diff --git a/conftest.py b/conftest.py index 38883a4e..9cad16c8 100644 --- a/conftest.py +++ b/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" diff --git a/scripts/pkg_gen/create_packages.py b/scripts/pkg_gen/create_packages.py index 2259b1b4..b79be4b1 100644 --- a/scripts/pkg_gen/create_packages.py +++ b/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, diff --git a/scripts/pkg_gen/freesurfer-only.yaml b/scripts/pkg_gen/freesurfer-only.yaml new file mode 100644 index 00000000..dec14f82 --- /dev/null +++ b/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