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This HackMD is re-used under a CC-BY license from The Turing Way online coworking calls template

Environmental Data Science book ⛰ 🌳 🏙️ ❄️ 🔥 🌊 _ online coworking calls

What? EDS book is a *computational notebook community for open environmental data science.
EDS book team hosts 1-hr long coworking calls each month for the community members to work together in real time. No sign-ups needed! Read more about it in this chapter.

If you would like to receive automatic updates on these meetings, please subscribe to the calendar.

Join Zoom Meeting
https://turing-uk.zoom.us/j/98587750579?pwd=aEJoem1rSXVLdHl1eTdDVUo4MlYvQT09

Meeting ID: 985 8775 0579
Passcode: 397294

Who can join? This call is joined by EDS book core and community members contributing to the publishing and infrastructure working groups.

Monthly coworking calls are dedicated space for the Core team members to check in, cowork and exchange knowledge from their respective work, working group and/or subprojects.

Contact for any question: Alejandro Coca-Castro (acoca@turing.ac.uk)

Code of conduct

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Schedule:

Pomodoro clock

Duration Activity
Start 👋 Welcome
5 mins Introductions and personal goal setting
20 mins 🍅 1st Pomodoro session
5 mins ☕️ Break and report out
20 mins 🍅 2nd Pomodoro session

Chairing a Coworking Call

  • 5 mins - Check-in: Begin with a short general check-in with folks (how they are doing).
  • 2-3 mins - Managing Breakout: Ask folks what specific task or group they are working on.
  • Ending Pomodoro: Close the breakout room at the end of the Pomodoro. Bring people back in the room, and ask if there is anything they would like to report on - or if they have any questions that others can help address.
  • Break: Remind them of 5 mins break – use the cuckoo clock.
  • Repeat for the second breakout - the second Pomodoro might be shorter.

Notes

20-06-25

  • Alejandro

Agenda

09-05-25

  • Alejandro

Agenda

14-03-25

  • Alejandro

Agenda

  • EDS book
    • Checking implementation of JB2
      • 3 notebooks so far
      • Open issue to document steps

14-02-25

  • Cam
  • Alejandro

Agenda

10-01-25

Cancelled

13-12-24

Cancelled because Xmas

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08-11-24

  • Cam
  • Anne
  • Anne

Agenda

  • Intros

  • Cam's updates on the livestock

  • FAIR-impact

  • Closing X account, issue #261

    • Ricardo suggest considering

Notes

  • Intros

    • Cam, located in UK, author of an on-going submission using the DeepForest package
    • Anne, located in Norway, interested in good practices in notebooks

  • Pangeo

  • Cam Livestock notebook

    • Going through the submission process and main steps
    • One of the reviewers is the developer of the DeepForest package
    • The concept of .safetensors
    • Expected publication 1st/2nd week December!
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  • Anne FAIR-impact updates

    • Going through badges in the Sea Ice Python API notebook
    • Example with Zenodo
    • Example of the RoHub repository
      • Some notebooks don't have the notebook file and computational environment linked (icenet python api, reproducibility challenge 2023)
    • FAIR-impact
      • Improve the FAIRness of software
      • 3 weeks work
      • Low score for EDS book example, varational data assimilation
      • 15 principles
        • gofair.foundation
        • example with README (F2), missing keywords
        • missing metadata.json but it contains similar information of CITATION.cff
      • check the core repository and notebook repository
      • Feedback
        • test checking certain files requirement.txt, but
      • Conclusion
        • Very useful for the initiative
      • Next steps
        • FAIR-impact release a new version Feb 2025 (TBC)
          • still require documentation
        • Improvements in EDS book
          • metadata.jon > automate generation
          • README > add missing sections in notebook repository
        • Document requires approval, then Anne will archive in Zenodo

  • Alejandro:

Actions

  • Check RoHub

13-09-24

  • Cam
  • Alejandro

Notes

09-08-24

  • Cam
  • Alejandro

Notes

  • Cam: Queen Mary, interest in drone imagery

We discussed about the EDS book resource. The basic infrastructure of notebook repositories, Binder and review process.

Cam is keen to submit a notebook according to the features described the issue#249.
> drone imagery, ok with copyrights, currently stored in Google Drive
> annotation data, ok with copyright, manual annotations using a python library
> models, pretrained from DeepForest or from scratch, suggested to share model weights, because the resource limits e.g. Binder

We commented about other spaces to connect, including the collaboration cafe sessions hosted by the Turing Way.

19-07-24

  • Anne F
  • Alejandro

Notes

14-06-24

  • Anne F
  • Alejandro

Notes

Actions

  • Alejandro: Retrospective features > UX/UI
  • Anne F: wait reviewers' response

30-05-24

  • Anne F
  • Alejandro
  • Abner
  • Lindsay

Notes

15-05-24

  • Anne F
  • Alejandro

Notes

Superbloom
FAIRness
Hydroshare

https://www.hydroshare.org/apps/

Others

26-12-24

  • Anne F
  • Alejandro

Notes

15-12-23

  • Alejandro
  • Angus

Notes

  • Slides
  • EDS have a gallery - another example of someone who'd benefit from a MyST feature for this
  • Curious about lifecycle - is NeuroLibre a useful entity to raise here?
  • Mention of 2023 CI Reproducibility Challenge
  • ROHub - https://www.rohub.org/
  • W3id - https://w3id.org/
  • reviewnb - https://www.reviewnb.com/
  • Bug in MyST Safari? acocac.github.io
  • Can we embed metadata about e.g. %run scripts? Or provide quicker access to filesystem
  • Why is mystmd better than JB?
    • Referencing is easier
    • Better cross-referencing of e.g. figures
    • More metadata in main document.
    • Can we depend upon reproducible environment (conda lock)
      • What are repo2docker doing w.r.t lockfiles?

Actions

  • Angus: follow-up meeting in late January 2024

08-12-23

  • Alejandro
  • Rowan Cockett
  • Steve Purves
  • Anne F

Notes

  • Frontend

    • Custom dev for team
      • React
      • Core in MyST
    • Binder
      • Curvenote, Binder
    • Healthchecking

  • Terms, Timeline

    • Feb/Mar 2024

  • Actions

    • Proposal/Quote

Async

  • Features based on Roadmap discussed on 09-06-23

    • User Interface and Experience
      • Gallery: Tags and Filters (rapidsai)
      • Guides: Access and Friendly Guides (PyOpenSci/ROpenSci)
      • Notebooks: Pre-requisites and link to existing training (Pythia)
    • Core features
      • Notebooks:
        • Annotations & Metadata (MyST + Machine readable)
        • Health checking (GitHub actions)
        • Computationally expensive notebooks (custom Binder/JupyterHub/EGI Replay (create a EDSBook User))
        • Inline execution (thebe)
      • Website:
        • Flexible website (sphinx)
      • Review

  • Extras

    • UX
    • Internationalisation
    • Create template for new communities (could be tested with Bio-Imaging)
    • Data ROs for each relevant dataset used in the notebooks to allow users to discover the notebooks while searching for data. (are creating DOIs for the package)
    • Data: cache data for instance using EGI datahub (requires to use EGI Replay) or B2SHARE (could we get an account for EDSBook & dedicated storage?)
    • RO-Crate & Signposting to increase FAIRness.

  • Vision and Approach

    • A world-leading community-driven education platform using interactive computing to accelerate reproducible and open scientific discovery.
    • Cross-cuting (Python, R & Julia)
    • Fast-track service for next-generation journals with interactive, reusable components
    • Flexible and portable to free and customise computational resources (Binder, JupyterHub)
    • Advance on FAIR principles (RO-crate)

  • Plan

    • Co-creation
      • Feedback form to EDS book community/contributors
      • Mini-workshop with Turing Environment & Sustainability researchers

17-11-23

Existing collaborations:

  • The Turing Way
    • Summary of collaboration in BookDash November 23 working groups and collaborators share-out
    • #environmental-sustainability slack channel
  • Pangeo
    • Pangeo-EOSC
    • Destination Earth Initiative
  • NotebooksNow!
    • Reuse existing developments in pre-submission (subject to licence)
      • Metadata

Potential collaborations

Events:

07-09-23

  • CI2023 Reproducibility challenge
    • Early reception of CI2023 winning team notebook
    • Post for runner-up team
      • Team 2 - Change colours for charts
        • Keep same colours
      • Team 7 - Unresponsive
        • Editor change
        • Create issues for hacktoberfest (potential for authorship)
    • Blog post experience
      • Motivation
      • Timeline
      • Technologies
      • Testimonial
        • Challenge (Team 3)
        • Talk with Experts (Team 2, Viktor)
      • Acknowledgements
  • Hacktoboerst
    • Quantity is fun, quality is key.
    • Really worth it?
    • Dates:
      • Registration: anytime between September 26 and October 31
      • Valid PRs/Merge: Oct 1-31
    • FAQ
      • how do I encourage contributions to my repos?
        • good first or help wanted
      • Accepted PR/MRs enter a seven day review window, during which approval can be revoked by the maintainer or by our
      • Low quality PR/MR
        • Automated pull/merge requests: scripted opening pull requests to remove whitespace, fix typos or optimize images.
        • Disruptive pull/merge requests: taking someone else’s branch/commits and making a pull request.
        • Anything that a project maintainer flags as spam.
        • Anything that looks like an attempt to duplicate your pull request count for October.
        • Multiple pull/merge requests for the same issue that are unnecessary, for example five PR/MRs to remove a stray whitespace.
      • Steps
        • Add the “hacktoberfest” topic to your repository to opt-in to Hacktoberfest and indicate you’re looking for contributions.
        • Apply the “hacktoberfest” label to issues you want contributors to help with in your GitHub or GitLab project.

11-08-23

Sign-up

  • Alejandro
  • Anne

Notes

https://stackoverflow.com/questions/70990353/right-way-to-apply-pre-trained-scikit-learn-model-to-dask-array

https://github.com/gkirok/tutorials/blob/29fd0f58e18fcccab19a120669f2832d294af265/demos/netops/nuclio_infer.ipynb#L140

https://github.com/ryanjmccall/prod_mle_capstone/blob/027a62368703a52318354630114e59ac3012100c/src/notebooks/3_Scale_prototype.ipynb#L65

14-07-23

Sign-up

  • Alejandro
  • Anne

Notes

  • Discussion NERC CDE hackathon

    • Jasmin
      • Notebooks, a single kernel (image)
      • Pangeo
    • FAIRpipeline
      • Only support plain scripts

  • Adding metadata information in the notebook:

    • codemetadata (see below)
{
    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
    "@type": "SoftwareSourceCode",
    "license": "https://spdx.org/licenses/MIT",
    "codeRepository": "https://github.com/Redacted”",
    "dateCreated": "Redacted”",
    "datePublished": "Redacted”",
    "name": "Redacted”",
    "description": "Redacted”",
    "applicationCategory": "Redacted”",
    "funding": "Redacted”",
    "developmentStatus": "inactive",
    "funder": [
        {
            "@type": "Organization",
            "@id": "https://ror.org/Redacted”",
            "name": "Redacted”",
            "url": "Redacted”"
        },
        {
            "@type": "Organization",
            "@id": "https://ror.org/Redacted”",
            "name": "Redacted",
            "url": "Redacted”"
        }
    ],
    "programmingLanguage": [
        "Python 3"
    ],
    "runtimePlatform": [
        "CPython"
    ],
    "operatingSystem": [
        "macOS"
    ],
    "softwareRequirements": [
        "Python 3.9.6, virtual environment configuration and requirements.txt file included in github repository"
    ],
    "author": [
        {
            "@type": "Person",
            "givenName": "Redacted”",
            "familyName": "Redacted”",
            "affiliation": {
                "@type": "Organization",
                "name": "Redacted”"
            }
        },
        {
            "@type": "Person",
            "@id": “Redacted”,
            "givenName": "Redacted”",
            "familyName": "Redacted”",
            "affiliation": {
                "@type": "Organization",
                "name": "Redacted”"
            }
        }
    ]
}

Actions

30-06-23

Sign-up

  • Alejandro
  • Ricardo

Notes

  • [Method paper]:
  • Discussion on CIRC2023 Feedback
  • Where to store large files
    • Dockerised version
    • Cloud Storage , ARD
    • Archival Repositories, Zenodo
  • [CIRC2023 Paper]:
    • Blogpost
    • Livestreaming in Twitter

09-06-23

Sign-up

  • Alejandro
  • Anne

Notes

  • Roadmap

  • Roadmap Structure

    • Priorities

      • User Interface and Experience
        • Gallery: Tags and Filters (rapidsai)
        • Guides: Access and Friendly Guides (PyOpenSci/ROpenSci)
        • Notebooks: Pre-requisites and link to existing training (Pythia)
      • Core features
        • Notebooks:
          • Annotations & Metadata (MyST)
          • Health checking (GitHub actions)
          • Expensive notebooks (custom Binder/JupyterHub)
          • Inline execution (thebe)
        • Website:
          • Flexible website (sphinx)
        • Review
      • Outreach
        • Mapping [TODO]

    • Working groups

      • Governance (Core meeting of the Turing Way)
      • Infrastructure
      • Community & Outreach (Collab cafes)

  • Governance

    • The Turing Way

24-05-23

Sign-up

  • Alejandro
  • Cassandra

Notes

Turing TRIC-DT

  • 3 year project
  • Community manager
  • Data Sharing

Report

Ideas

  • Mentoring for reviewers
  • Sustainability project
    • how to growth community
  • Practical steps
    • Facilitate notebooks in EDS book
    • Keep connected
  • Make replicates of EDS book for infrastructure and health DTS
  • Potential to communicate target audience
    • Decision Makers, Journalist

18-04-23

Sign-up

  • Alejandro
  • Anne F

Notes

Pythia project

Pythia notes in:
https://docs.google.com/document/d/1lIioFOGvKsQDyfq0_kCecWcDYiH4HGip_whHo__9THU/edit#

Tipo

14-04-23

Sign-up

  • Alejandro
  • Anne F

Topic

  • CI2023 Reproducibility Challenge
    • Structure
    • Misc
      • check config.yml

Actions

  • Alejandro:

    • Timeline

      • check dates
      • ice-breaker activities, Monday
      • onboarding/clinics
        • EDS book, Monday
        • JupyterHub and EDS book
      • add checkpoints - Q&A, time, mondays
      • chat with the experts, Friday
        • Python
        • R
        • Julia

    • Applicants

      • reviewers, notebooks
      • link to the right URL for reviewers form - TO ADD

    • Judging

      • remove Contribution to the field / and add to Additional insights
      • HOW TO WEIGHT 75/25

    • Incentives

      • after teams in
        • Professional development: Participants will take clinic sessions before teams

    • Cloud EGI JupyterHub

      • Ask Ricardo to test

    • Team

      • logistics,
        • in Tip link to the other section

    • Tutorials / Resources

    • Subdomain, using edsbook.org

  • Anne

    • Section of storage (zenodo and EGI JupyterHub)
    • ~~Add Alejandro to admin EGI/EU ~~
    • Ask sebastian to add torch-image

  • Anne and Alejandro
    -how to score notebooks, Jupyter
    - matrix, and then ask Douglas

  • Targeting: live first version on Tuesday before CI2023 conference

Select a repo