Merge branch 'main' into STEMMUS_SCOPE_PG

.github/workflows/doc_deploy.yml

@@ -0,0 +1,27 @@
+# Deploy documentation when push to main
+
+name: Deploy docs
+
+on:
+  push:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r docs/requirements.txt
+      - name: Deploy docs
+        run: mkdocs gh-deploy --force

.github/workflows/lint.yml

@@ -32,3 +32,5 @@ jobs:
         run: mh_lint src/ --brief
       - name: Check style against standards
         run: mh_style src/ --brief
+      - name: Check global and persistent variables
+        run: mh_metric src/ --brief --ci

CHANGELOG.md

@@ -1,9 +1,27 @@
 # Unreleased
 
+**Added:**
+
+- Documentation using mkdocs and a github action workflow to publish the
+  documentation in [#264](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/264)
+
 **Changed:**
 
+<a name="1.6.1"></a>
+# [1.6.1](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.6.1) - 26 Sep 2024
+
+The 1.6.1 release comes with minor changes as:
 
 **Fixed:**
+- The bug in the calculation of the soil type index discussed in
+  [#252](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/252)
+- The EVAP is removed discussed in [#274](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/274) and fixed in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
+- The shape of Evap variable is changed to match BMI requirements discussed in [#274](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/274) and fixed in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
+
+**Added:**
+- The recharge index is exposed to BMI in [#257](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/257)
+- The Trap variable (after changing its shape) is exposed to BMI discussed in [#271](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/271) and added in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
+- The FullCSVfiles option is added in [#273](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/273)
 
 
 <a name="1.6.0"></a>
@@ -41,7 +59,7 @@ as well as various bugfixes.
 - Defining the indices of the first four layers discussed in
   [#237](https://github.com/EcoExtreML/STEMMUS_SCOPE/issues/237) and fixed in
   [#238](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/238)
-  
+
 <a name="1.5.0"></a>
 # [1.5.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.5.0) - 3 Jan 2024
 

README.md

@@ -3,44 +3,21 @@
 Integrated code of SCOPE and STEMMUS.
 
 SCOPE is a radiative transfer and energy balance model, and STEMMUS model is a two-phase mass and heat transfer model. For more information about the coupling between these two models, please check [this reference](https://gmd.copernicus.org/articles/14/1379/2021/). Before running the model, you need to prepare input data and a configuration file. This can be done using the python package
-[PyStemmusScope](https://pystemmusscope.readthedocs.io).  
+[PyStemmusScope](https://pystemmusscope.readthedocs.io).
 
 ![img](https://raw.githubusercontent.com/EcoExtreML/STEMMUS_SCOPE/main/docs/assets/imgs/coupling_scheme.png)
 (by Zeng & Su, 2021)
 
-## Running STEMMUS_SCOPE
-
-```mermaid
-flowchart LR
-  subgraph Platform
-    direction RL
-    b[Snellius]
-    c[CRIB]
-    d[Your own machine]
-  end
-  A(Data)
-  Platform --> A
-  B(Config file)
-  A --> B
-  C{{Run model}}
-  B --> C
-  click b "https://github.com/EcoExtreML/STEMMUS_SCOPE/tree/main/docs/STEMMUS_SCOPE_on_Snellius.md" "Run STEMMUS_SCOPE on Snellius" _blank
-  click c "https://github.com/EcoExtreML/STEMMUS_SCOPE/tree/main/docs/STEMMUS_SCOPE_on_CRIB.md" "Run STEMMUS_SCOPE on CRIB" _blank
-  click d "https://github.com/EcoExtreML/STEMMUS_SCOPE/tree/main/docs/STEMMUS_SCOPE_on_local_device.md" "Run STEMMUS_SCOPE on your own machine" _blank
-```
-About how to run `STEMMUS_SCOPE` on Snellius, check [./docs/STEMMUS_SCOPE_on_Snellius.md](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/docs/STEMMUS_SCOPE_on_Snellius.md).
-
-If you want to run `STEMMUS_SCOPE` on CRIB, check [./docs/STEMMUS_SCOPE_on_CRIB.md](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/docs/STEMMUS_SCOPE_on_CRIB.md).
-
-If you want to run `STEMMUS_SCOPE` on your own machine, check [./docs/STEMMUS_SCOPE_on_local_device.md](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/docs/STEMMUS_SCOPE_on_local_device.md).
-
-`STEMMUS_SCOPE` scope also has a Basic Model Interface (BMI) mode implemented. The full BMI is implemented in Python in [PyStemmusScope](https://github.com/EcoExtreML/STEMMUS_SCOPE_Processing/). For more information, check [./docs/STEMMUS_SCOPE_BMI.md](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/docs/STEMMUS_SCOPE_BMI.md).
+## Documentation
+
+The documentation of the STEMMUS_SCOPE model can be found [here](https://ecoextreml.github.io/STEMMUS_SCOPE/).
 
 ## Contributing
 
 If you want to contribute to the development of `STEMMUS_SCOPE`,
 have a look at the [contribution guidelines](https://github.com/EcoExtreML/STEMMUS_SCOPE/blob/main/CONTRIBUTING.md).
 
 ## How to cite us
+
 [![RSD](https://img.shields.io/badge/rsd-ecoextreml-00a3e3.svg)](https://research-software-directory.org/projects/ecoextreml)
 <!-- [![DOI](https://zenodo.org/badge/DOI/<replace-with-created-DOI>.svg)](https://doi.org/<replace-with-created-DOI>) -->