software collaboration tools and the salish sea meopar project · software collaboration tools and...
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Software Collaboration Toolsand the Salish Sea MEOPAR Project
Doug LatornellSusan Allen, Nancy Soontiens, Kate Le Souëf
Earth, Ocean and Atmospheric SciencesUniversity of British Columbia
salishsea.eos.ubc.ca/nemo.html
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MEOPAR
● Marine Environmental Observation Prediction and Response
● Network of Centres of Excellence● meopar.ca
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NEMO
● Nucleus for European Modelling of the Ocean● www.nemo-ocean.eu● Ocean model component of the DFO/EC/DND
CONCEPTS program● Regional scale configuration● Atmospheric forcing from Environment Canada models
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Salish Sea
● British Columbia mainland south coast
● Strait of Georgia● Strait of Juan de Fuca● Puget Sound● Johnstone Strait
Courtesy of B. Moore-Maley
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Salish Sea NEMO Model
● Resolution: ~500m horizontal; 1m to 20m depth● Time Scale: 1-10 days● Presently evaluating model skill via hindcast runs:
● Tidal amplitude and phase● Storm surge events● Stratification and deep water renewal over annual cycle
● Nancy Soontiens' talk -- Thu at 12:15 in Parent room
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Online Collaboration
● Software Tools + Web Services● Instantly share documentation, results, tools & code
among research team● Share results with collaborators and stakeholders● Publish our experience with NEMO for other users
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Think of the Researchers...
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Think of the Researchers...
● Research productivity, not cool tools● New things to learn, and habits to change or form● Tools need to be:
● Powerful● Low cognitive load● Widely applicable, reusable
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DocumentationTools
Distributed Version Control
Web Services
Automation Tools
Analysis Tools
Coordination Tools
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Documentation Tools
reStructuredTextSphinx
Distributed Version Control
Mercurial (hg)
Web Services
bitbucket.org readthedocs.org nbviewer.ipython.org drive.google.com
Automation Tools
Python
Analysis Tools
PythonIPython Notebook
Markdown
Coordination Tools
Google Drive
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle Drive
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Documentation
● Lots of good reasons to write documentation● ...And usually a few more reasons why not to...● Describe NEMO configuration experience
for future users● Describe working environment for new team members● Be kind to our future selves
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle Drive
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Simple Docs Update
$ cd docs$ edit code-notes/salishsea-nemo/spinup.rst…
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Simple Docs Update
$ cd docs$ edit code-notes/salishsea-nemo/spinup.rst…$ hg commit -m''Add info re: recent spin-up runs.''$ hg push
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle Drive
![Page 20: Software Collaboration Tools and the Salish Sea MEOPAR Project · Software Collaboration Tools and the Salish Sea MEOPAR Project Doug Latornell Susan Allen, Nancy Soontiens, Kate](https://reader033.vdocuments.net/reader033/viewer/2022060605/605a00d1648a8d05f93ba414/html5/thumbnails/20.jpg)
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Docs Update with Preview
$ cd docs$ edit code-notes/salishsea-nemo/quickstart.rst…$ make html$ open _build/html/code-notes/salishsea-nemo/quickstart.html <review, edit, make, as necessary>
$ hg commit -m''Change to use new `salishsea run` command.''$ hg push
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Widely Applicable, Reusable
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Pre-processing and Analysis
● Preparation of files for boundary conditions and forcing● Analysis of model results for verification and new
insights● Mixture of narrative, math, code, plots, animations, …● Scientific Python libraries provide the platform● IPython Notebook enables us to keep narrative, math,
code, plots, etc. together, and share with minimal effort
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle Drive
![Page 27: Software Collaboration Tools and the Salish Sea MEOPAR Project · Software Collaboration Tools and the Salish Sea MEOPAR Project Doug Latornell Susan Allen, Nancy Soontiens, Kate](https://reader033.vdocuments.net/reader033/viewer/2022060605/605a00d1648a8d05f93ba414/html5/thumbnails/27.jpg)
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle Drive
![Page 32: Software Collaboration Tools and the Salish Sea MEOPAR Project · Software Collaboration Tools and the Salish Sea MEOPAR Project Doug Latornell Susan Allen, Nancy Soontiens, Kate](https://reader033.vdocuments.net/reader033/viewer/2022060605/605a00d1648a8d05f93ba414/html5/thumbnails/32.jpg)
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Web Services
Researcher's Computer
P
ush
Not
ifica
tion
readthedocs.org/ salishsea-meopar-docs salishsea-meopar-tools
nbviewer.ipython.org/
UR
Ls
hg Repositories:
docstoolsanalysissalishsea-siteresultsNEMO-codeNEMO-forcingSS-run-sets...
OtherTeam
Members
The Internet
hg pullhg push
bitbucket.org/salishsea/
Tools: hg reStructuredText Sphinx Python IPython Notebook Markdown LaTeX
URLsGoogle DriveDoug Latornell (@dlatornell )Susan AllenNancy Soontiens