Switch to absolute imports and ensure the Ruff (linter and formatter)…

… exclude patterns are correctly represented in `pyproject.toml` (#969)

.pre-commit-config.yaml

@@ -1,9 +1,5 @@
 ---
 files: ^(.*\.(py|yaml))$
-# We need to match the exclude list in pyproject.toml because pre-commit.ci
-# passes filenames and these do not get passed through the tool.black filter
-# for example
-exclude: ^(\.[^/]*cache/.*|.*/freesurfer/contrib/.*)$
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.5.4

docs/source/changes.md

@@ -1,3 +1,5 @@
+{% include-markdown "./v1.10.md.inc" %}
+
 {% include-markdown "./v1.9.md.inc" %}
 
 {% include-markdown "./v1.8.md.inc" %}

docs/source/v1.10.md.inc

@@ -0,0 +1,21 @@
+## v1.10.0 (unreleased)
+
+[//]: # (### :new: New features & enhancements)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :warning: Behavior changes)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :package: Requirements)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+[//]: # (### :bug: Bug fixes)
+
+[//]: # (- Whatever (#000 by @whoever))
+
+### :medical_symbol: Code health
+
+- Switch from using relative to using absolute imports (#969 by @hoechenberger)

mne_bids_pipeline/steps/freesurfer/_01_recon_all.py

@@ -11,9 +11,9 @@
 
 from mne.utils import run_subprocess
 
-from ..._config_utils import get_fs_subjects_dir, get_subjects
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._config_utils import get_fs_subjects_dir, get_subjects
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
 
 fs_bids_app = Path(__file__).parent / "contrib" / "run.py"
 

mne_bids_pipeline/steps/freesurfer/_02_coreg_surfaces.py

@@ -10,14 +10,14 @@
 
 import mne.bem
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     get_fs_subject,
     get_fs_subjects_dir,
     get_subjects,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._run import _prep_out_files, failsafe_run
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._run import _prep_out_files, failsafe_run
 
 fs_bids_app = Path(__file__).parent / "contrib" / "run.py"
 

mne_bids_pipeline/steps/init/_01_init_derivatives_dir.py

@@ -9,9 +9,9 @@
 from mne_bids.config import BIDS_VERSION
 from mne_bids.utils import _write_json
 
-from ..._config_utils import _bids_kwargs, get_sessions, get_subjects
-from ..._logging import gen_log_kwargs, logger
-from ..._run import _prep_out_files, failsafe_run
+from mne_bids_pipeline._config_utils import _bids_kwargs, get_sessions, get_subjects
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._run import _prep_out_files, failsafe_run
 
 
 @failsafe_run()

mne_bids_pipeline/steps/init/_02_find_empty_room.py

@@ -4,18 +4,23 @@
 
 from mne_bids import BIDSPath
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _bids_kwargs,
     _pl,
     get_datatype,
     get_mf_reference_run,
     get_sessions,
     get_subjects,
 )
-from ..._import_data import _empty_room_match_path
-from ..._io import _write_json
-from ..._logging import gen_log_kwargs, logger
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._import_data import _empty_room_match_path
+from mne_bids_pipeline._io import _write_json
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 def get_input_fnames_find_empty_room(

mne_bids_pipeline/steps/preprocessing/_01_data_quality.py

@@ -5,7 +5,7 @@
 import mne
 import pandas as pd
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _do_mf_autobad,
     _pl,
     get_mf_cal_fname,
@@ -14,7 +14,7 @@
     get_sessions,
     get_subjects,
 )
-from ..._import_data import (
+from mne_bids_pipeline._import_data import (
     _bads_path,
     _get_mf_reference_run_path,
     _get_run_rest_noise_path,
@@ -23,12 +23,12 @@
     import_er_data,
     import_experimental_data,
 )
-from ..._io import _write_json
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _add_raw, _open_report
-from ..._run import _prep_out_files, failsafe_run, save_logs
-from ..._viz import plot_auto_scores
+from mne_bids_pipeline._io import _write_json
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _add_raw, _open_report
+from mne_bids_pipeline._run import _prep_out_files, failsafe_run, save_logs
+from mne_bids_pipeline._viz import plot_auto_scores
 
 
 def get_input_fnames_data_quality(

mne_bids_pipeline/steps/preprocessing/_02_head_pos.py

@@ -4,20 +4,16 @@
 
 import mne
 
-from ..._config_utils import (
-    get_runs_tasks,
-    get_sessions,
-    get_subjects,
-)
-from ..._import_data import (
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._import_data import (
     _get_run_rest_noise_path,
     _import_data_kwargs,
     import_experimental_data,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _open_report
-from ..._run import _prep_out_files, failsafe_run, save_logs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _open_report
+from mne_bids_pipeline._run import _prep_out_files, failsafe_run, save_logs
 
 
 def get_input_fnames_head_pos(

mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py

@@ -22,26 +22,31 @@
 import numpy as np
 from mne_bids import read_raw_bids
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _pl,
     get_mf_cal_fname,
     get_mf_ctc_fname,
     get_runs_tasks,
     get_sessions,
     get_subjects,
 )
-from ..._import_data import (
+from mne_bids_pipeline._import_data import (
     _get_mf_reference_run_path,
     _get_run_path,
     _get_run_rest_noise_path,
     _import_data_kwargs,
     import_er_data,
     import_experimental_data,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _add_raw, _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _add_raw, _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 # %% eSSS

mne_bids_pipeline/steps/preprocessing/_04_frequency_filter.py

@@ -23,22 +23,23 @@
 from mne.io.pick import _picks_to_idx
 from mne.preprocessing import EOGRegression
 
-from ..._config_utils import (
-    get_runs_tasks,
-    get_sessions,
-    get_subjects,
-)
-from ..._import_data import (
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._import_data import (
     _get_run_rest_noise_path,
     _import_data_kwargs,
     _read_raw_msg,
     import_er_data,
     import_experimental_data,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _add_raw, _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _add_raw, _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 def get_input_fnames_frequency_filter(

mne_bids_pipeline/steps/preprocessing/_05_regress_artifact.py

@@ -6,16 +6,21 @@
 from mne.io.pick import _picks_to_idx
 from mne.preprocessing import EOGRegression
 
-from ..._config_utils import (
-    get_runs_tasks,
-    get_sessions,
-    get_subjects,
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._import_data import (
+    _get_run_rest_noise_path,
+    _import_data_kwargs,
+    _read_raw_msg,
+)
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _add_raw, _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
 )
-from ..._import_data import _get_run_rest_noise_path, _import_data_kwargs, _read_raw_msg
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _add_raw, _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
 
 
 def get_input_fnames_regress_artifact(

mne_bids_pipeline/steps/preprocessing/_06a1_fit_ica.py

@@ -17,19 +17,24 @@
 from mne.preprocessing import ICA
 from mne_bids import BIDSPath
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
     get_sessions,
     get_subjects,
 )
-from ..._import_data import annotations_to_events, make_epochs
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._reject import _get_reject
-from ..._report import _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._import_data import annotations_to_events, make_epochs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._reject import _get_reject
+from mne_bids_pipeline._report import _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 def get_input_fnames_run_ica(

mne_bids_pipeline/steps/preprocessing/_06a2_find_ica_artifacts.py

@@ -16,17 +16,22 @@
 from mne.preprocessing import create_ecg_epochs, create_eog_epochs
 from mne_bids import BIDSPath
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
     get_sessions,
     get_subjects,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 def detect_bad_components(

mne_bids_pipeline/steps/preprocessing/_06b_run_ssp.py

@@ -12,19 +12,24 @@
 from mne.preprocessing import find_ecg_events, find_eog_events
 from mne_bids import BIDSPath
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _bids_kwargs,
     _pl,
     _proj_path,
     get_runs,
     get_sessions,
     get_subjects,
 )
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._reject import _get_reject
-from ..._report import _open_report
-from ..._run import _prep_out_files, _update_for_splits, failsafe_run, save_logs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._reject import _get_reject
+from mne_bids_pipeline._report import _open_report
+from mne_bids_pipeline._run import (
+    _prep_out_files,
+    _update_for_splits,
+    failsafe_run,
+    save_logs,
+)
 
 
 def _find_ecg_events(raw: mne.io.Raw, ch_name: str | None) -> np.ndarray:

mne_bids_pipeline/steps/preprocessing/_07_make_epochs.py

@@ -13,18 +13,18 @@
 import mne
 from mne_bids import BIDSPath
 
-from ..._config_utils import (
+from mne_bids_pipeline._config_utils import (
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
     get_sessions,
     get_subjects,
 )
-from ..._import_data import annotations_to_events, make_epochs
-from ..._logging import gen_log_kwargs, logger
-from ..._parallel import get_parallel_backend, parallel_func
-from ..._report import _open_report
-from ..._run import (
+from mne_bids_pipeline._import_data import annotations_to_events, make_epochs
+from mne_bids_pipeline._logging import gen_log_kwargs, logger
+from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
+from mne_bids_pipeline._report import _open_report
+from mne_bids_pipeline._run import (
     _prep_out_files,
     _sanitize_callable,
     _update_for_splits,