diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index bb62f385..b25ee25d 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.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: diff --git a/.gitignore b/.gitignore index 942699c1..a8fe3352 100644 --- a/.gitignore +++ b/.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 diff --git a/docs/source/conf.py b/docs/source/conf.py index ee9b39e0..862a5f78 100644 --- a/docs/source/conf.py +++ b/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__ diff --git a/nipype-auto-conv/requirements.txt b/nipype-auto-conv/requirements.txt index cb69c8a6..30ec42b5 100644 --- a/nipype-auto-conv/requirements.txt +++ b/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 diff --git a/nipype-auto-conv/specs/interfaces/flameo.yaml b/nipype-auto-conv/specs/interfaces/flameo.yaml index 9b4cd5ed..4a6cb818 100644 --- a/nipype-auto-conv/specs/interfaces/flameo.yaml +++ b/nipype-auto-conv/specs/interfaces/flameo.yaml @@ -53,7 +53,7 @@ inputs: # type=directory|default='stats': mask_file: generic/file # type=file|default=: mask file - t_con_file: fileformats.medimage_fsl.Con + t_con_file: fileformats.vendor.fsl.medimage.Con # type=file|default=: ascii matrix specifying t-contrasts var_cope_file: generic/file # type=file|default=: varcope weightings data file diff --git a/nipype-auto-conv/specs/interfaces/melodic.yaml b/nipype-auto-conv/specs/interfaces/melodic.yaml index cb561822..5a817844 100644 --- a/nipype-auto-conv/specs/interfaces/melodic.yaml +++ b/nipype-auto-conv/specs/interfaces/melodic.yaml @@ -54,13 +54,13 @@ inputs: # type=file|default=: file name of mask for thresholding mix: generic/file # type=file|default=: mixing matrix for mixture modelling / filtering - s_con: fileformats.medimage_fsl.Con + s_con: fileformats.vendor.fsl.medimage.Con # type=file|default=: t-contrast matrix across subject-domain s_des: generic/file # type=file|default=: design matrix across subject-domain smode: generic/file # type=file|default=: matrix of session modes for report generation - t_con: fileformats.medimage_fsl.Con + t_con: fileformats.vendor.fsl.medimage.Con # type=file|default=: t-contrast matrix across time-domain t_des: generic/file # type=file|default=: design matrix across time-domain diff --git a/nipype-auto-conv/specs/interfaces/randomise.yaml b/nipype-auto-conv/specs/interfaces/randomise.yaml index 1c8f18d7..e50dc34c 100644 --- a/nipype-auto-conv/specs/interfaces/randomise.yaml +++ b/nipype-auto-conv/specs/interfaces/randomise.yaml @@ -39,7 +39,7 @@ inputs: # type=file|default=: 4D input file mask: medimage/nifti1 # type=file|default=: mask image - tcon: fileformats.medimage_fsl.Con + tcon: fileformats.vendor.fsl.medimage.Con # type=file|default=: t contrasts file x_block_labels: generic/file # type=file|default=: exchangeability block labels file diff --git a/pydra/tasks/fsl/__init__.py b/pydra/tasks/fsl/__init__.py index 57df2e18..081862d6 100644 --- a/pydra/tasks/fsl/__init__.py +++ b/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" ) diff --git a/pydra/tasks/fsl/v6/model/flameo.py b/pydra/tasks/fsl/v6/model/flameo.py index b0319317..f3c6763f 100644 --- a/pydra/tasks/fsl/v6/model/flameo.py +++ b/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() diff --git a/pydra/tasks/fsl/v6/model/melodic.py b/pydra/tasks/fsl/v6/model/melodic.py index d796264b..dd29f50a 100644 --- a/pydra/tasks/fsl/v6/model/melodic.py +++ b/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() diff --git a/pydra/tasks/fsl/v6/model/randomise.py b/pydra/tasks/fsl/v6/model/randomise.py index 1350b157..1183de3a 100644 --- a/pydra/tasks/fsl/v6/model/randomise.py +++ b/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() diff --git a/pydra/tasks/fsl/v6/model/tests/test_flameo.py b/pydra/tasks/fsl/v6/model/tests/test_flameo.py index 1fb3b4e3..ae6542fc 100644 --- a/pydra/tasks/fsl/v6/model/tests/test_flameo.py +++ b/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 diff --git a/pydra/tasks/fsl/v6/model/tests/test_melodic.py b/pydra/tasks/fsl/v6/model/tests/test_melodic.py index aa5c4fa4..47e27c80 100644 --- a/pydra/tasks/fsl/v6/model/tests/test_melodic.py +++ b/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 diff --git a/pydra/tasks/fsl/v6/model/tests/test_randomise.py b/pydra/tasks/fsl/v6/model/tests/test_randomise.py index 47bf623d..7586bac6 100644 --- a/pydra/tasks/fsl/v6/model/tests/test_randomise.py +++ b/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 diff --git a/pyproject.toml b/pyproject.toml index ba6a6004..9ce8d610 100644 --- a/pyproject.toml +++ b/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] diff --git a/related-packages/fileformats-extras/README.rst b/related-packages/fileformats-extras/README.rst index 385482ca..6ba1eb71 100644 --- a/related-packages/fileformats-extras/README.rst +++ b/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 `__ +This is a extras module for the `fileformats-vendor-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. diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_fsl/__init__.py b/related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/__init__.py similarity index 88% rename from related-packages/fileformats-extras/fileformats/extras/medimage_fsl/__init__.py rename to related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/__init__.py index 9a674a94..f6db0e4f 100644 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_fsl/__init__.py +++ b/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, ) diff --git a/related-packages/fileformats-extras/fileformats/extras/medimage_fsl/tests/test_generate_sample_data.py b/related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/tests/test_generate_sample_data.py similarity index 78% rename from related-packages/fileformats-extras/fileformats/extras/medimage_fsl/tests/test_generate_sample_data.py rename to related-packages/fileformats-extras/fileformats/extras/vendor/fsl/medimage/tests/test_generate_sample_data.py index a213223b..e8e6a9c4 100644 --- a/related-packages/fileformats-extras/fileformats/extras/medimage_fsl/tests/test_generate_sample_data.py +++ b/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, ) diff --git a/related-packages/fileformats-extras/pyproject.toml b/related-packages/fileformats-extras/pyproject.toml index c6304d3b..0a4f3caf 100644 --- a/related-packages/fileformats-extras/pyproject.toml +++ b/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" diff --git a/related-packages/fileformats/README.rst b/related-packages/fileformats/README.rst index 36df02a7..b8119efc 100644 --- a/related-packages/fileformats/README.rst +++ b/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. diff --git a/related-packages/fileformats/fileformats/medimage_fsl/__init__.py b/related-packages/fileformats/fileformats/vendor/fsl/medimage/__init__.py similarity index 79% rename from related-packages/fileformats/fileformats/medimage_fsl/__init__.py rename to related-packages/fileformats/fileformats/vendor/fsl/medimage/__init__.py index 8ec8dec7..77ef7008 100644 --- a/related-packages/fileformats/fileformats/medimage_fsl/__init__.py +++ b/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 diff --git a/related-packages/fileformats/pyproject.toml b/related-packages/fileformats/pyproject.toml index d6feebc9..9d6db389 100644 --- a/related-packages/fileformats/pyproject.toml +++ b/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"