Merge branch 'main' into fix_division_by_zero

echopype/convert/parse_base.py

@@ -495,7 +495,13 @@ def _read_datagrams(self, fid):
 
             # XML datagrams store environment or instrument parameters for EK80
             if new_datagram["type"].startswith("XML"):
-                if new_datagram["subtype"] == "environment":
+                # Check that environment datagrams contain more than
+                # just drop_keel_offset and drop_keel_offset_is_manual
+                # Temporary fix for handling >1 EK80 environment datagrams described in:
+                # https://github.com/OSOceanAcoustics/echopype/issues/1386
+                if new_datagram["subtype"] == "environment" and set(
+                    ["drop_keel_offset", "drop_keel_offset_is_manual"]
+                ) != set(new_datagram["environment"].keys()):
                     self.environment = new_datagram["environment"]
                     self.environment["xml"] = new_datagram["xml"]
                     self.environment["timestamp"] = new_datagram["timestamp"]

echopype/tests/convert/test_convert_ek80.py

@@ -511,3 +511,23 @@ def test_parse_missing_sound_velocity_profile():
 
     # Remove Zarr File
     shutil.rmtree(save_path)
+
+
+@pytest.mark.unit
+def test_parse_ek80_with_invalid_env_datagrams():
+    """
+    Tests parsing EK80 RAW file with invalid environment datagrams. Checks that the EchoData object
+    contains the necessary environment variables for calibration.
+    """
+
+    # Parse RAW
+    ed = open_raw(
+        "echopype/test_data/ek80_invalid_env_datagrams/SH24-replay-D20240705-T070536.raw",
+        sonar_model="EK80",
+    )
+
+    # Check that each calibration specific variable exists, is not NaN, and is of type float64
+    for var in ["acidity", "depth", "salinity", "temperature", "sound_speed_indicative"]:
+        env_var = ed["Environment"][var]
+        assert env_var.notnull().all() and env_var.dtype == np.float64
+