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Merge pull request #548 from effigies/fix/extension
FIX: Add dots to extensions
2 parents 932e1e3 + 9904aff commit 5153624

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-25
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-25
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‎niworkflows/data/nipreps.json

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@
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},
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{
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"name": "extension",
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"pattern": "[._]*[a-zA-Z0-9]*?\\.([^/\\\\]+)$"
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"pattern": "[._]*[a-zA-Z0-9]*?(\\.[^/\\\\]+)$"
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},
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{
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"name": "atlas",
@@ -132,25 +132,25 @@
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}
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],
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"default_path_patterns": [
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"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}.{extension<nii|nii.gz|json>|nii.gz}",
136-
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
137-
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}]_hemi-{hemi<L|R>}_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat>}.{extension<surf.gii>}",
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"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}.{extension<nii|nii.gz|json>|nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg>}.{extension<nii|nii.gz|json>|nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}.{extension<nii|nii.gz|json>|nii.gz}",
143-
"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<AROMAnoiseICs>|AROMAnoiseICs}.{extension<csv|tsv>|csv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors>|regressors}.{extension<json|tsv>|tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<components|mixing>|components}.{extension<json|tsv|nii|nii.gz>|tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}.{extension<json>|json}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_den-{density}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}.{extension<dtseries.nii|dtseries.json|func.gii|func.json>}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|epiref|lowb|dseg>}.{extension<json|nii.gz|nii>|nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}.{extension<json|nii.gz|nii>|nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}.{extension<tsv|bval|bvec>|tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<fieldmap>}.{extension<nii|nii.gz|json>|nii.gz}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}.{extension<html|svg>}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}.{extension<html|svg>}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold>}.{extension<html|svg>}"
135+
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
136+
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
137+
"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}]_hemi-{hemi<L|R>}_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat>}{extension<.surf.gii>}",
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"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|phase|sbref|boldref|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<AROMAnoiseICs>|AROMAnoiseICs}{extension<.csv|.tsv>|.csv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors>|regressors}{extension<.json|.tsv>|.tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<components|mixing>|components}{extension<.json|.tsv|.nii|.nii.gz>|.tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<decomposition>|decomposition}{extension<.json>|.json}",
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"sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_den-{density}][_hemi-{hemi<L|R>}][_desc-{desc}]_{suffix<bold>}{extension<.dtseries.nii|.dtseries.json|.func.gii|.func.json>}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi|epiref|lowb|dseg>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>}{extension<.json|.nii.gz|.nii>|.nii.gz}",
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"sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dwi>}{extension<.tsv|.bval|.bvec>|.tsv}",
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"sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg>}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg>}",
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"sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_cohort-{cohort}][_desc-{desc}]_{suffix<bold>}{extension<.html|.svg>}"
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]
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}

‎niworkflows/reports/tests/test_core.py

Lines changed: 3 additions & 3 deletions
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@@ -27,7 +27,7 @@ def bids_sessions(tmpdir_factory):
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"sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}]"
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"[_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}]"
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"[_mod-{modality}][_run-{run}][_echo-{echo}][_space-{space}]"
30-
"[_desc-{desc}]_{suffix<dseg|T1w|bold>}.{extension<svg>}"
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"[_desc-{desc}]_{suffix<dseg|T1w|bold>}{extension<.svg>}"
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)
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subjects = ["01"]
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tasks = ["t1", "t2", "t3"]
@@ -49,7 +49,7 @@ def bids_sessions(tmpdir_factory):
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"ceagent": ce,
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"run": run,
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"desc": desc,
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"extension": "svg",
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"extension": ".svg",
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"suffix": "bold",
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"datatype": "figures",
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}
@@ -219,7 +219,7 @@ def test_generated_reportlets(bids_sessions, ordering):
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settings["sections"][3]["ordering"] = ordering
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report.index(settings["sections"])
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# expected number of reportlets
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expected_reportlets_num = len(report.layout.get(extension="svg"))
222+
expected_reportlets_num = len(report.layout.get(extension=".svg"))
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# bids_session uses these entities
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needed_entities = ["session", "task", "ceagent", "run"]
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# the last section is the most recently run

‎setup.cfg

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@ install_requires =
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nitransforms >= 20.0.0rc3,<20.2
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packaging
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pandas
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pybids >= 0.10.2
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pybids >= 0.11.1
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PyYAML
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scikit-image
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scikit-learn

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