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Merge pull request #69 from jhlegarreta/ref/clean-fmriprep-code-refs
REF: Change references to fMRIPrep for PETPrep
2 parents f76d249 + 60f2252 commit 25b92fb

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‎.versions.json‎

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@@ -1,91 +1,4 @@
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{
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"flagged": {
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"1.0.0": "Deprecated / too old",
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"1.0.1": "Phase-difference fieldmap bug",
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"1.0.2": "Phase-difference fieldmap bug",
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"1.0.3": "Phase-difference fieldmap bug",
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"1.0.4": "Phase-difference fieldmap bug",
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"1.0.5": "Phase-difference fieldmap bug",
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"1.0.6": "Phase-difference fieldmap bug",
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"1.0.6-1": "Phase-difference fieldmap bug",
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"1.0.6-2": "Phase-difference fieldmap bug",
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"1.0.7": "Phase-difference fieldmap bug",
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"1.0.8": "Phase-difference fieldmap bug",
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"1.0.9": "Phase-difference fieldmap bug",
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"1.0.10": "Phase-difference fieldmap bug",
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"1.0.11": "Phase-difference fieldmap bug",
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"1.0.12": "Phase-difference fieldmap bug",
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"1.0.13": "Phase-difference fieldmap bug",
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"1.0.14": "Phase-difference fieldmap bug",
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"1.0.15": "Phase-difference fieldmap bug",
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"1.1.0": "Phase-difference fieldmap bug",
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"1.1.1": "Phase-difference fieldmap bug",
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"1.1.2": "Phase-difference fieldmap bug",
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"1.1.3": "Phase-difference fieldmap bug",
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"1.1.4": "Phase-difference fieldmap bug",
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"1.1.5": "Phase-difference fieldmap bug",
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"1.1.6": "Phase-difference fieldmap bug",
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"1.1.7": "Phase-difference fieldmap bug",
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"1.1.8": "Phase-difference fieldmap bug",
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"1.2.0": "Phase-difference fieldmap bug",
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"1.2.1": "Phase-difference fieldmap bug",
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"1.2.2": "Phase-difference fieldmap bug",
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"1.2.3": "Phase-difference fieldmap bug",
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"1.2.4": "Phase-difference fieldmap bug",
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"1.2.5": "Phase-difference fieldmap bug",
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"1.2.6": "Phase-difference fieldmap bug",
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"1.2.6-1": "Phase-difference fieldmap bug",
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"1.3.0": "Phase-difference fieldmap bug",
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"1.3.0.post1": "Phase-difference fieldmap bug",
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"1.3.0.post2": "Phase-difference fieldmap bug",
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"1.3.0.post3": "Phase-difference fieldmap bug",
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"1.3.1": "Phase-difference fieldmap bug",
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"1.3.1.post1": "Phase-difference fieldmap bug",
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"1.3.1.post2": "Phase-difference fieldmap bug",
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"1.3.1.post3": "Phase-difference fieldmap bug",
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"1.3.1.post4": "Phase-difference fieldmap bug",
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"1.3.2": "Phase-difference fieldmap bug",
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"1.4.0a0": "Phase-difference fieldmap bug",
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"1.4.0a1": "Phase-difference fieldmap bug",
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"1.4.0": "Phase-difference fieldmap bug",
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"1.4.1rc1": "Phase-difference fieldmap bug",
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"1.4.1rc2": "Phase-difference fieldmap bug",
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"1.4.1rc3": "Phase-difference fieldmap bug",
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"1.4.1rc4": "Phase-difference fieldmap bug",
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"1.4.1rc5": "Phase-difference fieldmap bug",
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"1.4.1": "Phase-difference fieldmap bug",
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"1.5.0rc1": "Nipype unstable; Phase-difference fieldmap bug",
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"1.5.0rc2": "Nipype unstable; Phase-difference fieldmap bug",
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"1.5.0": "Nipype unstable; Phase-difference fieldmap bug",
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"1.5.1rc1": "Nipype unstable; Phase-difference fieldmap bug",
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"1.5.1rc2": "Nipype unstable; Phase-difference fieldmap bug",
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"1.5.1": "Phase-difference fieldmap bug",
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"1.5.2": "Phase-difference fieldmap bug",
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"1.5.3rc1": "Phase-difference fieldmap bug",
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"1.5.3rc2": "Phase-difference fieldmap bug",
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"1.5.3": "Phase-difference fieldmap bug",
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"1.5.4": "Phase-difference fieldmap bug",
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"1.5.5": "Phase-difference fieldmap bug",
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"1.5.6": "Phase-difference fieldmap bug",
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"1.5.7": "Phase-difference fieldmap bug",
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"1.5.8": "Phase-difference fieldmap bug",
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"1.5.9": "Phase-difference fieldmap bug",
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"20.0.0rc1": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.0rc2": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.0rc3": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.0": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.1": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.2": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
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"20.0.3": "Phase-difference fieldmap bug",
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"20.0.4": "Phase-difference fieldmap bug",
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"20.0.5": "Phase-difference fieldmap bug",
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"20.1.0rc1": "Phase-difference fieldmap bug",
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"20.1.0rc2": "Phase-difference fieldmap bug",
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"20.1.0": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307",
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"20.1.1": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307",
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"20.1.2": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307",
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"20.1.3": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307",
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"20.2.0": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307",
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"20.2.1": "Functional outputs in standard space can be wrong depending on the original data's orientation headers - see https://github.com/nipreps/fmriprep/issues/2307"
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}
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}

‎CONTRIBUTING.md‎

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# Contributing to *fMRIPrep*
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# Contributing to *PETPrep*
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*PETPrep* is a project of the [*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).

‎docs/_static/sbatch.slurm‎

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@@ -19,9 +19,9 @@ LOCAL_FREESURFER_DIR="$STUDY/data/derivatives/freesurfer-6.0.1"
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# Prepare some writeable bind-mount points.
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TEMPLATEFLOW_HOST_HOME=$HOME/.cache/templateflow
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FMRIPREP_HOST_CACHE=$HOME/.cache/petprep
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PETPREP_HOST_CACHE=$HOME/.cache/petprep
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mkdir -p ${TEMPLATEFLOW_HOST_HOME}
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mkdir -p ${FMRIPREP_HOST_CACHE}
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mkdir -p ${PETPREP_HOST_CACHE}
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# Prepare derivatives folder
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mkdir -p ${BIDS_DIR}/${DERIVS_DIR}

‎notebooks/README.md‎

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# fmriprep-notebooks
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A repository for notebooks associated with FMRIPREP
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# petprep-notebooks
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A repository for notebooks associated with PETPrep

‎petprep/cli/parser.py‎

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action='store_true',
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default=False,
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help='Opt-out of sending tracking information of this run to '
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'the PETPREP developers. This information helps to '
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'improve FMRIPREP and provides an indicator of real '
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'the PETPrep developers. This information helps to '
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'improve PETPrep and provides an indicator of real '
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'world usage crucial for obtaining funding.',
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)
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g_other.add_argument(

‎petprep/cli/run.py‎

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#
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# https://www.nipreps.org/community/licensing/
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#
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"""fMRI preprocessing workflow."""
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"""PET preprocessing workflow."""
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from .. import config
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‎petprep/cli/tests/test_version.py‎

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monkeypatch.setattr(requests, 'get', mock_get)
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# Initially, cache should not exist
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cachefile = Path.home() / '.cache' / 'fmriprep' / 'latest'
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cachefile = Path.home() / '.cache' / 'petprep' / 'latest'
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assert not cachefile.exists()
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# First check actually fetches from pypi
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monkeypatch.setattr(requests, 'get', mock_get)
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# Initially, cache should not exist
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cachefile = Path.home() / '.cache' / 'fmriprep' / 'latest'
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cachefile = Path.home() / '.cache' / 'petprep' / 'latest'
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cachefile.parent.mkdir(parents=True, exist_ok=True)
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assert not cachefile.exists()
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def test_readonly(tmp_path, monkeypatch):
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"""Test behavior when $HOME/.cache/fmriprep/latest can't be written out."""
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"""Test behavior when $HOME/.cache/petprep/latest can't be written out."""
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home_path = Path('/home/readonly') if getenv('TEST_READONLY_FILESYSTEM') else tmp_path
205205
monkeypatch.setenv('HOME', str(home_path))
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cachedir = home_path / '.cache'
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# Make sure creating the folder will raise the exception.
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with pytest.raises(OSError, match=r'Read-only file system|Permission denied'):
215-
(cachedir / 'fmriprep').mkdir(parents=True)
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(cachedir / 'petprep').mkdir(parents=True)
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# Should not raise
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check_latest()

‎petprep/cli/version.py‎

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date = None
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outdated = None
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now = datetime.now(tz=timezone.utc)
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cachefile = Path.home() / '.cache' / 'fmriprep' / 'latest'
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cachefile = Path.home() / '.cache' / 'petprep' / 'latest'
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try:
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cachefile.parent.mkdir(parents=True, exist_ok=True)
4848
except OSError:
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if latest is None or outdated is True:
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response = None
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with suppress(Exception):
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response = requests.get(url='https://pypi.org/pypi/fmriprep/json', timeout=1.0)
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response = requests.get(url='https://pypi.org/pypi/petprep/json', timeout=1.0)
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7171
if response and response.status_code == 200:
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versions = [Version(rel) for rel in response.json()['releases'].keys()]
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def is_flagged():
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"""Check whether current version is flagged."""
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# https://raw.githubusercontent.com/nipreps/fmriprep/master/.versions.json
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# https://raw.githubusercontent.com/nipreps/petprep/master/.versions.json
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flagged = ()
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response = None
9191
with suppress(Exception):
9292
response = requests.get(
9393
url="""\
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https://raw.githubusercontent.com/nipreps/fmriprep/master/.versions.json""",
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https://raw.githubusercontent.com/nipreps/petprep/master/.versions.json""",
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timeout=1.0,
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)
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‎petprep/cli/workflow.py‎

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All the checks and the construction of the workflow are done
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inside this function that has pickleable inputs and output
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dictionary (``retval``) to allow isolation using a
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``multiprocessing.Process`` that allows fmriprep to enforce
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``multiprocessing.Process`` that allows petprep to enforce
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a hard-limited memory-scope.
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"""

‎petprep/conftest.py‎

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1818
def copytree_or_skip(source, target):
19-
data_dir = ir_files('fmriprep') / source
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data_dir = ir_files('petprep') / source
2020
if not data_dir.exists():
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pytest.skip(f'Cannot chdir into {data_dir!r}. Probably in a zipped distribution.')
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