Fixups for making Quick Look plots in production

README.md

@@ -110,6 +110,7 @@ First time use with Docker on a server using a service account:
     `CALIBRATION_VOL=<mount_location>`
     `WORK_VOL=<auv-python_home>/data`
     `HOST_NAME=<name_of_host>`
+    `GMT_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/`
 After installation and when logging into the server again mission data can be processed thusly:
 * Setting up environment and printing help message:   
     `sudo -u docker_user -i`  

docker-compose.yml

@@ -4,7 +4,8 @@
 # LRAUV_VOL=/Volumes/LRAUV
 # CALIBRATION_VOL=/Volumes/DMO
 # WORK_VOL=/opt/docker_auv-python_vols/data
-# HOST_NAME=MBARI2597.shhore.mbari.org
+# HOST_NAME=MBARI2597.shore.mbari.org
+# GMT_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu/
 
 # Required in shell environment:
 # export DOCKER_USER_ID=$(id -u)

docker/Dockerfile

@@ -20,6 +20,7 @@ RUN apt-get update \
         rsync \
         # GMT6 dependencies
         gmt \
+        libgmt-dev \
         gmt-dcw \
         gmt-gshhg \
     && rm -rf /var/lib/apt/lists/*

pyproject.toml

@@ -23,7 +23,7 @@ dependencies = [
     "numpy>=2.2.6",
     "pooch>=1.8.2",
     "pyarrow>=20.0.0",
-    "pygmt>=0.17.0",
+    "pygmt==0.16",
     "pyproj>=3.7.1",
     "pysolar>=0.13",
     "rolling>=0.5.0",

src/data/create_products.py

@@ -321,7 +321,7 @@ def _get_bathymetry(self, lons: np.ndarray, lats: np.ndarray) -> np.ndarray:
             Array of bathymetry depths (positive down) in meters, or None if pygmt unavailable
         """
         if not PYGMT_AVAILABLE:
-            self.logger.debug("pygmt not available, cannot retrieve bathymetry")
+            self.logger.warning("pygmt not available, will not be plotting bottom depths")
             return None
 
         # Use local Monterey Bay grid if available and coordinates are in range
@@ -1342,5 +1342,5 @@ def process_command_line(self):
     p_start = time.time()
     cp.plot_2column()
     cp.plot_biolume()
-    # cp.gulper_odv()
+    cp.gulper_odv()
     cp.logger.info("Time to process: %.2f seconds", (time.time() - p_start))

src/data/process.py

@@ -673,8 +673,8 @@ def create_products(self, mission: str) -> None:
         cp.logger.setLevel(self._log_levels[self.config["verbose"]])
         cp.logger.addHandler(self.log_handler)
 
-        # cp.plot_biolume()
-        # cp.plot_2column()
+        cp.plot_biolume()
+        cp.plot_2column()
         if "dorado" in cp.auv_name.lower():
             cp.gulper_odv()
         cp.logger.removeHandler(self.log_handler)