Hot Fix: structured_log function no longer with us

workflow/log_utils.py

@@ -1,8 +1,8 @@
 r"""Structured Logging Utilities for `logging`.
 
-This module support for different structured-logging formats (JSON and
+This module supports different structured-logging formats (JSON and
 text) and decorators for logging function calls and command
-executions. The logging functions can capture and structure log
+executions. The logging functions capture and structure log
 messages along with additional contextual information such as function
 arguments, execution status, and timestamps.
 
@@ -13,12 +13,12 @@
 >>> def foo(a, b):
 >>>     return a + b
 >>> foo(1, 2)
-2024-09-18 22:00:51.498268+00:00	INFO	example	MainThread	called	 function=foo	id=...	a=1	b=2
-2024-09-18 22:00:51.498268+00:00	INFO	example	MainThread	completed	 function=foo	id=...	result=3
+{"timestamp": "2025-02-25T22:00:51.498268Z", "level": "info", "logger": "example", "thread": "MainThread", "event": "called", "function": "foo", "id": "...", "a": 1, "b": 2}
+{"timestamp": "2025-02-25T22:00:51.498268Z", "level": "info", "logger": "example", "thread": "MainThread", "event": "completed", "function": "foo", "id": "...", "result": 3}
 3
 >>> logger = get_logger('example')
->>> logger.info(structured_log('hello world', counter=1))
-2024-09-18 22:00:51.498268+00:00	INFO	example	MainThread	hello world	 counter=1
+>>> logger.info('hello world', counter=1)
+{"timestamp": "2025-02-25T22:00:51.498268Z", "level": "info", "logger": "example", "thread": "MainThread", "event": "hello world", "counter": 1}
 """
 
 import functools

workflow/scripts/bb_sim.py

@@ -125,14 +125,10 @@ def bb_simulate_station(
     logger = log_utils.get_logger(__name__)
 
     if np.isnan(lf_acc).any():
-        logger.error(
-            log_utils.structured_log("Station LF had NaN waveform", station=station)
-        )
+        logger.error("Station LF had NaN waveform", station=station)
         raise ValueError(f"Station {station_name} had NaN waveform")
     if np.isnan(hf_acc).any():
-        logger.error(
-            log_utils.structured_log("Station HF had NaN waveform", station=station)
-        )
+        logger.error("Station HF had NaN waveform", station=station)
         raise ValueError(f"Station {station_name} had NaN waveform")
 
     pga = np.max(np.abs(hf_acc), axis=0) / 981.0
@@ -181,9 +177,13 @@ def bb_simulate_station(
 def combine_hf_and_lf(
     realisation_ffp: Annotated[Path, typer.Argument(dir_okay=False, exists=True)],
     station_vs30_ffp: Annotated[Path, typer.Argument(dir_okay=False, exists=True)],
-    low_frequency_waveform_directory: Annotated[Path, typer.Argument(file_okay=False, exists=True)],
+    low_frequency_waveform_directory: Annotated[
+        Path, typer.Argument(file_okay=False, exists=True)
+    ],
     high_frequency_waveform_file: Annotated[Path, typer.Argument(exists=True)],
-    velocity_model_directory: Annotated[Path, typer.Argument(file_okay=False, exists=True)],
+    velocity_model_directory: Annotated[
+        Path, typer.Argument(file_okay=False, exists=True)
+    ],
     output_ffp: Annotated[Path, typer.Argument(dir_okay=False, writable=True)],
 ):
     """Combine low-frequency and high-frequency seismic waveforms.

workflow/scripts/check_domain.py

@@ -26,6 +26,7 @@
 -------------
 See the output of `check-domain --help`.
 """
+
 from pathlib import Path
 from typing import Annotated
 
@@ -76,10 +77,8 @@ def check_domain(
     hausdorf_distance = shapely.hausdorff_distance(srf_geometry, domain.domain.polygon)
     if hausdorf_distance < 1000:
         logger.warning(
-            log_utils.structured_log(
-                "SRF geometry is close the edge of the domain. This could indicate a patch outside the domain, but may not be an error in its own right.",
-                closest_distance=hausdorf_distance,
-            ),
+            "SRF geometry is close the edge of the domain. This could indicate a patch outside the domain, but may not be an error in its own right.",
+            closest_distance=hausdorf_distance,
         )
         raise typer.Exit(code=1)
 
@@ -95,9 +94,7 @@ def check_domain(
         ]
     ):
         logger.error(
-            log_utils.structured_log(
-                "The expected velocity model size does not match the computed velocity model size",
-                expected_size=velocity_model_estimated_size,
-            ),
+            "The expected velocity model size does not match the computed velocity model size",
+            expected_size=velocity_model_estimated_size,
         )
         raise typer.Exit(code=1)

workflow/scripts/check_srf.py

@@ -100,37 +100,27 @@ def check_srf(
         )
         if not np.isclose(srf_magnitude, magnitude, atol=5e-3):
             logger.error(
-                log_utils.structured_log(
-                    "Mismatch SRF magnitude",
-                    srf_magnitude=srf_magnitude,
-                    realisation_magnitude=magnitude,
-                )
+                "Mismatch SRF magnitude",
+                srf_magnitude=srf_magnitude,
+                realisation_magnitude=magnitude,
             )
             raise typer.Exit(code=1)
     except RealisationParseError:
         pass
 
     if srf_magnitude >= 11:
-        logger.error(
-            log_utils.structured_log(
-                "Implausible SRF magnitude", srf_magnitude=magnitude
-            )
-        )
+        logger.error("Implausible SRF magnitude", srf_magnitude=magnitude)
         raise typer.Exit(code=1)
 
     if (srf_file.points["dep"] < 0).any():
         logger.error(
-            log_utils.structured_log(
-                "Negative SRF depth detected", min_depth=srf_file.points["depth"].min()
-            )
+            "Negative SRF depth detected", min_depth=srf_file.points["depth"].min()
         )
         raise typer.Exit(code=1)
 
     if not np.isclose(srf_file.points["tinit"].min(), 0):
         logger.warning(
-            log_utils.structured_log(
-                "SRF does not begin at zero (this may not be an error depending on SRF setup)",
-                tinit=srf_file.points["tinit"].min(),
-            )
+            "SRF does not begin at zero (this may not be an error depending on SRF setup)",
+            tinit=srf_file.points["tinit"].min(),
         )
         raise typer.Exit(code=1)

workflow/scripts/generate_velocity_model_parameters.py

@@ -84,7 +84,6 @@ def get_nz_outline_polygon() -> Polygon:
     return shapely.union(south_island, north_island)
 
 
-
 def estimate_simulation_duration(
     bounding_box: BoundingBox,
     magnitude: float,
@@ -150,6 +149,7 @@ def estimate_simulation_duration(
     )
     # import here rather than at the module level because openquake is slow to import
     from empirical.util import openquake_wrapper_vectorized as openquake
+
     ds = np.exp(
         openquake.oq_run(GMM.AS_16, TectType.ACTIVE_SHALLOW, oq_dataframe, "Ds595")[
             "Ds595_mean"
@@ -250,11 +250,15 @@ def generate_velocity_model_parameters(
     rupture_magnitude = total_magnitude(np.array(list(magnitudes.values())))
 
     rrups = {
-        fault_name: np.interp(magnitudes[fault_name], velocity_model_parameters.rrup_interpolants[:, 0], velocity_model_parameters.rrup_interpolants[:, 1])
+        fault_name: np.interp(
+            magnitudes[fault_name],
+            velocity_model_parameters.rrup_interpolants[:, 0],
+            velocity_model_parameters.rrup_interpolants[:, 1],
+        )
         for fault_name, fault in source_config.source_geometries.items()
     }
     logger = log_utils.get_logger(__name__)
-    logger.debug(log_utils.structured_log("computed rrups", rrups=rrups))
+    logger.debug("computed rrups", rrups=rrups)
 
     initial_fault = source_config.source_geometries[rupture_propagation.initial_fault]
     max_depth = get_max_depth(

workflow/scripts/hf_sim.py

@@ -149,11 +149,7 @@ def hf_simulate_station(
             hf_sim_input_str = "\n".join(str(line) for line in hf_sim_input)
 
             print("---\n" + hf_sim_input_str + "\n---")
-            logger.info(
-                log_utils.structured_log(
-                    "running hf", station=name, input=hf_sim_input_str
-                )
-            )
+            logger.info("running hf", station=name, input=hf_sim_input_str)
             output = subprocess.run(
                 str(hf_sim_path),
                 input=hf_sim_input_str,
@@ -162,20 +158,14 @@ def hf_simulate_station(
                 stderr=subprocess.PIPE,
             )
         except subprocess.CalledProcessError as e:
-            logger.error(
-                log_utils.structured_log(
-                    "hf failed", station=name, stdout=e.stdout, stderr=e.stderr
-                )
-            )
+            logger.error("hf failed", station=name, stdout=e.stdout, stderr=e.stderr)
             raise
         epicentre_distance = np.fromstring(output.stderr, dtype="f4", sep="\n")
         logger.info(
-            log_utils.structured_log(
-                "hf succeeded",
-                station=name,
-                epicentre_distance=epicentre_distance,
-                stderr=output.stderr,
-            )
+            "hf succeeded",
+            station=name,
+            epicentre_distance=epicentre_distance,
+            stderr=output.stderr,
         )
 
         if epicentre_distance.size != 1:
@@ -194,20 +184,14 @@ def run_hf(
         Path,
         typer.Argument(exists=True),
     ],
-    station_file: Annotated[
-        Path, typer.Argument(exists=True)
-    ],
-    out_file: Annotated[
-        Path, typer.Argument(file_okay=False)
-    ],
+    station_file: Annotated[Path, typer.Argument(exists=True)],
+    out_file: Annotated[Path, typer.Argument(file_okay=False)],
     hf_sim_path: Annotated[Path, typer.Option()] = Path(
         "/EMOD3D/tools/hb_high_binmod_v6.0.3"
     ),
     work_directory: Annotated[
         Path,
-        typer.Option(
-            exists=True, writable=True, file_okay=False
-        ),
+        typer.Option(exists=True, writable=True, file_okay=False),
     ] = Path("/out"),
 ):
     """Run the HF (High-Frequency) simulation and generate the HF output file.

workflow/scripts/realisation_to_srf.py

@@ -229,28 +229,20 @@ def generate_fault_srf(
     srf_file_path = output_directory / "srf" / (name + ".srf")
     with open(srf_file_path, "w", encoding="utf-8") as srf_file_handle:
         logger = log_utils.get_logger(__name__)
-        logger.info(
-            log_utils.structured_log("executing command", cmd=" ".join(genslip_cmd))
-        )
+        logger.info("executing command", cmd=" ".join(genslip_cmd))
         try:
             proc = subprocess.run(
                 genslip_cmd, stdout=srf_file_handle, stderr=subprocess.PIPE, check=True
             )
         except subprocess.CalledProcessError as e:
             logger.error(
-                log_utils.structured_log(
-                    "failed",
-                    exception=e.output.decode("utf-8"),
-                    code=e.returncode,
-                    stderr=e.stderr.decode("utf-8"),
-                )
+                "failed",
+                exception=e.output.decode("utf-8"),
+                code=e.returncode,
+                stderr=e.stderr.decode("utf-8"),
             )
             raise
-        logger.info(
-            log_utils.structured_log(
-                "command completed", stderr=proc.stderr.decode("utf-8")
-            )
-        )
+        logger.info("command completed", stderr=proc.stderr.decode("utf-8"))
 
 
 def concatenate_csr_arrays(csr_arrays: list[csr_array]) -> csr_array:
@@ -427,12 +419,10 @@ def process_fault(fault_name: str) -> None:
             logger = log_utils.get_logger(__name__)
             fault_srf.points["tinit"] += time_delay
             logger.info(
-                log_utils.structured_log(
-                    "computed delay",
-                    fault_name=fault_name,
-                    delay=time_delay,
-                    srf_min=fault_srf.points["tinit"].min(),
-                )
+                "computed delay",
+                fault_name=fault_name,
+                delay=time_delay,
+                srf_min=fault_srf.points["tinit"].min(),
             )
 
         srf_file_map[fault_name] = fault_srf
@@ -550,10 +540,16 @@ def generate_fault_srfs_parallel(
 @cli.from_docstring(app)
 @log_call()
 def generate_srf(
-    realisation_ffp: Annotated[Path, typer.Argument(exists=True, readable=True, dir_okay=False)],
+    realisation_ffp: Annotated[
+        Path, typer.Argument(exists=True, readable=True, dir_okay=False)
+    ],
     output_srf_filepath: Annotated[Path, typer.Argument(writable=True, dir_okay=False)],
-    work_directory: Annotated[Path, typer.Option(exists=True, file_okay=False)] = Path("/out"),
-    genslip_path: Annotated[Path, typer.Option(readable=True, dir_okay=False)] = Path("/EMOD3D/tools/genslip_v5.4.2"),
+    work_directory: Annotated[Path, typer.Option(exists=True, file_okay=False)] = Path(
+        "/out"
+    ),
+    genslip_path: Annotated[Path, typer.Option(readable=True, dir_okay=False)] = Path(
+        "/EMOD3D/tools/genslip_v5.4.2"
+    ),
 ):
     """Generate an SRF file from a given realisation specification.