Use ".nc4" extensions for files containing NetCDF4 data types.

src/data/align.py

@@ -226,10 +226,10 @@ def process_cal(self) -> Path:  # noqa: C901, PLR0912, PLR0915
         """Process calibrated netCDF file using instance attributes."""
         if self.mission and self.auv_name:
             netcdfs_dir = Path(self.base_path, self.auv_name, MISSIONNETCDFS, self.mission)
-            src_file = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_cal.nc")
+            src_file = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_cal.nc4")
         elif self.log_file:
             netcdfs_dir = Path(BASE_LRAUV_PATH, f"{Path(self.log_file).parent}")
-            src_file = Path(netcdfs_dir, f"{Path(self.log_file).stem}_cal.nc")
+            src_file = Path(netcdfs_dir, f"{Path(self.log_file).stem}_cal.nc4")
         else:
             msg = "Must provide either mission and vehicle or log_file"
             raise ValueError(msg)
@@ -712,9 +712,9 @@ def write_combined_netcdf(self, netcdfs_dir: Path) -> None:
         """Write aligned combined data to NetCDF file"""
         if self.log_file:
             # For LRAUV log files, use the log file stem for output name
-            out_fn = Path(netcdfs_dir, f"{Path(self.log_file).stem}_align.nc")
+            out_fn = Path(netcdfs_dir, f"{Path(self.log_file).stem}_align.nc4")
         else:
-            out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_align.nc")
+            out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_align.nc4")
 
         self.aligned_nc.attrs = self.global_metadata()
         self.logger.info("Writing aligned combined data to %s", out_fn)
@@ -730,7 +730,7 @@ def write_combined_netcdf(self, netcdfs_dir: Path) -> None:
     def write_netcdf(self, netcdfs_dir: Path) -> None:
         """Write aligned netCDF file using instance attributes."""
         self.aligned_nc.attrs = self.global_metadata()
-        out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_align.nc")
+        out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_align.nc4")
         self.logger.info("Writing aligned data to %s", out_fn)
         if out_fn.exists():
             self.logger.debug("Removing file %s", out_fn)

src/data/calibrate.py

@@ -3297,7 +3297,7 @@ def _process(self, sensor, logs_dir, netcdfs_dir):  # noqa: C901, PLR0912
     def write_netcdf(self, netcdfs_dir: Path) -> None:
         """Write calibrated netCDF file using instance attributes."""
         self.combined_nc.attrs = self.global_metadata()
-        out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_cal.nc")
+        out_fn = Path(netcdfs_dir, f"{self.auv_name}_{self.mission}_cal.nc4")
         self.logger.info("Writing calibrated instrument data to %s", out_fn)
         if Path(out_fn).exists():
             Path(out_fn).unlink()

src/data/process.py

@@ -561,10 +561,10 @@ def resample(self, mission: str = "", log_file: str = "") -> None:
         )
         resamp.logger.setLevel(self._log_levels[self.config["verbose"]])
         resamp.logger.addHandler(self.log_handler)
-        file_name = f"{resamp.auv_name}_{resamp.mission}_align.nc"
+        file_name = f"{resamp.auv_name}_{resamp.mission}_align.nc4"
         if resamp.log_file:
             netcdfs_dir = Path(BASE_LRAUV_PATH, Path(resamp.log_file).parent)
-            nc_file = Path(netcdfs_dir, f"{Path(resamp.log_file).stem}_align.nc")
+            nc_file = Path(netcdfs_dir, f"{Path(resamp.log_file).stem}_align.nc4")
         else:
             nc_file = Path(
                 self.config["base_path"],

src/data/resample.py

@@ -387,7 +387,7 @@ def resample_coordinates(self, instr: str, mf_width: int, freq: str) -> None:
             if self.log_file:
                 msg = f"A CTD depth was not found in {self.ds.encoding['source']}"
             else:
-                msg = f"{instr}_depth not found in {self.auv_name}_{self.mission}_align.nc"
+                msg = f"{instr}_depth not found in {self.auv_name}_{self.mission}_align.nc4"
             raise InvalidAlignFile(msg) from None
         try:
             self.df_o[f"{instr}_latitude"] = self.ds[f"{instr}_latitude"].to_pandas()
@@ -1831,7 +1831,7 @@ def resample_mission(  # noqa: C901, PLR0912, PLR0915, PLR0913
             "standard_name": "time",
             "long_name": "Time (UTC)",
         }
-        out_fn = str(nc_file).replace("_align.nc", f"_{freq}.nc")
+        out_fn = str(nc_file).replace("_align.nc4", f"_{freq}.nc")
         if self.flash_threshold and self.flash_threshold != FLASH_THRESHOLD:
             # Append flash_threshold to output filename
             ft_ending = f"_ft{self.flash_threshold:.0E}.nc".replace("E+", "E")
@@ -1899,9 +1899,9 @@ def process_command_line(self):
     resamp.process_command_line()
     if resamp.args.log_file:
         netcdfs_dir = Path(BASE_LRAUV_PATH, f"{Path(resamp.args.log_file).parent}")
-        nc_file = Path(netcdfs_dir, f"{Path(resamp.args.log_file).stem}_align.nc")
+        nc_file = Path(netcdfs_dir, f"{Path(resamp.args.log_file).stem}_align.nc4")
     else:
-        file_name = f"{resamp.args.auv_name}_{resamp.args.mission}_align.nc"
+        file_name = f"{resamp.args.auv_name}_{resamp.args.mission}_align.nc4"
         nc_file = Path(
             BASE_PATH,
             resamp.args.auv_name,

src/data/test_process_dorado.py

@@ -31,9 +31,9 @@ def test_process_dorado(complete_dorado_processing):
     # but it will alert us if a code change unexpectedly changes the file size.
     # If code changes are expected to change the file size then we should
     # update the expected size here.
-    EXPECTED_SIZE_GITHUB = 621404
-    EXPECTED_SIZE_ACT = 621402
-    EXPECTED_SIZE_LOCAL = 621452
+    EXPECTED_SIZE_GITHUB = 621408
+    EXPECTED_SIZE_ACT = 621406
+    EXPECTED_SIZE_LOCAL = 621456
     if str(proc.args.base_path).startswith("/home/runner"):
         # The size is different in GitHub Actions, maybe due to different metadata
         assert nc_file.stat().st_size == EXPECTED_SIZE_GITHUB  # noqa: S101
@@ -50,9 +50,9 @@ def test_process_dorado(complete_dorado_processing):
     check_md5 = True
     if check_md5:
         # Check that the MD5 hash has not changed
-        EXPECTED_MD5_GITHUB = "3bab0300e575c1d752a35f49e49e340e"
-        EXPECTED_MD5_ACT = "bb1d539284bee531a00c4d4d99580bf0"
-        EXPECTED_MD5_LOCAL = "9137be5a2ed840cfca94a723285355ec"
+        EXPECTED_MD5_GITHUB = "7c7a3e844988d3bb6ec2a951824bc0d5"
+        EXPECTED_MD5_ACT = "fac632c321b4956b6015d6de97958f8a"
+        EXPECTED_MD5_LOCAL = "c4a13d6e7ec7f35ae5aafa97ea9a2279"
         if str(proc.args.base_path).startswith("/home/runner"):
             # The MD5 hash is different in GitHub Actions, maybe due to different metadata
             assert hashlib.md5(open(nc_file, "rb").read()).hexdigest() == EXPECTED_MD5_GITHUB  # noqa:  PTH123, S101, S324, SIM115

src/data/test_process_i2map.py

@@ -30,9 +30,9 @@ def test_process_i2map(complete_i2map_processing):
     # but it will alert us if a code change unexpectedly changes the file size.
     # If code changes are expected to change the file size then we should
     # update the expected size here.
-    EXPECTED_SIZE_GITHUB = 52682
-    EXPECTED_SIZE_ACT = 52652
-    EXPECTED_SIZE_LOCAL = 52782
+    EXPECTED_SIZE_GITHUB = 52686
+    EXPECTED_SIZE_ACT = 52656
+    EXPECTED_SIZE_LOCAL = 52786
     if str(proc.args.base_path).startswith("/home/runner"):
         # The size is different in GitHub Actions, maybe due to different metadata
         assert nc_file.stat().st_size == EXPECTED_SIZE_GITHUB  # noqa: S101