fixed bug related to updated fileformats to_mime

Author: tclose

conftest.py

@@ -13,13 +13,6 @@
 EXAMPLE_WORKFLOWS_DIR = EXAMPLE_SPECS_DIR / "workflow"
 
 
-@File.generate_sample_data.register
-def file_generate_sample_data(file: File, dest_dir: Path):
-    a_file = dest_dir / "a_file.x"
-    a_file.write_text("a sample file")
-    return [a_file]
-
-
 @pytest.fixture
 def gen_test_conftest():
     return PKG_DIR / "scripts" / "pkg_gen" / "resources" / "conftest.py"

scripts/pkg_gen/create_packages.py

@@ -323,7 +323,7 @@ def combine_types(type_, prev_type):
                         InputsConverter,
                         {
                             "types": {
-                                n: fileformats.core.utils.to_mime(t)
+                                n: fileformats.core.utils.to_mime(t, official=False)
                                 for n, t in input_types.items()
                             }
                         },
@@ -333,7 +333,7 @@ def combine_types(type_, prev_type):
                         OutputsConverter,
                         {
                             "types": {
-                                n: fileformats.core.utils.to_mime(t)
+                                n: fileformats.core.utils.to_mime(t, official=False)
                                 for n, t in output_types.items()
                             },
                             "templates": output_templates,

scripts/pkg_gen/freesurfer-only.yaml

@@ -0,0 +1,88 @@
+packages:
+- freesurfer
+interfaces:
+  freesurfer:
+  - ParseDICOMDir
+  - UnpackSDICOMDir
+  - MRIConvert
+  - Resample
+  - ReconAll
+  - BBRegister
+  - ApplyVolTransform
+  - Smooth
+  - DICOMConvert
+  - RobustRegister
+  - FitMSParams
+  - SynthesizeFLASH
+  - MNIBiasCorrection
+  - WatershedSkullStrip
+  - Normalize
+  - CANormalize
+  - CARegister
+  - CALabel
+  - MRIsCALabel
+  - SegmentCC
+  - SegmentWM
+  - EditWMwithAseg
+  - ConcatenateLTA
+  - MRISPreproc
+  - MRISPreprocReconAll
+  - GLMFit
+  - OneSampleTTest
+  - Binarize
+  - Concatenate
+  - SegStats
+  - SegStatsReconAll
+  - Label2Vol
+  - MS_LDA
+  - Label2Label
+  - Label2Annot
+  - SphericalAverage
+  - SampleToSurface
+  - SurfaceSmooth
+  - SurfaceTransform
+  - Surface2VolTransform
+  - SurfaceSnapshots
+  - ApplyMask
+  - MRIsConvert
+  - MRITessellate
+  - MRIPretess
+  - MRIMarchingCubes
+  - SmoothTessellation
+  - MakeAverageSubject
+  - ExtractMainComponent
+  - Tkregister2
+  - AddXFormToHeader
+  - CheckTalairachAlignment
+  - TalairachAVI
+  - TalairachQC
+  - RemoveNeck
+  - MRIFill
+  - MRIsInflate
+  - Sphere
+  - FixTopology
+  - EulerNumber
+  - RemoveIntersection
+  - MakeSurfaces
+  - Curvature
+  - CurvatureStats
+  - Jacobian
+  - MRIsCalc
+  - VolumeMask
+  - ParcellationStats
+  - Contrast
+  - RelabelHypointensities
+  - Aparc2Aseg
+  - Apas2Aseg
+  - MRIsExpand
+  - MRIsCombine
+  - RobustTemplate
+  - FuseSegmentations
+  - MPRtoMNI305
+  - RegisterAVItoTalairach
+  - EMRegister
+  - Register
+  - Paint
+  - MRICoreg
+  - GTMSeg
+  - GTMPVC