Merge pull request #81 from jeromekelleher/logging-again

Basic logging via daiquiri

app.py

@@ -1,19 +1,23 @@
-import logging
 import pathlib
 import sys
+import time
 import traceback
 
+import daiquiri
 import panel as pn
 import tskit
 
 import model
 import pages
 
 
-logger = logging.Logger(__file__)
+daiquiri.setup(level="INFO")
+logger = daiquiri.getLogger("app")
+
 
 # Usage: panel serve app.py --args /path/to/trees-file
 path = pathlib.Path(sys.argv[1])
+logger.info(f"Loading {path}")
 tsm = model.TSModel(tskit.load(path), path.name)
 
 pn.extension(sizing_mode="stretch_width")
@@ -31,9 +35,13 @@
 
 
 def show(page):
+    logger.info(f"Showing page {page}")
     yield pn.indicators.LoadingSpinner(value=True, width=50, height=50)
     try:
+        before = time.time()
         content = pages[page](tsm)
+        duration = time.time() - before
+        logger.info(f"Loaded page {page} in {duration:.2f}s")
     except Exception as e:
         error_message = f"An error occurred: {str(e)}"
         error_traceback = traceback.format_exc().replace("\n", "<br>")

model.py

@@ -1,11 +1,14 @@
 import dataclasses
 from functools import cached_property
 
+import daiquiri
 import numba
 import numpy as np
 import pandas as pd
 import tskit
 
+logger = daiquiri.getLogger("model")
+
 spec = [
     ("num_edges", numba.int64),
     ("sequence_length", numba.float64),
@@ -287,6 +290,7 @@ def summary_df(self):
         df = pd.DataFrame(
             {"property": [d[0] for d in data], "value": [d[1] for d in data]}
         )
+        logger.info("Computed summary dataframe")
         return df.set_index("property")
 
     def _repr_html_(self):
@@ -355,6 +359,7 @@ def mutations_df(self):
             }
         )
 
+        logger.info("Computed mutations dataframe")
         return df.astype(
             {
                 "id": "int",
@@ -395,6 +400,7 @@ def edges_df(self):
             }
         )
 
+        logger.info("Computed edges dataframe")
         return df.astype(
             {
                 "left": "float64",
@@ -424,6 +430,7 @@ def nodes_df(self):
                 "is_sample": is_sample,
             }
         )
+        logger.info("Computed nodes dataframe")
         return df.astype(
             {
                 "time": "float64",
@@ -460,6 +467,7 @@ def trees_df(self):
             }
         )
 
+        logger.info("Computed trees dataframe")
         return df.astype(
             {
                 "left": "int",

requirements.txt

@@ -1,8 +1,9 @@
+daiquiri
 panel
 hvplot
 xarray
 datashader
 tskit
 seaborn
 pre-commit
-pytest
+pytest