From 6bc98ba67ef3292f3b8fb5e980afbf7c01038600 Mon Sep 17 00:00:00 2001
From: Jesse Cusack <jesse.cusack@oregonstate.edu>
Date: Tue, 27 Jan 2026 14:28:42 -0800
Subject: [PATCH 1/2] stop thermo calcs if not specified

---
 src/glide/cli.py        |  2 +-
 src/glide/config.py     | 25 ++++++++++++++-----------
 src/glide/process_l1.py |  8 +++++++-
 3 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/src/glide/cli.py b/src/glide/cli.py
index 0f80e7b..eee8acd 100644
--- a/src/glide/cli.py
+++ b/src/glide/cli.py
@@ -425,7 +425,7 @@ def get_raw_base_name(raw_file: Path) -> str:
 @app.command()
 @log_args
 def cfg(
-    out_file: _out_file_annotation = "default.config.yaml",
+    out_file: _out_file_annotation = "default.config.yml",
 ) -> None:
     """
     Output the default configuration file.
diff --git a/src/glide/config.py b/src/glide/config.py
index 2deaef0..b26d4ad 100644
--- a/src/glide/config.py
+++ b/src/glide/config.py
@@ -45,12 +45,11 @@ def _load_core() -> tuple[dict, dict, dict]:
     with open(core_file) as f:
         docs = [doc for doc in safe_load_all(f)]
 
-    core_variables = docs[0] if docs else {}
-    flight_attitude = docs[1] if len(docs) > 1 else {}
-    derived_thermo = docs[2] if len(docs) > 2 else {}
-
-    return core_variables, flight_attitude, derived_thermo
+    core = docs[0] if docs else {}
+    flight = docs[1] if len(docs) > 1 else {}
+    thermo = docs[2] if len(docs) > 2 else {}
 
+    return core, flight, thermo
 
 def _apply_qc_overrides(variables: dict, qc_overrides: dict) -> dict:
     """Apply QC parameter overrides to variable definitions.
@@ -121,7 +120,7 @@ def load_config(file: str | None = None) -> dict:
         - merged_variables: variables for higher-level processing
     """
     # Load core definitions
-    core_variables, flight_attitude, derived_thermo = _load_core()
+    core, flight, thermo = _load_core()
 
     # Load user config
     if file is None:
@@ -141,18 +140,18 @@ def load_config(file: str | None = None) -> dict:
 
     # Extract include toggles (default to True for backward compatibility)
     include = include_config.get("include", {})
-    include_flight = include.get("flight_attitude", True)
-    include_thermo = include.get("derived_thermo", True)
+    include_flight = include.get("flight", True)
+    include_thermo = include.get("thermo", True)
 
     # Build variable set: start with core
-    variables = copy.deepcopy(core_variables)
+    variables = copy.deepcopy(core)
 
     # Add optional suites if enabled
     if include_flight:
-        variables.update(copy.deepcopy(flight_attitude))
+        variables.update(copy.deepcopy(flight))
         _log.debug("Including flight_attitude suite")
     if include_thermo:
-        variables.update(copy.deepcopy(derived_thermo))
+        variables.update(copy.deepcopy(thermo))
         _log.debug("Including derived_thermo suite")
 
     # Apply QC overrides
@@ -193,6 +192,10 @@ def load_config(file: str | None = None) -> dict:
         variables=variables,
         slocum=slocum_name_map,
         merged_variables=merged_vars,
+        include=dict(
+            flight=include_flight,
+            thermo=include_thermo,
+        ),
     )
 
     return config
diff --git a/src/glide/process_l1.py b/src/glide/process_l1.py
index 65d75c3..21975fa 100644
--- a/src/glide/process_l1.py
+++ b/src/glide/process_l1.py
@@ -205,7 +205,13 @@ def merge(
 
 
 def calculate_thermodynamics(ds: xr.Dataset, config: dict) -> xr.Dataset:
-    """Should be applied after merging flight and science."""
+    """Should be applied after merging flight and science.
+    
+    Skips calculation if thermo suite is disabled in config.
+    """
+    if not config.get("include", {}).get("thermo", True):
+        _log.debug("Skipping thermodynamics (disabled in config)")
+        return ds
 
     _log.debug("Calculating thermodynamics")
 

From 2c6e4a19fbaee03d4fcd41bbdff3489d2decebe1 Mon Sep 17 00:00:00 2001
From: Jesse Cusack <jesse.cusack@oregonstate.edu>
Date: Wed, 28 Jan 2026 08:43:41 -0800
Subject: [PATCH 2/2] formatting

---
 src/glide/config.py     | 1 +
 src/glide/process_l1.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/glide/config.py b/src/glide/config.py
index b26d4ad..04ade5b 100644
--- a/src/glide/config.py
+++ b/src/glide/config.py
@@ -51,6 +51,7 @@ def _load_core() -> tuple[dict, dict, dict]:
 
     return core, flight, thermo
 
+
 def _apply_qc_overrides(variables: dict, qc_overrides: dict) -> dict:
     """Apply QC parameter overrides to variable definitions.
 
diff --git a/src/glide/process_l1.py b/src/glide/process_l1.py
index 21975fa..ccfd8ae 100644
--- a/src/glide/process_l1.py
+++ b/src/glide/process_l1.py
@@ -206,7 +206,7 @@ def merge(
 
 def calculate_thermodynamics(ds: xr.Dataset, config: dict) -> xr.Dataset:
     """Should be applied after merging flight and science.
-    
+
     Skips calculation if thermo suite is disabled in config.
     """
     if not config.get("include", {}).get("thermo", True):