Meta issue referencing extension updates

[jcfr]

These pull requests were created in the context of #2011

List of pull requests intended to fix and consolidate extension metadata:

• ENH: Update extension metadata naterex23/SlicerAblationPlanner#3
• ENH: Update extension metadata jamesobutler/ModelClip#2
• ENH: Update extension metadata lassoan/AnomalousFiltersExtension#2
• ENH: Update extension metadata SlicerIGT/PercutaneousApproachAnalysis#1
• ENH: Update extension metadata QIICR/PkModeling#11
• ENH: Update extension metadata SlicerIGT/PortPlacement#3
• ENH: Update extension metadata netstim/SlicerANTs#9
• ENH: Update extension metadata jcfr/SlicerToKiwiExporter#9
• ENH: Update extension metadata SlicerDMRI/SlicerWMA#12
• ENH: Update extension metadata NrgXnat/XNATSlicer#3 | Email ✉️ sent on June 13th
• ENH: Update extension metadata SlicerAirwaySegmentation#1
• ENH: Update extension metadata DCBIA-OrthoLab/AnglePlanes-Extension#21
• ENH: Update extension metadata pzaffino/SlicerArduinoController#3
• ENH: Update extension metadata Atracsys/SlicerAstmPhantomTest#4
• ENH: Update extension metadata ToothAndClaw/SlicerAuto3dgm#7
• ENH: Update extension metadata Auditory-Biophysics-Lab/Slicer-BoneThicknessMapping#7 | Email ✉️ sent on June 13th
• ENH: Update extension metadata jamesobutler/SlicerBrainVolumeRefinement#1
• ENH: Update extension metadata lassoan/SlicerBreastImplantAnalyzer#1
• ENH: Update extension metadata ikolesov/CarreraSlice#13 | Email ✉️ sent on June 13th, June 19th
• ENH: Update extension metadata fedorov/ChangeTrackerPy#20
• ENH: Update extension metadata acil-bwh/SlicerCIP#43
• ENH: Update extension metadata lassoan/SlicerCleverSegmentation#1
• ENH: Update extension metadata DCBIA-OrthoLab/CMFreg#39
• ENH: Update extension metadata CurveMaker#17 | Email ✉️ sent on June 13th
• ENH: Update extension metadata DCBIA-OrthoLab/DatabaseInteractorExtension#12
• ENH: Update extension metadata SlicerRt/SlicerDebuggingTools#17
• ENH: Update extension metadata gaudot/SlicerDentalSegmentator#2
• ENH: Update extension metadata SlicerDeveloperToolsForExtensions#30
• ENH: Update extension metadata pnlbwh/SlicerDiffusionQC#49
• ENH: Update extension metadata lassoan/SlicerDRRGenerator#2
• ENH: Update extension metadata QIICR/DSC_Analysis#5
• ENH: Update extension metadata DCBIA-OrthoLab/EasyClip-Extension#14
• ENH: Update extension metadata ErodeDilateLabel#3 | Email ✉️ sent on June 13th
• ENH: Update extension metadata SlicerRt/FilmDosimetryAnalysis#3
• ENH: Update extension metadata SlicerRt/GelDosimetryAnalysis#11
• ENH: Update extension metadata FredericBr/SlicerGeodesic#4
• ENH: Update extension metadata lpfang/GyroGuide#2 | Email ✉️ sent on June 13th
• ENH: Update extension metadata ImagingDataCommons/SlicerIDCBrowser#35
• ENH: Update extension metadata gpernelle/iGyne#4 | Email ✉️ sent on June 13th
• ENH: Update extension metadata finetjul/ImageMaker#2
• ENH: Update extension metadata PerkLab/SlicerMatlabBridge#8
• ENH: Update extension metadata SlicerMorph/SlicerMEMOS#19
• ENH: Update extension metadata DCBIA-OrthoLab/MeshStatisticsExtension#18
• ENH: Update extension metadata NIRALUser/MeshToLabelMap#12
• ENH: Update extension metadata MHubAI/SlicerMHubRunner#4
• ENH: Update extension metadata NIRALUser/3DMetricTools#14
• ENH: Update extension metadata Project-MONAI/MONAILabel#1675
• ENH: Update extension metadata Project-MONAI/SlicerMONAIViz#38
• ENH: Update extension metadata SlicerProstate/mpReview#180
• ENH: Update extension metadata kyliekeijzer/Slicer-PET-MUST-segmenter#4
• ENH: Update extension metadata needlefinder/NeedleFinder#2 | Email ✉️ sent on June 13th
• ENH: Update extension metadata NVIDIA/ai-assisted-annotation-client#109
• ENH: Update extension metadata OrthodonticAnalysis/SlicerOrthodonticAnalysis#4 | Email ✉️ sent on June 13th
• ENH: Update extension metadata aangelos28/PBNRR#6
• ENH: Update extension metadata PerkTutor/PerkTutor#76
• ENH: Update extension metadata QIICR/Slicer-PETDICOMExtension#23 | Email ✉️ sent on June 12th
• ENH: Update extension metadata QIICR/PET-IndiC#7
• ENH: Update extension metadata gti-fing/SlicerPetSpectAnalysis#5 | Email ✉️ sent on June 12th
• ENH: Update extension metadata QIICR/PETTumorSegmentation#22
• ENH: Update extension metadata DCBIA-OrthoLab/PickAndPaintExtension#25
• ENH: Update extension metadata KitwareMedical/SlicerPipelines#25
• ENH: Update extension metadata fepegar/SlicerPyTorch#16
• ENH: Update extension metadata DCBIA-OrthoLab/Q3DCExtension#106
• ENH: Update extension metadata QIICR/QuantitativeReporting#275
• ENH: Update extension metadata gsi-biomotion/SlicerRegistrationQA#17
• ENH: Update extension metadata R-Vessel-X/SlicerRVXVesselnessFilters#7 | Email ✉️ sent on June 12th
• ENH: Update extension metadata Sunderlandkyl/ScatteredTransform#1 | Email ✉️ sent on June 12th
• ENH: Update extension metadata gaoyi/SegmentationAidedRegistration#8 | Email ✉️ sent on June 12th
• ENH: Update extension metadata mazurowski-lab/SlicerSegmentWithSAM#16 | Email ✉️ sent on June 12th, June 19th
• ENH: Update extension metadata NIRALUser/ShapePopulationViewer#64
• ENH: Update extension metadata DCBIA-OrthoLab/ShapeVariationAnalyzer#70
• ENH: Update extension metadata KitwareMedical/SlicerSkeletalRepresentation#63
• ENH: Update extension metadata PerkLab/SlicerSkinMouldGenerator#3
• ENH: Update extension metadata hina-shah/SlicerBatchAnonymize#21 | Email ✉️ sent on July 3rd
• ENH: Update extension metadata JoostJM/SlicerCaseIterator#21 | Email ✉️ sent on June 12th, June 19th
• ENH: Update extension metadata KitwareMedical/SlicerCBCTToothSegmentation#4
• ENH: Update extension metadata MedicalImageAnalysisTutorials/SlicerCervicalSpine#8
• ENH: Update extension metadata MedicalImageAnalysisTutorials/SlicerCochlea#43 | Email ✉️ sent on June 12th
• ENH: Update extension metadata DCBIA-OrthoLab/SlicerConda#5
• ENH: Update extension metadata SlicerDMRI/SlicerDcm2nii#10
• ENH: Update extension metadata DCBIA-OrthoLab/SlicerDentalModelSeg#30
• ENH: Update extension metadata QIICR/SlicerDevelopmentToolbox#45
• ENH: Update extension metadata SlicerDMRI/SlicerDMRI#235 | Email ✉️ sent on June 12th
• ENH: Update extension metadata SlicerFab/SlicerFab#15 | Email ✉️ sent on June 12th
• ENH: Update extension metadata PerkLab/SlicerFreeSurfer#20
• ENH: Update extension metadata SlicerIGT/SlicerIGT#219
• ENH: Update extension metadata QIICR/SlicerLayoutButtons#3
• ENH: Update extension metadata ALive-research/Slicer-Liver#265
• ENH: Update extension metadata KitwareMedical/SlicerLookingGlass#27
• ENH: Update extension metadata netstim/SlicerNetstim#18
• ENH: Update extension metadata HOA-2/SlicerNeuroSegmentation#25
• ENH: Update extension metadata PerkLab/SlicerOpenAnatomy#20
• ENH: Update extension metadata SlicerOpenCV#79
• ENH: Update extension metadata jamesobutler/SlicerRegularizedFastMarching#1
• ENH: Update extension metadata SlicerRt/SlicerRT#243
• ENH: Update extension metadata sjh26/SlicerThemes#3
• ENH: Update extension metadata MarinaSandonis/SlicerTissueSegmentation#2 | Email ✉️ sent on June 12th
• ENH: Update extension metadata KitwareMedical/SlicerVirtualMouseCursor#3
• ENH: Update extension metadata KitwareMedical/SlicerVirtualReality#174
• ENH: Update extension metadata vmtk/SlicerExtension-VMTK#114
• ENH: Update extension metadata NIRALUser/SPHARM-PDM#86
• ENH: Update extension metadata JBeninca/SlicerStereotaxia#10
• ENH: Update extension metadata mturja-vf-ic-bd/SlicerSurfaceLearner#9 | Email ✉️ sent on June 12th, June 19th
• ENH: Update extension metadata SlicerHeart/SlicerSurfaceMarkup#14
• ENH: Update extension metadata gattia/Slicer-T2mapping#5
• ENH: Update extension metadata QIICR/TCIABrowser#69
• ENH: Update extension metadata SlicerMicro/Slicer-TITAN#4 | Email ✉️ sent on June 12th, June 18th
• ENH: Update extension metadata faustomilletari/TOMAAT-Slicer#16 | Email ✉️ sent on June 12th, June 18th
• ENH: Update extension metadata fedesemeraro/SlicerTomoSAM#18 | Email ✉️ sent on June 12th, June 18th
• ENH: Update extension metadata fepegar/SlicerTorchIO#15
• ENH: Update extension metadata pnlbwh/ukftractography#159
• ENH: Update extension metadata PerkLab/SlicerVolumeClip#3
• ENH: Update extension metadata SlicerIGT/ResectionPlanner#5
• ENH: Update extension metadata SlicerRt/SegmentRegistration#9
• ENH: Update extension metadata moselhy/SlicerSequenceRegistration#6
• ENH: Update extension metadata sebastianandress/Slicer-SurfaceFragmentsRegistration#5
• ENH: Update extension metadata sebastianandress/Slicer-SurfaceWrapSolidify#9
• ENH: Update extension metadata QIICR/T1Mapping#2 | Email ✉️ sent on June 12th
• ENH: Update extension metadata SkullStripper#12
• ENH: Update extension metadata SlicerIGT/aigt#58
• ENH: Update extension metadata lassoan/SlicerAutoscroll#1
• ENH: Update extension metadata openigtlink/SlicerOpenIGTLink#131
• ENH: Update extension metadata ETS-vis-interactive/SlicerPRISMRendering#35
• ENH: Update extension metadata SlicerProstate/SlicerProstate#56
• ENH: Update extension metadata KitwareMedical/SlicerPythonTestRunner#7
• ENH: Update extension metadata AIM-Harvard/SlicerRadiomics#81
• ENH: Update extension metadata harellab/SlicerUHFMRTools#10
• ENH: Update extension metadata VASST/VASSTAlgorithms#4
• ENH: Update extension metadata KitwareMedical/ShapeRegressionExtension#34

[fedorov]

@jcfr can you please review this comment: QIICR/SlicerDevelopmentToolbox#45 (comment) ?

Extension build stopped working today, which coincided with your PR...

[jcfr]

Thanks for pointing this out, I will have a look later when back on the 👨‍💻

[jcfr]

List of pull requests and issues intended to fix and consolidate extension metadata for extension not yet integrated:

• DOC: Fix extension homepage url rbumm/SlicerPACSConnector#5
• ENH: Update extension metadata mturja-vf-ic-bd/SlicerDeepLearningUI#30
• ENH: Update extension metadata fatihtalu/Slicer-ThicknessMap#7
• ENH: Update extension metadata AnnaPSQ/Slicer-SLICSegmentEditorEffect#1
• ENH: Update extension metadata SenonETS/SlicerIGSpineDeformity#3
• ENH: Update extension metadata AlistairMcCutcheon/SlicerMSLesionVisualiser#1
• https://github.com/Rediminds/SlicerRediMinds/pull/2
• ENH: Update extension metadata SlicerDMRI/SlicerTractParcellation#4
• ENH: Update extension metadata lapdMouse/Slicer-lapdMouseBrowser#1
• ENH: Update extension metadata laboratory-for-translational-medicine/SlicerCineTrack#144
• ENH: Update extension metadata mazurowski-lab/SlicerSegmentHumanBody#4
• ENH: Update extension metadata CSIM-Toolkits/SlicerDiffusionComplexityMap#1
• ENH: Update extension metadata LOAMRI/Slicer-DTI-ALPS#1
• ENH: Update extension metadata UWA-Medical-Physics/SlicerBatchBrainMRTumorSegmentation#1
• ENH: Update extension metadata saimasafdar2021/Slicer_SurfaceModelNodesSelector#1
• Update extension metadata and formatting tweaks dmolony3/SlicerFractionalMyocardialMass#5
• ENH: Update extension metadata WashUMusculoskeletalCore/Slicer-MusculoskeletalAnalysis#18
• ENH: Update extension metadata gongmingjun/SlicerDentureRegistration#10
• https://gitlab.kitware.com/vtk/meshing/SlicerVESPA/-/merge_requests/3

For future reference, following code was used to generate the s4ext from json:

import json
import sys
from pathlib import Path

extensions_index_dir = Path("/home/jcfr/Projects/ExtensionsIndex")
updated_extensions_index_dir = extensions_index_dir

def parse_s4ext(ext_file_path):
    """Parse a Slicer extension description file.
    :param ext_file_path: Path to a Slicer extension description file.
    """
    ext_metadata = {}
    with open(ext_file_path) as ext_file:
        for line in ext_file:
            if not line.strip() or line.startswith("#"):
                continue
            fields = [field.strip() for field in line.split(' ', 1)]
            assert(len(fields) <= 2)
            ext_metadata[fields[0]] = fields[1] if len(fields) == 2 else None
    return ext_metadata

# Collect s4ext files
s4ext_filepaths = list(extensions_index_dir.glob("*.s4ext"))

print(f"Found {len(s4ext_filepaths)} extension files (.s4ext)")

# Parse s4ext files and generate corresponding json files
for index, filepath in enumerate(s4ext_filepaths):

    metadata = parse_s4ext(filepath)
    #print("filepath", filepath)
    updated_metadata = {
        "$schema": "https://raw.githubusercontent.com/Slicer/Slicer/main/Schemas/slicer-extension-catalog-entry-schema-v1.0.0.json#",
        "scm_url": metadata["scmurl"],
        "scm_revision": metadata["scmrevision"],
        "build_dependencies": [] if metadata.get("depends", "NA") == "NA" else metadata["depends"].split(" "),
        "category": metadata["category"],
        "build_subdirectory": metadata["build_subdirectory"],
    }

    with open(updated_extensions_index_dir / f"{filepath.stem}.json", 'w') as fileContents:
        fileContents.write(json.dumps(updated_metadata, sort_keys=True, indent=2))
        fileContents.write("\n")

print(f"Generated {index + 1} extension files (.json)")

from pprint import pprint as pp

print(f"\nMetadata of extension #{index + 1} ({filepath.stem}):\n")
pp(updated_metadata)