TST: Rerun CIs (#781)

mne_bids_pipeline/steps/preprocessing/_07a_apply_ica.py

@@ -56,6 +56,7 @@ def get_input_fnames_apply_ica(
         processing="ica", suffix="components", extension=".tsv"
     )
     in_files["epochs"] = bids_basename.copy().update(suffix="epo", extension=".fif")
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 

mne_bids_pipeline/steps/preprocessing/_07b_apply_ssp.py

@@ -41,6 +41,7 @@ def get_input_fnames_apply_ssp(
     )
     in_files = dict()
     in_files["epochs"] = bids_basename.copy().update(suffix="epo", check=False)
+    _update_for_splits(in_files, "epochs", single=True)
     in_files["proj"] = bids_basename.copy().update(suffix="proj", check=False)
     return in_files
 
@@ -60,7 +61,7 @@ def apply_ssp(
     # compute SSP on first run of raw
     out_files = dict()
     out_files["epochs"] = (
-        in_files["epochs"].copy().update(processing="ssp", check=False)
+        in_files["epochs"].copy().update(processing="ssp", split=None, check=False)
     )
     msg = f"Input epochs: {in_files['epochs'].basename}"
     logger.info(**gen_log_kwargs(message=msg))

mne_bids_pipeline/steps/preprocessing/_08_ptp_reject.py

@@ -48,6 +48,7 @@ def get_input_fnames_drop_ptp(
     )
     in_files = dict()
     in_files["epochs"] = bids_path.copy().update(processing=cfg.spatial_filter)
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -63,7 +64,14 @@ def drop_ptp(
     in_files: dict,
 ) -> dict:
     out_files = dict()
-    out_files["epochs"] = in_files["epochs"].copy().update(processing="clean")
+    out_files["epochs"] = (
+        in_files["epochs"]
+        .copy()
+        .update(
+            processing="clean",
+            split=None,
+        )
+    )
     msg = f'Input:  {in_files["epochs"].basename}'
     logger.info(**gen_log_kwargs(message=msg))
     msg = f'Output: {out_files["epochs"].basename}'

mne_bids_pipeline/steps/sensor/_01_make_evoked.py

@@ -17,7 +17,13 @@
 from ..._logging import gen_log_kwargs, logger
 from ..._parallel import parallel_func, get_parallel_backend
 from ..._report import _open_report, _sanitize_cond_tag, _all_conditions
-from ..._run import failsafe_run, save_logs, _sanitize_callable, _prep_out_files
+from ..._run import (
+    failsafe_run,
+    save_logs,
+    _sanitize_callable,
+    _prep_out_files,
+    _update_for_splits,
+)
 
 
 def get_input_fnames_evoked(
@@ -43,6 +49,7 @@ def get_input_fnames_evoked(
     )
     in_files = dict()
     in_files["epochs"] = fname_epochs
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -59,7 +66,14 @@ def run_evoked(
 ) -> dict:
     out_files = dict()
     out_files["evoked"] = (
-        in_files["epochs"].copy().update(suffix="ave", processing=None, check=False)
+        in_files["epochs"]
+        .copy()
+        .update(
+            suffix="ave",
+            processing=None,
+            check=False,
+            split=None,
+        )
     )
 
     msg = f'Input: {in_files["epochs"].basename}'

mne_bids_pipeline/steps/sensor/_02_decoding_full_epochs.py

@@ -35,7 +35,7 @@
 from ..._logging import gen_log_kwargs, logger
 from ..._decoding import LogReg
 from ..._parallel import parallel_func, get_parallel_backend
-from ..._run import failsafe_run, save_logs, _prep_out_files
+from ..._run import failsafe_run, save_logs, _prep_out_files, _update_for_splits
 from ..._report import (
     _open_report,
     _contrasts_to_names,
@@ -68,6 +68,7 @@ def get_input_fnames_epochs_decoding(
     )
     in_files = dict()
     in_files["epochs"] = fname_epochs
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -89,7 +90,7 @@ def run_epochs_decoding(
     msg = f"Contrasting conditions: {condition1} – {condition2}"
     logger.info(**gen_log_kwargs(message=msg))
     out_files = dict()
-    bids_path = in_files["epochs"].copy()
+    bids_path = in_files["epochs"].copy().update(split=None)
 
     epochs = mne.read_epochs(in_files.pop("epochs"))
     _restrict_analyze_channels(epochs, cfg)

mne_bids_pipeline/steps/sensor/_03_decoding_time_by_time.py

@@ -38,7 +38,7 @@
 )
 from ..._decoding import LogReg
 from ..._logging import gen_log_kwargs, logger
-from ..._run import failsafe_run, save_logs, _prep_out_files
+from ..._run import failsafe_run, save_logs, _prep_out_files, _update_for_splits
 from ..._parallel import get_parallel_backend, get_parallel_backend_name
 from ..._report import (
     _open_report,
@@ -73,6 +73,7 @@ def get_input_fnames_time_decoding(
     )
     in_files = dict()
     in_files["epochs"] = fname_epochs
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -98,7 +99,7 @@ def run_time_decoding(
     msg = f"Contrasting conditions ({kind}): {condition1} – {condition2}"
     logger.info(**gen_log_kwargs(message=msg))
     out_files = dict()
-    bids_path = in_files["epochs"].copy()
+    bids_path = in_files["epochs"].copy().update(split=None)
 
     epochs = mne.read_epochs(in_files.pop("epochs"))
     _restrict_analyze_channels(epochs, cfg)

mne_bids_pipeline/steps/sensor/_04_time_frequency.py

@@ -22,7 +22,7 @@
     _restrict_analyze_channels,
 )
 from ..._logging import gen_log_kwargs, logger
-from ..._run import failsafe_run, save_logs, _prep_out_files
+from ..._run import failsafe_run, save_logs, _prep_out_files, _update_for_splits
 from ..._parallel import get_parallel_backend, parallel_func
 from ..._report import _open_report, _sanitize_cond_tag
 
@@ -53,6 +53,7 @@ def get_input_fnames_time_frequency(
     )
     in_files = dict()
     in_files["epochs"] = fname_epochs
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -73,7 +74,7 @@ def run_time_frequency(
     msg = f"Reading {epochs_path.basename}"
     logger.info(**gen_log_kwargs(message=msg))
     epochs = mne.read_epochs(epochs_path)
-    bids_path = epochs_path.copy().update(processing=None)
+    bids_path = epochs_path.copy().update(processing=None, split=None)
     del epochs_path
     _restrict_analyze_channels(epochs, cfg)
 

mne_bids_pipeline/steps/sensor/_05_decoding_csp.py

@@ -27,7 +27,7 @@
 from ..._decoding import LogReg, _handle_csp_args
 from ..._logging import logger, gen_log_kwargs
 from ..._parallel import parallel_func, get_parallel_backend
-from ..._run import failsafe_run, save_logs, _prep_out_files
+from ..._run import failsafe_run, save_logs, _prep_out_files, _update_for_splits
 from ..._report import (
     _open_report,
     _sanitize_cond_tag,
@@ -132,6 +132,7 @@ def get_input_fnames_csp(
     )
     in_files = dict()
     in_files["epochs"] = fname_epochs
+    _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 
@@ -157,7 +158,7 @@ def one_subject_decoding(
     msg = f"Contrasting conditions: {condition1} – {condition2}"
     logger.info(**gen_log_kwargs(msg))
 
-    bids_path = in_files["epochs"].copy().update(processing=None)
+    bids_path = in_files["epochs"].copy().update(processing=None, split=None)
     epochs = mne.read_epochs(in_files.pop("epochs"))
     _restrict_analyze_channels(epochs, cfg)
 

mne_bids_pipeline/steps/sensor/_06_make_cov.py

@@ -20,7 +20,13 @@
 from ..._logging import gen_log_kwargs, logger
 from ..._parallel import get_parallel_backend, parallel_func
 from ..._report import _open_report, _sanitize_cond_tag, _all_conditions
-from ..._run import failsafe_run, save_logs, _sanitize_callable, _prep_out_files
+from ..._run import (
+    failsafe_run,
+    save_logs,
+    _sanitize_callable,
+    _prep_out_files,
+    _update_for_splits,
+)
 
 
 def get_input_fnames_cov(
@@ -47,9 +53,8 @@ def get_input_fnames_cov(
         root=cfg.deriv_root,
         check=False,
     )
-    in_files["report_info"] = fname_epochs.copy().update(
-        processing="clean", suffix="epo"
-    )
+    in_files["report_info"] = fname_epochs.copy().update(processing="clean")
+    _update_for_splits(in_files, "report_info", single=True)
     fname_evoked = fname_epochs.copy().update(
         suffix="ave", processing=None, check=False
     )
@@ -83,6 +88,7 @@ def get_input_fnames_cov(
     else:
         assert cov_type == "epochs", cov_type
         in_files["epochs"] = fname_epochs
+        _update_for_splits(in_files, "epochs", single=True)
     return in_files
 
 

mne_bids_pipeline/tests/configs/config_ds000248_base.py

@@ -26,6 +26,8 @@
 def noise_cov(bp):
     # Use pre-stimulus period as noise source
     bp = bp.copy().update(processing="clean", suffix="epo")
+    if not bp.fpath.exists():
+        bp.update(split="01")
     epo = mne.read_epochs(bp)
     cov = mne.compute_covariance(epo, rank="info", tmax=0)
     return cov