[workflow] Renamed snakemake.yaml to buildinfo.yaml.

Applications/Utils/ExtractBoundary.py

 # Usage, e.g.:
-#   python3 ExtractBoundary.py ./snakemake.yaml
+#   python3 ExtractBoundary.py ./buildinfo.yaml
+#
+# buildinfo.yaml contains variables such as Data_BINARY_DIR
 
 import os, parsl, sys, yaml
 from parsl import python_app, bash_app
 from parsl.data_provider.files import File
 
 output_path = "FileIO"
-elem_types = ['tri', 'quad']
+elem_types = ["tri", "quad"]
 
 parsl.load()
 
@@ -14,7 +16,7 @@ config = dict()
 with open(sys.argv[1]) as f:
     config = yaml.safe_load(f)
 
-os.environ["PATH"] += os.pathsep + os.pathsep.join([config['BIN_DIR']])
+os.environ["PATH"] += os.pathsep + os.pathsep.join([config["BIN_DIR"]])
 os.chdir(f"{config['Data_BINARY_DIR']}/{output_path}")
 
 print(f"{config['Data_BINARY_DIR']}/{output_path}")
@@ -22,8 +24,9 @@ print(f"{config['Data_BINARY_DIR']}/{output_path}")
 
 # Apps
 @bash_app
-def generate_meshes(elem_type, outputs=[],
-                    stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME):
+def generate_meshes(
+    elem_type, outputs=[], stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME
+):
     return f"""generateStructuredMesh -e {elem_type} \
             --lx 1 --ly 1 \
             --nx 10 --ny 10 \
@@ -31,17 +34,20 @@ def generate_meshes(elem_type, outputs=[],
 
 
 @bash_app
-def extract_boundary(elem_type, inputs=[], outputs=[],
-                     stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME):
+def extract_boundary(
+    elem_type, inputs=[], outputs=[], stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME
+):
     return f"""ExtractBoundary -i {inputs[0].filepath} \
             -o square_1x1_{elem_type}_boundary.vtu"""
 
 
 # compares the files in inputs[0] and inputs[1]
 @bash_app
-def vtk_diff(fields, inputs=[], outputs=[],
-             stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME):
+def vtk_diff(
+    fields, inputs=[], outputs=[], stderr=parsl.AUTO_LOGNAME, stdout=parsl.AUTO_LOGNAME
+):
     import os
+
     script = ""
     if os.path.exists(outputs[0]):
         os.remove(outputs[0])
@@ -64,17 +70,22 @@ def vtk_diff(fields, inputs=[], outputs=[],
 # Workflow
 for elem_type in elem_types:
     gm = generate_meshes(elem_type, outputs=[File(f"input_square_1x1_{elem_type}.vtu")])
-    eb = extract_boundary(elem_type, inputs=[gm.outputs[0]], outputs=[File(f"square_1x1_{elem_type}_boundary.vtu")])
+    eb = extract_boundary(
+        elem_type,
+        inputs=[gm.outputs[0]],
+        outputs=[File(f"square_1x1_{elem_type}_boundary.vtu")],
+    )
     diff = vtk_diff(
         fields=[
             # second field name can be omitted if identical
             ["bulk_node_ids", 0, 0],
             ["bulk_element_ids", 0, 0],
-            ["bulk_face_ids", 0, 0]
+            ["bulk_face_ids", 0, 0],
         ],
         inputs=[
             eb.outputs[0],
-            f"{config['Data_SOURCE_DIR']}/{output_path}/{eb.outputs[0].filename}"
+            f"{config['Data_SOURCE_DIR']}/{output_path}/{eb.outputs[0].filename}",
         ],
-        outputs=[File(f"square_1x1_{elem_type}_boundary_diff.out")])
+        outputs=[File(f"square_1x1_{elem_type}_boundary_diff.out")],
+    )
     print(diff.result())

Applications/Utils/ExtractBoundary.smk

 # Usage, e.g.:
-#   snakemake -s ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/Tests/snakemake.yaml
+#   snakemake -s ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/buildinfo.yaml
+#
+# buildinfo.yaml contains variables such as Data_BINARY_DIR
+
 output_path = "FileIO"
 
 import os

Applications/Utils/Tests.cmake

@@ -310,7 +310,7 @@ if(SNAKEMAKE AND NOT OGS_USE_MPI)
     add_test(NAME snakemake_ExtractBoundary
         COMMAND ${SNAKEMAKE}
                  -j 1
-                 --configfile ${PROJECT_BINARY_DIR}/snakemake.yaml
+                 --configfile ${PROJECT_BINARY_DIR}/buildinfo.yaml
                  -s ${CMAKE_CURRENT_SOURCE_DIR}/ExtractBoundary.smk
     )
 endif()
@@ -318,7 +318,7 @@ if(PARSL AND NOT OGS_USE_MPI)
     add_test(NAME parsl_ExtractBoundary
         COMMAND ${Python3_EXECUTABLE}
             ${CMAKE_CURRENT_SOURCE_DIR}/ExtractBoundary.py
-            ${PROJECT_BINARY_DIR}/snakemake.yaml
+            ${PROJECT_BINARY_DIR}/buildinfo.yaml
     )
 endif()
 

scripts/cmake/test/Test.cmake

@@ -95,4 +95,4 @@ set_target_properties(ctest ctest-large ctest-cleanup ctest-large-cleanup
 add_dependencies(ctest ogs)
 add_dependencies(ctest-large ogs)
 
-configure_file(${PROJECT_SOURCE_DIR}/scripts/test/snakemake.in.yaml ${PROJECT_BINARY_DIR}/snakemake.yaml)
+configure_file(${PROJECT_SOURCE_DIR}/scripts/test/buildinfo.in.yaml ${PROJECT_BINARY_DIR}/buildinfo.yaml)