More fixes following operational testing

.vscode/launch.json

@@ -467,9 +467,11 @@
             // Test --update_ssds_provenance with a short log_file 
             //"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250128_20250131/20250131T051404/202501310514_202501310535.nc4", "--update_ssds_provenance"]
             // Test ahi mission that has Backseat Planktivore data with --update_ssds_provenance
-            "args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250414_20250418/20250415T040019/202504150400_202504152346.nc4", "--update_ssds_provenance"]
+            //"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250414_20250418/20250415T040019/202504150400_202504152346.nc4", "--update_ssds_provenance"]
             // Make per log file .html files to test with lrauv_deployment_plots and --update_ssds_provenance
             //"args": ["-v", "1", "--auv_name", "ahi", "--start", "20251022T000000", "--end", "20251024T000000", "--update_ssds_provenance", "--clobber"]
+            // Make per log file .html files to test with lrauv_deployment_plots and --update_ssds_provenance to test dynamic map bounds
+            "args": ["-v", "1", "--auv_name", "ahi", "--start", "20260409T000000", "--end", "20260415T000000", "--update_ssds_provenance", "--clobber"]
         },
         {
             "name": "lrauv_deployment_plots",

src/data/create_products.py

@@ -1062,22 +1062,48 @@ def _plot_track_map(  # noqa: PLR0915
         # Store original position
         pos = map_ax.get_position()
 
-        # Set fixed axis limits for Monterey Bay area (in Web Mercator) FIRST
-        lon_bounds = [-122.41, -121.77]
-        lat_bounds = [36.5, 37.0]
+        # Use fixed Monterey Bay bounds when the track fits within them; otherwise
+        # compute bounds dynamically from the data with a 10% margin.
+        fixed_lon_bounds = [-122.41, -121.77]
+        fixed_lat_bounds = [36.5, 37.0]
+        valid_lons = lons[~np.isnan(lons)]
+        valid_lats = lats[~np.isnan(lats)]
+        if (
+            valid_lons.size > 0
+            and valid_lats.size > 0
+            and valid_lons.min() >= fixed_lon_bounds[0]
+            and valid_lons.max() <= fixed_lon_bounds[1]
+            and valid_lats.min() >= fixed_lat_bounds[0]
+            and valid_lats.max() <= fixed_lat_bounds[1]
+        ):
+            lon_bounds = fixed_lon_bounds
+            lat_bounds = fixed_lat_bounds
+        else:
+            lon_margin = (valid_lons.max() - valid_lons.min()) * 0.1 or 0.05
+            lat_margin = (valid_lats.max() - valid_lats.min()) * 0.1 or 0.05
+            lon_bounds = [valid_lons.min() - lon_margin, valid_lons.max() + lon_margin]
+            lat_bounds = [valid_lats.min() - lat_margin, valid_lats.max() + lat_margin]
         x_bounds, y_bounds = transformer.transform(lon_bounds, lat_bounds)
         map_ax.set_xlim(x_bounds)
         map_ax.set_ylim(y_bounds)
 
         # Make the plot square by using equal aspect with explicit box adjustment
         map_ax.set_aspect("equal", adjustable="box")
 
-        # Plot the track with profile_number coloring in Web Mercator coordinates
+        # Plot the track colored by a cumulative profile number that keeps
+        # incrementing across concatenated log files (profile_number resets to
+        # zero at the start of each log file).
         profile_numbers = self.ds["profile_number"].to_numpy()
+        cumulative_profile = profile_numbers.copy().astype(float)
+        offset = 0
+        for i in range(1, len(profile_numbers)):
+            if profile_numbers[i] < profile_numbers[i - 1]:
+                offset += profile_numbers[i - 1]
+            cumulative_profile[i] = profile_numbers[i] + offset
         scatter = map_ax.scatter(
             x_merc,
             y_merc,
-            c=profile_numbers,
+            c=cumulative_profile,
             cmap="jet",
             s=1,
             alpha=0.6,
@@ -1104,7 +1130,7 @@ def _plot_track_map(  # noqa: PLR0915
         # Now position map aligned with left edge of reference, 50% width
         # Use a square aspect ratio based on the y-dimension
         map_height = pos.height
-        aspect_ratio = (37.0 - 36.5) / (122.41 - 121.77)  # data aspect ratio
+        aspect_ratio = (lat_bounds[1] - lat_bounds[0]) / (lon_bounds[1] - lon_bounds[0])
         map_width = map_height / aspect_ratio * 0.7  # scale to fit nicely
 
         # Align map top with the nighttime indicator top when ref axes is available.

src/data/lrauv_deployment_plots.py

@@ -159,36 +159,23 @@ def _concat_datasets(self, nc_files: list[Path | str]) -> xr.Dataset | None:
 
         Accepts both local Paths and OPeNDAP URL strings — xr.open_dataset
         handles both transparently.
-        Tries xr.open_mfdataset first; falls back to manual concat on failure.
         Uses join='outer' so every variable present in any log_file is retained
         (absent values filled with NaN).
         """
         if not nc_files:
             return None
 
-        paths = [str(p) for p in nc_files]
-        try:
-            self.logger.info("Concatenating %d files via open_mfdataset", len(paths))
-            return xr.open_mfdataset(
-                paths,
-                combine="by_coords",
-                join="outer",
-                parallel=True,
-                chunks="auto",
-            )
-        except Exception as exc:  # noqa: BLE001
-            self.logger.warning("open_mfdataset failed (%s), falling back to xr.concat", exc)
-
         datasets = []
         for p in nc_files:
             try:
-                datasets.append(xr.open_dataset(p))
+                datasets.append(xr.open_dataset(str(p)))
             except OSError as e:
                 self.logger.warning("Skipping %s: %s", p, e)
 
         if not datasets:
             return None
 
+        self.logger.info("Concatenating %d dataset(s) via xr.concat", len(datasets))
         return xr.concat(datasets, dim="time", join="outer")
 
     def _deployment_has_outputs(self, deployment_dir: Path, plot_name_stem: str) -> bool:
@@ -408,17 +395,21 @@ def _send_notify_email(
             std_png = None
         web_url = get_web_url(str(std_html)) if std_html else ""
 
+        sent_on = datetime.now(tz=UTC).astimezone().strftime("%Y-%m-%d %H:%M:%S %Z")
         plain = (
             f"New LRAUV deployment plots: {deployment_name}\n\n"
-            f"  View this and related information on the web:\n  {web_url}"
+            f"  View this and related information on the web:\n  {web_url}\n\n"
+            f"Sent on: {sent_on}"
         )
         img_tag = (
             '<img src="cid:std_plot" alt="Standard plot" style="max-width:100%"><br>'
             if std_png
             else ""
         )
         html_body = (
-            f'{img_tag}<p><a href="{web_url}">View this and related information on the web</a></p>'
+            f"{img_tag}"
+            f'<p><a href="{web_url}">View this and related information on the web</a></p>'
+            f"<p><small>Sent on: {sent_on}</small></p>"
         )
 
         outer = MIMEMultipart("related")
@@ -608,6 +599,7 @@ def _write_per_png_html(  # noqa: C901, PLR0913
             grouped.setdefault(log_dir, []).append(url)
 
         # Collect per-row data first so we can suppress empty columns
+        nt = 'target="_blank" rel="noopener"'  # new-tab attributes for all links
         rows: list[dict] = []
         for log_dir in sorted(grouped):
             nc_urls = grouped[log_dir]
@@ -616,9 +608,11 @@ def _write_per_png_html(  # noqa: C901, PLR0913
             rows.append(
                 {
                     "dir": log_dir,
-                    "plots": "<br>".join(f'<a href="{u}">{lbl}</a>' for u, lbl in png_links),
-                    "dap": "".join(f'<a href="{nc_url}.html">OPeNDAP</a>' for nc_url in nc_urls),
-                    "stoqs": f'<a href="{log_stoqs_url}">STOQS</a>' if log_stoqs_url else "",
+                    "plots": "<br>".join(f'<a href="{u}" {nt}>{lbl}</a>' for u, lbl in png_links),
+                    "dap": "".join(
+                        f'<a href="{nc_url}.html" {nt}>OPeNDAP</a>' for nc_url in nc_urls
+                    ),
+                    "stoqs": f'<a href="{log_stoqs_url}" {nt}>STOQS</a>' if log_stoqs_url else "",
                 }
             )
 
@@ -646,7 +640,7 @@ def _write_per_png_html(  # noqa: C901, PLR0913
         other_plots_line = ""
         if other_png_paths:
             sibling_links = [
-                f'<a href="{Path(p).with_suffix(".html").name}">{Path(p).name}</a>'
+                f'<a href="{Path(p).with_suffix(".html").name}" {nt}>{Path(p).name}</a>'
                 for p in other_png_paths
                 if Path(p).exists()
             ]
@@ -659,7 +653,7 @@ def _write_per_png_html(  # noqa: C901, PLR0913
         if stoqs_url:
             after_scheme = stoqs_url.split("//", 1)[-1] if "//" in stoqs_url else stoqs_url
             db_label = after_scheme.split("/")[1] if "/" in after_scheme else after_scheme
-            stoqs_line = f'<p>View these data in <a href="{stoqs_url}">{db_label}</a></p>\n'
+            stoqs_line = f'<p>View these data in <a href="{stoqs_url}" {nt}>{db_label}</a></p>\n'
 
         if png_file_path is not None and png_file_path.exists():
             b64 = base64.b64encode(png_file_path.read_bytes()).decode("ascii")
@@ -673,7 +667,7 @@ def _write_per_png_html(  # noqa: C901, PLR0913
         footer = (
             "<hr>\n"
             "<p><small>Created by "
-            f'<a href="{script_github_url}">lrauv_deployment_plots.py</a>'
+            f'<a href="{script_github_url}" {nt}>lrauv_deployment_plots.py</a>'
             f" on {created_ts}</small></p>\n"
         )
         html = (

src/data/make_permalink.py

@@ -8,7 +8,7 @@
 import csv
 import json
 import sys
-from datetime import UTC, datetime
+from datetime import UTC, datetime, timedelta
 from pathlib import Path
 
 import lzstring
@@ -96,7 +96,8 @@ def stoqs_url_from_ds(ds: xr.Dataset, base_url: str | None = None, auv_name: str
     # --- times ---
     times_np = ds.cf["time"].to_numpy()
     stime = pd.Timestamp(times_np[0]).to_pydatetime().replace(tzinfo=UTC)
-    etime = pd.Timestamp(times_np[-1]).to_pydatetime().replace(tzinfo=UTC)
+    # Subtract 1 second from the end time to avoid picking up the next Activity in the STOQS UI
+    etime = pd.Timestamp(times_np[-1]).to_pydatetime().replace(tzinfo=UTC) - timedelta(seconds=1)
 
     # --- depths ---
     depths_np = ds.cf["depth"].to_numpy()