/src/saltproc.tests.test_simulation.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_simulation module -====================================== - -.. automodule:: saltproc.tests.test_simulation - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.tests.test_sparger.rst b/docs/src/saltproc.tests.test_sparger.rst deleted file mode 100644 index b475f4cf9..000000000 --- a/docs/src/saltproc.tests.test_sparger.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.tests.test\_sparger module -=================================== - -.. automodule:: saltproc.tests.test_sparger - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/src/saltproc.version.rst b/docs/src/saltproc.version.rst deleted file mode 100644 index 9d7ecdbdf..000000000 --- a/docs/src/saltproc.version.rst +++ /dev/null @@ -1,7 +0,0 @@ -saltproc.version module -======================= - -.. automodule:: saltproc.version - :members: - :undoc-members: - :show-inheritance: From 539e614535642edbc877f19ef8b7ab70088d0e83 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 20 Jan 2022 10:36:28 -0600 Subject: [PATCH 16/70] remove crift from integration tests --- .../tests/integration_tests/no_repro/int_test | 104 ------------------ 1 file changed, 104 deletions(-) delete mode 100644 saltproc/tests/integration_tests/no_repro/int_test diff --git a/saltproc/tests/integration_tests/no_repro/int_test b/saltproc/tests/integration_tests/no_repro/int_test deleted file mode 100644 index f2e81e8aa..000000000 --- a/saltproc/tests/integration_tests/no_repro/int_test +++ /dev/null @@ -1,104 +0,0 @@ -include "/home/ooblack/projects/saltproc/saltproc/tests/integration_tests/no_repro/int_test_mat" - - -%therm zrh_h 900 hzr05.32t hzr06.32t % 900K H-Zr -%set acelib "/projects/sciteam/bahg/serpent/xsdata/jeff312/sss_jeff312.xsdata" -include "/home/ooblack/projects/saltproc/saltproc/tests/integration_tests/no_repro/../../test_geo.inp" -%set declib "/projects/sciteam/bahg/serpent/xsdata/jeff312/sss_jeff33.dec" -%set nfylib "/projects/sciteam/bahg/serpent/xsdata/jeff312/sss_jeff33.nfy" -set power 1.250000000E+09 dep daystep 3.00000E+00 -%set sfylib "/projects/sciteam/bahg/serpent/xsdata/jeff312/sss_jeff33.sfy" - -set acelib "sss_jeff312.xsdata" -set declib "sss_jeff33.dec" -set nfylib "sss_jeff33.nfy" -set sfylib "sss_jeff33.sfy" -% --- Neutron population and criticality cycles: - -set pop 100 20 5 -%set gcu -1 -% --- Depletion parameters -% --- Options for burnup calculation: -set bumode 2 % CRAM method -set pcc 1 % Predictor-corrector calculation on -%set xscalc 2 % Cross sections from spectrum -%set bunorm 2 -%set opti 1 - -%set power 1.250E+09 dep daytot 3 - -%set printm 1 0.0 - -set inventory all - -%set rfw 1 restart -%set rfr idx 321 restart -set seed 46549345296 - -mat zrh -5.66 tmp 900 rgb 68 1 84 moder zrh_h 1001 %moder zrh_z 40090 % g/cm3 UNVERIFIED -40090.09c -0.49793 % Mass fraction of Zr -90 -40091.09c -0.10980 % Mass fraction of Zr -91 -40092.09c -0.16967 % Mass fraction of Zr -92 -40094.09c -0.17569 % Mass fraction of Zr -94 -40096.09c -0.028908 % Mass fraction of Zr -96 -1001.09c -0.018007 % Mass fraction of H - 1 -1002.09c -0.0000041389 % Mass fraction of H - 2 -%therm zrh_h h-zr.15t % h-zr.26t % Scattering XS for H from MCNP ACE lib -%therm zrh_z zr-h.15t % zr-h.26t % Scattering XS for Zr from MCNP ACE lib -therm zrh_h 900 hzr05.32t hzr06.32t % 900K H-Zr for JEFF-3.1.2 ACE lib (BW) - -mat sic -3.21 tmp 900 % g/cm3 UNVERIFIED -14028.09c -0.64365 % Mass fraction of Si - 28 -14029.09c -0.033866 % Mass fraction of Si - 29 -14030.09c -0.02312 % Mass fraction of Si - 30 -6000.09c -0.29936 % Mass fraction of C - -mat hast -8.86 tmp 900 rgb 127 205 187 % g/cm3 for mixture -%28000.09c -6.29060 % Mass fraction of Ni -28058.09c -4.28245176 % Mass fraction of Ni-58 -28060.09c -1.649584 % Mass fraction of Ni-60 -28061.09c -0.07171284 % Mass fraction of Ni-61 -28061.09c -0.22866331 % Mass fraction of Ni-62 -28064.09c -0.058251 % Mass fraction of Ni-64 -%24000.09c -0.62020 % Mass fraction of Cr -24050.09c -0.0269477 % Mass fraction of Cr-50 -24052.09c -0.51965938 % Mass fraction of Cr-52 -24053.09c -0.0589252 % Mass fraction of Cr-53 -24054.09c -0.01466773 % Mass fraction of Cr-54 -%42000.09c -1.41760 % Mass fraction of Mo -42092.09c -0.2076784 % Mass fraction of Mo-92 -42094.09c -0.13027744 % Mass fraction of Mo-94 -42095.09c -0.22497312 % Mass fraction of Mo-95 -42096.09c -0.23631392 % Mass fraction of Mo-96 -42097.09c -0.13580608 % Mass fraction of Mo-97 -42098.09c -0.34433504 % Mass fraction of Mo-98 -42100.09c -0.13807424 % Mass fraction of Mo-100 -%26000.09c -0.28441 % Mass fraction of Fe -26054.09c -0.016637985 % Mass fraction of Fe-54 -26056.09c -0.260946175 % Mass fraction of Fe-56 -26057.09c -0.006029492 % Mass fraction of Fe-57 -26058.09c -7.96348E-4 % Mass fraction of Fe-58 -%14000.09c -0.08063 % Mass fraction of Si -14028.09c -0.07434086 % Mass fraction of Si-28 -14029.09c -3.78961E-3 % Mass fraction of Si-29 -14030.09c -2.249953E-3 % Mass fraction of Si-30 -25055.09c -0.05316 % Mass fraction of Mn-55 (100% abundance) -23000.09c -0.04430 % Mass fraction of V -6000.09c -0.00532 % Mass fraction of C -27059.09c -0.00177 % Mass fraction of Co-59 (100% abundance) -%74000.09c -0.02658 % Mass fraction of W -74182.09c -7.0437E-3 % Mass fraction of W-182 -74183.09c -3.803598E-3 % Mass fraction of W-183 -74184.09c -8.144112E-3 % Mass fraction of W-184 -74186.09c -7.556694E-3 % Mass fraction of W-186 -13027.09c -0.01772 % Mass fraction of Al-28 (100% abundance) -%22000.09c -0.01772 % Mass fraction of Ti -22046.09c -1.4619E-3 % Mass fraction of Ti-46 -22047.09c -1.318368E-3 % Mass fraction of Ti-47 -22048.09c -0.013063184 % Mass fraction of Ti-48 -22049.09c -9.58652E-4 % Mass fraction of Ti-49 -22050.09c -9.17896E-4 % Mass fraction of Ti-50 - -mat air -0.001225 tmp 900 -8016.09c 0.21 -7014.09c 0.79 From 5c41d5829860c213b85abb74c43242c02c0d931c Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 11:56:40 -0600 Subject: [PATCH 17/70] Revert "doc->docs" This reverts commit cea25adc281b262a444df85b60c4cc73c5e85976. --- docs/Makefile | 177 --------------------------------------- docs/conf.py | 187 ------------------------------------------ docs/examples.rst | 29 ------- docs/index.rst | 80 ------------------ docs/installation.rst | 86 ------------------- docs/overview.rst | 87 -------------------- docs/src/index.rst | 7 -- 7 files changed, 653 deletions(-) delete mode 100644 docs/Makefile delete mode 100644 docs/conf.py delete mode 100644 docs/examples.rst delete mode 100644 docs/index.rst delete mode 100644 docs/installation.rst delete mode 100644 docs/overview.rst delete mode 100644 docs/src/index.rst diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index f554f954e..000000000 --- a/docs/Makefile +++ /dev/null @@ -1,177 +0,0 @@ -# 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 ' where 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/pyrk.qhcp" - @echo "To view the help file:" - @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyrk.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/pyrk" - @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyrk" - @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." diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index b0382bb1a..000000000 --- a/docs/conf.py +++ /dev/null @@ -1,187 +0,0 @@ -# -*- coding: utf-8 -*- -# -# Configuration file for the Sphinx documentation builder. -# -# This file does only contain a selection of the most common options. For a -# full list see the documentation: -# http://www.sphinx-doc.org/en/master/config - -# -- 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 -import sphinx_rtd_theme -sys.path.append(os.path.abspath('../')) -sys.path.append(os.path.abspath('../saltproc')) - -# -- Project information ----------------------------------------------------- - -project = u'Saltproc' -copyright = u'2018, Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' -author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' - -# The short X.Y version -version = '0.3' -# The full version, including alpha/beta/rc tags -release = '0.3.1-dev' - - -# -- 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.doctest', - 'sphinx.ext.intersphinx', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.napoleon', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'sphinx.ext.viewcode', -] - -# Napoleon settings -napoleon_google_docstring = False -napoleon_numpy_docstring = True -napoleon_include_init_with_doc = True -napoleon_include_private_with_doc = True -napoleon_include_special_with_doc = True -napoleon_use_admonition_for_examples = True -napoleon_use_admonition_for_notes = True -napoleon_use_admonition_for_references = True -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'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# 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 - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path . -exclude_patterns = ['_build'] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# 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 = "sphinx_rtd_theme" -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] -html_show_copyright = False - -# 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 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'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# The default sidebars (for documents that don't match any pattern) are -# defined by theme itself. Builtin themes are using these templates by -# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', -# 'searchbox.html']``. -# -# html_sidebars = {} - - -# -- Options for HTMLHelp output --------------------------------------------- - -# Output file base name for HTML help builder. -htmlhelp_basename = 'saltprocdoc' - - -# -- 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 = [ - ('index', 'saltproc.tex', u'SaltProc Documentation', - author, 'manual'), -] - - -# -- Options for manual page output ------------------------------------------ - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'saltproc', u'Saltproc Documentation', - [author], 1) -] - - -# -- 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, 'Saltproc', 'Saltproc Documentation', - author, 'Saltproc', - 'SaltProc is a tool for online reprocessing for Molten Salt Reactors.', - 'Miscellaneous'), -] - -# autodoc default options -autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance', - 'inherited-members', 'private-members'] diff --git a/docs/examples.rst b/docs/examples.rst deleted file mode 100644 index 4f1f2c98f..000000000 --- a/docs/examples.rst +++ /dev/null @@ -1,29 +0,0 @@ -Examples -========= - -A number of examples are present in the `examples directory`_ provided with the source code. - -.. _examples directory: https://github.com/arfc/saltproc/tree/master/examples - -Transatomic Power Molten Salt Reactor example can be run with: - - -.. code-block:: bash - - cd /path/to/saltproc - python saltproc -i examples/tap/tap_main.json - - -In the example above, ``path/to/saltproc`` is, of course, the path to the main -saltproc directory, containing ``setup.py``. The ``tap_main.json`` is the main -Saltproc input file, which contains paths to Serpent input file -(``tap.serpent``), DOT-file with reprocessing scheme (``tap.dot``), and -reprocessing system components' detailed description (``tap_objects.json``). - - -Similarly, Molten Salt Breeder Reactor example can be run with: - - -.. code-block:: bash - - python saltproc -i examples/msbr/msbr_main.json diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index dd5ad5830..000000000 --- a/docs/index.rst +++ /dev/null @@ -1,80 +0,0 @@ -.. Saltproc documentation master file, created by - sphinx-quickstart on Tue Jul 3 14:26:54 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -SaltProc -========= - -**SaltProc** is a python package for liquid-fueled nuclear reactor depletion -calculations. It couples directly with the Serpent 2 Monte Carlo depletion -software to enable online reprocessing system modeling in depletion -calculation. - -**SaltProc** welcomes your contributions. It already relies on many libraries -in the Scientific Python ecosystem including `pyne`_, `numpy`_, `matplotlib`_, -`networkx`_, and `pydotplus`_. - -.. _pyne: http://pyne.io/ -.. _numpy: http://numpy.org -.. _matplotlib: http://matplotlib.org -.. _networkx: http://networkx.github.io -.. _pydotplus: https://pydotplus.readthedocs.io/ - - -Documentation -------------- - -.. toctree:: - :maxdepth: 1 - - overview - installation - examples - src/index - How to cite - -Indices and tables ------------------- - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - - - -Citation --------- - -Up-to-date information about citing SaltProc can be found within the `citation`_ -file. - -.. _citation: https://github.com/arfc/saltproc/blob/master/CITATION.md - - -Get in touch ------------- - -- Please report bugs, suggest feature ideas, and browse the source code `on GitHub`_. -- There, new contributors can also find `a guide to contributing`_. -- Good start point for new contributors is `current open issues`_. - -.. _a guide to contributing: https://github.com/arfc/saltproc/blob/master/CONTRIBUTING.md -.. _current open issues: https://github.com/arfc/saltproc/issues?q=is%3Aopen+is%3Aissue -.. _on GitHub: http://github.com/arfc/saltproc - -Acknowledgment --------------- - -SaltProc uses `Shablona`_ template which is universal solution for small -scientific python projects developed at University of Washington `eScience Insititute`_. - -.. _Shablona: https://github.com/uwescience/shablona -.. _eScience Insititute: https://escience.washington.edu - -License -------- - -SaltProc is available under the open source `BSD 3-clause License`__. - -__ https://raw.githubusercontent.com/arfc/saltproc/master/LICENSE diff --git a/docs/installation.rst b/docs/installation.rst deleted file mode 100644 index d6ebce79c..000000000 --- a/docs/installation.rst +++ /dev/null @@ -1,86 +0,0 @@ -Installation -============ - -SaltProc has the following dependencies: - - #. `Python`_ (>=3.5) - #. `Serpent`_ (>=2.1.31) - #. `PyNE`_ (>=0.5.11) - #. `NumPy`_ (>=1.14.0) - #. `PyTables`_ - #. `NetworkX`_ - #. `PyDotPlus`_ - -.. _Serpent: http://montecarlo.vtt.fi -.. _PyNE: http://pyne.io -.. _Python: http://python.org -.. _NumPy: http://numpy.org -.. _PyTables: http://pytables.org -.. _NetworkX: http://networkx.github.io -.. _PyDotPlus: https://pydotplus.readthedocs.io/ -.. _pytest: https://docs.pytest.org -.. _sphinx: https://www.sphinx-doc.org -.. _sphinx-rtd-theme: https://sphinx-rtd-theme.readthedocs.io -.. _matplotlib: http://matplotlib.org -.. _ViTables: http://vitables.org -.. _GitHub: http://github.com/arfc/saltproc - - -Optional Depenendencies: - #. `pytest`_ (for testing) - #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation) - #. `matplotlib`_ - #. `ViTables`_ - - - -Most of the dependencies are readily available through package managers. -Once all the dependencies are installed, SaltProc can be installed. -Clone the source from the SaltProc repository from `GitHub`_. -Then run the following commands from the directory above cloned repository: - -.. code-block:: bash - - git clone git@github.com:arfc/saltproc.git - cd saltproc/ - pip install . - -Please let us know if you run into trouble. - -Cross Section Configuration ---------------------------- -SaltProc can use any cross section library that Serpent can. See `this page on the Serpent wiki`_ for information on how to configure the libraries. - -.. _this page on the Serpent wiki: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries - -Testing -------- -The SaltProc test suite has two types of tests: unit tests and regression tests. -The unit tests check that the individual functions and classes of the ``saltproc`` -module return the correct type of variables and correct values, where applicable. -The regression tests run a full SaltProc simulation and check the final result -with a precalculated result. -The integration tests require the `JEFF 3.1.2 cross section library`_ as well -as neutron induces and spontaneous fission product yield data from JEFF 3.3. -The publicly available versions of JEFF 3.1.2 cannot be used with Serpent right -out of the box due to `Serpent's notation for isomeric states`_. The scripts in -``scripts/xsdata`` download all necessary libraries and perform all the necessary processing on them for use in Serpent 2. -We recommend using them for your convenience. -See the `README`_ for more information. - -.. _Serpent's notation for isomeric states: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries -.. _JEFF 3.1.2 cross section library: https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_31/JEFF312/ -.. _README: https://github.com/arfc/saltproc/blob/master/scripts/README.md - -To run the tests, execute: - -.. code-block:: bash - - pytest saltproc/ - -from the root directory of SaltProc. If you just want to run the unit tests, execute - -.. code-block:: bash - - pytest --ignore saltproc/tests/integration_tests saltproc/ - diff --git a/docs/overview.rst b/docs/overview.rst deleted file mode 100644 index 82d263510..000000000 --- a/docs/overview.rst +++ /dev/null @@ -1,87 +0,0 @@ -Overview -========= - -SaltProc couples directly with the Monte Carlo neutron transport code Serpent 2 -and enables sophisticated, multi-component online fuel reprocessing system -modeling. SaltProc is the first open-source tool for liquid-fueled MSR -depletion simulation with the following capabilities: - -- neutron poison removal with user-defined efficiency, -- make-up mass loss by fresh fuel injection, -- reactivity control by adjusting fuel feed rate or geometry change, -- can model any reactor design, -- potentially, can couple with any depletion tool (i.e., MCNP, SCALE, OpenMC). - - -How SaltProc works -------------------- - -SaltProc is a driver for Serpent to simulate online fuel salt reprocessing for -Molten Salt Reactors. It performs following major functions: - - - runs SERPENT - - parses and stores Serpent output data in HDF5 - - modifies parsed material composition (`reprocesses`) - - creates Serpent input file - - -The code logic flow is the following: - - 1. Runs Serpent (`saltproc.depcode.run_depcode()`) - 2. Parses through the output `*_dep.m` file and creates PyNE Material object - for each burnable material. - 3. Processes Fuel (`saltproc.app.reprocessing()` and `saltproc.refill`): - - * Passes fuel composition throughout Processes objects (reprocessing system - components) to remove poisons with specific efficiency. - * Adds back fissile and/or fertile material to make-up loss of material. - - 4. Records data: - - - Depleted fuel composition (`materials/fuel/before_reproc` table in HDF5) - - Reprocessed fuel composition (`materials/fuel/after_reproc` table in - HDF5) - - Multiplication factor at the beginning and at the end of depletion step - (`simulation_parameters/keff_bds`, `simulation_parameters/keff_eds`) - - Effective Delayed Neutron Fraction (:math:`\beta_{eff}`) at the end of - the depletion step (`simulation_parameters/beta_eff_eds`) - - Waste and feed streams from each `Process` (`materials/in_out_streams/`) - - 5. Repeats 1-4. - -Updates -------- - -March 2021: - -Besides the existing flexibility like fixed removal efficiency definition for -each target isotope defined in the object input file, Saltproc code now -comprises `Sparging System package` that calculates removal efficiencies for -various target isotopes (i.e., Xe, Kr, and H). To enable this feature, use -the `"self"` command in the input file in the `"efficiency"` object names of -Sparger and Separator components. Each component can be employed separately. -An example is given below. In the example, capacity and mass flow rate are in -`g/s` unit while volume is in `cm`:math:`^3` unit. - -"sparger": { "capacity": 9920000, - "efficiency": "self", - "mass_flowrate": 9920000, - "volume": 10000000 }, -"entrainment_separator": { "capacity": 9920000, - "efficiency": "self", - "mass_flowrate": 9920000, - "volume": 11 } - -The Future ------------ - -A number of features will be implemented in SaltProc soon. Support of various -depletion codes (e.g., OpenMC) will be added. - - -.. warning:: - - SaltProc is a relatively new project and is still under heavy development. - Although we will make our best effort to maintain compatibility with the - current API, inevitably the API will change in future versions as SaltProc - matures. diff --git a/docs/src/index.rst b/docs/src/index.rst deleted file mode 100644 index f09f9d4c0..000000000 --- a/docs/src/index.rst +++ /dev/null @@ -1,7 +0,0 @@ -SaltProc API -============= - -This is automatically generated API documentation from SaltProc source files. - -Click the "modules" (:ref:`modindex`) link to browse the modules. -Or, dive right into the autogenerated :doc:`saltproc` docs. From 446dd53c1fa2316ef0c0528518fd43053e560271 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 11:57:15 -0600 Subject: [PATCH 18/70] Revert "doc->docs" This reverts commit 061c29f1a703ffbdaaa8f9a53114621caac68e53. --- doc/Makefile | 177 ++++++++++++++++++++++++++++++++++++++++ doc/conf.py | 187 +++++++++++++++++++++++++++++++++++++++++++ doc/examples.rst | 29 +++++++ doc/index.rst | 80 ++++++++++++++++++ doc/installation.rst | 86 ++++++++++++++++++++ doc/overview.rst | 87 ++++++++++++++++++++ doc/src/index.rst | 7 ++ 7 files changed, 653 insertions(+) create mode 100644 doc/Makefile create mode 100644 doc/conf.py create mode 100644 doc/examples.rst create mode 100644 doc/index.rst create mode 100644 doc/installation.rst create mode 100644 doc/overview.rst create mode 100644 doc/src/index.rst diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 000000000..f554f954e --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,177 @@ +# 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 ' where 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/pyrk.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyrk.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/pyrk" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyrk" + @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." diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 000000000..b0382bb1a --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,187 @@ +# -*- coding: utf-8 -*- +# +# Configuration file for the Sphinx documentation builder. +# +# This file does only contain a selection of the most common options. For a +# full list see the documentation: +# http://www.sphinx-doc.org/en/master/config + +# -- 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 +import sphinx_rtd_theme +sys.path.append(os.path.abspath('../')) +sys.path.append(os.path.abspath('../saltproc')) + +# -- Project information ----------------------------------------------------- + +project = u'Saltproc' +copyright = u'2018, Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' +author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' + +# The short X.Y version +version = '0.3' +# The full version, including alpha/beta/rc tags +release = '0.3.1-dev' + + +# -- 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.doctest', + 'sphinx.ext.intersphinx', + 'sphinx.ext.todo', + 'sphinx.ext.coverage', + 'sphinx.ext.napoleon', + 'sphinx.ext.mathjax', + 'sphinx.ext.ifconfig', + 'sphinx.ext.viewcode', +] + +# Napoleon settings +napoleon_google_docstring = False +napoleon_numpy_docstring = True +napoleon_include_init_with_doc = True +napoleon_include_private_with_doc = True +napoleon_include_special_with_doc = True +napoleon_use_admonition_for_examples = True +napoleon_use_admonition_for_notes = True +napoleon_use_admonition_for_references = True +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'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The master toctree document. +master_doc = 'index' + +# 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 + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path . +exclude_patterns = ['_build'] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# 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 = "sphinx_rtd_theme" +html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] +html_show_copyright = False + +# 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 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'] + +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# The default sidebars (for documents that don't match any pattern) are +# defined by theme itself. Builtin themes are using these templates by +# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', +# 'searchbox.html']``. +# +# html_sidebars = {} + + +# -- Options for HTMLHelp output --------------------------------------------- + +# Output file base name for HTML help builder. +htmlhelp_basename = 'saltprocdoc' + + +# -- 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 = [ + ('index', 'saltproc.tex', u'SaltProc Documentation', + author, 'manual'), +] + + +# -- Options for manual page output ------------------------------------------ + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'saltproc', u'Saltproc Documentation', + [author], 1) +] + + +# -- 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, 'Saltproc', 'Saltproc Documentation', + author, 'Saltproc', + 'SaltProc is a tool for online reprocessing for Molten Salt Reactors.', + 'Miscellaneous'), +] + +# autodoc default options +autodoc_default_flags = ['members', 'undoc-members', 'show-inheritance', + 'inherited-members', 'private-members'] diff --git a/doc/examples.rst b/doc/examples.rst new file mode 100644 index 000000000..4f1f2c98f --- /dev/null +++ b/doc/examples.rst @@ -0,0 +1,29 @@ +Examples +========= + +A number of examples are present in the `examples directory`_ provided with the source code. + +.. _examples directory: https://github.com/arfc/saltproc/tree/master/examples + +Transatomic Power Molten Salt Reactor example can be run with: + + +.. code-block:: bash + + cd /path/to/saltproc + python saltproc -i examples/tap/tap_main.json + + +In the example above, ``path/to/saltproc`` is, of course, the path to the main +saltproc directory, containing ``setup.py``. The ``tap_main.json`` is the main +Saltproc input file, which contains paths to Serpent input file +(``tap.serpent``), DOT-file with reprocessing scheme (``tap.dot``), and +reprocessing system components' detailed description (``tap_objects.json``). + + +Similarly, Molten Salt Breeder Reactor example can be run with: + + +.. code-block:: bash + + python saltproc -i examples/msbr/msbr_main.json diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 000000000..dd5ad5830 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,80 @@ +.. Saltproc documentation master file, created by + sphinx-quickstart on Tue Jul 3 14:26:54 2018. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +SaltProc +========= + +**SaltProc** is a python package for liquid-fueled nuclear reactor depletion +calculations. It couples directly with the Serpent 2 Monte Carlo depletion +software to enable online reprocessing system modeling in depletion +calculation. + +**SaltProc** welcomes your contributions. It already relies on many libraries +in the Scientific Python ecosystem including `pyne`_, `numpy`_, `matplotlib`_, +`networkx`_, and `pydotplus`_. + +.. _pyne: http://pyne.io/ +.. _numpy: http://numpy.org +.. _matplotlib: http://matplotlib.org +.. _networkx: http://networkx.github.io +.. _pydotplus: https://pydotplus.readthedocs.io/ + + +Documentation +------------- + +.. toctree:: + :maxdepth: 1 + + overview + installation + examples + src/index + How to cite + +Indices and tables +------------------ + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + + + +Citation +-------- + +Up-to-date information about citing SaltProc can be found within the `citation`_ +file. + +.. _citation: https://github.com/arfc/saltproc/blob/master/CITATION.md + + +Get in touch +------------ + +- Please report bugs, suggest feature ideas, and browse the source code `on GitHub`_. +- There, new contributors can also find `a guide to contributing`_. +- Good start point for new contributors is `current open issues`_. + +.. _a guide to contributing: https://github.com/arfc/saltproc/blob/master/CONTRIBUTING.md +.. _current open issues: https://github.com/arfc/saltproc/issues?q=is%3Aopen+is%3Aissue +.. _on GitHub: http://github.com/arfc/saltproc + +Acknowledgment +-------------- + +SaltProc uses `Shablona`_ template which is universal solution for small +scientific python projects developed at University of Washington `eScience Insititute`_. + +.. _Shablona: https://github.com/uwescience/shablona +.. _eScience Insititute: https://escience.washington.edu + +License +------- + +SaltProc is available under the open source `BSD 3-clause License`__. + +__ https://raw.githubusercontent.com/arfc/saltproc/master/LICENSE diff --git a/doc/installation.rst b/doc/installation.rst new file mode 100644 index 000000000..d6ebce79c --- /dev/null +++ b/doc/installation.rst @@ -0,0 +1,86 @@ +Installation +============ + +SaltProc has the following dependencies: + + #. `Python`_ (>=3.5) + #. `Serpent`_ (>=2.1.31) + #. `PyNE`_ (>=0.5.11) + #. `NumPy`_ (>=1.14.0) + #. `PyTables`_ + #. `NetworkX`_ + #. `PyDotPlus`_ + +.. _Serpent: http://montecarlo.vtt.fi +.. _PyNE: http://pyne.io +.. _Python: http://python.org +.. _NumPy: http://numpy.org +.. _PyTables: http://pytables.org +.. _NetworkX: http://networkx.github.io +.. _PyDotPlus: https://pydotplus.readthedocs.io/ +.. _pytest: https://docs.pytest.org +.. _sphinx: https://www.sphinx-doc.org +.. _sphinx-rtd-theme: https://sphinx-rtd-theme.readthedocs.io +.. _matplotlib: http://matplotlib.org +.. _ViTables: http://vitables.org +.. _GitHub: http://github.com/arfc/saltproc + + +Optional Depenendencies: + #. `pytest`_ (for testing) + #. `sphinx`_ and `sphinx-rtd-theme`_ (for building documentation) + #. `matplotlib`_ + #. `ViTables`_ + + + +Most of the dependencies are readily available through package managers. +Once all the dependencies are installed, SaltProc can be installed. +Clone the source from the SaltProc repository from `GitHub`_. +Then run the following commands from the directory above cloned repository: + +.. code-block:: bash + + git clone git@github.com:arfc/saltproc.git + cd saltproc/ + pip install . + +Please let us know if you run into trouble. + +Cross Section Configuration +--------------------------- +SaltProc can use any cross section library that Serpent can. See `this page on the Serpent wiki`_ for information on how to configure the libraries. + +.. _this page on the Serpent wiki: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries + +Testing +------- +The SaltProc test suite has two types of tests: unit tests and regression tests. +The unit tests check that the individual functions and classes of the ``saltproc`` +module return the correct type of variables and correct values, where applicable. +The regression tests run a full SaltProc simulation and check the final result +with a precalculated result. +The integration tests require the `JEFF 3.1.2 cross section library`_ as well +as neutron induces and spontaneous fission product yield data from JEFF 3.3. +The publicly available versions of JEFF 3.1.2 cannot be used with Serpent right +out of the box due to `Serpent's notation for isomeric states`_. The scripts in +``scripts/xsdata`` download all necessary libraries and perform all the necessary processing on them for use in Serpent 2. +We recommend using them for your convenience. +See the `README`_ for more information. + +.. _Serpent's notation for isomeric states: https://serpent.vtt.fi/mediawiki/index.php/Installing_and_running_Serpent#Setting_up_the_data_libraries +.. _JEFF 3.1.2 cross section library: https://www.oecd-nea.org/dbforms/data/eva/evatapes/jeff_31/JEFF312/ +.. _README: https://github.com/arfc/saltproc/blob/master/scripts/README.md + +To run the tests, execute: + +.. code-block:: bash + + pytest saltproc/ + +from the root directory of SaltProc. If you just want to run the unit tests, execute + +.. code-block:: bash + + pytest --ignore saltproc/tests/integration_tests saltproc/ + diff --git a/doc/overview.rst b/doc/overview.rst new file mode 100644 index 000000000..82d263510 --- /dev/null +++ b/doc/overview.rst @@ -0,0 +1,87 @@ +Overview +========= + +SaltProc couples directly with the Monte Carlo neutron transport code Serpent 2 +and enables sophisticated, multi-component online fuel reprocessing system +modeling. SaltProc is the first open-source tool for liquid-fueled MSR +depletion simulation with the following capabilities: + +- neutron poison removal with user-defined efficiency, +- make-up mass loss by fresh fuel injection, +- reactivity control by adjusting fuel feed rate or geometry change, +- can model any reactor design, +- potentially, can couple with any depletion tool (i.e., MCNP, SCALE, OpenMC). + + +How SaltProc works +------------------- + +SaltProc is a driver for Serpent to simulate online fuel salt reprocessing for +Molten Salt Reactors. It performs following major functions: + + - runs SERPENT + - parses and stores Serpent output data in HDF5 + - modifies parsed material composition (`reprocesses`) + - creates Serpent input file + + +The code logic flow is the following: + + 1. Runs Serpent (`saltproc.depcode.run_depcode()`) + 2. Parses through the output `*_dep.m` file and creates PyNE Material object + for each burnable material. + 3. Processes Fuel (`saltproc.app.reprocessing()` and `saltproc.refill`): + + * Passes fuel composition throughout Processes objects (reprocessing system + components) to remove poisons with specific efficiency. + * Adds back fissile and/or fertile material to make-up loss of material. + + 4. Records data: + + - Depleted fuel composition (`materials/fuel/before_reproc` table in HDF5) + - Reprocessed fuel composition (`materials/fuel/after_reproc` table in + HDF5) + - Multiplication factor at the beginning and at the end of depletion step + (`simulation_parameters/keff_bds`, `simulation_parameters/keff_eds`) + - Effective Delayed Neutron Fraction (:math:`\beta_{eff}`) at the end of + the depletion step (`simulation_parameters/beta_eff_eds`) + - Waste and feed streams from each `Process` (`materials/in_out_streams/`) + + 5. Repeats 1-4. + +Updates +------- + +March 2021: + +Besides the existing flexibility like fixed removal efficiency definition for +each target isotope defined in the object input file, Saltproc code now +comprises `Sparging System package` that calculates removal efficiencies for +various target isotopes (i.e., Xe, Kr, and H). To enable this feature, use +the `"self"` command in the input file in the `"efficiency"` object names of +Sparger and Separator components. Each component can be employed separately. +An example is given below. In the example, capacity and mass flow rate are in +`g/s` unit while volume is in `cm`:math:`^3` unit. + +"sparger": { "capacity": 9920000, + "efficiency": "self", + "mass_flowrate": 9920000, + "volume": 10000000 }, +"entrainment_separator": { "capacity": 9920000, + "efficiency": "self", + "mass_flowrate": 9920000, + "volume": 11 } + +The Future +----------- + +A number of features will be implemented in SaltProc soon. Support of various +depletion codes (e.g., OpenMC) will be added. + + +.. warning:: + + SaltProc is a relatively new project and is still under heavy development. + Although we will make our best effort to maintain compatibility with the + current API, inevitably the API will change in future versions as SaltProc + matures. diff --git a/doc/src/index.rst b/doc/src/index.rst new file mode 100644 index 000000000..f09f9d4c0 --- /dev/null +++ b/doc/src/index.rst @@ -0,0 +1,7 @@ +SaltProc API +============= + +This is automatically generated API documentation from SaltProc source files. + +Click the "modules" (:ref:`modindex`) link to browse the modules. +Or, dive right into the autogenerated :doc:`saltproc` docs. From 4fe57be8fd8967363d2d8b01f023f96ff4151674 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 12:30:44 -0600 Subject: [PATCH 19/70] created doc-environment.yml --- doc/doc-environment.yml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 doc/doc-environment.yml diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml new file mode 100644 index 000000000..f511e9f65 --- /dev/null +++ b/doc/doc-environment.yml @@ -0,0 +1,14 @@ +name: saltrpoc-doc-env +channels: + - conda-forge + - defaults +dependencies: + - pyne>=0.5.11 + - numpy>=1.14.0 + - pytables + - networkx + - pydotplus + - pytest + - sphinx + - sphinx_rtd_theme + - gitpython From e4c6aff933a0175cf9cfde59aba633e39483880b Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 12:38:23 -0600 Subject: [PATCH 20/70] env typo fix --- doc/doc-environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index f511e9f65..6498231a6 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -1,4 +1,4 @@ -name: saltrpoc-doc-env +name: saltproc-doc-env channels: - conda-forge - defaults From cfc6157e1cc1b8e290b99820e7285fb67d1748c9 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 13:04:19 -0600 Subject: [PATCH 21/70] update doc-environment.yml --- doc/doc-environment.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index 6498231a6..fa6cab883 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -10,5 +10,10 @@ dependencies: - pydotplus - pytest - sphinx + - sphinx-intl - sphinx_rtd_theme - gitpython + - rsync + - pip: + - pystemmer + - rinohtype From 3a7f111e986c33ee73755fe4a337bfd8d1ce2235 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 13:33:32 -0600 Subject: [PATCH 22/70] update doc-environment.yml --- doc/doc-environment.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index fa6cab883..184428989 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -10,10 +10,6 @@ dependencies: - pydotplus - pytest - sphinx - - sphinx-intl - sphinx_rtd_theme - - gitpython - - rsync - pip: - - pystemmer - - rinohtype + - sphinxcontrib-versioning From bb63eb957f70463c571148cfb15ad35182585561 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 13:50:09 -0600 Subject: [PATCH 23/70] add sphinx_multiversion to conf.py --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index b0382bb1a..63daea088 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -49,7 +49,7 @@ 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', -] + 'sphinx_multiversion'] # Napoleon settings napoleon_google_docstring = False From 392d0a4201e0878841a79009b31662232fcac821 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 13:50:21 -0600 Subject: [PATCH 24/70] update doc-environment.yml --- doc/doc-environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index 184428989..1de8cb023 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -12,4 +12,4 @@ dependencies: - sphinx - sphinx_rtd_theme - pip: - - sphinxcontrib-versioning + - sphinx-multiversion From 0bb73ba75832e6f9d996fe7c0fe9bc9a826673e1 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 13:53:31 -0600 Subject: [PATCH 25/70] add _templates/versions.html --- doc/_templates/versions.html | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 doc/_templates/versions.html diff --git a/doc/_templates/versions.html b/doc/_templates/versions.html new file mode 100644 index 000000000..31a125789 --- /dev/null +++ b/doc/_templates/versions.html @@ -0,0 +1,27 @@ +{%- if current_version %} +
+ + Other Versions + v: {{ current_version.name }} + + +
+ {%- if versions.tags %} +
+
Tags
+ {%- for item in versions.tags %} +
{{ item.name }}
+ {%- endfor %} +
+ {%- endif %} + {%- if versions.branches %} +
+
Branches
+ {%- for item in versions.branches %} +
{{ item.name }}
+ {%- endfor %} +
+ {%- endif %} +
+
+{%- endif %} From cd3b2fe4197e3b10b026ba36aa062f52e10768e5 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:19:08 -0600 Subject: [PATCH 26/70] add conf settigns for sphinx-multiverison' --- doc/conf.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index 63daea088..1a82f2353 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -29,6 +29,24 @@ # The full version, including alpha/beta/rc tags release = '0.3.1-dev' +# -- sphinx-multiversion configuration --------------------------------------- +# Whitelist pattern for tags (set to None to ignore all tags) +smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' + +# Whitelist pattern for branches (set to None to ignore all branches) +smv_branch_whitelist = r'^master*$' + +# Whitelist pattern for remotes (set to None to use local branches only) +smv_remote_whitelist = None + +# Pattern for released versions +smv_released_pattern = r'^tags/.*$' + +# Format for versioned output directories inside the build directory +smv_outputdir_format = '{ref.name}' + +# Determines whether remote or local git branches/tags are preferred if their output dirs conflict +smv_prefer_remote_refs = False # -- General configuration --------------------------------------------------- From 6b6b86b4f221adcabd1bd883b62eeab7ec97c35c Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:22:40 -0600 Subject: [PATCH 27/70] remove build saltproc in deploy-docs --- .github/workflows/deploy-docs.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index f8aac2d81..7a29675ae 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -52,9 +52,6 @@ jobs: run: mamba env update -n saltproc-env -f environment.yml if: steps.dependencies-cache.outputs.cache-hit != 'true' - - name: Install SaltProc - run: pip install . - - name: Check packages run: conda list From 128a1deef013a3ed36e1017bb2d11c553bcba2fd Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:36:37 -0600 Subject: [PATCH 28/70] modify deploy-docs workflow to work with sphinx-multiversion --- .github/workflows/deploy-docs.yml | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 7a29675ae..0eb3f92d1 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -2,12 +2,16 @@ name: Deploy SaltProc docs on: + release: + type: [published] push: - branches: - - master + #branches: + # - master paths: - 'doc/**' - 'saltproc/**' + # enable worflow to be run manually + workflow_dispatch: env: CACHE_NUMBER: 0 #change to manually reset cache @@ -29,7 +33,7 @@ jobs: with: miniforge-variant: Mambaforge # mamba is faster than base conda miniforge-version: latest - activate-environment: saltproc-env + activate-environment: saltproc-doc-env use-mamba: true use-only-tar-bz2: true - run: | @@ -43,27 +47,24 @@ jobs: id: dependencies-cache with: path: | - /usr/share/miniconda3/envs/saltproc-env + /usr/share/miniconda3/envs/doc-saltproc-env ~/.cache/pip - key: depcache-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} + key: depcache-${{ hashFiles(''doc-environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} # Install dependencies - name: Update environment - run: mamba env update -n saltproc-env -f environment.yml + run: mamba env update -n saltproc-doc-env -f doc-environment.yml if: steps.dependencies-cache.outputs.cache-hit != 'true' - name: Check packages run: conda list - name: Build Sphinx Documentation - run: | - cd doc - sphinx-apidoc --separate --force --output-dir=src/ ../saltproc - make clean - make html + run: sphinx-multiversion doc doc/_build/html - name: Deploy documentation to gh-pages branch uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./doc/_build/html + commmit_message: update docs: ${{ github.event.head_commit.message }} From 9b93f395e89fe1b8b9d4ef50e252bb12392ab7e9 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:41:39 -0600 Subject: [PATCH 29/70] update cache-depenencies worflow --- .github/workflows/cache-dependencies.yml | 41 +++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/.github/workflows/cache-dependencies.yml b/.github/workflows/cache-dependencies.yml index ff2a9520c..5c9dbd813 100644 --- a/.github/workflows/cache-dependencies.yml +++ b/.github/workflows/cache-dependencies.yml @@ -9,7 +9,7 @@ env: CACHE_NUMBER: 0 jobs: - cache-dependencies: + cache-build-dependencies: runs-on: ubuntu-latest defaults: run: @@ -18,6 +18,7 @@ jobs: steps: - uses: actions/checkout@v2 +## TESTING CACHE ## # Setup conda - name: Set up conda uses: conda-incubator/setup-miniconda@v2 @@ -50,5 +51,43 @@ jobs: - name: Install SaltProc run: pip install . + cache-doc-dependencies: + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + + steps: + - uses: actions/checkout@v2 + +## DOCUMENTATION CACHE ## + - name: Set up conda + uses: conda-incubator/setup-miniconda@v2 + with: + miniforge-variant: Mambaforge # mamba is faster than base conda + miniforge-version: latest + activate-environment: saltproc-doc-env + use-mamba: true + use-only-tar-bz2: true + - run: | + conda config --env --set pip_interop_enabled True + +# check for existing cache + - name: Set cache date + run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV + + - uses: actions/cache@v2 + id: dependencies-cache + with: + path: | + /usr/share/miniconda3/envs/saltproc-doc-env + ~/.cache/pip + key: depcache-${{ hashFiles('doc/doc-environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} + +# Install dependencies + - name: Update environment + run: mamba env update -n saltproc-doc-env -f doc/doc-environment.yml + if: steps.dependencies-cache.outputs.cache-hit != 'true' + - name: Check packages run: conda list From f82732c64378e6e04501c6c7330a6ac59219d92d Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:42:32 -0600 Subject: [PATCH 30/70] typo fix --- .github/workflows/deploy-docs.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 0eb3f92d1..b992284dd 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -47,13 +47,13 @@ jobs: id: dependencies-cache with: path: | - /usr/share/miniconda3/envs/doc-saltproc-env + /usr/share/miniconda3/envs/saltproc-doc-env ~/.cache/pip - key: depcache-${{ hashFiles(''doc-environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} + key: depcache-${{ hashFiles('doc/doc-environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }} # Install dependencies - name: Update environment - run: mamba env update -n saltproc-doc-env -f doc-environment.yml + run: mamba env update -n saltproc-doc-env -f doc/doc-environment.yml if: steps.dependencies-cache.outputs.cache-hit != 'true' - name: Check packages From aa343f64b9f675632e9a37446262c7d2d34fe6da Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:46:58 -0600 Subject: [PATCH 31/70] typo fixes in deploy-docs.yml --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index b992284dd..1b7fdf0e6 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -67,4 +67,4 @@ jobs: with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./doc/_build/html - commmit_message: update docs: ${{ github.event.head_commit.message }} + commit_message: update docs at commit ${{ github.event.head_commit.message }} From 46963c10d4b530c23b5d3fef052abacd4028ace1 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 14:50:12 -0600 Subject: [PATCH 32/70] add path specifier for push trigger in test-saltproc workflow --- .github/workflows/deploy-docs.yml | 6 +++--- .github/workflows/test-saltproc.yml | 3 +++ 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 1b7fdf0e6..b50a157be 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -7,9 +7,9 @@ on: push: #branches: # - master - paths: - - 'doc/**' - - 'saltproc/**' + #paths: + # - 'doc/**' + # - 'saltproc/**' # enable worflow to be run manually workflow_dispatch: diff --git a/.github/workflows/test-saltproc.yml b/.github/workflows/test-saltproc.yml index bd1448762..5d137416a 100644 --- a/.github/workflows/test-saltproc.yml +++ b/.github/workflows/test-saltproc.yml @@ -3,6 +3,9 @@ name: Test SaltProc on: push: + paths: + - 'saltproc/**' + - 'saltproc/tests/**' pull_request: workflow_dispatch: workflow_run: From 96dce8192ea86578bea5b6c0d56260c6ee5d6c30 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 15:17:16 -0600 Subject: [PATCH 33/70] use prebuid package to allow us to make api pages --- doc/conf.py | 4 +++- doc/doc-environment.yml | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 1a82f2353..478fc6d34 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -34,7 +34,7 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^master*$' +smv_branch_whitelist = r'^(master|vc-docs)*$' # Whitelist pattern for remotes (set to None to use local branches only) smv_remote_whitelist = None @@ -48,6 +48,8 @@ # Determines whether remote or local git branches/tags are preferred if their output dirs conflict smv_prefer_remote_refs = False +smv_prebuild_command = "sphinx-apidoc --force --separate -o doc/src saltproc/" + # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index 1de8cb023..3632ca1d7 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -12,4 +12,4 @@ dependencies: - sphinx - sphinx_rtd_theme - pip: - - sphinx-multiversion + - sphinx-multiversion-pre-post-build From 2d772b95459038fcac92388331724d50d244fe9d Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 15:45:19 -0600 Subject: [PATCH 34/70] use sphinxcontrib_apidoc instead of the prerelease package --- doc/conf.py | 10 ++++++++-- doc/doc-environment.yml | 3 ++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 478fc6d34..0fe703dfd 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -34,7 +34,7 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master|vc-docs)*$' +smv_branch_whitelist = r'^(master|vc-docs|generalize-simulation)*$' # Whitelist pattern for remotes (set to None to use local branches only) smv_remote_whitelist = None @@ -48,7 +48,6 @@ # Determines whether remote or local git branches/tags are preferred if their output dirs conflict smv_prefer_remote_refs = False -smv_prebuild_command = "sphinx-apidoc --force --separate -o doc/src saltproc/" # -- General configuration --------------------------------------------------- @@ -60,6 +59,7 @@ # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + 'sphinxcontrib.apidoc', 'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', @@ -71,6 +71,12 @@ 'sphinx.ext.viewcode', 'sphinx_multiversion'] +# apidoc settings +apidoc_module_dir = '../saltproc/' +apidoc_output_dir = 'src/' +apidoc_excluded_paths = [] +apidoc_separate_modules = True + # Napoleon settings napoleon_google_docstring = False napoleon_numpy_docstring = True diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index 3632ca1d7..363498764 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -12,4 +12,5 @@ dependencies: - sphinx - sphinx_rtd_theme - pip: - - sphinx-multiversion-pre-post-build + - sphinx-multiversion + - sphinxcontrib-apidoc From c082fe87152476fbe6b79cc88f255506d64b87c1 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 15:51:24 -0600 Subject: [PATCH 35/70] try to add all subfolders of built docs --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index b50a157be..f0d0d162b 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -66,5 +66,5 @@ jobs: uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./doc/_build/html + publish_dir: ./doc/_build/html/** commit_message: update docs at commit ${{ github.event.head_commit.message }} From 506b1da8cb9dcb22bac78af939a5c17110cd0b9d Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 15:53:24 -0600 Subject: [PATCH 36/70] try to add all version subfolders of built docs --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index f0d0d162b..ccc673156 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -66,5 +66,5 @@ jobs: uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./doc/_build/html/** + publish_dir: ./doc/_build/html/* commit_message: update docs at commit ${{ github.event.head_commit.message }} From 244c44fd4385b264b533d4cedb0c7c89b15f6ac4 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:03:33 -0600 Subject: [PATCH 37/70] resolve revert conflicct --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index ccc673156..b50a157be 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -66,5 +66,5 @@ jobs: uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: ./doc/_build/html/* + publish_dir: ./doc/_build/html commit_message: update docs at commit ${{ github.event.head_commit.message }} From 815ecde765d4637f8ec539bea13418a2dc23322a Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:04:07 -0600 Subject: [PATCH 38/70] try using remote branches/tags for sphinx-multiversion --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 0fe703dfd..efe74610a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -46,7 +46,7 @@ smv_outputdir_format = '{ref.name}' # Determines whether remote or local git branches/tags are preferred if their output dirs conflict -smv_prefer_remote_refs = False +smv_prefer_remote_refs = True # -- General configuration --------------------------------------------------- From 22af7798944fbf494497e03e1e52578c1e8e83f7 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:09:15 -0600 Subject: [PATCH 39/70] try using fetch-depth 0 w/ checkout action so we can build versioned ocs --- .github/workflows/deploy-docs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index b50a157be..b7355e163 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -26,6 +26,8 @@ jobs: steps: - uses: actions/checkout@v2 + with: + fetch-depth: 0 # Setup conda - name: Set up conda From 93ba835f74d183aa6d44c3629e5f06643dbc877f Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:19:34 -0600 Subject: [PATCH 40/70] try preferring remote branhces --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index efe74610a..353b2b3d0 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -37,7 +37,7 @@ smv_branch_whitelist = r'^(master|vc-docs|generalize-simulation)*$' # Whitelist pattern for remotes (set to None to use local branches only) -smv_remote_whitelist = None +smv_remote_whitelist = r'^(origin)$' # Pattern for released versions smv_released_pattern = r'^tags/.*$' From e919e17e648a158a2a25b8d4efc1cba6cbaded4e Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:33:38 -0600 Subject: [PATCH 41/70] restrcuture environments --- doc/doc-environment.yml | 3 --- environment.yml | 2 -- 2 files changed, 5 deletions(-) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index 363498764..c5e204418 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -6,9 +6,6 @@ dependencies: - pyne>=0.5.11 - numpy>=1.14.0 - pytables - - networkx - - pydotplus - - pytest - sphinx - sphinx_rtd_theme - pip: diff --git a/environment.yml b/environment.yml index ba1607054..3cb0f07e7 100644 --- a/environment.yml +++ b/environment.yml @@ -9,7 +9,5 @@ dependencies: - networkx - pydotplus - pytest - - sphinx - - sphinx_rtd_theme - pip: - argparse==1.4.0 From f40e45f74b5011f0c7b50a73d3d48823a7fe2996 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:37:18 -0600 Subject: [PATCH 42/70] remove extra testing branches --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 353b2b3d0..ea07d5e76 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -34,7 +34,7 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master|vc-docs|generalize-simulation)*$' +smv_branch_whitelist = r'^(master)*$' # Whitelist pattern for remotes (set to None to use local branches only) smv_remote_whitelist = r'^(origin)$' From a3f17389a55999cb9ff34b74b0720f04621ac851 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:41:14 -0600 Subject: [PATCH 43/70] pep8 fixes --- doc/conf.py | 3 ++- saltproc/version.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index ea07d5e76..b47f0f6d4 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -45,7 +45,8 @@ # Format for versioned output directories inside the build directory smv_outputdir_format = '{ref.name}' -# Determines whether remote or local git branches/tags are preferred if their output dirs conflict +# Determines whether remote or local git branches/tags are preferred +# if their output dirs conflict smv_prefer_remote_refs = True diff --git a/saltproc/version.py b/saltproc/version.py index d6647a702..ee3f9f91e 100644 --- a/saltproc/version.py +++ b/saltproc/version.py @@ -6,7 +6,7 @@ _version_minor = 3 _version_micro = '1' # use '' for first of series, number for 1 and above _version_extra = 'dev' -#_version_extra = '0' # Uncomment this for full releases +# _version_extra = '0' # Uncomment this for full releases # Construct full version string from these. _ver = [_version_major, _version_minor] From 5a95c3582c485fd0dceaf852cf1634bfe14e501f Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:42:07 -0600 Subject: [PATCH 44/70] remove .readthedocs.yaml --- .readthedocs.yaml | 18 ------------------ 1 file changed, 18 deletions(-) delete mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml deleted file mode 100644 index 1ef94b015..000000000 --- a/.readthedocs.yaml +++ /dev/null @@ -1,18 +0,0 @@ -version: 2 - -build: - os: "ubuntu-20.04" - tools: - python: "mambaforge-4.10" - -conda: - environment: environment.yml - -python: - install: - - method: pip - path: . - -sphinx: - configuration: docs/conf.py - # fail_on_warning: true From 530a68b136b334665bd3e8c65f6253d00d95d831 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 16:47:20 -0600 Subject: [PATCH 45/70] add manual triggers for workflows, remove commented out commands --- .github/workflows/cache-dependencies.yml | 4 ++++ .github/workflows/deploy-docs.yml | 12 ++++++------ .github/workflows/test-saltproc.yml | 3 ++- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/.github/workflows/cache-dependencies.yml b/.github/workflows/cache-dependencies.yml index 5c9dbd813..d77ca8d62 100644 --- a/.github/workflows/cache-dependencies.yml +++ b/.github/workflows/cache-dependencies.yml @@ -4,6 +4,8 @@ name: Cache dependencies on: schedule: - cron: '0 9 * * 1' # run every monday @ 9AM + # enable worflow to be run manually + workflow_dispatch: env: CACHE_NUMBER: 0 @@ -51,6 +53,8 @@ jobs: - name: Install SaltProc run: pip install . + - name: Check packages + run: conda list cache-doc-dependencies: runs-on: ubuntu-latest defaults: diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index b7355e163..8c1e1eba1 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -3,13 +3,13 @@ name: Deploy SaltProc docs on: release: - type: [published] + type: [published] push: - #branches: - # - master - #paths: - # - 'doc/**' - # - 'saltproc/**' + branches: + - master + paths: + - 'doc/**' + - 'saltproc/**' # enable worflow to be run manually workflow_dispatch: diff --git a/.github/workflows/test-saltproc.yml b/.github/workflows/test-saltproc.yml index 5d137416a..c66303ff4 100644 --- a/.github/workflows/test-saltproc.yml +++ b/.github/workflows/test-saltproc.yml @@ -7,10 +7,11 @@ on: - 'saltproc/**' - 'saltproc/tests/**' pull_request: - workflow_dispatch: workflow_run: workflows: ["Cache dependencies"] types: [completed] + # enable worflow to be run manually + workflow_dispatch: env: CACHE_NUMBER: 0 #change to manually reset cache From 6961b30e0f5d220a3915c1d700ec163b32a9f3ba Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:28:33 -0600 Subject: [PATCH 46/70] add redirect page --- .github/workflows/deploy-docs.yml | 4 +++- doc/redirect.html | 9 +++++++++ 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 doc/redirect.html diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 8c1e1eba1..bedfc11fe 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -62,7 +62,9 @@ jobs: run: conda list - name: Build Sphinx Documentation - run: sphinx-multiversion doc doc/_build/html + run: | + sphinx-multiversion doc doc/_build/html + cp doc/redirect.html doc/_build/html/index.html - name: Deploy documentation to gh-pages branch uses: peaceiris/actions-gh-pages@v3 diff --git a/doc/redirect.html b/doc/redirect.html new file mode 100644 index 000000000..ddb84db41 --- /dev/null +++ b/doc/redirect.html @@ -0,0 +1,9 @@ + + + + Redirecting to master branch + + + + + From 02ba34077484afa9d85ddd241ae10dac562a90ac Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:31:45 -0600 Subject: [PATCH 47/70] test redirect page --- .github/workflows/deploy-docs.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index bedfc11fe..591df20df 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -5,11 +5,11 @@ on: release: type: [published] push: - branches: - - master - paths: - - 'doc/**' - - 'saltproc/**' + #branches: + # - master + #paths: + # - 'doc/**' + # - 'saltproc/**' # enable worflow to be run manually workflow_dispatch: @@ -71,4 +71,4 @@ jobs: with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./doc/_build/html - commit_message: update docs at commit ${{ github.event.head_commit.message }} + commit_message: update docs at commit: ${{ github.event.head_commit.message }} From d52606d09c5b44f398e60aac8c045c46769bb73a Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:32:27 -0600 Subject: [PATCH 48/70] typo fix --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 591df20df..dd7379f17 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -71,4 +71,4 @@ jobs: with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./doc/_build/html - commit_message: update docs at commit: ${{ github.event.head_commit.message }} + commit_message: update docs at commit\: ${{ github.event.head_commit.message }} From 655cb1262e32382866686fe3a026f9acd1bcdf56 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:33:17 -0600 Subject: [PATCH 49/70] typo fix --- .github/workflows/deploy-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index dd7379f17..4a94a7ad2 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -71,4 +71,4 @@ jobs: with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./doc/_build/html - commit_message: update docs at commit\: ${{ github.event.head_commit.message }} + commit_message: "update docs at commit: ${{ github.event.head_commit.message }}" From 5e0af0ede9c029661251c66a0b3ad3bc2f6c3acf Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:39:43 -0600 Subject: [PATCH 50/70] add upstream to the remotes whitelist for sphinx-multiversion config --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index b47f0f6d4..ebe14e09b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -37,7 +37,7 @@ smv_branch_whitelist = r'^(master)*$' # Whitelist pattern for remotes (set to None to use local branches only) -smv_remote_whitelist = r'^(origin)$' +smv_remote_whitelist = r'^(origin|upstream)$' # Pattern for released versions smv_released_pattern = r'^tags/.*$' From 4f32938556a3ba99a27332fb3f4f744beaa8a47d Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:47:05 -0600 Subject: [PATCH 51/70] add another branch to demonstrate deployment --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index ebe14e09b..152809326 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -34,7 +34,7 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master)*$' +smv_branch_whitelist = r'^(master|generalize-simulation)*$' # Whitelist pattern for remotes (set to None to use local branches only) smv_remote_whitelist = r'^(origin|upstream)$' From 2e00786f2fa3684b1d93a8c2e23c44f415812264 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 21 Jan 2022 17:48:47 -0600 Subject: [PATCH 52/70] changes for merging --- .github/workflows/deploy-docs.yml | 10 +++++----- doc/conf.py | 2 +- doc/redirect.html | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 4a94a7ad2..c091583cc 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -5,11 +5,11 @@ on: release: type: [published] push: - #branches: - # - master - #paths: - # - 'doc/**' - # - 'saltproc/**' + branches: + - master + paths: + - 'doc/**' + - 'saltproc/**' # enable worflow to be run manually workflow_dispatch: diff --git a/doc/conf.py b/doc/conf.py index 152809326..ebe14e09b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -34,7 +34,7 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master|generalize-simulation)*$' +smv_branch_whitelist = r'^(master)*$' # Whitelist pattern for remotes (set to None to use local branches only) smv_remote_whitelist = r'^(origin|upstream)$' diff --git a/doc/redirect.html b/doc/redirect.html index ddb84db41..b9e7244ac 100644 --- a/doc/redirect.html +++ b/doc/redirect.html @@ -4,6 +4,6 @@ Redirecting to master branch - + From d5d78431afa57cc53095e5cbb043a1b1c40b4346 Mon Sep 17 00:00:00 2001 From: yardasol Date: Mon, 24 Jan 2022 11:50:20 -0600 Subject: [PATCH 53/70] add packages needed for sphinx-apidoc to work --- doc/doc-environment.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/doc-environment.yml b/doc/doc-environment.yml index c5e204418..eb15230d2 100644 --- a/doc/doc-environment.yml +++ b/doc/doc-environment.yml @@ -6,6 +6,8 @@ dependencies: - pyne>=0.5.11 - numpy>=1.14.0 - pytables + - networkx + - pydotplus - sphinx - sphinx_rtd_theme - pip: From 905f97d45c08d25024c3dc5447bbf873fe999202 Mon Sep 17 00:00:00 2001 From: yardasol Date: Mon, 24 Jan 2022 11:51:02 -0600 Subject: [PATCH 54/70] update readme install instructions --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 917df73af..dd7378112 100644 --- a/README.md +++ b/README.md @@ -31,9 +31,8 @@ following steps 1. `pip install sphinx` 2. `pip install sphinx_rtd_theme`. 3. `cd doc/` -4. `sphinx-apidoc --separate --force --output-dir=src/ ../saltproc` -5. `make clean` -6. `make html` +4. `make clean` +5. `make html` After these steps, the website will be found in `saltproc/doc/_build/html`. From b93761e51704bd760df0636d5b44a82a9d1f4237 Mon Sep 17 00:00:00 2001 From: yardasol Date: Mon, 24 Jan 2022 11:54:26 -0600 Subject: [PATCH 55/70] minor adjustments to instructions for building documentation --- README.md | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index dd7378112..40af6c6c6 100644 --- a/README.md +++ b/README.md @@ -24,15 +24,14 @@ Detailed installation instructions can be found in the The documentation for SaltProc can be found at [arfc.github.io/saltproc/](http://arfc.github.io/saltproc/). -Additionally, the entire contents of that -website can be built from the doc directory in the source code using the -following steps - -1. `pip install sphinx` -2. `pip install sphinx_rtd_theme`. -3. `cd doc/` -4. `make clean` -5. `make html` +The entire contents of that +website can be built from the `doc` directory in the repositiory using +the following steps + +1. `pip install sphinx sphinx_rtd_theme` +2. `cd doc/` +3. `make clean` +4. `make html` After these steps, the website will be found in `saltproc/doc/_build/html`. From 18da4bbfee951e3de2d53acf6442c4d072a56067 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 10:23:16 -0600 Subject: [PATCH 56/70] update author, copyright in conf.py --- doc/conf.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index ebe14e09b..70bc2cac9 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -21,8 +21,9 @@ # -- Project information ----------------------------------------------------- project = u'Saltproc' -copyright = u'2018, Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' -author = u'Andrei Rykhlevskii, Jin Whan Bae, Kathryn D. Huff' +author = u'Oleksandr Yardas, Andrei Rykhlevskii,\ + Jin Whan Bae, Kathryn D. Huff' +copyright = u'2021, ' + author # The short X.Y version version = '0.3' From f60282bd75003bd41849cb729d25c51cfd84cf9f Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 10:28:15 -0600 Subject: [PATCH 57/70] update version --- saltproc/version.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/saltproc/version.py b/saltproc/version.py index ee3f9f91e..7cf0bee3f 100644 --- a/saltproc/version.py +++ b/saltproc/version.py @@ -3,8 +3,8 @@ # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z" _version_major = 0 -_version_minor = 3 -_version_micro = '1' # use '' for first of series, number for 1 and above +_version_minor = 4 +_version_micro = '0' # use '' for first of series, number for 1 and above _version_extra = 'dev' # _version_extra = '0' # Uncomment this for full releases From ac67c321dd074a9a37248cc62d50d540e6fe6cb2 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 10:43:20 -0600 Subject: [PATCH 58/70] try importing __version from version.py --- doc/conf.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 70bc2cac9..c3e0003fb 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -18,6 +18,9 @@ sys.path.append(os.path.abspath('../')) sys.path.append(os.path.abspath('../saltproc')) +from saltproc.version import __version__ + + # -- Project information ----------------------------------------------------- project = u'Saltproc' @@ -26,19 +29,19 @@ copyright = u'2021, ' + author # The short X.Y version -version = '0.3' +version = '0.4.0-dev' # The full version, including alpha/beta/rc tags -release = '0.3.1-dev' +release = __version__ # -- sphinx-multiversion configuration --------------------------------------- # Whitelist pattern for tags (set to None to ignore all tags) smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master)*$' +smv_branch_whitelist = r'^(master|vc-docs)*$' # Whitelist pattern for remotes (set to None to use local branches only) -smv_remote_whitelist = r'^(origin|upstream)$' +smv_remote_whitelist = None#r'^(origin|upstream)$' # Pattern for released versions smv_released_pattern = r'^tags/.*$' @@ -48,7 +51,7 @@ # Determines whether remote or local git branches/tags are preferred # if their output dirs conflict -smv_prefer_remote_refs = True +smv_prefer_remote_refs = False#True # -- General configuration --------------------------------------------------- From 6e418d100d89119f5a86de28046b8e5de5db0f8f Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 10:45:30 -0600 Subject: [PATCH 59/70] remove build testing params --- doc/conf.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index c3e0003fb..e07e6675a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -29,7 +29,7 @@ copyright = u'2021, ' + author # The short X.Y version -version = '0.4.0-dev' +version = __version__ # The full version, including alpha/beta/rc tags release = __version__ @@ -38,10 +38,10 @@ smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$' # Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = r'^(master|vc-docs)*$' +smv_branch_whitelist = r'^(master)*$' # Whitelist pattern for remotes (set to None to use local branches only) -smv_remote_whitelist = None#r'^(origin|upstream)$' +smv_remote_whitelist = r'^(origin|upstream)$' # Pattern for released versions smv_released_pattern = r'^tags/.*$' @@ -51,7 +51,7 @@ # Determines whether remote or local git branches/tags are preferred # if their output dirs conflict -smv_prefer_remote_refs = False#True +smv_prefer_remote_refs = False # -- General configuration --------------------------------------------------- From 56e9bddc91fa941d575507d1583ffd999ff8a9c4 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 12:32:18 -0600 Subject: [PATCH 60/70] prefer remote refs --- doc/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index e07e6675a..d3f05b6ab 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -51,7 +51,7 @@ # Determines whether remote or local git branches/tags are preferred # if their output dirs conflict -smv_prefer_remote_refs = False +smv_prefer_remote_refs = True # -- General configuration --------------------------------------------------- From 26bacd191ea678089934c99c6782e87c3450e436 Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 12:42:15 -0600 Subject: [PATCH 61/70] pep8 fixes --- doc/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index d3f05b6ab..7c779c00f 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -17,7 +17,6 @@ import sphinx_rtd_theme sys.path.append(os.path.abspath('../')) sys.path.append(os.path.abspath('../saltproc')) - from saltproc.version import __version__ From 415e8ead59828a1d9a76800b937359a14f5bb3fe Mon Sep 17 00:00:00 2001 From: yardasol Date: Thu, 27 Jan 2022 12:44:19 -0600 Subject: [PATCH 62/70] add explanation comment --- doc/conf.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/conf.py b/doc/conf.py index 7c779c00f..cb132df80 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -17,6 +17,9 @@ import sphinx_rtd_theme sys.path.append(os.path.abspath('../')) sys.path.append(os.path.abspath('../saltproc')) +# autopep8 will make a stink about this but +# we need to have saltproc on ouy syspath +# before we can import it from saltproc.version import __version__ From 7cc11b76b16e4aa6deab93e29e04ab3f62722cd3 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 11:55:54 -0600 Subject: [PATCH 63/70] update descriptions in version.py --- saltproc/version.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/saltproc/version.py b/saltproc/version.py index 7cf0bee3f..591e9c3d4 100644 --- a/saltproc/version.py +++ b/saltproc/version.py @@ -3,8 +3,8 @@ # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z" _version_major = 0 -_version_minor = 4 -_version_micro = '0' # use '' for first of series, number for 1 and above +_version_minor = 3 +_version_micro = '1' # use '' for first of series, number for 1 and above _version_extra = 'dev' # _version_extra = '0' # Uncomment this for full releases @@ -26,15 +26,16 @@ "Topic :: Scientific/Engineering"] # Description should be a one-liner: -description = "saltproc: the on-line reprocessing driver for SERPENT" +description = "saltproc: the on-line reprocessing driver for monte-carlo codes" # Long description will go up on the pypi page long_description = """ SaltProc ======== -Saltproc is a on-line reprocessing driver for SERPENT, which -runs SEPRENT from a given input file and parameters and performs -user-defined processing of the fuel salt by adding or removing -waste, fissile, and fertile streams. +SaltProc is an on-line reprocessing driver for monte-carlo +particle transport codes with depletion capabilites. SaltProc +runs the monte-carlo simulation from a given input file and +parameters, then performs user-defined processing of the fuel +salt by adding or removing waste, fissile, and fertile streams. License ======= @@ -71,7 +72,7 @@ NAME = "saltproc" MAINTAINER = "Oleksandr Yardas" -MAINTAINER_EMAIL = "arfc@googlegroups.com" +MAINTAINER_EMAIL = "oyardas2@illinois.edu" DESCRIPTION = description LONG_DESCRIPTION = long_description URL = "http://github.com/arfc/saltproc" From f67358d04a9f1b8df2cff2635780e5f876a72922 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 15:07:49 -0600 Subject: [PATCH 64/70] update readme instructions --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 40af6c6c6..b826cfd43 100644 --- a/README.md +++ b/README.md @@ -28,7 +28,7 @@ The entire contents of that website can be built from the `doc` directory in the repositiory using the following steps -1. `pip install sphinx sphinx_rtd_theme` +1. `conda env create -f doc/doc-environment.yml` 2. `cd doc/` 3. `make clean` 4. `make html` From 552b92255e2339adee045a4d8be116f53fe75eeb Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 15:12:49 -0600 Subject: [PATCH 65/70] update install instructions in docs --- doc/installation.rst | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/doc/installation.rst b/doc/installation.rst index d6ebce79c..f31968190 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -34,15 +34,27 @@ Optional Depenendencies: -Most of the dependencies are readily available through package managers. -Once all the dependencies are installed, SaltProc can be installed. Clone the source from the SaltProc repository from `GitHub`_. -Then run the following commands from the directory above cloned repository: .. code-block:: bash git clone git@github.com:arfc/saltproc.git + +All of the dependencies are readily available through package managers. +You can download the required ones using the provided `environment.yml` +file in the repository: + +.. code-block:: bash + cd saltproc/ + conda env create -f environment.yml + +Once all the dependencies are installed, SaltProc can be installed by +running the following commands from within the cloned directory +repository: + +.. code-block:: bash + pip install . Please let us know if you run into trouble. From 679187cda3e505e8e7fe9f2c1d3e95a11f4d6459 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 15:25:16 -0600 Subject: [PATCH 66/70] add note on using mamba --- doc/installation.rst | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/doc/installation.rst b/doc/installation.rst index f31968190..15ece1525 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -24,7 +24,8 @@ SaltProc has the following dependencies: .. _matplotlib: http://matplotlib.org .. _ViTables: http://vitables.org .. _GitHub: http://github.com/arfc/saltproc - +.. _conda package manager: https://docs.conda.io/en/latest/ +.. _mamba: https://github.com/mamba-org/mamba Optional Depenendencies: #. `pytest`_ (for testing) @@ -40,8 +41,11 @@ Clone the source from the SaltProc repository from `GitHub`_. git clone git@github.com:arfc/saltproc.git -All of the dependencies are readily available through package managers. -You can download the required ones using the provided `environment.yml` +All of the dependencies are readily available through the `conda package manager`_. + +.. note:: We recommend using the `mamba`_ CLI tool to install packages quickly. SaltProc has a compltex package dependency structure which can result is long environment solve times in the default ``conda`` solver. ``mamba`` is a reimplementation of ``conda`` in ``C++`` and we have found it is significantly faster. + +You can download the required ones using the provided ``environment.yml`` file in the repository: .. code-block:: bash From e980a3beb1ffcdcad5bedf8f36c92cef5a0f2b66 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 15:29:29 -0600 Subject: [PATCH 67/70] add mamba blurb to readme --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index b826cfd43..23bf9ac37 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,9 @@ the following steps After these steps, the website will be found in `saltproc/doc/_build/html`. +_Note_: We recommend using [`mamba`](https://github.com/mamba-org/mamba) CLI tool to install packages quickly. SaltProc has a compltex package dependency structure which can result is long environment solve times in the default ``conda`` solver. ``mamba`` is a reimplementation of ``conda`` in ``C++`` and we have found it is significantly faster. + + ## License The license for this work can be found From 9967207c9cfb69e118faa4d33a87d744e7b183f6 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 16:46:52 -0600 Subject: [PATCH 68/70] README.md --- doc/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/installation.rst b/doc/installation.rst index 15ece1525..faf7b7a79 100644 --- a/doc/installation.rst +++ b/doc/installation.rst @@ -45,7 +45,7 @@ All of the dependencies are readily available through the `conda package manager .. note:: We recommend using the `mamba`_ CLI tool to install packages quickly. SaltProc has a compltex package dependency structure which can result is long environment solve times in the default ``conda`` solver. ``mamba`` is a reimplementation of ``conda`` in ``C++`` and we have found it is significantly faster. -You can download the required ones using the provided ``environment.yml`` +You can download the required ones using ``conda`` on the provided ``environment.yml`` file in the repository: .. code-block:: bash @@ -55,7 +55,7 @@ file in the repository: Once all the dependencies are installed, SaltProc can be installed by running the following commands from within the cloned directory -repository: +repository (assuming the `saltproc-env` environment is active): .. code-block:: bash From 44bf02a72c30df3401645a0fbe5034c0173843ed Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 16:47:27 -0600 Subject: [PATCH 69/70] added @munkm suggestions --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 23bf9ac37..eb49f4fc0 100644 --- a/README.md +++ b/README.md @@ -25,8 +25,7 @@ Detailed installation instructions can be found in the The documentation for SaltProc can be found at [arfc.github.io/saltproc/](http://arfc.github.io/saltproc/). The entire contents of that -website can be built from the `doc` directory in the repositiory using -the following steps +website can be built from the `doc` directory in the repositiory using the following steps with the [`conda`](https://docs.conda.io/en/latest/) tool: 1. `conda env create -f doc/doc-environment.yml` 2. `cd doc/` From 9f31ce4f37ae37025a84ba5ffdd06d64c5860be3 Mon Sep 17 00:00:00 2001 From: yardasol Date: Fri, 28 Jan 2022 16:52:31 -0600 Subject: [PATCH 70/70] update maintainer email --- saltproc/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/saltproc/version.py b/saltproc/version.py index 591e9c3d4..bdfb452b8 100644 --- a/saltproc/version.py +++ b/saltproc/version.py @@ -72,7 +72,7 @@ NAME = "saltproc" MAINTAINER = "Oleksandr Yardas" -MAINTAINER_EMAIL = "oyardas2@illinois.edu" +MAINTAINER_EMAIL = "arfc@googlegroups.com" DESCRIPTION = description LONG_DESCRIPTION = long_description URL = "http://github.com/arfc/saltproc"