Remove unnecessary dependencies

.github/workflows/lint.yml

@@ -32,6 +32,6 @@ jobs:
         run: python -m pip install \
           flake8 flake8-absolute-import flake8-black flake8-docstrings \
           flake8-isort flake8-pyproject flake8-unused-arguments \
-          flake8-use-fstring flake8-warnings pep8-naming
+          flake8-use-fstring pep8-naming
       - name: Check aslprep
         run: python -m flake8 aslprep

.readthedocs.yaml

@@ -3,19 +3,11 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.9"
 
 sphinx:
   configuration: docs/conf.py
 
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.8"
-  jobs:
-    post_checkout:
-      - git fetch --unshallow
-
 python:
   install:
     - method: pip

aslprep/config.py

@@ -390,23 +390,37 @@ def init(cls):
             import re
 
             from bids.layout import BIDSLayout
+            from bids.layout.index import BIDSLayoutIndexer
 
-            work_dir = cls.work_dir / "bids.db"
-            work_dir.mkdir(exist_ok=True, parents=True)
-            cls._layout = BIDSLayout(
-                str(cls.bids_dir),
+            # Recommended after PyBIDS 12.1
+            _indexer = BIDSLayoutIndexer(
                 validate=False,
-                # database_path=str(work_dir),
                 ignore=(
                     "code",
                     "stimuli",
                     "sourcedata",
                     "models",
-                    "derivatives",
-                    re.compile(r"^\."),
+                    re.compile(r"\/\.\w+|^\.\w+"),
+                    re.compile(
+                        r"sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|dwi|eeg|ieeg|meg|func)"
+                    ),
                 ),
             )
+            cls._layout = BIDSLayout(
+                str(cls.bids_dir),
+                indexer=_indexer,
+            )
+
         cls.layout = cls._layout
+        if cls.bids_filters:
+            from bids.layout import Query
+
+            # unserialize pybids Query enum values
+            for acq, filters in cls.bids_filters.items():
+                cls.bids_filters[acq] = {
+                    k: getattr(Query, v[7:-4]) if not isinstance(v, Query) and "Query" in v else v
+                    for k, v in filters.items()
+                }
 
 
 # These variables are not necessary anymore

aslprep/utils/asl.py

@@ -44,7 +44,11 @@ def select_processing_target(aslcontext):
     """Determine how to handle ASL and M0 data based on dataset configuration."""
     import pandas as pd
 
-    aslcontext_df = pd.read_table(aslcontext)
+    try:
+        aslcontext_df = pd.read_table(aslcontext)
+    except:
+        raise ValueError(aslcontext)
+
     voltypes = aslcontext_df["volume_type"].tolist()
 
     if "control" in voltypes and "label" in voltypes:

aslprep/workflows/base.py

@@ -109,7 +109,7 @@ def init_single_subject_wf(subject_id):
     """
     name = f"single_subject_{subject_id}_wf"
     subject_data, layout = collect_data(
-        config.execution.bids_dir,
+        config.execution._layout,
         subject_id,
         bids_filters=config.execution.bids_filters,
     )

pyproject.toml

@@ -12,29 +12,27 @@ classifiers = [
     "Intended Audience :: Science/Research",
     "Topic :: Scientific/Engineering :: Image Recognition",
     "License :: OSI Approved :: BSD License",
-    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
 ]
 license = {file = "LICENSE.md"}
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
-    'importlib_resources; python_version < "3.9"',
+    'importlib_resources; python_version < "3.10"',
     "indexed_gzip >= 0.8.8",
     "jinja2 < 3.1",
     "looseversion == 1.0.3",
     "networkx ~= 2.8.8",  # nipype needs networkx, but 3+ isn"t compatible with nipype 1.8.5
     "nibabel >= 3.0",
     "niflow-nipype1-workflows",
     "nilearn == 0.10.0",
-    "nipype >= 1.8.5",
-    "nitime",
+    "nipype[nipy] >= 1.8.5",
     "nitransforms >= 21.0.0",
     "niworkflows ~= 1.7.3",
     "numpy >= 1.17.3",
     "pandas >= 0.24.0",
     "patsy",
     "psutil >= 5.4",
     "pybids >= 0.13.2",
-    "pyslim",
     "pyyaml",
     "sdcflows",
     "sentry-sdk >= 0.6.9",