Merge pull request #6 from pmlmodelling/merge_from_public

Merge from public
pmlmodelling · Jul 22, 2024 · 384950f · 384950f
2 parents 48724b8 + 70cf437
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,10 @@
+#### Description of Work
+
+Fixes
+
+#### Testing Instructions
+
+1.
+2.
+3.
+
diff --git a/.github/workflows/ersem.yml b/.github/workflows/ersem.yml
@@ -41,11 +41,11 @@ jobs:
           with:
               python-version: '3.x'
         - name: Installing GOTM-FABM-ERSEM dependences
-          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -b $BRANCH -f '-DCMAKE_Fortran_FLAGS="-fcheck=all"'
         - name: Running tutorial
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-tut-config-setup.sh
@@ -70,7 +70,7 @@ jobs:
         - name: Building and installing FABM0d-GOTM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh -b $BRANCH
+              ./github-actions/fabm0d-gotm-ersem/fabm0d-gotm-ersem-build.sh -b $BRANCH -f '-DCMAKE_Fortran_FLAGS="-fcheck=all"'
         - name: Running tutorial
           run: |
               ./github-actions/fabm0d-gotm-ersem/aquarium-tut-config-setup.sh
@@ -90,11 +90,11 @@ jobs:
           with:
               python-version: '3.x'
         - name: Installing GOTM-FABM-ERSEM dependences
-          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh 
+          run: ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-dep-debian.sh
         - name: Building and installing GOTM-FABM-ERSEM
           run: |
               BRANCH=${{ github.head_ref }}
-              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg"" -b $BRANCH
+              ./github-actions/gotm-fabm-ersem/gotm-fabm-ersem-build.sh -f "-DCMAKE_Fortran_FLAGS="-pg -fcheck=all"" -b $BRANCH
         - name: Running config
           run: |
               ./github-actions/gotm-fabm-ersem/gotm-profiling.sh

diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,6 @@ docs/source/module_index.rst
 
 # the ERSEM setups repo should be cloned each time
 docs/source/ersem-setups
+
+# removing vscode files
+.vscode
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,6 +5,12 @@
 # Required
 version: 2
 
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
@@ -15,6 +21,7 @@ formats:
    - pdf
 
 python:
-  version: 3.8
   install:
   - requirements: docs/requirements.txt
+  - method: pip
+    path: .
diff --git a/README.md b/README.md
@@ -1,23 +1,31 @@
-![Tests](https://github.com/pmlmodelling/ersem/workflows/build-ersem/badge.svg) 
+![Tests](https://img.shields.io/github/actions/workflow/status/pmlmodelling/ersem/ersem.yml?label=tests&style=flat-square) 
 [![Documentation Status](https://readthedocs.org/projects/ersem/badge/?version=latest)](https://ersem.readthedocs.io/en/latest/?badge=latest)
 
 # ERSEM
 
 ![ERSEM diagram](docs/images/ERSEM.png)
 
-[ERSEM](http://ersem.com) is a marine ecosystem model. It describes the
-biogeochemical cycling of carbon, nitrogen, phosphorus, silicon, oxygen and
-iron through pelagic and benthic ecosystems. 
+[ERSEM](http://ersem.com) is a marine biogeochemical and ecosystem model. It describes the
+cycling of carbon, nitrogen, phosphorus, silicon, oxygen and iron through 
+the lower trophic level pelagic and benthic ecosystems. 
 
 - **Installation Instructions:** conda: https://ersem.readthedocs.io/en/latest/tutorials/index.html#conda-installation, source: https://ersem.readthedocs.io/en/latest/developers/index.html
 - **User Documentation & Example Usage:** https://ersem.readthedocs.io/en/latest/
 - **Automated Tests:** Run via GitHub Actions https://github.com/pmlmodelling/ersem/actions
 - **Acknowledgements:** https://ersem.readthedocs.io/en/latest/acknowledgements.html
 - **License:** https://ersem.readthedocs.io/en/latest/license.html
 
+# Support
+
+We strongly encourage everyone using the ERSEM code to register as a user by filling a
+[short registration form](https://forms.office.com/r/X0iXv8AvTC). 
+We’d love to get a better understanding of who is using the ERSEM code and for what 
+applications, as it will help us to provide the best support to the user community. 
+It will also allow you to receive information and news on the latest model developments.
+
 # How to cite
 
-If you would like to refer to ERSEM in publications, please cite:
+To refer to ERSEM in publications, please cite:
 
 Butenschön, M., Clark, J., Aldridge, J.N., Allen, J.I., Artioli, Y.,
 Blackford, J., Bruggeman, J., Cazenave, P., Ciavatta, S., Kay, S., Lessin, G.,
@@ -27,9 +35,7 @@ biogeochemistry and the ecosystem dynamics of the lower trophic levels.
 Geoscientific Model Development, 9(4), 1293–1339.
 doi: [10.5194/gmd-9-1293-2016](https://doi.org/10.5194/gmd-9-1293-2016).
 
-If you would like to refer to the ERSEM source code, you can do so by its Zenodo DOI:
+To refer specifically to the ERSEM source code, you may use its Zenodo DOI:
 
 [![DOI](https://zenodo.org/badge/302390544.svg)](https://zenodo.org/badge/latestdoi/302390544)
 
-To refer to the ERSEM website, please use <http://ersem.com>.
-
diff --git a/docs/images/C1D_PAPA_ERSEM_plots.png b/docs/images/C1D_PAPA_ERSEM_plots.png
diff --git a/docs/images/N1_p_NEMO.png b/docs/images/N1_p_NEMO.png
diff --git a/docs/images/N3_n_NEMO.png b/docs/images/N3_n_NEMO.png
diff --git a/docs/images/O2_o_NEMO.png b/docs/images/O2_o_NEMO.png
diff --git a/docs/images/O3_c_NEMO.png b/docs/images/O3_c_NEMO.png
diff --git a/docs/images/P1_Chl_NEMO.png b/docs/images/P1_Chl_NEMO.png
diff --git a/docs/images/R6_c_NEMO.png b/docs/images/R6_c_NEMO.png
diff --git a/docs/images/pyfabm_fig.png b/docs/images/pyfabm_fig.png
diff --git a/docs/images/sal_NEMO.png b/docs/images/sal_NEMO.png
diff --git a/docs/images/temp_NEMO.png b/docs/images/temp_NEMO.png
diff --git a/docs/source/developers/gotm-dev.rst b/docs/source/developers/gotm-dev.rst
@@ -19,8 +19,7 @@ To install GOTM-FABM-ERSEM, we suggest you use the following script below
     :linenos:
 
 
-If you experience NetCDF issues when running ``make install``, see `tips
-and tricks/troubleshooting <#tips-and-trickstroubleshooting>`__.
+If you experience NetCDF issues when running ``make install``, see :ref:`trouble`.
 
 Now you should have a GOTM executable with FABM and ERSEM support at
 ``~/local/gotm/bin/gotm``.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -23,9 +23,9 @@ Welcome to ERSEM's documentation!
    ERSEM tutorials <tutorials/index>
    troubleshooting
    developers/index
+   workflow
    module_index
    license
    acknowledgements
-   support
    references
 
diff --git a/docs/source/model_info/description.rst b/docs/source/model_info/description.rst
@@ -1,43 +1,43 @@
 .. _description:
 
 #################
-ERSEM area models
+ERSEM model domains
 #################
 
-ERSEM is used in a variety of different models, the table bellow outlines several
-of these models.
+ERSEM is used in a variety of geographical regions, coupled to different physical (hydrodynamic) models.
+The table bellow outlines several of these setups.
 
 
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| Area                          | Includes       | Spatial Scale                    | Quality (data used) |
-+                               +----------+-----+-----------------------+----------+                     +
-|                               | Hydro    | BGC | Domain                | Res.(km) |                     |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| Water column (GOTM-ERSEM)     | X        | X   | Any                   | N/A      | 4,6,8,14,16,22      |
-|                               |          |     | location              |          |                     |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| Global (NEMO)                 | X        | X   | Global                | 111      | 8,11,19,20,21       |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| North Atlantic (NEMO)         | X        | X   | 205-BON               | 28       | 8,11,19,20,21       |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| North Atlantic (NEMO shelf)   | X        | X   | 20N-80N               | 7        | 8,11,19,20,21       |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| Irish and Celtic Seas (FVCOM) | X        | X   | 41.8-56.8N9, .6-Z.SW  | 3.5      | 7,23,24,25          |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| NW European shelf (NEMO)      |          | X   | 40N-6SN, ZOW-13E      | 7        | 3,8,11,12,13,14,19  |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| NW European shelf (POLCOMS)   | X        | X   | 40N-6SN, 20W-13E      | 10       | 3,8,9,10,11,12,     |
-|                               |          |     |                       |          | 13,14,15,16,17,19   |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| NW European shelf (POLCOMS    | X        | X   | 40N-6S                | 10       | 2,3,8,9,10,12,13,   |
-| + data assimilation)          |          |     | N,ZOW-13E             |          | 14,15,17            |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| AMM7NW European-Baltric-GCOMS | X        | X   | 46.4-63N, 17.SW-13E   | 10       | 3,8,11,14,17,18     |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| WEC                           | X        | X   | 41.5-50.9N, 7.6-1.2SW | 1.9      | 2,4,8,12,13,14      |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
-| WEC (data assimilation)       | X        | X   | 41.5-50.9N, 7.6-1.2SW | 7        | 1,2,4,8,12,13,14    |
-+-------------------------------+----------+-----+-----------------------+----------+---------------------+
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| Area                          |               | Spatial Scale                    | Quality (data used) |
++                               +---------------+-----------------------+----------+                     +
+|                               |               | Domain                | Res.(km) |                     |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| Water column (GOTM-ERSEM)     |               | Various               | N/A      | 4,6,8,14,16,22      |
+|                               |               | locations             |          |                     |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| Global (NEMO)                 |               | Global                | 111      | 8,11,19,20,21       |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| North Atlantic (NEMO)         |               | 20N-8ON               | 28       | 8,11,19,20,21       |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| North Atlantic (NEMO shelf)   |               | 20N-80N               | 7        | 8,11,19,20,21       |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| Irish and Celtic Seas (FVCOM) |               | 41.8-56.8N, 9.6-2.5W  | 3.5      | 7,23,24,25          |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| NW European shelf (NEMO)      |               | 40N-65N, 2OW-13E      | 7        | 3,8,11,12,13,14,19  |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| NW European shelf (POLCOMS)   |               | 40N-65N, 20W-13E      | 10       | 3,8,9,10,11,12,     |
+|                               |               |                       |          | 13,14,15,16,17,19   |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| NW European shelf (POLCOMS    |               | 40N-65N, 20w-13E      | 10       | 2,3,8,9,10,12,13,   |
+| + data assimilation)          |               |                       |          | 14,15,17            |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| AMM7NW European-Baltic-GCOMS  |               | 46.4-63N, 17.5W-13E   | 10       | 3,8,11,14,17,18     |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| Western European Channel (WEC)|               | 48.5-50.9N, 7.6-1.25W | 1.9      | 2,4,8,12,13,14      |
++-------------------------------+---------------+-----------------------+----------+---------------------+
+| WEC (data assimilation)       |               | 48.5-50.9N, 7.6-1.25W | 7        | 1,2,4,8,12,13,14    |
++-------------------------------+---------------+-----------------------+----------+---------------------+
 
 
 Key
@@ -46,36 +46,35 @@ Key
 .. hlist::
     :columns: 3
 
-    - 1. Glocolour ocean colour
+    - 1. GlobColour ocean colour
     - 2. ESA CCI ocean colour
-    - 3. North Sea Project cru1ses
+    - 3. North Sea Project cruises
     - 4. Western Channel Observatory
-    - 5. Tide sauses 
+    - 5. Tide gauges 
     - 6. Smart Buoy data 
     - 7. NCEP reanalysis
     - 8. World Ocean Atlas
-    - 9. ICES temperature andsalinity
+    - 9. ICES temperature and salinity
     - 10. ICES nutrients and chlorophyll
-    - 11. IPCC climate forcing (HADGEMI,PSL, ECHAM)
+    - 11. IPCC climate forcing (HADGEM, IPSL, ECHAM)
     - 12. EA riverine nutrients data 
-    - 13. Europeanriver data
-    - 14. ECMWF reanalysis meteorolosv
-    - 15. DMIreanalysis meteorology
+    - 13. European river data
+    - 14. ECMWF reanalysis meteorology
+    - 15. DMI reanalysis meteorology
     - 16. ESSC ocean reanalysis
     - 17. GLORYS reanalysis
     - 18. GLOBAL NEWS river data
     - 19. GLODAP
     - 20. DFS atmospheric reanalysis
-    - 21. GEM/GLORI river data
+    - 21. GEMS-GLORI river data
     - 22. BATS data
-    - 23. HF Radar and CTD Data.
+    - 23. HF Radar and CTD Data
     - 24. NTSLF data
-    - 25. CEH river discharge and temperature.
+    - 25. CEH river discharge and temperature
 
 
 .. note::
-    The table of area models is not yet complete, please ERSEM's issue
-    tracking for updates.
+    The table of regional setups is not yet complete, please stay tuned for updates.
 
 Existing uses:
 ~~~~~~~~~~~~~~
@@ -89,14 +88,14 @@ Existing uses:
 - **Environmental change:** climate change impacts, ocean acidification, 
   multiple stressors, and sustainable fisheries.
 - Run operationally by the UK Met Office to predict water quality.
-- Estimation of the carbon budget of the UK shelf.
+- Estimation of the carbon and nutrient budgets of the UK shelf.
 
 
 Potential new uses:
 ~~~~~~~~~~~~~~~~~~~
 
 - Understanding shelf seas carbon ("blue carbon") and nutrient budgets 
-  {past and future climate).
+  (past and future climate).
 - Expansion to represent biodiversity-relevant processes over a range 
   of spatial and temporal scales, and simulate changes in function in 
   the context of ecosystem services.

diff --git a/docs/source/support.rst b/docs/source/support.rst
diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst
@@ -22,6 +22,7 @@ Here we describe several tutorials for the common use cases for ERSEM.
    gotm
    fvcom
    nemo
+   nemo1d
 
 .. _conda-install: