Merge branch 'develop' into feature/new_abiotic_model

.github/workflows/ci.yml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - uses: pre-commit/[email protected]
 
   test:
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ "3.9" , "3.10", "3.11" ]
+        python-version: [ "3.10", "3.11" ]
 
     steps:
     - uses: actions/checkout@v3
@@ -40,7 +40,7 @@ jobs:
       run: poetry run pytest --cov-report xml
 
     - name: Upload coverage to Codecov
-      if: (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9')
+      if: (matrix.os == 'ubuntu-latest' && matrix.python-version == '3.10')
       uses: codecov/codecov-action@v3
 
   docs_build:
@@ -50,7 +50,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
       - name: Install Poetry
         uses: abatilo/[email protected]

.pre-commit-config.yaml

@@ -27,3 +27,8 @@ repos:
     rev: v0.33.0
     hooks:
     - id: markdownlint
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.13.0
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]

docs/source/conf.py

@@ -110,6 +110,10 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "virtual_rainforest.models.abiotic.energy_balance.EnergyBalance"),
     # Something off about JSONSchema intersphinx mapping?
     ("py:obj", "virtual_rainforest.core.schema.ValidatorWithDefaults.ID_OF"),
+    # HACK - sphinx seems to thing GRID_STRUCTURE_SIG is a tuple not a type alias
+    ("py:obj", "virtual_rainforest.core.grid.GRID_STRUCTURE_SIG.__repr__"),
+    ("py:obj", "virtual_rainforest.core.grid.GRID_STRUCTURE_SIG.count"),
+    ("py:obj", "virtual_rainforest.core.grid.GRID_STRUCTURE_SIG.index"),
 ]
 intersphinx_mapping = {
     "numpy": ("https://numpy.org/doc/stable/", None),

docs/source/data_recipes/CDS_toolbox_template.md

@@ -22,9 +22,11 @@ of the Virtual Rainforest. This document describes how to download climate data
 the Copernicus [Climate Data Store](https://cds.climate.copernicus.eu/) (CDS) and basic
 pre-processing options using the
 [CDS toolbox](https://cds.climate.copernicus.eu/cdsapp#!/toolbox).
-At present, the pre-processing does not include scaling or topographic adjustment.
+You need to create a user account to access all data and functionalities.
 
-NOTE: You need to create a user account to access all data and functionalities.
+```{note}
+At present, the pre-processing does not include scaling or topographic adjustment.
+```
 
 ## Climate input variables
 
@@ -33,7 +35,7 @@ variables (or derivatives) at each time step (default: monthly means):
 
 * Air temperature (typically 2m; mean, minimum, and maximum)
 * Air humidity (typically 2m; relative or specific humidity)
-* Air pressure (typically mean sealevel or surface pressure)
+* Air pressure (typically mean sea level or surface pressure)
 * Wind speed (typically 10m)
 * Precipitation
 
@@ -63,12 +65,15 @@ simulations:
 
   ERA5-Land is a reanalysis dataset providing a consistent view of the evolution of land
   variables over several decades at an enhanced resolution compared to ERA5 (0.1 x 0.1
-  deg resolution).
+  deg).
 
   The full documentation and download link can be accessed
   [here for hourly data](https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land?tab=overview)
   and [here for monthly data](https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-land-monthly-means?tab=overview)
 
+  Example code to manipulate downloaded ERA5-Land data as used in the `vr_run` example
+  is available [here](../../../virtual_rainforest/example_data/generation_scripts/climate_example_data.py).
+
 * WFDE5
 
   This global dataset provides bias-corrected reconstruction of near-surface
@@ -77,7 +82,9 @@ simulations:
   available in hourly and daily time steps for the period 1979-2019 in 0.5 x 0.5 deg
   resolution.
 
-  The full documentation and download link can be accessed [here](https://cds.climate.copernicus.eu/cdsapp#!/dataset/derived-near-surface-meteorological-variables?tab=overview).
+  The full documentation and download link can be accessed
+  [here](https://cds.climate.copernicus.eu/cdsapp#!/dataset/derived-near-surface-meteorological-variables?tab=overview)
+  .
 
 * CORDEX-SEA
 
@@ -90,15 +97,15 @@ simulations:
 
   The full documentation and download link can be accessed [here](https://cds.climate.copernicus.eu/cdsapp#!/dataset/projections-cordex-domains-single-levels?tab=overview).
 
-* Atmospheric CO2
+* Atmospheric $\ce{CO_{2}}$
 
-  Observed global CO2 levels (Mauna Loa, NOAA/GML) are available in monthly or annual
-  resolution (1958 - present) [here](https://gml.noaa.gov/ccgg/trends/graph.html).
-  Monthly data derived from satellite observation (2002 - present) is available
+  Observed global $\ce{CO_{2}}$ levels (Mauna Loa, NOAA/GML) are available in monthly or
+  annual resolution (1958 - present) [here](https://gml.noaa.gov/ccgg/trends/graph.html)
+  .  Monthly data derived from satellite observation (2002 - present) is available
   [here](https://cds.climate.copernicus.eu/cdsapp#!/dataset/satellite-carbon-dioxide?tab=overview)
-  . Alternatively, reconstructed gridded monthly CO2 data for the historical period
-  (1953 - 2013) and future CMIP6 scenarios (2015 - 2150) can be downloaded
-  [here](https://zenodo.org/record/5021361){cite:p}`cheng_wei_global_2021`.
+  . Alternatively, reconstructed gridded monthly $\ce{CO_{2}}$ data for the historical
+  period (1953 - 2013) and future CMIP6 scenarios (2015 - 2150) can be downloaded
+  [here](https://zenodo.org/record/5021361) {cite:p}`cheng_wei_global_2021`.
 
 ## Step-by-step example
 
@@ -109,7 +116,7 @@ data, navigate to the tab 'Download Data'.
 ### Selection
 
 This is an example of a selection of tabs to download historical '2m air temperature'
-from the CORDEX-SEA:
+from the CORDEX-SEA (you can download multiple variables and years in one request):
 
 * Domain (South-East Asia),
 * Experiment (here: 'historical', RCPs available)
@@ -121,10 +128,12 @@ from the CORDEX-SEA:
 * Ensemble member (r1i1p1)
 * Start year and End year (here: 2001-2005)
 
-Once you selected the data, you can either download the dataset for further processing,
-[see here](./ERA5_preprocessing_example.md) an example of how to manipulate ERA5 data
-using xarray, or click on 'show Toolbox request' at the bottom of the page, copy the
-code, and open the CDS toolbox editor.
+Once you selected the data, you can either download the dataset for further processing
+or click on 'show Toolbox request' at the bottom of the page, copy the code, and open
+the CDS toolbox editor.
+
+The code to manipulate climate data as used in the `vr_run` example is available
+[here](../../../virtual_rainforest/example_data/generation_scripts/climate_example_data.py).
 
 ### Toolbox template CORDEX-SEA