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@joestubbs
joestubbs committed Nov 12, 2021
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29 changes: 10 additions & 19 deletions docs/Makefile
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Expand Up @@ -2,32 +2,23 @@
#

# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXAUTOBUILD = sphinx-autobuild
SPHINXPROJ = TACCCloudAPIs
SOURCEDIR = .
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
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SPHINXPROJ = ChameleonCloudDocumentation
#SOURCEDIR = source
SOURCEDIR =
BUILDDIR = build

# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
@echo " livehtml to watch the source directory for changes and rebuild the html"

.PHONY: help Makefile clean
.PHONY: help Makefile

livehtml:
sphinx-autobuild --port 7898 -b html $(ALLSPHINXOPTS) "$(SOURCEDIR)" $(BUILDDIR)/html

# 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)

clean:
rm -rf $(BUILDDIR)/*

livehtml:
@$(SPHINXAUTOBUILD) -b html $(SPHINXOPTS) "$(SOURCEDIR)" "$(BUILDDIR)/html"
36 changes: 17 additions & 19 deletions docs/conf.py
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Expand Up @@ -12,13 +12,13 @@
# 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 os
# import sys
from recommonmark.parser import CommonMarkParser
#from recommonmark.parser import CommonMarkParser
# sys.path.insert(0, os.path.abspath('.'))

# -- RTD configuration -------------------------------------------------------
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
#on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

# -- Project information -----------------------------------------------------

Expand All @@ -43,23 +43,21 @@
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.doctest',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx_fontawesome'
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
]


# 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'
source_parsers = {
'.md': CommonMarkParser,
}
source_suffix = '.rst'

# The master toctree document.
master_doc = 'index'
Expand All @@ -74,7 +72,7 @@
# 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']
# exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
Expand All @@ -85,13 +83,13 @@
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'default'
if not on_rtd:
import sphinx_rtd_theme
html_theme = 'sphinx_rtd_theme'
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
else:
html_theme = 'default'
html_theme = 'sphinx_rtd_theme'
# if not on_rtd:
# import sphinx_rtd_theme
# html_theme = 'sphinx_rtd_theme'
# html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
# else:
# html_theme = 'default'

# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
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4 changes: 2 additions & 2 deletions docs/index.rst
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Expand Up @@ -37,8 +37,8 @@ TACC Cloud Papers, Projects & Partnerships
:maxdepth: 2
:caption: Papers Reference

Research Papers & Projects <https://tacc-cloud.readthedocs.io/en/latest/resources/papers.html>
Partnerships <https://tacc-cloud.readthedocs.io/en/latest/resources/partnerships.html>
resources/papers
resources/partnerships



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95 changes: 84 additions & 11 deletions docs/resources/papers.rst
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Expand Up @@ -9,13 +9,93 @@

Users of our services are encouraged to cite Tapis, Abaco and Chameleon in publications that result from using TACC Cloud resources. Please use the following reference(s):

Abaco
Tapis
-----
Stubbs J., Vaughn M., and Looney J. 2018. Rapid Development of Scalable, Distributed Computation with Abaco. Proceedings of the 10th International Workshop on Science Gateways(2018).

Tapis
Reference Paper
| 1) *Tapis: An API Platform for Reproducible, Distributed Computational Research.*
| Advances in Intelligent Systems and Computing. 2021.
| Book chapter; DOI: 10.1007/978-3-030-73100-7_61
| Part of ISSN: 2194-5357
| Part of ISSN: 2194-5365
Additional Papers
| 2) *Tapis v3 Streams API: Time‐series and data‐driven event support in science gateway infrastructure.*
| Concurrency and Computation: Practice and Experience. 2021-10-10.
| Journal article; DOI: 10.1002/cpe.6103
| Part of ISSN: 1532-0626
| Part of ISSN: 1532-0634
| 3) *Prediction of whole-cell transcriptional response with machine learning.*
| Bioinformatics. 2021-09-27
| Journal article; DOI: 10.1093/bioinformatics/btab676
| Part of ISSN: 1367-4803
| Part of ISSN: 1460-2059
| 4) *Building Tapis v3 Streams API Support for Real-Time Streaming Data Event-Driven Workflows.*
| Practice and Experience in Advanced Research Computing. 2021-07-17.
| Conference paper; DOI: 10.1145/3437359.3465567
| 5) *Real-World, Self-Hosted Kubernetes Experience*
| Practice and Experience in Advanced Research Computing. 2021-07-17
| Conference paper; DOI: 10.1145/3437359.3465603
| 6) *Sustainability in the Tapis Framework.*
| Proceedings of the 54th Hawaii International Conference on System Sciences. 2021
| Conference Paper; DOI: 10.24251/hicss.2021.874
| 7) *Tapis API Development with Python: Best Practices In Scientific REST API Implementation.*
| Practice and Experience in Advanced Research Computing. 2020-07-26
| Conference paper; DOI: 10.1145/3311790.3396647
| 8) *SSH-Backed API Performance Case Study.*
| Benchmarking, Measuring, and Optimizing. 2020.
| Book chapter; DOI: 10.1007/978-3-030-49556-5_27
| Part of ISSN: 0302-9743
| Part of ISSN: 1611-3349
| 9) *Building Science Gateway Infrastructure in the Middle of the Pacific and Beyond.*
| Proceedings of the Practice and Experience on Advanced Research Computing. 2018-07-22
| Conference paper; DOI: 10.1145/3219104.3219151
| 10) *Virtualizing the Stampede2 Supercomputer with Applications to HPC in the Cloud.*
| Proceedings of the Practice and Experience on Advanced Research Computing. 2018-07-22
| Conference paper; DOI: 10.1145/3219104.3219131
| 11) *Distributed Systems of Microservices Using Docker and Serfnode.*
| 7th International Workshop on Science Gateways (IWSG). 2015-06.
| Conference paper; DOI: 10.1109/iwsg.2015.16
Abaco
-----
Dooley, Rion, Steven R. Brandt, and John Fonner. "The Agave Platform: An Open, Science-as-a-Service Platform for Digital Science." Proceedings of the Practice and Experience on Advanced Research Computing. ACM, 2018.
Reference Paper
| 1) *Rapid development of scalable, distributed computation with Abaco*.
| Proceedings of the 10th International Workshop on Science Gateways (2018).
| Conference paper; http://ceur-ws.org/Vol-2357/paper3.pdf
Additional Papers
| 2) *Tapis v3 Streams API: Time‐series and data‐driven event support in science gateway infrastructure.*
| Concurrency and Computation: Practice and Experience. 2021-10-10.
| Journal-article; DOI: 10.1002/cpe.6103
| Part of ISSN: 1532-0626
| Part of ISSN: 1532-0634
| 3) *Prediction of whole-cell transcriptional response with machine learning.*
| Bioinformatics. 2021-09-27
| Journal article; DOI: 10.1093/bioinformatics/btab676
| Part of ISSN: 1367-4803
| Part of ISSN: 1460-2059
| 4) *The Abaco Platform: A Performance and Scalability Study on the Jetstream Cloud.*
| Advances in Parallel & Distributed Processing, and Applications. 2021
| Conference paper; DOI: 10.1007/978-3-030-69984-0_77
| Part of ISBN: 978-3-030-69984-0
| 5) *GenApp, containers and Abaco.*
| Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning). 2019-07-28.
| Conference paper; DOI: 10.1145/3332186.3332191


Chameleon
---------
Expand All @@ -25,13 +105,6 @@ JetStream
---------
Stewart, C.A., Cockerill, T.M., Foster, I., Hancock, D., Merchant, N., Skidmore, E., Stanzione, D., Taylor, J., Tuecke, S., Turner, G., Vaughn, M., and Gaffney, N.I., Jetstream: a self-provisioned, scalable science and engineering cloud environment. 2015, In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure. St. Louis, Missouri. ACM: 2792774. p. 1-8. http://dx.doi.org/10.1145/2792745.2792774

**Papers**

Tapis Reference
---------
Joe Stubbs, Richard Cardone, Mike Packard, Anagha Jamthe, Smruti Padhy, Steve Terry, Julia Looney, Joseph Meiring, Steve Black, Maytal Dahan, Sean Cleveland†, Gwen Jacobs. Tapis: An API Platform for Reproducible, Distributed Computational Research. Future of Information and Communications Conference (FICC) 2021. 29-30 April 2021 in Vancouver, Canada.


.. raw:: html
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