From aff5f2d5516bd6df0860bc761e955bd3fcd5d1d5 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Tue, 5 Aug 2025 23:43:04 +0930 Subject: [PATCH 1/9] cleaned up pyproject.toml --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 97bf8f1..09cd00b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -92,7 +92,7 @@ python = ["3.11", "3.12", "3.13"] [tool.pytest.ini_options] minversion = "6.0" -testpaths = ["pydra/tasks/ants"] +testpaths = ["pydra/tasks/afni"] log_cli_level = "INFO" xfail_strict = true addopts = [ @@ -102,7 +102,7 @@ addopts = [ "--strict-markers", # "--doctest-modules", # "--doctest-continue-on-failure", - "--cov=pydra.tasks.ants", + "--cov=pydra.tasks.afni", "--cov-report=xml", "--cov-config=pyproject.toml", ] From ffef6f4ccf19271ba0605694b3e48bca9ba0d69d Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 08:35:51 +0930 Subject: [PATCH 2/9] fixed ci-cd workflow --- .github/workflows/ci-cd.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index 9433e9d..9769005 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.github/workflows/ci-cd.yaml @@ -150,7 +150,7 @@ jobs: --cov fileformats.extras.medimage_afni --cov-report xml . deploy-fileformats: - needs: [devcheck, test] + needs: [test] runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 From b86887463fcc28682674b2a6cf6c64ec3fccf393 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 08:53:48 +0930 Subject: [PATCH 3/9] updated ci-cd --- .github/workflows/ci-cd.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index 9769005..f0de095 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.github/workflows/ci-cd.yaml @@ -150,7 +150,7 @@ jobs: --cov fileformats.extras.medimage_afni --cov-report xml . deploy-fileformats: - needs: [test] + needs: [build, test, fileformats-test] runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 From 56c2e7df19ff678360e49953723cb7c463690970 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 08:54:49 +0930 Subject: [PATCH 4/9] updated references to afni package version --- pydra/tasks/afni/v25/model/deconvolve.py | 4 ++-- pydra/tasks/afni/v25/model/remlfit.py | 2 +- pydra/tasks/afni/v25/model/synthesize.py | 2 +- pydra/tasks/afni/v25/model/tests/test_deconvolve.py | 2 +- pydra/tasks/afni/v25/model/tests/test_remlfit.py | 2 +- pydra/tasks/afni/v25/model/tests/test_synthesize.py | 2 +- pydra/tasks/afni/v25/preprocess/align_epi_anat_py.py | 6 +++--- pydra/tasks/afni/v25/preprocess/allineate.py | 4 ++-- pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py | 2 +- pydra/tasks/afni/v25/preprocess/auto_tlrc.py | 4 ++-- pydra/tasks/afni/v25/preprocess/automask.py | 2 +- pydra/tasks/afni/v25/preprocess/bandpass.py | 2 +- pydra/tasks/afni/v25/preprocess/blur_in_mask.py | 2 +- pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py | 2 +- pydra/tasks/afni/v25/preprocess/clip_level.py | 4 ++-- pydra/tasks/afni/v25/preprocess/degree_centrality.py | 4 ++-- pydra/tasks/afni/v25/preprocess/despike.py | 2 +- pydra/tasks/afni/v25/preprocess/detrend.py | 2 +- pydra/tasks/afni/v25/preprocess/ecm.py | 2 +- pydra/tasks/afni/v25/preprocess/fim.py | 2 +- pydra/tasks/afni/v25/preprocess/fourier.py | 2 +- pydra/tasks/afni/v25/preprocess/hist.py | 2 +- pydra/tasks/afni/v25/preprocess/lfcd.py | 2 +- pydra/tasks/afni/v25/preprocess/maskave.py | 2 +- pydra/tasks/afni/v25/preprocess/means.py | 2 +- pydra/tasks/afni/v25/preprocess/net_corr.py | 4 ++-- pydra/tasks/afni/v25/preprocess/outlier_count.py | 2 +- pydra/tasks/afni/v25/preprocess/quality_index.py | 2 +- pydra/tasks/afni/v25/preprocess/qwarp.py | 6 +++--- pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py | 6 +++--- pydra/tasks/afni/v25/preprocess/retroicor.py | 2 +- pydra/tasks/afni/v25/preprocess/roi_stats.py | 2 +- pydra/tasks/afni/v25/preprocess/seg.py | 2 +- pydra/tasks/afni/v25/preprocess/skull_strip.py | 2 +- pydra/tasks/afni/v25/preprocess/t_corr_1d.py | 2 +- pydra/tasks/afni/v25/preprocess/t_corr_map.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_correlate.py | 2 +- pydra/tasks/afni/v25/preprocess/t_norm.py | 2 +- pydra/tasks/afni/v25/preprocess/t_project.py | 2 +- pydra/tasks/afni/v25/preprocess/t_shift.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_smooth.py | 2 +- .../tasks/afni/v25/preprocess/tests/test_alignepianatpy.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_allineate.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_automask.py | 2 +- .../tasks/afni/v25/preprocess/tests/test_autotcorrelate.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_autotlrc.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_bandpass.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_blurinmask.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_blurtofwhm.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_cliplevel.py | 2 +- .../afni/v25/preprocess/tests/test_degreecentrality.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_despike.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_detrend.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_ecm.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_fim.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_fourier.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_hist.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_lfcd.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_maskave.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_means.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_netcorr.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_outliercount.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_qualityindex.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_qwarp.py | 2 +- .../tasks/afni/v25/preprocess/tests/test_qwarpplusminus.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_retroicor.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_roistats.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_seg.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_skullstrip.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tcorr1d.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tcorrelate.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tcorrmap.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tnorm.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tproject.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tshift.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_tsmooth.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_volreg.py | 2 +- pydra/tasks/afni/v25/preprocess/tests/test_warp.py | 2 +- pydra/tasks/afni/v25/preprocess/volreg.py | 2 +- pydra/tasks/afni/v25/preprocess/warp.py | 4 ++-- pydra/tasks/afni/v25/svm/svm_test.py | 2 +- pydra/tasks/afni/v25/svm/svm_train.py | 2 +- pydra/tasks/afni/v25/svm/tests/test_svmtest.py | 2 +- pydra/tasks/afni/v25/svm/tests/test_svmtrain.py | 2 +- pydra/tasks/afni/v25/utils/a_boverlap.py | 4 ++-- pydra/tasks/afni/v25/utils/afn_ito_nifti.py | 2 +- pydra/tasks/afni/v25/utils/autobox.py | 2 +- pydra/tasks/afni/v25/utils/axialize.py | 2 +- pydra/tasks/afni/v25/utils/brick_stat.py | 4 ++-- pydra/tasks/afni/v25/utils/bucket.py | 2 +- pydra/tasks/afni/v25/utils/calc.py | 2 +- pydra/tasks/afni/v25/utils/cat.py | 4 ++-- pydra/tasks/afni/v25/utils/cat_matvec.py | 2 +- pydra/tasks/afni/v25/utils/center_mass.py | 2 +- pydra/tasks/afni/v25/utils/convert_dset.py | 2 +- pydra/tasks/afni/v25/utils/copy.py | 2 +- pydra/tasks/afni/v25/utils/dot.py | 4 ++-- pydra/tasks/afni/v25/utils/edge_3.py | 4 ++-- pydra/tasks/afni/v25/utils/eval.py | 2 +- pydra/tasks/afni/v25/utils/fwh_mx.py | 2 +- pydra/tasks/afni/v25/utils/gcor.py | 2 +- pydra/tasks/afni/v25/utils/local_bistat.py | 2 +- pydra/tasks/afni/v25/utils/localstat.py | 2 +- pydra/tasks/afni/v25/utils/mask_tool.py | 2 +- pydra/tasks/afni/v25/utils/merge.py | 2 +- pydra/tasks/afni/v25/utils/notes.py | 2 +- pydra/tasks/afni/v25/utils/nwarp_adjust.py | 2 +- pydra/tasks/afni/v25/utils/nwarp_apply.py | 2 +- pydra/tasks/afni/v25/utils/nwarp_cat.py | 4 ++-- pydra/tasks/afni/v25/utils/one_d_tool_py.py | 2 +- pydra/tasks/afni/v25/utils/re_ho.py | 2 +- pydra/tasks/afni/v25/utils/refit.py | 2 +- pydra/tasks/afni/v25/utils/resample.py | 2 +- pydra/tasks/afni/v25/utils/t_cat.py | 2 +- pydra/tasks/afni/v25/utils/t_cat_sub_brick.py | 4 ++-- pydra/tasks/afni/v25/utils/t_stat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_aboverlap.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_afnitonifti.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_autobox.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_axialize.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_brickstat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_bucket.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_calc.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_cat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_catmatvec.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_centermass.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_convertdset.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_copy.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_dot.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_edge3.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_eval.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_fwhmx.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_gcor.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_localbistat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_localstat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_masktool.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_merge.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_notes.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_nwarpadjust.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_nwarpapply.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_nwarpcat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_onedtoolpy.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_refit.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_reho.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_resample.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_tcat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_tcatsubbrick.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_to3d.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_tstat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_undump.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_unifize.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_zcat.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_zcutup.py | 2 +- pydra/tasks/afni/v25/utils/tests/test_zeropad.py | 2 +- pydra/tasks/afni/v25/utils/to_3d.py | 2 +- pydra/tasks/afni/v25/utils/undump.py | 4 ++-- pydra/tasks/afni/v25/utils/unifize.py | 4 ++-- pydra/tasks/afni/v25/utils/z_cut_up.py | 2 +- pydra/tasks/afni/v25/utils/zcat.py | 2 +- pydra/tasks/afni/v25/utils/zeropad.py | 2 +- 160 files changed, 184 insertions(+), 184 deletions(-) diff --git a/pydra/tasks/afni/v25/model/deconvolve.py b/pydra/tasks/afni/v25/model/deconvolve.py index 9eae7f0..cc8325d 100644 --- a/pydra/tasks/afni/v25/model/deconvolve.py +++ b/pydra/tasks/afni/v25/model/deconvolve.py @@ -3,7 +3,7 @@ from fileformats.medimage import Nifti1 from fileformats.medimage_afni import OneD import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path from pathlib._local import Path @@ -134,7 +134,7 @@ class Deconvolve(shell.Task["Deconvolve.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.model.deconvolve import Deconvolve + >>> from pydra.tasks.afni.v25.model.deconvolve import Deconvolve >>> task = Deconvolve() >>> task.inputs.in_files = [Nifti1.mock("functional.nii"), Nifti1.mock("functional2.nii")] diff --git a/pydra/tasks/afni/v25/model/remlfit.py b/pydra/tasks/afni/v25/model/remlfit.py index 93ecee6..567af4c 100644 --- a/pydra/tasks/afni/v25/model/remlfit.py +++ b/pydra/tasks/afni/v25/model/remlfit.py @@ -140,7 +140,7 @@ class Remlfit(shell.Task["Remlfit.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.model.remlfit import Remlfit + >>> from pydra.tasks.afni.v25.model.remlfit import Remlfit >>> task = Remlfit() >>> task.inputs.in_files = [Nifti1.mock("functional.nii"), Nifti1.mock("functional2.nii")] diff --git a/pydra/tasks/afni/v25/model/synthesize.py b/pydra/tasks/afni/v25/model/synthesize.py index 1a94c89..5f0c81a 100644 --- a/pydra/tasks/afni/v25/model/synthesize.py +++ b/pydra/tasks/afni/v25/model/synthesize.py @@ -19,7 +19,7 @@ class Synthesize(shell.Task["Synthesize.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.model.synthesize import Synthesize + >>> from pydra.tasks.afni.v25.model.synthesize import Synthesize >>> task = Synthesize() >>> task.inputs.cbucket = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/model/tests/test_deconvolve.py b/pydra/tasks/afni/v25/model/tests/test_deconvolve.py index 3a379f3..911e7e5 100644 --- a/pydra/tasks/afni/v25/model/tests/test_deconvolve.py +++ b/pydra/tasks/afni/v25/model/tests/test_deconvolve.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.model.deconvolve import Deconvolve +from pydra.tasks.afni.v25.model.deconvolve import Deconvolve import pytest diff --git a/pydra/tasks/afni/v25/model/tests/test_remlfit.py b/pydra/tasks/afni/v25/model/tests/test_remlfit.py index 90851d4..a57cc86 100644 --- a/pydra/tasks/afni/v25/model/tests/test_remlfit.py +++ b/pydra/tasks/afni/v25/model/tests/test_remlfit.py @@ -3,7 +3,7 @@ from fileformats.medimage_afni import OneD import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.model.remlfit import Remlfit +from pydra.tasks.afni.v25.model.remlfit import Remlfit import pytest diff --git a/pydra/tasks/afni/v25/model/tests/test_synthesize.py b/pydra/tasks/afni/v25/model/tests/test_synthesize.py index 64c22ae..ee02906 100644 --- a/pydra/tasks/afni/v25/model/tests/test_synthesize.py +++ b/pydra/tasks/afni/v25/model/tests/test_synthesize.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.model.synthesize import Synthesize +from pydra.tasks.afni.v25.model.synthesize import Synthesize import pytest diff --git a/pydra/tasks/afni/v25/preprocess/align_epi_anat_py.py b/pydra/tasks/afni/v25/preprocess/align_epi_anat_py.py index 7b74674..d08ad13 100644 --- a/pydra/tasks/afni/v25/preprocess/align_epi_anat_py.py +++ b/pydra/tasks/afni/v25/preprocess/align_epi_anat_py.py @@ -2,8 +2,8 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.base import Info -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.base import Info +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix from pydra.compose import shell import typing as ty @@ -220,7 +220,7 @@ class AlignEpiAnatPy(shell.Task["AlignEpiAnatPy.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.preprocess.align_epi_anat_py import AlignEpiAnatPy + >>> from pydra.tasks.afni.v25.preprocess.align_epi_anat_py import AlignEpiAnatPy >>> task = AlignEpiAnatPy() >>> task.inputs.in_file = File.mock() diff --git a/pydra/tasks/afni/v25/preprocess/allineate.py b/pydra/tasks/afni/v25/preprocess/allineate.py index 17cfd2c..3674184 100644 --- a/pydra/tasks/afni/v25/preprocess/allineate.py +++ b/pydra/tasks/afni/v25/preprocess/allineate.py @@ -4,7 +4,7 @@ from fileformats.medimage import Nifti1 from fileformats.text import TextFile import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import ( +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import ( fname_presuffix, split_filename, ) @@ -120,7 +120,7 @@ class Allineate(shell.Task["Allineate.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from fileformats.text import TextFile >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.allineate import Allineate + >>> from pydra.tasks.afni.v25.preprocess.allineate import Allineate >>> task = Allineate() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py b/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py index 3f3fd6a..01a30b5 100644 --- a/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py +++ b/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py @@ -19,7 +19,7 @@ class AutoTcorrelate(shell.Task["AutoTcorrelate.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.auto_tcorrelate import AutoTcorrelate + >>> from pydra.tasks.afni.v25.preprocess.auto_tcorrelate import AutoTcorrelate >>> task = AutoTcorrelate() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/auto_tlrc.py b/pydra/tasks/afni/v25/preprocess/auto_tlrc.py index 2a0d7cc..8d5f4ed 100644 --- a/pydra/tasks/afni/v25/preprocess/auto_tlrc.py +++ b/pydra/tasks/afni/v25/preprocess/auto_tlrc.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pydra.compose import shell import typing as ty @@ -46,7 +46,7 @@ class AutoTLRC(shell.Task["AutoTLRC.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.preprocess.auto_tlrc import AutoTLRC + >>> from pydra.tasks.afni.v25.preprocess.auto_tlrc import AutoTLRC >>> task = AutoTLRC() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/preprocess/automask.py b/pydra/tasks/afni/v25/preprocess/automask.py index ba09556..e003b33 100644 --- a/pydra/tasks/afni/v25/preprocess/automask.py +++ b/pydra/tasks/afni/v25/preprocess/automask.py @@ -17,7 +17,7 @@ class Automask(shell.Task["Automask.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.automask import Automask + >>> from pydra.tasks.afni.v25.preprocess.automask import Automask >>> task = Automask() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/bandpass.py b/pydra/tasks/afni/v25/preprocess/bandpass.py index fb72d10..5149160 100644 --- a/pydra/tasks/afni/v25/preprocess/bandpass.py +++ b/pydra/tasks/afni/v25/preprocess/bandpass.py @@ -19,7 +19,7 @@ class Bandpass(shell.Task["Bandpass.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.bandpass import Bandpass + >>> from pydra.tasks.afni.v25.preprocess.bandpass import Bandpass >>> task = Bandpass() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/blur_in_mask.py b/pydra/tasks/afni/v25/preprocess/blur_in_mask.py index 0c3c97b..33b7c6c 100644 --- a/pydra/tasks/afni/v25/preprocess/blur_in_mask.py +++ b/pydra/tasks/afni/v25/preprocess/blur_in_mask.py @@ -19,7 +19,7 @@ class BlurInMask(shell.Task["BlurInMask.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.blur_in_mask import BlurInMask + >>> from pydra.tasks.afni.v25.preprocess.blur_in_mask import BlurInMask >>> task = BlurInMask() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py b/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py index e2bb39f..cb355e9 100644 --- a/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py +++ b/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py @@ -19,7 +19,7 @@ class BlurToFWHM(shell.Task["BlurToFWHM.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.blur_to_fwhm import BlurToFWHM + >>> from pydra.tasks.afni.v25.preprocess.blur_to_fwhm import BlurToFWHM >>> task = BlurToFWHM() >>> task.inputs.in_file = Nifti1.mock("epi.nii") diff --git a/pydra/tasks/afni/v25/preprocess/clip_level.py b/pydra/tasks/afni/v25/preprocess/clip_level.py index 357ab9e..e971e7a 100644 --- a/pydra/tasks/afni/v25/preprocess/clip_level.py +++ b/pydra/tasks/afni/v25/preprocess/clip_level.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import load_json, save_json +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import load_json, save_json import os from pydra.compose import shell @@ -56,7 +56,7 @@ class ClipLevel(shell.Task["ClipLevel.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.preprocess.clip_level import ClipLevel + >>> from pydra.tasks.afni.v25.preprocess.clip_level import ClipLevel >>> task = ClipLevel() >>> task.inputs.in_file = Nifti1.mock("anatomical.nii") diff --git a/pydra/tasks/afni/v25/preprocess/degree_centrality.py b/pydra/tasks/afni/v25/preprocess/degree_centrality.py index ffe7954..b5d53a0 100644 --- a/pydra/tasks/afni/v25/preprocess/degree_centrality.py +++ b/pydra/tasks/afni/v25/preprocess/degree_centrality.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename import os from pathlib import Path from pathlib._local import Path @@ -48,7 +48,7 @@ class DegreeCentrality(shell.Task["DegreeCentrality.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.degree_centrality import DegreeCentrality + >>> from pydra.tasks.afni.v25.preprocess.degree_centrality import DegreeCentrality >>> task = DegreeCentrality() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/despike.py b/pydra/tasks/afni/v25/preprocess/despike.py index 5cdf072..992dad3 100644 --- a/pydra/tasks/afni/v25/preprocess/despike.py +++ b/pydra/tasks/afni/v25/preprocess/despike.py @@ -17,7 +17,7 @@ class Despike(shell.Task["Despike.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.despike import Despike + >>> from pydra.tasks.afni.v25.preprocess.despike import Despike >>> task = Despike() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/detrend.py b/pydra/tasks/afni/v25/preprocess/detrend.py index 170f819..091331a 100644 --- a/pydra/tasks/afni/v25/preprocess/detrend.py +++ b/pydra/tasks/afni/v25/preprocess/detrend.py @@ -17,7 +17,7 @@ class Detrend(shell.Task["Detrend.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.detrend import Detrend + >>> from pydra.tasks.afni.v25.preprocess.detrend import Detrend >>> task = Detrend() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/ecm.py b/pydra/tasks/afni/v25/preprocess/ecm.py index 20b5716..400b4eb 100644 --- a/pydra/tasks/afni/v25/preprocess/ecm.py +++ b/pydra/tasks/afni/v25/preprocess/ecm.py @@ -19,7 +19,7 @@ class ECM(shell.Task["ECM.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.ecm import ECM + >>> from pydra.tasks.afni.v25.preprocess.ecm import ECM >>> task = ECM() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/fim.py b/pydra/tasks/afni/v25/preprocess/fim.py index 9dc331f..6394874 100644 --- a/pydra/tasks/afni/v25/preprocess/fim.py +++ b/pydra/tasks/afni/v25/preprocess/fim.py @@ -19,7 +19,7 @@ class Fim(shell.Task["Fim.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.fim import Fim + >>> from pydra.tasks.afni.v25.preprocess.fim import Fim >>> task = Fim() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/fourier.py b/pydra/tasks/afni/v25/preprocess/fourier.py index f97eb0b..3dad434 100644 --- a/pydra/tasks/afni/v25/preprocess/fourier.py +++ b/pydra/tasks/afni/v25/preprocess/fourier.py @@ -17,7 +17,7 @@ class Fourier(shell.Task["Fourier.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.fourier import Fourier + >>> from pydra.tasks.afni.v25.preprocess.fourier import Fourier >>> task = Fourier() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/hist.py b/pydra/tasks/afni/v25/preprocess/hist.py index 7ca16e9..66da08c 100644 --- a/pydra/tasks/afni/v25/preprocess/hist.py +++ b/pydra/tasks/afni/v25/preprocess/hist.py @@ -33,7 +33,7 @@ class Hist(shell.Task["Hist.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.hist import Hist + >>> from pydra.tasks.afni.v25.preprocess.hist import Hist >>> task = Hist() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/lfcd.py b/pydra/tasks/afni/v25/preprocess/lfcd.py index e26840d..c466ee1 100644 --- a/pydra/tasks/afni/v25/preprocess/lfcd.py +++ b/pydra/tasks/afni/v25/preprocess/lfcd.py @@ -19,7 +19,7 @@ class LFCD(shell.Task["LFCD.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.lfcd import LFCD + >>> from pydra.tasks.afni.v25.preprocess.lfcd import LFCD >>> task = LFCD() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/maskave.py b/pydra/tasks/afni/v25/preprocess/maskave.py index 1426f46..de4af35 100644 --- a/pydra/tasks/afni/v25/preprocess/maskave.py +++ b/pydra/tasks/afni/v25/preprocess/maskave.py @@ -19,7 +19,7 @@ class Maskave(shell.Task["Maskave.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.maskave import Maskave + >>> from pydra.tasks.afni.v25.preprocess.maskave import Maskave >>> task = Maskave() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/means.py b/pydra/tasks/afni/v25/preprocess/means.py index 4b4ee6b..c12f34c 100644 --- a/pydra/tasks/afni/v25/preprocess/means.py +++ b/pydra/tasks/afni/v25/preprocess/means.py @@ -19,7 +19,7 @@ class Means(shell.Task["Means.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.means import Means + >>> from pydra.tasks.afni.v25.preprocess.means import Means >>> task = Means() >>> task.inputs.in_file_a = Nifti1.mock("im1.nii") diff --git a/pydra/tasks/afni/v25/preprocess/net_corr.py b/pydra/tasks/afni/v25/preprocess/net_corr.py index 403304f..709dc70 100644 --- a/pydra/tasks/afni/v25/preprocess/net_corr.py +++ b/pydra/tasks/afni/v25/preprocess/net_corr.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path from pathlib._local import Path @@ -66,7 +66,7 @@ class NetCorr(shell.Task["NetCorr.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.net_corr import NetCorr + >>> from pydra.tasks.afni.v25.preprocess.net_corr import NetCorr >>> task = NetCorr() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/outlier_count.py b/pydra/tasks/afni/v25/preprocess/outlier_count.py index 57f06eb..c950860 100644 --- a/pydra/tasks/afni/v25/preprocess/outlier_count.py +++ b/pydra/tasks/afni/v25/preprocess/outlier_count.py @@ -60,7 +60,7 @@ class OutlierCount(shell.Task["OutlierCount.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.outlier_count import OutlierCount + >>> from pydra.tasks.afni.v25.preprocess.outlier_count import OutlierCount >>> task = OutlierCount() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/quality_index.py b/pydra/tasks/afni/v25/preprocess/quality_index.py index dfaee93..2130fab 100644 --- a/pydra/tasks/afni/v25/preprocess/quality_index.py +++ b/pydra/tasks/afni/v25/preprocess/quality_index.py @@ -20,7 +20,7 @@ class QualityIndex(shell.Task["QualityIndex.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.quality_index import QualityIndex + >>> from pydra.tasks.afni.v25.preprocess.quality_index import QualityIndex >>> task = QualityIndex() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/qwarp.py b/pydra/tasks/afni/v25/preprocess/qwarp.py index d7a0957..f3ec89d 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp.py @@ -2,8 +2,8 @@ from fileformats.generic import File from fileformats.medimage import Nifti1, NiftiGz import logging -from pydra.tasks.afni.v25_2_06.base import Info -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.base import Info +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path from pathlib._local import Path @@ -186,7 +186,7 @@ class Qwarp(shell.Task["Qwarp.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1, NiftiGz >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.qwarp import Qwarp + >>> from pydra.tasks.afni.v25.preprocess.qwarp import Qwarp >>> task = Qwarp() >>> task.inputs.in_file = "sub-01_dir-LR_epi.nii.gz" diff --git a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py index 0d68f87..0b5a7b0 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py @@ -2,8 +2,8 @@ from fileformats.generic import File from fileformats.medimage import NiftiGz import logging -from pydra.tasks.afni.v25_2_06.base import Info -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.base import Info +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path from pathlib._local import Path @@ -186,7 +186,7 @@ class QwarpPlusMinus(shell.Task["QwarpPlusMinus.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import NiftiGz >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.qwarp_plus_minus import QwarpPlusMinus + >>> from pydra.tasks.afni.v25.preprocess.qwarp_plus_minus import QwarpPlusMinus >>> task = QwarpPlusMinus() >>> task.inputs.source_file = File.mock() diff --git a/pydra/tasks/afni/v25/preprocess/retroicor.py b/pydra/tasks/afni/v25/preprocess/retroicor.py index 5ea5b01..7422039 100644 --- a/pydra/tasks/afni/v25/preprocess/retroicor.py +++ b/pydra/tasks/afni/v25/preprocess/retroicor.py @@ -37,7 +37,7 @@ class Retroicor(shell.Task["Retroicor.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.retroicor import Retroicor + >>> from pydra.tasks.afni.v25.preprocess.retroicor import Retroicor >>> task = Retroicor() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/roi_stats.py b/pydra/tasks/afni/v25/preprocess/roi_stats.py index 4a10ce0..fcde7ab 100644 --- a/pydra/tasks/afni/v25/preprocess/roi_stats.py +++ b/pydra/tasks/afni/v25/preprocess/roi_stats.py @@ -47,7 +47,7 @@ class ROIStats(shell.Task["ROIStats.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.roi_stats import ROIStats + >>> from pydra.tasks.afni.v25.preprocess.roi_stats import ROIStats >>> from pydra.utils.typing import MultiInputObj >>> task = ROIStats() diff --git a/pydra/tasks/afni/v25/preprocess/seg.py b/pydra/tasks/afni/v25/preprocess/seg.py index 498123c..bd79016 100644 --- a/pydra/tasks/afni/v25/preprocess/seg.py +++ b/pydra/tasks/afni/v25/preprocess/seg.py @@ -43,7 +43,7 @@ class Seg(shell.Task["Seg.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.preprocess.seg import Seg + >>> from pydra.tasks.afni.v25.preprocess.seg import Seg >>> task = Seg() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/preprocess/skull_strip.py b/pydra/tasks/afni/v25/preprocess/skull_strip.py index 6d6b910..71a30ec 100644 --- a/pydra/tasks/afni/v25/preprocess/skull_strip.py +++ b/pydra/tasks/afni/v25/preprocess/skull_strip.py @@ -17,7 +17,7 @@ class SkullStrip(shell.Task["SkullStrip.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.skull_strip import SkullStrip + >>> from pydra.tasks.afni.v25.preprocess.skull_strip import SkullStrip >>> task = SkullStrip() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_corr_1d.py b/pydra/tasks/afni/v25/preprocess/t_corr_1d.py index 73a55c7..fb93c3d 100644 --- a/pydra/tasks/afni/v25/preprocess/t_corr_1d.py +++ b/pydra/tasks/afni/v25/preprocess/t_corr_1d.py @@ -19,7 +19,7 @@ class TCorr1D(shell.Task["TCorr1D.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_corr_1d import TCorr1D + >>> from pydra.tasks.afni.v25.preprocess.t_corr_1d import TCorr1D >>> task = TCorr1D() >>> task.inputs.xset = Nifti1.mock("u_rc1s1_Template.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_corr_map.py b/pydra/tasks/afni/v25/preprocess/t_corr_map.py index 949d717..0e82d5e 100644 --- a/pydra/tasks/afni/v25/preprocess/t_corr_map.py +++ b/pydra/tasks/afni/v25/preprocess/t_corr_map.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -160,7 +160,7 @@ class TCorrMap(shell.Task["TCorrMap.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_corr_map import TCorrMap + >>> from pydra.tasks.afni.v25.preprocess.t_corr_map import TCorrMap >>> task = TCorrMap() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_correlate.py b/pydra/tasks/afni/v25/preprocess/t_correlate.py index 50d1b77..51bf118 100644 --- a/pydra/tasks/afni/v25/preprocess/t_correlate.py +++ b/pydra/tasks/afni/v25/preprocess/t_correlate.py @@ -19,7 +19,7 @@ class TCorrelate(shell.Task["TCorrelate.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_correlate import TCorrelate + >>> from pydra.tasks.afni.v25.preprocess.t_correlate import TCorrelate >>> task = TCorrelate() >>> task.inputs.xset = Nifti1.mock("u_rc1s1_Template.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_norm.py b/pydra/tasks/afni/v25/preprocess/t_norm.py index 6e8f66c..2ba6363 100644 --- a/pydra/tasks/afni/v25/preprocess/t_norm.py +++ b/pydra/tasks/afni/v25/preprocess/t_norm.py @@ -17,7 +17,7 @@ class TNorm(shell.Task["TNorm.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_norm import TNorm + >>> from pydra.tasks.afni.v25.preprocess.t_norm import TNorm >>> task = TNorm() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_project.py b/pydra/tasks/afni/v25/preprocess/t_project.py index 538a06a..4e9baf8 100644 --- a/pydra/tasks/afni/v25/preprocess/t_project.py +++ b/pydra/tasks/afni/v25/preprocess/t_project.py @@ -19,7 +19,7 @@ class TProject(shell.Task["TProject.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_project import TProject + >>> from pydra.tasks.afni.v25.preprocess.t_project import TProject >>> task = TProject() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_shift.py b/pydra/tasks/afni/v25/preprocess/t_shift.py index b2d0207..07077f2 100644 --- a/pydra/tasks/afni/v25/preprocess/t_shift.py +++ b/pydra/tasks/afni/v25/preprocess/t_shift.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename import os from pathlib import Path from pathlib._local import Path @@ -78,7 +78,7 @@ class TShift(shell.Task["TShift.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_shift import TShift + >>> from pydra.tasks.afni.v25.preprocess.t_shift import TShift >>> task = TShift() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/t_smooth.py b/pydra/tasks/afni/v25/preprocess/t_smooth.py index fb7b25b..6dd0d2b 100644 --- a/pydra/tasks/afni/v25/preprocess/t_smooth.py +++ b/pydra/tasks/afni/v25/preprocess/t_smooth.py @@ -19,7 +19,7 @@ class TSmooth(shell.Task["TSmooth.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.t_smooth import TSmooth + >>> from pydra.tasks.afni.v25.preprocess.t_smooth import TSmooth >>> task = TSmooth() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_alignepianatpy.py b/pydra/tasks/afni/v25/preprocess/tests/test_alignepianatpy.py index b39f33e..4f9cb9a 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_alignepianatpy.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_alignepianatpy.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.align_epi_anat_py import AlignEpiAnatPy +from pydra.tasks.afni.v25.preprocess.align_epi_anat_py import AlignEpiAnatPy import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_allineate.py b/pydra/tasks/afni/v25/preprocess/tests/test_allineate.py index 3e13472..77d9877 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_allineate.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_allineate.py @@ -3,7 +3,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.allineate import Allineate +from pydra.tasks.afni.v25.preprocess.allineate import Allineate import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_automask.py b/pydra/tasks/afni/v25/preprocess/tests/test_automask.py index 9446c8e..6838598 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_automask.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_automask.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.automask import Automask +from pydra.tasks.afni.v25.preprocess.automask import Automask import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_autotcorrelate.py b/pydra/tasks/afni/v25/preprocess/tests/test_autotcorrelate.py index 36d1ee1..0643d0c 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_autotcorrelate.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_autotcorrelate.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.auto_tcorrelate import AutoTcorrelate +from pydra.tasks.afni.v25.preprocess.auto_tcorrelate import AutoTcorrelate import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_autotlrc.py b/pydra/tasks/afni/v25/preprocess/tests/test_autotlrc.py index f488e31..8c74f1f 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_autotlrc.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_autotlrc.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.auto_tlrc import AutoTLRC +from pydra.tasks.afni.v25.preprocess.auto_tlrc import AutoTLRC import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_bandpass.py b/pydra/tasks/afni/v25/preprocess/tests/test_bandpass.py index d478823..0f05a3f 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_bandpass.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_bandpass.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.bandpass import Bandpass +from pydra.tasks.afni.v25.preprocess.bandpass import Bandpass import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_blurinmask.py b/pydra/tasks/afni/v25/preprocess/tests/test_blurinmask.py index b6043fb..1ac225c 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_blurinmask.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_blurinmask.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.blur_in_mask import BlurInMask +from pydra.tasks.afni.v25.preprocess.blur_in_mask import BlurInMask import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_blurtofwhm.py b/pydra/tasks/afni/v25/preprocess/tests/test_blurtofwhm.py index fb0922c..6501ea9 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_blurtofwhm.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_blurtofwhm.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.blur_to_fwhm import BlurToFWHM +from pydra.tasks.afni.v25.preprocess.blur_to_fwhm import BlurToFWHM import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_cliplevel.py b/pydra/tasks/afni/v25/preprocess/tests/test_cliplevel.py index d933edf..db0b429 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_cliplevel.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_cliplevel.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.clip_level import ClipLevel +from pydra.tasks.afni.v25.preprocess.clip_level import ClipLevel import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_degreecentrality.py b/pydra/tasks/afni/v25/preprocess/tests/test_degreecentrality.py index 0c70c81..86a2e16 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_degreecentrality.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_degreecentrality.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.degree_centrality import DegreeCentrality +from pydra.tasks.afni.v25.preprocess.degree_centrality import DegreeCentrality import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_despike.py b/pydra/tasks/afni/v25/preprocess/tests/test_despike.py index 86f1add..d670bda 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_despike.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_despike.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.despike import Despike +from pydra.tasks.afni.v25.preprocess.despike import Despike import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_detrend.py b/pydra/tasks/afni/v25/preprocess/tests/test_detrend.py index 7ff2a5d..af76911 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_detrend.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_detrend.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.detrend import Detrend +from pydra.tasks.afni.v25.preprocess.detrend import Detrend import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_ecm.py b/pydra/tasks/afni/v25/preprocess/tests/test_ecm.py index 6411442..9215fc8 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_ecm.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_ecm.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.ecm import ECM +from pydra.tasks.afni.v25.preprocess.ecm import ECM import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_fim.py b/pydra/tasks/afni/v25/preprocess/tests/test_fim.py index 623a4d9..db7223e 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_fim.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_fim.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.fim import Fim +from pydra.tasks.afni.v25.preprocess.fim import Fim import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_fourier.py b/pydra/tasks/afni/v25/preprocess/tests/test_fourier.py index 96b940b..39e029f 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_fourier.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_fourier.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.fourier import Fourier +from pydra.tasks.afni.v25.preprocess.fourier import Fourier import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_hist.py b/pydra/tasks/afni/v25/preprocess/tests/test_hist.py index f7473a6..b02d384 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_hist.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_hist.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.hist import Hist +from pydra.tasks.afni.v25.preprocess.hist import Hist import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_lfcd.py b/pydra/tasks/afni/v25/preprocess/tests/test_lfcd.py index 727db66..41f4fa0 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_lfcd.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_lfcd.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.lfcd import LFCD +from pydra.tasks.afni.v25.preprocess.lfcd import LFCD import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_maskave.py b/pydra/tasks/afni/v25/preprocess/tests/test_maskave.py index 86180f4..625687b 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_maskave.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_maskave.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.maskave import Maskave +from pydra.tasks.afni.v25.preprocess.maskave import Maskave import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_means.py b/pydra/tasks/afni/v25/preprocess/tests/test_means.py index 995df0c..f2d1f74 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_means.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_means.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.means import Means +from pydra.tasks.afni.v25.preprocess.means import Means import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_netcorr.py b/pydra/tasks/afni/v25/preprocess/tests/test_netcorr.py index cdf6bad..ee852be 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_netcorr.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_netcorr.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.net_corr import NetCorr +from pydra.tasks.afni.v25.preprocess.net_corr import NetCorr import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_outliercount.py b/pydra/tasks/afni/v25/preprocess/tests/test_outliercount.py index 26f7941..b389425 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_outliercount.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_outliercount.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.outlier_count import OutlierCount +from pydra.tasks.afni.v25.preprocess.outlier_count import OutlierCount import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_qualityindex.py b/pydra/tasks/afni/v25/preprocess/tests/test_qualityindex.py index 1746cb4..227df9e 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_qualityindex.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_qualityindex.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.quality_index import QualityIndex +from pydra.tasks.afni.v25.preprocess.quality_index import QualityIndex import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_qwarp.py b/pydra/tasks/afni/v25/preprocess/tests/test_qwarp.py index 8fe368b..a900e1f 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_qwarp.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_qwarp.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1, NiftiGz import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.qwarp import Qwarp +from pydra.tasks.afni.v25.preprocess.qwarp import Qwarp import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_qwarpplusminus.py b/pydra/tasks/afni/v25/preprocess/tests/test_qwarpplusminus.py index e5e75ae..dd4e9c3 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_qwarpplusminus.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_qwarpplusminus.py @@ -2,7 +2,7 @@ from fileformats.medimage import NiftiGz import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.qwarp_plus_minus import QwarpPlusMinus +from pydra.tasks.afni.v25.preprocess.qwarp_plus_minus import QwarpPlusMinus import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_retroicor.py b/pydra/tasks/afni/v25/preprocess/tests/test_retroicor.py index 978d9b2..407d59e 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_retroicor.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_retroicor.py @@ -3,7 +3,7 @@ from fileformats.medimage_afni import OneD import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.retroicor import Retroicor +from pydra.tasks.afni.v25.preprocess.retroicor import Retroicor import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_roistats.py b/pydra/tasks/afni/v25/preprocess/tests/test_roistats.py index a7b74a2..0ba5891 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_roistats.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_roistats.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.roi_stats import ROIStats +from pydra.tasks.afni.v25.preprocess.roi_stats import ROIStats import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_seg.py b/pydra/tasks/afni/v25/preprocess/tests/test_seg.py index 5275519..92f878b 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_seg.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_seg.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.seg import Seg +from pydra.tasks.afni.v25.preprocess.seg import Seg import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_skullstrip.py b/pydra/tasks/afni/v25/preprocess/tests/test_skullstrip.py index 3c97e1d..b9532bb 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_skullstrip.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_skullstrip.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.skull_strip import SkullStrip +from pydra.tasks.afni.v25.preprocess.skull_strip import SkullStrip import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tcorr1d.py b/pydra/tasks/afni/v25/preprocess/tests/test_tcorr1d.py index 457939e..14e8751 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tcorr1d.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tcorr1d.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_corr_1d import TCorr1D +from pydra.tasks.afni.v25.preprocess.t_corr_1d import TCorr1D import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tcorrelate.py b/pydra/tasks/afni/v25/preprocess/tests/test_tcorrelate.py index 47110b5..b5a7ba1 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tcorrelate.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tcorrelate.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_correlate import TCorrelate +from pydra.tasks.afni.v25.preprocess.t_correlate import TCorrelate import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tcorrmap.py b/pydra/tasks/afni/v25/preprocess/tests/test_tcorrmap.py index 1be5089..d578f54 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tcorrmap.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tcorrmap.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_corr_map import TCorrMap +from pydra.tasks.afni.v25.preprocess.t_corr_map import TCorrMap import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tnorm.py b/pydra/tasks/afni/v25/preprocess/tests/test_tnorm.py index 87d47e0..1bdf93e 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tnorm.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tnorm.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_norm import TNorm +from pydra.tasks.afni.v25.preprocess.t_norm import TNorm import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tproject.py b/pydra/tasks/afni/v25/preprocess/tests/test_tproject.py index 62cabf2..5eacd76 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tproject.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tproject.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_project import TProject +from pydra.tasks.afni.v25.preprocess.t_project import TProject import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tshift.py b/pydra/tasks/afni/v25/preprocess/tests/test_tshift.py index 6d92219..0ad5ce6 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tshift.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tshift.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_shift import TShift +from pydra.tasks.afni.v25.preprocess.t_shift import TShift import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_tsmooth.py b/pydra/tasks/afni/v25/preprocess/tests/test_tsmooth.py index 65cc399..27fb01c 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_tsmooth.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_tsmooth.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.t_smooth import TSmooth +from pydra.tasks.afni.v25.preprocess.t_smooth import TSmooth import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_volreg.py b/pydra/tasks/afni/v25/preprocess/tests/test_volreg.py index 82088e2..0e91f0b 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_volreg.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_volreg.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.volreg import Volreg +from pydra.tasks.afni.v25.preprocess.volreg import Volreg import pytest diff --git a/pydra/tasks/afni/v25/preprocess/tests/test_warp.py b/pydra/tasks/afni/v25/preprocess/tests/test_warp.py index f365085..5af671f 100644 --- a/pydra/tasks/afni/v25/preprocess/tests/test_warp.py +++ b/pydra/tasks/afni/v25/preprocess/tests/test_warp.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.preprocess.warp import Warp +from pydra.tasks.afni.v25.preprocess.warp import Warp import pytest diff --git a/pydra/tasks/afni/v25/preprocess/volreg.py b/pydra/tasks/afni/v25/preprocess/volreg.py index 9bc34b6..f4664dd 100644 --- a/pydra/tasks/afni/v25/preprocess/volreg.py +++ b/pydra/tasks/afni/v25/preprocess/volreg.py @@ -36,7 +36,7 @@ class Volreg(shell.Task["Volreg.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.volreg import Volreg + >>> from pydra.tasks.afni.v25.preprocess.volreg import Volreg >>> task = Volreg() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/preprocess/warp.py b/pydra/tasks/afni/v25/preprocess/warp.py index a2735ea..016d6b7 100644 --- a/pydra/tasks/afni/v25/preprocess/warp.py +++ b/pydra/tasks/afni/v25/preprocess/warp.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import ( +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import ( fname_presuffix, split_filename, ) @@ -52,7 +52,7 @@ class Warp(shell.Task["Warp.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.preprocess.warp import Warp + >>> from pydra.tasks.afni.v25.preprocess.warp import Warp >>> task = Warp() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/svm/svm_test.py b/pydra/tasks/afni/v25/svm/svm_test.py index df918b5..7b29e2c 100644 --- a/pydra/tasks/afni/v25/svm/svm_test.py +++ b/pydra/tasks/afni/v25/svm/svm_test.py @@ -17,7 +17,7 @@ class SVMTest(shell.Task["SVMTest.Outputs"]): >>> from fileformats.generic import File >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.svm.svm_test import SVMTest + >>> from pydra.tasks.afni.v25.svm.svm_test import SVMTest """ diff --git a/pydra/tasks/afni/v25/svm/svm_train.py b/pydra/tasks/afni/v25/svm/svm_train.py index 54719ad..d89f8bf 100644 --- a/pydra/tasks/afni/v25/svm/svm_train.py +++ b/pydra/tasks/afni/v25/svm/svm_train.py @@ -17,7 +17,7 @@ class SVMTrain(shell.Task["SVMTrain.Outputs"]): >>> from fileformats.generic import File >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.svm.svm_train import SVMTrain + >>> from pydra.tasks.afni.v25.svm.svm_train import SVMTrain """ diff --git a/pydra/tasks/afni/v25/svm/tests/test_svmtest.py b/pydra/tasks/afni/v25/svm/tests/test_svmtest.py index a56f044..8203165 100644 --- a/pydra/tasks/afni/v25/svm/tests/test_svmtest.py +++ b/pydra/tasks/afni/v25/svm/tests/test_svmtest.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.svm.svm_test import SVMTest +from pydra.tasks.afni.v25.svm.svm_test import SVMTest import pytest diff --git a/pydra/tasks/afni/v25/svm/tests/test_svmtrain.py b/pydra/tasks/afni/v25/svm/tests/test_svmtrain.py index c417d66..095169c 100644 --- a/pydra/tasks/afni/v25/svm/tests/test_svmtrain.py +++ b/pydra/tasks/afni/v25/svm/tests/test_svmtrain.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.svm.svm_train import SVMTrain +from pydra.tasks.afni.v25.svm.svm_train import SVMTrain import pytest diff --git a/pydra/tasks/afni/v25/utils/a_boverlap.py b/pydra/tasks/afni/v25/utils/a_boverlap.py index 493f5f3..36903f9 100644 --- a/pydra/tasks/afni/v25/utils/a_boverlap.py +++ b/pydra/tasks/afni/v25/utils/a_boverlap.py @@ -3,7 +3,7 @@ from fileformats.medimage import Nifti1 from fileformats.text import TextFile import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -46,7 +46,7 @@ class ABoverlap(shell.Task["ABoverlap.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from fileformats.text import TextFile >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.a_boverlap import ABoverlap + >>> from pydra.tasks.afni.v25.utils.a_boverlap import ABoverlap >>> task = ABoverlap() >>> task.inputs.in_file_a = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/afn_ito_nifti.py b/pydra/tasks/afni/v25/utils/afn_ito_nifti.py index b4c7d04..265170a 100644 --- a/pydra/tasks/afni/v25/utils/afn_ito_nifti.py +++ b/pydra/tasks/afni/v25/utils/afn_ito_nifti.py @@ -22,7 +22,7 @@ class AFNItoNIFTI(shell.Task["AFNItoNIFTI.Outputs"]): >>> from fileformats.medimage_afni import ThreeD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.afn_ito_nifti import AFNItoNIFTI + >>> from pydra.tasks.afni.v25.utils.afn_ito_nifti import AFNItoNIFTI >>> task = AFNItoNIFTI() >>> task.inputs.in_file = ThreeD.mock("afni_output.3D") diff --git a/pydra/tasks/afni/v25/utils/autobox.py b/pydra/tasks/afni/v25/utils/autobox.py index d1916d5..b9a8dd6 100644 --- a/pydra/tasks/afni/v25/utils/autobox.py +++ b/pydra/tasks/afni/v25/utils/autobox.py @@ -79,7 +79,7 @@ class Autobox(shell.Task["Autobox.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.autobox import Autobox + >>> from pydra.tasks.afni.v25.utils.autobox import Autobox >>> task = Autobox() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/axialize.py b/pydra/tasks/afni/v25/utils/axialize.py index 397d9ec..77cfe4f 100644 --- a/pydra/tasks/afni/v25/utils/axialize.py +++ b/pydra/tasks/afni/v25/utils/axialize.py @@ -17,7 +17,7 @@ class Axialize(shell.Task["Axialize.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.axialize import Axialize + >>> from pydra.tasks.afni.v25.utils.axialize import Axialize >>> task = Axialize() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/brick_stat.py b/pydra/tasks/afni/v25/utils/brick_stat.py index f8f651b..d16c56c 100644 --- a/pydra/tasks/afni/v25/utils/brick_stat.py +++ b/pydra/tasks/afni/v25/utils/brick_stat.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import load_json, save_json +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import load_json, save_json import os from pydra.compose import shell import typing as ty @@ -57,7 +57,7 @@ class BrickStat(shell.Task["BrickStat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.utils.brick_stat import BrickStat + >>> from pydra.tasks.afni.v25.utils.brick_stat import BrickStat >>> task = BrickStat() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/bucket.py b/pydra/tasks/afni/v25/utils/bucket.py index fbea86b..c6dc3c8 100644 --- a/pydra/tasks/afni/v25/utils/bucket.py +++ b/pydra/tasks/afni/v25/utils/bucket.py @@ -29,7 +29,7 @@ class Bucket(shell.Task["Bucket.Outputs"]): ------- >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.bucket import Bucket + >>> from pydra.tasks.afni.v25.utils.bucket import Bucket >>> task = Bucket() >>> task.inputs.in_file = [('functional.nii',"{2..$}"), ('functional.nii',"{1}")] diff --git a/pydra/tasks/afni/v25/utils/calc.py b/pydra/tasks/afni/v25/utils/calc.py index d1d1bb6..4434eed 100644 --- a/pydra/tasks/afni/v25/utils/calc.py +++ b/pydra/tasks/afni/v25/utils/calc.py @@ -39,7 +39,7 @@ class Calc(shell.Task["Calc.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.calc import Calc + >>> from pydra.tasks.afni.v25.utils.calc import Calc >>> task = Calc() >>> task.inputs.in_file_a = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/cat.py b/pydra/tasks/afni/v25/utils/cat.py index d6d49f5..15ae126 100644 --- a/pydra/tasks/afni/v25/utils/cat.py +++ b/pydra/tasks/afni/v25/utils/cat.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage_afni import OneD import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -46,7 +46,7 @@ class Cat(shell.Task["Cat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.cat import Cat + >>> from pydra.tasks.afni.v25.utils.cat import Cat >>> task = Cat() >>> task.inputs.out_file = "catout.1d" diff --git a/pydra/tasks/afni/v25/utils/cat_matvec.py b/pydra/tasks/afni/v25/utils/cat_matvec.py index 15b6eff..7fe5b0c 100644 --- a/pydra/tasks/afni/v25/utils/cat_matvec.py +++ b/pydra/tasks/afni/v25/utils/cat_matvec.py @@ -32,7 +32,7 @@ class CatMatvec(shell.Task["CatMatvec.Outputs"]): ------- >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.cat_matvec import CatMatvec + >>> from pydra.tasks.afni.v25.utils.cat_matvec import CatMatvec >>> task = CatMatvec() >>> task.inputs.in_file = [("structural.BRIK::WARP_DATA","I")] diff --git a/pydra/tasks/afni/v25/utils/center_mass.py b/pydra/tasks/afni/v25/utils/center_mass.py index 39fa0f9..5fed9c2 100644 --- a/pydra/tasks/afni/v25/utils/center_mass.py +++ b/pydra/tasks/afni/v25/utils/center_mass.py @@ -47,7 +47,7 @@ class CenterMass(shell.Task["CenterMass.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.center_mass import CenterMass + >>> from pydra.tasks.afni.v25.utils.center_mass import CenterMass >>> task = CenterMass() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/convert_dset.py b/pydra/tasks/afni/v25/utils/convert_dset.py index 0db9413..7fc2574 100644 --- a/pydra/tasks/afni/v25/utils/convert_dset.py +++ b/pydra/tasks/afni/v25/utils/convert_dset.py @@ -36,7 +36,7 @@ class ConvertDset(shell.Task["ConvertDset.Outputs"]): >>> from fileformats.medimage import Gifti >>> from fileformats.medimage_afni import Dset >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.convert_dset import ConvertDset + >>> from pydra.tasks.afni.v25.utils.convert_dset import ConvertDset >>> task = ConvertDset() >>> task.inputs.in_file = Gifti.mock("lh.pial_converted.gii") diff --git a/pydra/tasks/afni/v25/utils/copy.py b/pydra/tasks/afni/v25/utils/copy.py index f75faff..a6e648c 100644 --- a/pydra/tasks/afni/v25/utils/copy.py +++ b/pydra/tasks/afni/v25/utils/copy.py @@ -18,7 +18,7 @@ class Copy(shell.Task["Copy.Outputs"]): >>> from copy import deepcopy >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.copy import Copy + >>> from pydra.tasks.afni.v25.utils.copy import Copy >>> task = Copy() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/dot.py b/pydra/tasks/afni/v25/utils/dot.py index b95d162..879aa4e 100644 --- a/pydra/tasks/afni/v25/utils/dot.py +++ b/pydra/tasks/afni/v25/utils/dot.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.text import TextFile import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -44,7 +44,7 @@ class Dot(shell.Task["Dot.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.text import TextFile >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.dot import Dot + >>> from pydra.tasks.afni.v25.utils.dot import Dot >>> task = Dot() >>> task.inputs.in_files = [File.mock("functional.nii[0]"), File.mock("structural.nii")] diff --git a/pydra/tasks/afni/v25/utils/edge_3.py b/pydra/tasks/afni/v25/utils/edge_3.py index aeb824c..4a987c1 100644 --- a/pydra/tasks/afni/v25/utils/edge_3.py +++ b/pydra/tasks/afni/v25/utils/edge_3.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -44,7 +44,7 @@ class Edge3(shell.Task["Edge3.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.edge_3 import Edge3 + >>> from pydra.tasks.afni.v25.utils.edge_3 import Edge3 >>> task = Edge3() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/eval.py b/pydra/tasks/afni/v25/utils/eval.py index 5b574c8..b9ffa5c 100644 --- a/pydra/tasks/afni/v25/utils/eval.py +++ b/pydra/tasks/afni/v25/utils/eval.py @@ -39,7 +39,7 @@ class Eval(shell.Task["Eval.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.eval import Eval + >>> from pydra.tasks.afni.v25.utils.eval import Eval >>> task = Eval() >>> task.inputs.in_file_a = OneD.mock("seed.1D") diff --git a/pydra/tasks/afni/v25/utils/fwh_mx.py b/pydra/tasks/afni/v25/utils/fwh_mx.py index 373fe8f..e1c6b07 100644 --- a/pydra/tasks/afni/v25/utils/fwh_mx.py +++ b/pydra/tasks/afni/v25/utils/fwh_mx.py @@ -126,7 +126,7 @@ class FWHMx(shell.Task["FWHMx.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.fwh_mx import FWHMx + >>> from pydra.tasks.afni.v25.utils.fwh_mx import FWHMx >>> task = FWHMx() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/gcor.py b/pydra/tasks/afni/v25/utils/gcor.py index ab41813..317a80c 100644 --- a/pydra/tasks/afni/v25/utils/gcor.py +++ b/pydra/tasks/afni/v25/utils/gcor.py @@ -29,7 +29,7 @@ class GCOR(shell.Task["GCOR.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.utils.gcor import GCOR + >>> from pydra.tasks.afni.v25.utils.gcor import GCOR >>> task = GCOR() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/local_bistat.py b/pydra/tasks/afni/v25/utils/local_bistat.py index 39c41e7..a0ff046 100644 --- a/pydra/tasks/afni/v25/utils/local_bistat.py +++ b/pydra/tasks/afni/v25/utils/local_bistat.py @@ -39,7 +39,7 @@ class LocalBistat(shell.Task["LocalBistat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.local_bistat import LocalBistat + >>> from pydra.tasks.afni.v25.utils.local_bistat import LocalBistat >>> from pydra.utils.typing import MultiInputObj >>> task = LocalBistat() diff --git a/pydra/tasks/afni/v25/utils/localstat.py b/pydra/tasks/afni/v25/utils/localstat.py index e78b8a3..d47ad99 100644 --- a/pydra/tasks/afni/v25/utils/localstat.py +++ b/pydra/tasks/afni/v25/utils/localstat.py @@ -63,7 +63,7 @@ class Localstat(shell.Task["Localstat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.localstat import Localstat + >>> from pydra.tasks.afni.v25.utils.localstat import Localstat >>> from pydra.utils.typing import MultiInputObj >>> task = Localstat() diff --git a/pydra/tasks/afni/v25/utils/mask_tool.py b/pydra/tasks/afni/v25/utils/mask_tool.py index bb29071..59e35cb 100644 --- a/pydra/tasks/afni/v25/utils/mask_tool.py +++ b/pydra/tasks/afni/v25/utils/mask_tool.py @@ -17,7 +17,7 @@ class MaskTool(shell.Task["MaskTool.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.mask_tool import MaskTool + >>> from pydra.tasks.afni.v25.utils.mask_tool import MaskTool >>> task = MaskTool() >>> task.inputs.in_file = [Nifti1.mock("f"), Nifti1.mock("u"), Nifti1.mock("n"), Nifti1.mock("c"), Nifti1.mock("t"), Nifti1.mock("i"), Nifti1.mock("o"), Nifti1.mock("n"), Nifti1.mock("a"), Nifti1.mock("l"), Nifti1.mock("."), Nifti1.mock("n"), Nifti1.mock("i"), Nifti1.mock("i")] diff --git a/pydra/tasks/afni/v25/utils/merge.py b/pydra/tasks/afni/v25/utils/merge.py index 349fa4f..bd8f8ec 100644 --- a/pydra/tasks/afni/v25/utils/merge.py +++ b/pydra/tasks/afni/v25/utils/merge.py @@ -17,7 +17,7 @@ class Merge(shell.Task["Merge.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.merge import Merge + >>> from pydra.tasks.afni.v25.utils.merge import Merge >>> task = Merge() >>> task.inputs.in_files = [Nifti1.mock("functional.nii"), Nifti1.mock("functional2.nii")] diff --git a/pydra/tasks/afni/v25/utils/notes.py b/pydra/tasks/afni/v25/utils/notes.py index bfe7083..c63d6b3 100644 --- a/pydra/tasks/afni/v25/utils/notes.py +++ b/pydra/tasks/afni/v25/utils/notes.py @@ -36,7 +36,7 @@ class Notes(shell.Task["Notes.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import Head >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.notes import Notes + >>> from pydra.tasks.afni.v25.utils.notes import Notes >>> task = Notes() >>> task.inputs.in_file = Head.mock("functional.HEAD") diff --git a/pydra/tasks/afni/v25/utils/nwarp_adjust.py b/pydra/tasks/afni/v25/utils/nwarp_adjust.py index f17f1d5..8de9bc2 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_adjust.py +++ b/pydra/tasks/afni/v25/utils/nwarp_adjust.py @@ -34,7 +34,7 @@ class NwarpAdjust(shell.Task["NwarpAdjust.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import NiftiGz >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.nwarp_adjust import NwarpAdjust + >>> from pydra.tasks.afni.v25.utils.nwarp_adjust import NwarpAdjust >>> task = NwarpAdjust() >>> task.inputs.warps = [NiftiGz.mock("func2anat_InverseWarp.nii.gz"), NiftiGz.mock("func2anat_InverseWarp.nii.gz"), NiftiGz.mock("func2anat_InverseWarp.nii.gz"), NiftiGz.mock("func2anat_InverseWarp.nii.gz"), NiftiGz.mock("func2anat_InverseWarp.nii.gz")] diff --git a/pydra/tasks/afni/v25/utils/nwarp_apply.py b/pydra/tasks/afni/v25/utils/nwarp_apply.py index 2ff68a6..445d84d 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_apply.py +++ b/pydra/tasks/afni/v25/utils/nwarp_apply.py @@ -17,7 +17,7 @@ class NwarpApply(shell.Task["NwarpApply.Outputs"]): >>> from fileformats.generic import File >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.nwarp_apply import NwarpApply + >>> from pydra.tasks.afni.v25.utils.nwarp_apply import NwarpApply >>> task = NwarpApply() >>> task.inputs.in_file = "Fred+orig" diff --git a/pydra/tasks/afni/v25/utils/nwarp_cat.py b/pydra/tasks/afni/v25/utils/nwarp_cat.py index 77f5907..3b855a4 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_cat.py +++ b/pydra/tasks/afni/v25/utils/nwarp_cat.py @@ -1,5 +1,5 @@ import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -46,7 +46,7 @@ class NwarpCat(shell.Task["NwarpCat.Outputs"]): ------- >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.nwarp_cat import NwarpCat + >>> from pydra.tasks.afni.v25.utils.nwarp_cat import NwarpCat >>> task = NwarpCat() >>> task.inputs.in_files = ["Q25_warp+tlrc.HEAD", ("IDENT", "structural.nii")] diff --git a/pydra/tasks/afni/v25/utils/one_d_tool_py.py b/pydra/tasks/afni/v25/utils/one_d_tool_py.py index 2fd2d88..bcbfadb 100644 --- a/pydra/tasks/afni/v25/utils/one_d_tool_py.py +++ b/pydra/tasks/afni/v25/utils/one_d_tool_py.py @@ -44,7 +44,7 @@ class OneDToolPy(shell.Task["OneDToolPy.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.one_d_tool_py import OneDToolPy + >>> from pydra.tasks.afni.v25.utils.one_d_tool_py import OneDToolPy >>> task = OneDToolPy() >>> task.inputs.in_file = OneD.mock("f1.1D") diff --git a/pydra/tasks/afni/v25/utils/re_ho.py b/pydra/tasks/afni/v25/utils/re_ho.py index 4a6cf73..3d2a892 100644 --- a/pydra/tasks/afni/v25/utils/re_ho.py +++ b/pydra/tasks/afni/v25/utils/re_ho.py @@ -51,7 +51,7 @@ class ReHo(shell.Task["ReHo.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.re_ho import ReHo + >>> from pydra.tasks.afni.v25.utils.re_ho import ReHo >>> task = ReHo() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/refit.py b/pydra/tasks/afni/v25/utils/refit.py index 54b6ead..13b9d68 100644 --- a/pydra/tasks/afni/v25/utils/refit.py +++ b/pydra/tasks/afni/v25/utils/refit.py @@ -33,7 +33,7 @@ class Refit(shell.Task["Refit.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pydra.tasks.afni.v25_2_06.utils.refit import Refit + >>> from pydra.tasks.afni.v25.utils.refit import Refit >>> task = Refit() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/resample.py b/pydra/tasks/afni/v25/utils/resample.py index 56e094e..4efc793 100644 --- a/pydra/tasks/afni/v25/utils/resample.py +++ b/pydra/tasks/afni/v25/utils/resample.py @@ -19,7 +19,7 @@ class Resample(shell.Task["Resample.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.resample import Resample + >>> from pydra.tasks.afni.v25.utils.resample import Resample >>> task = Resample() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/t_cat.py b/pydra/tasks/afni/v25/utils/t_cat.py index 42966ab..2f7f8f3 100644 --- a/pydra/tasks/afni/v25/utils/t_cat.py +++ b/pydra/tasks/afni/v25/utils/t_cat.py @@ -17,7 +17,7 @@ class TCat(shell.Task["TCat.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.t_cat import TCat + >>> from pydra.tasks.afni.v25.utils.t_cat import TCat >>> task = TCat() >>> task.inputs.in_files = [Nifti1.mock("functional.nii"), Nifti1.mock("functional2.nii")] diff --git a/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py b/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py index 946d134..6369b9b 100644 --- a/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py +++ b/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py @@ -1,5 +1,5 @@ import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import fname_presuffix +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -27,7 +27,7 @@ class TCatSubBrick(shell.Task["TCatSubBrick.Outputs"]): ------- >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.t_cat_sub_brick import TCatSubBrick + >>> from pydra.tasks.afni.v25.utils.t_cat_sub_brick import TCatSubBrick >>> task = TCatSubBrick() >>> task.inputs.in_files = [('functional.nii', "'{2..$}'"), ('functional2.nii', "'{2..$}'")] diff --git a/pydra/tasks/afni/v25/utils/t_stat.py b/pydra/tasks/afni/v25/utils/t_stat.py index 4064dd4..730203e 100644 --- a/pydra/tasks/afni/v25/utils/t_stat.py +++ b/pydra/tasks/afni/v25/utils/t_stat.py @@ -19,7 +19,7 @@ class TStat(shell.Task["TStat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.t_stat import TStat + >>> from pydra.tasks.afni.v25.utils.t_stat import TStat >>> task = TStat() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/tests/test_aboverlap.py b/pydra/tasks/afni/v25/utils/tests/test_aboverlap.py index 0fb940c..659c66a 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_aboverlap.py +++ b/pydra/tasks/afni/v25/utils/tests/test_aboverlap.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.a_boverlap import ABoverlap +from pydra.tasks.afni.v25.utils.a_boverlap import ABoverlap import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_afnitonifti.py b/pydra/tasks/afni/v25/utils/tests/test_afnitonifti.py index 79337e5..b25371b 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_afnitonifti.py +++ b/pydra/tasks/afni/v25/utils/tests/test_afnitonifti.py @@ -1,7 +1,7 @@ from fileformats.medimage_afni import ThreeD import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.afn_ito_nifti import AFNItoNIFTI +from pydra.tasks.afni.v25.utils.afn_ito_nifti import AFNItoNIFTI import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_autobox.py b/pydra/tasks/afni/v25/utils/tests/test_autobox.py index 5a8a700..38941c8 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_autobox.py +++ b/pydra/tasks/afni/v25/utils/tests/test_autobox.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.autobox import Autobox +from pydra.tasks.afni.v25.utils.autobox import Autobox import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_axialize.py b/pydra/tasks/afni/v25/utils/tests/test_axialize.py index 99d0989..6bde14c 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_axialize.py +++ b/pydra/tasks/afni/v25/utils/tests/test_axialize.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.axialize import Axialize +from pydra.tasks.afni.v25.utils.axialize import Axialize import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_brickstat.py b/pydra/tasks/afni/v25/utils/tests/test_brickstat.py index 400e36b..60254f5 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_brickstat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_brickstat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.brick_stat import BrickStat +from pydra.tasks.afni.v25.utils.brick_stat import BrickStat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_bucket.py b/pydra/tasks/afni/v25/utils/tests/test_bucket.py index 85c53c5..2d2b63c 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_bucket.py +++ b/pydra/tasks/afni/v25/utils/tests/test_bucket.py @@ -1,6 +1,6 @@ import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.bucket import Bucket +from pydra.tasks.afni.v25.utils.bucket import Bucket import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_calc.py b/pydra/tasks/afni/v25/utils/tests/test_calc.py index 2f6dd99..e710115 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_calc.py +++ b/pydra/tasks/afni/v25/utils/tests/test_calc.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.calc import Calc +from pydra.tasks.afni.v25.utils.calc import Calc import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_cat.py b/pydra/tasks/afni/v25/utils/tests/test_cat.py index b1f2a98..60b2c96 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_cat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_cat.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.cat import Cat +from pydra.tasks.afni.v25.utils.cat import Cat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_catmatvec.py b/pydra/tasks/afni/v25/utils/tests/test_catmatvec.py index c5dfd70..6fca496 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_catmatvec.py +++ b/pydra/tasks/afni/v25/utils/tests/test_catmatvec.py @@ -1,6 +1,6 @@ import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.cat_matvec import CatMatvec +from pydra.tasks.afni.v25.utils.cat_matvec import CatMatvec import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_centermass.py b/pydra/tasks/afni/v25/utils/tests/test_centermass.py index cdb39cb..7e97d78 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_centermass.py +++ b/pydra/tasks/afni/v25/utils/tests/test_centermass.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.center_mass import CenterMass +from pydra.tasks.afni.v25.utils.center_mass import CenterMass import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_convertdset.py b/pydra/tasks/afni/v25/utils/tests/test_convertdset.py index b82b1c3..a874839 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_convertdset.py +++ b/pydra/tasks/afni/v25/utils/tests/test_convertdset.py @@ -1,7 +1,7 @@ from fileformats.medimage import Gifti import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.convert_dset import ConvertDset +from pydra.tasks.afni.v25.utils.convert_dset import ConvertDset import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_copy.py b/pydra/tasks/afni/v25/utils/tests/test_copy.py index fee0b75..193d36a 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_copy.py +++ b/pydra/tasks/afni/v25/utils/tests/test_copy.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.copy import Copy +from pydra.tasks.afni.v25.utils.copy import Copy import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_dot.py b/pydra/tasks/afni/v25/utils/tests/test_dot.py index 2b9223e..0b3a5c6 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_dot.py +++ b/pydra/tasks/afni/v25/utils/tests/test_dot.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.dot import Dot +from pydra.tasks.afni.v25.utils.dot import Dot import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_edge3.py b/pydra/tasks/afni/v25/utils/tests/test_edge3.py index bbfca29..8ac8b7c 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_edge3.py +++ b/pydra/tasks/afni/v25/utils/tests/test_edge3.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.edge_3 import Edge3 +from pydra.tasks.afni.v25.utils.edge_3 import Edge3 import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_eval.py b/pydra/tasks/afni/v25/utils/tests/test_eval.py index 455d7f0..c2b7140 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_eval.py +++ b/pydra/tasks/afni/v25/utils/tests/test_eval.py @@ -2,7 +2,7 @@ from fileformats.medimage_afni import OneD import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.eval import Eval +from pydra.tasks.afni.v25.utils.eval import Eval import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_fwhmx.py b/pydra/tasks/afni/v25/utils/tests/test_fwhmx.py index 885b090..f2e7744 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_fwhmx.py +++ b/pydra/tasks/afni/v25/utils/tests/test_fwhmx.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.fwh_mx import FWHMx +from pydra.tasks.afni.v25.utils.fwh_mx import FWHMx import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_gcor.py b/pydra/tasks/afni/v25/utils/tests/test_gcor.py index 6571875..1143a42 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_gcor.py +++ b/pydra/tasks/afni/v25/utils/tests/test_gcor.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.gcor import GCOR +from pydra.tasks.afni.v25.utils.gcor import GCOR import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_localbistat.py b/pydra/tasks/afni/v25/utils/tests/test_localbistat.py index 390e7c3..167873b 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_localbistat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_localbistat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.local_bistat import LocalBistat +from pydra.tasks.afni.v25.utils.local_bistat import LocalBistat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_localstat.py b/pydra/tasks/afni/v25/utils/tests/test_localstat.py index e4414b1..0b7578b 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_localstat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_localstat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.localstat import Localstat +from pydra.tasks.afni.v25.utils.localstat import Localstat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_masktool.py b/pydra/tasks/afni/v25/utils/tests/test_masktool.py index 08bb7de..3437b42 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_masktool.py +++ b/pydra/tasks/afni/v25/utils/tests/test_masktool.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.mask_tool import MaskTool +from pydra.tasks.afni.v25.utils.mask_tool import MaskTool import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_merge.py b/pydra/tasks/afni/v25/utils/tests/test_merge.py index 6028d88..6a4c336 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_merge.py +++ b/pydra/tasks/afni/v25/utils/tests/test_merge.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.merge import Merge +from pydra.tasks.afni.v25.utils.merge import Merge import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_notes.py b/pydra/tasks/afni/v25/utils/tests/test_notes.py index 1179eec..26826eb 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_notes.py +++ b/pydra/tasks/afni/v25/utils/tests/test_notes.py @@ -1,7 +1,7 @@ from fileformats.medimage_afni import Head import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.notes import Notes +from pydra.tasks.afni.v25.utils.notes import Notes import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_nwarpadjust.py b/pydra/tasks/afni/v25/utils/tests/test_nwarpadjust.py index 270e7f1..66bbbe1 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_nwarpadjust.py +++ b/pydra/tasks/afni/v25/utils/tests/test_nwarpadjust.py @@ -2,7 +2,7 @@ from fileformats.medimage import NiftiGz import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.nwarp_adjust import NwarpAdjust +from pydra.tasks.afni.v25.utils.nwarp_adjust import NwarpAdjust import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_nwarpapply.py b/pydra/tasks/afni/v25/utils/tests/test_nwarpapply.py index f441cc5..ddc200c 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_nwarpapply.py +++ b/pydra/tasks/afni/v25/utils/tests/test_nwarpapply.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.nwarp_apply import NwarpApply +from pydra.tasks.afni.v25.utils.nwarp_apply import NwarpApply import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_nwarpcat.py b/pydra/tasks/afni/v25/utils/tests/test_nwarpcat.py index e203b92..f4dc99e 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_nwarpcat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_nwarpcat.py @@ -1,6 +1,6 @@ import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.nwarp_cat import NwarpCat +from pydra.tasks.afni.v25.utils.nwarp_cat import NwarpCat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_onedtoolpy.py b/pydra/tasks/afni/v25/utils/tests/test_onedtoolpy.py index 3752b11..5aef1c5 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_onedtoolpy.py +++ b/pydra/tasks/afni/v25/utils/tests/test_onedtoolpy.py @@ -2,7 +2,7 @@ from fileformats.medimage_afni import OneD import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.one_d_tool_py import OneDToolPy +from pydra.tasks.afni.v25.utils.one_d_tool_py import OneDToolPy import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_refit.py b/pydra/tasks/afni/v25/utils/tests/test_refit.py index b251c40..be4207e 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_refit.py +++ b/pydra/tasks/afni/v25/utils/tests/test_refit.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.refit import Refit +from pydra.tasks.afni.v25.utils.refit import Refit import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_reho.py b/pydra/tasks/afni/v25/utils/tests/test_reho.py index 8002919..7d9c5e1 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_reho.py +++ b/pydra/tasks/afni/v25/utils/tests/test_reho.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.re_ho import ReHo +from pydra.tasks.afni.v25.utils.re_ho import ReHo import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_resample.py b/pydra/tasks/afni/v25/utils/tests/test_resample.py index 3fdd331..ba5d284 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_resample.py +++ b/pydra/tasks/afni/v25/utils/tests/test_resample.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.resample import Resample +from pydra.tasks.afni.v25.utils.resample import Resample import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_tcat.py b/pydra/tasks/afni/v25/utils/tests/test_tcat.py index 7b91981..9a3177c 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_tcat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_tcat.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.t_cat import TCat +from pydra.tasks.afni.v25.utils.t_cat import TCat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_tcatsubbrick.py b/pydra/tasks/afni/v25/utils/tests/test_tcatsubbrick.py index 85ae34d..87a91bb 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_tcatsubbrick.py +++ b/pydra/tasks/afni/v25/utils/tests/test_tcatsubbrick.py @@ -1,6 +1,6 @@ import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.t_cat_sub_brick import TCatSubBrick +from pydra.tasks.afni.v25.utils.t_cat_sub_brick import TCatSubBrick import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_to3d.py b/pydra/tasks/afni/v25/utils/tests/test_to3d.py index 014f6e0..236be6e 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_to3d.py +++ b/pydra/tasks/afni/v25/utils/tests/test_to3d.py @@ -1,7 +1,7 @@ from fileformats.generic import Directory import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.to_3d import To3D +from pydra.tasks.afni.v25.utils.to_3d import To3D import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_tstat.py b/pydra/tasks/afni/v25/utils/tests/test_tstat.py index 2b758b4..a9b8d2a 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_tstat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_tstat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.t_stat import TStat +from pydra.tasks.afni.v25.utils.t_stat import TStat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_undump.py b/pydra/tasks/afni/v25/utils/tests/test_undump.py index f1f3dcd..478d424 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_undump.py +++ b/pydra/tasks/afni/v25/utils/tests/test_undump.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.undump import Undump +from pydra.tasks.afni.v25.utils.undump import Undump import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_unifize.py b/pydra/tasks/afni/v25/utils/tests/test_unifize.py index ebf7be1..b563648 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_unifize.py +++ b/pydra/tasks/afni/v25/utils/tests/test_unifize.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.unifize import Unifize +from pydra.tasks.afni.v25.utils.unifize import Unifize import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_zcat.py b/pydra/tasks/afni/v25/utils/tests/test_zcat.py index 53d112d..dddeb78 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_zcat.py +++ b/pydra/tasks/afni/v25/utils/tests/test_zcat.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.zcat import Zcat +from pydra.tasks.afni.v25.utils.zcat import Zcat import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_zcutup.py b/pydra/tasks/afni/v25/utils/tests/test_zcutup.py index 9eed457..d10b44f 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_zcutup.py +++ b/pydra/tasks/afni/v25/utils/tests/test_zcutup.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.z_cut_up import ZCutUp +from pydra.tasks.afni.v25.utils.z_cut_up import ZCutUp import pytest diff --git a/pydra/tasks/afni/v25/utils/tests/test_zeropad.py b/pydra/tasks/afni/v25/utils/tests/test_zeropad.py index 45531ab..0fbc206 100644 --- a/pydra/tasks/afni/v25/utils/tests/test_zeropad.py +++ b/pydra/tasks/afni/v25/utils/tests/test_zeropad.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from nipype2pydra.testing import PassAfterTimeoutWorker -from pydra.tasks.afni.v25_2_06.utils.zeropad import Zeropad +from pydra.tasks.afni.v25.utils.zeropad import Zeropad import pytest diff --git a/pydra/tasks/afni/v25/utils/to_3d.py b/pydra/tasks/afni/v25/utils/to_3d.py index 8af0007..ae3b143 100644 --- a/pydra/tasks/afni/v25/utils/to_3d.py +++ b/pydra/tasks/afni/v25/utils/to_3d.py @@ -17,7 +17,7 @@ class To3D(shell.Task["To3D.Outputs"]): >>> from fileformats.generic import Directory >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.to_3d import To3D + >>> from pydra.tasks.afni.v25.utils.to_3d import To3D >>> task = To3D() >>> task.inputs.out_file = "dicomdir.nii" diff --git a/pydra/tasks/afni/v25/utils/undump.py b/pydra/tasks/afni/v25/utils/undump.py index 3a565a1..fae383c 100644 --- a/pydra/tasks/afni/v25/utils/undump.py +++ b/pydra/tasks/afni/v25/utils/undump.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -44,7 +44,7 @@ class Undump(shell.Task["Undump.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.undump import Undump + >>> from pydra.tasks.afni.v25.utils.undump import Undump >>> task = Undump() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/unifize.py b/pydra/tasks/afni/v25/utils/unifize.py index 2912a5f..aa6bba7 100644 --- a/pydra/tasks/afni/v25/utils/unifize.py +++ b/pydra/tasks/afni/v25/utils/unifize.py @@ -2,7 +2,7 @@ from fileformats.generic import File from fileformats.medimage import Nifti1 import logging -from pydra.tasks.afni.v25_2_06.nipype_ports.utils.filemanip import split_filename +from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path from pathlib._local import Path from pydra.compose import shell @@ -44,7 +44,7 @@ class Unifize(shell.Task["Unifize.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.unifize import Unifize + >>> from pydra.tasks.afni.v25.utils.unifize import Unifize >>> task = Unifize() >>> task.inputs.in_file = Nifti1.mock("structural.nii") diff --git a/pydra/tasks/afni/v25/utils/z_cut_up.py b/pydra/tasks/afni/v25/utils/z_cut_up.py index 22b8290..b3f300e 100644 --- a/pydra/tasks/afni/v25/utils/z_cut_up.py +++ b/pydra/tasks/afni/v25/utils/z_cut_up.py @@ -17,7 +17,7 @@ class ZCutUp(shell.Task["ZCutUp.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.z_cut_up import ZCutUp + >>> from pydra.tasks.afni.v25.utils.z_cut_up import ZCutUp >>> task = ZCutUp() >>> task.inputs.in_file = Nifti1.mock("functional.nii") diff --git a/pydra/tasks/afni/v25/utils/zcat.py b/pydra/tasks/afni/v25/utils/zcat.py index 8a0b830..7920365 100644 --- a/pydra/tasks/afni/v25/utils/zcat.py +++ b/pydra/tasks/afni/v25/utils/zcat.py @@ -17,7 +17,7 @@ class Zcat(shell.Task["Zcat.Outputs"]): >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.zcat import Zcat + >>> from pydra.tasks.afni.v25.utils.zcat import Zcat >>> task = Zcat() >>> task.inputs.in_files = [Nifti1.mock("functional2.nii"), Nifti1.mock("functional3.nii")] diff --git a/pydra/tasks/afni/v25/utils/zeropad.py b/pydra/tasks/afni/v25/utils/zeropad.py index 1a97c3b..6ad3e2a 100644 --- a/pydra/tasks/afni/v25/utils/zeropad.py +++ b/pydra/tasks/afni/v25/utils/zeropad.py @@ -34,7 +34,7 @@ class Zeropad(shell.Task["Zeropad.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from pathlib._local import Path - >>> from pydra.tasks.afni.v25_2_06.utils.zeropad import Zeropad + >>> from pydra.tasks.afni.v25.utils.zeropad import Zeropad >>> task = Zeropad() >>> task.inputs.in_files = Nifti1.mock("functional.nii") From 2cea41cd15f7799e1d41d2aef239ddf4759cf9f9 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 09:06:39 +0930 Subject: [PATCH 5/9] fixed up errors in unittests --- nipype-auto-conv/specs/interfaces/fwh_mx.yaml | 2 +- nipype-auto-conv/specs/interfaces/qwarp.yaml | 2 +- nipype-auto-conv/specs/interfaces/qwarp_plus_minus.yaml | 2 +- pydra/tasks/afni/v25/preprocess/qwarp.py | 4 ++-- pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py | 4 ++-- pydra/tasks/afni/v25/utils/fwh_mx.py | 2 +- pydra/tasks/afni/v25/utils/nwarp_adjust.py | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/nipype-auto-conv/specs/interfaces/fwh_mx.yaml b/nipype-auto-conv/specs/interfaces/fwh_mx.yaml index e964c2d..486a30d 100644 --- a/nipype-auto-conv/specs/interfaces/fwh_mx.yaml +++ b/nipype-auto-conv/specs/interfaces/fwh_mx.yaml @@ -184,7 +184,7 @@ tests: # type=bool|default=False: if in_file has more than one sub-brick, compute the final estimate as the geometric mean of the individual sub-brick FWHM estimates arith: # type=bool|default=False: if in_file has more than one sub-brick, compute the final estimate as the arithmetic mean of the individual sub-brick FWHM estimates - combine: + combine_: # type=bool|default=False: combine the final measurements along each axis compat: # type=bool|default=False: be compatible with the older 3dFWHM diff --git a/nipype-auto-conv/specs/interfaces/qwarp.yaml b/nipype-auto-conv/specs/interfaces/qwarp.yaml index 288dd9f..2b519f1 100644 --- a/nipype-auto-conv/specs/interfaces/qwarp.yaml +++ b/nipype-auto-conv/specs/interfaces/qwarp.yaml @@ -236,7 +236,7 @@ tests: # type=int|default=0: This option instructs the program to pad the warp by an extra'EE' voxels (and then 3dQwarp starts optimizing it).This option is seldom needed, but can be useful if youmight later catenate the nonlinear warp -- via 3dNwarpCat --with an affine transformation that contains a large shift.Under that circumstance, the nonlinear warp might be shiftedpartially outside its original grid, so expanding that gridcan avoid this problem.Note that this option perforce turns off '-nopadWARP'. ballopt: # type=bool|default=False: Normally, the incremental warp parameters are optimized insidea rectangular 'box' (24 dimensional for cubic patches, 81 forquintic patches), whose limits define the amount of distortionallowed at each step. Using '-ballopt' switches these limitsto be applied to a 'ball' (interior of a hypersphere), whichcan allow for larger incremental displacements. Use thisoption if you think things need to be able to move farther. - baxopt: + boxopt: # type=bool|default=False: Use the 'box' optimization limits instead of the 'ball'[this is the default at present].Note that if '-workhard' is used, then ball and box optimizationare alternated in the different iterations at each level, sothese two options have no effect in that case. verb: # type=bool|default=False: more detailed description of the process diff --git a/nipype-auto-conv/specs/interfaces/qwarp_plus_minus.yaml b/nipype-auto-conv/specs/interfaces/qwarp_plus_minus.yaml index d05d49c..1366d8f 100644 --- a/nipype-auto-conv/specs/interfaces/qwarp_plus_minus.yaml +++ b/nipype-auto-conv/specs/interfaces/qwarp_plus_minus.yaml @@ -170,7 +170,7 @@ tests: # type=int|default=0: This option instructs the program to pad the warp by an extra'EE' voxels (and then 3dQwarp starts optimizing it).This option is seldom needed, but can be useful if youmight later catenate the nonlinear warp -- via 3dNwarpCat --with an affine transformation that contains a large shift.Under that circumstance, the nonlinear warp might be shiftedpartially outside its original grid, so expanding that gridcan avoid this problem.Note that this option perforce turns off '-nopadWARP'. ballopt: # type=bool|default=False: Normally, the incremental warp parameters are optimized insidea rectangular 'box' (24 dimensional for cubic patches, 81 forquintic patches), whose limits define the amount of distortionallowed at each step. Using '-ballopt' switches these limitsto be applied to a 'ball' (interior of a hypersphere), whichcan allow for larger incremental displacements. Use thisoption if you think things need to be able to move farther. - baxopt: + boxopt: # type=bool|default=False: Use the 'box' optimization limits instead of the 'ball'[this is the default at present].Note that if '-workhard' is used, then ball and box optimizationare alternated in the different iterations at each level, sothese two options have no effect in that case. verb: # type=bool|default=False: more detailed description of the process diff --git a/pydra/tasks/afni/v25/preprocess/qwarp.py b/pydra/tasks/afni/v25/preprocess/qwarp.py index f3ec89d..0cb7937 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp.py @@ -163,7 +163,7 @@ def _gen_filename(name, inputs): ["duplo", "allsave", "iwarp", "plusminus"], ["duplo", "gridlist", "plusminus"], ["plusminus", "gridlist", "allsave", "iniwarp", "duplo", "maxlev", "inilev"], - ["workhard", "baxopt", "ballopt"], + ["workhard", "boxopt", "ballopt"], ["allsave", "expad", "nopadWARP"], ["wball", "wmask"], ["quiet", "verb"], @@ -419,7 +419,7 @@ class Qwarp(shell.Task["Qwarp.Outputs"]): help="Normally, the incremental warp parameters are optimized insidea rectangular 'box' (24 dimensional for cubic patches, 81 forquintic patches), whose limits define the amount of distortionallowed at each step. Using '-ballopt' switches these limitsto be applied to a 'ball' (interior of a hypersphere), whichcan allow for larger incremental displacements. Use thisoption if you think things need to be able to move farther.", argstr="-ballopt", ) - baxopt: bool = shell.arg( + boxopt: bool = shell.arg( help="Use the 'box' optimization limits instead of the 'ball'[this is the default at present].Note that if '-workhard' is used, then ball and box optimizationare alternated in the different iterations at each level, sothese two options have no effect in that case.", argstr="-boxopt", ) diff --git a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py index 0b5a7b0..6bcbde3 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py @@ -163,7 +163,7 @@ def _gen_filename(name, inputs): ["duplo", "allsave", "iwarp", "plusminus"], ["duplo", "gridlist", "plusminus"], ["plusminus", "gridlist", "allsave", "iniwarp", "duplo", "maxlev", "inilev"], - ["workhard", "baxopt", "ballopt"], + ["workhard", "boxopt", "ballopt"], ["allsave", "expad", "nopadWARP"], ["wball", "wmask"], ["quiet", "verb"], @@ -358,7 +358,7 @@ class QwarpPlusMinus(shell.Task["QwarpPlusMinus.Outputs"]): help="Normally, the incremental warp parameters are optimized insidea rectangular 'box' (24 dimensional for cubic patches, 81 forquintic patches), whose limits define the amount of distortionallowed at each step. Using '-ballopt' switches these limitsto be applied to a 'ball' (interior of a hypersphere), whichcan allow for larger incremental displacements. Use thisoption if you think things need to be able to move farther.", argstr="-ballopt", ) - baxopt: bool = shell.arg( + boxopt: bool = shell.arg( help="Use the 'box' optimization limits instead of the 'ball'[this is the default at present].Note that if '-workhard' is used, then ball and box optimizationare alternated in the different iterations at each level, sothese two options have no effect in that case.", argstr="-boxopt", ) diff --git a/pydra/tasks/afni/v25/utils/fwh_mx.py b/pydra/tasks/afni/v25/utils/fwh_mx.py index e1c6b07..346f0c9 100644 --- a/pydra/tasks/afni/v25/utils/fwh_mx.py +++ b/pydra/tasks/afni/v25/utils/fwh_mx.py @@ -168,7 +168,7 @@ class FWHMx(shell.Task["FWHMx.Outputs"]): help="if in_file has more than one sub-brick, compute the final estimate as the arithmetic mean of the individual sub-brick FWHM estimates", argstr="-arith", ) - combine: bool = shell.arg( + combine_: bool = shell.arg( help="combine the final measurements along each axis", argstr="-combine" ) compat: bool = shell.arg( diff --git a/pydra/tasks/afni/v25/utils/nwarp_adjust.py b/pydra/tasks/afni/v25/utils/nwarp_adjust.py index 8de9bc2..c1a9996 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_adjust.py +++ b/pydra/tasks/afni/v25/utils/nwarp_adjust.py @@ -56,7 +56,7 @@ class NwarpAdjust(shell.Task["NwarpAdjust.Outputs"]): outputtype: ty.Any = shell.arg(help="AFNI output filetype") class Outputs(shell.Outputs): - out_file: Path = shell.outarg( + out_file: File | None = shell.outarg( help="Output mean dataset, only needed if in_files are also given. The output dataset will be on the common grid shared by the source datasets.", argstr="-prefix {out_file}", requires=["in_files"], From 39f2696b176377069877344286f1c2fe59c20099 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 09:51:45 +0930 Subject: [PATCH 6/9] updated pathlib._local to pathlib --- pydra/tasks/afni/v25/model/deconvolve.py | 4 ++-- pydra/tasks/afni/v25/model/remlfit.py | 4 ++-- pydra/tasks/afni/v25/model/synthesize.py | 4 ++-- pydra/tasks/afni/v25/preprocess/allineate.py | 4 ++-- pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py | 4 ++-- pydra/tasks/afni/v25/preprocess/automask.py | 4 ++-- pydra/tasks/afni/v25/preprocess/bandpass.py | 4 ++-- pydra/tasks/afni/v25/preprocess/blur_in_mask.py | 4 ++-- pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py | 4 ++-- pydra/tasks/afni/v25/preprocess/degree_centrality.py | 4 ++-- pydra/tasks/afni/v25/preprocess/despike.py | 4 ++-- pydra/tasks/afni/v25/preprocess/detrend.py | 4 ++-- pydra/tasks/afni/v25/preprocess/ecm.py | 4 ++-- pydra/tasks/afni/v25/preprocess/fim.py | 4 ++-- pydra/tasks/afni/v25/preprocess/fourier.py | 4 ++-- pydra/tasks/afni/v25/preprocess/hist.py | 4 ++-- pydra/tasks/afni/v25/preprocess/lfcd.py | 4 ++-- pydra/tasks/afni/v25/preprocess/maskave.py | 4 ++-- pydra/tasks/afni/v25/preprocess/means.py | 4 ++-- pydra/tasks/afni/v25/preprocess/net_corr.py | 4 ++-- pydra/tasks/afni/v25/preprocess/outlier_count.py | 4 ++-- pydra/tasks/afni/v25/preprocess/quality_index.py | 4 ++-- pydra/tasks/afni/v25/preprocess/qwarp.py | 4 ++-- pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py | 4 ++-- pydra/tasks/afni/v25/preprocess/retroicor.py | 4 ++-- pydra/tasks/afni/v25/preprocess/roi_stats.py | 4 ++-- pydra/tasks/afni/v25/preprocess/skull_strip.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_corr_1d.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_corr_map.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_correlate.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_norm.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_project.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_shift.py | 4 ++-- pydra/tasks/afni/v25/preprocess/t_smooth.py | 4 ++-- pydra/tasks/afni/v25/preprocess/volreg.py | 4 ++-- pydra/tasks/afni/v25/preprocess/warp.py | 4 ++-- pydra/tasks/afni/v25/svm/svm_test.py | 4 ++-- pydra/tasks/afni/v25/svm/svm_train.py | 4 ++-- pydra/tasks/afni/v25/utils/a_boverlap.py | 4 ++-- pydra/tasks/afni/v25/utils/afn_ito_nifti.py | 4 ++-- pydra/tasks/afni/v25/utils/autobox.py | 4 ++-- pydra/tasks/afni/v25/utils/axialize.py | 4 ++-- pydra/tasks/afni/v25/utils/bucket.py | 4 ++-- pydra/tasks/afni/v25/utils/calc.py | 4 ++-- pydra/tasks/afni/v25/utils/cat.py | 4 ++-- pydra/tasks/afni/v25/utils/cat_matvec.py | 4 ++-- pydra/tasks/afni/v25/utils/center_mass.py | 4 ++-- pydra/tasks/afni/v25/utils/convert_dset.py | 4 ++-- pydra/tasks/afni/v25/utils/copy.py | 4 ++-- pydra/tasks/afni/v25/utils/dot.py | 4 ++-- pydra/tasks/afni/v25/utils/edge_3.py | 4 ++-- pydra/tasks/afni/v25/utils/eval.py | 4 ++-- pydra/tasks/afni/v25/utils/fwh_mx.py | 4 ++-- pydra/tasks/afni/v25/utils/local_bistat.py | 4 ++-- pydra/tasks/afni/v25/utils/localstat.py | 4 ++-- pydra/tasks/afni/v25/utils/mask_tool.py | 4 ++-- pydra/tasks/afni/v25/utils/merge.py | 4 ++-- pydra/tasks/afni/v25/utils/notes.py | 4 ++-- pydra/tasks/afni/v25/utils/nwarp_adjust.py | 4 ++-- pydra/tasks/afni/v25/utils/nwarp_apply.py | 4 ++-- pydra/tasks/afni/v25/utils/nwarp_cat.py | 4 ++-- pydra/tasks/afni/v25/utils/one_d_tool_py.py | 4 ++-- pydra/tasks/afni/v25/utils/re_ho.py | 4 ++-- pydra/tasks/afni/v25/utils/resample.py | 4 ++-- pydra/tasks/afni/v25/utils/t_cat.py | 4 ++-- pydra/tasks/afni/v25/utils/t_cat_sub_brick.py | 4 ++-- pydra/tasks/afni/v25/utils/t_stat.py | 4 ++-- pydra/tasks/afni/v25/utils/to_3d.py | 4 ++-- pydra/tasks/afni/v25/utils/undump.py | 4 ++-- pydra/tasks/afni/v25/utils/unifize.py | 4 ++-- pydra/tasks/afni/v25/utils/z_cut_up.py | 4 ++-- pydra/tasks/afni/v25/utils/zcat.py | 4 ++-- pydra/tasks/afni/v25/utils/zeropad.py | 4 ++-- 73 files changed, 146 insertions(+), 146 deletions(-) diff --git a/pydra/tasks/afni/v25/model/deconvolve.py b/pydra/tasks/afni/v25/model/deconvolve.py index cc8325d..d331ab0 100644 --- a/pydra/tasks/afni/v25/model/deconvolve.py +++ b/pydra/tasks/afni/v25/model/deconvolve.py @@ -6,7 +6,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -133,7 +133,7 @@ class Deconvolve(shell.Task["Deconvolve.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.model.deconvolve import Deconvolve >>> task = Deconvolve() diff --git a/pydra/tasks/afni/v25/model/remlfit.py b/pydra/tasks/afni/v25/model/remlfit.py index 567af4c..ff982f4 100644 --- a/pydra/tasks/afni/v25/model/remlfit.py +++ b/pydra/tasks/afni/v25/model/remlfit.py @@ -5,7 +5,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -139,7 +139,7 @@ class Remlfit(shell.Task["Remlfit.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.model.remlfit import Remlfit >>> task = Remlfit() diff --git a/pydra/tasks/afni/v25/model/synthesize.py b/pydra/tasks/afni/v25/model/synthesize.py index 5f0c81a..b1d0777 100644 --- a/pydra/tasks/afni/v25/model/synthesize.py +++ b/pydra/tasks/afni/v25/model/synthesize.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Synthesize(shell.Task["Synthesize.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.model.synthesize import Synthesize >>> task = Synthesize() diff --git a/pydra/tasks/afni/v25/preprocess/allineate.py b/pydra/tasks/afni/v25/preprocess/allineate.py index 3674184..a8036d6 100644 --- a/pydra/tasks/afni/v25/preprocess/allineate.py +++ b/pydra/tasks/afni/v25/preprocess/allineate.py @@ -11,7 +11,7 @@ import os import os.path as op from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -119,7 +119,7 @@ class Allineate(shell.Task["Allineate.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from fileformats.text import TextFile - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.allineate import Allineate >>> task = Allineate() diff --git a/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py b/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py index 01a30b5..c3aa06e 100644 --- a/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py +++ b/pydra/tasks/afni/v25/preprocess/auto_tcorrelate.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class AutoTcorrelate(shell.Task["AutoTcorrelate.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.auto_tcorrelate import AutoTcorrelate >>> task = AutoTcorrelate() diff --git a/pydra/tasks/afni/v25/preprocess/automask.py b/pydra/tasks/afni/v25/preprocess/automask.py index e003b33..db8816d 100644 --- a/pydra/tasks/afni/v25/preprocess/automask.py +++ b/pydra/tasks/afni/v25/preprocess/automask.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Automask(shell.Task["Automask.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.automask import Automask >>> task = Automask() diff --git a/pydra/tasks/afni/v25/preprocess/bandpass.py b/pydra/tasks/afni/v25/preprocess/bandpass.py index 5149160..2a4c6bf 100644 --- a/pydra/tasks/afni/v25/preprocess/bandpass.py +++ b/pydra/tasks/afni/v25/preprocess/bandpass.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Bandpass(shell.Task["Bandpass.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.bandpass import Bandpass >>> task = Bandpass() diff --git a/pydra/tasks/afni/v25/preprocess/blur_in_mask.py b/pydra/tasks/afni/v25/preprocess/blur_in_mask.py index 33b7c6c..ff2eb0d 100644 --- a/pydra/tasks/afni/v25/preprocess/blur_in_mask.py +++ b/pydra/tasks/afni/v25/preprocess/blur_in_mask.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class BlurInMask(shell.Task["BlurInMask.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.blur_in_mask import BlurInMask >>> task = BlurInMask() diff --git a/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py b/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py index cb355e9..2f9fb34 100644 --- a/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py +++ b/pydra/tasks/afni/v25/preprocess/blur_to_fwhm.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class BlurToFWHM(shell.Task["BlurToFWHM.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.blur_to_fwhm import BlurToFWHM >>> task = BlurToFWHM() diff --git a/pydra/tasks/afni/v25/preprocess/degree_centrality.py b/pydra/tasks/afni/v25/preprocess/degree_centrality.py index b5d53a0..6ac1e8f 100644 --- a/pydra/tasks/afni/v25/preprocess/degree_centrality.py +++ b/pydra/tasks/afni/v25/preprocess/degree_centrality.py @@ -5,7 +5,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -47,7 +47,7 @@ class DegreeCentrality(shell.Task["DegreeCentrality.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.degree_centrality import DegreeCentrality >>> task = DegreeCentrality() diff --git a/pydra/tasks/afni/v25/preprocess/despike.py b/pydra/tasks/afni/v25/preprocess/despike.py index 992dad3..d5950b8 100644 --- a/pydra/tasks/afni/v25/preprocess/despike.py +++ b/pydra/tasks/afni/v25/preprocess/despike.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Despike(shell.Task["Despike.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.despike import Despike >>> task = Despike() diff --git a/pydra/tasks/afni/v25/preprocess/detrend.py b/pydra/tasks/afni/v25/preprocess/detrend.py index 091331a..ccb336f 100644 --- a/pydra/tasks/afni/v25/preprocess/detrend.py +++ b/pydra/tasks/afni/v25/preprocess/detrend.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Detrend(shell.Task["Detrend.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.detrend import Detrend >>> task = Detrend() diff --git a/pydra/tasks/afni/v25/preprocess/ecm.py b/pydra/tasks/afni/v25/preprocess/ecm.py index 400b4eb..d776c38 100644 --- a/pydra/tasks/afni/v25/preprocess/ecm.py +++ b/pydra/tasks/afni/v25/preprocess/ecm.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class ECM(shell.Task["ECM.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.ecm import ECM >>> task = ECM() diff --git a/pydra/tasks/afni/v25/preprocess/fim.py b/pydra/tasks/afni/v25/preprocess/fim.py index 6394874..c53d6bb 100644 --- a/pydra/tasks/afni/v25/preprocess/fim.py +++ b/pydra/tasks/afni/v25/preprocess/fim.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Fim(shell.Task["Fim.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.fim import Fim >>> task = Fim() diff --git a/pydra/tasks/afni/v25/preprocess/fourier.py b/pydra/tasks/afni/v25/preprocess/fourier.py index 3dad434..b792229 100644 --- a/pydra/tasks/afni/v25/preprocess/fourier.py +++ b/pydra/tasks/afni/v25/preprocess/fourier.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Fourier(shell.Task["Fourier.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.fourier import Fourier >>> task = Fourier() diff --git a/pydra/tasks/afni/v25/preprocess/hist.py b/pydra/tasks/afni/v25/preprocess/hist.py index 66da08c..a50bd0b 100644 --- a/pydra/tasks/afni/v25/preprocess/hist.py +++ b/pydra/tasks/afni/v25/preprocess/hist.py @@ -3,7 +3,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell @@ -32,7 +32,7 @@ class Hist(shell.Task["Hist.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.hist import Hist >>> task = Hist() diff --git a/pydra/tasks/afni/v25/preprocess/lfcd.py b/pydra/tasks/afni/v25/preprocess/lfcd.py index c466ee1..3c3c440 100644 --- a/pydra/tasks/afni/v25/preprocess/lfcd.py +++ b/pydra/tasks/afni/v25/preprocess/lfcd.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class LFCD(shell.Task["LFCD.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.lfcd import LFCD >>> task = LFCD() diff --git a/pydra/tasks/afni/v25/preprocess/maskave.py b/pydra/tasks/afni/v25/preprocess/maskave.py index de4af35..b079ebe 100644 --- a/pydra/tasks/afni/v25/preprocess/maskave.py +++ b/pydra/tasks/afni/v25/preprocess/maskave.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Maskave(shell.Task["Maskave.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.maskave import Maskave >>> task = Maskave() diff --git a/pydra/tasks/afni/v25/preprocess/means.py b/pydra/tasks/afni/v25/preprocess/means.py index c12f34c..e9cf405 100644 --- a/pydra/tasks/afni/v25/preprocess/means.py +++ b/pydra/tasks/afni/v25/preprocess/means.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Means(shell.Task["Means.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.means import Means >>> task = Means() diff --git a/pydra/tasks/afni/v25/preprocess/net_corr.py b/pydra/tasks/afni/v25/preprocess/net_corr.py index 709dc70..4795fd1 100644 --- a/pydra/tasks/afni/v25/preprocess/net_corr.py +++ b/pydra/tasks/afni/v25/preprocess/net_corr.py @@ -5,7 +5,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -65,7 +65,7 @@ class NetCorr(shell.Task["NetCorr.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.net_corr import NetCorr >>> task = NetCorr() diff --git a/pydra/tasks/afni/v25/preprocess/outlier_count.py b/pydra/tasks/afni/v25/preprocess/outlier_count.py index c950860..2851f3f 100644 --- a/pydra/tasks/afni/v25/preprocess/outlier_count.py +++ b/pydra/tasks/afni/v25/preprocess/outlier_count.py @@ -5,7 +5,7 @@ import os import os.path as op from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -59,7 +59,7 @@ class OutlierCount(shell.Task["OutlierCount.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.outlier_count import OutlierCount >>> task = OutlierCount() diff --git a/pydra/tasks/afni/v25/preprocess/quality_index.py b/pydra/tasks/afni/v25/preprocess/quality_index.py index 2130fab..19fe33d 100644 --- a/pydra/tasks/afni/v25/preprocess/quality_index.py +++ b/pydra/tasks/afni/v25/preprocess/quality_index.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell @@ -19,7 +19,7 @@ class QualityIndex(shell.Task["QualityIndex.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.quality_index import QualityIndex >>> task = QualityIndex() diff --git a/pydra/tasks/afni/v25/preprocess/qwarp.py b/pydra/tasks/afni/v25/preprocess/qwarp.py index 0cb7937..7884952 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp.py @@ -6,7 +6,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -185,7 +185,7 @@ class Qwarp(shell.Task["Qwarp.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1, NiftiGz - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.qwarp import Qwarp >>> task = Qwarp() diff --git a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py index 6bcbde3..8c86cad 100644 --- a/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py +++ b/pydra/tasks/afni/v25/preprocess/qwarp_plus_minus.py @@ -6,7 +6,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -185,7 +185,7 @@ class QwarpPlusMinus(shell.Task["QwarpPlusMinus.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import NiftiGz - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.qwarp_plus_minus import QwarpPlusMinus >>> task = QwarpPlusMinus() diff --git a/pydra/tasks/afni/v25/preprocess/retroicor.py b/pydra/tasks/afni/v25/preprocess/retroicor.py index 7422039..46160aa 100644 --- a/pydra/tasks/afni/v25/preprocess/retroicor.py +++ b/pydra/tasks/afni/v25/preprocess/retroicor.py @@ -4,7 +4,7 @@ from fileformats.medimage_afni import OneD import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -36,7 +36,7 @@ class Retroicor(shell.Task["Retroicor.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.retroicor import Retroicor >>> task = Retroicor() diff --git a/pydra/tasks/afni/v25/preprocess/roi_stats.py b/pydra/tasks/afni/v25/preprocess/roi_stats.py index fcde7ab..b91fc19 100644 --- a/pydra/tasks/afni/v25/preprocess/roi_stats.py +++ b/pydra/tasks/afni/v25/preprocess/roi_stats.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell from pydra.utils.typing import MultiInputObj @@ -46,7 +46,7 @@ class ROIStats(shell.Task["ROIStats.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.roi_stats import ROIStats >>> from pydra.utils.typing import MultiInputObj diff --git a/pydra/tasks/afni/v25/preprocess/skull_strip.py b/pydra/tasks/afni/v25/preprocess/skull_strip.py index 71a30ec..2a95754 100644 --- a/pydra/tasks/afni/v25/preprocess/skull_strip.py +++ b/pydra/tasks/afni/v25/preprocess/skull_strip.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class SkullStrip(shell.Task["SkullStrip.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.skull_strip import SkullStrip >>> task = SkullStrip() diff --git a/pydra/tasks/afni/v25/preprocess/t_corr_1d.py b/pydra/tasks/afni/v25/preprocess/t_corr_1d.py index fb93c3d..2592314 100644 --- a/pydra/tasks/afni/v25/preprocess/t_corr_1d.py +++ b/pydra/tasks/afni/v25/preprocess/t_corr_1d.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class TCorr1D(shell.Task["TCorr1D.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_corr_1d import TCorr1D >>> task = TCorr1D() diff --git a/pydra/tasks/afni/v25/preprocess/t_corr_map.py b/pydra/tasks/afni/v25/preprocess/t_corr_map.py index 0e82d5e..5176c5b 100644 --- a/pydra/tasks/afni/v25/preprocess/t_corr_map.py +++ b/pydra/tasks/afni/v25/preprocess/t_corr_map.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -159,7 +159,7 @@ class TCorrMap(shell.Task["TCorrMap.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_corr_map import TCorrMap >>> task = TCorrMap() diff --git a/pydra/tasks/afni/v25/preprocess/t_correlate.py b/pydra/tasks/afni/v25/preprocess/t_correlate.py index 51bf118..43a679b 100644 --- a/pydra/tasks/afni/v25/preprocess/t_correlate.py +++ b/pydra/tasks/afni/v25/preprocess/t_correlate.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class TCorrelate(shell.Task["TCorrelate.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_correlate import TCorrelate >>> task = TCorrelate() diff --git a/pydra/tasks/afni/v25/preprocess/t_norm.py b/pydra/tasks/afni/v25/preprocess/t_norm.py index 2ba6363..7d1d119 100644 --- a/pydra/tasks/afni/v25/preprocess/t_norm.py +++ b/pydra/tasks/afni/v25/preprocess/t_norm.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class TNorm(shell.Task["TNorm.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_norm import TNorm >>> task = TNorm() diff --git a/pydra/tasks/afni/v25/preprocess/t_project.py b/pydra/tasks/afni/v25/preprocess/t_project.py index 4e9baf8..7330de5 100644 --- a/pydra/tasks/afni/v25/preprocess/t_project.py +++ b/pydra/tasks/afni/v25/preprocess/t_project.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class TProject(shell.Task["TProject.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_project import TProject >>> task = TProject() diff --git a/pydra/tasks/afni/v25/preprocess/t_shift.py b/pydra/tasks/afni/v25/preprocess/t_shift.py index 07077f2..f6d8b9a 100644 --- a/pydra/tasks/afni/v25/preprocess/t_shift.py +++ b/pydra/tasks/afni/v25/preprocess/t_shift.py @@ -5,7 +5,7 @@ from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -77,7 +77,7 @@ class TShift(shell.Task["TShift.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_shift import TShift >>> task = TShift() diff --git a/pydra/tasks/afni/v25/preprocess/t_smooth.py b/pydra/tasks/afni/v25/preprocess/t_smooth.py index 6dd0d2b..dfdbae6 100644 --- a/pydra/tasks/afni/v25/preprocess/t_smooth.py +++ b/pydra/tasks/afni/v25/preprocess/t_smooth.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class TSmooth(shell.Task["TSmooth.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.t_smooth import TSmooth >>> task = TSmooth() diff --git a/pydra/tasks/afni/v25/preprocess/volreg.py b/pydra/tasks/afni/v25/preprocess/volreg.py index f4664dd..b61a513 100644 --- a/pydra/tasks/afni/v25/preprocess/volreg.py +++ b/pydra/tasks/afni/v25/preprocess/volreg.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -35,7 +35,7 @@ class Volreg(shell.Task["Volreg.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.volreg import Volreg >>> task = Volreg() diff --git a/pydra/tasks/afni/v25/preprocess/warp.py b/pydra/tasks/afni/v25/preprocess/warp.py index 016d6b7..b55c46e 100644 --- a/pydra/tasks/afni/v25/preprocess/warp.py +++ b/pydra/tasks/afni/v25/preprocess/warp.py @@ -7,7 +7,7 @@ split_filename, ) from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -51,7 +51,7 @@ class Warp(shell.Task["Warp.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.preprocess.warp import Warp >>> task = Warp() diff --git a/pydra/tasks/afni/v25/svm/svm_test.py b/pydra/tasks/afni/v25/svm/svm_test.py index 7b29e2c..1920701 100644 --- a/pydra/tasks/afni/v25/svm/svm_test.py +++ b/pydra/tasks/afni/v25/svm/svm_test.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class SVMTest(shell.Task["SVMTest.Outputs"]): ------- >>> from fileformats.generic import File - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.svm.svm_test import SVMTest """ diff --git a/pydra/tasks/afni/v25/svm/svm_train.py b/pydra/tasks/afni/v25/svm/svm_train.py index d89f8bf..3b12b34 100644 --- a/pydra/tasks/afni/v25/svm/svm_train.py +++ b/pydra/tasks/afni/v25/svm/svm_train.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class SVMTrain(shell.Task["SVMTrain.Outputs"]): ------- >>> from fileformats.generic import File - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.svm.svm_train import SVMTrain """ diff --git a/pydra/tasks/afni/v25/utils/a_boverlap.py b/pydra/tasks/afni/v25/utils/a_boverlap.py index 36903f9..c37edab 100644 --- a/pydra/tasks/afni/v25/utils/a_boverlap.py +++ b/pydra/tasks/afni/v25/utils/a_boverlap.py @@ -5,7 +5,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -45,7 +45,7 @@ class ABoverlap(shell.Task["ABoverlap.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 >>> from fileformats.text import TextFile - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.a_boverlap import ABoverlap >>> task = ABoverlap() diff --git a/pydra/tasks/afni/v25/utils/afn_ito_nifti.py b/pydra/tasks/afni/v25/utils/afn_ito_nifti.py index 265170a..de29fde 100644 --- a/pydra/tasks/afni/v25/utils/afn_ito_nifti.py +++ b/pydra/tasks/afni/v25/utils/afn_ito_nifti.py @@ -2,7 +2,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -21,7 +21,7 @@ class AFNItoNIFTI(shell.Task["AFNItoNIFTI.Outputs"]): ------- >>> from fileformats.medimage_afni import ThreeD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.afn_ito_nifti import AFNItoNIFTI >>> task = AFNItoNIFTI() diff --git a/pydra/tasks/afni/v25/utils/autobox.py b/pydra/tasks/afni/v25/utils/autobox.py index b9a8dd6..b1d14cb 100644 --- a/pydra/tasks/afni/v25/utils/autobox.py +++ b/pydra/tasks/afni/v25/utils/autobox.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import re import typing as ty @@ -78,7 +78,7 @@ class Autobox(shell.Task["Autobox.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.autobox import Autobox >>> task = Autobox() diff --git a/pydra/tasks/afni/v25/utils/axialize.py b/pydra/tasks/afni/v25/utils/axialize.py index 77cfe4f..681887b 100644 --- a/pydra/tasks/afni/v25/utils/axialize.py +++ b/pydra/tasks/afni/v25/utils/axialize.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Axialize(shell.Task["Axialize.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.axialize import Axialize >>> task = Axialize() diff --git a/pydra/tasks/afni/v25/utils/bucket.py b/pydra/tasks/afni/v25/utils/bucket.py index c6dc3c8..57fc990 100644 --- a/pydra/tasks/afni/v25/utils/bucket.py +++ b/pydra/tasks/afni/v25/utils/bucket.py @@ -1,6 +1,6 @@ import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -28,7 +28,7 @@ class Bucket(shell.Task["Bucket.Outputs"]): Examples ------- - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.bucket import Bucket >>> task = Bucket() diff --git a/pydra/tasks/afni/v25/utils/calc.py b/pydra/tasks/afni/v25/utils/calc.py index 4434eed..e047034 100644 --- a/pydra/tasks/afni/v25/utils/calc.py +++ b/pydra/tasks/afni/v25/utils/calc.py @@ -3,7 +3,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -38,7 +38,7 @@ class Calc(shell.Task["Calc.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.calc import Calc >>> task = Calc() diff --git a/pydra/tasks/afni/v25/utils/cat.py b/pydra/tasks/afni/v25/utils/cat.py index 15ae126..6a9b121 100644 --- a/pydra/tasks/afni/v25/utils/cat.py +++ b/pydra/tasks/afni/v25/utils/cat.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -45,7 +45,7 @@ class Cat(shell.Task["Cat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.cat import Cat >>> task = Cat() diff --git a/pydra/tasks/afni/v25/utils/cat_matvec.py b/pydra/tasks/afni/v25/utils/cat_matvec.py index 7fe5b0c..37da035 100644 --- a/pydra/tasks/afni/v25/utils/cat_matvec.py +++ b/pydra/tasks/afni/v25/utils/cat_matvec.py @@ -1,6 +1,6 @@ import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -31,7 +31,7 @@ class CatMatvec(shell.Task["CatMatvec.Outputs"]): Examples ------- - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.cat_matvec import CatMatvec >>> task = CatMatvec() diff --git a/pydra/tasks/afni/v25/utils/center_mass.py b/pydra/tasks/afni/v25/utils/center_mass.py index 5fed9c2..3bc1c1f 100644 --- a/pydra/tasks/afni/v25/utils/center_mass.py +++ b/pydra/tasks/afni/v25/utils/center_mass.py @@ -5,7 +5,7 @@ import numpy as np import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -46,7 +46,7 @@ class CenterMass(shell.Task["CenterMass.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.center_mass import CenterMass >>> task = CenterMass() diff --git a/pydra/tasks/afni/v25/utils/convert_dset.py b/pydra/tasks/afni/v25/utils/convert_dset.py index 7fc2574..8955df0 100644 --- a/pydra/tasks/afni/v25/utils/convert_dset.py +++ b/pydra/tasks/afni/v25/utils/convert_dset.py @@ -4,7 +4,7 @@ import logging import os.path as op from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -35,7 +35,7 @@ class ConvertDset(shell.Task["ConvertDset.Outputs"]): >>> from fileformats.medimage import Gifti >>> from fileformats.medimage_afni import Dset - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.convert_dset import ConvertDset >>> task = ConvertDset() diff --git a/pydra/tasks/afni/v25/utils/copy.py b/pydra/tasks/afni/v25/utils/copy.py index a6e648c..4f5eab0 100644 --- a/pydra/tasks/afni/v25/utils/copy.py +++ b/pydra/tasks/afni/v25/utils/copy.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -17,7 +17,7 @@ class Copy(shell.Task["Copy.Outputs"]): >>> from copy import deepcopy >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.copy import Copy >>> task = Copy() diff --git a/pydra/tasks/afni/v25/utils/dot.py b/pydra/tasks/afni/v25/utils/dot.py index 879aa4e..981664b 100644 --- a/pydra/tasks/afni/v25/utils/dot.py +++ b/pydra/tasks/afni/v25/utils/dot.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -43,7 +43,7 @@ class Dot(shell.Task["Dot.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.text import TextFile - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.dot import Dot >>> task = Dot() diff --git a/pydra/tasks/afni/v25/utils/edge_3.py b/pydra/tasks/afni/v25/utils/edge_3.py index 4a987c1..751c990 100644 --- a/pydra/tasks/afni/v25/utils/edge_3.py +++ b/pydra/tasks/afni/v25/utils/edge_3.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -43,7 +43,7 @@ class Edge3(shell.Task["Edge3.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.edge_3 import Edge3 >>> task = Edge3() diff --git a/pydra/tasks/afni/v25/utils/eval.py b/pydra/tasks/afni/v25/utils/eval.py index b9ffa5c..ea6aec1 100644 --- a/pydra/tasks/afni/v25/utils/eval.py +++ b/pydra/tasks/afni/v25/utils/eval.py @@ -3,7 +3,7 @@ from fileformats.medimage_afni import OneD import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -38,7 +38,7 @@ class Eval(shell.Task["Eval.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.eval import Eval >>> task = Eval() diff --git a/pydra/tasks/afni/v25/utils/fwh_mx.py b/pydra/tasks/afni/v25/utils/fwh_mx.py index 346f0c9..7502674 100644 --- a/pydra/tasks/afni/v25/utils/fwh_mx.py +++ b/pydra/tasks/afni/v25/utils/fwh_mx.py @@ -6,7 +6,7 @@ import os import os.path as op from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -125,7 +125,7 @@ class FWHMx(shell.Task["FWHMx.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.fwh_mx import FWHMx >>> task = FWHMx() diff --git a/pydra/tasks/afni/v25/utils/local_bistat.py b/pydra/tasks/afni/v25/utils/local_bistat.py index a0ff046..5672ecd 100644 --- a/pydra/tasks/afni/v25/utils/local_bistat.py +++ b/pydra/tasks/afni/v25/utils/local_bistat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell from pydra.utils.typing import MultiInputObj import typing as ty @@ -38,7 +38,7 @@ class LocalBistat(shell.Task["LocalBistat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.local_bistat import LocalBistat >>> from pydra.utils.typing import MultiInputObj diff --git a/pydra/tasks/afni/v25/utils/localstat.py b/pydra/tasks/afni/v25/utils/localstat.py index d47ad99..662e079 100644 --- a/pydra/tasks/afni/v25/utils/localstat.py +++ b/pydra/tasks/afni/v25/utils/localstat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell from pydra.utils.typing import MultiInputObj import typing as ty @@ -62,7 +62,7 @@ class Localstat(shell.Task["Localstat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.localstat import Localstat >>> from pydra.utils.typing import MultiInputObj diff --git a/pydra/tasks/afni/v25/utils/mask_tool.py b/pydra/tasks/afni/v25/utils/mask_tool.py index 59e35cb..375295c 100644 --- a/pydra/tasks/afni/v25/utils/mask_tool.py +++ b/pydra/tasks/afni/v25/utils/mask_tool.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class MaskTool(shell.Task["MaskTool.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.mask_tool import MaskTool >>> task = MaskTool() diff --git a/pydra/tasks/afni/v25/utils/merge.py b/pydra/tasks/afni/v25/utils/merge.py index bd8f8ec..6e17653 100644 --- a/pydra/tasks/afni/v25/utils/merge.py +++ b/pydra/tasks/afni/v25/utils/merge.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Merge(shell.Task["Merge.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.merge import Merge >>> task = Merge() diff --git a/pydra/tasks/afni/v25/utils/notes.py b/pydra/tasks/afni/v25/utils/notes.py index c63d6b3..ed4963d 100644 --- a/pydra/tasks/afni/v25/utils/notes.py +++ b/pydra/tasks/afni/v25/utils/notes.py @@ -4,7 +4,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -35,7 +35,7 @@ class Notes(shell.Task["Notes.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import Head - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.notes import Notes >>> task = Notes() diff --git a/pydra/tasks/afni/v25/utils/nwarp_adjust.py b/pydra/tasks/afni/v25/utils/nwarp_adjust.py index c1a9996..5af7f61 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_adjust.py +++ b/pydra/tasks/afni/v25/utils/nwarp_adjust.py @@ -3,7 +3,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -33,7 +33,7 @@ class NwarpAdjust(shell.Task["NwarpAdjust.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import NiftiGz - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.nwarp_adjust import NwarpAdjust >>> task = NwarpAdjust() diff --git a/pydra/tasks/afni/v25/utils/nwarp_apply.py b/pydra/tasks/afni/v25/utils/nwarp_apply.py index 445d84d..0211a94 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_apply.py +++ b/pydra/tasks/afni/v25/utils/nwarp_apply.py @@ -1,7 +1,7 @@ from fileformats.generic import File import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class NwarpApply(shell.Task["NwarpApply.Outputs"]): ------- >>> from fileformats.generic import File - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.nwarp_apply import NwarpApply >>> task = NwarpApply() diff --git a/pydra/tasks/afni/v25/utils/nwarp_cat.py b/pydra/tasks/afni/v25/utils/nwarp_cat.py index 3b855a4..b44a13b 100644 --- a/pydra/tasks/afni/v25/utils/nwarp_cat.py +++ b/pydra/tasks/afni/v25/utils/nwarp_cat.py @@ -1,7 +1,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -45,7 +45,7 @@ class NwarpCat(shell.Task["NwarpCat.Outputs"]): Examples ------- - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.nwarp_cat import NwarpCat >>> task = NwarpCat() diff --git a/pydra/tasks/afni/v25/utils/one_d_tool_py.py b/pydra/tasks/afni/v25/utils/one_d_tool_py.py index bcbfadb..87479c7 100644 --- a/pydra/tasks/afni/v25/utils/one_d_tool_py.py +++ b/pydra/tasks/afni/v25/utils/one_d_tool_py.py @@ -4,7 +4,7 @@ import logging import os from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -43,7 +43,7 @@ class OneDToolPy(shell.Task["OneDToolPy.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage_afni import OneD - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.one_d_tool_py import OneDToolPy >>> task = OneDToolPy() diff --git a/pydra/tasks/afni/v25/utils/re_ho.py b/pydra/tasks/afni/v25/utils/re_ho.py index 3d2a892..ae2d0a0 100644 --- a/pydra/tasks/afni/v25/utils/re_ho.py +++ b/pydra/tasks/afni/v25/utils/re_ho.py @@ -3,7 +3,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -50,7 +50,7 @@ class ReHo(shell.Task["ReHo.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.re_ho import ReHo >>> task = ReHo() diff --git a/pydra/tasks/afni/v25/utils/resample.py b/pydra/tasks/afni/v25/utils/resample.py index 4efc793..bec8b84 100644 --- a/pydra/tasks/afni/v25/utils/resample.py +++ b/pydra/tasks/afni/v25/utils/resample.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class Resample(shell.Task["Resample.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.resample import Resample >>> task = Resample() diff --git a/pydra/tasks/afni/v25/utils/t_cat.py b/pydra/tasks/afni/v25/utils/t_cat.py index 2f7f8f3..68b376b 100644 --- a/pydra/tasks/afni/v25/utils/t_cat.py +++ b/pydra/tasks/afni/v25/utils/t_cat.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class TCat(shell.Task["TCat.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.t_cat import TCat >>> task = TCat() diff --git a/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py b/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py index 6369b9b..3887ab0 100644 --- a/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py +++ b/pydra/tasks/afni/v25/utils/t_cat_sub_brick.py @@ -1,7 +1,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import fname_presuffix from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -26,7 +26,7 @@ class TCatSubBrick(shell.Task["TCatSubBrick.Outputs"]): Examples ------- - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.t_cat_sub_brick import TCatSubBrick >>> task = TCatSubBrick() diff --git a/pydra/tasks/afni/v25/utils/t_stat.py b/pydra/tasks/afni/v25/utils/t_stat.py index 730203e..eb1572f 100644 --- a/pydra/tasks/afni/v25/utils/t_stat.py +++ b/pydra/tasks/afni/v25/utils/t_stat.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -18,7 +18,7 @@ class TStat(shell.Task["TStat.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.t_stat import TStat >>> task = TStat() diff --git a/pydra/tasks/afni/v25/utils/to_3d.py b/pydra/tasks/afni/v25/utils/to_3d.py index ae3b143..a89f76c 100644 --- a/pydra/tasks/afni/v25/utils/to_3d.py +++ b/pydra/tasks/afni/v25/utils/to_3d.py @@ -1,7 +1,7 @@ from fileformats.generic import Directory import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class To3D(shell.Task["To3D.Outputs"]): ------- >>> from fileformats.generic import Directory - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.to_3d import To3D >>> task = To3D() diff --git a/pydra/tasks/afni/v25/utils/undump.py b/pydra/tasks/afni/v25/utils/undump.py index fae383c..4c193d8 100644 --- a/pydra/tasks/afni/v25/utils/undump.py +++ b/pydra/tasks/afni/v25/utils/undump.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -43,7 +43,7 @@ class Undump(shell.Task["Undump.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.undump import Undump >>> task = Undump() diff --git a/pydra/tasks/afni/v25/utils/unifize.py b/pydra/tasks/afni/v25/utils/unifize.py index aa6bba7..fcc2f49 100644 --- a/pydra/tasks/afni/v25/utils/unifize.py +++ b/pydra/tasks/afni/v25/utils/unifize.py @@ -4,7 +4,7 @@ import logging from pydra.tasks.afni.v25.nipype_ports.utils.filemanip import split_filename from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -43,7 +43,7 @@ class Unifize(shell.Task["Unifize.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.unifize import Unifize >>> task = Unifize() diff --git a/pydra/tasks/afni/v25/utils/z_cut_up.py b/pydra/tasks/afni/v25/utils/z_cut_up.py index b3f300e..4aac099 100644 --- a/pydra/tasks/afni/v25/utils/z_cut_up.py +++ b/pydra/tasks/afni/v25/utils/z_cut_up.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class ZCutUp(shell.Task["ZCutUp.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.z_cut_up import ZCutUp >>> task = ZCutUp() diff --git a/pydra/tasks/afni/v25/utils/zcat.py b/pydra/tasks/afni/v25/utils/zcat.py index 7920365..d00b906 100644 --- a/pydra/tasks/afni/v25/utils/zcat.py +++ b/pydra/tasks/afni/v25/utils/zcat.py @@ -1,7 +1,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -16,7 +16,7 @@ class Zcat(shell.Task["Zcat.Outputs"]): ------- >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.zcat import Zcat >>> task = Zcat() diff --git a/pydra/tasks/afni/v25/utils/zeropad.py b/pydra/tasks/afni/v25/utils/zeropad.py index 6ad3e2a..92e5ba2 100644 --- a/pydra/tasks/afni/v25/utils/zeropad.py +++ b/pydra/tasks/afni/v25/utils/zeropad.py @@ -2,7 +2,7 @@ from fileformats.medimage import Nifti1 import logging from pathlib import Path -from pathlib._local import Path +from pathlib import Path from pydra.compose import shell import typing as ty @@ -33,7 +33,7 @@ class Zeropad(shell.Task["Zeropad.Outputs"]): >>> from fileformats.generic import File >>> from fileformats.medimage import Nifti1 - >>> from pathlib._local import Path + >>> from pathlib import Path >>> from pydra.tasks.afni.v25.utils.zeropad import Zeropad >>> task = Zeropad() From 03e6c0be1a72a1a78975a9e242605ecdc59cf7a1 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 6 Aug 2025 10:55:55 +0930 Subject: [PATCH 7/9] disable cov ci fail --- .github/workflows/ci-cd.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index f0de095..a053fdc 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.github/workflows/ci-cd.yaml @@ -120,7 +120,7 @@ jobs: - name: Upload coverage to Codecov uses: codecov/codecov-action@v5 with: - fail_ci_if_error: true + fail_ci_if_error: false token: ${{ secrets.CODECOV_TOKEN }} fileformats-test: From 5d381dd6190a9d565296636a63094ec51ae0a2ed Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Tue, 19 Aug 2025 13:00:45 +1000 Subject: [PATCH 8/9] updated ci-cd to use neurocommand ants install --- .github/workflows/ci-cd.yaml | 103 ++++++++++++++++++----------------- tox.ini | 3 + 2 files changed, 55 insertions(+), 51 deletions(-) diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml index a053fdc..358f1a6 100644 --- a/.github/workflows/ci-cd.yaml +++ b/.github/workflows/ci-cd.yaml @@ -27,10 +27,10 @@ permissions: id-token: write env: # Define environment variables - AFNI_VERSION: 25.2.06 - AFNI_INSTALL_PATH: /opt/afni - # Force tox and pytest to use color + SCIGET_NAME: afni + SCIGET_VERSION: 25.2.06 FORCE_COLOR: true + jobs: build: @@ -56,53 +56,39 @@ jobs: steps: - - name: Install prerequisite packages - run: sudo apt install -y cmake - - name: Removed unnecessary tools to free space run: | sudo rm -rf /usr/share/dotnet sudo rm -rf "$AGENT_TOOLSDIRECTORY" - - name: Create AFNI install directory + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Revert version to most recent version tag on Nipype or Nipype2Pydra update + if: github.event_name == 'repository_dispatch' + run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}') + + - name: Install Apptainer and Lmod run: | - sudo mkdir -p ${{ env.AFNI_INSTALL_PATH }} - sudo chown $USER ${{ env.AFNI_INSTALL_PATH }} + sudo add-apt-repository -y ppa:apptainer/ppa + sudo apt-get update + sudo apt-get install -y lmod apptainer - - name: Cache AFNI Install - id: cache-install - uses: actions/cache@v4 - with: - path: ${{ env.AFNI_INSTALL_PATH }} - key: afni-${{ env.AFNI_VERSION }}-${{ runner.os }} - - # - name: Install AFNI Package - # if: steps.cache-install.outputs.cache-hit != 'true' - # run: | - # pushd ${{ env.AFNI_INSTALL_PATH }} - # curl -O https://afni.nimh.nih.gov/pub/dist/bin/linux_openmp64/AFNI_${{ env.AFNI_VERSION }}_Linux_openmp64.tar.gz - # tar -xzf AFNI_${{ env.AFNI_VERSION }}_Linux_openmp64.tar.gz - # rm AFNI_${{ env.AFNI_VERSION }}_Linux_openmp64.tar.gz - # echo "PATH=${{ env.AFNI_INSTALL_PATH }}/AFNI_${{ env.AFNI_VERSION }}_Linux_openmp64:$PATH" >> $GITHUB_ENV - # echo "LD_LIBRARY_PATH=${{ env.AFNI_INSTALL_PATH }}/AFNI_${{ env.AFNI_VERSION }}_Linux_openmp64/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV - # popd - - # # - name: Install AFNI Package - # # if: steps.cache-install.outputs.cache-hit != 'true' - # # run: | - # # pushd ~ - # # curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_24_64_a_admin.txt - # # curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_24_64_b_user.tcsh - # # curl -O https://raw.githubusercontent.com/afni/afni/master/src/other_builds/OS_notes.linux_ubuntu_24_64_c_nice.tcsh - # # sudo bash OS_notes.linux_ubuntu_24_64_a_admin.txt 2>&1 | tee o.ubuntu_24_a.txt - # # tcsh OS_notes.linux_ubuntu_24_64_b_user.tcsh 2>&1 | tee o.ubuntu_24_b.txt - # # afni_system_check.py -check_all - # # echo "PATH=${{ env.AFNI_INSTALL_PATH }}/bin:$PATH" >> $GITHUB_ENV - # # echo "LD_LIBRARY_PATH=${{ env.AFNI_INSTALL_PATH }}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV - # # popd + - name: Install Neurocommand + run: | + git clone https://github.com/NeuroDesk/neurocommand.git + pushd neurocommand + pip3 install -r neurodesk/requirements.txt --user + bash build.sh --cli + echo "APPTAINER_BINDPATH=`pwd -P`" >> $GITHUB_ENV - - name: Checkout repo - uses: actions/checkout@v4 + source /etc/profile.d/lmod.sh + ./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}' + SCIGET_BUILDVERSION=$(./containers.sh "${{ env.SCIGET_NAME }}" | grep -E "^\s*\|\s*${{ env.SCIGET_NAME }}\s*\|\s*${{ env.SCIGET_VERSION }}\s*\|" | awk -F '|' '{gsub(/ /,"",$4); print $4}') + + ./local/fetch_containers.sh ${{ env.SCIGET_NAME }} ${{ env.SCIGET_VERSION }} $SCIGET_BUILDVERSION + echo "SCIGET_BUILDVERSION=$SCIGET_BUILDVERSION" >> $GITHUB_ENV + popd - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 @@ -127,7 +113,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.8', '3.12'] + python-version: ['3.11', '3.13'] steps: - uses: actions/checkout@v3 - name: Revert version to most recent tag on upstream update @@ -153,26 +139,33 @@ jobs: needs: [build, test, fileformats-test] runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + + - uses: actions/checkout@v4 with: submodules: recursive fetch-depth: 0 + - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.x' + - name: Install build tools run: python -m pip install build twine + - name: Build source and wheel distributions run: python -m build ./related-packages/fileformats + - name: Check distributions run: twine check ./related-packages/fileformats/dist/* + - name: Check for PyPI token on tag id: deployable if: github.event_name == 'release' env: PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_API_TOKEN }}" run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI if: steps.deployable.outputs.DEPLOY uses: pypa/gh-action-pypi-publish@release/v1 @@ -185,26 +178,33 @@ jobs: needs: [deploy-fileformats] runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + + - uses: actions/checkout@v4 with: submodules: recursive fetch-depth: 0 + - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: - python-version: '3.11' + python-version: '3.x' + - name: Install build tools run: python -m pip install build twine + - name: Build source and wheel distributions run: python -m build ./related-packages/fileformats-extras + - name: Check distributions run: twine check ./related-packages/fileformats-extras/dist/* + - name: Check for PyPI token on tag id: deployable if: github.event_name == 'release' env: PYPI_API_TOKEN: "${{ secrets.PYPI_FILEFORMATS_EXTRAS_API_TOKEN }}" run: if [ -n "$PYPI_API_TOKEN" ]; then echo "DEPLOY=true" >> $GITHUB_OUTPUT; fi + - name: Upload to PyPI if: steps.deployable.outputs.DEPLOY uses: pypa/gh-action-pypi-publish@release/v1 @@ -214,9 +214,8 @@ jobs: packages-dir: ./related-packages/fileformats-extras/dist deploy: - needs: [build, test] + needs: [build, test, deploy-fileformats, deploy-fileformats-extras] runs-on: ubuntu-latest - if: github.event_name == 'release' permissions: attestations: write id-token: write @@ -227,7 +226,9 @@ jobs: name: Packages path: dist - name: Upload to PyPI + if: github.event_name == 'release' uses: pypa/gh-action-pypi-publish@release/v1 + # Deploy on tags if PYPI_API_TOKEN is defined in the repository secrets. # Secrets are not accessible in the if: condition [0], so set an output variable [1] diff --git a/tox.ini b/tox.ini index 5835e20..353aad7 100644 --- a/tox.ini +++ b/tox.ini @@ -47,6 +47,9 @@ setenv = pre: UV_INDEX_STRATEGY=unsafe-best-match uv_resolution = min: lowest-direct +deps = + -e ./related-packages/fileformats + -e ./related-packages/fileformats-extras commands = pytest pydra/tasks/afni --cov=pydra.tasks.afni --cov-report term-missing --durations=20 --durations-min=1.0 {posargs:-n auto} From b923bfc20bc79267eb7e97bd1bca81d69541e1ed Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 1 Sep 2025 11:32:15 +1000 Subject: [PATCH 9/9] fixed name of generated package from ants to afnit --- nipype-auto-conv/generate | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype-auto-conv/generate b/nipype-auto-conv/generate index d0be32c..4db770e 100755 --- a/nipype-auto-conv/generate +++ b/nipype-auto-conv/generate @@ -25,7 +25,7 @@ echo "Running nipype2pydra conversion..." nipype2pydra convert $conv_dir/specs $conv_dir/.. echo "Committing converted tasks to ${CURRENT_BRANCH}-auto-conv..." -git add pydra/tasks/ants +git add pydra/tasks/afni git commit -m "Auto-converted Nipype tasks to Pydra tasks" || echo true echo "Rebasing '$CURRENT_BRANCH' to apply changes..."