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name: build | ||
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on: | ||
pull_request: | ||
branches: [ master ] | ||
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jobs: | ||
build: | ||
runs-on: ubuntu-latest | ||
container: dedalusproject/dedalus-conda | ||
steps: | ||
- uses: actions/checkout@v2 | ||
with: | ||
ref: 'v2.0-refactor' | ||
- name: build | ||
run: /opt/conda/envs/dedalus/bin/pip install -e . | ||
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- name: test | ||
run: /opt/conda/envs/dedalus/bin/pytest | ||
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*.egg | ||
MANIFEST | ||
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# ipython | ||
.ipynb_checkpoints/ | ||
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# Eigentools | ||
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Eigentools is a set of tools for studying linear eigenvalue problems. The underlying eigenproblems are solved using [Dedalus](http://dedalus-project.org). | ||
Eigentools is a set of tools for studying linear eigenvalue problems. The underlying eigenproblems are solved using [Dedalus](http://dedalus-project.org), which provides a domain-specific language for partial differential equations. Eigentools extends Dedalus's `EigenvalueProblem` object and provides | ||
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Eigentools was developed with support from the Research Corporation under award Scialog Collaborative Award (TDA) ID# 24231. | ||
* automatic rejection of unresolved eigenvalues | ||
* simple plotting of specified eigenmodes | ||
* simple plotting of spectra | ||
* computation of $\epsilon$-pseudospectra for any Differential-Algebraic Equations with **user-specifiable norms** | ||
* tools to find critical parameters for linear stability analysis | ||
* ability to project eigenmode onto 2- or 3-D domain for visualization | ||
* ability to output projected eigenmodes as Dedalus-formatted HDF5 file to be used as initial conditions for Initial Value Problems | ||
* simple plotting of drift ratios (both ordinal and nearest) to evaluate tolerance for eigenvalue rejection | ||
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## Installation | ||
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Eigentools requires [Dedalus](http://dedalus-project.org), which can be installed along with all of its dependencies using conda via [its install script](https://dedalus-project.readthedocs.io/en/latest/pages/installation.html#conda-installation-recommended). | ||
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Once Dedalus is installed, eigentools can be pip installed in the same conda environment via | ||
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``` | ||
pip install eigentools | ||
``` | ||
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## Documentation | ||
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API Documentation can be found at [Read the Docs](eigentools.readthedocs.io). | ||
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## Developers | ||
The core development team consists of | ||
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* Jeff Oishi (<jsoishi@gmail.com>) | ||
* Evan Anders (<Evan.Anders@colorado.edu>) | ||
* Keaton Burns (<keaton.burns@gmail.com>) | ||
* Susan Clark (<susanclark19@gmail.com>) | ||
* Evan Anders (<evan.anders@northwestern.edu>) | ||
* Ben Brown (<bpbrown@gmail.com>) | ||
* Keaton Burns (<keaton.burns@gmail.com>) | ||
* Geoff Vasil (<geoffrey.m.vasil@gmail.com>) | ||
* Daniel Lecoanet (<daniel.lecoanet@northwestern.edu>) | ||
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## Support | ||
Eigentools was developed with support from the Research Corporation under award Scialog Collaborative Award (TDA) ID# 24231. | ||
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<!-- LocalWords: Eigentools eigenproblems Dedalus EigenvalueProblem | ||
--> | ||
<!-- LocalWords: eigenmodes pseudospectra eigenmode HDF conda Oishi | ||
--> | ||
<!-- LocalWords: eigentools Anders Geoff Vasil Lecoanet Scialog TDA | ||
--> |
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# Minimal makefile for Sphinx documentation | ||
# | ||
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# You can set these variables from the command line. | ||
SPHINXOPTS = | ||
SPHINXBUILD = sphinx-build | ||
SPHINXPROJ = Eigentools | ||
SOURCEDIR = . | ||
BUILDDIR = _build | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile | ||
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# Catch-all target: route all unknown targets to Sphinx using the new | ||
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). | ||
%: Makefile | ||
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) |
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# -*- 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 | ||
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# -- Path setup -------------------------------------------------------------- | ||
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# If extensions (or modules to document with autodoc) are in another directory, | ||
# add these directories to sys.path here. If the directory is relative to the | ||
# documentation root, use os.path.abspath to make it absolute, like shown here. | ||
# | ||
# import os | ||
# import sys | ||
# sys.path.insert(0, os.path.abspath('.')) | ||
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# -- Project information ----------------------------------------------------- | ||
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project = 'Eigentools' | ||
copyright = '2020 Dedalus Collaboration' | ||
author = 'Dedalus Collaboration' | ||
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# The short X.Y version | ||
version = '' | ||
# The full version, including alpha/beta/rc tags | ||
release = '' | ||
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# -- General configuration --------------------------------------------------- | ||
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# If your documentation needs a minimal Sphinx version, state it here. | ||
# | ||
# needs_sphinx = '1.0' | ||
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# Add any Sphinx extension module names here, as strings. They can be | ||
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom | ||
# ones. | ||
extensions = [] | ||
extensions += ['sphinx.ext.mathjax'] | ||
extensions += ['autoapi.extension'] | ||
extensions += ['sphinx.ext.viewcode'] | ||
extensions += ['sphinx.ext.napoleon'] | ||
extensions += ['nbsphinx'] | ||
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add_module_names = False | ||
autoapi_type = 'python' | ||
autoapi_dirs = ['../eigentools'] | ||
autoapi_file_patterns = ['*.py'] | ||
autoapi_options = ['members', 'undoc-members'] | ||
autoapi_python_class_content = 'both' | ||
autoapi_add_toctree_entry = False | ||
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napoleon_use_param = False | ||
napoleon_use_keyword = False | ||
napoleon_use_ivar = True | ||
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# Add any paths that contain templates here, relative to this directory. | ||
templates_path = ['_templates'] | ||
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# The suffix(es) of source filenames. | ||
# You can specify multiple suffix as a list of string: | ||
# | ||
# source_suffix = ['.rst', '.md'] | ||
source_suffix = '.rst' | ||
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# The master toctree document. | ||
master_doc = 'index' | ||
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# 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 | ||
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# 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', 'Thumbs.db', '.DS_Store'] | ||
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# The name of the Pygments (syntax highlighting) style to use. | ||
pygments_style = 'sphinx' | ||
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# -- Options for HTML output ------------------------------------------------- | ||
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# 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_logo = 'epic12_4_exp_2_1.25.png' | ||
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# 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 = {} | ||
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# 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'] | ||
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# 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 = {} | ||
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# -- Options for HTMLHelp output --------------------------------------------- | ||
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# Output file base name for HTML help builder. | ||
htmlhelp_basename = 'Eigentoolsdoc' | ||
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# -- Options for LaTeX output ------------------------------------------------ | ||
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latex_elements = { | ||
# The paper size ('letterpaper' or 'a4paper'). | ||
# | ||
# 'papersize': 'letterpaper', | ||
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# The font size ('10pt', '11pt' or '12pt'). | ||
# | ||
# 'pointsize': '10pt', | ||
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# Additional stuff for the LaTeX preamble. | ||
# | ||
# 'preamble': '', | ||
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# Latex figure (float) alignment | ||
# | ||
# 'figure_align': 'htbp', | ||
} | ||
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# Grouping the document tree into LaTeX files. List of tuples | ||
# (source start file, target name, title, | ||
# author, documentclass [howto, manual, or own class]). | ||
latex_documents = [ | ||
(master_doc, 'Eigentools.tex', 'Eigentools Documentation', | ||
'Dedalus Collaboration', 'manual'), | ||
] | ||
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# -- Options for manual page output ------------------------------------------ | ||
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# One entry per manual page. List of tuples | ||
# (source start file, name, description, authors, manual section). | ||
man_pages = [ | ||
(master_doc, 'dedalusproject', 'Eigentools Documentation', | ||
[author], 1) | ||
] | ||
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# -- Options for Texinfo output ---------------------------------------------- | ||
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# 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, 'Eigentools', 'Eigentools Documentation', | ||
author, 'DedalusProject', 'One line description of project.', | ||
'Miscellaneous'), | ||
] |
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Eigentools | ||
********** | ||
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Eigentools is a set of tools for studying linear eigenvalue problems. The underlying eigenproblems are solved using [Dedalus](http://dedalus-project.org), which provides a domain-specific language for partial differential equations. Eigentools extends Dedalus's `EigenvalueProblem` object and provides | ||
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||
* automatic rejection of unresolved eigenvalues | ||
* simple plotting of specified eigenmodes | ||
* simple plotting of spectra | ||
* computation of $\epsilon$-pseudospectra for any Differential-Algebraic Equations with **user-specifiable norms** | ||
* tools to find critical parameters for linear stability analysis | ||
* ability to project eigenmode onto 2- or 3-D domain for visualization | ||
* ability to output projected eigenmodes as Dedalus-formatted HDF5 file to be used as initial conditions for Initial Value Problems | ||
* simple plotting of drift ratios (both ordinal and nearest) to evaluate tolerance for eigenvalue rejection | ||
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Doc Contents | ||
============ | ||
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.. toctree:: | ||
:maxdepth: 2 | ||
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Eigentools API reference <autoapi/eigentools/index> | ||
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Developers | ||
========== | ||
The core development team consists of | ||
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* Jeff Oishi (<jsoishi@gmail.com>) | ||
* Keaton Burns (<keaton.burns@gmail.com>) | ||
* Susan Clark (<susanclark19@gmail.com>) | ||
* Evan Anders (<evan.anders@northwestern.edu>) | ||
* Ben Brown (<bpbrown@gmail.com>) | ||
* Geoff Vasil (<geoffrey.m.vasil@gmail.com>) | ||
* Daniel Lecoanet (<daniel.lecoanet@northwestern.edu>) | ||
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Support | ||
======= | ||
Eigentools was developed with support from the Research Corporation under award Scialog Collaborative Award (TDA) ID# 24231. | ||
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