fix ignoring sessions that have no data (#1035)

.circleci/config.yml

@@ -49,7 +49,7 @@ jobs:
           command: |
             pip install --upgrade --progress-bar off pip
             # TODO: Restore https://api.github.com/repos/mne-tools/mne-bids/zipball/main pending https://github.com/mne-tools/mne-bids/pull/1349/files#r1885104885
-            pip install --upgrade --progress-bar off "autoreject @ https://api.github.com/repos/autoreject/autoreject/zipball/master" "mne[hdf5] @ git+https://github.com/mne-tools/mne-python@main" "mne-bids[full]" numba
+            pip install --upgrade --progress-bar off "autoreject @ https://api.github.com/repos/autoreject/autoreject/zipball/master" "mne[hdf5] @ git+https://github.com/mne-tools/mne-python@main" "mne-bids[full] @ git+https://github.com/mne-tools/mne-bids@main" numba
             pip install -ve .[tests]
             pip install "PyQt6!=6.6.1" "PyQt6-Qt6!=6.6.1,!=6.6.2,!=6.6.3,!=6.7.0"
       - run:

.github/workflows/run-tests.yml

@@ -22,7 +22,7 @@ jobs:
       with:
         python-version: "3.12"
     - run: pip install --upgrade pip
-    - run: pip install -ve .[tests] codespell tomli --only-binary="numpy,scipy,pandas,matplotlib,pyarrow,numexpr"
+    - run: pip install -ve .[tests] "mne-bids[full] @ git+https://github.com/mne-tools/mne-bids@main" codespell tomli --only-binary="numpy,scipy,pandas,matplotlib,pyarrow,numexpr"
     - run: make codespell-error
     - run: pytest mne_bids_pipeline -m "not dataset_test"
     - uses: codecov/codecov-action@v5

mne_bids_pipeline/_config_import.py

@@ -6,12 +6,14 @@
 import pathlib
 from dataclasses import field
 from functools import partial
+from inspect import signature
 from types import SimpleNamespace
 from typing import Any
 
 import matplotlib
 import mne
 import numpy as np
+from mne_bids import get_entity_vals
 from pydantic import BaseModel, ConfigDict, ValidationError
 
 from ._logging import gen_log_kwargs, logger
@@ -324,6 +326,16 @@ def _check_config(config: SimpleNamespace, config_path: PathLike | None) -> None
             "Please set process_empty_room = True"
         )
 
+    if (
+        config.allow_missing_sessions
+        and "ignore_suffixes" not in signature(get_entity_vals).parameters
+    ):
+        raise ConfigError(
+            "You've requested to `allow_missing_sessions`, but this functionality "
+            "requires a newer version of `mne_bids` than you have available. Please "
+            "update MNE-BIDS (or if on the latest version, install the dev version)."
+        )
+
     bl = config.baseline
     if bl is not None:
         if (bl[0] is not None and bl[0] < config.epochs_tmin) or (

mne_bids_pipeline/_config_utils.py

@@ -4,6 +4,7 @@
 import functools
 import pathlib
 from collections.abc import Iterable, Sized
+from inspect import signature
 from types import ModuleType, SimpleNamespace
 from typing import Any, Literal, TypeVar
 
@@ -142,26 +143,52 @@ def _get_sessions(config: SimpleNamespace) -> tuple[str, ...]:
     return tuple(str(x) for x in sessions)
 
 
-def get_subjects_sessions(config: SimpleNamespace) -> dict[str, list[str] | list[None]]:
-    subj_sessions: dict[str, list[str] | list[None]] = dict()
+def get_subjects_sessions(
+    config: SimpleNamespace,
+) -> dict[str, tuple[None] | tuple[str, ...]]:
+    subjects = get_subjects(config)
     cfg_sessions = _get_sessions(config)
-    for subject in get_subjects(config):
-        # Only traverse through the current subject's directory
+    # easy case first: datasets that don't have (named) sessions
+    if not cfg_sessions:
+        return {subj: (None,) for subj in subjects}
+
+    # find which tasks to ignore when deciding if a subj has data for a session
+    ignore_datatypes = _get_ignore_datatypes(config)
+    if config.task == "":
+        ignore_tasks = None
+    else:
+        all_tasks = _get_entity_vals_cached(
+            root=config.bids_root,
+            entity_key="task",
+            ignore_datatypes=ignore_datatypes,
+        )
+        ignore_tasks = tuple(set(all_tasks) - set([config.task]))
+
+    # loop over subjs and check for available sessions
+    subj_sessions: dict[str, tuple[None] | tuple[str, ...]] = dict()
+    kwargs = (
+        dict(ignore_suffixes=("scans", "coordsystem"))
+        if "ignore_suffixes" in signature(mne_bids.get_entity_vals).parameters
+        else dict()
+    )
+    for subject in subjects:
         valid_sessions_subj = _get_entity_vals_cached(
             config.bids_root / f"sub-{subject}",
             entity_key="session",
-            ignore_datatypes=_get_ignore_datatypes(config),
+            ignore_tasks=ignore_tasks,
+            ignore_acquisitions=("calibration", "crosstalk"),
+            ignore_datatypes=ignore_datatypes,
+            **kwargs,
         )
-        missing_sessions = set(cfg_sessions) - set(valid_sessions_subj)
+        missing_sessions = sorted(set(cfg_sessions) - set(valid_sessions_subj))
         if missing_sessions and not config.allow_missing_sessions:
             raise RuntimeError(
                 f"Subject {subject} is missing session{_pl(missing_sessions)} "
-                f"{tuple(sorted(missing_sessions))}, and "
-                "`config.allow_missing_sessions` is False"
+                f"{missing_sessions}, and `config.allow_missing_sessions` is False"
             )
-        subj_sessions[subject] = sorted(set(cfg_sessions) & set(valid_sessions_subj))
-        if subj_sessions[subject] == []:
-            subj_sessions[subject] = [None]
+        keep_sessions = tuple(sorted(set(cfg_sessions) & set(valid_sessions_subj)))
+        if len(keep_sessions):
+            subj_sessions[subject] = keep_sessions
     return subj_sessions
 
 

mne_bids_pipeline/tests/test_run.py

@@ -258,7 +258,7 @@ def test_missing_sessions(
     context = (
         nullcontext()
         if allow_missing_sessions
-        else pytest.raises(RuntimeError, match=r"Subject 1 is missing session \('b',\)")
+        else pytest.raises(RuntimeError, match=r"Subject 1 is missing session \['b'\]")
     )
     # run
     command = [