update logging to redirect everything to logfile, if provided

src/disp_s1/_log.py

@@ -0,0 +1,17 @@
+import logging
+from logging import Formatter
+from pathlib import Path
+
+from dolphin._types import Filename
+
+
+def setup_file_logging(filename: Filename) -> None:
+    """Redirect all logging to a file."""
+    logger = logging.getLogger()
+    # In addition to stderr, log to a file if requested
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
+    file_handler = logging.FileHandler(filename)
+    file_handler.setLevel(logging.DEBUG)
+    formatter = Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+    file_handler.setFormatter(formatter)
+    logger.addHandler(file_handler)

src/disp_s1/main.py

@@ -16,7 +16,7 @@
 from dolphin.workflows._utils import _create_burst_cfg, _remove_dir_if_empty
 from dolphin.workflows.config import Workflow
 
-from disp_s1 import product
+from disp_s1 import _log, product
 from disp_s1.pge_runconfig import RunConfig
 
 
@@ -39,7 +39,10 @@ def run(
         PGE-specific metadata for the output product.
     """
     # Set the logging level for all `dolphin.` modules
-    logger = get_log(name="disp_s1", debug=debug, filename=cfg.log_file)
+    logger = get_log(name="disp_s1", debug=debug)
+    if cfg.log_file:
+        _log.setup_file_logging(cfg.log_file)
+
     logger.debug(pformat(cfg.model_dump()))
     cfg.create_dir_tree(debug=debug)
 

src/disp_s1/plotting.py

@@ -136,7 +136,9 @@ def __dir__(self):
         return list(self._attr_cache.keys())
 
 
-def create_explorer_widget(hf: h5py.File, load_less_than: float = 1e3):
+def create_explorer_widget(
+    hf: h5py.File, load_less_than: float = 1e3
+) -> widgets.Widget:
     """Make a widget in Jupyter to explore a h5py file.
 
     Examples
@@ -145,7 +147,7 @@ def create_explorer_widget(hf: h5py.File, load_less_than: float = 1e3):
     >>> create_explorer_widget(hf)
     """
 
-    def _make_thumbnail(image):
+    def _make_thumbnail(image) -> widgets.Image:
         # Create a thumbnail of the dataset
         fig, ax = plt.subplots(figsize=(5, 5))
         ax.imshow(image, cmap="gray", vmax=np.nanpercentile(image, 99))
@@ -157,7 +159,7 @@ def _make_thumbnail(image):
         # Display the thumbnail in an Image widget
         return widgets.Image(value=buf.read(), format="png")
 
-    def _add_widgets(item, level: int = 0):
+    def _add_widgets(item, level: int = 0) -> widgets.Widget:
         """Recursively add widgets to the accordion widget."""
         if isinstance(item, h5py.Group):
             # Add a new accordion widget for the group