Fixes for problems found when testing LRAUV archive step

.vscode/launch.json

@@ -334,7 +334,8 @@
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber"]
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber", "--no_cleanup"]
-            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup"]
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup"]
+            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup", "--clobber"]
             //"args": ["-v", "1", "--auv_name", "tethys", "--start", "20120901", "--end", "20121101", "--noinput"]
         },
 

src/data/AUV.py

@@ -256,7 +256,7 @@ def nudge_positions(  # noqa: C901, PLR0912, PLR0913, PLR0915
         seg_min = float(lat.cf["T"].data[segi][-1] - lat.cf["T"].data[segi][0]) / 1.0e9 / 60
 
     logger.info(
-        f"{seg_count + 1:4d}: {'-':>12} {'-':>12} {'-':>12} {len(segi):-9d} {seg_min:9.2f} {'-':>14} {'-':>14}",  # noqa: E501, G004
+        f"{seg_count + 1:5d}: {'-':>12} {'-':>12} {'-':>12} {len(segi):-9d} {seg_min:9.2f} {'-':>14} {'-':>14}",  # noqa: E501, G004
     )
     segment_count = seg_count
     segment_minsum = seg_minsum

src/data/archive.py

@@ -172,7 +172,7 @@ def copy_to_AUVTCD(self, nc_file_base: Path, freq: str = FREQ) -> None:  # noqa:
     def copy_to_M3(self, resampled_nc_file: str) -> None:
         pass
 
-    def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None:
+    def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None:  # noqa: C901, PLR0912
         "Copy the intermediate and resampled netCDF file(s) to the archive LRAUV location"
         src_dir = Path(BASE_LRAUV_PATH, Path(log_file).parent)
         dst_dir = Path(LRAUV_VOL, Path(log_file).parent)
@@ -196,7 +196,7 @@ def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None:
                     "%-75s exists, but is not being archived because --clobber is not specified.",
                     src_file.name,
                 )
-        for ftype in (f"{freq}.nc", "cal.nc", "align.nc"):
+        for ftype in (f"{freq}.nc", "combined.nc", "align.nc"):
             src_file = Path(src_dir, f"{Path(log_file).stem}_{ftype}")
             dst_file = Path(dst_dir, src_file.name)
             if self.args.clobber:
@@ -211,6 +211,19 @@ def copy_to_LRAUV(self, log_file: str, freq: str = FREQ) -> None:
                     "%-36s exists, but is not being archived because --clobber is not specified.",  # noqa: E501
                     src_file.name,
                 )
+        # Copy the processing.log file last so that we get everything
+        src_file = Path(src_dir, f"{Path(log_file).stem}_{LOG_NAME}")
+        dst_file = Path(dst_dir, src_file.name)
+        if src_file.exists():
+            if self.args.clobber:
+                self.logger.info("copyfile %s %s", src_file, dst_dir)
+                shutil.copyfile(src_file, dst_file)
+                self.logger.info("copyfile %s %s done.", src_file, dst_dir)
+            else:
+                self.logger.info(
+                    "%26s exists, but is not being archived because --clobber is not specified.",  # noqa: E501
+                    src_file.name,
+                )
 
     def process_command_line(self):
         parser = argparse.ArgumentParser(

src/data/process.py

@@ -785,7 +785,7 @@ def process_log_file(self, log_file: str) -> None:
         netcdfs_dir = Path(BASE_LRAUV_PATH, Path(log_file).parent)
         Path(netcdfs_dir).mkdir(parents=True, exist_ok=True)
         self.log_handler = logging.FileHandler(
-            Path(BASE_LRAUV_PATH, f"{log_file}_extract.log"), mode="w+"
+            Path(netcdfs_dir, f"{Path(log_file).stem}_processing.log"), mode="w+"
         )
         self.log_handler.setLevel(self._log_levels[self.args.verbose])
         self.log_handler.setFormatter(AUV_NetCDF._formatter)

src/data/resample.py

@@ -78,6 +78,17 @@ def _build_global_metadata(self) -> None:
             )
             gitcommit = "<failed to get git commit>"
         iso_now = datetime.now(tz=UTC).isoformat().split(".")[0] + "Z"
+
+        # Ensure that only the latitude and longitude variables have
+        # standard_name attributes equal to "latitude" and "longitude" so that
+        # the .cf[] accessor works correctly
+        for var in self.resampled_nc.data_vars:
+            if self.resampled_nc[var].attrs.get("standard_name") in ["latitude", "longitude"]:
+                if var in {"latitude", "longitude"}:
+                    continue
+                self.logger.info("Removing standard_name attribute from variable %s", var)
+                del self.resampled_nc[var].attrs["standard_name"]
+
         # Common dynamic attributes for all auv platforms
         self.metadata["time_coverage_start"] = str(min(self.resampled_nc.time.values))
         self.metadata["time_coverage_end"] = str(max(self.resampled_nc.time.values))
@@ -1050,7 +1061,7 @@ def resample_variable(  # noqa: PLR0913
                     .resample(freq.lower())
                     .mean()
                 )
-                self.df_r[variable].loc[instr_data.index] = instr_data
+                self.df_r.loc[instr_data.index, variable] = instr_data
             else:
                 self.df_r[variable] = (
                     self.df_o[f"{variable}_mf"]