Merge branch 'main' into PHS

.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

.github/workflows/publish-container.yml

@@ -0,0 +1,58 @@
+#
+name: Create and publish the STEMMUS_SCOPE container image 📦
+
+on:
+  release:
+    types: [published]
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      # 
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see "[AUTOTITLE](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds)." 
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

CHANGELOG.md

@@ -2,6 +2,27 @@
 
 **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)
+
+**Added:**
+- The recharge index is exposed to BMI in [#257](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/257)
+
+
+<a name="1.6.0"></a>
+# [1.6.0](https://github.com/EcoExtreML/STEMMUS_SCOPE/releases/tag/1.6.0) - 3 Aug 2024
+
+The 1.6.0 release comes with changes to support groundwater coupling via the Basic Model Interface,
+as well as various bugfixes.
+
+**Changed:**
+
 - Added changes to support groundwater coupling via BMI in
   [#221](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/221) and
   [#234](https://github.com/EcoExtreML/STEMMUS_SCOPE/pull/234)

Dockerfile

@@ -1,16 +1,17 @@
 FROM demartis/matlab-runtime:R2023a@sha256:9d6b3acd29b974ca0a0c77eca09a34488dcece290c8a4bd04dafaa7c4a5665b2
 LABEL maintainer="Bart Schilperoort <[email protected]>"
-LABEL org.opencontainers.image.source = "https://github.com/EcoExtreML/STEMMUS_SCOPE"
+LABEL org.opencontainers.image.source="https://github.com/EcoExtreML/STEMMUS_SCOPE"
 
-RUN wget https://github.com/EcoExtreML/STEMMUS_SCOPE/raw/main/run_model_on_snellius/exe/STEMMUS_SCOPE --no-check-certificate
+#RUN wget https://github.com/EcoExtreML/STEMMUS_SCOPE/raw/main/run_model_on_snellius/exe/STEMMUS_SCOPE --no-check-certificate
+COPY run_model_on_snellius/exe/STEMMUS_SCOPE ./STEMMUS_SCOPE
 
 # Make sure the file is executable
 RUN chmod +x ./STEMMUS_SCOPE
 
 # Allow MCR to have a cache directory which all users can access
 RUN mkdir /temp/
 RUN chmod 777 /temp/
-ENV MCR_CACHE_ROOT /temp/
+ENV MCR_CACHE_ROOT=/temp/
 
 CMD ./STEMMUS_SCOPE "" bmi
 # Build the image with: `docker build . -t stemmus_scope`

miss_hit.cfg

@@ -4,3 +4,11 @@ suppress_rule: "naming_functions"
 suppress_rule: "naming_parameters"
 suppress_rule: "naming_scripts"
 suppress_rule: "operator_after_continuation"
+metric "globals": limit 0
+metric "persistent": limit 0
+metric "file_length": disable
+metric "function_length": disable
+metric "npath": disable
+metric "cnest": disable
+metric "parameters": disable
+metric "cyc": disable

src/+groundwater/calculateGroundwaterRecharge.m

@@ -103,13 +103,14 @@ soilThick               cumulative soil layers thickness (from top to bottom)
         warning('Index of the bottom layer boundary that includes groundwater head ~= index of the recharge layer + 1!');
     end
 
-    % Outputs to be exported in csv
+    % Outputs to be exported in csv or exposed to BMI
     gwfluxes.QLh = QLh_flip(indxRchrg);
     gwfluxes.QLT = QLT_flip(indxRchrg);
     gwfluxes.QLa = QLa_flip(indxRchrg);
     gwfluxes.QVH = QVH_flip(indxRchrg);
     gwfluxes.QVT = QVT_flip(indxRchrg);
     gwfluxes.QVa = QVa_flip(indxRchrg);
+    gwfluxes.indxRchrg = indxRchrg;
     % gwfluxes.recharge_init = recharge_init;
     % gwfluxes.S = S;
     % gwfluxes.sy = sy;

src/STEMMUS_SCOPE.m

@@ -807,6 +807,7 @@
             end
         else
             gwfluxes.recharge = 0;
+            gwfluxes.indxRchrg = NaN;
         end
 
         % set SoilVariables for the rest of the loop