Error when Calling a created CLI script

[markus-stoll]

Call a created CLI:
./bunnyCGAL_HiFlow3.msml.py -h

returns

WARNING  Could not load imported repository /home/nschoch/HiFlow3_Project/MSML/msml/examples/BunnyExample/msml-repository.xml at .
WARNING  Could not load imported repository /home/nschoch/.config/msml/msml-repository.xml at .
INFO     READING alphabet...
INFO     Alphabet Paths:  
[Path(u'/home/nschoch/HiFlow3_Project/MSML/msml/share/alphabet')]
INFO     found 77 xml files in the alphabet search path
WARNING  _logical type Geometry requested, but does not exist WARNING  _logical type vector requested, but does not exist WARNING  _logical type vector.matID requested, but does not exist WARNING  _logical type PointSet requested, but does not exist WARNING  _logical type PointSet requested, but does not exist CRITICAL Slot pulse in parent surfacePressureOnMesh does not have a physical type defined. This can cause conversion errors.
WARNING  _logical type bool requested, but does not exist
ERROR    MiscPython Operators unavaiable because of ImportError: No  
module named scipy
ERROR    msml.ext.misc_python.generateBeamDisplacementsFromParaCoeffs  
is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromParaCoeffs'
ERROR    msml.ext.misc_python.copy_file is not available  
(function/attribute not found), got exception message ''module' object has no attribute 'copy_file'
ERROR     
msml.ext.misc_python.generateBeamDisplacementsFromSplineCoeffs is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromSplineCoeffs'
ERROR    msml.ext.misc.measureMeshQuality is not available  
(function/attribute not found), got exception message ''module' object has no attribute 'measureMeshQuality'
ERROR    msml.ext.misc.calculateHausdorffDistance is not available  
(function/attribute not found), got exception message ''module' object has no attribute 'calculateHausdorffDistance'
INFO     Need convert value of <var input_vol_mesh : <Sort: <class  
'msml.sortdef.MSMLString'>, <class 'msml.sortdef.Mesh'>> = bunnyVolumeMeshCGAL.vtk>
INFO     Need convert value of <var input_surf_mesh : <Sort: <class  
'msml.sortdef.VTK'>, <class 'msml.sortdef.TriangularSurface'>> = Bunny6000Surface.vtk>
INFO     Need convert value of <var gen_1_ : <Sort: <type 'bool'>,  
None> = false>
INFO     Need convert value of <var gen_2_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 3>
INFO     Need convert value of <var gen_3_ : <Sort: <type 'bool'>,  
None> = false>
INFO     Need convert value of <var gen_4_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 0.02>
INFO     Need convert value of <var gen_5_ : <Sort: <type 'bool'>,  
None> = false>
INFO     Need convert value of <var gen_6_ : <Sort: <type 'bool'>,  
None> = false>
INFO     Need convert value of <var gen_7_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 20>
INFO     Need convert value of <var gen_8_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 0.006>
INFO     Need convert value of <var gen_9_ : <Sort: <type 'bool'>,  
None> = false>
INFO     Need convert value of <var gen_10_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 0.004>
INFO     Need convert value of <var gen_11_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.045 0.06>
INFO     Need convert value of <var gen_12_ : <Sort: <class  
'msml.sortdef.MSMLString'>, None> = points>
INFO     Need convert value of <var gen_13_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.19 0.06>
INFO     Need convert value of <var gen_14_ : <Sort: <class  
'msml.sortdef.MSMLString'>, None> = elements>
INFO     Need convert value of <var gen_15_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = -0.1 0.16 -0.07 0.07 0.19 0.06>
INFO     Need convert value of <var gen_16_ : <Sort: <class  
'msml.sortdef.MSMLString'>, None> = points>
ERROR    Parameter name of Element mass is not specified in definition.
INFO     Need convert value of <var gen_17_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = 0.5 -0.06 -0.3>
INFO     Need convert value of <var gen_18_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 1.000>
INFO     Need convert value of <var gen_19_ : <Sort: <class  
'msml.sortdef.MSMLInt'>, None> = 4166>
INFO     Need convert value of <var gen_20_ : <Sort: <class  
'msml.sortdef.MSMLFloat'>, None> = 0.488>
INFO     Need convert value of <var gen_21_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = 0.01 0.0 -0.03>
INFO     Need convert value of <var gen_22_ : <Sort: <class  
'msml.sortdef.MSMLListF'>, None> = 0.0 0.02 0.0>
ERROR    some features are not supported by exporter
ERROR    -- msml_file: set(['object_element_displacement_supported',  
'output_supported', 'object_element_mass_supported', 'env_timeintegration_Newmark_supported',
'environment_multiple_simulation_steps_supported',
'constraints_supported', 'env_processingunit_CPU_supported',
'material_region_supported',
'env_preconditioner_SGAUSS_SEIDEL_supported',
'object_element_linearElasticMaterial_supported',
'sets_elements_supported', 'object_element_surfacePressure_supported',
'object_element_displacementConstraint_supported',
'amount_constraints_n', 'sets_surface_supported', 'environment_simulation_steps_supported', 'scene_objects_supported', 'object_element_fixedConstraint_supported', 'sets_nodes_supported',
'env_linearsolver_CG_supported'])
ERROR    -- supported:  
frozenset(['object_element_displacement_supported',
'output_supported', 'object_element_mass_supported', 'env_processingunit_CPU_supported', 'constraints_supported', 'material_region_supported', 'env_linearsolver_iterativeCG_supported',
'env_preconditioner_None_supported',
'object_element_linearElasticMaterial_supported',
'scene_objects_supported',
'env_timeintegration_dynamicImplicitEuler_supported',
'sets_surface_supported', 'sets_elements_supported', 'environment_simulation_steps_supported',
'interbody_contact_simulation_supported',
'object_element_fixedConstraint_supported', 'sets_nodes_supported'])
ERROR    -- not matched: set(['env_linearsolver_CG_supported',  
'environment_multiple_simulation_steps_supported',
'amount_constraints_n', 'object_element_surfacePressure_supported',
'env_timeintegration_Newmark_supported',
'env_preconditioner_SGAUSS_SEIDEL_supported',
'object_element_displacementConstraint_supported'])
Traceback (most recent call last):
   File "./bunnyCGAL_HiFlow3.msml.py", line 27, in <module>
     main()
   File "./bunnyCGAL_HiFlow3.msml.py", line 23, in main
     executor_options = {}
   File
"/home/nschoch/HiFlow3_Project/MSML/msml/src/msml/api/clisupport.py",
line 170, in cli_app
     variables = get_arguments(mfile)
   File
"/home/nschoch/HiFlow3_Project/MSML/msml/src/msml/api/clisupport.py",
line 205, in get_arguments
     parser = clictk.build_argument_parser(exe)
   File
"/usr/local/lib/python2.7/dist-packages/clictk/argparseutil.py", line 26, in build_argument_parser
     for p in executable:
TypeError: iter() returned non-iterator of type 'tuple'

[markus-stoll]

You need to add role="input" for all vars that should be used as input.
Does this help?

[NicolaiSchoch]

Yes, but now there is another new error:

nschoch@numhpc0023:/HiFlow3_Project/MSML/msml/examples/BunnyExample$ python bunnyCGAL_HiFlow3.msml.py
WARNING Could not load imported repository /home/nschoch/HiFlow3_Project/MSML/msml/examples/BunnyExample/msml-repository.xml at .
WARNING Could not load imported repository /home/nschoch/.config/msml/msml-repository.xml at .
INFO READING alphabet...
INFO Alphabet Paths: [Path(u'/home/nschoch/HiFlow3_Project/MSML/msml/share/alphabet')]
INFO found 77 xml files in the alphabet search path
WARNING logical type Geometry requested, but does not exist
WARNING logical type vector requested, but does not exist
WARNING logical type vector.matID requested, but does not exist
WARNING logical type PointSet requested, but does not exist
WARNING logical type PointSet requested, but does not exist
CRITICAL Slot pulse in parent surfacePressureOnMesh does not have a physical type defined. This can cause conversion errors.
WARNING logical type bool requested, but does not exist
ERROR MiscPython Operators unavaiable because of ImportError: No module named scipy
ERROR msml.ext.misc_python.generateBeamDisplacementsFromParaCoeffs is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromParaCoeffs'
ERROR msml.ext.misc_python.copy_file is not available (function/attribute not found), got exception message ''module' object has no attribute 'copy_file'
ERROR msml.ext.misc_python.generateBeamDisplacementsFromSplineCoeffs is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromSplineCoeffs'
ERROR msml.ext.misc.measureMeshQuality is not available (function/attribute not found), got exception message ''module' object has no attribute 'measureMeshQuality'
ERROR msml.ext.misc.calculateHausdorffDistance is not available (function/attribute not found), got exception message ''module' object has no attribute 'calculateHausdorffDistance'
INFO Need convert value of <var input_vol_mesh : <Sort: <class 'msml.sortdef.MSMLString'>, <class 'msml.sortdef.Mesh'>> = bunnyVolumeMeshCGAL.vtk>
INFO Need convert value of <var input_surf_mesh : <Sort: <class 'msml.sortdef.VTK'>, <class 'msml.sortdef.TriangularSurface'>> = Bunny6000Surface.vtk>
INFO Need convert value of <var gen_1 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_2 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3>
INFO Need convert value of <var gen_3 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_4 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.02>
INFO Need convert value of <var gen_5 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_6 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_7_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 20>
INFO Need convert value of <var gen_8_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.006>
INFO Need convert value of <var gen_9_ : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_10_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.004>
INFO Need convert value of <var gen_11_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.045 0.06>
INFO Need convert value of <var gen_12_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points>
INFO Need convert value of <var gen_13_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.19 0.06>
INFO Need convert value of <var gen_14_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements>
INFO Need convert value of <var gen_15_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.16 -0.07 0.07 0.19 0.06>
INFO Need convert value of <var gen_16_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points>
ERROR Parameter name of Element mass is not specified in definition.
INFO Need convert value of <var gen_17_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.5 -0.06 -0.3>
INFO Need convert value of <var gen_18_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 1.000>
INFO Need convert value of <var gen_19_ : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 4166>
INFO Need convert value of <var gen_20_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.488>
INFO Need convert value of <var gen_21_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.01 0.0 -0.03>
INFO Need convert value of <var gen_22_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.0 0.02 0.0>
ERROR some features are not supported by exporter
ERROR -- msml_file: set(['object_element_displacement_supported', 'output_supported', 'object_element_mass_supported', 'env_timeintegration_Newmark_supported', 'environment_multiple_simulation_steps_supported', 'constraints_supported', 'env_processingunit_CPU_supported', 'material_region_supported', 'env_preconditioner_SGAUSS_SEIDEL_supported', 'object_element_linearElasticMaterial_supported', 'sets_elements_supported', 'object_element_surfacePressure_supported', 'object_element_displacementConstraint_supported', 'amount_constraints_n', 'sets_surface_supported', 'environment_simulation_steps_supported', 'scene_objects_supported', 'object_element_fixedConstraint_supported', 'sets_nodes_supported', 'env_linearsolver_CG_supported'])
ERROR -- supported: frozenset(['object_element_displacement_supported', 'output_supported', 'object_element_mass_supported', 'env_processingunit_CPU_supported', 'constraints_supported', 'material_region_supported', 'env_linearsolver_iterativeCG_supported', 'env_preconditioner_None_supported', 'object_element_linearElasticMaterial_supported', 'scene_objects_supported', 'env_timeintegration_dynamicImplicitEuler_supported', 'sets_surface_supported', 'sets_elements_supported', 'environment_simulation_steps_supported', 'interbody_contact_simulation_supported', 'object_element_fixedConstraint_supported', 'sets_nodes_supported'])
ERROR -- not matched: set(['env_linearsolver_CG_supported', 'environment_multiple_simulation_steps_supported', 'amount_constraints_n', 'object_element_surfacePressure_supported', 'env_timeintegration_Newmark_supported', 'env_preconditioner_SGAUSS_SEIDEL_supported', 'object_element_displacementConstraint_supported'])
WARNING Could not load imported repository /home/nschoch/HiFlow3_Project/MSML/msml/examples/BunnyExample/msml-repository.xml at .
WARNING Could not load imported repository /home/nschoch/.config/msml/msml-repository.xml at .
INFO READING alphabet...
INFO Alphabet Paths: [Path(u'/home/nschoch/HiFlow3_Project/MSML/msml/share/alphabet')]
INFO found 77 xml files in the alphabet search path
WARNING logical type Geometry requested, but does not exist
WARNING logical type vector requested, but does not exist
WARNING logical type vector.matID requested, but does not exist
WARNING logical type PointSet requested, but does not exist
WARNING logical type PointSet requested, but does not exist
CRITICAL Slot pulse in parent surfacePressureOnMesh does not have a physical type defined. This can cause conversion errors.
WARNING logical type bool requested, but does not exist
ERROR MiscPython Operators unavaiable because of ImportError: No module named scipy
ERROR msml.ext.misc_python.generateBeamDisplacementsFromParaCoeffs is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromParaCoeffs'
ERROR msml.ext.misc_python.copy_file is not available (function/attribute not found), got exception message ''module' object has no attribute 'copy_file'
ERROR msml.ext.misc_python.generateBeamDisplacementsFromSplineCoeffs is not available (function/attribute not found), got exception message ''module' object has no attribute 'generateBeamDisplacementsFromSplineCoeffs'
ERROR msml.ext.misc.measureMeshQuality is not available (function/attribute not found), got exception message ''module' object has no attribute 'measureMeshQuality'
ERROR msml.ext.misc.calculateHausdorffDistance is not available (function/attribute not found), got exception message ''module' object has no attribute 'calculateHausdorffDistance'
INFO Need convert value of <var input_vol_mesh : <Sort: <class 'msml.sortdef.MSMLString'>, <class 'msml.sortdef.Mesh'>> = bunnyVolumeMeshCGAL.vtk>
INFO Need convert value of <var input_surf_mesh : <Sort: <class 'msml.sortdef.VTK'>, <class 'msml.sortdef.TriangularSurface'>> = Bunny6000Surface.vtk>
INFO Need convert value of <var gen_1 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_2 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 3>
INFO Need convert value of <var gen_3 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_4 : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.02>
INFO Need convert value of <var gen_5 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_6 : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_7_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 20>
INFO Need convert value of <var gen_8_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.006>
INFO Need convert value of <var gen_9_ : <Sort: <type 'bool'>, None> = false>
INFO Need convert value of <var gen_10_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.004>
INFO Need convert value of <var gen_11_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.045 0.06>
INFO Need convert value of <var gen_12_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points>
INFO Need convert value of <var gen_13_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.03 -0.07 0.07 0.19 0.06>
INFO Need convert value of <var gen_14_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = elements>
INFO Need convert value of <var gen_15_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = -0.1 0.16 -0.07 0.07 0.19 0.06>
INFO Need convert value of <var gen_16_ : <Sort: <class 'msml.sortdef.MSMLString'>, None> = points>
ERROR Parameter name of Element mass is not specified in definition.
INFO Need convert value of <var gen_17_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.5 -0.06 -0.3>
INFO Need convert value of <var gen_18_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 1.000>
INFO Need convert value of <var gen_19_ : <Sort: <class 'msml.sortdef.MSMLInt'>, None> = 4166>
INFO Need convert value of <var gen_20_ : <Sort: <class 'msml.sortdef.MSMLFloat'>, None> = 0.488>
INFO Need convert value of <var gen_21_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.01 0.0 -0.03>
INFO Need convert value of <var gen_22_ : <Sort: <class 'msml.sortdef.MSMLListF'>, None> = 0.0 0.02 0.0>
ERROR some features are not supported by exporter
ERROR -- msml_file: set(['object_element_displacement_supported', 'output_supported', 'object_element_mass_supported', 'env_timeintegration_Newmark_supported', 'environment_multiple_simulation_steps_supported', 'constraints_supported', 'env_processingunit_CPU_supported', 'material_region_supported', 'env_preconditioner_SGAUSS_SEIDEL_supported', 'object_element_linearElasticMaterial_supported', 'sets_elements_supported', 'object_element_surfacePressure_supported', 'object_element_displacementConstraint_supported', 'amount_constraints_n', 'sets_surface_supported', 'environment_simulation_steps_supported', 'scene_objects_supported', 'object_element_fixedConstraint_supported', 'sets_nodes_supported', 'env_linearsolver_CG_supported'])
ERROR -- supported: frozenset(['object_element_displacement_supported', 'output_supported', 'object_element_mass_supported', 'env_processingunit_CPU_supported', 'constraints_supported', 'material_region_supported', 'env_linearsolver_iterativeCG_supported', 'env_preconditioner_None_supported', 'object_element_linearElasticMaterial_supported', 'scene_objects_supported', 'env_timeintegration_dynamicImplicitEuler_supported', 'sets_surface_supported', 'sets_elements_supported', 'environment_simulation_steps_supported', 'interbody_contact_simulation_supported', 'object_element_fixedConstraint_supported', 'sets_nodes_supported'])
ERROR -- not matched: set(['env_linearsolver_CG_supported', 'environment_multiple_simulation_steps_supported', 'amount_constraints_n', 'object_element_surfacePressure_supported', 'env_timeintegration_Newmark_supported', 'env_preconditioner_SGAUSS_SEIDEL_supported', 'object_element_displacementConstraint_supported'])
Traceback (most recent call last):
File "bunnyCGAL_HiFlow3.msml.py", line 27, in
main()
File "bunnyCGAL_HiFlow3.msml.py", line 23, in main
executor_options = {}
File "/home/nschoch/HiFlow3_Project/MSML/msml/src/msml/api/clisupport.py", line 170, in cli_app
variables = get_arguments(mfile)
File "/home/nschoch/HiFlow3_Project/MSML/msml/src/msml/api/clisupport.py", line 226, in get_arguments
value = os.path.abspath(value)
File "/usr/lib/python2.7/posixpath.py", line 343, in abspath
if not isabs(path):
File "/usr/lib/python2.7/posixpath.py", line 53, in isabs
return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'
nschoch@numhpc0023:/HiFlow3_Project/MSML/msml/examples/BunnyExample$

[NicolaiSchoch]

And executing:
nschoch@numhpc0023:~/HiFlow3_Project/MSML/msml/examples/BunnyExample$ ./bunnyCGAL_HiFlow3.msml.py -h

does not yield anything at all...

And executing
nschoch@numhpc0023:~/HiFlow3_Project/MSML/msml/examples/BunnyExample$ ./bunnyCGAL_HiFlow3.msml.py --xml
yields:
MSML<title>bunnyCGAL_HiFlow3.msml.xml</title>...Offered Parametersn/ainput_surf_meshinput_surf_mesh input_surf_meshBunny6000Surface.vtkinput

[NicolaiSchoch]

Okay, I guess it generally works now. :-)

The workflow should be:

1.) Test pipeline execution
python ../../src/msml.py exec bunnyCGAL_HiFlow3.msml.xml -e hiflow3

2.) Generate CLI script via
python ../../src/msml.py cli bunnyCGAL_HiFlow3.msml.xml -e hiflow3
This produces the file ``bunnyCGAL_HiFlow3.msml.py`

3.) Check out the CLI xml file via
python bunnyCGAL_HiFlow3.msml.py --xml > bunnyCGAL_HiFlow3.msml.py.CLIinfo.xml
in order to figure out how to use the variables as parameters for the CLI execution.
E.g. here, the "name" of the input variable is input_surf_mesh

4.) Execute CLI script via
python bunnyCGAL_HiFlow3.msml.py --input_surf_mesh Bunny6000Surface.vtk
possibly direct simulation output from console into history.txt file via
python bunnyCGAL_HiFlow3.msml.py --input_surf_mesh Bunny6000Surface.vtk > history.txt

---

What still doesn't work, is the --help or -h option... these don't produce anything... do they?
I cannot find any implementation of this functionality either... as opposed to the --xml option, which is in src/msml/api/clisupport.py.
However, they somehow should, as mentioned in areku's post on 11 Feb in #217.
Then, one could omit step 3) in the above description, and directly know how to handle step 4).

Any ideas how to get the --help work?

[NicolaiSchoch]

Am I right in thinking, that such produced CLI scripts are supposted to be feasible for handling in MITK CGS workbench (once the MITK support has created the corresponding plugin/interface), or is there anything further for us to be done from this stage on?

[wadoon]

See b015d97
Fixed in branch release_cand_1.0

Additionally, update pyclictk:

pip install -U pyclictk 

Current Version is 0.2.3

[NicolaiSchoch]

Ah, perfect! Thanks!! :)
Is there a reason, why this functionality is not in experimental branch yet?
Any objection to adding it there, too?

[wadoon]

This is a small patch. I have just checked out the default branch.
You should be able to cherry-pick this commit. It is just a change of three lines.

[NicolaiSchoch]

Ah, yes, that works!

However, the --help still does not produce the output, which you pasted in issue 217:

(msml)➜  msml git:(experimental) ✗ python test.py --help
usage: test.py [-h] [--pr float] [--input_surf_mesh file.vtk] [--gen_1_ bool]
               [--ym float] [--gen_4_ vector.float] [--gen_3_ string]
               [--gen_2_ vector.float] [--gen_6_ float] [--input_vol_mesh str]
               [--gen_5_ string] [--xml]

optional arguments:
  -h, --help  show this help message and exit
  --xml       show cli xml

[markus-stoll]

cherry picked, the fix is now also available on experimental.

[markus-stoll]

Does everything work (except --help)? How is the MITK integration?
Make sure your needed data types are available in CTK (SFB S01 issue nr 167).

[NicolaiSchoch]

Yes, so far, everything seems to work fine; except for the "--help".

Alexander, do you remember, where and how you produced the output which you pasted in issue 217 (see also above)?
I cannot find it.
Maybe we could also cherry-pick this part in order to have it in the experimental branch?

About the MITK integration:
The data types should be fine; they fit to CTK as far as possible.
I talked to Andy about ways to test the MITK integration via MITK's CLI modules plugin, which is not yet in MITK CGS Workbench but will be in the soon-to-come next release.
We can still test it by using the standard MITK release 2015-05 and installing the plugin via CMake.
-- I did not yet do this.

However, along with Patrick I managed to use the CLI mitral valve preprocessing script for setting up a "cognitive app" prototype, which is now available in the SFB redmine/git (SFB B01 Cognitive Apps).