Merge remote-tracking branch 'origin/main' into wflow.jl

.github/workflows/ci.yml → .github/workflows/openapi.yml

@@ -1,12 +1,18 @@
-name: Validate OpenAPI
+name: Validate OpenAPI.yaml
 
 on:
   push:
     paths:
       - "openapi.yaml"
-  pull_request:
+      - .github/workflows/openapi.yml
+  pull_request_target:
     paths:
       - "openapi.yaml"
+      - .github/workflows/openapi.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   lintspec:
@@ -38,19 +44,3 @@ jobs:
 
       - name: Yamllint
         run: yamllint openapi.yaml
-
-  python:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-      - name: Setup Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-          cache: "pip"
-      - name: Install ruff
-        run: pip install ruff
-      - name: Run ruff
-        run: ruff check python/remotebmi

.github/workflows/python.yml

@@ -0,0 +1,56 @@
+name: Python
+
+on:
+  push:
+    paths:
+      - "openapi.yaml"
+      - "python/remotebmi/**"
+      - "python/tests/**"
+      - .github/workflows/python.yml
+  pull_request_target:
+    paths:
+      - "openapi.yaml"
+      - "python/remotebmi/**"
+      - "python/tests/**"
+      - .github/workflows/python.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    working-directory: python
+
+jobs:
+  lint-format:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - name: Install ruff
+        run: pip install ruff
+      - name: Run ruff check
+        run: ruff check
+      - name: Run ruff format
+        run: ruff format --check
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: "pip"
+      - name: Install dependencies
+        run: pip install -e .[dev]
+      - name: Run tests
+        run: pytest tests

.github/workflows/r.yml

@@ -0,0 +1,65 @@
+name: R
+
+on:
+  push:
+    paths:
+      - "R/remotebmi/**"
+      - .github/workflows/r.yml
+  pull_request_target:
+    paths:
+      - "R/remotebmi/**"
+      - .github/workflows/r.yml
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  id-token: write # This is required for requesting the JWT
+
+jobs:
+  r:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck, any::covr, any::xml2
+          needs: check, coverage
+          working-directory: R/remotebmi
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: R/remotebmi
+      - name: Test coverage
+        working-directory: R/remotebmi
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./R/remotebmi/cobertura.xml
+          plugin: noop
+          disable_search: true
+          use_oidc: true
+      - name: Show testthat output
+        if: always()
+        run: |
+            ## --------------------------------------------------------------------
+            find '${{ runner.temp }}/R/remotebmi/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+            name: coverage-test-failures
+            path: ${{ runner.temp }}/R/remotebmi/package

.gitignore

@@ -30,4 +30,6 @@ python/heat.toml
 RemoteBMI.jl/example/Project.toml
 RemoteBMI.jl/example/heat.toml
 openapi-generator-cli.jar
-openapitools.json
+openapitools.json
+PEQ_Hupsel.dat
+walrus.yml

CONTRIBUTING.md

@@ -1,5 +1,11 @@
 # Contributing
 
+## AI Assistance
+
+The documentation/software code in this repository can and has been partly generated and/or refined using
+GitHub CoPilot. All AI-output has been verified for correctness,
+accuracy and completeness, adapted where needed, and approved by the author.
+
 ## Add another language
 
 A directory of the name of the language should be created in the root of the repository.

R/remotebmi/.Rbuildignore

@@ -0,0 +1 @@
+^LICENSE\.md$

R/remotebmi/DESCRIPTION

@@ -0,0 +1,21 @@
+Package: remotebmi
+Title: BMI over http
+Version: 0.0.0.9000
+Authors@R: 
+    person("Stefan", "Verhoeven", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "https://orcid.org/0000-0002-5821-2060"))
+Description: Runs a BMI model as a http json web service.
+URL: https://github.com/eWaterCycle/remotebmi
+License: Apache License (>= 2)
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports: 
+    fiery,
+    reqres,
+    routr
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+Remotes:
+    eWaterCycle/bmi-r