Merge pull request #244 from alan-turing-institute/add-nb-icenet-library

Notebook - Sea ice forecasting using the IceNet library
alan-turing-institute · Jul 3, 2024 · 4848da8 · 4848da8
2 parents b5afe33 + 2b0f127
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diff --git a/.gitmodules b/.gitmodules
@@ -50,3 +50,7 @@
 	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
diff --git a/book/_bibliography/references.bib b/book/_bibliography/references.bib
@@ -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
@@ -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}
+}
diff --git a/book/_toc.yml b/book/_toc.yml
@@ -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
@@ -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

diff --git a/book/notebooks/gallery.md b/book/notebooks/gallery.md
@@ -5,6 +5,42 @@
 ::::{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
@@ -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">
@@ -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

diff --git a/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b b/book/notebooks/gallery/67a1e320-7c47-4ea9-8df8-e868326bc90b
diff --git a/book/publishing/guidelines/guidelines-eic.md b/book/publishing/guidelines/guidelines-eic.md
@@ -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.
 
@@ -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. 

diff --git a/misc/rohub/register.py b/misc/rohub/register.py
@@ -10,20 +10,20 @@
 
 # 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']
@@ -48,40 +48,34 @@
 # edition
 authors=[
         {"agent_type": "user",
-         "display_name": "Mukulika Pahari",
-         "name": "Mukulika Pahari",
-         "email": "mukulikapahari@gmail.com",
-         "orcid_id": None,
-         "affiliation": "University of Mumbai"},
+         "display_name": "Bryn Noel Ubald",
+         "name": "Bryn Noel Ubald",
+         "email": "bryald@bas.ac.uk",
+         "orcid_id": "0000-0002-0206-7140",
+         "affiliation": "British Antarctic Survey"},
         {"agent_type": "user",
-         "display_name": "Rutika Bhoir",
-         "name": "Rutika Bhoir",
-         "email": "rutikabhoir1316@gmail.com",
-         "orcid_id": None,
-         "affiliation": "University of Mumbai"},
+         "display_name": "James Byrne",
+         "name": "James Byrne",
+         "email": "jambyr@bas.ac.uk",
+         "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": "tina.odaka@ifremer.fr",
-     "orcid_id": "0000-0002-1500-0156",
-     "affiliation": "Ifremer"},
+     "display_name": "Wei Ji",
+     "name": "Wei Ji",
+     "email": "weiji@developmentseed.org",
+     "orcid_id": "0000-0003-2354-1988",
+     "affiliation": "Development Seed"},
     {"agent_type": "user",
-     "display_name": "Caroline Arnold",
-     "name": "Caroline Arnold",
-     "email": "arnold@dkrz.de",
-     "orcid_id": "0000-0002-9458-1517",
-     "affiliation": "German Climate Computing Center"},
-    {"agent_type": "user",
-     "display_name": "Paolo Pelucchi",
-     "name": "Paolo Pelucchi",
-     "email": "paolo.pelucchi@uv.es",
-     "orcid_id": None,
-     "affiliation": "Universitat de València"},
+     "display_name": "William Gregory",
+     "name": "William Gregory",
+     "email": "wg4031@princeton.edu",
+     "orcid_id": "0000-0001-8176-1642",
+     "affiliation": "Princeton University"},
         ]
 
 ro.set_contributors(agents=reviewers)