seabirdfilehandler 0.6.0__py3-none-any.whl → 0.6.1__py3-none-any.whl

seabirdfilehandler/cnvfile.py

@@ -59,10 +59,10 @@ class CnvFile(DataFile):
     ):
         super().__init__(path_to_file, only_header)
         self.validation_modules = self.obtaining_validation_modules()
-        self.start_time = self.reading_start_time()
         self.parameters = Parameters(
             self.data, self.data_table_description, only_header
         )
+        self.start_time = self.reading_start_time()
         if create_dataframe:
             self.df = self.create_dataframe()
         if absolute_time_calculation:
@@ -79,21 +79,15 @@ class CnvFile(DataFile):
         self.df = self.parameters.get_pandas_dataframe()
         return self.df
 
-    def reading_start_time(
-        self,
-        time_source: str = "System UTC",
-    ) -> datetime | None:
+    def reading_start_time(self) -> datetime | None:
         """
         Extracts the Cast start time from the metadata header.
         """
-        for line in self.sbe9_data:
-            if line.startswith(time_source):
-                start_time = line.split("=")[1]
-                start_time = datetime.strptime(
-                    start_time, " %b %d %Y %H:%M:%S "
-                )
-                return start_time
-        return None
+        start_time = (
+            self.parameters.data_table_misc["start_time"].split("[")[0].strip()
+        )
+        start_time = datetime.strptime(start_time, "%b %d %Y %H:%M:%S")
+        return start_time
 
     def absolute_time_calculation(self) -> bool:
         """

seabirdfilehandler/parameter.py

@@ -104,11 +104,19 @@ class Parameters(UserDict):
         )
         parameter_dict = {}
         list_of_metadata_shortnames = list(metadata.keys())
+        # if column number and metadata number is different, we are propably
+        # working with duplicate_columns and will drop the duplicates
         if self.full_data_array.shape[1] != len(list_of_metadata_shortnames):
-            raise AssertionError(
-                f"Array column width {
-                    self.full_data_array.shape[1]
-                } does not fit metadata length {len(metadata)}"
+            self.full_data_array = np.delete(
+                self.full_data_array, self.duplicate_columns, 1
+            )
+            assert self.full_data_array.shape[1] == len(
+                list_of_metadata_shortnames
+            )
+            # rewrite the column number in the metadata header
+            self.data_table_stats["nquan"] = str(
+                int(self.data_table_stats["nquan"])
+                - len(self.duplicate_columns)
             )
         for i in range(self.full_data_array.shape[1]):
             column_data = self.full_data_array[:, i]
@@ -286,14 +294,10 @@ class Parameters(UserDict):
         assert data.shape[1] == len(columns)
         df = pd.DataFrame(data=data, columns=columns)
         for column in df.columns:
-            if column.lower() not in [
-                "latitude",
-                "longitude",
-                "event",
-                "cast",
-                "flag",
-            ]:
+            try:
                 df[column].astype("float64")
+            except ValueError:
+                df[columns].astype("str")
         return df
 
     def with_name_type(self, name_type: str = "shortname"):

{seabirdfilehandler-0.6.0.dist-info → seabirdfilehandler-0.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: seabirdfilehandler
-Version: 0.6.0
+Version: 0.6.1
 Summary: Library of parsers to interact with SeaBird CTD files.
 Keywords: CTD,parser,seabird,data
 Author: Emil Michels

{seabirdfilehandler-0.6.0.dist-info → seabirdfilehandler-0.6.1.dist-info}/RECORD

@@ -1,16 +1,16 @@
 seabirdfilehandler/__init__.py,sha256=XMmhfwZ3YPzR3sLTi8AHN6mSlrQA1tLEpw02_fI7Rr0,278
 seabirdfilehandler/bottlefile.py,sha256=qCh506J3MWZXM11243aw_oJRocVB0ZIipXQLEgkD5M0,6046
 seabirdfilehandler/bottlelogfile.py,sha256=MtMmEebdAktO3mk6KbmJC7dfx9sRLbV5qqDQt2qtpJE,4310
-seabirdfilehandler/cnvfile.py,sha256=j7IR3EgCrGD3riKOzFSKFNW6lkuzZYGYkxI_czcD8XU,10196
+seabirdfilehandler/cnvfile.py,sha256=IvCHjcgI-mgtJodSzlQ5bfyJWZ-D-3Lk5Z5Hh3BLfps,10048
 seabirdfilehandler/datafiles.py,sha256=9r0Mh3zPYJJ3CoybgOBH4Dsq43kLDnca9m8s_V0cYU8,9378
 seabirdfilehandler/file_collection.py,sha256=8uLoN55h00_EmiEa4mbyaSJZst7w8NhODv7DrtzEAwc,15021
 seabirdfilehandler/geomar_ctd_file_parser.py,sha256=4eCnkE0mvPKC8Dic8sXP4xpfwnk3K2MQcGFBf6loT8k,2655
 seabirdfilehandler/hexfile.py,sha256=TBplwbWHrTuJzv2qlx6xYNtoX43I2YUabDmaGZuBEDQ,2144
-seabirdfilehandler/parameter.py,sha256=CjC8T5wfbThryqVNjTcAolug9gi_BnInfZzkEfmKm5E,14561
+seabirdfilehandler/parameter.py,sha256=MDVNGC1PZPf6IMN7r6Y3A3cg52AKXoyau1foEDQ1uoI,14877
 seabirdfilehandler/utils.py,sha256=5KXdB8Hdv65dv5tPyXxNMct1mCEOyA3S8XP54AFAnx0,1745
 seabirdfilehandler/validation_modules.py,sha256=eZ6x0giftUtlxnRMOnK_vCkgccdwUXPrDjajFa-E6n0,4698
 seabirdfilehandler/xmlfiles.py,sha256=XqqbVNjyINySoe2ZC_qJglkAqshavZxT2-jorDOSj7Y,5084
-seabirdfilehandler-0.6.0.dist-info/LICENSE,sha256=Ifd1VPmYv32oJd2QVh3wIQP9X05vYJlcY6kONz360ws,34603
-seabirdfilehandler-0.6.0.dist-info/METADATA,sha256=-HcIPCv4_SMttVtN0kXdr-UKJy5iUsFx0Onde2YXQwE,2307
-seabirdfilehandler-0.6.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-seabirdfilehandler-0.6.0.dist-info/RECORD,,
+seabirdfilehandler-0.6.1.dist-info/LICENSE,sha256=Ifd1VPmYv32oJd2QVh3wIQP9X05vYJlcY6kONz360ws,34603
+seabirdfilehandler-0.6.1.dist-info/METADATA,sha256=4BNXjQ4Xgm5OQCyLkPK3C4l0OkFiD_e--dfjcYedS04,2307
+seabirdfilehandler-0.6.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+seabirdfilehandler-0.6.1.dist-info/RECORD,,