Make @deprecate log a warning (mlflow#1569)

* Make deprecations actually log a warning

* Updating stack level

* Warn only once and on function usage

* Setting warning filter

* Add in-line comment

mlflow/__init__.py

@@ -24,21 +24,22 @@
 
 For a lower level API, see the :py:mod:`mlflow.tracking` module.
 """
-
 from mlflow.version import VERSION as __version__
+from mlflow.utils.logging_utils import _configure_mlflow_loggers
+import mlflow.tracking.fluent
 
 # Filter annoying Cython warnings that serve no good purpose, and so before
 # importing other modules.
 # See: https://github.com/numpy/numpy/pull/432/commits/170ed4e33d6196d7
 import warnings
 warnings.filterwarnings("ignore", message="numpy.dtype size changed")  # noqa: E402
 warnings.filterwarnings("ignore", message="numpy.ufunc size changed")  # noqa: E402
+# log a deprecated warning only once per function per module
+warnings.filterwarnings("module", category=DeprecationWarning)
 
 # pylint: disable=wrong-import-position
 import mlflow.projects as projects  # noqa
 import mlflow.tracking as tracking  # noqa
-import mlflow.tracking.fluent
-from mlflow.utils.logging_utils import _configure_mlflow_loggers
 
 _configure_mlflow_loggers(root_module_name=__name__)
 

mlflow/pyfunc/__init__.py

@@ -281,7 +281,7 @@ def load_model(model_uri, suppress_warnings=False):
     return load_pyfunc(model_uri, suppress_warnings)
 
 
-@deprecated("pyfunc.load_model", 1.0)
+@deprecated("mlflow.pyfunc.load_model", 1.0)
 def load_pyfunc(model_uri, suppress_warnings=False):
     """
     Load a model stored in Python function format.

mlflow/utils/annotations.py

@@ -1,3 +1,4 @@
+import warnings
 from functools import wraps
 
 
@@ -21,15 +22,29 @@ def deprecated(alternative=None, since=None):
     :param func: A function to mark
     :returns Decorated function.
     """
-    def deprecated_func(func):
+
+    def deprecated_decorator(func):
         since_str = " since %s" % since if since else ""
-        notice = ".. Warning:: Deprecated%s: This method will be removed in " % since_str + \
-                 "a near future release."
+        notice = (
+            ".. Warning:: ``{function_name}`` is deprecated{since_string}. This method will be"
+            " removed in a near future release".format(
+                function_name='.'.join([func.__module__, func.__name__]),
+                since_string=since_str)
+        )
         if alternative is not None and alternative.strip():
             notice += " Use ``%s`` instead." % alternative
-        func.__doc__ = notice + "\n" + func.__doc__
-        return func
-    return deprecated_func
+
+        @wraps(func)
+        def deprecated_func(*args, **kwargs):
+            warnings.warn(notice, category=DeprecationWarning, stacklevel=2)
+            return func(*args, **kwargs)
+
+        if func.__doc__ is not None:
+            deprecated_func.__doc__ = notice + "\n" + func.__doc__
+
+        return deprecated_func
+
+    return deprecated_decorator
 
 
 def keyword_only(func):