trying and failing to get logging-on-demand by tools/entrypoint scripts

apis/python/README-dev.md

@@ -1,8 +1,8 @@
 * Most things are configured using GitHub Actions at `../../.github/workflows`
 * Pre-push suggestions:
-  * `black .`
-  * `isort .`
-  * `flake8`
+  * `black . tools/[a-z]*`
+  * `isort . tools/[a-z]*`
+  * `flake8 . tools/[a-z]*`
   * `python -m pytest tests`
 * PyPI:
   * https://pypi.org/project/tiledbsc/

apis/python/examples/uniformizer.py

@@ -50,8 +50,14 @@ def main() -> int:
     parser = _create_args_parser()
     args = parser.parse_args()
 
-    # XXX
     if args.verbose:
+        # tiledbsc.logging.logger.setLevel(logging.INFO)
+        # logger = logging.getLogger('tiledbsc')
+        # logger.setLevel(logging.INFO)
+        # logging.getLogger("tiledbsc").setLevel(logging.INFO)
+        # Not able to get any of the above to 'stick'. The following sets level for the whole app,
+        # not just the tiledbsc library, but that's an acceptable workaround since this CLI does
+        # nothing except invoke the tiledbsc library.
         logging.basicConfig(level=logging.INFO)
 
     uniformizer = Uniformizer(

apis/python/src/tiledbsc/logging.py

@@ -0,0 +1,3 @@
+import logging
+
+logger = logging.getLogger(__name__)  # Nominally __name__ is 'tiledbsc'

apis/python/tools/ingestor

@@ -23,7 +23,7 @@ import tiledb
 
 import tiledbsc
 import tiledbsc.io
-import tiledbsc.logger
+import tiledbsc.logging
 import tiledbsc.util
 
 
@@ -98,7 +98,16 @@ select `relative=True`. (This is the default.)
     soma_options = tiledbsc.SOMAOptions()
 
     write_soco = args.soco
-    # XXX verbose = not args.quiet
+    verbose = not args.quiet
+    if verbose:
+        # tiledbsc.logging.logger.setLevel(logging.INFO)
+        # logger = logging.getLogger('tiledbsc')
+        # logger.setLevel(logging.INFO)
+        # logging.getLogger("tiledbsc").setLevel(logging.INFO)
+        # Not able to get any of the above to 'stick'. The following sets level for the whole app,
+        # not just the tiledbsc library, but that's an acceptable workaround since this CLI does
+        # nothing except invoke the tiledbsc library.
+        logging.basicConfig(level=logging.INFO)
 
     if args.relative is not None:
         relative = args.relative[0]
@@ -208,7 +217,9 @@ def ingest_one(
     else:
         if os.path.exists(output_path):
             if ifexists == "continue":
-                tiledbsc.logger.info(f"Already exists; continuing: {output_path}")
+                tiledbsc.logging.logger.info(
+                    f"Already exists; continuing: {output_path}"
+                )
                 return
             elif ifexists == "abort":
                 logging.error(f"Already exists; aborting: {output_path}")
@@ -229,7 +240,7 @@ def ingest_one(
         # Do the ingest into TileDB.
         tiledbsc.io.from_h5ad(soma, input_path)
 
-    tiledbsc.logger.info(f"Wrote {output_path}")
+    tiledbsc.logging.logger.info(f"Wrote {output_path}")
 
     if write_soco:
         soco = tiledbsc.SOMACollection(soco_dir, soma_options=soma_options)
@@ -238,8 +249,10 @@ def ingest_one(
             raise Exception(f"Could not create SOCO at {soco.uri}")
         soco.add(soma)
 
-        tiledbsc.logger.info("")
-        tiledbsc.logger.info(f"Added SOMA {soma.name} to SOMACollection {soco_dir}")
+        tiledbsc.logging.logger.info("")
+        tiledbsc.logging.logger.info(
+            f"Added SOMA {soma.name} to SOMACollection {soco_dir}"
+        )
 
 
 # ================================================================

apis/python/tools/outgestor

@@ -22,7 +22,7 @@ import tiledb
 
 import tiledbsc
 import tiledbsc.io
-import tiledbsc.logger
+import tiledbsc.logging
 import tiledbsc.util
 
 
@@ -76,11 +76,21 @@ def main():
         if not os.path.exists(outdir):
             os.mkdir(outdir)
 
-    # XXX verbose = not args.quiet
+    verbose = not args.quiet
+    if verbose:
+        # tiledbsc.logging.logger.setLevel(logging.INFO)
+        # logger = logging.getLogger('tiledbsc')
+        # logger.setLevel(logging.INFO)
+        # logging.getLogger("tiledbsc").setLevel(logging.INFO)
+        # Not able to get any of the above to 'stick'. The following sets level for the whole app,
+        # not just the tiledbsc library, but that's an acceptable workaround since this CLI does
+        # nothing except invoke the tiledbsc library.
+        logging.basicConfig(level=logging.INFO)
+
     soma = tiledbsc.SOMA(input_path)
     tiledbsc.io.to_h5ad(soma, output_path)
 
-    tiledbsc.logger.info(f"Wrote {output_path}")
+    tiledbsc.logging.logger.info(f"Wrote {output_path}")
 
 
 if __name__ == "__main__":