Environmental Data Science book ⛰ 🌳 🏙️ ❄️ 🔥 🌊 Publishing working group [PUBLIC ARCHIVE]

Meeting 03-02-23

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• Alejandro
• Thijs

Agenda and notes

• Visualisation package for reproducible figures (RFs)
  • Motivation
    • Multipanel
    • Time-efficient
    • Reproducible and traceable figures
  • Features
    • Shared axis
    • Imported images into code-generated RFs
  • Principles

Next steps

• Thijs
  • Explore potential of notebooks metadata to automatically generate thumbnails
• Alejandro
  • Read more about notebooks metadata
• All
  • Meeting after Notebook File Workshop

Meeting 21-09-22

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• Alejandro
• Nick

Agenda and notes

Post-print, Land cover notebook

• Notebook PR
• Steps
  • PR
    • All reviewers recommend the notebook for publication
    • Check all cells generate outputs in Binder
    • Open ReviewNB, solve comments except TODOs (typos, minor changes)
      • write: "closing conversation", resolved, so that there is a record of who closed each discussion.
    • All ok, next step is merging to the main branch
  • Main branch
    • Wait until GH action runs, inspect Render branch
  • Create post-print branch
    • refactor files
      • move environment.yml file to .binder folder
      • in .github/workflows/publish.yml, change path environment-file to ``.binder/environment.yml`
      • create lock files and move to .lock folder
        • install conda-lock
          • pip install conda-lock
          • conda install -c conda-forge conda-lock
        • conda-lock -f .binder/environment.yml -p osx-64 -p linux-64 -p win-64
    • Generate outputs (figures and/or tables)
      • Add cell at the end of the notebook
      • All interactive plotting should be declared as a variables, including when opts.
      • Create Zenodo Repository
        • Date should be same the expected release/publication date
    • Create a RoHub RO
      • register the notebook using register.py
    • Add Citation cells
    • Add RoHub and Binder Badges
    • Replace Rohub link in README, verify other items
    • Replace reference using reference.bib
    • Set cells tags using jupyter book
    • Check spelling, typos, grammars
    • Inspect the notebook in Binder
    • Merge branch
  • Check render locally
    • check all outputs ok
  • Update submodule in EDS book PR
  • Confirm all ok with author
  • Create twitter
    • Create animation
    • Thread

Next steps

• anyone
  • create a bash to facilitate post-print preparation
• anyone
  • are outputs valuable?
    • automated in HoloView, see https://holoviews.org/user_guide/Exporting_and_Archiving.html#exporting-notebooks
• Alejandro > hvplot developers
  • why saving hvplot outputs as PNG

Meeting 25-08-22

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• Alejandro
• Nick
• Tim

Agenda and notes

Updates

• CDE Expert Network Recruitment 2022 - CDE
• [FOSS4G Pangeo 101]
  • GitHub
  • Jupyter Book
• AGU22

Discussion

• Diagram for submission
  • Issue
• Dependencies
  • Version
  • OS (Tim), e.g. conflict(s) found using Windows 10 https://github.com/Environmental-DS-Book/wildfires-exploration-fires_modis/blob/main/wildfires-exploration-fires_modis.ipynb
  • Packages
    • pipgrid (dependencies)
      • also requirements.txt
    • pyvis.network
  • pygeon uses pipgrid, scrappes from anaconda (number of libraries),

Next steps

• Nick:
  • check pipgrip to inform the available OS.
  • make public the repo
• Tim
  • participating in MetOffice community in practice

Resources

• Pangeo 2i2c Binder
  • Fill form

Meeting 25-07-22

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• Alejandro
• Nick
• Tim

Agenda and notes

• Communication, Twitter

• EnvDS book, navigate to project folder

  • gmail
    • Tim: [e-mail]
    • Nick: [e-mail]

• Dashboard

  • pygeons
    • Ecosystem
      https://github.com/pygieons/pygieons/tree/main/src/pygieons

• Discussion on GEE
  *

• STAC

  • https://stacspec.org/en/tutorials/access-sentinel-2-data-aws/

• Minor issues of Tim's notebook

  • environment > yaml, yml
  • training, public repository - not part of any previous trainings, but may be deployed in the future
  • Notebook is not within a public repo, but is under the same funding stream as the public repo https://github.com/informatics-lab/causality/tree/master/causality_paper (check acknowledgement of BAMS paper for funding details)

Actions

• Nick: experiment with environment.yml of the notebooks
• Alejandro: how to serve panel in HTML
  • hosted as jupyter book

Meeting 27-06-22

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• Alejandro
• Nick
• Tim

Agenda and notes

• Tim’s notebook revision and publication
  • Nick feedback:
    • Clone locally
      • But it would be better if Binder badge can be used
    • ReviewNB
      • ok
    • Communication
      • make clear how reviewer communicate with editors and authors
  • Tim feedback:
    • Copy existing notebook as the templates weren't available in March 2022
    • Ok to set roles: editors, authors and reviewers
  • Alejandro Role of the editor
    • Contact corresponding author
      • Responsability all co-authors are happy to be listed and citation with DOI
      • Stress it in the submission guidelines
• Discussion of the dashboard related to Nick’s research
  • Present prototype of dashboard
  • Working on dataset
  • Proposed approach:
    • Separate repository per theme dashboard
    • Test if the App can be saved as HTML, then we can render in a new branch and call it as a submodule in the main EnvDS book repo
• Updates of the submission guidelines according to Tim’s submission
• AOB
  • Tim asks about future co-working sessions
    • Joint show and tell with the Pangeo Europe community
    • Set a monthly date for general co-working/collaboration cafe session with the community for new notebooks, ideas, etc.
  • Presentations of the EnvDS book
    • Fireside chat, 30 July, 4 pm
    • CEDS, 4-6 July
    • ASG community meeting, 6-7 July

Actions

• Tim:
  • complete review round 2
• Nick:
  • prototype with small database
  • make a public repository
• Alejandro:
  • send invite the next meeting 25th July
  • update guidelines for submission and reviewing
  • set a new date for collaboration cafe/co-working session