updated tools for future sdi12 analog mix

pyproject.toml

@@ -40,10 +40,17 @@ dependencies = [
     "cloud-sql-python-connector>=1.0.0",
     "google-auth>=2.0.0",
     "google-cloud-secret-manager>=2.16.0",
-    "pg8000>=1.29.0",
+    "pg8000>=1.31.5",  # CVE-2025-61385: SQL injection fix
     "yagmail>=0.15.293",
     "keyring>=25.6.0",
     "pyserial>=3.5",
+    # Security fixes for transitive dependencies
+    "urllib3>=2.6.3",  # CVE-2026-21441: decompression bomb fixes
+    "aiohttp>=3.13.3",  # CVE-2025-69223: zip bomb and DoS fixes
+    "authlib>=1.6.4",  # CVE-2025-59420: JWT crit headers fix
+    "starlette>=0.49.1",  # CVE-2025-62727: Range header DoS fix
+    "fonttools>=4.60.2",  # CVE-2025-66034: arbitrary file write fix
+    "filelock>=3.20.1",  # CVE-2025-68146: TOCTOU symlink attack fix
 ]
 
 [project.optional-dependencies]
@@ -61,8 +68,8 @@ visualization = [
     "plotly>=5.0.0",
 ]
 mcp = [
-    "mcp[cli]>=0.1.0",
-    "fastmcp>=0.1.0",
+    "mcp[cli]>=1.23.0",  # CVE-2025-66416: DNS rebinding protection fix
+    "fastmcp>=2.14.0",  # Multiple security fixes including MCP 1.23+ update
 ]
 dev = [
     "pytest>=7.0.0",

src/rtgs_lab_tools/device_configuration/cli.py

@@ -348,6 +348,9 @@ def decode_both(ctx, system_uid, sensor_uid, verbose, log_file, no_postgres_log,
 @click.option("--num-co2", type=int, default=0, help="Number of CO2 sensors")
 @click.option("--num-o2", type=int, default=0, help="Number of O2 sensors")
 @click.option("--num-pressure", type=int, default=0, help="Number of pressure sensors")
+@click.option(
+    "--num-analog-mux", type=int, default=0, help="Number of analog mux sensors"
+)
 @add_common_options
 @click.pass_context
 @handle_common_errors("create-config")
@@ -368,6 +371,7 @@ def create_config(
     num_co2,
     num_o2,
     num_pressure,
+    num_analog_mux,
     verbose,
     log_file,
     no_postgres_log,
@@ -398,6 +402,7 @@ def create_config(
                     "numCO2": num_co2,
                     "numO2": num_o2,
                     "numPressure": num_pressure,
+                    "numAnalogMux": num_analog_mux,
                 },
             }
         }
@@ -432,6 +437,7 @@ def create_config(
             "num_co2": num_co2,
             "num_o2": num_o2,
             "num_pressure": num_pressure,
+            "num_analog_mux": num_analog_mux,
             "note": note,
         }
         results = {

src/rtgs_lab_tools/device_configuration/configurations/config.json

@@ -1,22 +1,22 @@
 {
     "config": {
-      "system": {
-        "logPeriod": 300,
-        "backhaulCount": 1,
-        "powerSaveMode": 2,
-        "loggingMode": 2,
-        "numAuxTalons": 1,
-        "numI2CTalons": 1,
-        "numSDI12Talons": 1
-      },
-      "sensors": {
-        "numET": 0,
-        "numHaar": 0,
-        "numSoil": 2,
-        "numApogeeSolar": 0,
-        "numCO2": 0,
-        "numO2": 0,
-        "numPressure": 0
-      }
+        "system": {
+            "logPeriod": 300,
+            "backhaulCount": 4,
+            "powerSaveMode": 1,
+            "loggingMode": 0,
+            "numAuxTalons": 1,
+            "numI2CTalons": 1,
+            "numSDI12Talons": 1
+        },
+        "sensors": {
+            "numET": 0,
+            "numHaar": 0,
+            "numSoil": 1,
+            "numApogeeSolar": 0,
+            "numCO2": 0,
+            "numO2": 0,
+            "numPressure": 0
+        }
     }
-  }
+}

src/rtgs_lab_tools/device_configuration/particle_client.py

@@ -157,6 +157,7 @@ def calculate_config_uid(config: Dict[str, Any]) -> Tuple[int, int]:
             | (sensors.get("numCO2", 0) << 12)
             | (sensors.get("numO2", 0) << 8)
             | (sensors.get("numPressure", 0) << 4)
+            | sensors.get("numAnalogMux", 0)
         )
 
         return system_uid, sensor_uid

src/rtgs_lab_tools/device_configuration/uid_decoding.py

@@ -50,6 +50,7 @@ def decode_sensor_configuration_uid(uid: int) -> Dict[str, int]:
     config["num_co2"] = (uid >> 12) & 0xF  # 4 bits at position 12-15
     config["num_o2"] = (uid >> 8) & 0xF  # 4 bits at position 8-11
     config["num_pressure"] = (uid >> 4) & 0xF  # 4 bits at position 4-7
+    config["num_analog_mux"] = uid & 0xF  # 4 bits at position 0-3
 
     return config
 
@@ -98,6 +99,7 @@ def format_sensor_config(uid: int) -> str:
         f"Num CO2 Sensors:      {config['num_co2']}",
         f"Num O2 Sensors:       {config['num_o2']}",
         f"Num Pressure Sensors: {config['num_pressure']}",
+        f"Num Analog Mux:       {config['num_analog_mux']}",
     ]
     return "\n".join(lines)
 

src/rtgs_lab_tools/mcp_server/rtgs_lab_tools_mcp_server.py

@@ -786,6 +786,7 @@ async def device_configuration_create_config(
     num_co2: int = 0,
     num_o2: int = 0,
     num_pressure: int = 0,
+    num_analog_mux: int = 0,
     note: Optional[str] = None,
 ) -> Dict[str, Any]:
     """
@@ -810,6 +811,7 @@ async def device_configuration_create_config(
         num_co2: Number of CO2 sensors (default: 0)
         num_o2: Number of O2 sensors (default: 0)
         num_pressure: Number of pressure sensors (default: 0)
+        num_analog_mux: Number of analog mux sensors (default: 0)
         note: Description for this operation (optional)
 
     Returns:
@@ -861,6 +863,8 @@ async def device_configuration_create_config(
             str(num_o2),
             "--num-pressure",
             str(num_pressure),
+            "--num-analog-mux",
+            str(num_analog_mux),
         ]
 
         if note:
@@ -890,6 +894,7 @@ async def device_configuration_create_config(
                     "numCO2": num_co2,
                     "numO2": num_o2,
                     "numPressure": num_pressure,
+                    "numAnalogMux": num_analog_mux,
                 },
             }
         }

tests/device_configuration/test_uid_decoding.py

@@ -78,7 +78,7 @@ def test_decode_basic_sensor_config(self):
         """Test decoding a basic sensor configuration UID."""
         # Create a test UID with known values
         # num_et=0, num_haar=0, num_soil=1, num_apogee_solar=0,
-        # num_co2=0, num_o2=0, num_pressure=0
+        # num_co2=0, num_o2=0, num_pressure=0, num_analog_mux=0
         # 0x00100000 = 1048576
         uid = 0x00100000
 
@@ -91,6 +91,7 @@ def test_decode_basic_sensor_config(self):
         assert config["num_co2"] == 0
         assert config["num_o2"] == 0
         assert config["num_pressure"] == 0
+        assert config["num_analog_mux"] == 0
 
     def test_decode_zero_sensor_uid(self):
         """Test decoding a zero sensor UID."""
@@ -113,6 +114,7 @@ def test_decode_max_sensor_values(self):
         assert config["num_co2"] == 0xF  # 4 bits
         assert config["num_o2"] == 0xF  # 4 bits
         assert config["num_pressure"] == 0xF  # 4 bits
+        assert config["num_analog_mux"] == 0xF  # 4 bits
 
     def test_decode_sensor_config_bit_masks(self):
         """Test specific bit mask operations for sensor config."""
@@ -128,6 +130,7 @@ def test_decode_sensor_config_bit_masks(self):
         assert config["num_co2"] == (0x12345678 >> 12) & 0xF
         assert config["num_o2"] == (0x12345678 >> 8) & 0xF
         assert config["num_pressure"] == (0x12345678 >> 4) & 0xF
+        assert config["num_analog_mux"] == 0x12345678 & 0xF
 
 
 class TestFormatSystemConfig:
@@ -182,6 +185,7 @@ def test_format_sensor_config_basic(self):
         assert "Num CO2 Sensors:      0" in formatted
         assert "Num O2 Sensors:       0" in formatted
         assert "Num Pressure Sensors: 0" in formatted
+        assert "Num Analog Mux:       0" in formatted
 
     def test_format_sensor_config_zero(self):
         """Test formatting a zero sensor configuration."""