sierra-research 1.3.5__py3-none-any.whl → 1.3.11__py3-none-any.whl

sierra/core/config.py

@@ -45,7 +45,7 @@ def mpl_init():
     import matplotlib.pyplot as plt
 
     # Set MPL style
-    plt.style.use('seaborn-colorblind')
+    plt.style.use('seaborn-v0_8-colorblind')
 
 
 # Actually initialize matplotlib

sierra/core/generators/exp_creator.py

@@ -148,7 +148,7 @@ class ExpCreator:
                         run_exp_def: definition.XMLExpDef,
                         cmds_generator,
                         run_num: int) -> None:
-        run_output_dir = "{0}_{1}_output".format(self.template_stem, run_num)
+        run_output_dir = "{0}_run{1}_output".format(self.template_stem, run_num)
 
         # If the project defined per-run configuration, apply
         # it. Otherwise, just apply the configuration in the SIERRA core.

sierra/core/graphs/heatmap.py

@@ -211,7 +211,7 @@ class DualHeatmap:
         # Scaffold graph. We can use either dataframe for setting the graph
         # size; we assume they have the same dimensions.
         #
-        fig, axes = plt.subplots(ncols=2)
+        fig, axes = plt.subplots(nrows=1, ncols=2)
         Heatmap.set_graph_size(dfs[0], fig)
 
         y = np.arange(len(dfs[0].columns))

sierra/core/graphs/stacked_line_graph.py

@@ -222,7 +222,9 @@ class StackedLineGraph:
 
         return dfs
 
-    def _read_models(self) -> tp.Tuple[pd.DataFrame, tp.List[str]]:
+    # 2024/09/13 [JRH]: The union is for compatability with type checkers in
+    # python {3.8,3.11}.
+    def _read_models(self) -> tp.Tuple[pd.DataFrame, tp.Union[tp.List[str], tp.List[bytes]]]:
         if self.model_root is not None:
             model_fpath = self.model_root / \
                 (self.input_stem + config.kModelsExt['model'])

sierra/core/graphs/summary_line_graph.py

@@ -332,7 +332,9 @@ class SummaryLineGraph:
 
         return dfs
 
-    def _read_models(self) -> tp.Tuple[pd.DataFrame, tp.List[str]]:
+    # 2024/09/13 [JRH]: The union is for compatability with type checkers in
+    # python {3.8,3.11}.
+    def _read_models(self) -> tp.Tuple[pd.DataFrame, tp.Union[tp.List[str], tp.List[bytes]]]:
         if self.model_root is None:
             return (None, [])
 

sierra/core/pipeline/stage3/statistics_calculator.py

@@ -229,11 +229,11 @@ class ExpCSVGatherer:
 
         self.logger.info('Processing .csvs: %s...', exp_output_root.name)
 
-        pattern = "{}_{}_output".format(re.escape(self.gather_opts['template_input_leaf']),
-                                        r'\d+')
+        pattern = "{}_run{}_output".format(re.escape(self.gather_opts['template_input_leaf']),
+                                           r'\d+')
 
         runs = list(exp_output_root.iterdir())
-        assert(all(re.match(pattern, r.name) for r in runs)),\
+        assert (all(re.match(pattern, r.name) for r in runs)), \
             f"Extra files/not all dirs in '{exp_output_root}' are exp runs"
 
         # Maps (unique .csv stem, optional parent dir) to the averaged dataframe
@@ -299,7 +299,7 @@ class ExpCSVGatherer:
             reader = storage.DataFrameReader(self.gather_opts['storage_medium'])
             df = reader(item_path, index_col=False)
 
-            if df.dtypes[0] == 'object':
+            if df.dtypes.iloc[0] == 'object':
                 df[df.columns[0]] = df[df.columns[0]].apply(lambda x: float(x))
 
             if item not in gathered:
@@ -373,7 +373,7 @@ class ExpCSVGatherer:
                                   str(path1))
                 continue
 
-            assert (utils.path_exists(path1) and utils.path_exists(path2)),\
+            assert (utils.path_exists(path1) and utils.path_exists(path2)), \
                 f"Either {path1} or {path2} does not exist"
 
             # Verify both dataframes have same # columns, and that
@@ -385,15 +385,15 @@ class ExpCSVGatherer:
             assert (len(df1.columns) == len(df2.columns)), \
                 (f"Dataframes from {path1} and {path2} do not have "
                  "the same # columns")
-            assert(sorted(df1.columns) == sorted(df2.columns)),\
+            assert (sorted(df1.columns) == sorted(df2.columns)), \
                 f"Columns from {path1} and {path2} not identical"
 
             # Verify the length of all columns in both dataframes is the same
             for c1 in df1.columns:
-                assert(all(len(df1[c1]) == len(df1[c2]) for c2 in df1.columns)),\
+                assert (all(len(df1[c1]) == len(df1[c2]) for c2 in df1.columns)), \
                     f"Not all columns from {path1} have same length"
 
-                assert(all(len(df1[c1]) == len(df2[c2]) for c2 in df1.columns)),\
+                assert (all(len(df1[c1]) == len(df2[c2]) for c2 in df1.columns)), \
                     (f"Not all columns from {path1} and {path2} have "
                      "the same length")
 

sierra/core/pipeline/stage4/graph_collator.py

@@ -124,7 +124,7 @@ class UnivarGraphCollator:
 
             data_df = storage.DataFrameReader('storage.csv')(csv_ipath)
 
-            assert target['col'] in data_df.columns.values,\
+            assert target['col'] in data_df.columns.values, \
                 "{0} not in columns of {1}".format(target['col'],
                                                    target['src_stem'] + stat.df_ext)
 
@@ -221,7 +221,7 @@ class BivarGraphCollator:
 
             data_df = storage.DataFrameReader('storage.csv')(csv_ipath)
 
-            assert target['col'] in data_df.columns.values,\
+            assert target['col'] in data_df.columns.values, \
                 "{0} not in columns of {1}, which has {2}".format(target['col'],
                                                                   csv_ipath,
                                                                   data_df.columns)
@@ -238,10 +238,11 @@ class BivarGraphCollator:
             # in sequence, to generate a SEQUENCE of 2D dataframes.
             for row in data_df[target['col']].index:
                 if row in stat.df_seq.keys():
-                    stat.df_seq[row].loc[xlabel][ylabel] = data_df[target['col']][row]
+                    stat.df_seq[row].loc[xlabel][ylabel] = data_df.loc[row,
+                                                                       target['col']]
                 else:
                     df = pd.DataFrame(columns=stat.ylabels, index=stat.xlabels)
-                    df.loc[xlabel][ylabel] = data_df[target['col']][row]
+                    df.loc[xlabel][ylabel] = data_df.loc[row, target['col']]
                     stat.df_seq[row] = df
 
 

sierra/core/startup.py

@@ -74,8 +74,8 @@ def _linux_pkg_checks() -> None:
 
     dist = distro.id()
     os_info = distro.os_release_info()
-    if any(candidate in os_info['id_like'] for candidate in ['debian',
-                                                             'ubuntu']):
+    if any(candidate in os_info['id'] for candidate in ['debian',
+                                                        'ubuntu']):
         _apt_pkg_checks(dist)
     else:
         logging.warning(("Unknown Linux distro '%s' detected: skipping package "

sierra/core/utils.py

@@ -365,7 +365,7 @@ def df_fill(df: pd.DataFrame, policy: str) -> pd.DataFrame:
 
 
 @retry(OSError, tries=10, delay=0.100, backoff=1.1)  # type:ignore
-def pickle_dump(obj: object, f: tp.IO) -> None:
+def pickle_dump(obj: object, f) -> None:
     pickle.dump(obj, f)
 
 

sierra/version.py

@@ -9,4 +9,4 @@
 
 # Project packages
 
-__version__ = "1.3.5"
+__version__ = "1.3.11"