[T] Added snakemake wrapper for vtkdiff.

Applications/Utils/ExtractBoundary.smk

 # Usage, e.g.:
-#   # generateStructuredMesh and ExtractBoundary have to be in the path
-#   snakemake -s ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/Tests/snakemake.yaml -d $HOME/code/ogs6/build/Tests/Data/FileIO
+#   snakemake -s ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/Tests/snakemake.yaml
+output_path = "FileIO"
 
 import os
 os.environ["PATH"] += os.pathsep + os.pathsep.join([config['BIN_DIR']])
+workdir: f"{config['Data_BINARY_DIR']}/{output_path}"
 
 # "entry point", otherwise one would had to specify output files as snakemake
 # arguments
@@ -36,9 +37,12 @@ rule vtkdiff:
         "square_1x1_{type}_boundary.vtu"
     output:
         "square_1x1_{type}_boundary_diff.out"
-    shell:
-        """
-        vtkdiff {input} {config[Data_SOURCE_DIR]}/FileIO/square_1x1_{wildcards.type}_boundary.vtu -a bulk_node_ids -b bulk_node_ids --abs 0 --rel 0 > {output}
-        vtkdiff {input} {config[Data_SOURCE_DIR]}/FileIO/square_1x1_{wildcards.type}_boundary.vtu -a bulk_element_ids -b bulk_element_ids --abs 0 --rel 0 >> {output}
-        vtkdiff {input} {config[Data_SOURCE_DIR]}/FileIO/square_1x1_{wildcards.type}_boundary.vtu -a bulk_face_ids -b bulk_face_ids --abs 0 --rel 0 >> {output}
-        """
+    params:
+        fields = [
+            # second field name can be omitted if identical
+            ["bulk_node_ids", 0, 0],
+            ["bulk_element_ids", 0, 0],
+            ["bulk_face_ids", 0, 0]
+        ]
+    wrapper:
+        f"file://{config['SOURCE_DIR']}/scripts/snakemake/vtkdiff"

Applications/Utils/Tests.cmake

@@ -311,7 +311,6 @@ if(SNAKEMAKE AND NOT OGS_USE_MPI)
         COMMAND ${SNAKEMAKE}
                  -j 1
                  --configfile ${PROJECT_BINARY_DIR}/snakemake.yaml
-                 -d ${Data_BINARY_DIR}/FileIO/
                  -s ${CMAKE_CURRENT_SOURCE_DIR}/ExtractBoundary.smk
     )
 endif()

scripts/snakemake/vtkdiff/wrapper.py

+"""Snakemake wrapper for vtkdiff."""
+
+__author__ = "Lars Bilke"
+__copyright__ = "Copyright 2020, OpenGeoSys Community"
+__license__ = "BSD"
+
+import os
+from snakemake.shell import shell
+
+output_path = os.getcwd().replace(snakemake.config['Data_BINARY_DIR'], "")
+
+for field in snakemake.params.fields:
+    field_a = field[0]
+    offset = 0
+    if len(field) == 4:
+        offset = 1
+    field_b = field[0 + offset]
+    abs_tol = field[1 + offset]
+    rel_tol = field[2 + offset]
+
+    shell(
+        """
+        rm {snakemake.output[0]} || true
+        vtkdiff {snakemake.input[0]} \
+          {snakemake.config[Data_SOURCE_DIR]}/{output_path}/{snakemake.input[0]} \
+          -a {field_a} -b {field_b} \
+          --abs {abs_tol} --rel {rel_tol} > {snakemake.output[0]}
+        """
+    )