Diagnostics reading error

nt2/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "1.5.1"
+__version__ = "1.5.2"
 
 import nt2.containers.data as nt2_data
 

nt2/containers/data.py

@@ -1,6 +1,7 @@
 from typing import Callable, Any, Union, Optional, List, Dict
 
 import sys
+import logging
 
 if sys.version_info >= (3, 12):
     from typing import override
@@ -248,7 +249,11 @@ def __init__(
         self.__coordinate_system = coord_system
 
         super(Data, self).__init__(path=path, reader=self.__reader, remap=remap)
-        self.__diagnostics = Diagnostics(path)
+        try:
+            self.__diagnostics = Diagnostics(path)
+        except Exception as e:
+            logging.warning(f"Failed to read diagnostics: {e}")
+            self.__diagnostics = None
 
     def makeMovie(
         self,
@@ -314,6 +319,8 @@ def attrs(self) -> Dict[str, Any]:
     @property
     def diagnostics(self) -> Union[pd.DataFrame, None]:
         """pd.DataFrame or None: The diagnostics output if .out file is found, None otherwise."""
+        if self.__diagnostics is None:
+            return None
         return self.__diagnostics.df
 
     def to_str(self) -> str:

nt2/containers/diagnostics.py

@@ -76,21 +76,19 @@ def to_ns(value: float, unit: str) -> float:
                         data["species_min"][specie[0]] = []
                         data["species_max"][specie[0]] = []
                     data["species"][specie[0]].append(int(float(specie[1])))
-                    if len(specie) == 6:
+                    if len(specie) == 6 and specie[3] != "" and specie[5] != "":
                         data["species_min"][specie[0]].append(int(float(specie[3])))
                         data["species_max"][specie[0]].append(int(float(specie[5])))
 
                 for key in data["species"].keys():
                     assert len(data["species"][key]) == len(
                         data["steps"]
                     ), f"Number of species entries for {key} does not match number of steps"
-                    assert (
-                        len(data["species_min"][key]) == len(data["steps"])
-                        or len("species_min") == 0
+                    assert (len(data["species_min"][key]) == len(data["steps"])) or (
+                        len(data["species_min"][key]) == 0
                     ), f"Number of species min entries for {key} does not match number of steps"
-                    assert (
-                        len(data["species_max"][key]) == len(data["steps"])
-                        or len("species_max") == 0
+                    assert (len(data["species_max"][key]) == len(data["steps"])) or (
+                        len(data["species_max"][key]) == 0
                     ), f"Number of species max entries for {key} does not match number of steps"
 
             self.df = pd.DataFrame(index=data["steps"])
@@ -100,7 +98,11 @@ def to_ns(value: float, unit: str) -> float:
                 self.df[key] = data["substeps"][key]
             for key in data["species"].keys():
                 self.df[f"species_{key}"] = data["species"][key]
-                self.df[f"species_{key}_min"] = data["species_min"][key]
-                self.df[f"species_{key}_max"] = data["species_max"][key]
+                if (
+                    len(data["species_min"][key]) > 0
+                    and len(data["species_max"][key]) > 0
+                ):
+                    self.df[f"species_{key}_min"] = data["species_min"][key]
+                    self.df[f"species_{key}_max"] = data["species_max"][key]
 
             del data