moved fileformats under vendor.fsl

Author: tclose

.github/workflows/ci-cd.yaml

@@ -129,10 +129,10 @@ jobs:
     - name: Install task package
       run: |
         pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-        python -c "import fileformats.medimage_fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
+        python -c "import fileformats.vendor.fsl as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
     - name: Test fileformats with pytest
       run: >-
-        pytest ./related-packages -sv --cov fileformats.medimage_fsl
+        pytest ./related-packages -sv --cov fileformats.vendor.fsl.medimage
         --cov fileformats.extras.medimage_fsl --cov-report xml .
 
   deploy-fileformats:

.gitignore

@@ -178,6 +178,6 @@ cython_debug/
 
 # Generated files
 /pydra/tasks/fsl/_version.py
-/related-packages/fileformats/fileformats/medimage_fsl/_version.py
-/related-packages/fileformats-extras/fileformats/extras/medimage_fsl/_version.py
+/related-packages/fileformats/fileformats/vendor/fsl/_version.py
+/related-packages/fileformats-extras/fileformats/extras/vendor/fsl/_version.py
 /pydra/tasks/fsl/auto

nipype-auto-conv/requirements.txt

@@ -7,6 +7,6 @@ PyYAML>=6.0
 fileformats >=0.8
 fileformats-medimage >=0.4
 fileformats-datascience >= 0.1
-fileformats-medimage-fsl
+fileformats-vendor-fsl
 traits
 nipype2pydra

nipype-auto-conv/specs/interfaces/flameo.yaml

@@ -53,7 +53,7 @@ inputs:
     # type=directory|default='stats':
     mask_file: generic/file
     # type=file|default=<undefined>: mask file
-    t_con_file: fileformats.medimage_fsl.Con
+    t_con_file: fileformats.vendor.fsl.medimage.Con
     # type=file|default=<undefined>: ascii matrix specifying t-contrasts
     var_cope_file: generic/file
     # type=file|default=<undefined>: varcope weightings data file

nipype-auto-conv/specs/interfaces/melodic.yaml

@@ -54,13 +54,13 @@ inputs:
     # type=file|default=<undefined>: file name of mask for thresholding
     mix: generic/file
     # type=file|default=<undefined>: mixing matrix for mixture modelling / filtering
-    s_con: fileformats.medimage_fsl.Con
+    s_con: fileformats.vendor.fsl.medimage.Con
     # type=file|default=<undefined>: t-contrast matrix across subject-domain
     s_des: generic/file
     # type=file|default=<undefined>: design matrix across subject-domain
     smode: generic/file
     # type=file|default=<undefined>: matrix of session modes for report generation
-    t_con: fileformats.medimage_fsl.Con
+    t_con: fileformats.vendor.fsl.medimage.Con
     # type=file|default=<undefined>: t-contrast matrix across time-domain
     t_des: generic/file
     # type=file|default=<undefined>: design matrix across time-domain

nipype-auto-conv/specs/interfaces/randomise.yaml

@@ -39,7 +39,7 @@ inputs:
     # type=file|default=<undefined>: 4D input file
     mask: medimage/nifti1
     # type=file|default=<undefined>: mask image
-    tcon: fileformats.medimage_fsl.Con
+    tcon: fileformats.vendor.fsl.medimage.Con
     # type=file|default=<undefined>: t contrasts file
     x_block_labels: generic/file
     # type=file|default=<undefined>: exchangeability block labels file

pydra/tasks/fsl/v6/model/flameo.py

@@ -2,7 +2,7 @@
 from fileformats.datascience import TextMatrix
 from fileformats.generic import Directory, File
 from fileformats.medimage import NiftiGz
-from fileformats.medimage_fsl import Con
+from fileformats.vendor.fsl.medimage import Con
 from glob import glob
 import logging
 from pydra.tasks.fsl.v6.nipype_ports.utils.misc import human_order_sorted
@@ -165,7 +165,7 @@ class FLAMEO(shell.Task["FLAMEO.Outputs"]):
     >>> from fileformats.datascience import TextMatrix
     >>> from fileformats.generic import Directory, File
     >>> from fileformats.medimage import NiftiGz
-    >>> from fileformats.medimage_fsl import Con
+    >>> from fileformats.vendor.fsl.medimage import Con
     >>> from pydra.tasks.fsl.v6.model.flameo import FLAMEO
 
     >>> task = FLAMEO()

pydra/tasks/fsl/v6/model/melodic.py

@@ -1,6 +1,6 @@
 import attrs
 from fileformats.generic import Directory, File
-from fileformats.medimage_fsl import Con
+from fileformats.vendor.fsl.medimage import Con
 import logging
 import os
 from pydra.compose import shell
@@ -52,7 +52,7 @@ class MELODIC(shell.Task["MELODIC.Outputs"]):
     -------
 
     >>> from fileformats.generic import Directory, File
-    >>> from fileformats.medimage_fsl import Con
+    >>> from fileformats.vendor.fsl.medimage import Con
     >>> from pydra.tasks.fsl.v6.model.melodic import MELODIC
 
     >>> task = MELODIC()

pydra/tasks/fsl/v6/model/randomise.py

@@ -2,7 +2,7 @@
 from fileformats.datascience import TextMatrix
 from fileformats.generic import File
 from fileformats.medimage import Nifti1
-from fileformats.medimage_fsl import Con
+from fileformats.vendor.fsl.medimage import Con
 from glob import glob
 import logging
 from pydra.tasks.fsl.v6.nipype_ports.utils.filemanip import fname_presuffix
@@ -141,7 +141,7 @@ class Randomise(shell.Task["Randomise.Outputs"]):
     >>> from fileformats.datascience import TextMatrix
     >>> from fileformats.generic import File
     >>> from fileformats.medimage import Nifti1
-    >>> from fileformats.medimage_fsl import Con
+    >>> from fileformats.vendor.fsl.medimage import Con
     >>> from pydra.tasks.fsl.v6.model.randomise import Randomise
 
     >>> task = Randomise()

pydra/tasks/fsl/v6/model/tests/test_flameo.py

@@ -1,7 +1,7 @@
 from fileformats.datascience import TextMatrix
 from fileformats.generic import Directory, File
 from fileformats.medimage import NiftiGz
-from fileformats.medimage_fsl import Con
+from fileformats.vendor.fsl.medimage import Con
 import logging
 from nipype2pydra.testing import PassAfterTimeoutWorker
 from pydra.tasks.fsl.v6.model.flameo import FLAMEO