[pre-commit.ci] pre-commit autoupdate (#38)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.5.0](astral-sh/ruff-pre-commit@v0.3.5...v0.5.0) - [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](codespell-project/codespell@v2.2.6...v2.3.0) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rm architecture constraint * fix ruff --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mscheltienne <mathieu.scheltienne@fcbg.ch>
mscheltienne · Jul 2, 2024 · 8931105 · 8931105
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commit 8931105
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diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -32,7 +32,6 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          architecture: 'x64'
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ repos:
             files: eeg_flow
 
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.3.5
+      rev: v0.5.0
       hooks:
           - id: ruff
             name: ruff linter
@@ -20,7 +20,7 @@ repos:
             files: eeg_flow
 
     - repo: https://github.com/codespell-project/codespell
-      rev: v2.2.6
+      rev: v2.3.0
       hooks:
           - id: codespell
             args: [--write-changes]

diff --git a/eeg_flow/tasks/__init__.py b/eeg_flow/tasks/__init__.py
@@ -7,10 +7,10 @@
 )
 from .convert_xdf_to_fiff import convert_xdf_to_fiff  # noqa: F401
 from .create_behavioral_metadata import create_behavioral_metadata  # noqa: F401
-from .epochs_evoked import ( # noqa: F401
+from .epochs_evoked import (  # noqa: F401
     create_epochs_evoked_and_behavioral_metadata,
-    response_to_CSD
-)  
+    response_to_CSD,
+)
 from .ica_decomposition import (  # noqa: F401
     apply_ica,
     compare_labels,

diff --git a/eeg_flow/tasks/epochs_evoked.py b/eeg_flow/tasks/epochs_evoked.py
@@ -39,10 +39,11 @@
 
 _TOO_QUICK_THRESHOLD: float = 0.2
 
+
 def response_to_CSD(
     participant: str,
     group: str,
-    task: str,  
+    task: str,
     run: int,
     BC_response: str,
     *,
@@ -66,12 +67,14 @@ def response_to_CSD(
         derivatives_folder_root, participant, group, task, run
     )
 
-     # lock the output derivative files
+    # lock the output derivative files
     # create locks
-    #"400200resp","2000resp","400200resp_CSD","2000resp_CSD"
+    # "400200resp","2000resp","400200resp_CSD","2000resp_CSD"
     derivatives = [
-        derivatives_folder / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-cleaned-epo.fif",
-        derivatives_folder / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-ave.fif",
+        derivatives_folder
+        / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-cleaned-epo.fif",
+        derivatives_folder
+        / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-ave.fif",
     ]
 
     locks = lock_files(*derivatives, timeout=timeout)
@@ -82,23 +85,30 @@ def response_to_CSD(
 
         # load previous steps (normal epoching)
         epochs = read_epochs(
-            derivatives_folder / f"{fname_stem}_step8_responselocked-{BC_response}-cleaned-epo.fif",
+            derivatives_folder
+            / f"{fname_stem}_step8_responselocked-{BC_response}-cleaned-epo.fif",
+        )
+        epochs_CSD = compute_current_source_density(
+            epochs.interpolate_bads(), stiffness=3, n_legendre_terms=15, verbose=100
         )
-        epochs_CSD = compute_current_source_density(epochs.interpolate_bads(), stiffness=3, n_legendre_terms=15, verbose=100)
 
         evoked = read_evokeds(
-            derivatives_folder / f"{fname_stem}_step8_responselocked-{BC_response}-ave.fif",
+            derivatives_folder
+            / f"{fname_stem}_step8_responselocked-{BC_response}-ave.fif",
         )[0]
-        evoked_CSD = compute_current_source_density(evoked.interpolate_bads(), stiffness=3, n_legendre_terms=15, verbose=100)
-
+        evoked_CSD = compute_current_source_density(
+            evoked.interpolate_bads(), stiffness=3, n_legendre_terms=15, verbose=100
+        )
+
         # save epochs, drop-log and evoked files
         if epochs_CSD is not None and evoked_CSD is not None:
             epochs_CSD.save(
                 derivatives_folder
-                / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-cleaned-epo.fif"
+                / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-cleaned-epo.fif"  # noqa: E501
             )
             evoked_CSD.save(
-                derivatives_folder / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-ave.fif"
+                derivatives_folder
+                / f"{fname_stem}_step8b_responselocked-{BC_response}_CSD-ave.fif"
             )
 
     except FileNotFoundError:
@@ -181,16 +191,21 @@ def create_epochs_evoked_and_behavioral_metadata(
         derivatives_folder / f"{fname_stem}_step8_responselocked-ave.fif",
     ]
 
-    window_response_bc = ["400200resp","2000resp"]
+    window_response_bc = ["400200resp", "2000resp"]
     for window in window_response_bc:
-        derivatives.extend([derivatives_folder / f"{fname_stem}_step8_responselocked-{window}-cleaned-epo.fif",
-        derivatives_folder
-        / "plots"
-        / f"{fname_stem}_step8_responselocked-{window}-epochs-rejected.svg",
-        derivatives_folder
-        / f"{fname_stem}_step8_responselocked-{window}-cleaned-epo-drop-log.csv",
-        derivatives_folder / f"{fname_stem}_step8_responselocked-{window}-ave.fif",
-    ])
+        derivatives.extend(
+            [
+                derivatives_folder
+                / f"{fname_stem}_step8_responselocked-{window}-cleaned-epo.fif",
+                derivatives_folder
+                / "plots"
+                / f"{fname_stem}_step8_responselocked-{window}-epochs-rejected.svg",
+                derivatives_folder
+                / f"{fname_stem}_step8_responselocked-{window}-cleaned-epo-drop-log.csv",  # noqa: E501
+                derivatives_folder
+                / f"{fname_stem}_step8_responselocked-{window}-ave.fif",
+            ]
+        )
 
     locks = lock_files(*derivatives, timeout=timeout)
 
@@ -217,21 +232,18 @@ def create_epochs_evoked_and_behavioral_metadata(
             fig_drops_response,
             count_stim_before_response,
             count_stim_after_response,
-
             epochs_response_400200resp,
             evoked_response_400200resp,
             drop_reasons_response_400200resp,
             fig_drops_response_400200resp,
             count_stim_before_response_400200resp,
             count_stim_after_response_400200resp,
-
             epochs_response_2000resp,
             evoked_response_2000resp,
             drop_reasons_response_2000resp,
             fig_drops_response_2000resp,
             count_stim_before_response_2000resp,
             count_stim_after_response_2000resp,
-
         ) = _create_epochs_evoked_and_behavioral_metadata(raw)
 
         # save epochs, drop-log and evoked files
@@ -290,14 +302,18 @@ def create_epochs_evoked_and_behavioral_metadata(
                     ",Total,Rejected,Bad,PTP\n"
                     f"Response,{count_stim_before_response[64]},{count_stim_before_response[64] - count_stim_after_response[64]},{drop_reasons_response['response']['bad_segment']},{drop_reasons_response['response']['ptp']}\n"  # noqa: E501
                 )
-
-        if epochs_response_400200resp is not None and evoked_response_400200resp is not None:
+
+        if (
+            epochs_response_400200resp is not None
+            and evoked_response_400200resp is not None
+        ):
             epochs_response_400200resp.save(
                 derivatives_folder
                 / f"{fname_stem}_step8_responselocked-400200resp-cleaned-epo.fif"
             )
             evoked_response_400200resp.save(
-                derivatives_folder / f"{fname_stem}_step8_responselocked-400200resp-ave.fif"
+                derivatives_folder
+                / f"{fname_stem}_step8_responselocked-400200resp-ave.fif"
             )
             fig_drops_response_400200resp.get_axes()[0].set_title(
                 f"{fname_stem}: {fig_drops.get_axes()[0].get_title()}"
@@ -310,20 +326,24 @@ def create_epochs_evoked_and_behavioral_metadata(
             )
             with open(
                 derivatives_folder
-                / f"{fname_stem}_step8_responselocked-400200resp-cleaned-epo-drop-log.csv",
+                / f"{fname_stem}_step8_responselocked-400200resp-cleaned-epo-drop-log.csv",  # noqa: E501
                 "w",
             ) as file:
                 file.write(
                     ",Total,Rejected,Bad,PTP\n"
                     f"Response,{count_stim_before_response_400200resp[64]},{count_stim_before_response_400200resp[64] - count_stim_after_response_400200resp[64]},{drop_reasons_response_400200resp['response']['bad_segment']},{drop_reasons_response_400200resp['response']['ptp']}\n"  # noqa: E501
                 )
-        if epochs_response_2000resp is not None and evoked_response_2000resp is not None:
+        if (
+            epochs_response_2000resp is not None
+            and evoked_response_2000resp is not None
+        ):
             epochs_response_2000resp.save(
                 derivatives_folder
                 / f"{fname_stem}_step8_responselocked-2000resp-cleaned-epo.fif"
             )
             evoked_response_2000resp.save(
-                derivatives_folder / f"{fname_stem}_step8_responselocked-2000resp-ave.fif"
+                derivatives_folder
+                / f"{fname_stem}_step8_responselocked-2000resp-ave.fif"
             )
             fig_drops_response_2000resp.get_axes()[0].set_title(
                 f"{fname_stem}: {fig_drops.get_axes()[0].get_title()}"
@@ -336,13 +356,13 @@ def create_epochs_evoked_and_behavioral_metadata(
             )
             with open(
                 derivatives_folder
-                / f"{fname_stem}_step8_responselocked-2000resp-cleaned-epo-drop-log.csv",
+                / f"{fname_stem}_step8_responselocked-2000resp-cleaned-epo-drop-log.csv",  # noqa: E501
                 "w",
             ) as file:
                 file.write(
                     ",Total,Rejected,Bad,PTP\n"
                     f"Response,{count_stim_before_response_2000resp[64]},{count_stim_before_response_2000resp[64] - count_stim_after_response_2000resp[64]},{drop_reasons_response_2000resp['response']['bad_segment']},{drop_reasons_response_2000resp['response']['ptp']}\n"  # noqa: E501
-                )  
+                )
 
     except FileNotFoundError:
         logger.error(
@@ -393,14 +413,12 @@ def _create_epochs_evoked_and_behavioral_metadata(
     plt.Figure,
     Counter,
     Counter,
-
     Optional[Epochs],
     Optional[Evoked],
     dict[str, dict[str, int]],
     plt.Figure,
     Counter,
     Counter,
-
     Optional[Epochs],
     Optional[Evoked],
     dict[str, dict[str, int]],
@@ -487,7 +505,7 @@ def _create_epochs_evoked_and_behavioral_metadata(
             fig_drops_response,
         ) = _drop_bad_epochs(epochs_response, events_response, reject, response=True)
 
-        #redo for other baseline correction
+        # redo for other baseline correction
         epochs_response_400200resp = Epochs(
             raw=raw,
             tmin=-0.4,
@@ -507,9 +525,11 @@ def _create_epochs_evoked_and_behavioral_metadata(
             count_stim_after_response_400200resp,
             drop_reasons_response_400200resp,
             fig_drops_response_400200resp,
-        ) = _drop_bad_epochs(epochs_response_400200resp, events_response, reject, response=True)
+        ) = _drop_bad_epochs(
+            epochs_response_400200resp, events_response, reject, response=True
+        )
 
-        #redo for other baseline correction
+        # redo for other baseline correction
         epochs_response_2000resp = Epochs(
             raw=raw,
             tmin=-0.2,
@@ -529,7 +549,9 @@ def _create_epochs_evoked_and_behavioral_metadata(
             count_stim_after_response_2000resp,
             drop_reasons_response_2000resp,
             fig_drops_response_2000resp,
-        ) = _drop_bad_epochs(epochs_response_2000resp, events_response, reject, response=True)
+        ) = _drop_bad_epochs(
+            epochs_response_2000resp, events_response, reject, response=True
+        )
 
     else:
         metadata = None
@@ -575,22 +597,25 @@ def _create_epochs_evoked_and_behavioral_metadata(
         fig_drops_response,
         count_stim_before_response,
         count_stim_after_response,
-
         epochs_response_400200resp,
-        None if epochs_response_400200resp is None else epochs_response_400200resp.average(),
+        None
+        if epochs_response_400200resp is None
+        else epochs_response_400200resp.average(),
         drop_reasons_response_400200resp,
         fig_drops_response_400200resp,
         count_stim_before_response_400200resp,
         count_stim_after_response_400200resp,
-
         epochs_response_2000resp,
-        None if epochs_response_2000resp is None else epochs_response_2000resp.average(),
+        None
+        if epochs_response_2000resp is None
+        else epochs_response_2000resp.average(),
         drop_reasons_response_2000resp,
         fig_drops_response_2000resp,
         count_stim_before_response_2000resp,
-        count_stim_after_response_2000resp,       
+        count_stim_after_response_2000resp,
     )
 
+
 def _make_metadata(
     events: NDArray[+ScalarIntType],
     events_id: dict[str, int],

diff --git a/eeg_flow/utils/_checks.py b/eeg_flow/utils/_checks.py
@@ -40,7 +40,7 @@ def ensure_int(item: Any, item_name: Optional[str] = None) -> int:
             raise TypeError
         item = int(operator.index(item))
     except TypeError:
-        item_name = "Item" if item_name is None else "'%s'" % item_name
+        item_name = "Item" if item_name is None else f"'{item_name}'"
         raise TypeError(f"{item_name} must be an integer, got {type(item)} instead.")
 
     return item
@@ -119,7 +119,7 @@ def check_type(item: Any, types: tuple, item_name: Optional[str] = None) -> None
         else:
             type_name[-1] = "or " + type_name[-1]
             type_name = ", ".join(type_name)
-        item_name = "Item" if item_name is None else "'%s'" % item_name
+        item_name = "Item" if item_name is None else f"'{item_name}'"
         raise TypeError(
             f"{item_name} must be an instance of {type_name}, got {type(item)} instead."
         )
@@ -150,15 +150,15 @@ def check_value(
         When the value of the item is not one of the valid options.
     """
     if item not in allowed_values:
-        item_name = "" if item_name is None else " '%s'" % item_name
+        item_name = "" if item_name is None else f" '{item_name}'"
         extra = "" if extra is None else " " + extra
         msg = (
             "Invalid value for the{item_name} parameter{extra}. "
             "{options}, but got {item!r} instead."
         )
         allowed_values = tuple(allowed_values)  # e.g., if a dict was given
         if len(allowed_values) == 1:
-            options = "The only allowed value is %s" % repr(allowed_values[0])
+            options = f"The only allowed value is {repr(allowed_values[0])}"
         elif len(allowed_values) == 2:
             options = (
                 f"Allowed values are {repr(allowed_values[0])} "