flexibly handle addition of direct use of logging CLI by pipeline aut…

…hor; databio#158 (comment)

docs/changelog.md

@@ -3,22 +3,22 @@
 ## [0.12.0] -- unreleased
 ### Added
 - Use profile to determine total elapsed time
+- `logging` functions directly on `PipelineManager`
+- Re-export `add_logging_options` from `logmuse`, for direct use by a pipeline author.
+- `logger_via_cli` that defaults to the `strict=False` behavior of the same-named function from `logmuse`
 
 ## [0.11.3] -- 2019-06-17
 ### Fixed
 - Fixed a bug that caused an OSError removing lock files for some filesystems.
 
-
 ## [0.11.2] -- 2019-06-06
 ### Fixed
 - Elevate `attmap` depdendency bound to require inclusion of improved path expansion behavior.
 
-
 ## [0.11.1] -- 2019-05-30
 ### Fixed
 - Elevate `attmap` dependency bound to require inclusion of a bugfix there.
 
-
 ## [0.11.0] -- 2019-05-13
 - Improve python3 handling of integers and strings
 - Fixed a bug with cleanup scripts in `dirty` mode
@@ -29,7 +29,6 @@
 - Some performance improvements for ngstk functions
 - Allow `ngstk.input_to_fastq` to yield gzipped fastq files
 
-
 ## [0.10.0] -- 2019-03-22
 - Fixed a bug that raised exception with empty commands
 - Fixed the pipeline profiling issues

pypiper/__init__.py

@@ -5,3 +5,6 @@
 from .pipeline import *
 from .exceptions import *
 from .stage import *
+
+# Implicitly re-export so logmuse usage by pipeline author routes through here.
+from logmuse import add_logging_options

pypiper/manager.py

@@ -31,8 +31,8 @@
 from .flags import *
 from .utils import \
     check_shell, checkpoint_filepath, clear_flags, default_pipeline_config, \
-    flag_name, get_proc_name, is_multi_target, make_lock_name, parse_cmd, \
-    pipeline_filepath, CHECKPOINT_SPECIFICATIONS
+    flag_name, get_proc_name, is_multi_target, logger_via_cli, make_lock_name, \
+    parse_cmd, pipeline_filepath, CHECKPOINT_SPECIFICATIONS
 from .const import PROFILE_COLNAMES
 from ._version import __version__
 import __main__
@@ -321,13 +321,18 @@ def __init__(
             self.config = None
 
         logger_kwargs = logger_kwargs or {}
-        try:
-            name = logger_kwargs.pop("name")
-        except KeyError:
-            pass
+        default_logname = ".".join([__name__, self.__class__.__name__, self.name])
+        if not args:
+            # strict is only for logger_via_cli.
+            kwds = {k: v for k, v in logger_kwargs.items() if k != "strict"}
+            try:
+                name = kwds.pop("name")
+            except KeyError:
+                name = default_logname
+            self._logger = init_logger(name, **kwds)
         else:
-            name = ".".join([__name__, self.__class__.__name__, self.name])
-        self._logger = init_logger(name, **logger_kwargs)
+            logger_kwargs.setdefault("name", default_logname)
+            self._logger = logger_via_cli(args, **logger_kwargs)
 
     @property
     def _completed(self):

pypiper/utils.py

@@ -30,7 +30,7 @@
 # Conceptually, reserve this for functions expected to be used in other
 # packages, and import from utils within pypiper for other functions.
 __all__ = ["add_pypiper_args", "build_command", "check_all_commands",
-           "determine_uncallable", "get_first_value", "head"]
+           "determine_uncallable", "get_first_value", "head", "logger_via_cli"]
 
 
 CHECKPOINT_SPECIFICATIONS = ["start_point", "stop_before", "stop_after"]
@@ -588,6 +588,22 @@ def is_sam_or_bam(file_name):
     return ext in [".bam", ".sam"]
 
 
+def logger_via_cli(opts, **kwargs):
+    """
+    Build and initialize logger from CLI specification.
+
+    :param argparse.Namespace opts: parse of command-line interface
+    :param kwargs: keyword arguments to pass along to underlying logmuse function
+    :return logging.Logger: newly created and configured logger
+    """
+    from copy import deepcopy
+    import logmuse
+    kwds = deepcopy(kwargs)
+    # By default, don't require the logging options to have been added to the parser.
+    kwds.setdefault("strict", False)
+    return logmuse.logger_via_cli(opts, **kwds)
+
+
 def make_lock_name(original_path, path_base_folder):
     """
     Create name for lock file from an absolute path.

requirements/reqs-pypiper.txt

@@ -1,5 +1,5 @@
 attmap>=0.12.5
-logmuse>=0.2.0
+logmuse>=0.2.1
 psutil
 pandas
 ubiquerg>=0.4.5

tests/test_packaging.py

@@ -8,7 +8,8 @@
 
 
 @pytest.mark.parametrize(["obj_name", "typecheck"], [
-    ("check_all_commands", isfunction), ("determine_uncallable", isfunction)])
+    ("add_logging_options", isfunction), ("check_all_commands", isfunction),
+    ("determine_uncallable", isfunction), ("logger_via_cli", isfunction)])
 def test_top_level_exports(obj_name, typecheck):
     """ At package level, validate object availability and type. """
     import pypiper