[Debian-med-packaging] Bug#1015102: heudiconv: FTBFS: FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data-reproin]
Lucas Nussbaum
lucas at debian.org
Sat Jul 16 14:49:48 BST 2022
Source: heudiconv
Version: 0.11.3-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220716 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> install -d /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home
> pybuild --configure -i python{version} -p "3.9 3.10"
> I: pybuild base:239: python3.9 setup.py config
> running config
> I: pybuild base:239: python3.10 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> pybuild --build -i python{version} -p "3.9 3.10"
> I: pybuild base:239: /usr/bin/python3.9 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/queue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/dicoms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/due.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> copying heudiconv/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external
> copying heudiconv/external/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external
> copying heudiconv/external/pydicom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external
> copying heudiconv/external/dcmstack.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external
> copying heudiconv/external/dlad.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/anonymize_script.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_dicoms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_monitor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_tarballs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_regression.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_queue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_heuristics.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/monitor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_PhoenixReport.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/reproin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/cmrr_heuristic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_ME.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/test_b0dwi_for_fmap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/studyforrest_phase2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/banda-bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_with_ses.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/uc_bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/test_reproin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/multires_7Tbold.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/convertall.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/example.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external/tests
> copying heudiconv/external/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external/tests
> copying heudiconv/external/tests/test_dlad.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/external/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/axasc35.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/phantom.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm
> copying heudiconv/tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00003.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00002.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/01-anat-scout
> copying heudiconv/tests/data/01-anat-scout/0001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/01-anat-scout
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/Phoenix
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA
> copying heudiconv/tests/data/Phoenix/01+AA/01+AA+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument
> copying heudiconv/tests/data/Phoenix/99+PhoenixDocument/99+PhoenixDocument+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument
> copying heudiconv/tests/data/sample_nifti_params.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/sample_nifti.nii.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data
> I: pybuild base:239: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/queue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/dicoms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/due.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> copying heudiconv/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external
> copying heudiconv/external/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external
> copying heudiconv/external/pydicom.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external
> copying heudiconv/external/dcmstack.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external
> copying heudiconv/external/dlad.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/anonymize_script.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_dicoms.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_monitor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_tarballs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_convert.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_regression.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_queue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> copying heudiconv/tests/test_heuristics.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/monitor.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/cli
> copying heudiconv/cli/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_PhoenixReport.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/reproin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/cmrr_heuristic.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_ME.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/test_b0dwi_for_fmap.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/studyforrest_phase2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/banda-bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/bids_with_ses.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/uc_bids.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/test_reproin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/multires_7Tbold.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/convertall.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> copying heudiconv/heuristics/example.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external/tests
> copying heudiconv/external/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external/tests
> copying heudiconv/external/tests/test_dlad.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/external/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/axasc35.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/phantom.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm
> copying heudiconv/tests/data/01-fmap_acq-3mm/1.3.12.2.1107.5.2.43.66112.2016101409263663466202201.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/01-fmap_acq-3mm
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00003.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> copying heudiconv/tests/data/b0dwiForFmap/b0dwi_for_fmap+00002.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/b0dwiForFmap
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/01-anat-scout
> copying heudiconv/tests/data/01-anat-scout/0001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/01-anat-scout
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/Phoenix
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA
> copying heudiconv/tests/data/Phoenix/01+AA/01+AA+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/Phoenix/01+AA
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument
> copying heudiconv/tests/data/Phoenix/99+PhoenixDocument/99+PhoenixDocument+00001.dcm -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/Phoenix/99+PhoenixDocument
> copying heudiconv/tests/data/sample_nifti_params.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data
> copying heudiconv/tests/data/sample_nifti.nii.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data
> dh_auto_test -O--buildsystem=pybuild
> pybuild --test --test-pytest -i python{version} -p "3.9 3.10"
> I: pybuild pybuild:300: cp -a heudiconv/tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/
> I: pybuild base:239: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build; python3.9 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.9.13, pytest-7.1.2, pluggy-1.0.0
> rootdir: /<<PKGBUILDDIR>>
> collected 99 items / 1 skipped
>
> heudiconv/external/tests/test_dlad.py . [ 1%]
> heudiconv/heuristics/test_reproin.py ........ [ 9%]
> heudiconv/tests/test_bids.py ..................................s [ 44%]
> heudiconv/tests/test_convert.py .......... [ 54%]
> heudiconv/tests/test_dicoms.py ... [ 57%]
> heudiconv/tests/test_heuristics.py .F......... [ 68%]
> heudiconv/tests/test_main.py .............. [ 82%]
> heudiconv/tests/test_queue.py ... [ 85%]
> heudiconv/tests/test_regression.py sss. [ 89%]
> heudiconv/tests/test_tarballs.py . [ 90%]
> heudiconv/tests/test_utils.py ......... [100%]
>
> =================================== FAILURES ===================================
> _ test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data-reproin] _
>
> tmpdir = local('/tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0')
> heuristic = 'reproin'
> invocation = '--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data'
>
> @pytest.mark.parametrize('heuristic', ['reproin', 'convertall'])
> @pytest.mark.parametrize(
> 'invocation', [
> "--files %s" % TESTS_DATA_PATH, # our new way with automated groupping
> "-d %s/{subject}/* -s 01-fmap_acq-3mm" % TESTS_DATA_PATH # "old" way specifying subject
> # should produce the same results
> ])
> @pytest.mark.skipif(Dataset is None, reason="no datalad")
> def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
> is_bids = True if heuristic == 'reproin' else False
> arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
> % (heuristic, tmpdir)
> if is_bids:
> arg += " -b"
> arg += " --datalad "
> args = (
> arg + invocation
> ).split(' ')
>
> # Test some safeguards
> if invocation == "--files %s" % TESTS_DATA_PATH:
> # Multiple subjects must not be specified -- only a single one could
> # be overridden from the command line
> with pytest.raises(ValueError):
> runner(args + ['--subjects', 'sub1', 'sub2'])
>
> if heuristic != 'reproin':
> # if subject is not overridden, raise error
> with pytest.raises(NotImplementedError):
> runner(args)
> return
>
> runner(args)
> ds = Dataset(str(tmpdir))
> assert ds.is_installed()
> assert not ds.repo.dirty
> head = ds.repo.get_hexsha()
>
> # and if we rerun -- should fail
> lgr.info(
> "RERUNNING, expecting to FAIL since the same everything "
> "and -c specified so we did conversion already"
> )
> with pytest.raises(RuntimeError):
> runner(args)
>
> # but there should be nothing new
> assert not ds.repo.dirty
> > assert head == ds.repo.get_hexsha()
> E AssertionError: assert '2c32d90c7252...452338c3a611a' == '52121805b02b...b36be77769e34'
> E - 52121805b02b454149686a4ae12b36be77769e34
> E + 2c32d90c7252c966ebdba876f6f452338c3a611a
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py:93: AssertionError
> ----------------------------- Captured stdout call -----------------------------
> create(ok): /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0 (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): head (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): advanced applications libraries (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): advanced applications libraries (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): advanced applications libraries (file)
> save(ok): head (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): dbictest1/info/dbictest1.auto.txt (file)
> add(ok): dbictest1/info/dbictest1.edit.txt (file)
> add(ok): dbictest1/info/dicominfo.tsv (file)
> add(ok): dbictest1/info/filegroup.json (file)
> add(ok): dbictest1/info/heuristic.py (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-dbictest1/anat/sub-dbictest1_scout.dicom.tgz (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 14)
> save (ok: 2)
> add(ok): advanced applications libraries (file)
> save(ok): head (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Development (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Functional (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Functional (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): Functional (file)
> save(ok): Development (dataset)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): o6jgilro/info/dicominfo.tsv (file)
> add(ok): o6jgilro/info/filegroup.json (file)
> add(ok): o6jgilro/info/heuristic.py (file)
> add(ok): o6jgilro/info/o6jgilro.auto.txt (file)
> add(ok): o6jgilro/info/o6jgilro.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-o6jgilro/anat/sub-o6jgilro_32ch-head-coil_scout.dicom.tgz (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 14)
> save (ok: 2)
> add(ok): Functional (file)
> save(ok): Development (dataset)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Halchenko (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Yarik (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): 950_bids_test4 (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): 950_bids_test4 (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): 950_bids_test4 (file)
> save(ok): Halchenko/Yarik (dataset)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): Halchenko (dataset)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 5)
> save (notneeded: 1, ok: 3)
> 220716-05:53:06,695 nipype.workflow INFO:
> [Node] Setting-up "convert" in "/tmp/dcm2niixim54mcyi/convert".
> 220716-05:53:06,698 nipype.workflow INFO:
> [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
> 220716-05:53:06,722 nipype.interface INFO:
> stdout 2022-07-16T05:53:06.722711:Chris Rorden's dcm2niiX version v1.0.20211006 (JP2:OpenJPEG) GCC11.3.0 x86-64 (64-bit Linux)
> 220716-05:53:06,723 nipype.interface INFO:
> stdout 2022-07-16T05:53:06.722711:Found 1 DICOM file(s)
> 220716-05:53:06,723 nipype.interface INFO:
> stdout 2022-07-16T05:53:06.722711:Convert 1 DICOM as /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1)
> 220716-05:53:06,723 nipype.interface INFO:
> stdout 2022-07-16T05:53:06.722711:Warning: Check that 2D images are not mirrored.
> 220716-05:53:06,723 nipype.interface INFO:
> stdout 2022-07-16T05:53:06.722711:Conversion required 0.004130 seconds (0.004125 for core code).
> 220716-05:53:06,762 nipype.workflow INFO:
> [Node] Finished "convert", elapsed time 0.062181s.
> 220716-05:53:06,780 nipype.workflow INFO:
> [Node] Setting-up "embedder" in "/tmp/embedmetajpecif6z/embedder".
> 220716-05:53:06,783 nipype.workflow INFO:
> [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
> 220716-05:53:06,821 nipype.workflow INFO:
> [Node] Finished "embedder", elapsed time 0.036873s.
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): phantom1sid1/ses-localizer/info/dicominfo_ses-localizer.tsv (file)
> add(ok): phantom1sid1/ses-localizer/info/filegroup_ses-localizer.json (file)
> add(ok): phantom1sid1/ses-localizer/info/heuristic.py (file)
> add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.auto.txt (file)
> add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-phantom1sid1/ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz (file)
> add(ok): sourcedata/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.dicom.tgz (file)
> add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json (file)
> add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.nii.gz (file)
> add(ok): sub-phantom1sid1/ses-localizer/sub-phantom1sid1_ses-localizer_scans.tsv (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 18)
> save (ok: 2)
> add(ok): 950_bids_test4 (file)
> save(ok): Halchenko/Yarik (dataset)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): Halchenko (dataset)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 5)
> save (notneeded: 2, ok: 3)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Research (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): MCBI_TESTING (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): MCBI_TESTING (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): MCBI_TESTING (file)
> save(ok): Research (dataset)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): crlab/info/crlab.auto.txt (file)
> add(ok): crlab/info/crlab.edit.txt (file)
> add(ok): crlab/info/dicominfo.tsv (file)
> add(ok): crlab/info/filegroup.json (file)
> add(ok): crlab/info/heuristic.py (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 12)
> save (ok: 2)
> add(ok): MCBI_TESTING (file)
> save(ok): Research (dataset)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Investigators (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Winawer (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Winawer (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): Winawer (file)
> save(ok): Investigators (dataset)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): ke6hl9lm/info/dicominfo.tsv (file)
> add(ok): ke6hl9lm/info/filegroup.json (file)
> add(ok): ke6hl9lm/info/heuristic.py (file)
> add(ok): ke6hl9lm/info/ke6hl9lm.auto.txt (file)
> add(ok): ke6hl9lm/info/ke6hl9lm.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 12)
> save (ok: 2)
> add(ok): Winawer (file)
> save(ok): Investigators (dataset)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> action summary:
> save (notneeded: 2)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 2)
> save (notneeded: 3, ok: 1)
> action summary:
> save (notneeded: 2)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 2)
> save (notneeded: 3, ok: 1)
> ------------------------------ Captured log call -------------------------------
> WARNING heudiconv.main:main.py:302 Could not check for version updates: Connection to server could not be made
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> WARNING heudiconv:reproin.py:434 Could not determine the series name by looking at protocol_name, series_description fields
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> INFO nipype.workflow:nodes.py:450 [Node] Setting-up "convert" in "/tmp/dcm2niixim54mcyi/convert".
> INFO nipype.workflow:nodes.py:713 [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:06.722711:Chris Rorden's dcm2niiX version v1.0.20211006 (JP2:OpenJPEG) GCC11.3.0 x86-64 (64-bit Linux)
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:06.722711:Found 1 DICOM file(s)
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> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Investigators/Winawer
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Investigators/Winawer/.heudiconv
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Investigators/Winawer
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: done
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> INFO datalad.core.local.save:log.py:431 Total: starting
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Investigators/Winawer
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Investigators
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0
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> INFO datalad.core.local.save:log.py:431 Total: done
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> WARNING heudiconv.main:main.py:302 Could not check for version updates: Connection to server could not be made
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries/sub-dbictest1
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0
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> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional/sub-o6jgilro
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: starting
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0/Development
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
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> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-9/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> =============================== warnings summary ===============================
> heudiconv/utils.py:262
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/utils.py:262: DeprecationWarning: invalid escape sequence \]
> js_ = re.sub(" *\]", "]", js_)
>
> heudiconv/utils.py:269
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/utils.py:269: DeprecationWarning: invalid escape sequence \w
> '(?<!\w{3})' # negative lookbehind for the month
>
> heudiconv/utils.py:271
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/utils.py:271: DeprecationWarning: invalid escape sequence \d
> '(?! [123]\d{3})' # negative lookahead for a year
>
> heudiconv/utils.py:275
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/utils.py:275: DeprecationWarning: invalid escape sequence \[
> js_ = re.sub('\[ ', '[', js_)
>
> heudiconv/heuristics/test_reproin.py:117
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics/test_reproin.py:117: DeprecationWarning: invalid escape sequence \+
> [('scout_run\+', 'THESCOUT-runX'),
>
> heudiconv/heuristics/reproin.py:903
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/heuristics/reproin.py:903: DeprecationWarning: invalid escape sequence \d
> reg = re.match("sid0*(\d+)$", subjectid)
>
> heudiconv/bids.py:179
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/bids.py:179: DeprecationWarning: invalid escape sequence \_
> for fpath in find_files('.*_task-.*\_bold\.json',
>
> heudiconv/bids.py:182
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/bids.py:182: DeprecationWarning: invalid escape sequence \.
> exclude="/\.(datalad|heudiconv)/"):
>
> heudiconv/bids.py:188
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/bids.py:188: DeprecationWarning: invalid escape sequence \.
> task = re.sub('.*_(task-[^_\.]*(_acq-[^_\.]*)?)_.*', r'\1', fpath)
>
> heudiconv/parser.py:25
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/parser.py:25: DeprecationWarning: invalid escape sequence \.
> _VCS_REGEX = '%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (op.sep, op.sep)
>
> heudiconv/parser.py:164
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/parser.py:164: DeprecationWarning: invalid escape sequence \.
> '.*', topdir=f, exclude_vcs=True, exclude="/\.datalad/"))
>
> heudiconv/convert.py:898
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/convert.py:898: DeprecationWarning: invalid escape sequence \w
> meta_info['TaskName'] = (re.search('(?<=_task-)\w+',
>
> heudiconv/tests/test_heuristics.py:124
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py:124: DeprecationWarning: invalid escape sequence \d
> '^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}.[\d]{6}$',
>
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_main.py::test_cache
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/parser.py:200: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
> lgr.warn("Heuristic is missing an `infotoids` method, assigning "
>
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py: 6 warnings
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_dicoms.py: 3 warnings
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py: 8 warnings
> /usr/lib/python3/dist-packages/dcmstack/dcmmeta.py:1536: DeprecationWarning: get_affine method is deprecated.
> Please use the ``img.affine`` property instead.
>
> * deprecated from version: 2.5.1
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
> affine = np.dot(np.diag([-1., -1., 1., 1.]), dcm_wrp.get_affine())
>
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata
> /usr/lib/python3/dist-packages/dcmstack/dcmstack.py:839: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> self._files_info[file_idx][0].nii_img.get_data()
>
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data-reproin]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[-d /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/{subject}/* -s 01-fmap_acq-3mm-reproin]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[-d /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data/{subject}/* -s 01-fmap_acq-3mm-reproin]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_scans_keys_reproin[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_scout_conversion
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_notop[bidsoptions0]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_notop[bidsoptions1]
> .pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion
> /usr/lib/python3/dist-packages/dcmstack/dcmstack.py:845: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> self._files_info[file_idx][0].nii_img.get_data()[:, :, 0]
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build/heudiconv/tests/data-reproin]
> ============ 1 failed, 94 passed, 5 skipped, 49 warnings in 45.36s =============
> E: pybuild pybuild:369: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_heudiconv/build; python3.9 -m pytest
> I: pybuild pybuild:300: cp -a heudiconv/tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/
> I: pybuild base:239: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build; python3.10 -m pytest
> ============================= test session starts ==============================
> platform linux -- Python 3.10.5, pytest-7.1.2, pluggy-1.0.0
> rootdir: /<<PKGBUILDDIR>>
> collected 99 items / 1 skipped
>
> heudiconv/external/tests/test_dlad.py . [ 1%]
> heudiconv/heuristics/test_reproin.py ........ [ 9%]
> heudiconv/tests/test_bids.py ..................................s [ 44%]
> heudiconv/tests/test_convert.py .......... [ 54%]
> heudiconv/tests/test_dicoms.py ... [ 57%]
> heudiconv/tests/test_heuristics.py .F......... [ 68%]
> heudiconv/tests/test_main.py .............. [ 82%]
> heudiconv/tests/test_queue.py ... [ 85%]
> heudiconv/tests/test_regression.py sss. [ 89%]
> heudiconv/tests/test_tarballs.py . [ 90%]
> heudiconv/tests/test_utils.py ......... [100%]
>
> =================================== FAILURES ===================================
> _ test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data-reproin] _
>
> tmpdir = local('/tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0')
> heuristic = 'reproin'
> invocation = '--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data'
>
> @pytest.mark.parametrize('heuristic', ['reproin', 'convertall'])
> @pytest.mark.parametrize(
> 'invocation', [
> "--files %s" % TESTS_DATA_PATH, # our new way with automated groupping
> "-d %s/{subject}/* -s 01-fmap_acq-3mm" % TESTS_DATA_PATH # "old" way specifying subject
> # should produce the same results
> ])
> @pytest.mark.skipif(Dataset is None, reason="no datalad")
> def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
> is_bids = True if heuristic == 'reproin' else False
> arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
> % (heuristic, tmpdir)
> if is_bids:
> arg += " -b"
> arg += " --datalad "
> args = (
> arg + invocation
> ).split(' ')
>
> # Test some safeguards
> if invocation == "--files %s" % TESTS_DATA_PATH:
> # Multiple subjects must not be specified -- only a single one could
> # be overridden from the command line
> with pytest.raises(ValueError):
> runner(args + ['--subjects', 'sub1', 'sub2'])
>
> if heuristic != 'reproin':
> # if subject is not overridden, raise error
> with pytest.raises(NotImplementedError):
> runner(args)
> return
>
> runner(args)
> ds = Dataset(str(tmpdir))
> assert ds.is_installed()
> assert not ds.repo.dirty
> head = ds.repo.get_hexsha()
>
> # and if we rerun -- should fail
> lgr.info(
> "RERUNNING, expecting to FAIL since the same everything "
> "and -c specified so we did conversion already"
> )
> with pytest.raises(RuntimeError):
> runner(args)
>
> # but there should be nothing new
> assert not ds.repo.dirty
> > assert head == ds.repo.get_hexsha()
> E AssertionError: assert '8b30aa64c6c4...27b57f802e72e' == 'd3faa6eaeb37...fa5d8b030692d'
> E - d3faa6eaeb37ad50978c99b6c37fa5d8b030692d
> E + 8b30aa64c6c45d0f910e663c46127b57f802e72e
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py:93: AssertionError
> ----------------------------- Captured stdout call -----------------------------
> create(ok): /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0 (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): head (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): advanced applications libraries (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): advanced applications libraries (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): advanced applications libraries (file)
> save(ok): head (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): dbictest1/info/dbictest1.auto.txt (file)
> add(ok): dbictest1/info/dbictest1.edit.txt (file)
> add(ok): dbictest1/info/dicominfo.tsv (file)
> add(ok): dbictest1/info/filegroup.json (file)
> add(ok): dbictest1/info/heuristic.py (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-dbictest1/anat/sub-dbictest1_scout.dicom.tgz (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 14)
> save (ok: 2)
> add(ok): advanced applications libraries (file)
> save(ok): head (dataset)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Development (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Functional (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Functional (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): Functional (file)
> save(ok): Development (dataset)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): o6jgilro/info/dicominfo.tsv (file)
> add(ok): o6jgilro/info/filegroup.json (file)
> add(ok): o6jgilro/info/heuristic.py (file)
> add(ok): o6jgilro/info/o6jgilro.auto.txt (file)
> add(ok): o6jgilro/info/o6jgilro.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-o6jgilro/anat/sub-o6jgilro_32ch-head-coil_scout.dicom.tgz (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 14)
> save (ok: 2)
> add(ok): Functional (file)
> save(ok): Development (dataset)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Halchenko (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Yarik (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): 950_bids_test4 (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): 950_bids_test4 (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): 950_bids_test4 (file)
> save(ok): Halchenko/Yarik (dataset)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): Halchenko (dataset)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 5)
> save (notneeded: 1, ok: 3)
> 220716-05:53:48,422 nipype.workflow INFO:
> [Node] Setting-up "convert" in "/tmp/dcm2niixu0i0an2g/convert".
> 220716-05:53:48,424 nipype.workflow INFO:
> [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
> 220716-05:53:48,441 nipype.interface INFO:
> stdout 2022-07-16T05:53:48.441096:Chris Rorden's dcm2niiX version v1.0.20211006 (JP2:OpenJPEG) GCC11.3.0 x86-64 (64-bit Linux)
> 220716-05:53:48,441 nipype.interface INFO:
> stdout 2022-07-16T05:53:48.441096:Found 1 DICOM file(s)
> 220716-05:53:48,441 nipype.interface INFO:
> stdout 2022-07-16T05:53:48.441096:Convert 1 DICOM as /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1)
> 220716-05:53:48,441 nipype.interface INFO:
> stdout 2022-07-16T05:53:48.441096:Warning: Check that 2D images are not mirrored.
> 220716-05:53:48,441 nipype.interface INFO:
> stdout 2022-07-16T05:53:48.441096:Conversion required 0.005438 seconds (0.005435 for core code).
> 220716-05:53:48,483 nipype.workflow INFO:
> [Node] Finished "convert", elapsed time 0.057785s.
> 220716-05:53:48,505 nipype.workflow INFO:
> [Node] Setting-up "embedder" in "/tmp/embedmetax47g95tm/embedder".
> 220716-05:53:48,508 nipype.workflow INFO:
> [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
> 220716-05:53:48,533 nipype.workflow INFO:
> [Node] Finished "embedder", elapsed time 0.02498s.
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): phantom1sid1/ses-localizer/info/dicominfo_ses-localizer.tsv (file)
> add(ok): phantom1sid1/ses-localizer/info/filegroup_ses-localizer.json (file)
> add(ok): phantom1sid1/ses-localizer/info/heuristic.py (file)
> add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.auto.txt (file)
> add(ok): phantom1sid1/ses-localizer/info/phantom1sid1_ses-localizer.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> add(ok): sourcedata/README (file)
> add(ok): sourcedata/sub-phantom1sid1/ses-localizer/anat/sub-phantom1sid1_ses-localizer_scout.dicom.tgz (file)
> add(ok): sourcedata/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.dicom.tgz (file)
> add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json (file)
> add(ok): sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.nii.gz (file)
> add(ok): sub-phantom1sid1/ses-localizer/sub-phantom1sid1_ses-localizer_scans.tsv (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 18)
> save (ok: 2)
> add(ok): 950_bids_test4 (file)
> save(ok): Halchenko/Yarik (dataset)
> add(ok): Yarik (file)
> add(ok): .gitmodules (file)
> save(ok): Halchenko (dataset)
> add(ok): Halchenko (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 5)
> save (notneeded: 2, ok: 3)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Research (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): MCBI_TESTING (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): MCBI_TESTING (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): MCBI_TESTING (file)
> save(ok): Research (dataset)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): crlab/info/crlab.auto.txt (file)
> add(ok): crlab/info/crlab.edit.txt (file)
> add(ok): crlab/info/dicominfo.tsv (file)
> add(ok): crlab/info/filegroup.json (file)
> add(ok): crlab/info/heuristic.py (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 12)
> save (ok: 2)
> add(ok): MCBI_TESTING (file)
> save(ok): Research (dataset)
> add(ok): Research (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Investigators (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): Winawer (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): Winawer (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): .gitattributes (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 1)
> save (ok: 1)
> add(ok): Winawer (file)
> save(ok): Investigators (dataset)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 1, ok: 2)
> add(ok): .heudiconv (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> create(ok): .heudiconv (dataset)
> action summary:
> add (ok: 2)
> create (ok: 1)
> save (ok: 1)
> add(ok): ke6hl9lm/info/dicominfo.tsv (file)
> add(ok): ke6hl9lm/info/filegroup.json (file)
> add(ok): ke6hl9lm/info/heuristic.py (file)
> add(ok): ke6hl9lm/info/ke6hl9lm.auto.txt (file)
> add(ok): ke6hl9lm/info/ke6hl9lm.edit.txt (file)
> save(ok): .heudiconv (dataset)
> add(ok): .heudiconv (file)
> add(ok): CHANGES (file)
> add(ok): README (file)
> add(ok): dataset_description.json (file)
> add(ok): participants.json (file)
> add(ok): participants.tsv (file)
> add(ok): scans.json (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 12)
> save (ok: 2)
> add(ok): Winawer (file)
> save(ok): Investigators (dataset)
> add(ok): Investigators (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 3)
> save (notneeded: 2, ok: 2)
> action summary:
> save (notneeded: 2)
> add(ok): head (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 2)
> save (notneeded: 3, ok: 1)
> action summary:
> save (notneeded: 2)
> add(ok): Development (file)
> add(ok): .gitmodules (file)
> save(ok): . (dataset)
> action summary:
> add (ok: 2)
> save (notneeded: 3, ok: 1)
> ------------------------------ Captured log call -------------------------------
> WARNING heudiconv.main:main.py:302 Could not check for version updates: Connection to server could not be made
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries/sub-dbictest1
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries/.heudiconv
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
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> WARNING heudiconv:reproin.py:434 Could not determine the series name by looking at protocol_name, series_description fields
> WARNING heudiconv:reproin.py:619 Could not figure out where to stick 1 sequences: ['99-Phoenix Document']
> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional/sub-o6jgilro
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> INFO nipype.workflow:nodes.py:450 [Node] Setting-up "convert" in "/tmp/dcm2niixu0i0an2g/convert".
> INFO nipype.workflow:nodes.py:713 [Node] Executing "convert" <nipype.interfaces.dcm2nii.Dcm2niix>
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:48.441096:Chris Rorden's dcm2niiX version v1.0.20211006 (JP2:OpenJPEG) GCC11.3.0 x86-64 (64-bit Linux)
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:48.441096:Found 1 DICOM file(s)
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:48.441096:Convert 1 DICOM as /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff_heudiconv137_e2_ph (64x64x1x1)
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:48.441096:Warning: Check that 2D images are not mirrored.
> INFO nipype.interface:subprocess.py:69 stdout 2022-07-16T05:53:48.441096:Conversion required 0.005438 seconds (0.005435 for core code).
> INFO nipype.workflow:nodes.py:720 [Node] Finished "convert", elapsed time 0.057785s.
> WARNING heudiconv.convert:convert.py:902 Failed to find task field in /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Halchenko/Yarik/950_bids_test4/sub-phantom1sid1/ses-localizer/fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json.
> INFO nipype.workflow:nodes.py:450 [Node] Setting-up "embedder" in "/tmp/embedmetax47g95tm/embedder".
> INFO nipype.workflow:nodes.py:713 [Node] Executing "embedder" <nipype.interfaces.utility.wrappers.Function>
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> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Investigators
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> WARNING heudiconv.main:main.py:302 Could not check for version updates: Connection to server could not be made
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti.json since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti.nii.gz since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.dicoms:dicoms.py:119 Ignoring /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/sample_nifti_params.txt since not quite a "normal" DICOM: 'FileDataset' object has no attribute 'SeriesNumber'
> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries/sub-dbictest1
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head/advanced applications libraries
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/head
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> WARNING heudiconv.bids:bids.py:901 We cannot add the IntendedFor field: no fmap/ in /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional/sub-o6jgilro
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: starting
> INFO datalad.core.local.save:log.py:431
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional/.heudiconv
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development/Functional
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0/Development
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: processed result for /tmp/pytest-of-user42/pytest-10/test_reproin_largely_smoke___f0
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> INFO datalad.core.local.save:log.py:431 Total: done
> INFO datalad.ui.dialog:log.py:431 Clear progress bars
> INFO datalad.ui.dialog:log.py:431 Refresh progress bars
> =============================== warnings summary ===============================
> heudiconv/utils.py:262
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/utils.py:262: DeprecationWarning: invalid escape sequence '\]'
> js_ = re.sub(" *\]", "]", js_)
>
> heudiconv/utils.py:269
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/utils.py:269: DeprecationWarning: invalid escape sequence '\w'
> '(?<!\w{3})' # negative lookbehind for the month
>
> heudiconv/utils.py:271
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/utils.py:271: DeprecationWarning: invalid escape sequence '\d'
> '(?! [123]\d{3})' # negative lookahead for a year
>
> heudiconv/utils.py:275
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/utils.py:275: DeprecationWarning: invalid escape sequence '\['
> js_ = re.sub('\[ ', '[', js_)
>
> ../../../../../../usr/lib/python3/dist-packages/nipype/__init__.py:15
> /usr/lib/python3/dist-packages/nipype/__init__.py:15: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
> from distutils.version import LooseVersion
>
> heudiconv/heuristics/test_reproin.py:117
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics/test_reproin.py:117: DeprecationWarning: invalid escape sequence '\+'
> [('scout_run\+', 'THESCOUT-runX'),
>
> heudiconv/heuristics/reproin.py:903
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/heuristics/reproin.py:903: DeprecationWarning: invalid escape sequence '\d'
> reg = re.match("sid0*(\d+)$", subjectid)
>
> heudiconv/bids.py:179
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/bids.py:179: DeprecationWarning: invalid escape sequence '\_'
> for fpath in find_files('.*_task-.*\_bold\.json',
>
> heudiconv/bids.py:182
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/bids.py:182: DeprecationWarning: invalid escape sequence '\.'
> exclude="/\.(datalad|heudiconv)/"):
>
> heudiconv/bids.py:188
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/bids.py:188: DeprecationWarning: invalid escape sequence '\.'
> task = re.sub('.*_(task-[^_\.]*(_acq-[^_\.]*)?)_.*', r'\1', fpath)
>
> heudiconv/parser.py:25
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/parser.py:25: DeprecationWarning: invalid escape sequence '\.'
> _VCS_REGEX = '%s\.(?:git|gitattributes|svn|bzr|hg)(?:%s|$)' % (op.sep, op.sep)
>
> heudiconv/parser.py:164
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/parser.py:164: DeprecationWarning: invalid escape sequence '\.'
> '.*', topdir=f, exclude_vcs=True, exclude="/\.datalad/"))
>
> heudiconv/convert.py:898
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/convert.py:898: DeprecationWarning: invalid escape sequence '\w'
> meta_info['TaskName'] = (re.search('(?<=_task-)\w+',
>
> heudiconv/tests/test_heuristics.py:124
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py:124: DeprecationWarning: invalid escape sequence '\d'
> '^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}.[\d]{6}$',
>
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_main.py::test_cache
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/parser.py:200: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
> lgr.warn("Heuristic is missing an `infotoids` method, assigning "
>
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py: 6 warnings
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_dicoms.py: 3 warnings
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py: 8 warnings
> /usr/lib/python3/dist-packages/dcmstack/dcmmeta.py:1536: DeprecationWarning: get_affine method is deprecated.
> Please use the ``img.affine`` property instead.
>
> * deprecated from version: 2.5.1
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
> affine = np.dot(np.diag([-1., -1., 1., 1.]), dcm_wrp.get_affine())
>
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_convert.py::test_b0dwi_for_fmap
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_dicoms.py::test_embed_dicom_and_nifti_metadata
> /usr/lib/python3/dist-packages/dcmstack/dcmstack.py:839: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> self._files_info[file_idx][0].nii_img.get_data()
>
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data-reproin]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[-d /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/{subject}/* -s 01-fmap_acq-3mm-reproin]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[-d /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data/{subject}/* -s 01-fmap_acq-3mm-reproin]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_scans_keys_reproin[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_scout_conversion
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_notop[bidsoptions0]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_notop[bidsoptions1]
> .pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/test_heuristics.py::test_phoenix_doc_conversion
> /usr/lib/python3/dist-packages/dcmstack/dcmstack.py:845: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).
>
> * deprecated from version: 3.0
> * Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
> self._files_info[file_idx][0].nii_img.get_data()[:, :, 0]
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> FAILED heudiconv/tests/test_heuristics.py::test_reproin_largely_smoke[--files /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build/heudiconv/tests/data-reproin]
> ============ 1 failed, 94 passed, 5 skipped, 50 warnings in 33.99s =============
> E: pybuild pybuild:369: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_heudiconv/build; python3.10 -m pytest
> rm -fr -- /tmp/dh-xdg-rundir-PTAzUKZZ
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.9 3.10" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2022/07/16/heudiconv_0.11.3-1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220716;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220716&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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