From 26bfaf488a70e485c934f0210959295313346252 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 19 Mar 2024 17:31:59 +0100 Subject: [PATCH 1/2] fix: wrong package string for Loaders --- mriqc/data/config.py | 2 +- mriqc/interfaces/common/ensure_size.py | 2 +- mriqc/reports/group.py | 2 +- mriqc/reports/individual.py | 2 +- mriqc/testing.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/mriqc/data/config.py b/mriqc/data/config.py index cfb9a593..5cb2e664 100644 --- a/mriqc/data/config.py +++ b/mriqc/data/config.py @@ -37,7 +37,7 @@ class GroupTemplate: def __init__(self): import jinja2 - self.template_str = Loader(__package__)("data/reports/group.html") + self.template_str = Loader("mriqc")("data/reports/group.html") self.env = jinja2.Environment( loader=jinja2.FileSystemLoader(searchpath="/"), trim_blocks=True, diff --git a/mriqc/interfaces/common/ensure_size.py b/mriqc/interfaces/common/ensure_size.py index f6c9f331..0ac4ae5c 100644 --- a/mriqc/interfaces/common/ensure_size.py +++ b/mriqc/interfaces/common/ensure_size.py @@ -43,7 +43,7 @@ OUT_MASK_NAME = "{prefix}_resmask{ext}" REF_FILE_NAME = "resample_ref.nii.gz" REF_MASK_NAME = "mask_ref.nii.gz" -load_data = Loader(__package__) +load_data = Loader("mriqc") class EnsureSizeInputSpec(BaseInterfaceInputSpec): diff --git a/mriqc/reports/group.py b/mriqc/reports/group.py index 3b586030..d642dbc7 100644 --- a/mriqc/reports/group.py +++ b/mriqc/reports/group.py @@ -43,7 +43,7 @@ def gen_html(csv_file, mod, csv_failed=None, out_file=None): else: from io import BytesIO as TextIO - load_data = Loader(__package__) + load_data = Loader("mriqc") QCGROUPS = { "T1w": [ diff --git a/mriqc/reports/individual.py b/mriqc/reports/individual.py index 392f9115..43209e8c 100644 --- a/mriqc/reports/individual.py +++ b/mriqc/reports/individual.py @@ -26,7 +26,7 @@ from nireports.assembler.report import Report from niworkflows.data import Loader -_load_data = Loader(__package__) +_load_data = Loader("mriqc") def generate_reports(): diff --git a/mriqc/testing.py b/mriqc/testing.py index d2acb4a5..6eac654a 100644 --- a/mriqc/testing.py +++ b/mriqc/testing.py @@ -28,7 +28,7 @@ from niworkflows.data import Loader -_load_data = Loader(__package__) +_load_data = Loader("mriqc") @contextmanager From 1d993d84efa24ef2167e589a35a6aac4a3c1d137 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 19 Mar 2024 17:33:59 +0100 Subject: [PATCH 2/2] fix: variable name --- mriqc/cli/parser.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mriqc/cli/parser.py b/mriqc/cli/parser.py index ecd2b715..b4e82ec9 100644 --- a/mriqc/cli/parser.py +++ b/mriqc/cli/parser.py @@ -535,14 +535,14 @@ def parse_args(args=None, namespace=None): # Force initialization of the BIDSLayout config.execution.init() - participant_labels = [ + participant_label = [ d.name[4:] for d in config.execution.bids_dir.glob("sub-*") if d.is_dir() and d.exists() ] if config.execution.participant_label is not None: selected_label = set(config.execution.participant_label) - if (missing_subjects := selected_label - set(participant_labels)): + if (missing_subjects := selected_label - set(participant_label)): parser.error( "One or more participant labels were not found in the BIDS directory: " f"{', '.join(missing_subjects)}."