removed nextflow scripts, template for tool workflow generation in txt format

Author: dtyagi

.github/workflows/run-benchmark.yml

@@ -48,7 +48,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd $GITHUB_WORKSPACE/benchmarks/common/
-          python simulation_tool_snakefile_generator.py --tool fenics --simulation_script run_fenics_simulation.py --environment_file environment_simulation.yml
+          python simulation_tool_snakefile_generator.py --benchmark_name linear-elastic-plate-with-hole --tool fenics --simulation_script run_fenics_simulation.py --environment_file environment_simulation.yml
 
       - name: run_linear-elastic-plate-with-hole-benchmarks_snakemake
         shell: bash -l {0}
@@ -67,13 +67,6 @@ jobs:
             --report-metadata4ing-paramscript ../common/parameter_extractor.py \
             --report-metadata4ing-filename snakemake_provenance_kratos
           unzip snakemake_provenance_kratos -d snakemake_provenance_kratos
-      
-      - name: run_linear-elastic-plate-with-hole-benchmarks_nextflow
-        shell: bash -l {0}
-        run: |
-          cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/
-          nextflow run main.nf -params-file workflow_config.json --tool="fenics" -c ../common/nextflow.config -plugins [email protected]
-          nextflow run main.nf -params-file workflow_config.json --tool="kratos"  -c ../common/nextflow.config -plugins [email protected]
 
       - name: Archive Linear Elastic plate with a hole benchmark data for snakemake fenics
         uses: actions/upload-artifact@v4
@@ -89,13 +82,6 @@ jobs:
             path: |
               benchmarks/linear-elastic-plate-with-hole/snakemake_provenance_kratos/
 
-      - name: Archive Linear Elastic plate with a hole benchmark data for nextflow fenics
-        uses: actions/upload-artifact@v4
-        with:
-            name: nextflow_results_linear-elastic-plate-with-hole
-            path: |
-              benchmarks/linear-elastic-plate-with-hole/nextflow_results/
-
   process-artifacts:
     runs-on: ubuntu-latest
     needs: tests
@@ -107,13 +93,13 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: snakemake_fenics_result_linear-elastic-plate-with-hole
-          path: ./snakemake_provenance
+          path: ./snakemake_fenics_provenance
 
       - name: Download snakemake kratos artifact
         uses: actions/download-artifact@v4
         with:
           name: snakemake_kratos_result_linear-elastic-plate-with-hole
-          path: ./snakemake_provenance
+          path: ./snakemake_kratos_provenance
 
       - name: Setup Mambaforge with postprocessing env
         uses: conda-incubator/setup-miniconda@v3
@@ -126,7 +112,7 @@ jobs:
       - name: Run plotting script
         shell: bash -l {0}
         run: |
-          python benchmarks/linear-elastic-plate-with-hole/plot_metrics.py ./snakemake_provenance
+          python benchmarks/linear-elastic-plate-with-hole/plot_metrics.py ./snakemake_fenics_provenance ./snakemake_kratos_provenance
 
       - name: Upload PDF plot as artifact
         uses: actions/upload-artifact@v4

benchmarks/common/nextflow.config

@@ -11,7 +11,7 @@
 from pathlib import Path
 
 
-def generate_snakefile(tool_name: str, environment_file: str, simulation_script: str, output_path: str = None):
+def generate_snakefile(benchmark_name: str, tool_name: str, environment_file: str, simulation_script: str, output_path: str = None):
     """
     Generate a Snakefile for a simulation tool.
     
@@ -22,40 +22,23 @@ def generate_snakefile(tool_name: str, environment_file: str, simulation_script:
         output_path: Optional path where to save the Snakefile. If None, saves to {tool_name}/Snakefile
     """
 
-    # Template for the Snakefile
+    # Load template from external file
+    template_path = Path(__file__).parent / "snakefile_template.txt"
+    with open(template_path, 'r') as f:
+        snakefile_template = f.read()
 
-    snakefile_template = f'''import json
-import os
-
-tool = "{tool_name}"
-result_dir = "snakemake_results/" + config["benchmark"] 
-configuration_to_parameter_file = config["configuration_to_parameter_file"]
-configurations = config["configurations"]
-
-
-rule run_{tool_name}_simulation:
-    input: 
-        script = "{{tool}}/{simulation_script}",
-        parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
-        mesh = f"{{result_dir}}/mesh/mesh_{{{{configuration}}}}.msh",
-    output:
-        zip = f"{{result_dir}}/{{{{tool}}}}/solution_field_data_{{{{configuration}}}}.zip",
-        metrics = f"{{result_dir}}/{{{{tool}}}}/solution_metrics_{{{{configuration}}}}.json",
-    conda:
-        "{environment_file}",
-    shell:
-        """
-        python3 {{input.script}} --input_parameter_file {{input.parameters}} --input_mesh_file {{input.mesh}} --output_solution_file_zip {{output.zip}} --output_metrics_file {{output.metrics}}
-        """
-    '''
+    # Replace placeholders with actual values
+    snakefile_content = snakefile_template.replace("{TOOL_NAME}", tool_name) \
+                                          .replace("{SIMULATION_SCRIPT}", simulation_script) \
+                                          .replace("{ENVIRONMENT_FILE}", environment_file)
 
     # Determine output path
     if output_path is None:
-        output_path = f"../linear-elastic-plate-with-hole/{tool_name}/Snakefile"
+        output_path = f"../{benchmark_name}/{tool_name}/Snakefile"
 
     # Write the Snakefile
     with open(output_path, 'w') as f:
-        f.write(snakefile_template)
+        f.write(snakefile_content)
 
     print(f"Snakefile generated successfully: {output_path}")
 
@@ -78,7 +61,13 @@ def main():
 
     """
     )
-    
+    parser.add_argument(
+        '--benchmark_name',
+        type=str,
+        required=True,
+        help='Name of the benchmark (same as the benchmark directory name)'
+    )
+        
     parser.add_argument(
         '--tool',
         type=str,
@@ -103,6 +92,7 @@ def main():
     args = parser.parse_args()
 
     generate_snakefile(
+        benchmark_name=args.benchmark_name,
         tool_name=args.tool,
         environment_file=args.environment_file,
         simulation_script=args.simulation_script

benchmarks/common/simulation_tool_snakefile_generator.py

@@ -0,0 +1,23 @@
+import json
+import os
+
+tool = "{TOOL_NAME}"
+result_dir = "snakemake_results/" + config["benchmark"] 
+configuration_to_parameter_file = config["configuration_to_parameter_file"]
+configurations = config["configurations"]
+
+
+rule run_{TOOL_NAME}_simulation:
+    input: 
+        script = f"{tool}/{SIMULATION_SCRIPT}",
+        parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
+        mesh = f"{result_dir}/{tool}/mesh/mesh_{{configuration}}.msh",
+    output:
+        zip = f"{result_dir}/{tool}/solution_field_data_{{configuration}}.zip",
+        metrics = f"{result_dir}/{tool}/solution_metrics_{{configuration}}.json",
+    conda:
+        "{ENVIRONMENT_FILE}",
+    shell:
+        """
+        python3 {input.script} --input_parameter_file {input.parameters} --input_mesh_file {input.mesh} --output_solution_file_zip {output.zip} --output_metrics_file {output.metrics}
+        """

benchmarks/common/snakefile_template.txt

@@ -11,7 +11,7 @@ benchmark_uri = config["benchmark_uri"]
 
 rule all:
     input:
-        expand(f"{result_dir}/{{tool}}/summary.json", tool=tool),
+        f"{result_dir}/{tool}/summary.json"
 
 rule create_mesh:    
     input:
@@ -21,20 +21,18 @@ rule create_mesh:
         # otherwise, you could just write configuration_to_parameter_file(configuration)
         parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
     output:
-        mesh = f"{result_dir}/mesh/mesh_{{configuration}}.msh",
+        mesh = f"{result_dir}/{tool}/mesh/mesh_{{configuration}}.msh",
     conda: "environment_mesh.yml"
     shell:
         """
         python3 {input.script} --input_parameter_file {input.parameters} --output_mesh_file {output.mesh}
         """
 
 # Include tool-specific rules
-# The should have at least the mesh file and the parameters as input
+# They should have at least the mesh file and the parameters as input
 # and output for each configuration a 
 # solution_metrics_{configuration}.json and 
-# and solution_field_data_{configuration}.zip whee all the visualization files are stored
-# (e.g. vtk)
-#for tool in tools:
+# and solution_field_data_{configuration}.zip where all the visualization files are stored (e.g. vtk)
 include: f"{tool}/Snakefile"
 
 
@@ -44,7 +42,7 @@ rule summary:
         # (snakemake_results/linear-elastic-plate-with-hole/fenics/summary.json)
         script = "../common/summarize_results.py",
         parameters = expand("{param}", param=[configuration_to_parameter_file[c] for c in configurations]),
-        mesh = expand(f"{result_dir}/mesh/mesh_{{configuration}}.msh", configuration=configurations),
+        mesh = expand(f"{result_dir}/{tool}/mesh/mesh_{{configuration}}.msh", configuration=configurations),
         metrics = lambda wildcards: expand(
             f"{result_dir}/{{tool}}/solution_metrics_{{configuration}}.json",
             tool=[wildcards.tool], configuration=configurations

benchmarks/linear-elastic-plate-with-hole/Snakefile

@@ -12,7 +12,7 @@ kratos_material_template = f"{tool}/StructuralMaterials_template.json"
 rule mesh_to_mdpa:
     input:
         parameters = lambda wildcards: configuration_to_parameter_file[wildcards.configuration],
-        mesh = f"{result_dir}/mesh/mesh_{{configuration}}.msh",
+        mesh = f"{result_dir}/{tool}/mesh/mesh_{{configuration}}.msh",
         script = f"{tool}/msh_to_mdpa.py",
     output:
         mdpa = f"{result_dir}/{tool}/mesh_{{configuration}}.mdpa",