From d8066aae19cae4f41fe04b0603c86d09fd2394ca Mon Sep 17 00:00:00 2001
From: Lars Bilke <lars.bilke@ufz.de>
Date: Thu, 25 Jul 2024 10:06:14 +0200
Subject: [PATCH] [T] Rewritten GMSH2OGS_Extractoundary snakemake test to
pytest.
---
.../Utils/GMSH2OGS_ExtractBoundary.smk | 86 -------------------
.../GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk | 85 ------------------
Applications/Utils/Tests.cmake | 21 -----
.../{MeshLib => Utils/GMSH2OGS}/A2-gmsh.msh | 0
.../{MeshLib => Utils/GMSH2OGS}/A2-gmsh4.msh | 0
Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_0.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_1.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_2.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_3.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_4.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_5.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_6.vtu | 0
.../Data/{MeshLib => Utils/GMSH2OGS}/A2_7.vtu | 0
.../test_gmsh2ogs_extract_boundary.py | 79 +++++++++++++++++
15 files changed, 79 insertions(+), 192 deletions(-)
delete mode 100644 Applications/Utils/GMSH2OGS_ExtractBoundary.smk
delete mode 100644 Applications/Utils/GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2-gmsh.msh (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2-gmsh4.msh (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_0.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_1.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_2.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_3.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_4.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_5.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_6.vtu (100%)
rename Tests/Data/{MeshLib => Utils/GMSH2OGS}/A2_7.vtu (100%)
create mode 100644 Tests/Data/Utils/GMSH2OGS/test_gmsh2ogs_extract_boundary.py
diff --git a/Applications/Utils/GMSH2OGS_ExtractBoundary.smk b/Applications/Utils/GMSH2OGS_ExtractBoundary.smk
deleted file mode 100644
index fec4376e1c4..00000000000
--- a/Applications/Utils/GMSH2OGS_ExtractBoundary.smk
+++ /dev/null
@@ -1,86 +0,0 @@
-# Usage, e.g.:
-# snakemake -s GMSH2OGS_ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/buildinfo.yaml
-#
-# buildinfo.yaml contains variables such as Data_BINARY_DIR
-
-import os
-os.environ["PATH"] += os.pathsep + os.pathsep.join([config['BIN_DIR']])
-workdir: f"{config['Data_BINARY_DIR']}/MeshLib"
-
-#import ipdb
-#ipdb.set_trace()
-
-VTKDIFF = f"file://{config['SOURCE_DIR']}/scripts/snakemake/vtkdiff"
-SOURCE_DIR = f"{config['Data_SOURCE_DIR']}/MeshLib"
-
-MESH_NAME = "A2"
-BULK_MESH = f"{MESH_NAME}.vtu"
-GMSH_MESH = f"{MESH_NAME}-gmsh.msh"
-GMSH2OGS = f"{config['BIN_DIR']}/GMSH2OGS --gmsh2_physical_id"
-
-INNER_BOUNDARIES = "[12]"
-OUTER_BOUNDARIES = "[034567]"
-
-ALL_REFERENCE_FILES = glob_wildcards(f"{SOURCE_DIR}/{{file, {MESH_NAME}.*}}.vtu").file
-
-rule all:
- input:
- expand("{file}.vtkdiff.out", file=ALL_REFERENCE_FILES)
-
-rule gmsh2ogs:
- input:
- f"{SOURCE_DIR}/{GMSH_MESH}"
- output:
- expand("{file}.vtu", file=ALL_REFERENCE_FILES)
- shell:
- "{GMSH2OGS} -i {input} -o {BULK_MESH} -e -b -v"
-
-rule vtkdiff_geometry_bulk:
- input:
- a = f"{SOURCE_DIR}/{BULK_MESH}",
- b = BULK_MESH
- output:
- f"{MESH_NAME}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["MaterialIDs", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_boundary:
- input:
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids"
- params:
- check_mesh = True,
- fields = [["bulk_node_ids", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_inner:
- input:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids",
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x, {INNER_BOUNDARIES}}}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["number_bulk_elements", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_outer:
- input:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids",
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x, {OUTER_BOUNDARIES}}}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["bulk_element_ids", 0, 0]]
- wrapper:
- VTKDIFF
diff --git a/Applications/Utils/GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk b/Applications/Utils/GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk
deleted file mode 100644
index 73d35e5b580..00000000000
--- a/Applications/Utils/GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk
+++ /dev/null
@@ -1,85 +0,0 @@
-# Usage, e.g.:
-# snakemake -s GMSH2OGS_ExtractBoundary.smk -j 1 --configfile $HOME/code/ogs6/build/buildinfo.yaml
-#
-# buildinfo.yaml contains variables such as Data_BINARY_DIR
-
-import os
-os.environ["PATH"] += os.pathsep + os.pathsep.join([config['BIN_DIR']])
-workdir: f"{config['Data_BINARY_DIR']}/MeshLib"
-
-#import ipdb
-#ipdb.set_trace()
-
-VTKDIFF = f"file://{config['SOURCE_DIR']}/scripts/snakemake/vtkdiff"
-SOURCE_DIR = f"{config['Data_SOURCE_DIR']}/MeshLib"
-GMSH2OGS = f"{config['BIN_DIR']}/GMSH2OGS"
-
-MESH_NAME = "A2"
-BULK_MESH = f"{MESH_NAME}.vtu"
-GMSH_MESH = f"{MESH_NAME}-gmsh4.msh"
-INNER_BOUNDARIES = "[12]"
-OUTER_BOUNDARIES = "[034567]"
-
-ALL_REFERENCE_FILES = glob_wildcards(f"{SOURCE_DIR}/{{file, {MESH_NAME}.*}}.vtu").file
-
-rule all:
- input:
- expand("{file}.vtkdiff.out", file=ALL_REFERENCE_FILES)
-
-rule gmsh2ogs:
- input:
- f"{SOURCE_DIR}/{GMSH_MESH}"
- output:
- expand("{file}.vtu", file=ALL_REFERENCE_FILES)
- shell:
- "{GMSH2OGS} -i {input} -o {BULK_MESH} -e -b -v"
-
-rule vtkdiff_geometry_bulk:
- input:
- a = f"{SOURCE_DIR}/{BULK_MESH}",
- b = BULK_MESH
- output:
- f"{MESH_NAME}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["MaterialIDs", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_boundary:
- input:
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids"
- params:
- check_mesh = True,
- fields = [["bulk_node_ids", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_inner:
- input:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids",
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x, {INNER_BOUNDARIES}}}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["number_bulk_elements", 0, 0]]
- wrapper:
- VTKDIFF
-
-rule vtkdiff_geometry_outer:
- input:
- f"{MESH_NAME}_{{x}}.vtkdiff.out-bulk_node_ids",
- a = f"{SOURCE_DIR}/{MESH_NAME}_{{x}}.vtu",
- b = f"{MESH_NAME}_{{x}}.vtu"
- output:
- f"{MESH_NAME}_{{x, {OUTER_BOUNDARIES}}}.vtkdiff.out"
- params:
- check_mesh = True,
- fields = [["bulk_element_ids", 0, 0]]
- wrapper:
- VTKDIFF
diff --git a/Applications/Utils/Tests.cmake b/Applications/Utils/Tests.cmake
index 5a109f848d6..a76ac034d43 100644
--- a/Applications/Utils/Tests.cmake
+++ b/Applications/Utils/Tests.cmake
@@ -839,27 +839,6 @@ if(TARGET VerticalSliceFromLayers AND GMSH)
endif()
-if(TARGET GMSH2OGS AND SNAKEMAKE AND TEE_TOOL_PATH)
- add_test(NAME snakemake_GMSH2OGS_ExtractBoundary
- COMMAND ${SNAKEMAKE} --cores all
- --configfile ${PROJECT_BINARY_DIR}/buildinfo.yaml
- -s ${CMAKE_CURRENT_SOURCE_DIR}/GMSH2OGS_ExtractBoundary.smk
- )
-
- add_test(NAME snakemake_GMSH2OGS_Gmsh4_ExtractBoundary
- COMMAND ${SNAKEMAKE} --cores all
- --configfile ${PROJECT_BINARY_DIR}/buildinfo.yaml
- -s ${CMAKE_CURRENT_SOURCE_DIR}/GMSH2OGS_ExtractBoundary_MeshByGmsh4.smk
- )
- set_tests_properties(
- snakemake_GMSH2OGS_ExtractBoundary
- snakemake_GMSH2OGS_Gmsh4_ExtractBoundary
- PROPERTIES LABELS "default" RUN_SERIAL TRUE
- )
-
- add_dependencies(ctest GMSH2OGS)
-endif()
-
foreach(criterion ElementSize EdgeRatio EquiAngleSkew RadiusEdgeRatio SizeDifference)
AddTest(
NAME TrianglesGoodElementQuality_${criterion}_Test
diff --git a/Tests/Data/MeshLib/A2-gmsh.msh b/Tests/Data/Utils/GMSH2OGS/A2-gmsh.msh
similarity index 100%
rename from Tests/Data/MeshLib/A2-gmsh.msh
rename to Tests/Data/Utils/GMSH2OGS/A2-gmsh.msh
diff --git a/Tests/Data/MeshLib/A2-gmsh4.msh b/Tests/Data/Utils/GMSH2OGS/A2-gmsh4.msh
similarity index 100%
rename from Tests/Data/MeshLib/A2-gmsh4.msh
rename to Tests/Data/Utils/GMSH2OGS/A2-gmsh4.msh
diff --git a/Tests/Data/MeshLib/A2.vtu b/Tests/Data/Utils/GMSH2OGS/A2.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2.vtu
diff --git a/Tests/Data/MeshLib/A2_0.vtu b/Tests/Data/Utils/GMSH2OGS/A2_0.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_0.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_0.vtu
diff --git a/Tests/Data/MeshLib/A2_1.vtu b/Tests/Data/Utils/GMSH2OGS/A2_1.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_1.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_1.vtu
diff --git a/Tests/Data/MeshLib/A2_2.vtu b/Tests/Data/Utils/GMSH2OGS/A2_2.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_2.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_2.vtu
diff --git a/Tests/Data/MeshLib/A2_3.vtu b/Tests/Data/Utils/GMSH2OGS/A2_3.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_3.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_3.vtu
diff --git a/Tests/Data/MeshLib/A2_4.vtu b/Tests/Data/Utils/GMSH2OGS/A2_4.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_4.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_4.vtu
diff --git a/Tests/Data/MeshLib/A2_5.vtu b/Tests/Data/Utils/GMSH2OGS/A2_5.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_5.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_5.vtu
diff --git a/Tests/Data/MeshLib/A2_6.vtu b/Tests/Data/Utils/GMSH2OGS/A2_6.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_6.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_6.vtu
diff --git a/Tests/Data/MeshLib/A2_7.vtu b/Tests/Data/Utils/GMSH2OGS/A2_7.vtu
similarity index 100%
rename from Tests/Data/MeshLib/A2_7.vtu
rename to Tests/Data/Utils/GMSH2OGS/A2_7.vtu
diff --git a/Tests/Data/Utils/GMSH2OGS/test_gmsh2ogs_extract_boundary.py b/Tests/Data/Utils/GMSH2OGS/test_gmsh2ogs_extract_boundary.py
new file mode 100644
index 00000000000..a3dea98cc2d
--- /dev/null
+++ b/Tests/Data/Utils/GMSH2OGS/test_gmsh2ogs_extract_boundary.py
@@ -0,0 +1,79 @@
+import os
+from pathlib import Path
+
+import pytest
+from ogs import cli
+
+
+@pytest.mark.parametrize(
+ ("mesh", "gmsh2_physical_id"), [("A2-gmsh.msh", True), ("A2-gmsh4.msh", False)]
+)
+def test_gmsh2ogs_extract_boundary(tmp_path, mesh, gmsh2_physical_id):
+ os.chdir(Path(__file__).resolve().parent)
+ mesh_file = Path(f"{tmp_path}/A2.vtu")
+
+ cli.GMSH2OGS(
+ gmsh2_physical_id=gmsh2_physical_id,
+ i=mesh,
+ o=mesh_file,
+ e=True,
+ boundaries=True,
+ validation=True,
+ )
+ assert mesh_file.exists()
+
+ # geometry bulk
+ assert cli.vtkdiff(mesh_file, "A2.vtu", mesh_check=None) == 0
+ assert (
+ cli.vtkdiff(
+ mesh_file,
+ "A2.vtu",
+ a="MaterialIDs",
+ b="MaterialIDs",
+ abs=0,
+ rel=0,
+ )
+ == 0
+ )
+
+ for x in range(8):
+ # geometry boundary
+ assert (
+ cli.vtkdiff(f"{tmp_path}/A2_{x}.vtu", f"A2_{x}.vtu", mesh_check=None) == 0
+ )
+ assert (
+ cli.vtkdiff(
+ f"{tmp_path}/A2_{x}.vtu",
+ f"A2_{x}.vtu",
+ a="bulk_node_ids",
+ b="bulk_node_ids",
+ abs=0,
+ rel=0,
+ )
+ == 0
+ )
+ if x in [1, 2]: # inner boundarie
+ assert (
+ cli.vtkdiff(
+ f"{tmp_path}/A2_{x}.vtu",
+ f"A2_{x}.vtu",
+ a="number_bulk_elements",
+ b="number_bulk_elements",
+ abs=0,
+ rel=0,
+ )
+ == 0
+ )
+
+ if x in [0, 3, 4, 5, 6, 7]: # outer boundarie
+ assert (
+ cli.vtkdiff(
+ f"{tmp_path}/A2_{x}.vtu",
+ f"A2_{x}.vtu",
+ a="bulk_element_ids",
+ b="bulk_element_ids",
+ abs=0,
+ rel=0,
+ )
+ == 0
+ )
--
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