Geophysical research
powered by open-source

Leonardo Uieda | @leouieda

Talk at the GDSL - University of Liverpool - 4 March 2020

First a bit of history

Undergraduate

BSc Geophysics | Instituto de Astronomia, Geofísica e Ciências Atmosféricas - Universidade de São Paulo

Brief stint as a paleomagnetist getting stung by hornets.

Project #1

tesseroids.leouieda.com

C command-line programs for gravity modelling

doi:10.6084/m9.figshare.1495525

doi:10.1038/srep21050

"The signal has been calculated for the spherical geometry with the software Tesseroids"

doi:10.1038/srep21050

Grad School

MSc + PhD Geophysics | Observatório Nacional - Rio de Janeiro (photo credit Leandro Ciuffo; CC-BY)

Inverse problems:

  • Given observed gravity disturbances
  • Estimate density anomalies
  • Ill-posed problem
  • Some methods exist
  • Mine: "Planting inversion"

Uieda and Barbosa (2012) doi:10.1190/geo2011-0388.1

Inverse problems:

  • Given observed gravity disturbances
  • Estimate density anomalies
  • Ill-posed problem
  • Some methods exist
  • Mine: "Planting inversion"

Uieda and Barbosa (2012) doi:10.1190/geo2011-0388.1

Inverse problems:

  • Given observed gravity disturbances
  • Estimate density anomalies
  • Ill-posed problem
  • Some methods exist
  • Mine: "Planting inversion"

Uieda and Barbosa (2012) doi:10.1190/geo2011-0388.1

Project #2

www.fatiando.org

First commit of the fatiando library: 928515b0fc

First website and example gallery from 2011. (Google+ 😂)

In 2018 started a massive rewrite breaking into separate tools.

Postdoc

Project #3

www.generic-mapping-tools.org

C program and API for mapping geophysical data

Started in the 80s by Paul Wessel and Walter Smith (white-haired gentlemen in the middle).

GMT is crucial infrastructure software for marine geoscience and seismology

My postdoc was starting PyGMT

doi:10.6084/m9.figshare.11320280

Back to the present

GMT's biggest challenge:

sustainability

How Paul can retire in peace 🏝:

  • Lower barriers for contribution
    (: moved to GitHub)
  • Automate the boring stuff
    (: setup CI and bots)
  • Nurture a sense of community
    (: new Discourse forum)
  • Formalize governance roles
    (: still figuring it out)
  • General house cleaning
    (: new NSF grant 🤞)

Fatiando a Terra 2.0 🚀

How to build tools that can scale, will last, and are trustworthy

Santiago Soler
@santisoler

Breath of fresh air

  • PhD student from Argentina
  • Collaborating since 2016
  • Leading some of our packages
  • Inspired writing down my process
  • Visiting Liverpool in June

Machine learning inspired spatial data processing and interpolation

doi:10.21105/joss.00957

Manage data registries: download, cache, update, unzip, etc

Used by other packages to manage sample data:
Verde, Harmonica, MetPy, scikit-image (PR 3945), and yt (PR 2417)

doi:10.21105/joss.01943

Documentation is crucial

  • Undocumented code will not be widely used
  • Writing docs makes your code better
  • Forces to think clearly about design
  • ... and use your own code in examples
  • Document before you implement
  • "DDD: documentation driven development"

Nurturing our small community

  • Code of Conduct
    for everyone
  • Contributing Guide
    for new developers
  • Maintenance Guide
    for new maintainers
  • New Authorship Guidelines
    for giving (academic) credit

Nurturing our small community

  • Code of Conduct
    for everyone
  • Contributing Guide
    for new developers
  • Maintenance Guide
    for new maintainers
  • New Authorship Guidelines
    for giving (academic) credit

Guide updates ()

Code checks ()

  • For every commit/PR
  • Check code style (black)
  • Run tests (pytest)
  • Check test coverage (codecov)
  • Build the docs (sphinx)
  • Multiple combinations of OS, Python, dependencies

Deployment ()

  • New tag created on GitHub (v1.0.0)
  • Build HTML docs in new folder and push to gh-pages
  • Point /latest to the new folder
  • Build source/wheel and push to PyPI
  • conda-forge bot picks it up from there

Towards the future

Open-source enables reproducibility and reuse

Credit for software work

A developer friendly gold open-access journal

joss.theoj.org

(JOSS logo is licensed CC-BY-4.0)

Training

  • Software Carpentry:
    • Programming with Python
    • Version control (Git + Github)
    • Bash shell
  • Software Sustainability Institute:
    • Fellowship 2020
    • Workshops on best practices

Conclusion

Let's talk

  • Workshops at SOES
  • Automation for OSS projects
  • Building reproducible workflows
  • Publishing your code in JOSS
  • Ice loss from GRACE gravity data
    (Santiago Soler visiting in June)

Contact

This presentation by Leonardo Uieda is licensed under a Creative Commons Attribution 4.0 International License.