renamed references to pydra-* to pydra-tasks-*

.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.medimage 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

docs/source/conf.py

@@ -8,7 +8,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = "pydra-fsl"
+project = "pydra-tasks-fsl"
 author = "Pydra Development Team"
 copyright = f"2022-2023, {author}"
 release = __version__

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/__init__.py

@@ -15,7 +15,7 @@
     from ._version import __version__
 except ImportError:
     raise RuntimeError(
-        "pydra-fsl has not been properly installed, please run "
+        "pydra-tasks-fsl has not been properly installed, please run "
         f"`pip install -e {str(pkg_path)}` to install a development version"
     )
 

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

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

@@ -1,5 +1,5 @@
 from fileformats.generic import File
-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.melodic import MELODIC

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

@@ -1,7 +1,7 @@
 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
 import logging
 from nipype2pydra.testing import PassAfterTimeoutWorker
 from pydra.tasks.fsl.v6.model.randomise import Randomise

pyproject.toml

@@ -12,7 +12,7 @@ dependencies = [
   "fileformats >=0.15.4",
   "fileformats-datascience >=0.3.2",
   "fileformats-medimage >=0.10.5",
-  "fileformats-medimage-fsl",
+  "fileformats-vendor-fsl",
   "looseversion>=1.3.0",
 ]
 license = { file = "LICENSE" }
@@ -59,7 +59,7 @@ test = [
   "fileformats-extras",
   "fileformats-datascience-extras",
   "fileformats-medimage-extras",
-  "fileformats-medimage-fsl-extras",
+  "fileformats-vendor-fsl-extras",
 ]
 
 [tool.hatch.build]

related-packages/fileformats-extras/README.rst

@@ -5,7 +5,7 @@ FileFormats-medimage-fsl Extras
     :target: https://github.com/nipype/pydra-freesurfer/actions/workflows/ci-cd.yaml
 
 
-This is a extras module for the `fileformats-medimage-fsl <https://github.com/nipype/pydra-fsl/>`__
+This is a extras module for the `fileformats-vendor-fsl <https://github.com/nipype/pydra-fsl/>`__
 fileformats extension package, which provides additional functionality to format classes (i.e. aside
 from basic identification and validation), such as conversion tools, metadata parsers,
 sample data generators, etc...
@@ -16,7 +16,7 @@ Quick Installation
 
 This extension can be installed for Python 3 using *pip*::
 
-    $ pip3 install fileformats-medimage-fsl-extras
+    $ pip3 install fileformats-vendor-fsl-extras
 
 This will install the package, base packages, and any other dependencies required to
 implement the extra functionality.

related-packages/fileformats-extras/fileformats/extras/medimage_fsl/__init__.py → related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/__init__.py

@@ -3,7 +3,7 @@
 import typing as ty
 from random import Random
 from fileformats.core import FileSet, SampleFileGenerator
-from fileformats.medimage_fsl import (
+from fileformats.vendor.fsl.medimage import (
     Con,
 )
 

related-packages/fileformats-extras/fileformats/extras/medimage_fsl/tests/test_generate_sample_data.py → related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/tests/test_generate_sample_data.py

@@ -1,5 +1,5 @@
 import pytest
-from fileformats.medimage_fsl import (
+from fileformats.vendor.fsl.medimage import (
     Con,
 )
 

related-packages/fileformats-extras/pyproject.toml

@@ -3,13 +3,13 @@ requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
-name = "fileformats-medimage-fsl-extras"
+name = "fileformats-vendor-fsl-extras"
 description = "Extensions to add functionality to tool-specific *fileformats* classes"
 readme = "README.rst"
 requires-python = ">=3.8"
 dependencies = [
     "fileformats",
-    "fileformats-medimage-fsl",
+    "fileformats-vendor-fsl",
     "pydra >= 0.23.0a"
 ]
 license = {file = "LICENSE"}
@@ -58,21 +58,21 @@ converters = [
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-fsl"
+repository = "https://github.com/nipype/pydra-tasks-fsl"
 
 [tool.hatch.version]
 source = "vcs"
 raw-options = { root = "../.." }
 
 [tool.hatch.build.hooks.vcs]
-version-file = "fileformats/extras/medimage_fsl/_version.py"
+version-file = "fileformats/extras/vendor/fsl/_version.py"
 
 [tool.hatch.build.targets.wheel]
 packages = ["fileformats"]
 
 [tool.black]
 target-version = ['py38']
-exclude = "fileformats/extras/medimage_fsl/_version.py"
+exclude = "fileformats/extras/vendor/fsl/_version.py"
 
 [tool.codespell]
 ignore-words = ".codespell-ignorewords"

related-packages/fileformats/README.rst

@@ -13,7 +13,7 @@ Quick Installation
 
 This extension can be installed for Python 3 using *pip*::
 
-    $ pip3 install fileformats-medimage-fsl
+    $ pip3 install fileformats-vendor-fsl
 
 This will install the format extensions and dependent base packages.
 

related-packages/fileformats/fileformats/medimage_fsl/__init__.py → related-packages/fileformats/fileformats/vendor/fsl/medimage/__init__.py

@@ -1,4 +1,4 @@
-from ._version import __version__  # noqa: F401
+from .._version import __version__  # noqa: F401
 from fileformats.generic import File, Directory
 
 

related-packages/fileformats/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
-name = "fileformats-medimage-fsl"
+name = "fileformats-vendor-fsl"
 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"
@@ -51,25 +51,25 @@ test = [
     "pytest-env>=0.6.2",
     "pytest-cov>=2.12.1",
     "codecov",
-    "fileformats-medimage-fsl-extras",
+    "fileformats-vendor-fsl-extras",
 ]
 
 [project.urls]
-repository = "https://github.com/nipype/pydra-fsl"
+repository = "https://github.com/nipype/pydra-tasks-fsl"
 
 [tool.hatch.version]
 source = "vcs"
 raw-options = { root = "../.." }
 
 [tool.hatch.build.hooks.vcs]
-version-file = "fileformats/medimage_fsl/_version.py"
+version-file = "fileformats/vendor/fsl/_version.py"
 
 [tool.hatch.build.targets.wheel]
 packages = ["fileformats"]
 
 [tool.black]
 target-version = ['py38']
-exclude = "fileformats/medimage_fsl/_version.py"
+exclude = "fileformats/vendor/fsl/_version.py"
 
 [tool.codespell]
 ignore-words = ".codespell-ignorewords"