seabirdfilehandler 0.7.0__tar.gz → 0.7.2__tar.gz

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: seabirdfilehandler
-Version: 0.7.0
+Version: 0.7.2
 Summary: Library of parsers to interact with SeaBird CTD files.
 Keywords: CTD,parser,seabird,data
 Author: Emil Michels

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/pyproject.toml

@@ -20,7 +20,7 @@ urls.homepage = "https://ctd-software.pages.io-warnemuende.de/seabirdfilehandler
 urls.repository = "https://git.io-warnemuende.de/CTD-Software/SeabirdFileHandler"
 urls.documentation = "https://ctd-software.pages.io-warnemuende.de/seabirdfilehandler"
 dynamic = []
-version = "0.7.0"
+version = "0.7.2"
 
 [tool.poetry]
 

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/src/seabirdfilehandler/cnvfile.py

@@ -95,7 +95,7 @@ class CnvFile(DataFile):
 
         """
         time_parameter = None
-        for parameter in self.df.columns:
+        for parameter in self.parameters.keys():
             if parameter.lower().startswith("time"):
                 time_parameter = parameter
         if time_parameter and self.start_time:
@@ -106,8 +106,9 @@ class CnvFile(DataFile):
                         timedelta(days=float(time)) + self.start_time
                         if time_parameter == "timeJ"
                         else timedelta(seconds=float(time)) + self.start_time
-                        for time in self.df[time_parameter]
-                    ]
+                        for time in self.parameters[time_parameter].data
+                    ],
+                    dtype=str,
                 ),
             )
             return True
@@ -159,7 +160,7 @@ class CnvFile(DataFile):
     def array2cnv(self) -> list:
         result = []
         for row in self.parameters.full_data_array:
-            formatted_row = "".join(f"{elem:11}" for elem in row)
+            formatted_row = "".join(elem.rjust(11) for elem in row)
             result.append(formatted_row + "\n")
         return result
 
@@ -216,23 +217,21 @@ class CnvFile(DataFile):
         self.data = self.array2cnv()
         self.file_data = [*self.header, *self.data]
 
-    def add_processing_metadata(self, addition: str | list):
+    def add_processing_metadata(self, module: str, key: str, value: str):
         """
         Adds new processing lines to the list of processing module information
 
         Parameters
         ----------
-        addition: str:
-            the new information line
+        module: str :
+            the name of the processing module
+        key: str :
+            the description of the value
+        value: str :
+            the information
 
         """
-        if isinstance(addition, str):
-            addition = [addition]
-        self.processing_steps.append(
-            self.processing_steps.create_step_instance(
-                module=addition[0].split("_")[0], raw_info=addition
-            )
-        )
+        self.processing_steps.add_info(module, key, value)
         self._update_header()
 
     def add_station_and_event_column(self) -> bool:

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/src/seabirdfilehandler/file_collection.py

@@ -445,7 +445,7 @@ class CnvCollection(FileCollection):
         A list of ProcessingSteps.
         """
         individual_processing_steps = [
-            file.processing_steps for file in self.data
+            file.processing_steps.modules for file in self.data
         ]
         for index, step_info in enumerate(individual_processing_steps):
             if step_info != individual_processing_steps[0]:

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/src/seabirdfilehandler/parameter.py

@@ -78,7 +78,7 @@ class Parameters(UserDict):
                     for i in range(0, len(line) - n, n)
                 ]
             )
-        return np.array(row_list, dtype=float)
+        return np.array(row_list, dtype="str")
 
     def create_parameter_instances(
         self,
@@ -176,7 +176,7 @@ class Parameters(UserDict):
             for line in post
         }
 
-    def add_parameter(self, parameter: Parameter):
+    def add_parameter(self, parameter: Parameter, position: str = ""):
         """
         Adds one parameter instance to the collection.
 
@@ -186,13 +186,36 @@ class Parameters(UserDict):
             The new parameter
 
         """
-        self.data[parameter.name] = parameter
+        position_index = -1
+        # add to parameter dict at given
+        if position:
+            new_dict = {}
+            for index, (key, value) in enumerate(self.data.items()):
+                new_dict[key] = value
+                if key == position:
+                    new_dict[parameter.name] = parameter
+                    position_index = index + 1
+            self.data = new_dict
+
+        else:
+            self.data[parameter.name] = parameter
+
+        # update metadata dict
+        self.metadata = {
+            parameter.name: parameter.metadata
+            for parameter in self.data.values()
+        }
+        # add to full numpy data array
+        self.full_data_array = np.insert(
+            self.full_data_array, position_index, parameter.data, axis=1
+        )
 
     def create_parameter(
         self,
         data: np.ndarray | int | float | str,
         metadata: dict = {},
         name: str = "",
+        position: str = "",
     ) -> Parameter:
         """
         Creates a new parameter instance with the given data and metadata.
@@ -233,7 +256,7 @@ class Parameters(UserDict):
                 shape=self.full_data_array.shape[0],
             )
         parameter = Parameter(data=data, metadata=metadata)
-        self.add_parameter(parameter)
+        self.add_parameter(parameter, position)
         return parameter
 
     def add_default_metadata(
@@ -426,6 +449,7 @@ class Parameter:
         self.data = data
         self.metadata = metadata
         self.name = metadata["shortname"]
+        self.parse_to_float()
         self.update_span()
 
     def __str__(self) -> str:
@@ -457,6 +481,15 @@ class Parameter:
         except KeyError:
             return
 
+    def parse_to_float(self):
+        """
+        Tries to parse the data array type to float.
+        """
+        try:
+            self.data = self.data.astype("float64")
+        except ValueError:
+            pass
+
     def update_span(self):
         """
         Updates the data span.

{seabirdfilehandler-0.7.0 → seabirdfilehandler-0.7.2}/src/seabirdfilehandler/processing_steps.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 from collections import UserList
+import copy
 
 
 class CnvProcessingSteps(UserList):
@@ -28,6 +29,7 @@ class CnvProcessingSteps(UserList):
     def _form_processing_info(self) -> list:
         out_list = []
         for module in self.data:
+            module = copy.deepcopy(module)
             if "vars" in module.metadata and module.name != "wildedit":
                 module.metadata["date"] = (
                     module.metadata["date"]
@@ -167,6 +169,39 @@ class CnvProcessingSteps(UserList):
                 return self.data[index]
         return None
 
+    def add_info(
+        self,
+        module: str,
+        key: str,
+        value: str,
+    ) -> ProcessingStep | None:
+        """
+        Adds new processing lines to the list of processing module information
+
+        Parameters
+        ----------
+        module: str :
+            the name of the processing module
+        key: str :
+            the description of the value
+        value: str :
+            the information
+
+        Returns
+        -------
+        the altered ProcessingStep
+
+        """
+        if module in self.modules:
+            step_info = self.get_step(module)
+            if step_info:
+                step_info.metadata[key] = value
+        else:
+            step_info = ProcessingStep(name=module, metadata={key: value})
+            self.data.append(step_info)
+            self.modules.append(module)
+        return step_info
+
 
 class ProcessingStep:
     """