Fix bug in profiling code and create profiling CI

.github/workflows/pyrealm_profiling_without_benchmarking.yaml

@@ -0,0 +1,43 @@
+name: Profiling without benchmarking
+
+# This runs when a PR is opened, synchronised or reopened
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_call:
+
+jobs:
+  test:
+    uses: ./.github/workflows/pyrealm_ci.yaml
+    secrets: inherit
+
+  profiling:
+    needs: test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        ref: ${{ github.head_ref }}
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+
+    - name: Install Poetry
+      uses: abatilo/[email protected]
+      with:
+        poetry-version: 1.8.2
+
+    - name: Install dependencies and add env vars
+      run: |
+        poetry install
+        sudo apt-get install graphviz
+        calculatedSha=$(git rev-parse --short ${{ github.sha }})
+        echo "COMMIT_SHORT_SHA=$calculatedSha" >> $GITHUB_ENV
+
+    - name: Run the profiling test suite, using time to get peak memory usage
+      id: profiling
+      run: poetry run /usr/bin/time -v pytest -m "profiling" --profile-svg

tests/profiling/pmodel/test_profiling_pmodel.py

@@ -14,12 +14,12 @@ def test_profiling_pmodel(pmodel_profile_data):
 
     # Profiling the PModel submodule
     # Standard C3 PModel
-    pmod_c3 = PModel(env=pm_env, kphio=1 / 8)
+    pmod_c3 = PModel(env=pm_env, reference_kphio=1 / 8)
     pmod_c3.estimate_productivity(fapar=fapar, ppfd=ppfd)
     pmod_c3.summarize()
 
     # Standard C4 PModel
-    pmod_c4 = PModel(env=pm_env, kphio=1 / 8, method_optchi="c4")
+    pmod_c4 = PModel(env=pm_env, reference_kphio=1 / 8, method_optchi="c4")
     pmod_c4.estimate_productivity(fapar=fapar, ppfd=ppfd)
     pmod_c4.summarize()