Merge pull request #1407 from virtualcell/nightly_testing_patch

Nightly testing patch

.github/workflows/NightlyBMDB_CLI.yml

@@ -6,7 +6,7 @@ on:
 
 env:
   python-version: "3.10"
-  poetry-version: "1.2.1"
+  poetry-version: "2.0"
 
 jobs:
   build:
@@ -379,5 +379,11 @@ jobs:
       - name: Post results to slack part 3 (report.md from exec-report CLI command)
         run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="$(cat ${GITHUB_WORKSPACE}/report.md)" https://slack.com/api/chat.postMessage
 
-      - name: Post results to slack part 4
+      - name: Post results to slack part 4 (sound alarm if changed results)
+        run: |
+          if grep -q "Unmatched Results Statistics" "$(cat ${GITHUB_WORKSPACE}/report.md)"; then
+            curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="@here BMDB Nightly Testing has reported a change in execution results!! Please Investigate" https://slack.com/api/chat.postMessage
+          fi
+
+      - name: Post results to slack part 5
         run: curl -X POST -F token="${{ secrets.SLACK_BOT_TOKEN }}" -F channel=${{ secrets.SLACK_CHANNEL_VCELL_DEV_TOKEN }} -F text="To see detailed logs of the BMDB results, see - ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}. Go see what happened!" https://slack.com/api/chat.postMessage

pom.xml

@@ -194,13 +194,6 @@
 
 
 	<repositories>
-		<!-- needed for javax.media.jai -->
-		<repository>
-			<id>com.springsource.repository.bundles.external</id>
-			<name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name>
-			<url>https://repository.springsource.com/maven/bundles/external</url>
-		</repository>
-
 		<!-- needed for com.mxgraph.jgraphx -->
 		<repository>
 			<id>com.alfresco.repository.public</id>

pythonVtk/pyproject.toml

@@ -1,5 +1,5 @@
 [tool.poetry]
-name = "pythonvtk"
+name = "python_vtk"
 version = "0.1.0"
 description = ""
 authors = ["Jim Schaff <[email protected]>"]

pythonVtk/vtkService/makeLittleVtk.py → pythonVtk/python_vtk/vtkService/makeLittleVtk.py

@@ -1,30 +1,30 @@
-import vtk
-
-import vtkService.vtkService as vtkService
-
-x = [1, 2, 3, 4]
-y = [1, 2, 3, 4]
-ugrid = vtk.vtkUnstructuredGrid()
-points = vtk.vtkPoints()
-points.SetDataTypeToDouble()
-xyToNode = [[] for i in range(len(x))]
-index = 0
-for i, xCoord in enumerate(x):
-    for yCoord in y:
-        points.InsertNextPoint(xCoord, yCoord, 0.0)
-        xyToNode[i].append(index)
-        index += 1
-ugrid.SetPoints(points)
-
-# Add the volume elements
-for i, xCoord in enumerate(x[:-1]):
-    for j, yCoord in enumerate(y[:-1]):
-        idList = vtk.vtkIdList()
-        idList.InsertNextId(xyToNode[i][j])
-        idList.InsertNextId(xyToNode[i + 1][j])
-        idList.InsertNextId(xyToNode[i + 1][j + 1])
-        idList.InsertNextId(xyToNode[i][j + 1])
-        ugrid.InsertNextCell(vtk.VTK_QUAD, idList)
-
-vtkService.writevtk(ugrid, "abc.vtu")
-vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu")
+import vtk
+
+import python_vtk.vtkService.vtkService as vtkService
+
+x = [1, 2, 3, 4]
+y = [1, 2, 3, 4]
+ugrid = vtk.vtkUnstructuredGrid()
+points = vtk.vtkPoints()
+points.SetDataTypeToDouble()
+xyToNode = [[] for i in range(len(x))]
+index = 0
+for i, xCoord in enumerate(x):
+    for yCoord in y:
+        points.InsertNextPoint(xCoord, yCoord, 0.0)
+        xyToNode[i].append(index)
+        index += 1
+ugrid.SetPoints(points)
+
+# Add the volume elements
+for i, xCoord in enumerate(x[:-1]):
+    for j, yCoord in enumerate(y[:-1]):
+        idList = vtk.vtkIdList()
+        idList.InsertNextId(xyToNode[i][j])
+        idList.InsertNextId(xyToNode[i + 1][j])
+        idList.InsertNextId(xyToNode[i + 1][j + 1])
+        idList.InsertNextId(xyToNode[i][j + 1])
+        ugrid.InsertNextCell(vtk.VTK_QUAD, idList)
+
+vtkService.writevtk(ugrid, "abc.vtu")
+vtkService.writeDataArrayToNewVtkFile("abc.vtu", "var", [1., 2., 3., 4., 5., 6., 7., 8., 9.], "abc_var.vtu")

pythonVtk/vtkService/vtkAddData_not_used.py → pythonVtk/python_vtk/vtkService/vtkAddData_not_used.py

@@ -1,41 +1,41 @@
-import argparse
-
-import numpy as np
-import vtk
-
-from vtkService.vtkService import writeDataArrayToNewVtkFile
-
-
-def main():
-    #    try:
-    parser = argparse.ArgumentParser()
-    parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid")
-    parser.add_argument("varname", help="name of cell data variable")
-    parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid")
-    args = parser.parse_args()
-
-    # deserialize raw bytes into VarDataAdd
-    reader = vtk.vtkXMLUnstructuredGridReader()
-    reader.SetFileName(args.invtkfile)
-    reader.Update()
-    mesh = reader.GetOutput()
-    assert isinstance(mesh, vtk.vtkUnstructuredGrid)
-    num_cells = mesh.GetCells().GetSize()
-
-    # write 0..N-1 into data
-    npdata = np.arange(0, num_cells, 0.1)
-
-    writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile)
-    print("done")
-
-
-# except:
-#     e = sys.exc_info()[0]
-#     print("exception "+e)
-#     sys.exit(-1)
-# else:
-#     sys.exit(0)
-
-
-if __name__ == '__main__':
-    main()
+import argparse
+
+import numpy as np
+import vtk
+
+from python_vtk.vtkService.vtkService import writeDataArrayToNewVtkFile
+
+
+def main():
+    #    try:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("invtkfile", help="filename of input vtk mesh (VTK XML unstructured grid")
+    parser.add_argument("varname", help="name of cell data variable")
+    parser.add_argument("outvtkfile", help="filename of output vtk mesh (VTK XML unstructured grid")
+    args = parser.parse_args()
+
+    # deserialize raw bytes into VarDataAdd
+    reader = vtk.vtkXMLUnstructuredGridReader()
+    reader.SetFileName(args.invtkfile)
+    reader.Update()
+    mesh = reader.GetOutput()
+    assert isinstance(mesh, vtk.vtkUnstructuredGrid)
+    num_cells = mesh.GetCells().GetSize()
+
+    # write 0..N-1 into data
+    npdata = np.arange(0, num_cells, 0.1)
+
+    writeDataArrayToNewVtkFile(args.invtkfile, args.varname, npdata, args.outvtkfile)
+    print("done")
+
+
+# except:
+#     e = sys.exc_info()[0]
+#     print("exception "+e)
+#     sys.exit(-1)
+# else:
+#     sys.exit(0)
+
+
+if __name__ == '__main__':
+    main()