fix: E722, E701, F401, F507 lint errors and configure suppressions

- E722: Replace 55 bare `except:` with `except Exception:` (32 files)
- E701: Split 29 single-line compound statements onto separate lines
- F401: Add `__all__` to 5 `__init__.py` re-export files, noqa 2 keras
  availability checks
- F507: Fix format string placeholder mismatch in glif_optimizer_neuron
- Configure ruff and flake8 to suppress E402, E741, F403, F405

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: galenlynch

.flake8

@@ -1,2 +1,9 @@
 [flake8]
-extend-ignore = E203
+max-line-length = 120
+extend-ignore =
+    E203,
+    E402,
+    E741,
+    F403,
+    F405,
+    W503

allensdk/api/queries/biophysical_api.py

@@ -237,7 +237,7 @@ def is_well_known_file_type(self, wkf, name):
         '''
         try:
             return wkf['well_known_file_type']['name'] == name
-        except:
+        except Exception:
             return False
 
     def get_well_known_file_ids(self, neuronal_model_id):

allensdk/api/queries/cell_types_api.py

@@ -361,7 +361,7 @@ def save_reconstruction(self, specimen_id, file_name):
         try:
             file_url = results[0]['neuron_reconstructions'][
                 0]['well_known_files'][0]['download_link']
-        except:
+        except Exception:
             raise Exception("Specimen %d has no reconstruction" % specimen_id)
 
         self.retrieve_file_over_http(self.api_url + file_url, file_name)
@@ -394,7 +394,7 @@ def save_reconstruction_markers(self, specimen_id, file_name):
         try:
             file_url = results[0]['neuron_reconstructions'][
                 0]['well_known_files'][0]['download_link']
-        except:
+        except Exception:
             raise LookupError("Specimen %d has no marker file" % specimen_id)
 
         self.retrieve_file_over_http(self.api_url + file_url, file_name)

allensdk/brain_observatory/brain_observatory_exceptions.py

@@ -33,11 +33,14 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 #
-class BrainObservatoryAnalysisException(Exception): pass
+class BrainObservatoryAnalysisException(Exception):
+    pass
 
-class MissingStimulusException(Exception): pass
+class MissingStimulusException(Exception):
+    pass
 
-class NoEyeTrackingException(Exception): pass
+class NoEyeTrackingException(Exception):
+    pass
 
 class EpochSeparationException(Exception):
 

allensdk/brain_observatory/brain_observatory_plotting.py

@@ -59,7 +59,7 @@ def plot_drifting_grating_traces(dg, save_dir):
                 (blank[str(nc)].std() / len(blank[str(nc)]))
             blank_n = blank[str(nc)].mean() - \
                 (blank[str(nc)].std() / len(blank[str(nc)]))
-        except:
+        except Exception:
             blank_p = blank.iloc[:, nc].apply(
                 np.mean) + (blank.iloc[:, nc].apply(np.std) / blank.iloc[:, nc].apply(len))
             blank_n = blank.iloc[:, nc].apply(
@@ -76,7 +76,7 @@ def plot_drifting_grating_traces(dg, save_dir):
                     ) + (subset_response[str(nc)][:-1].std() / len(subset_response[str(nc)]))
                     subset_response_n = subset_response[str(nc)].mean(
                     ) - (subset_response[str(nc)][:-1].std() / len(subset_response[str(nc)]))
-                except:
+                except Exception:
                     subset_response_p = subset_response.iloc[:, nc].apply(
                         np.mean) + (subset_response.iloc[:, nc].apply(np.std) / subset_response.iloc[:, nc].apply(len))
                     subset_response_n = subset_response.iloc[:, nc].apply(
@@ -87,17 +87,17 @@ def plot_drifting_grating_traces(dg, save_dir):
                 try:
                     ax.fill_between(xtime, subset_response_p,
                                     subset_response_n, color='b', alpha=0.5)
-                except:
+                except Exception:
                     pass
                 try:
                     ax.fill_between(xtime, blank_p, blank_n,
                                     color='k', alpha=0.5)
-                except:
+                except Exception:
                     pass
                 try:
                     ax.plot(xtime, subset_response[
                             str(nc)].mean(), color='b', lw=2)
-                except:
+                except Exception:
                     pass
                 ax.plot(xtime, subset_response[
                         str(nc)].mean(), color='b', lw=2)
@@ -162,7 +162,7 @@ def plot_ns_traces(nsa, save_dir):
             try:
                 ax.fill_between(xtime, subset_response_p,
                                 subset_response_n, color='b', alpha=0.5)
-            except:
+            except Exception:
                 xtime = xtime[:-1]
                 ax.fill_between(xtime, subset_response_p,
                                 subset_response_n, color='b', alpha=0.5)
@@ -762,7 +762,7 @@ def _plot_3sb(sg, nm1, ns, save_dir):
         ) - (subset[str(nc)].std() / np.sqrt(len(subset[str(nc)])))
         try:
             ax13.fill_between(xtime, subset_p, subset_n, color='b', alpha=0.5)
-        except:
+        except Exception:
             xtime = xtime[:-1]
             ax13.fill_between(xtime, subset_p, subset_n, color='b', alpha=0.5)
         blank = sg.sweep_response[(sg.stim_table.orientation == 0) & (
@@ -860,7 +860,7 @@ def _plot_3sb(sg, nm1, ns, save_dir):
         try:
             ax12.fill_between(xtime, subset_response_p,
                               subset_response_n, color='b', alpha=0.5)
-        except:
+        except Exception:
             xtime = xtime[:-1]
             ax12.fill_between(xtime, subset_response_p,
                               subset_response_n, color='b', alpha=0.5)

allensdk/brain_observatory/ecephys/ecephys_project_api/__init__.py

@@ -2,3 +2,11 @@
 from .ecephys_project_lims_api import EcephysProjectLimsApi
 from .ecephys_project_warehouse_api import EcephysProjectWarehouseApi
 from .ecephys_project_fixed_api import EcephysProjectFixedApi, MissingDataError
+
+__all__ = [
+    "EcephysProjectApi",
+    "EcephysProjectLimsApi",
+    "EcephysProjectWarehouseApi",
+    "EcephysProjectFixedApi",
+    "MissingDataError",
+]

allensdk/brain_observatory/ecephys/ecephys_session_api/__init__.py

@@ -1,3 +1,9 @@
 from .ecephys_session_api import EcephysSessionApi
 from .ecephys_nwb_session_api import EcephysNwbSessionApi
-from .ecephys_nwb1_session_api import EcephysNwb1Api
+from .ecephys_nwb1_session_api import EcephysNwb1Api
+
+__all__ = [
+    "EcephysSessionApi",
+    "EcephysNwbSessionApi",
+    "EcephysNwb1Api",
+]

allensdk/brain_observatory/ecephys/stimulus_analysis/__init__.py

@@ -4,4 +4,14 @@
 from .flashes import Flashes
 from .dot_motion import DotMotion
 from .natural_movies import NaturalMovies
-from .receptive_field_mapping import ReceptiveFieldMapping
+from .receptive_field_mapping import ReceptiveFieldMapping
+
+__all__ = [
+    "StaticGratings",
+    "NaturalScenes",
+    "DriftingGratings",
+    "Flashes",
+    "DotMotion",
+    "NaturalMovies",
+    "ReceptiveFieldMapping",
+]

allensdk/brain_observatory/observatory_plots.py

@@ -196,7 +196,8 @@ def plot_representational_similarity(rs, dims=None, dim_labels=None, colors=None
                          cbar_size="7%",
                          cbar_pad=0.05)
 
-        for ax in grid: pass
+        for ax in grid:
+            pass
     else:
         ax = plt.gca()
 

allensdk/brain_observatory/receptive_field_analysis/fitgaussian2D.py

@@ -37,7 +37,8 @@
 from scipy import optimize
 
 
-class GaussianFitError(RuntimeError): pass
+class GaussianFitError(RuntimeError):
+    pass
 
 
 def gaussian2D(height, center_x, center_y, width_x, width_y, rotation):