update Readme and enforce strict channel priority in github ci

Author: joergfunger

.github/workflows/run-benchmark.yml

@@ -32,6 +32,9 @@ jobs:
             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
 

benchmarks/linear-elastic-plate-with-hole/README.md

@@ -1,9 +1,59 @@
 # Infinite plate with hole benchmark in FEniCSx
 
-This directory contains:
+## Problem Definition
 
-* `Snakefile`: A snakefile to run the benchmark.
-* `run_simulation.py`: The main script to run the benchmark.
-* `create_input_files.py`: A script to create the input files for the benchmark.
-* `environment.yml`: A conda environment file to create the environment needed to run the benchmark.
-* `parameters_*.json`: A set of parameters files for the benchmark. Each file will create a new instance of the benchmark with different parameters.
+See the [documentation](../../docs/benchmarks/linear%20elasticity/index.md) for a detailed problem definition and mathematical formulation.
+
+## Running the Benchmark
+
+1. **Generate Configuration Files**
+
+   Before running the benchmark, generate the configuration files using:
+   ```bash
+   python generate_config.py
+   ```
+   This script creates a workflow_config.json that defines what configurations are computed (in the starndard case one for each parameter_file_*.json) and what tools are used.
+
+2. **Run the Benchmark**
+
+   The benchmark is managed via Snakemake. You can run all tools or specify a subset (e.g., only fenics) by editing the generated config or passing parameters via the command line:
+   ```bash
+   snakemake --use-conda --cores all
+   ```
+   To run only a specific tool or specific configuration (e.g. for testing), update the config file or use:
+   ```bash
+   snakemake --use-conda --cores all --config tools=fenics
+   ```
+
+3. **Collect Provenance**
+
+   After running, provenance data is collected automatically and stored in .snakemake. If you want to use the reporter plugin ([metadata4ing](https://github.com/izus-fokus/snakemake-report-plugin-metadata4ing)) to generate an ROCrate, call snakemake again (make sure the plugin is added to the environment):
+   ```bash
+   snakemake --use-conda --cores all --reporter metadata4ing
+   ```
+   Output and provenance files are stored in the `snakemake_results/` directory and as zipped archives.
+
+## Hierarchical Structure of Snakefiles
+
+The workflow is organized hierarchically:
+- The main `Snakefile` orchestrates the benchmark and includes sub-workflows for each tool.
+- Each tool (e.g., fenics) has its own rules and output structure.
+
+### Inputs
+
+Each tool's rule must accept:
+- A parameter/configuration file (e.g., `parameters_*.json`) specifying geometry, material properties, boundary conditions, and solver settings.
+- A mesh file (*.msh from gmsh) generated with the rule generate_mesh.
+
+### Outputs
+
+Each tool's rule must produce:
+- **Solution field results**: This zip-file should include all the data used to plot the output like strains, stresses or displacements of the solution field.
+- **Metrics file**: JSON-File summarizing key metrics (e.g., max Mises stress at Gauss points or maximum mises stress obtained when projecting to the nodes).
+- All output files should be placed in the designated results directory (e.g., `snakemake_results/{benchmark}/{tool}/solution_field_data_{configuration}.zip`). `snakemake_results/` is generated from the level where snakemake is executed, but this directory is then zipped.
+
+To add another simulation tool:
+  - Create a new subdirectory for the tool.
+  - Create a new Snakefile with at least one rule that produces the outputs (metrics and solution fields)
+  - Ensure the rule accepts the standardized parameter file and mesh/input files.
+  - Update the main `Snakefile` to include the new tool's rules.