Moved fileformats package under vendor namespace

.github/workflows/ci-cd.yaml

@@ -72,7 +72,7 @@ jobs:
         git clone https://github.com/tclose/mrtrix3.git $MRTRIX_HOME/src
         cd $MRTRIX_HOME/src
         git checkout print-pydra-dev
-        git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-task-mrtrix3 release"
+        git tag -a $MRTRIX_VERSION -m"Tag used to create a pydra-tasks-mrtrix3 release"
         git describe --abbrev=0
 # echo "MRTRIX_VERSION=$(git describe --tags --abbrev=0)" >> $GITHUB_ENV
 # git checkout $MRTRIX_VERSION

docs/requirements.txt

@@ -6,5 +6,5 @@ fileformats >= 0.8
 fileformats-extras >= 0.2.1
 fileformats-medimage >= 0.4.4
 fileformats-medimage-extras >= 0.1.5
-fileformats-medimage-mrtrix3
-fileformats-medimage-mrtrix3-extras
+fileformats-vendor-mrtrix3
+fileformats-vendor-mrtrix3-extras

generate.py

@@ -14,7 +14,7 @@
 import black.report
 import black.parsing
 from fileformats.core import FileSet
-from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, ImageOut, Tracks
+from fileformats.vendor.mrtrix3.medimage import ImageFormat, ImageIn, ImageOut, Tracks
 from pydra.compose import shell
 from pydra.compose.base import NO_DEFAULT
 from pydra.utils.typing import MultiInputObj
@@ -323,7 +323,7 @@ def auto_gen_test(cmd_name: str, output_dir: Path, log_errors: bool, pkg_version
 import pytest
 from fileformats.generic import File, Directory, FsObject  # noqa
 from fileformats.medimage import Nifti1  # noqa
-from fileformats.medimage_mrtrix3 import ImageFormat, ImageIn, Tracks  # noqa
+from fileformats.vendor.mrtrix3.medimage import ImageFormat, ImageIn, Tracks  # noqa
 from pydra.tasks.mrtrix3.{pkg_version} import {pascal_case_task_name(cmd_name)}
 """
 

pydra/tasks/mrtrix3/manual/mrcalc.py

@@ -2,7 +2,7 @@
 from pathlib import Path  # noqa: F401
 from enum import Enum
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/afdconnectivity.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/amp2response.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/amp2sh.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/connectome2tck.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/connectomeedit.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/connectomestats.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dcmedit.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dcminfo.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirflip.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirgen.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirmerge.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirorder.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirrotate.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirsplit.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dirstat.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dwi2adc.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dwi2fod.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_3dautomask.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_ants.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_b02template.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_consensus.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_fslbet.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_hdbet.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_legacy.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_mean.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_mtnorm.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_synthstrip.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2mask_trace.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_dhollander.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_fa.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_manual.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_msmt_5tt.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_tax.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2response_tournier.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwi2tensor.py

@@ -3,7 +3,7 @@
 import typing as ty
 from pathlib import Path  # noqa: F401
 from fileformats.generic import File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import ImageIn, ImageOut, Tracks  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import ImageIn, ImageOut, Tracks  # noqa: F401
 from pydra.compose import shell
 from pydra.utils.typing import MultiInputObj
 

pydra/tasks/mrtrix3/v3_1/dwibiascorrect_ants.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwibiascorrect_fsl.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwibiascorrect_mtnorm.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell
 

pydra/tasks/mrtrix3/v3_1/dwibiasnormmask.py

@@ -3,7 +3,7 @@
 import typing
 from pathlib import Path  # noqa: F401
 from fileformats.generic import FsObject, File, Directory  # noqa: F401
-from fileformats.medimage_mrtrix3 import Tracks, ImageIn, ImageOut  # noqa: F401
+from fileformats.vendor.mrtrix3.medimage import Tracks, ImageIn, ImageOut  # noqa: F401
 from pydra.utils.typing import MultiInputObj
 from pydra.compose import shell