MNT: Fix flake8 errors

.flake8

@@ -8,4 +8,5 @@ max-line-length = 99
 extend-ignore = E203,E402,F401,D100,D101,D102,D103,D104,D105,D106,D107,D200
 docstring-convention = numpy
 # Ignore missing docstrings within unit testing functions.
-per-file-ignores = **/tests/:D100,D101,D102,D103,D104,D105,D106,D107
+# Ignore C420 Unnecessary dict comprehension
+per-file-ignores = **/tests/:D100,D101,D102,D103,D104,D105,D106,D107,C420

docs/examples/SIMA example.ipynb

@@ -76,7 +76,7 @@
     "sequences = [sima.Sequence.create(\"TIFF\", tiff) for tiff in tiffs[:1]]\n",
     "try:\n",
     "    dataset = sima.ImagingDataset(sequences, \"example.sima\")\n",
-    "except BaseException:\n",
+    "except Exception:\n",
     "    dataset = sima.ImagingDataset.load(\"example.sima\")"
    ]
   },

examples/SIMA example.ipynb

@@ -76,7 +76,7 @@
     "sequences = [sima.Sequence.create(\"TIFF\", tiff) for tiff in tiffs[:1]]\n",
     "try:\n",
     "    dataset = sima.ImagingDataset(sequences, \"example.sima\")\n",
-    "except BaseException:\n",
+    "except Exception:\n",
     "    dataset = sima.ImagingDataset.load(\"example.sima\")"
    ]
   },

fissa/core.py

@@ -383,7 +383,9 @@ def separate_trials(
             message_extra = " for ROI {}".format(label)
         warnings.warn(
             "{}Found values below zero in raw signal{}. Offsetting so minimum is 0."
-            "".format(header, message_extra)
+            "".format(header, message_extra),
+            UserWarning,
+            stacklevel=2,
         )
         X -= X.min()
 
@@ -1177,7 +1179,7 @@ def separation_prep(self, redo=False):
                 self.load(fname)
                 if self.raw is not None:
                     return
-            except BaseException as err:
+            except Exception as err:
                 print("An error occurred while loading {}".format(fname))
                 print(err)
                 print("Extraction will be redone and {} overwritten".format(fname))
@@ -1379,7 +1381,7 @@ def separate(self, redo_prep=False, redo_sep=False):
                 self.load(fname)
                 if self.result is not None:
                     return
-            except BaseException as err:
+            except Exception as err:
                 print("An error occurred while loading {}".format(fname))
                 print(err)
                 print(
@@ -1859,6 +1861,7 @@ def save_to_matlab(self, fname=None):
             "The experiment.save_to_matlab() method is deprecated."
             " Please use experiment.to_matfile() instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
         return self.to_matfile(fname=fname, legacy=True)
 

fissa/extraction.py

@@ -191,15 +191,19 @@ def image2array(image):
                         " with {} dimensions (page shaped {})."
                         " All dimensions before the final two (height and"
                         " width) will be treated as time-like and flattened."
-                        "".format(image, n_pages, page.ndim, page.shape)
+                        "".format(image, n_pages, page.ndim, page.shape),
+                        UserWarning,
+                        stacklevel=2,
                     )
                 elif page.ndim > 3 and (np.array(page.shape[:-2]) > 1).sum() > 1:
                     warnings.warn(
                         "TIFF {} has at least one page with {} dimensions"
                         " (page shaped {})."
                         " All dimensions before the final two (height and"
                         " width) will be treated as time-like and flattened."
-                        "".format(image, page.ndim, page.shape)
+                        "".format(image, page.ndim, page.shape),
+                        UserWarning,
+                        stacklevel=2,
                     )
                 shp = [-1] + list(page.shape[-2:])
                 frames.append(page.reshape(shp))
@@ -327,15 +331,19 @@ def getmean(data):
                     " with {} dimensions (page shaped {})."
                     " All dimensions before the final two (height and"
                     " width) will be treated as time-like and flattened."
-                    "".format("", n_pages, page.ndim, page.shape)
+                    "".format("", n_pages, page.ndim, page.shape),
+                    UserWarning,
+                    stacklevel=2,
                 )
             elif page.ndim > 3 and (np.array(page.shape[:-2]) > 1).sum() > 1:
                 warnings.warn(
                     "TIFF {} has at least one page with {} dimensions"
                     " (page shaped {})."
                     " All dimensions before the final two (height and"
                     " width) will be treated as time-like and flattened."
-                    "".format("", page.ndim, page.shape)
+                    "".format("", page.ndim, page.shape),
+                    UserWarning,
+                    stacklevel=2,
                 )
             shp = [-1] + list(page.shape[-2:])
             page = page.reshape(shp)

fissa/readimagejrois.py

@@ -275,7 +275,7 @@ def _getcoords(z=0):
             coords = _getcoords(z)
             coords = coords.astype("float")
             return {"polygons": coords}
-        except BaseException:
+        except Exception:
             raise ValueError(
                 "read_imagej_roi: ROI type {} not supported".format(roi_type)
             )

fissa/tests/base_test.py

@@ -79,7 +79,7 @@ def assert_starts_with(actual, desired):
     """
     try:
         assert len(actual) >= len(desired)
-    except BaseException:
+    except Exception:
         print(
             "Actual string too short ({} < {} characters)".format(
                 len(actual), len(desired)
@@ -89,7 +89,7 @@ def assert_starts_with(actual, desired):
         raise
     try:
         return assert_equal(str(actual)[: len(desired)], desired)
-    except BaseException as err:
+    except Exception as err:
         msg = "ACTUAL: {}".format(actual)
         if isinstance(getattr(err, "args", None), str):
             err.args += "\n" + msg

fissa/tests/generate_downsampled_resources.py

@@ -318,7 +318,7 @@ def _writecoords(points):
                 _writecoords(coords)
                 coords = coords.astype("float")
                 # return {'polygons': coords}
-            except BaseException:
+            except Exception:
                 raise ValueError(
                     "read_imagej_roi: ROI type {} not supported".format(roi_type)
                 )

fissa/tests/test_core.py

@@ -1251,7 +1251,7 @@ def test_load_none_force(self):
         # Make a save file which contains values set to `None`
         fname = os.path.join(self.output_dir, "dummy.npz")
         os.makedirs(self.output_dir)
-        np.savez_compressed(fname, **{field: None for field in fields})
+        np.savez_compressed(fname, **{field: None for field in fields})  # noqa: C420
         # Load the file and check the data appears as None, not np.array(None)
         exp.load(fname, force=True)
         for field in fields:
@@ -1281,7 +1281,7 @@ def test_load_scalar_force(self):
         # Make a save file which contains values set to a scalar
         fname = os.path.join(self.output_dir, "dummy.npz")
         os.makedirs(self.output_dir)
-        np.savez_compressed(fname, **{field: 1337 for field in fields})
+        np.savez_compressed(fname, **{field: 1337 for field in fields})  # noqa: C420
         # Load the file and check the data appears correctly
         exp.load(fname, force=True)
         for field in fields: