updated auto-generated yaml files with fileformats

.gitignore

@@ -137,10 +137,5 @@ dmypy.json
 # Mac garbarge
 .DS_store
 
-# Auto-generated version files
-/pydra/tasks/freesurfer/_version.py
-/fileformats/src/fileformats/medimage_freesurfer/_version.py
-/fileformts/extras/fileformats/extras/medimage_freesurfer/_version.py
-
-# Auto-converted (from Nipype) interfaces directory (needs to be stripped before packaging)
 /pydra/tasks/freesurfer/auto
+/pydra/tasks/freesurfer/_version.py

README.rst

@@ -2,10 +2,10 @@
 Pydra task package for freesurfer
 ===============================
 
-.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml/badge.svg
-   :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
-.. image:: https://codecov.io/gh/nipype/pydra-freesurfer/branch/main/graph/badge.svg?token=UIS0OGPST7
-   :target: https://codecov.io/gh/nipype/pydra-freesurfer
+.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/pythonpackage.yaml/badge.svg
+   :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/pythonpackage.yaml
+.. .. image:: https://codecov.io/gh/nipype/pydra-freesurfer/branch/main/graph/badge.svg?token=UIS0OGPST7
+..    :target: https://codecov.io/gh/nipype/pydra-freesurfer
 .. image:: https://img.shields.io/pypi/pyversions/pydra-freesurfer.svg
    :target: https://pypi.python.org/pypi/pydra-freesurfer/
    :alt: Supported Python versions

fileformats/extras/fileformats/extras/medimage_freesurfer/__init__.py

@@ -1 +1,108 @@
-from ._version import __version__
+from pathlib import Path
+import typing as ty
+from random import Random
+from fileformats.core import FileSet
+from fileformats.medimage_freesurfer import (
+    Orig,
+    Xfm,
+    Lta,
+    Stats,
+    Avg_curv,
+    Inflated,
+    Nofix,
+    Pial,
+    M3z,
+    Thickness,
+    Annot,
+    Label,
+    Ctab,
+    Out,
+    Area,
+    White,
+    Reg,
+)
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_orig_data(orig: Orig, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_xfm_data(xfm: Xfm, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_lta_data(lta: Lta, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_stats_data(stats: Stats, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_avg_curv_data(avg_curv: Avg_curv, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_inflated_data(inflated: Inflated, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_nofix_data(nofix: Nofix, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_pial_data(pial: Pial, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_m3z_data(m3z: M3z, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_thickness_data(thickness: Thickness, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_annot_data(annot: Annot, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_label_data(label: Label, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_ctab_data(ctab: Ctab, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_out_data(out: Out, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_area_data(area: Area, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_white_data(white: White, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError
+
+
+@FileSet.generate_sample_data.register
+def gen_sample_reg_data(reg: Reg, dest_dir: Path, seed: ty.Union[int, Random], stem: ty.Optional[str]):
+    raise NotImplementedError

fileformats/extras/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "fileformats-medimage-freesurfer-extras"
-description = "Classes for representing file formats used exclusively by the Freesurfer tool in Python classes for use in type hinting in data workflows"
+description = "Extensions to add functionality to tool-specific *fileformats* classes"
 readme = "README.rst"
 requires-python = ">=3.8"
 dependencies = [

fileformats/src/README.rst

@@ -1,12 +1,9 @@
 FileFormats Extension - medimage-freesurfer
 ====================================
-.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/tests.yml/badge.svg
-    :target: https://github.com/nipype/pydra-medimage-freesurfer/actions/workflows/tests.yml
-.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
-    :target: https://arcanaframework.github.io/fileformats/
-    :alt: Documentation Status
+.. image:: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yml/badge.svg
+    :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yml
 
-This is the "medimage-freesurfer" extension module for the
+This is the "freesurfer" extension module for the
 `fileformats <https://github.com/ArcanaFramework/fileformats-core>`__ package
 
 
@@ -15,7 +12,7 @@ Quick Installation
 
 This extension can be installed for Python 3 using *pip*::
 
-    $ pip3 install fileformats-medimage-freesurfer
+    $ pip3 install fileformats-freesurfer
 
 This will install the core package and any other dependencies
 

fileformats/src/fileformats/medimage_freesurfer/__init__.py

@@ -1 +1,86 @@
-from ._version import __version__
+from fileformats.generic import File
+
+
+class Orig(File):
+    ext = ".orig"
+    binary = True
+
+
+class Xfm(File):
+    ext = ".xfm"
+    binary = True
+
+
+class Lta(File):
+    ext = ".lta"
+    binary = True
+
+
+class Stats(File):
+    ext = ".stats"
+    binary = True
+
+
+class Avg_curv(File):
+    ext = ".avg_curv"
+    binary = True
+
+
+class Inflated(File):
+    ext = ".inflated"
+    binary = True
+
+
+class Nofix(File):
+    ext = ".nofix"
+    binary = True
+
+
+class Pial(File):
+    ext = ".pial"
+    binary = True
+
+
+class M3z(File):
+    ext = ".m3z"
+    binary = True
+
+
+class Thickness(File):
+    ext = ".thickness"
+    binary = True
+
+
+class Annot(File):
+    ext = ".annot"
+    binary = True
+
+
+class Label(File):
+    ext = ".label"
+    binary = True
+
+
+class Ctab(File):
+    ext = ".ctab"
+    binary = True
+
+
+class Out(File):
+    ext = ".out"
+    binary = True
+
+
+class Area(File):
+    ext = ".area"
+    binary = True
+
+
+class White(File):
+    ext = ".white"
+    binary = True
+
+
+class Reg(File):
+    ext = ".reg"
+    binary = True

fileformats/src/pyproject.toml

@@ -4,11 +4,12 @@ build-backend = "hatchling.build"
 
 [project]
 name = "fileformats-medimage-freesurfer"
-description = "Classes for representing different file formats solely used by the 'freesurfer' tool in Python classes for use in type hinting in data workflows"
+description = "Classes for representing different file formats in Python classes for use in type hinting in data workflows"
 readme = "README.rst"
 requires-python = ">=3.8"
 dependencies = [
-    "fileformats >= 0.4"
+    "fileformats >= 0.4",
+    "fileformats-medimage > = 0.2"
 ]
 license = {file = "LICENSE"}
 authors = [
@@ -50,6 +51,7 @@ test = [
     "pytest-env>=0.6.2",
     "pytest-cov>=2.12.1",
     "codecov",
+    "fileformats-medimage-medimage-extras",
 ]
 
 [project.urls]

nipype-auto-conv/generate

@@ -58,7 +58,7 @@ for fspath in sorted(SPECS_DIR.glob("**/*.yaml")):
     auto_init += f"from .{module_name} import {converter.task_name}\n"
 
 
-with open(auto_dir / "_version.py", "w") as f:
+with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "_version.py", "w") as f:
     f.write(
         f"""# Auto-generated by {__file__}, do not edit as it will be overwritten
 
@@ -68,5 +68,5 @@ post_release = (nipype_version + nipype2pydra_version).replace(".", "")
 """
     )
 
-with open(auto_dir / "__init__.py", "w") as f:
+with open(PKG_ROOT / "pydra" / "tasks" / PKG_NAME / "auto" / "__init__.py", "w") as f:
     f.write(auto_init)

nipype-auto-conv/specs/aparc_2_aseg.yaml

@@ -58,23 +58,23 @@ inputs:
     out_file: medimage/mgh-gz
     # type=file: Output aseg file
     # type=file|default=<undefined>: Full path of file to save the output segmentation in
-    lh_white: generic/file
+    lh_white: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.white
-    rh_white: generic/file
+    rh_white: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.white
-    lh_pial: generic/file
+    lh_pial: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/lh.pial
-    rh_pial: generic/file
+    rh_pial: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/rh.pial
     lh_ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: Input file must be <subject_id>/mri/lh.ribbon.mgz
     rh_ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: Input file must be <subject_id>/mri/rh.ribbon.mgz
     ribbon: medimage/mgh-gz
     # type=file|default=<undefined>: Input file must be <subject_id>/mri/ribbon.mgz
-    lh_annotation: generic/file
+    lh_annotation: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/label/lh.aparc.annot
-    rh_annotation: generic/file
+    rh_annotation: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file must be <subject_id>/label/rh.aparc.annot
     filled: generic/file
     # type=file|default=<undefined>: Implicit input filled file. Only required with FS v5.3.

nipype-auto-conv/specs/ca_register.yaml

@@ -59,7 +59,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: generic/file
+    out_file: medimage-freesurfer/m3z
     # type=file: The output file for CARegister
     # type=file|default=<undefined>: The output volume for CARegister
   callables:

nipype-auto-conv/specs/concatenate_lta.yaml

@@ -47,9 +47,9 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_lta1: generic/file
+    in_lta1: medimage-freesurfer/lta
     # type=file|default=<undefined>: maps some src1 to dst1
-    out_file: generic/file
+    out_file: medimage-freesurfer/lta
     # type=file: the combined LTA maps: src1 to dst2 = LTA2*LTA1
     # type=file|default=<undefined>: the combined LTA maps: src1 to dst2 = LTA2*LTA1
     tal_source_file: generic/file
@@ -69,7 +69,7 @@ outputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    out_file: generic/file
+    out_file: medimage-freesurfer/lta
     # type=file: the combined LTA maps: src1 to dst2 = LTA2*LTA1
     # type=file|default=<undefined>: the combined LTA maps: src1 to dst2 = LTA2*LTA1
   callables:

nipype-auto-conv/specs/contrast.yaml

@@ -37,13 +37,13 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    thickness: generic/file
+    thickness: medimage-freesurfer/thickness
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/?h.thickness
-    white: generic/file
+    white: medimage-freesurfer/white
     # type=file|default=<undefined>: Input file must be <subject_id>/surf/<hemisphere>.white
-    annotation: generic/file
+    annotation: medimage-freesurfer/annot
     # type=file|default=<undefined>: Input annotation file must be <subject_id>/label/<hemisphere>.aparc.annot
-    cortex: generic/file
+    cortex: medimage-freesurfer/label
     # type=file|default=<undefined>: Input cortex label must be <subject_id>/label/<hemisphere>.cortex.label
     orig: medimage/mgh-gz
     # type=file|default=<undefined>: Implicit input file mri/orig.mgz

nipype-auto-conv/specs/curvature.yaml

@@ -33,7 +33,7 @@ inputs:
   # from the nipype interface, but you may want to be more specific, particularly
   # for file types, where specifying the format also specifies the file that will be
   # passed to the field in the automatically generated unittests.
-    in_file: generic/file
+    in_file: medimage-freesurfer/pial
     # type=file|default=<undefined>: Input file for Curvature
   metadata:
   # dict[str, dict[str, any]] - additional metadata to set on any of the input fields (e.g. out_file: position: 1)