From 2c2288bfdb5f6ca43ce35146ea8e4d15afc29c06 Mon Sep 17 00:00:00 2001
From: Lloyd Izard <76954858+LOCEANlloydizard@users.noreply.github.com>
Date: Mon, 14 Sep 2026 20:33:34 -0700
Subject: [PATCH 1/4] Add SPASSO IWCPS recipe

---
 recipes/deploy/deploy_spasso_iwcps_2026.yaml |  8 ++++++++
 recipes/params/params_spasso_iwcps_2026.yaml | 16 ++++++++++++++++
 2 files changed, 24 insertions(+)
 create mode 100644 recipes/deploy/deploy_spasso_iwcps_2026.yaml
 create mode 100644 recipes/params/params_spasso_iwcps_2026.yaml

diff --git a/recipes/deploy/deploy_spasso_iwcps_2026.yaml b/recipes/deploy/deploy_spasso_iwcps_2026.yaml
new file mode 100644
index 0000000..e3c3b00
--- /dev/null
+++ b/recipes/deploy/deploy_spasso_iwcps_2026.yaml
@@ -0,0 +1,8 @@
+flow_start_time:
+
+flows:
+  fetch_spasso:
+    deployment_name: fetch-spasso-iwcps-2026
+    deployment_concurrency:
+      limit: 1
+      collision_strategy: CANCEL_NEW
\ No newline at end of file
diff --git a/recipes/params/params_spasso_iwcps_2026.yaml b/recipes/params/params_spasso_iwcps_2026.yaml
new file mode 100644
index 0000000..bd24fac
--- /dev/null
+++ b/recipes/params/params_spasso_iwcps_2026.yaml
@@ -0,0 +1,16 @@
+flows:
+  fetch_spasso:
+    host: "ftp-access.aviso.altimetry.fr"
+    port: 2221
+    remote_path: "data/Cruises/IWCPS_Leg5"
+
+    path_main: "D:/spasso/IWCPS_Leg5"
+
+    filename_pattern: "*"
+    new_file_num_limit: 1
+
+    username_env: "SPASSO_USERNAME"
+    password_env: "SPASSO_PASSWORD"
+
+    task_retries: 3
+    task_retry_delay_seconds: 30
\ No newline at end of file

From 7f64aa2532c43efbdc2726da505d39594d142c52 Mon Sep 17 00:00:00 2001
From: Lloyd Izard <76954858+LOCEANlloydizard@users.noreply.github.com>
Date: Fri, 18 Sep 2026 21:18:49 -0700
Subject: [PATCH 2/4] Update SPASSO IWCPS recipe and navigation

---
 .../deploy/deploy_spasso_iwcps_2026.yaml      |   4 +-
 .../params/params_spasso_iwcps_2026.yaml      |  28 ++-
 recipes_nrt/params/viz_spasso_iwcps_2026.yaml |  99 ++++++++
 scripts/watch_ship_navigation.py              | 228 ++++++++++++++++++
 4 files changed, 348 insertions(+), 11 deletions(-)
 create mode 100644 recipes_nrt/params/viz_spasso_iwcps_2026.yaml
 create mode 100644 scripts/watch_ship_navigation.py

diff --git a/recipes_nrt/deploy/deploy_spasso_iwcps_2026.yaml b/recipes_nrt/deploy/deploy_spasso_iwcps_2026.yaml
index e3c3b00..309c5a4 100644
--- a/recipes_nrt/deploy/deploy_spasso_iwcps_2026.yaml
+++ b/recipes_nrt/deploy/deploy_spasso_iwcps_2026.yaml
@@ -3,6 +3,4 @@ flow_start_time:
 flows:
   fetch_spasso:
     deployment_name: fetch-spasso-iwcps-2026
-    deployment_concurrency:
-      limit: 1
-      collision_strategy: CANCEL_NEW
\ No newline at end of file
+    interval: 15
\ No newline at end of file
diff --git a/recipes_nrt/params/params_spasso_iwcps_2026.yaml b/recipes_nrt/params/params_spasso_iwcps_2026.yaml
index bd24fac..7e18724 100644
--- a/recipes_nrt/params/params_spasso_iwcps_2026.yaml
+++ b/recipes_nrt/params/params_spasso_iwcps_2026.yaml
@@ -1,16 +1,28 @@
 flows:
   fetch_spasso:
-    host: "ftp-access.aviso.altimetry.fr"
+    host: "download host"
     port: 2221
-    remote_path: "data/Cruises/IWCPS_Leg5"
+    remote_path: "remote path"
 
-    path_main: "D:/spasso/IWCPS_Leg5"
+    path_main: "path/to/spasso"
 
-    filename_pattern: "*"
-    new_file_num_limit: 1
+    product_patterns:
+      - "Copernicus_PHY"
+      - "Copernicus_SST_L4"
+      - "Copernicus_SSS_L4"
+      - "Copernicus_CHL_L4"
+      - "FTLE_Copernicus_PHY"
+      - "OW_Copernicus_PHY"
+      - "KE_Copernicus_PHY"
+      - "LLADV_Copernicus_PHY"
 
-    username_env: "SPASSO_USERNAME"
-    password_env: "SPASSO_PASSWORD"
+    username_secret: "spasso-username"
+    password_secret: "spasso-password"
 
     task_retries: 3
-    task_retry_delay_seconds: 30
\ No newline at end of file
+    task_retry_delay_seconds: 30
+
+navigation:
+  port: "serial port"
+  baudrate: 4800
+  path_output: "path/to/navigation"
\ No newline at end of file
diff --git a/recipes_nrt/params/viz_spasso_iwcps_2026.yaml b/recipes_nrt/params/viz_spasso_iwcps_2026.yaml
new file mode 100644
index 0000000..9809718
--- /dev/null
+++ b/recipes_nrt/params/viz_spasso_iwcps_2026.yaml
@@ -0,0 +1,99 @@
+dashboard:
+  title: "App' title"
+
+  spasso_path: "path/to/spasso"
+  navigation_path: "path/to/navigation"
+  cartopy_path: "path/to/cartopy"
+
+  map_radius_km: 500
+  navigation_history_hours: 6
+  refresh_seconds: 60
+
+  plot:
+    width: 520
+    height: 400
+
+products:
+  sst:
+    title: "Sea Surface Temperature"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_SST_L4.nc"
+    variables:
+      - "analysed_sst"
+    cmap: "Turbo"
+    label: "SST (°C)"
+    transform: "kelvin_to_celsius"
+    clim: [10.0, 20.0]
+
+  sss:
+    title: "Sea Surface Salinity"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_SSS_L4.nc"
+    variables:
+      - "sos"
+    cmap: "Viridis"
+    label: "SSS"
+    clim: [30.0, 34.0]
+
+  chla:
+    title: "Chlorophyll-a"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_CHL_L4.nc"
+    variables:
+      - "CHL"
+    cmap: "Viridis"
+    label: "Chlorophyll-a (mg m⁻³)"
+    clim: [0.0, 5.0]
+
+  ftle:
+    title: "Finite Time Lyapunov Exponent"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_FTLE_Copernicus_PHY.nc"
+    variables:
+      - "ftle"
+    cmap: "Greys"
+    label: "FTLE"
+    zero_min: true
+
+  ke:
+    title: "Kinetic Energy"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_KE_Copernicus_PHY.nc"
+    variables:
+      - "ke"
+    cmap: "Viridis"
+    label: "KE"
+    zero_min: true
+
+  ow:
+    title: "Okubo-Weiss Parameter"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_OW_Copernicus_PHY.nc"
+    variables:
+      - "ow"
+    cmap: "RdBu_r"
+    label: "OW"
+
+currents:
+  title: "Surface Geostrophic Currents"
+  tab: "Currents / Diagnostics"
+
+  pattern: "????????_Copernicus_PHY.nc"
+
+  u_variable: "ugos"
+  v_variable: "vgos"
+
+  cmap: "Viridis"
+  label: "Current speed (m/s)"
+  zero_min: true
+
+  vectors:
+    enabled: true
+    step: 2
+    scale: 0.5
\ No newline at end of file
diff --git a/scripts/watch_ship_navigation.py b/scripts/watch_ship_navigation.py
new file mode 100644
index 0000000..ab25978
--- /dev/null
+++ b/scripts/watch_ship_navigation.py
@@ -0,0 +1,228 @@
+"""Continuously record ship navigation from an NMEA 0183 serial stream."""
+
+from __future__ import annotations
+
+import argparse
+from datetime import datetime, timezone
+from pathlib import Path
+
+import pandas as pd
+import serial
+import yaml
+import time
+
+def nmea_to_decimal(value: str, hemisphere: str) -> float:
+    """Convert an NMEA coordinate to decimal degrees."""
+    raw = float(value)
+
+    degrees = int(raw // 100)
+    minutes = raw - degrees * 100
+
+    decimal = degrees + minutes / 60.0
+
+    if hemisphere in {"S", "W"}:
+        decimal *= -1
+
+    return decimal
+
+
+def parse_rmc(sentence: str) -> dict[str, object] | None:
+    """Parse a valid GPRMC sentence."""
+    if not sentence.startswith("$GPRMC"):
+        return None
+
+    fields = sentence.split(",")
+
+    if len(fields) < 10 or fields[2] != "A":
+        return None
+
+    time_string = fields[1]
+    latitude = fields[3]
+    latitude_hemisphere = fields[4]
+    longitude = fields[5]
+    longitude_hemisphere = fields[6]
+    speed_knots = fields[7]
+    course_deg = fields[8]
+    date_string = fields[9]
+
+    if not all(
+        [
+            time_string,
+            date_string,
+            latitude,
+            latitude_hemisphere,
+            longitude,
+            longitude_hemisphere,
+        ]
+    ):
+        return None
+
+    timestamp = datetime.strptime(
+        date_string + time_string.split(".")[0],
+        "%d%m%y%H%M%S",
+    ).replace(tzinfo=timezone.utc)
+
+    return {
+        "timestamp_utc": timestamp,
+        "latitude": nmea_to_decimal(latitude, latitude_hemisphere),
+        "longitude": nmea_to_decimal(longitude, longitude_hemisphere),
+        "speed_knots": float(speed_knots) if speed_knots else None,
+        "course_deg": float(course_deg) if course_deg else None,
+    }
+
+
+def write_parquet_chunk(
+    records: list[dict[str, object]],
+    output_dir: Path,
+) -> Path:
+    """Write one completed navigation minute to Parquet."""
+    if not records:
+        raise ValueError("Cannot write an empty navigation chunk.")
+
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+    first_timestamp = records[0]["timestamp_utc"]
+
+    filename = (
+        f"ship_navigation_"
+        f"{first_timestamp:%Y%m%d_%H%M}.parquet"
+    )
+
+    output_path = output_dir / filename
+
+    dataframe = pd.DataFrame(records)
+    dataframe.to_parquet(output_path, index=False)
+
+    return output_path
+
+
+def load_navigation_config(config_path: Path) -> dict:
+    """Load navigation configuration from the cruise params YAML."""
+    with config_path.open("r", encoding="utf-8") as file:
+        config = yaml.safe_load(file)
+
+    if "navigation" not in config:
+        raise ValueError(
+            f"No 'navigation' section found in {config_path}"
+        )
+
+    return config["navigation"]
+
+
+def watch_navigation(
+    port: str,
+    baudrate: int,
+    output_dir: Path,
+) -> None:
+    """Continuously read GPS positions and write one Parquet file per minute."""
+    print(f"Reading navigation from {port} @ {baudrate} baud")
+    print(f"Writing navigation to {output_dir}")
+    print("Press Ctrl+C to stop.")
+
+    records: list[dict[str, object]] = []
+    current_minute = None
+
+    try:
+        while True:
+            try:
+                with serial.Serial(
+                    port=port,
+                    baudrate=baudrate,
+                    timeout=1,
+                ) as stream:
+                    print(f"Connected to {port}.")
+
+                    while True:
+                        sentence = (
+                            stream.readline()
+                            .decode("ascii", errors="ignore")
+                            .strip()
+                        )
+
+                        navigation = parse_rmc(sentence)
+
+                        if navigation is None:
+                            continue
+
+                        timestamp = navigation["timestamp_utc"]
+                        minute = timestamp.replace(
+                            second=0,
+                            microsecond=0,
+                        )
+
+                        if current_minute is None:
+                            current_minute = minute
+
+                        # A new UTC minute has started.
+                        if minute != current_minute:
+                            output_path = write_parquet_chunk(
+                                records,
+                                output_dir,
+                            )
+
+                            print(
+                                f"Saved {len(records)} positions -> "
+                                f"{output_path.name}"
+                            )
+
+                            records = []
+                            current_minute = minute
+
+                        records.append(navigation)
+
+                        print(
+                            f"{timestamp.isoformat()} | "
+                            f"lat={navigation['latitude']:.6f} | "
+                            f"lon={navigation['longitude']:.6f} | "
+                            f"speed={navigation['speed_knots']} kn | "
+                            f"course={navigation['course_deg']}°"
+                        )
+
+            except serial.SerialException as exc:
+                print(
+                    f"Serial connection lost: {exc}\n"
+                    f"Retrying {port} in 5 seconds..."
+                )
+                time.sleep(5)
+
+    except KeyboardInterrupt:
+        print("\nStopping navigation reader.")
+
+        # Preserve the unfinished minute when stopped manually.
+        if records:
+            output_path = write_parquet_chunk(
+                records,
+                output_dir,
+            )
+
+            print(
+                f"Saved final {len(records)} positions -> "
+                f"{output_path.name}"
+            )
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(
+        description="Record ship navigation from an NMEA serial stream."
+    )
+
+    parser.add_argument(
+        "--config",
+        type=Path,
+        required=True,
+        help="Path to the cruise parameter YAML.",
+    )
+
+    args = parser.parse_args()
+
+    navigation_config = load_navigation_config(args.config)
+
+    watch_navigation(
+        port=navigation_config["port"],
+        baudrate=int(navigation_config["baudrate"]),
+        output_dir=Path(navigation_config["path_output"]),
+    )
+
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file

From 96f26e852d09a7abbe6700e728a25787d00e70bf Mon Sep 17 00:00:00 2001
From: Lloyd Izard <76954858+LOCEANlloydizard@users.noreply.github.com>
Date: Fri, 18 Sep 2026 21:23:55 -0700
Subject: [PATCH 3/4] Consolidate SPASSO configuration

---
 .../params/params_spasso_iwcps_2026.yaml      | 106 +++++++++++++++++-
 recipes_nrt/params/viz_spasso_iwcps_2026.yaml |  99 ----------------
 2 files changed, 105 insertions(+), 100 deletions(-)
 delete mode 100644 recipes_nrt/params/viz_spasso_iwcps_2026.yaml

diff --git a/recipes_nrt/params/params_spasso_iwcps_2026.yaml b/recipes_nrt/params/params_spasso_iwcps_2026.yaml
index 7e18724..894e936 100644
--- a/recipes_nrt/params/params_spasso_iwcps_2026.yaml
+++ b/recipes_nrt/params/params_spasso_iwcps_2026.yaml
@@ -22,7 +22,111 @@ flows:
     task_retries: 3
     task_retry_delay_seconds: 30
 
+
 navigation:
   port: "serial port"
   baudrate: 4800
-  path_output: "path/to/navigation"
\ No newline at end of file
+  path_output: "path/to/navigation"
+
+
+dashboard:
+  title: "App title"
+
+  spasso_path: "path/to/spasso"
+  navigation_path: "path/to/navigation"
+  cartopy_path: "path/to/cartopy"
+
+  map_radius_km: 500
+  navigation_history_hours: 6
+  refresh_seconds: 60
+
+  plot:
+    width: 520
+    height: 400
+
+
+products:
+  sst:
+    title: "Sea Surface Temperature"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_SST_L4.nc"
+    variables:
+      - "analysed_sst"
+    cmap: "Turbo"
+    label: "SST (°C)"
+    transform: "kelvin_to_celsius"
+    clim: [10.0, 20.0]
+
+  sss:
+    title: "Sea Surface Salinity"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_SSS_L4.nc"
+    variables:
+      - "sos"
+    cmap: "Viridis"
+    label: "SSS"
+    clim: [30.0, 34.0]
+
+  chla:
+    title: "Chlorophyll-a"
+    tab: "Environmental"
+    patterns:
+      - "*_Copernicus_CHL_L4.nc"
+    variables:
+      - "CHL"
+    cmap: "Viridis"
+    label: "Chlorophyll-a (mg m⁻³)"
+    clim: [0.0, 5.0]
+
+  ftle:
+    title: "Finite Time Lyapunov Exponent"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_FTLE_Copernicus_PHY.nc"
+    variables:
+      - "ftle"
+    cmap: "Greys"
+    label: "FTLE"
+    zero_min: true
+
+  ke:
+    title: "Kinetic Energy"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_KE_Copernicus_PHY.nc"
+    variables:
+      - "ke"
+    cmap: "Viridis"
+    label: "KE"
+    zero_min: true
+
+  ow:
+    title: "Okubo-Weiss Parameter"
+    tab: "Currents / Diagnostics"
+    patterns:
+      - "*_OW_Copernicus_PHY.nc"
+    variables:
+      - "ow"
+    cmap: "RdBu_r"
+    label: "OW"
+
+
+currents:
+  title: "Surface Geostrophic Currents"
+  tab: "Currents / Diagnostics"
+
+  pattern: "????????_Copernicus_PHY.nc"
+
+  u_variable: "ugos"
+  v_variable: "vgos"
+
+  cmap: "Viridis"
+  label: "Current speed (m/s)"
+  zero_min: true
+
+  vectors:
+    enabled: true
+    step: 2
+    scale: 0.5
\ No newline at end of file
diff --git a/recipes_nrt/params/viz_spasso_iwcps_2026.yaml b/recipes_nrt/params/viz_spasso_iwcps_2026.yaml
deleted file mode 100644
index 9809718..0000000
--- a/recipes_nrt/params/viz_spasso_iwcps_2026.yaml
+++ /dev/null
@@ -1,99 +0,0 @@
-dashboard:
-  title: "App' title"
-
-  spasso_path: "path/to/spasso"
-  navigation_path: "path/to/navigation"
-  cartopy_path: "path/to/cartopy"
-
-  map_radius_km: 500
-  navigation_history_hours: 6
-  refresh_seconds: 60
-
-  plot:
-    width: 520
-    height: 400
-
-products:
-  sst:
-    title: "Sea Surface Temperature"
-    tab: "Environmental"
-    patterns:
-      - "*_Copernicus_SST_L4.nc"
-    variables:
-      - "analysed_sst"
-    cmap: "Turbo"
-    label: "SST (°C)"
-    transform: "kelvin_to_celsius"
-    clim: [10.0, 20.0]
-
-  sss:
-    title: "Sea Surface Salinity"
-    tab: "Environmental"
-    patterns:
-      - "*_Copernicus_SSS_L4.nc"
-    variables:
-      - "sos"
-    cmap: "Viridis"
-    label: "SSS"
-    clim: [30.0, 34.0]
-
-  chla:
-    title: "Chlorophyll-a"
-    tab: "Environmental"
-    patterns:
-      - "*_Copernicus_CHL_L4.nc"
-    variables:
-      - "CHL"
-    cmap: "Viridis"
-    label: "Chlorophyll-a (mg m⁻³)"
-    clim: [0.0, 5.0]
-
-  ftle:
-    title: "Finite Time Lyapunov Exponent"
-    tab: "Currents / Diagnostics"
-    patterns:
-      - "*_FTLE_Copernicus_PHY.nc"
-    variables:
-      - "ftle"
-    cmap: "Greys"
-    label: "FTLE"
-    zero_min: true
-
-  ke:
-    title: "Kinetic Energy"
-    tab: "Currents / Diagnostics"
-    patterns:
-      - "*_KE_Copernicus_PHY.nc"
-    variables:
-      - "ke"
-    cmap: "Viridis"
-    label: "KE"
-    zero_min: true
-
-  ow:
-    title: "Okubo-Weiss Parameter"
-    tab: "Currents / Diagnostics"
-    patterns:
-      - "*_OW_Copernicus_PHY.nc"
-    variables:
-      - "ow"
-    cmap: "RdBu_r"
-    label: "OW"
-
-currents:
-  title: "Surface Geostrophic Currents"
-  tab: "Currents / Diagnostics"
-
-  pattern: "????????_Copernicus_PHY.nc"
-
-  u_variable: "ugos"
-  v_variable: "vgos"
-
-  cmap: "Viridis"
-  label: "Current speed (m/s)"
-  zero_min: true
-
-  vectors:
-    enabled: true
-    step: 2
-    scale: 0.5
\ No newline at end of file

From 93fae90402573d355b4f72240b427d9d9b56d308 Mon Sep 17 00:00:00 2001
From: Lloyd Izard <76954858+LOCEANlloydizard@users.noreply.github.com>
Date: Sat, 19 Sep 2026 08:35:42 -0700
Subject: [PATCH 4/4] Update echodataflow checkout in monitoring CI

---
 .github/workflows/test_monitoring.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_monitoring.yaml b/.github/workflows/test_monitoring.yaml
index 058534c..a9b5127 100644
--- a/.github/workflows/test_monitoring.yaml
+++ b/.github/workflows/test_monitoring.yaml
@@ -17,12 +17,12 @@ jobs:
       - name: Checkout recipes
         uses: actions/checkout@v4
 
-      - name: Checkout echodataflow monitoring PR
+      - name: Checkout echodataflow
         uses: actions/checkout@v4
         with:
           repository: echostack-org/echodataflow
-          ref: refs/pull/174/head
           path: echodataflow
+          fetch-depth: 0
 
       - name: Set up Python
         uses: actions/setup-python@v5