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Merge pull request #244 from alan-turing-institute/add-nb-icenet-library
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Notebook - Sea ice forecasting using the IceNet library
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acocac authored Jul 3, 2024
2 parents b5afe33 + 2b0f127 commit 4848da8
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4 changes: 4 additions & 0 deletions .gitmodules
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path = book/notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3
url = https://github.com/eds-book-gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3.git
branch = render
[submodule "book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b"]
path = book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b
url = https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b.git
branch = render
21 changes: 19 additions & 2 deletions book/_bibliography/references.bib
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Expand Up @@ -139,7 +139,7 @@ @article{Andersson2021
volume = {12},
url = {https://doi.org/10.1038/s41467-021-25257-4},
year = {2021},
topic = {ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef}
topic = {ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef, 67a1e320-7c47-4ea9-8df8-e868326bc90b}
}

## 1b8921af-e77f-4ccf-ae38-4813cdceba0f
Expand Down Expand Up @@ -420,4 +420,21 @@ @article{filoche_2023
year={2023},
pages={e2},
topic = {39d9c177-11da-41b2-9b64-63f4c1c834b3}
}
}

### 67a1e320-7c47-4ea9-8df8-e868326bc90b
@misc{cocacastro2024_icenetnb,
author = {Coca-Castro, Alejandro and
This EDS book notebook contributors},
title = {{Sea ice forecasting using IceNet (Jupyter
Notebook) published in the Environmental Data
Science book}},
month = mar,
year = {2024},
publisher = {Zenodo},
version = {v1.0.5},
doi = {10.5281/zenodo.10808514},
url = {https://doi.org/10.5281/zenodo.10808514},
topic = {67a1e320-7c47-4ea9-8df8-e868326bc90b}
}
4 changes: 3 additions & 1 deletion book/_toc.yml
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Expand Up @@ -23,6 +23,8 @@ parts:
- file: notebooks/gallery
title: Gallery
sections:
- file: notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/notebook
title: Daily sea ice forecasting (IceNet)
- file: notebooks/gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/notebook
title: Variational data assimilation with deep prior (CIRC23)
- file: notebooks/gallery/93463cac-471a-469d-ad52-0514fd9b67f2/notebook
Expand All @@ -36,7 +38,7 @@ parts:
- file: notebooks/gallery/ea34568e-d86e-4720-be2f-3f826f66a26c/notebook
title: Rainfall NCEP/NCAR (NOAA)
- file: notebooks/gallery/ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef/notebook
title: Sea ice forecasting (IceNet)
title: Monthly sea ice forecasting (IceNet)
- file: notebooks/gallery/94486a7f-e046-461f-bbb9-334ec7b57040/notebook
title: Tree crown (DetectreeRGB)
- file: notebooks/gallery/bc30df18-fce2-42fa-aade-1ce5b7f3ca3c/notebook
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40 changes: 38 additions & 2 deletions book/notebooks/gallery.md
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::::{grid} 1 3 3 3
:gutter: 2

:::{grid-item-card} Daily sea ice forecasting <br> (IceNet library)
:margin: 3 0 0 0
:link: ./gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/notebook.html
:link-type: url
:text-align: center
:shadow: md

{bdg-primary}`Polar`
{bdg-secondary}`Modelling`
<br>
{bdg-warning}`Standard`
{bdg-info}`Python`
^^^

<img src="https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/blob/main/images/thumbnail.png?raw=True"/>

+++
Byrne & Ubald (2024)

<p align="center">
<a href="https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/blob/main/LICENSE">
<img alt="license" src="https://img.shields.io/badge/license-MIT-yellow.svg">
</a>
<a href="http://mybinder.org/v2/gh/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/main?labpath=notebook.ipynb">
<img alt="binder" src="https://mybinder.org/badge_logo.svg">
</a>
<a href="https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/actions/workflows/render.yaml">
<img alt="render" src="https://github.com/eds-book-gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b/actions/workflows/render.yaml/badge.svg">
</a>
<a href="https://zenodo.org/badge/latestdoi/777128102">
<img alt="doi" src="https://zenodo.org/badge/777128102.svg">
</a>
<br/>
</p>
:::

:::{grid-item-card} Variational data assimilation with deep prior (CIRC23)
:margin: 3 0 0 0
:link: ./gallery/39d9c177-11da-41b2-9b64-63f4c1c834b3/notebook.html
Expand Down Expand Up @@ -100,7 +136,7 @@ Malhotra *et al.* (2023)
<a href="https://github.com/eds-book-gallery/3286b92f-4fae-4cc6-a29e-e408bc844542/blob/main/LICENSE">
<img alt="license" src="https://img.shields.io/badge/license-MIT-yellow.svg">
</a>
<a href="http://mybinder.org/v2/gh/eds-book-gallery/3286b92f-4fae-4cc6-a29e-e408bc844542/postprint?labpath=notebook.ipynb">
<a href="http://mybinder.org/v2/gh/eds-book-gallery/3286b92f-4fae-4cc6-a29e-e408bc844542/main?labpath=notebook.ipynb">
<img alt="binder" src="https://mybinder.org/badge_logo.svg">
</a>
<a href="https://github.com/eds-book-gallery/3286b92f-4fae-4cc6-a29e-e408bc844542/actions/workflows/render.yaml">
Expand Down Expand Up @@ -221,7 +257,7 @@ Lam *et al.* (2022)
</p>
:::

:::{grid-item-card} Sea ice forecasting <br> (IceNet)
:::{grid-item-card} Monthly sea ice forecasting <br> (IceNet)
:margin: 3 0 0 0
:link: ./gallery/ac327c3a-5264-40a2-8c6e-1e8d7c4b37ef/notebook.html
:link-type: url
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13 changes: 2 additions & 11 deletions book/publishing/guidelines/guidelines-eic.md
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Expand Up @@ -30,12 +30,7 @@ Before moving to PRE-REVIEW, EiC open a new issue `Preparation` in the notebook
```

## Pre-review
EiC open a PRE-REVIEW issue containing all relevant information of the notebook including a link to the notebook idea issue.

Copy and paste the markdown below in the issue:

```{include} ../../templates/editor-in-chief/eic-prereview-template.md
```
EiC open a [PRE-REVIEW issue](https://github.com/alan-turing-institute/environmental-ds-book/issues/new?assignees=&labels=prereview&projects=&template=prereview-template.md&title=%5BPRE+REVIEW%5D) containing all relevant information of the notebook including a link to the notebook idea issue.

EiC assign an editor to moderate the review and find reviewers.

Expand All @@ -47,11 +42,7 @@ After the editor acceptance, EiC will update the heading at the top of the issue
Once reviewers agreed on the revision, EiC open a REVIEW issue.

## Review
The REVIEW issue aims to be a space where editor will moderate timings and conversation between authors and reviewers.
EiC open it and replace the default first comment the markdown template below:

```{include} ../../templates/editor-in-chief/eic-review-template.md
```
The [REVIEW issue](https://github.com/alan-turing-institute/environmental-ds-book/issues/new?assignees=&labels=review&projects=&template=review-template.md&title=%5BREVIEW%5D) aims to be a space where editor will moderate timings and conversation between authors and reviewers.

To facilitate the discussion, EiC creates a new branch `review` to add reviewers info (name, affiliation, GitHub handle) in the contribution section of the notebook.
Then EiC commit and push changes to create a PR in the notebook repository.
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68 changes: 31 additions & 37 deletions misc/rohub/register.py
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# metadata
metadata_contribution = {
'environment': 'ocean',
'environment': 'polar',
'topic': 'modelling',
'reponame': '39d9c177-11da-41b2-9b64-63f4c1c834b3',
'title': "Variational data assimilation with deep prior (CIRC23)",
'inputs': {'input1':{'name':'Codebase of the reproduced paper',
'url':'https://github.com/ArFiloche/Deepprior4DVar_CI22'},
'reponame': '67a1e320-7c47-4ea9-8df8-e868326bc90b',
'title': "Sea ice forecasting using the IceNet library",
'inputs': {'input1':{'name':'Codebase of the IceNet library',
'url':'https://github.com/icenet-ai/icenet/'},
},
'outputs': {'content': 'figures, models and results',
'url': "https://doi.org/10.5281/zenodo.8338556"},
'outputs': {'content': 'results',
'url': "https://doi.org/10.5281/zenodo.12612126"},
'author_GHuser': 'eds-book-gallery',
'references':{'ref1':{'name':'Deep prior in variational assimilation to estimate an ocean circulation without explicit regularization',
'url':"http://doi.org/10.1017/eds.2022.31"}},
'sketch': {'title':'Image showing an example of the estimated motion fields with various algorithms',
'path':'_temp/rohub/39d9c177-11da-41b2-9b64-63f4c1c834b3/plot.png'}
'references':{'ref1':{'name':'Seasonal Arctic sea ice forecasting with probabilistic deep learning',
'url':"https://doi.org/10.1038/s41467-021-25257-4"}},
'sketch': {'title':'Image showing an example of the forecasted sea ice',
'path':'_temp/rohub/67a1e320-7c47-4ea9-8df8-e868326bc90b/plot.png'}
}

title_nb = metadata_contribution['title']
Expand All @@ -48,40 +48,34 @@
# edition
authors=[
{"agent_type": "user",
"display_name": "Mukulika Pahari",
"name": "Mukulika Pahari",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "University of Mumbai"},
"display_name": "Bryn Noel Ubald",
"name": "Bryn Noel Ubald",
"email": "[email protected]",
"orcid_id": "0000-0002-0206-7140",
"affiliation": "British Antarctic Survey"},
{"agent_type": "user",
"display_name": "Rutika Bhoir",
"name": "Rutika Bhoir",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "University of Mumbai"},
"display_name": "James Byrne",
"name": "James Byrne",
"email": "[email protected]",
"orcid_id": "0000-0003-3731-2377",
"affiliation": "British Antarctic Survey"},
]

ro.set_authors(agents=authors)

reviewers=[
{"agent_type": "user",
"display_name": "Tina Odaka",
"name": "Tina Odaka",
"email": "[email protected]",
"orcid_id": "0000-0002-1500-0156",
"affiliation": "Ifremer"},
"display_name": "Wei Ji",
"name": "Wei Ji",
"email": "[email protected]",
"orcid_id": "0000-0003-2354-1988",
"affiliation": "Development Seed"},
{"agent_type": "user",
"display_name": "Caroline Arnold",
"name": "Caroline Arnold",
"email": "[email protected]",
"orcid_id": "0000-0002-9458-1517",
"affiliation": "German Climate Computing Center"},
{"agent_type": "user",
"display_name": "Paolo Pelucchi",
"name": "Paolo Pelucchi",
"email": "[email protected]",
"orcid_id": None,
"affiliation": "Universitat de València"},
"display_name": "William Gregory",
"name": "William Gregory",
"email": "[email protected]",
"orcid_id": "0000-0001-8176-1642",
"affiliation": "Princeton University"},
]

ro.set_contributors(agents=reviewers)
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