Looking at the schema allowing to validated the XML description, I noticed that the paramType is specified as a xsd:choice of name, flag, longflag, ... which is probably incorrect.

For example, I believe name is mandatory, at least flag or longflag should be specified, ...

See https://github.com/Slicer/SlicerExecutionModel/blob/master/ModuleDescriptionParser/ModuleDescription.xsd#L52

For reference, what motivated the creation of this issue if what's discussed here: http://www.na-mic.org/Bug/view.php?id=1828

Is ITK v4.5 really required? I was able build against ITK v4.3.1 (using all default build options) and things seem to still work fine (100% tests passed)

Sometimes it is useful to pass CMake variables into C++ code. The way to do it is to use the CMake configure_file() macro. It takes a *.h.in as input and generate a .h file.
SEMMacroBuildCLI already generate a *CLP.h file. It would be great if we could define pre-processor variables by passing a simple SEMMacroBuildCLI parameter. For example:
in cmake:

SEMMacroBuildCLI( MyCLI PREPROCESSOR MY_CMAKE_VARIABLE ...)

If MY_CMAKE_VARIABLE is True, that would generate in the CLP.h file:
#define MY_CMAKE_VARIABLE
which could then be used in the MyCLI.cxx file:

int main(int argc, char* argv[])
{
  PARSE_ARGS
#ifdefined MY_CMAKE_VARIABLE
  // do something here
#endif
  ...
}

I ran into this problem before, and now again: longflag is required, name is optional. This is counterintuitive.

Consider the following CLI XML specification:

<?xml version="1.0" encoding="UTF-8"?>
<executable>
  <category>IGT</category>
  <title>crashExample</title>
  <description><![CDATA[This is a CLI module for ...]]></description>
  <version>0.0.1</version>
  <contributor>Dženan Zukić (Kitware Inc.)</contributor>
  <acknowledgements>This work was funded by ...</acknowledgements>
  <parameters>
    <label>IO</label>
    <description><![CDATA[Input/output parameters]]></description>
    <image>
      <name>inputImage</name>
      <label>Input Image</label>
      <channel>input</channel>
      <flag>i</flag>
      <description><![CDATA[The input image]]></description>
    </image>
    <image>
      <name>outputImage</name>
      <label>Output Image</label>
      <channel>output</channel>
      <flag>o</flag>
      <description><![CDATA[The output image]]></description>
    </image>
  </parameters>
</executable>

PARSE_ARGS; crashes here with the following exception message: -o <std::string>, -- <std::string> -- Argument with same flag/name already exists!. That is because a->name is an empty string, and matches the the argument -i which also has empty string as a name.

If the name tags are replaced by longflags, the problem goes away:

<?xml version="1.0" encoding="UTF-8"?>
<executable>
  <category>IGT</category>
  <title>crashExample</title>
  <description><![CDATA[This is a CLI module for ...]]></description>
  <version>0.0.1</version>
  <contributor>Dženan Zukić (Kitware Inc.)</contributor>
  <acknowledgements>This work was funded by ...</acknowledgements>
  <parameters>
    <label>IO</label>
    <description><![CDATA[Input/output parameters]]></description>
    <image>
      <longflag>inputImage</longflag>
      <label>Input Image</label>
      <channel>input</channel>
      <flag>i</flag>
      <description><![CDATA[The input image]]></description>
    </image>
    <image>
      <longflag>outputImage</longflag>
      <label>Output Image</label>
      <channel>output</channel>
      <flag>o</flag>
      <description><![CDATA[The output image]]></description>
    </image>
  </parameters>
</executable>

See also https://github.com/Slicer/tclap/

ITK is needed only because itksys is used. Instead, kwsys should either be integrated (copying the source :( or using a git submodule :) )

command line applications typically have dashes in the names of their long flags.
It should be possible to have parameters such as:
--no-something
--use-something
...

SlicerExecutionModel_DEFAULT_CLI___OUTPUT_DIRECTORY and SlicerExecutionModel_DEFAULT_CLI_INSTALL___DESTINATION variables' default value is used when using SEMMacroBuildCLI.cmake because of find_package(SlicerExecutionModel REQUIRED GenerateCLP) (line 100). One solution is to set those varialbes as CACHE variables when setting their default value in SlicerExecutionModelConfig.cmake.

When compiling a target that has specific C++ requirements, one can use the new CMake function target_compile_features() [1].

There is currently no way of passing these requirements to SEMMacroBuildCLI, and the targets created in the macro are not exposed to the user.
It would be great to either be able:

1. to pass the requirements to the CMake macro or
2. to expose the list of targets created by the macro.

Note: Both solutions are not mutually exclusive and even if 1) is implemented, 2) might still be useful in certain corner cases.

[1] https://cmake.org/cmake/help/v3.6/command/target_compile_features.html

Only one file is installed: lib/ModuleDescriptionParser/libModuleDescriptionParser.so
Is this what's intended?

The description says: project that provides macros and associated tools.

When using the SEMMacroBuildCLI, the macro perfoms a find_package() step:
https://github.com/Slicer/SlicerExecutionModel/blob/master/CMake/SEMMacroBuildCLI.cmake#L103
This step leads to another find_package() step in UseGenerateCLP.cmake:
https://github.com/Slicer/SlicerExecutionModel/blob/master/GenerateCLP/UseGenerateCLP.cmake.in#L20
In this last step, the CMake variable ITK_LIBRARIES is reset.
This reset could lead to link errors, mostly related to the IO factory mechanism if the ITK_LIBRARIES is used again after calling the SEMMacroBuildCLI, i.e. if one calls the macro multiple times to compile multiple CLIs in the same CMakeLists.txt file.
When trying to compile the example available here (branch ITKLinkError):
https://github.com/fbudin69500/3D4DImageConversion/blob/ITKLinkError/CMakeLists.txt
It results in linking error messages:
Linking CXX executable bin/4DTo3DImages
lib/lib4DTo3DImagesLib.a(4DTo3DImages.cxx.o):(.data+0x3a0): undefined reference to itk::NiftiImageIOFactoryRegister__Private()' lib/lib4DTo3DImagesLib.a(4DTo3DImages.cxx.o):(.data+0x3a8): undefined reference toitk::NrrdImageIOFactoryRegister__Private()'
lib/lib4DTo3DImagesLib.a(4DTo3DImages.cxx.o):(.data+0x3b0): undefined reference to `itk::MetaImageIOFactoryRegister__Private()'

One easy solution for the user is to save the value of the ITK_LIBRARIES in a different variable. However, this should be done directly in SEMMacroBuild.

This issue is partly related to:
#8

We are creating a new vtkMRMLTableNode. See Slicer issue #3912 at http://na-mic.org/Mantis/view.php?id=3912
This ticket will track the development to add CLI support for this new data type in SEM.

In order for CLI to report progress, the following output is the standard:

<filter-start>
 <filter-name>...</filter-name>
 ...
</filter-start>
<filter-progress>
...

There is in Slicer (Base/CLI) some utility classes that observe ITK and VTK filters to automatically generate such output.
Such classes should be moved in SlicerExecutionModel as conveniency (and be enabled only if ITK_DIR or VTK_DIR are passed).
A generic progress watcher (whose itkPluginFilterWatcher and vtkPluginFilterWatcher should derive from) should also be added.

class SEMProgressWatcher
{
public:
  SEMProgressWatcher(const char* name, const char* comment = 0, ModuleProcessInformation* inf = 0, double fraction = 1.0, double start = 0.0);
  virtual void Start();
  virtual void SetProgress(double progress);
  virtual void End();
  virtual double GetProgress();
protected:
  void ReportStart();
  void ReportEnd();
  void ReportProgress();
};
class itkPluginFilterWatcher: public itkSimpleFilterWatcher, SEMProgressWatcher
{
...
};
class vtkPluginFilterWatcher: public SEMProgressWatcher
{
...
};

Pull Request #46 is adding CircleCI verification to this repository using Docker.
The actual Docker repository is a private one ( https://hub.docker.com/r/lucasgandel/slicerexecutionmodel/ ) and should be replaced by a new Organization for SlicerExecutionModel.
Once this organization is created, changes can be made to the pull request to point to that new repository.

I could not pinpoint what is the source of this issue, but I thought I report it here. See details in QIICR/dcmqi#498.

Currently, no errors / warnings are generated if flags are duplicated in the XML schema. You will then get indeterminate runtime errors.

ITK has updated its version of KWSys (the source of itksys).

InsightSoftwareConsortium/ITK@2c45eec

That update introduced a version of KWSys that does not contain the SharedForward.h.in file, as required by GenerateCLPLauncher.

SlicerExecutionModel (specifically the GenerateCLPLauncher) will not compile with ITK master.

The CMakeLists.txt file below is a simple example that demonstrates that including SEM before ITK causes find_package(ITK COMPONENTS ) to be corrupted.

SlicerExecutionModel hash 865e2a7 does not seem to exhibit this behavior.

cmake_minimum_required(VERSION 3.0)
project(test)

set(ITK_IO_MODULES_USED "")
set(ITK_MODULES_USED
ITKAnisotropicSmoothing
ITKBinaryMathematicalMorphology
ITKCommon
ITKConnectedComponents
ITKCurvatureFlow
ITKDeprecated
ITKDiffusionTensorImage
ITKDisplacementField
ITKDistanceMap
ITKFFT
ITKFastMarching
ITKHDF5
ITKIOBMP
ITKIOBioRad
ITKIODCMTK
ITKIOGDCM
ITKIOGE
ITKIOGIPL
ITKIOImageBase
ITKIOJPEG
ITKIOLSM
ITKIOMeta
ITKIONIFTI
ITKIONRRD
ITKIOPNG
ITKIORAW
MGHIO
ITKIOSpatialObjects
ITKIOStimulate
ITKIOTIFF
ITKIOTransformBase
ITKIOXML
ITKImageAdaptors
ITKImageCompare
ITKImageCompose
ITKImageFeature
ITKImageFilterBase
ITKImageFunction
ITKImageFusion
ITKImageGradient
ITKImageGrid
ITKImageIntensity
ITKImageSources
ITKImageStatistics
ITKLabelMap
ITKLabelVoting
ITKLevelSets
ITKMathematicalMorphology
ITKMesh
ITKMetricsv4
ITKOptimizers
ITKOptimizersv4
ITKPDEDeformableRegistration
ITKQuadEdgeMesh
ITKQuadEdgeMeshFiltering
ITKRegionGrowing
ITKRegistrationCommon
ITKRegistrationMethodsv4
ITKReview
ITKSmoothing
ITKSpatialObjects
ITKStatistics
ITKTestKernel
ITKThresholding
ITKTransform
ITKV3Compatibility
${ITK_VTK_COMPONENTS}
${ITK_IO_MODULES_USED}
)

option(SEMFIRST "Include SEM First" ON)

if(SEMFIRST)

THIS FAILS

find_package(SlicerExecutionModel REQUIRED GenerateCLP)
include(${GenerateCLP_USE_FILE})
include(${SlicerExecutionModel_USE_FILE})
include(${SlicerExecutionModel_CMAKE_DIR}/SEMMacroBuildCLI.cmake)
message(STATUS "YYYY ${ITK_INCLUDE_DIRS}")

find_package(ITK 4.5 COMPONENTS
${ITK_MODULES_USED}
REQUIRED
)
include(${ITK_USE_FILE})
message(STATUS "XXXX ${ITK_INCLUDE_DIRS}")
else()

THIS WORKS

find_package(ITK 4.5 COMPONENTS
${ITK_MODULES_USED}
REQUIRED
)
include(${ITK_USE_FILE})
find_package(SlicerExecutionModel REQUIRED GenerateCLP)
include(${GenerateCLP_USE_FILE})
include(${SlicerExecutionModel_USE_FILE})
include(${SlicerExecutionModel_CMAKE_DIR}/SEMMacroBuildCLI.cmake)
message(STATUS "YYYY ${ITK_INCLUDE_DIRS}")

message(STATUS "XXXX ${ITK_INCLUDE_DIRS}")

endif()

When running the install step of SlicerExecutionModel, only one file is installed:
<CMAKE_INSTALL_PREFIX>/lib/ModuleDescriptionParser/libModuleDescriptionParser.a
It is therefore not possible to install SlicerExecutionModel and use it. It would be great to have a real install step that would install all the necessary files to be able to actually install SlicerExecutionModel.

Sometimes it might be useful to disable warnings when compiling a CLI.
The naive manual solution to call set_target_properties(${MODULE_NAME}Lib PROPERTIES COMPILE_FLAGS "-Wno-overloaded-virtual") fails because "-Dmain-=ModuleEntryPoint" is no longer defined.

Comment associated with these issues could be integrated in the documentation:

• #7 (comment)
• #26 (comment)

See: http://na-mic.org/Mantis/view.php?id=2781

[100%] Building C object GenerateCLP/CMakeFiles/GenerateCLPLauncher.dir/GenerateCLPLauncher.c.o
/Users/zach/dev/covalic-score-build/SlicerExecutionModel-Build/GenerateCLP/GenerateCLPLauncher.c:15:4: error: expected identifier or '('
   "/Users/zach/dev/covalic-score-build/SlicerExecutionModel-Build/ModuleDescriptionParser/bin" CONFIG_DIR_POST \
   ^
In file included from /Users/zach/dev/covalic-score-build/SlicerExecutionModel-Build/GenerateCLP/GenerateCLPLauncher.c:29:
/Users/zach/dev/covalic-score-build/Insight-Build/Modules/ThirdParty/KWSys/src/itksys/SharedForward.h:720:76: error: expected expression
  static const char* search_path_build[] = {KWSYS_SHARED_FORWARD_PATH_BUILD, 0};
                                                                           ^
/Users/zach/dev/covalic-score-build/Insight-Build/Modules/ThirdParty/KWSys/src/itksys/SharedForward.h:721:80: error: expected expression
  static const char* search_path_install[] = {KWSYS_SHARED_FORWARD_PATH_INSTALL, 0};

ping @vovythevov @jcfr

Discussion: http://slicer-devel.65872.n3.nabble.com/Temporary-directory-for-CLI-modules-td4035464.html

Reason to reject initial patch from @ prastawa : Patch Slicer/Slicer#400 will be problematic when the CLI is executed directly without Slicer.

Proposal:

• CLI should always expect the environment variable SEM_TEMPORARY_DIR to be set
• SEM_TEMPORARY_DIR can be set in three different ways:
  1. Set by reading the value of an other environment variable. This other environment variable would be set configuring SlicerExecutionModel using for example -DSEM_TEMPORARY_DIR_ENVVAR_NAME:STRING=SLICER_TEMPORARY_DIR
  2. Set by reading the value of special parameter named --sem-temporary-dir. If specified, other environment variable would be ignored
  3. If neither (1) or (2) have been set, temporary directory will be set to the operating system default
• code in charge of reading the other environment variable, or special parameter would be embedded in the CLI thanks to code generated by GenerateCLP

See http://www.na-mic.org/Bug/view.php?id=4225

Cc: @vovythevov

For reference:

• #124 (comment)

As of August 13th 2021, all jobs are failing:

Source: https://app.circleci.com/pipelines/github/Slicer/SlicerExecutionModel/19/workflows/ed1fad58-f7e9-4df7-8887-ddf82dd7e454

Suggested plan:

• Remove these obsolete jobs:

  SlicerExecutionModel/.circleci/config.yml

  Lines 56 to 58 in f19d6e8

  	- itk-v4.8.0_use_system_libraries-off
  	- itk-v4.10.1_use_system_libraries-off
  	- itk-v4.13.0_use_system_libraries-off

• Update itk-master_use_system_libraries-off docker image

• Add itk-v5.1.2_use_system_libraries-off and itk-v5.2.1_use_system_libraries-off

For more details:

• https://github.com/Slicer/SlicerExecutionModel#adding-or-updating-a-testing-environment
• https://github.com/Slicer/SlicerExecutionModel/tree/master/test

Compilation error when building SlicerExecutionModel in a x86_64 GNU/Linux system.

[  7%] Building CXX object ModuleDescriptionParser/CMakeFiles/ModuleDescriptionParser.dir/ModuleDescriptionParser.cxx.o
In file included from include/ITK-4.9/expat.h:11:0,
                 from SlicerExecutionModel/ModuleDescriptionParser/ModuleDescriptionParser.cxx:24:
include/ITK-4.9/expatDllConfig.h:5:30: fatal error: itk_expat_mangle.h: No such file or directory
compilation terminated.