Merge branch 'develop' into bro-fix-variational-args

Author: b-r-oleary

cmdstanpy/cmdstan_args.py

@@ -597,12 +597,12 @@ def validate(self) -> None:
                     self._logger.info(
                         'created output directory: %s', self.output_dir
                     )
-                except (RuntimeError, PermissionError):
+                except (RuntimeError, PermissionError) as exc:
                     raise ValueError(
                         'invalid path for output files, no such dir: {}'.format(
                             self.output_dir
                         )
-                    )
+                    ) from exc
             if not os.path.isdir(self.output_dir):
                 raise ValueError(
                     'specified output_dir not a directory: {}'.format(
@@ -614,11 +614,11 @@ def validate(self) -> None:
                 with open(testpath, 'w+'):
                     pass
                 os.remove(testpath)  # cleanup
-            except Exception:
+            except Exception as exc:
                 raise ValueError(
                     'invalid path for output files,'
                     ' cannot write to dir: {}'.format(self.output_dir)
-                )
+                ) from exc
 
         if self.seed is None:
             rng = RandomState()

cmdstanpy/model.py

@@ -850,13 +850,13 @@ def generate_quantities(
                 runset._csv_files = sample_csv_files
                 sample_fit = CmdStanMCMC(runset)
                 sample_drawset = sample_fit.draws_as_dataframe()
-        except ValueError as e:
+        except ValueError as exc:
             raise ValueError(
                 'Invalid mcmc_sample, error:\n\t{}\n\t'
                 ' while processing files\n\t{}'.format(
-                    repr(e), '\n\t'.join(sample_csv_files)
+                    repr(exc), '\n\t'.join(sample_csv_files)
                 )
-            )
+            ) from exc
 
         generate_quantities_args = GenerateQuantitiesArgs(
             csv_files=sample_csv_files

cmdstanpy/stanfit.py

@@ -261,8 +261,8 @@ def save_csvfiles(self, dir: str = None) -> None:
             with open(test_path, 'w'):
                 pass
             os.remove(test_path)  # cleanup
-        except (IOError, OSError, PermissionError):
-            raise Exception('cannot save to path: {}'.format(dir))
+        except (IOError, OSError, PermissionError) as exc:
+            raise Exception('cannot save to path: {}'.format(dir)) from exc
 
         for i in range(self.chains):
             if not os.path.exists(self._csv_files[i]):

cmdstanpy/utils.py

@@ -444,8 +444,8 @@ def parse_rdump_value(rhs: str) -> Union[int, float, np.array]:
             val = float(rhs)
         else:
             val = int(rhs)
-    except TypeError:
-        raise ValueError('bad value in Rdump file: {}'.format(rhs))
+    except TypeError as exc:
+        raise ValueError('bad value in Rdump file: {}'.format(rhs)) from exc
     return val
 
 
@@ -686,10 +686,10 @@ def scan_metric(fd: TextIO, config_dict: Dict, lineno: int) -> int:
         )
     try:
         float(stepsize.strip())
-    except ValueError:
+    except ValueError as exc:
         raise ValueError(
             'line {}: invalid stepsize: {}'.format(lineno, stepsize)
-        )
+        ) from exc
     line = fd.readline().strip()
     lineno += 1
     if not (