added the fenics examples for linear elastic plate with hole benchmark (#70)

* added the fenics examples for linear elastic plate with hole benchmark

* rewritten the CI .yml to remove ambiguity.

* removed comments

Author: div-tyg

.github/workflows/run-benchmark-examples.yml

@@ -0,0 +1,54 @@
+name: Examples-CI
+on:
+  push:
+
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # Runs the workflow once per day at 3:15am
+  schedule:
+    - cron: '3 16 * * *'
+
+env:
+  CACHE_NUMBER: 1  # increase to reset cache manually
+  SNAKEMAKE_RESULT_FILE: metadata4ing_provenance
+  PROVENANACE_FILE_NAME: element_size_vs_max_mises_stress.pdf
+
+jobs:
+  run-examples:
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout repo content
+        uses: actions/checkout@v2
+
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+            miniforge-version: latest
+            activate-environment: model-validation 
+            use-mamba: true
+
+      - name: Set strict channel priority
+        run: conda config --set channel_priority strict
+        
+      - name: Update environment
+        run: mamba env update -n model-validation -f environment_benchmarks.yml
+
+      - name: Run linear-elastic-plate-with-hole using fenics
+        shell: bash -l {0}
+        run: |
+          cd $GITHUB_WORKSPACE/examples/linear-elastic-plate-with-hole/fenics/
+          python run_benchmark.py
+
+      - name: Archive results of the fenics run of linear-elastic-plate-with-hole
+        uses: actions/upload-artifact@v4
+        with:
+            name: snakemake_results_linear-elastic-plate-with-hole
+            path: |
+              examples/linear-elastic-plate-with-hole/fenics/results/
+
+
+

examples/linear-elastic-plate-with-hole/fenics/environment_simulation.yml

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+name: fenics_simulation
+# Environment file for fenics simulation scripts. Called by fenics tool workflow.
+
+channels:
+  - conda-forge
+
+channel_priority: strict
+
+dependencies:
+  - python=3.12
+  - fenics-dolfinx=0.9.*
+  - mpich
+  - petsc4py
+  - pint
+  - python-gmsh
+  - sympy

examples/linear-elastic-plate-with-hole/fenics/run_benchmark.py

@@ -0,0 +1,75 @@
+from pathlib import Path
+import zipfile
+import json
+import shutil
+import subprocess
+
+"""
+The script performs the following steps:
+
+1. Extracts the benchmark files from a zip archive (currently assuming that it is an RO-Crate of the benchmark).
+2. Iterates through the parameter configuration files, checks the "element-size" value, and if it meets the specified condition (>= 0.025)
+, it executes the Snakemake workflow for that configuration.
+
+The results of each run (and the files used by it) are stored in the directory with the configuration name.
+"""
+
+####################################################################################################
+####################################################################################################
+# Benchmark Extraction
+####################################################################################################
+####################################################################################################
+
+root_zipped_benchmark_dir = Path(__file__).resolve().parent.parent
+root_unzipped_benchmark_dir = Path(__file__).resolve().parent
+
+with zipfile.ZipFile(root_zipped_benchmark_dir / "linear-elastic-plate-with-hole.zip", 'r') as zip_ref:
+    # Extract all files
+    zip_ref.extractall(root_unzipped_benchmark_dir)
+    
+    
+#Creates a directory to store the conda environments. The environments are shared across different parameter configurations.
+#To avoid redundant creation of environments, this path will be passed to all snakemake files during execution.
+        
+shared_env_dir = root_unzipped_benchmark_dir / "conda_envs"
+shared_env_dir.mkdir(parents=True, exist_ok=True)  
+
+####################################################################################################
+####################################################################################################
+# Conditional execution of parameter configurations 
+####################################################################################################
+####################################################################################################
+  
+for file in root_unzipped_benchmark_dir.glob("parameters_*.json"):
+    with open(file, "r") as f:
+        data = json.load(f)
+        if data.get("element-size").get("value") >= 0.025:
+            
+            # Create output directory for the configuration
+            output_dir = root_unzipped_benchmark_dir / "results" / data.get("configuration")
+            output_dir.mkdir(parents=True, exist_ok=True) 
+            
+            # Copy the selected parameter file to the output directory with a standardised name
+            with open(output_dir / "parameters.json", "w") as outfile:
+                json.dump(data, outfile, indent=2)
+
+            # Copy files from benchmark_dir to output_dir, excluding non-matching parameter files.
+            for item in root_unzipped_benchmark_dir.iterdir():
+                if item.is_file():
+                    if item.name.startswith("parameters_") and item.suffix == ".json":
+                        continue
+                    else:
+                        shutil.copy(item, output_dir / item.name)
+                            
+            # Run the Snakemake workflow for the configuration
+            subprocess.run(["snakemake", "--use-conda", "--force", "--cores", "all", "--conda-prefix", str(shared_env_dir)], check=True, cwd=output_dir)
+            print("Workflow executed successfully.")
+            
+            # For the scenario where the snakemake workflow doesn't exist, one can directly run the simulation script using the subprocess module, e.g.:
+            #subprocess.run(["python", "run_fenics_simulation.py" \
+                            #"--input_parameter_file" "parameters.json" \
+                            #"--input_mesh_file" "mesh.msh" \
+                            #"--output_solution_file_zip" "solution_field_data.zip" \
+                            #"--output_metrics_file" "solution_metrics.json"], check=True, cwd=output_dir)
+                            
+            #Assuming the mesh.msh and parameters.json files are present/copied to the output_dir.