refactor: narrow overly broad except Exception catches to specific exception types

- base.py:137: Replace 'except Exception' with 'except (OSError, ImportError)' for filesystem initialization
- base.py:146: Replace 'except Exception' with 'except (OSError, json.JSONDecodeError)' for config loading
- sample_metadata.py:1867: Replace 'except Exception' with 'except (KeyError, NameError, SyntaxError, TypeError, AttributeError)' for pandas eval queries
- map_params.py:45: Replace 'except Exception' with 'except (ImportError, ModuleNotFoundError, AttributeError)' for basemap provider initialization

These changes prevent silent masking of unexpected bugs by only catching the specific exception types that each code block is designed to handle. Improves debuggability without altering intended error-handling behavior.

Fixes: Narrow overly broad exception handlers

Author: kunal-10-cloud

malariagen_data/anoph/base.py

@@ -134,7 +134,7 @@ def __init__(
             storage_options = dict()
         try:
             self._fs, self._base_path = _init_filesystem(self._url, **storage_options)
-        except Exception as exc:  # pragma: no cover
+        except (OSError, ImportError) as exc:  # pragma: no cover
             raise IOError(
                 "An error occurred establishing a connection to the storage system. Please see the nested exception for more details."
             ) from exc
@@ -143,7 +143,7 @@ def __init__(
         try:
             with self.open_file(self._config_path) as f:
                 self._config = json.load(f)
-        except Exception as exc:  # pragma: no cover
+        except (OSError, json.JSONDecodeError) as exc:  # pragma: no cover
             if (isinstance(exc, OSError) and "forbidden" in str(exc).lower()) or (
                 getattr(exc, "status", None) == 403
             ):

malariagen_data/anoph/map_params.py

@@ -42,7 +42,7 @@ def get_basemap_abbrevs() -> dict:
         for key, provider_fn in _basemap_abbrev_candidates.items():
             try:
                 _basemap_abbrevs[key] = provider_fn()
-            except Exception:
+            except (ImportError, ModuleNotFoundError, AttributeError):
                 warnings.warn(
                     f"Basemap provider {key!r} is not available and will be skipped.",
                     stacklevel=2,

malariagen_data/anoph/sample_metadata.py

@@ -1864,7 +1864,7 @@ def _locate_cohorts(*, cohorts, data, min_cohort_size):
         for coh, query in cohorts.items():
             try:
                 loc_coh = data.eval(query).values
-            except Exception as e:
+            except (KeyError, NameError, SyntaxError, TypeError, AttributeError) as e:
                 raise ValueError(
                     f"Invalid query for cohort {coh!r}: {query!r}. Error: {e}"
                 ) from e