code page and thumbnail fix

content/code/_index.md

@@ -5,7 +5,7 @@ heroSubHeading: 'Public repository and data access'
 heroBackground: '/images/photo-1542831371-29b0f74f9713.jpeg'
 ---
 
-#### Codes
+<!-- #### Codes
 
 Our codes are hosted on our Github [repository](https://github.com/m2lines).
 
@@ -30,4 +30,4 @@ Upcoming codes will be linked to this repository as they become available.
 
 #### Datasets
 
-All of the datasets used in M²LInES publications will be made openly available. When possible, they will be hosted on [Pangeo](https://pangeo.io/)
+All of the datasets used in M²LInES publications will be made openly available. When possible, they will be hosted on [Pangeo](https://pangeo.io/) -->

content/code/cm26.md

@@ -0,0 +1,13 @@
+---
+title: CM2.6
+jobtitle: Dataset
+datasettype: Cloud
+---
+<!-- Datasets: hosted on globus. access e.g.:
+```
+import xarray as xr
+import gcsfs
+fs = gcsfs.GCSFileSystem()
+fs.ls("gs://leap-persistent-ro/groundpepper/GFDL_cm2.6")
+ds = xr.open_dataset('gs://leap-persistent-ro/groundpepper/GFDL_cm2.6/GFDL_CM2_6_CONTROL_DAILY_SURF.zarr', engine='zarr')
+``` -->

content/code/datadrivenparam.md

@@ -0,0 +1,6 @@
+---
+title: Generative data-driven approaches for stochastic subgrid parameterizations
+jobtitle: Ocean Parameterization
+paper: https://arxiv.org/abs/2302.07984
+code: https://github.com/m2lines/pyqg_generative
+---

content/code/diffqg.md

@@ -0,0 +1,6 @@
+---
+title: Differentiable QG model
+jobtitle: Model
+paper: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2022MS003124
+code: https://github.com/hrkz/torchqg
+---

content/code/equationdiscovery.md

@@ -0,0 +1,6 @@
+---
+title: Equation Discovery
+jobtitle: Tutorial
+paper: https://onlinelibrary.wiley.com/doi/abs/10.1029/2022MS003258
+code: https://github.com/m2lines/EquationDisco
+---

content/code/gcm.md

@@ -0,0 +1,8 @@
+---
+title: "GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data"
+draft: false
+jobtitle: Package
+paper: https://joss.theoj.org/papers/10.21105/joss.03947
+Website: https://gcm-filters.readthedocs.io/en/latest/index.html
+code: https://github.com/ocean-eddy-cpt/gcm-filters
+---

content/code/icemodelerrors.md

@@ -0,0 +1,6 @@
+---
+title: Deep learning of systematic sea ice model errors from data assimilation increments
+jobtitle: Sea Ice Parameterization
+paper: https://arxiv.org/abs/2304.03832
+code: https://github.com/m2lines/seaice_DA-ML
+---

content/code/lorenz96.md

@@ -0,0 +1,6 @@
+---
+title: Machine Learning tutorial for Lorenz 96
+jobtitle: Tutorial
+Website: https://m2lines.github.io/L96_demo/intro.html
+code: https://github.com/m2lines/L96_demo
+---

content/code/mom6.md

@@ -0,0 +1,5 @@
+---
+title: Implementation of data-driven parameterizations in MOM6
+jobtitle: Model
+code: https://github.com/NOAA-GFDL/MOM6/pull/356
+---

content/code/momentumforcing.md

@@ -0,0 +1,6 @@
+---
+title: Stochastic parameterization of subgrid momentum forcing
+jobtitle: Ocean Parameterization
+paper: http://onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002534
+code: https://github.com/m2lines/gz21_ocean_momentum
+---

content/code/parampyqg.md

@@ -0,0 +1,6 @@
+---
+title: Implementation of parameterizations in pyqg
+jobtitle: Model
+code: https://github.com/pyqg/pyqg/pull/266
+paper:  https://onlinelibrary.wiley.com/doi/abs/10.1029/2022MS003258
+---

content/code/pyqg.md

@@ -0,0 +1,18 @@
+---
+title: Pyqg parameterization benchmarks
+jobtitle: Dataset
+datasettype: Benchmark
+paper: 'https://onlinelibrary.wiley.com/doi/abs/10.1029/2022MS003258'
+website: 'https://m2lines.github.io/MLwithQG/intro.html'
+code: 'https://github.com/m2lines/pyqg_parameterization_benchmarks'
+---
+
+<!-- Datasets: hosted on globus, access as described [here](https://github.com/m2lines/pyqg_parameterization_benchmarks/blob/master/notebooks/dataset_description.ipynb), e.g.:
+```
+import xarray as xr
+import fsspec
+# Datasets are hosted on globus as zarr files
+def get_dataset(path, base_url="https://g-402b74.00888.8540.data.globus.org"):
+    mapper = fsspec.get_mapper(f"{base_url}/{path}.zarr")
+    return xr.open_zarr(mapper, consolidated=True)
+``` -->

content/code/randomforest.md

@@ -0,0 +1,6 @@
+---
+title: Random forest to learn atmospheric parameterization
+jobtitle: Atmosphere Parameterization
+paper: https://www.nature.com/articles/s41467-020-17142-3
+code: https://github.com/m2lines/subgrid_parameterization
+---

content/code/shallowwater.md

@@ -0,0 +1,6 @@
+---
+title: Stacked shallow water model with stochastic subgrid momentum parameterization
+jobTitle: Model
+code: https://github.com/arthurBarthe/swe_stochastic_param/tree/0.1
+paper: http://onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002534
+---

content/code/subgridatmosphere.md

@@ -0,0 +1,7 @@
+---
+title: Neural Networks for Stable, Accurate and Physically Consistent Parameterization of Subgrid Atmospheric Processes
+jobtitle: Atmosphere Parameterization
+paper: https://onlinelibrary.wiley.com/doi/abs/10.1029/2020GL091363
+code: https://github.com/m2lines/convection-parameterization-in-CAM
+datasetused: https://drive.google.com/drive/folders/1TRPDL6JkcLjgTHJL9Ib_Z4XuPyvNVIyY
+---

content/code/transportatmosphere.md

@@ -0,0 +1,7 @@
+---
+title: Neural-Network Parameterization of Subgrid Momentum Transport in the Atmosphere
+jobtitle: Atmosphere Parameterization
+paper: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2023MS003606
+code: https://github.com/m2lines/momentum_parameterization
+datasetused: https://drive.google.com/drive/folders/1TRPDL6JkcLjgTHJL9Ib_Z4XuPyvNVIyY
+---

content/publications/_index.md

@@ -17,7 +17,7 @@ If you are interested in understanding how M²LInES is using machine learning to
   </div>
   <p>
     <strong>Aakash Sane, Brandon G. Reichl, Alistair Adcroft, Laure Zanna</strong><br>
-    <a href="https://arxiv.org/abs/2304.03832"><strong>Parameterizing vertical mixing coefficients in the Ocean
+    <a href="https://arxiv.org/abs/2306.09045"><strong>Parameterizing vertical mixing coefficients in the Ocean
     Surface Boundary Layer using Neural Networks</strong></a><br>
     <i>ArXiv 2023.</i> <strong>DOI</strong>: 10.48550/arXiv.2306.09045
   </p>

data/code/dataset/CM26.yml

@@ -0,0 +1,11 @@
+name: CM2.6
+type: Cloud
+description: |
+  Datasets: hosted on globus. access e.g.:
+  ```
+  import xarray as xr
+  import gcsfs
+  fs = gcsfs.GCSFileSystem()
+  fs.ls("gs://leap-persistent-ro/groundpepper/GFDL_cm2.6")
+  ds = xr.open_dataset('gs://leap-persistent-ro/groundpepper/GFDL_cm2.6/GFDL_CM2_6_CONTROL_DAILY_SURF.zarr', engine='zarr')
+  ```

data/code/dataset/pyqg.yml

@@ -0,0 +1,16 @@
+name: Pyqg parameterization benchmarks (Ross et al., 2023)
+type: Benchmark
+paper: 'https://onlinelibrary.wiley.com/doi/abs/10.1029/2022MS003258'
+website: 'https://m2lines.github.io/MLwithQG/intro.html'
+# code: 'https://github.com/m2lines/MLwithQG'
+code: 'https://github.com/m2lines/pyqg_parameterization_benchmarks'
+description: |
+  Datasets: hosted on globus, access as described [here](https://github.com/m2lines/pyqg_parameterization_benchmarks/blob/master/notebooks/dataset_description.ipynb), e.g.:
+  ```
+  import xarray as xr
+  import fsspec
+  # Datasets are hosted on globus as zarr files
+  def get_dataset(path, base_url="https://g-402b74.00888.8540.data.globus.org"):
+      mapper = fsspec.get_mapper(f"{base_url}/{path}.zarr")
+      return xr.open_zarr(mapper, consolidated=True)
+  ```

data/code/model/diff_qg.yml

@@ -0,0 +1,3 @@
+name: Differentiable QG model
+paper: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2022MS003124
+code: https://github.com/hrkz/torchqg

data/code/model/shallow_water.yml

@@ -0,0 +1,3 @@
+name: Stacked shallow water model with stochastic subgrid momentum parameterization
+code: https://github.com/arthurBarthe/swe_stochastic_param/tree/0.1
+paper: http://onlinelibrary.wiley.com/doi/abs/10.1029/2021MS002534

data/code/package/gcm_filter.yml

@@ -0,0 +1,4 @@
+name: "GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data"
+paper: https://joss.theoj.org/papers/10.21105/joss.03947
+website: https://gcm-filters.readthedocs.io/en/latest/index.html
+code: https://github.com/ocean-eddy-cpt/gcm-filters

data/code/tutorial/equation_discovery.yml

@@ -0,0 +1,4 @@
+name: Equation Discovery
+jobTitle: Tutorial
+paper: https://onlinelibrary.wiley.com/doi/abs/10.1029/2022MS003258
+code: https://github.com/m2lines/EquationDisco

data/code/tutorial/lorenz96.yml

@@ -0,0 +1,3 @@
+name: Machine Learning tutorial for Lorenz 96
+website: https://m2lines.github.io/L96_demo/intro.html
+code: https://github.com/m2lines/L96_demo

themes/hugo-hero-theme/layouts/code/list.html

@@ -1,27 +1,19 @@
-{{ define "header_css" }}{{ end }}
-{{ define "body_classes" }}page-work-list{{ end }}
+
+
+ {{ define "header_css" }}{{ end }}
+{{ define "body_classes" }}page-team-list{{ end }}
 {{ define "header_classes" }}{{ end }}
 
 {{ define "main" }}
 
 {{ partial "hero-image-setheight.html" (dict "background" .Params.heroBackground "heading" .Params.heroHeading "subheading" .Params.heroSubHeading "content" .)}}
-{{ if .Content }}
-<div class="container pt-6 pt-md-10">
-  <div class="row">
-    <div class="col-12">
-      <div class="page-intro">
-      {{ .Content }}
-    </div>
-    </div>
-  </div>
-</div>
-{{ end }}
 
-<div class="container pb-6 pt-6 pb-md-10 pt-md-10">
-  <div class="row">
-    {{ range .Pages.ByWeight }}
-    <div class="col-12 col-md-6 mb-2 ">{{ .Render "summary" }}</div>
-    {{ end }}
+
+<div class="container">
+  <div class="row  pt-6 pb-6">
+    <!-- {{ range where .Pages.ByWeight ".Params.promoted" "!=" true}} -->
+    <div class="col-12 col-md-6 mb-2">{{ .Render "summary" }}</div>
+    <!-- {{ end }} -->
   </div>
 </div>
 {{ end }}

themes/hugo-hero-theme/layouts/code/summary.html

@@ -1,13 +1,80 @@
-<div class="work work-summary">
-  {{ if .Params.thumbnail }}
-  <div class="work-image">
-    <a href="{{ .RelPermalink }}"><img src="{{ .Params.thumbnail | relURL }}"/></a>
+
+<div class="team team-summary">
+  <div class="team-meta">
+    {{ if .Params.Paper }}
+    <h2 class="team-name"><a target="_blank" href="{{ .Params.Paper }}">{{ .Title }}</a></h2>
+    {{ else }}
+    <h2 class="team-name">{{ .Title }}</h2>
+    {{ end }}
   </div>
-  {{ end }}
-  <div class="work-content">
-    <h2 class="work-title">
-      <a href="{{ .Permalink }}">{{ .Title }}</a>
-    </h2>
-    {{ .Content | truncate 120 "..."  }}
+  <div class="team-content">
+    {{ if or .Params.Jobtitle .Params.Code .Params.Website .Params.Description .Params.Datasetused }}
+    <div class="team-tags">
+      {{ with .Params.Website }}
+        <a href="{{ . }}" target="_blank" class="tag">Website</a>
+      {{ end }}
+      {{ with .Params.Jobtitle }}
+        <span class="tag">{{ . }}</span>
+      {{ end }}
+      {{ with .Params.Datasetused }}
+        <span class="tag">Dataset Used</span>
+      {{ end }}
+      {{ with .Params.Datasettype }}
+        <span class="tag">{{ . }}</span>
+      {{ end }}
+      {{ with .Params.Code }}
+        <a href="{{ . }}" target="_blank" class="tag">Code</a>
+      {{ end }}
+
+
+    </div>
+    <div class="content-text">
+      {{ .Content | markdownify | safeHTML }}
+    </div>
+    {{ end }}
+
   </div>
 </div>
+
+
+<!-- add css below -->
+<style>
+
+.tag {
+  display: inline-block;
+  margin-right: 10px;
+  padding: 2px 6px;
+  background-color: #ffffff;
+  color: #080808;
+  font-size: 15px; /* Adjust font size as needed */
+  border: 1px solid #ffffff00;
+  border-radius: 4px;
+  cursor: pointer;
+  transition: background-color 0.3s, color 0.3s, font-size 0.3s;
+}
+
+.tag:hover {
+  background-color: #080808;
+  color: #ffffff;
+  font-size: 16px; /* Increase font size on hover */
+}
+
+.team-content {
+  /* Set a maximum width for the content */
+  max-width: 90%; /* Adjust as needed */
+
+  /* Allow content to wrap within the div */
+  word-wrap: break-word;
+  overflow-wrap: break-word;
+
+  /* Add scrollbars for content that exceeds the div's dimensions */
+  overflow: auto;
+  /* Optional: Define a maximum height for the div to trigger scrolling */
+  max-height: 300px; /* Adjust as needed */
+}
+
+.content-text {
+  font-size: 14px; /* Adjust the font size as needed */
+}
+
+</style>