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---
tags: eds-book, coworking-call
---
*This HackMD is re-used under a CC-BY license from [_The Turing Way_ online coworking calls template](https://github.com/alan-turing-institute/the-turing-way/blob/main/book/website/community-handbook/coworking/coworking-weekly.md)*
# _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](https://edsbook.org/community/about.html#meeting-structure)*.
If you would like to receive automatic updates on these meetings, please [subscribe to the calendar](https://calendar.google.com/calendar/embed?src=environmental.ds.book%40gmail.com&ctz=Europe%2FLondon).
## Joining Link:
:::info
**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
* [Take a moment to read this](https://github.com/alan-turing-institute/environmental-ds-book/blob/master/CODE_OF_CONDUCT.md)
:hourglass_flowing_sand: **Schedule:**
---
**Pomodoro clock**
- [https://cuckoo.team/edsbook-coworking](https://cuckoo.team/edsbook-coworking)
| 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.
* Whoever joins the call first will be able to make you host (full right), you can then follow this instruction to make a breakout room: see Create breakout rooms.
* Use the online clock to set the timer for the first breakout room (20-25 mins: https://cuckoo.team/edsbook-coworking) - remind folks of CoC: https://github.com/alan-turing-institute/environmental-ds-book/blob/master/CODE_OF_CONDUCT.md - open the breakout room!
* 1 min before the clock hits the end of Pomodoro, broadcast to everyone that you will be closing rooms! (for Zoom broadcast see: Broadcast a message to all breakout rooms: https://support.zoom.us/hc/en-us/articles/8550395207693-Sharing-screen-and-broadcasting-to-breakout-rooms)
* **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
## 26-12-24
- Anne F
- Alejandro
#### Notes
- Recap
- EGU24
- Vannessa's work
- https://github.com/icenet-ai/icenet-ai.github.io/issues/9
- Climate Informatics
- https://github.com/alan-turing-institute/climate-informatics-2024-ae
- Ricardo asked about DGGS
- IGARSS
- Half day (3h)
- Anne asked morning
- Date TBC
- Set learning objectives
- Intro Pangeo
- Dask
- Applied ML
- Clustering (unsupervised)
- Random Forest
- CNN-Unet (pre-trained model)
- Resources
- https://projectpythia.org/landsat-ml-cookbook/notebooks/2.0_Spectral_Clustering_PC.html
- Turing
- Depriorisation in Turing 2.0 E&S GC
- Alternatives
- OLS Residence Fellowship, https://docs.google.com/document/d/11yPbX7xUyRkwTXyStibNQUO7x6p5BOz_5eoXZow6yoY/edit
- TTW joint activities
- Pangeo
- Oslo
- https://www.rohub.org/5c135a7b-70bf-45f3-9895-3103e0e29c11?activetab=overview
- IceNet notebook
- Check reviewers
- CW24 - TTW 5 year celebration
* [Slides](https://docs.google.com/presentation/d/1mzuz--sPMGX7-tDvB_hTqKksjfnP9BqHiFjN8Q_ziJI/edit?usp=sharing)
### 15-12-23
- Alejandro
- Angus
#### Notes
- [Slides](https://docs.google.com/presentation/d/1IdKnE5jRPR3rPaKkzUtw-5YaUhpsgjsonRlt05d8SgQ/edit#slide=id.g2579304b761_1_2783)
- EDS have a gallery - another example of someone who'd benefit from a MyST feature for this
- Pythia discoverability (<https://projectpythia.org>?)
- Also HSF training
- 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
- [name=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
* [Bot](https://joss.readthedocs.io/en/latest/editorial_bot.html)
* 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)
* [RoHub example](https://www.rohub.org/91046403-e0b7-41d3-8d60-4b540219ffa7?activetab=overview)
* 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](https://hackmd.io/@turingway/Sk8UuPy4a) 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**
* Pangeo
- Project Pythia
* ESA
* FAIR Image Analysis Galaxy working group (Bioimaging, Geo-image analysis)
* Turing >
- [Environment & Sustainability Grand Challenge](https://www.turing.ac.uk/research/environment-and-sustainability)
- [DeepSensor](https://github.com/tom-andersson/deepsensor)
- Biodiversity
- Computer vision > [scivision](https://sci.vision/)
- [Reproducible Digital Twins](https://www.turing.ac.uk/research/research-projects/tric-dt)
- [Environment & Sustainability Interest Group](https://www.turing.ac.uk/research/interest-groups/environment-and-sustainability)
* Galaxy
- Vanessa's work on the IceNet notebook
* [ELIXIR Environmental Impact](https://elixir-europe.org/focus-groups/environmental-impact)
**Events:**
* 21 Nov, [Environmental model code of long-term value organised](https://www.software.ac.uk/news/workshop-environmental-code-long-term-value), Alejandro
* 5 Dec, Webinar on Reproducibility Challenge for [FARR](https://www.farr-rcn.org/events), Alejandro
* 8 Dec, Presentation of [RELIANCE project and ROHub (including edsbook)](https://www.ub.uio.no/english/courses-events/events/dsc/2023/2023-12-07-dmn-fairdo.html), Anne
* AGU23, Reproducibility Challenge, Andrew McDonald
* 18 March 2024, [Machine Learning and Data Management for Earth Observation] organised by TU Berlin
### 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?
- https://github.com/the-turing-way/the-turing-way/pulls?q=is%3Apr+label%3Ahacktoberfest-accepted+is%3Aclosed
- https://github.com/the-turing-way/the-turing-way/issues/2700
- 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
- Discussion EDS book repositories
- Consultation with the community
- Core repo
- Notebooks Gallery
- Temp EDS book Org
- Reproducibility Challenge
- dask_ml
- https://ml.dask.org/modules/generated/dask_ml.wrappers.ParallelPostFit.html
"Most scikit-learn estimators will convert large Dask arrays to a single NumPy array, which may exhaust the memory of your worker. You probably want to always specify scoring."
- Add Anne as an editor to Team-2 notebook
- ML version notebook to test
- https://github.com/acocac/repro-challenge-team-3/blob/main/notebooks/notebook_ml.ipynb
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](https://jasmin.ac.uk/)
- Notebooks, a single kernel (image)
- Pangeo
- [FAIRpipeline](https://www.fairdatapipeline.org/)
- 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”"
}
}
]
}
```
- Information on possible metadata standard from NotebookNow!: https://docs.google.com/spreadsheets/d/1T2b0RHopBaKt7myF9hd4RVl_rid7ZShl4d2nf3U9Wo4/edit?usp=sharing
- NotebooksNow
- [MyST]() and [Quarto]() Templates
- Large files
- Zenodo / Mirror in Amazon using same DOI only when format is the same
- [Nanopublications](https://nanodash.petapico.org): connect multiple datasets in different formats
- https://knowledgepixels.com/
- CIRC2023
- Winning team
- Inmediate solution: light notebook without training step, load pretrained models
- Explore
- MinIO:
- ZARR-optimised version
- Intake (default loading, if not try other sources):
- Point to MinIO bucket
#### Actions
- Test MiniO in [TTW collaboration cafe](https://hackmd.io/@turingway/collaboration-cafe) on Wednesday 19 July
### 30-06-23
#### Sign-up
- Alejandro
- Ricardo
#### Notes
- [Method paper]:
- Suggestions > https://chss.uchicago.edu/directory/james-evans
- 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
* References
- [Pangeo](https://raw.githack.com/pangeo-data/pangeo/ab/add-roadmap-preview/roadmap.html)
- [Galaxy](https://galaxyproject.org/roadmap/)
- [Scivision](https://scivision.readthedocs.io/en/latest/scip/0003-roadmap.html)
- 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
* [Bot]()
* 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
- https://zenodo.org/record/7840266#.ZG3UtNbMLao
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
- Review
- ReviewNB
- Infrastructure
- Scheduling notebooks
- Metadata
- MyST & Ro-crate
- Hackathon
- https://projectpythia.org/pythia-cookoff-2023/index.html
### 14-04-23
#### Sign-up
- Alejandro
- Anne F
#### Topic
- CI2023 Reproducibility Challenge
- Structure
- Misc
- check config.yml
#### Actions
- [name=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
- Learning to code
- ~~fix Julia heading~~
- Julia
- ~~https://julialang.org/learning/tutorials/~~
- Subdomain, using edsbook.org
- [name=Anne]
- ~~Section of storage (zenodo and EGI JupyterHub)~~
- ~~Add Alejandro to admin EGI/EU ~~
- ~~Ask sebastian to add torch-image~~
- [name=Anne and Alejandro]
-how to score notebooks, Jupyter
- matrix, and then ask Douglas
- Targeting: live first version on Tuesday before CI2023 conference