From d5cbc591db9af753651ce82523bdbc636409af97 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Mon, 18 Apr 2022 02:08:40 -0400
Subject: [PATCH] batch replace 'except:' with 'except Exception:'

The latter will not catch `KeyboardInterrupt` and `SystemExit`. See https://stackoverflow.com/a/18982726/9567349.
---
 dpdata/fhi_aims/output.py       | 4 ++--
 dpdata/rdkit/sanitize.py        | 4 ++--
 dpdata/unit.py                  | 2 +-
 tests/test_pick_atom_idx.py     | 2 +-
 tests/test_to_ase.py            | 2 +-
 tests/test_to_pymatgen.py       | 2 +-
 tests/test_to_pymatgen_entry.py | 2 +-
 tests/test_water_ions.py        | 2 +-
 8 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/dpdata/fhi_aims/output.py b/dpdata/fhi_aims/output.py
index 99cb1203a..4ee819c3b 100755
--- a/dpdata/fhi_aims/output.py
+++ b/dpdata/fhi_aims/output.py
@@ -124,7 +124,7 @@ def analyze_block(lines, first_blk=False, md=True) :
     contents="\n".join(lines)
     try:
        natom=int(re.findall("Number of atoms.*([0-9]{1,})",lines)[0])
-    except:
+    except Exception:
        natom=0
 
     if first_blk:
@@ -154,7 +154,7 @@ def analyze_block(lines, first_blk=False, md=True) :
     try:
       _eng_patt=re.compile(eng_patt)
       energy=float(_eng_patt.search(contents).group().split()[-2])
-    except:
+    except Exception:
      energy=None
     
     if not energy:
diff --git a/dpdata/rdkit/sanitize.py b/dpdata/rdkit/sanitize.py
index 01f002e0f..0e1637402 100644
--- a/dpdata/rdkit/sanitize.py
+++ b/dpdata/rdkit/sanitize.py
@@ -22,7 +22,7 @@ def get_explicit_valence(atom, verbose=False):
                 print(
                     f"Explicit valence given by GetExplicitValence() and sum of bond order are inconsistent on {atom.GetSymbol()}{atom.GetIdx() + 1}, using sum of bond order.")
         return exp_val_calculated_from_bonds
-    except:
+    except Exception:
         return exp_val_calculated_from_bonds
 
 
@@ -37,7 +37,7 @@ def regularize_formal_charges(mol, sanitize=True, verbose=False):
         try:
             Chem.SanitizeMol(mol)
             return mol
-        except:
+        except Exception:
             return None
     else:
         return mol
diff --git a/dpdata/unit.py b/dpdata/unit.py
index 7b5aeffc4..299ac2bbb 100644
--- a/dpdata/unit.py
+++ b/dpdata/unit.py
@@ -35,7 +35,7 @@ def check_unit(unit):
                 raise RuntimeError(f"Invaild unit: {unit}")
             if lunit not in lconvs.keys():
                 raise RuntimeError(f"Invalid unit: {unit}")
-        except:
+        except Exception:
             raise RuntimeError(f"Invalid unit: {unit}")
 
 class Conversion(ABC):
diff --git a/tests/test_pick_atom_idx.py b/tests/test_pick_atom_idx.py
index 7e13cca97..bb6af61f7 100644
--- a/tests/test_pick_atom_idx.py
+++ b/tests/test_pick_atom_idx.py
@@ -5,7 +5,7 @@
 try:
    import parmed
    exist_module=True
-except:
+except Exception:
    exist_module=False
 
 class TestPickAtomIdx(unittest.TestCase, CompSys, IsNoPBC):
diff --git a/tests/test_to_ase.py b/tests/test_to_ase.py
index 1cd7200a9..4ea870c79 100644
--- a/tests/test_to_ase.py
+++ b/tests/test_to_ase.py
@@ -7,7 +7,7 @@
    from ase import Atoms
    from ase.io import write
    exist_module=True
-except:
+except Exception:
    exist_module=False
 
 @unittest.skipIf(not exist_module,"skip test_ase")
diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py
index 5922828b4..0077a0495 100644
--- a/tests/test_to_pymatgen.py
+++ b/tests/test_to_pymatgen.py
@@ -6,7 +6,7 @@
 try:
    from pymatgen import  Structure
    exist_module=True
-except:
+except Exception:
    exist_module=False
 
 @unittest.skipIf(not exist_module,"skip pymatgen")
diff --git a/tests/test_to_pymatgen_entry.py b/tests/test_to_pymatgen_entry.py
index ef7cb942f..e0a952be3 100644
--- a/tests/test_to_pymatgen_entry.py
+++ b/tests/test_to_pymatgen_entry.py
@@ -7,7 +7,7 @@
 try:
    from pymatgen.entries.computed_entries import ComputedStructureEntry
    exist_module=True
-except:
+except Exception:
    exist_module=False
 
 @unittest.skipIf(not exist_module,"skip pymatgen")
diff --git a/tests/test_water_ions.py b/tests/test_water_ions.py
index 3a9436b6d..f2fab203b 100644
--- a/tests/test_water_ions.py
+++ b/tests/test_water_ions.py
@@ -6,7 +6,7 @@
     import ase
     import ase.neighborlist    
     exist_ase=True
-except:
+except Exception:
     exist_ase=False
 
 class TestIons(unittest.TestCase):