Merge pull request pepkit#303 from vreuter/depr

Better deprecation localization
vreuter · May 6, 2019 · fa5a1b1 · fa5a1b1
2 parents 7139d14 + aa8f43d
commit fa5a1b1
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Showing 2 changed files with 18 additions and 25 deletions.
diff --git a/peppy/project.py b/peppy/project.py
@@ -66,8 +66,8 @@
 from .exceptions import PeppyError
 from .sample import merge_sample, Sample
 from .utils import \
-    add_project_sample_constants, copy, fetch_samples, infer_delimiter, is_url, \
-    non_null_value, type_check_strict, warn_derived_cols, warn_implied_cols
+    add_project_sample_constants, copy, fetch_samples, get_name_depr_msg, \
+    infer_delimiter, is_url, non_null_value, type_check_strict
 
 
 MAX_PROJECT_SAMPLES_REPR = 12
@@ -82,6 +82,8 @@
 GENOMES_KEY = "genomes"
 TRANSCRIPTOMES_KEY = "transcriptomes"
 IDEALLY_IMPLIED = [GENOMES_KEY, TRANSCRIPTOMES_KEY]
+_OLD_DERIVATIONS_KEY = "derived_columns"
+_OLD_IMPLICATIONS_KEY = "implied_columns"
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -264,11 +266,15 @@ def __setitem__(self, key, value):
         :param str key: Key to map to given value
         :param object value: Arbitrary value to bind to given key
         """
-        if key == "derived_columns":
-            warn_derived_cols()
+        if key == _OLD_DERIVATIONS_KEY:
+            warnings.warn(get_name_depr_msg(
+                _OLD_DERIVATIONS_KEY, "derived_attributes", self.__class__),
+                DeprecationWarning)
             key = DERIVATIONS_DECLARATION
-        elif key == "implied_columns":
-            warn_implied_cols()
+        elif key == _OLD_IMPLICATIONS_KEY:
+            warnings.warn(get_name_depr_msg(
+                _OLD_IMPLICATIONS_KEY, "implied_attributes", self.__class__),
+                DeprecationWarning)
             key = IMPLICATIONS_DECLARATION
         elif key == METADATA_KEY:
             value = _Metadata(value)
@@ -291,7 +297,9 @@ def derived_columns(self):
 
         :return list[str]: sample attribute names for which value is derived
         """
-        warn_derived_cols()
+        msg = get_name_depr_msg(
+            _OLD_DERIVATIONS_KEY, "derived_attributes", self.__class__)
+        warnings.warn(msg, DeprecationWarning)
         try:
             return self.derived_attributes
         except AttributeError:
@@ -304,7 +312,9 @@ def implied_columns(self):
 
         :return list[str]: sample attribute names for which value is implied by other(s)
         """
-        warn_implied_cols()
+        msg = get_name_depr_msg(
+            _OLD_IMPLICATIONS_KEY, "implied_attributes", self.__class__)
+        warnings.warn(msg, DeprecationWarning)
         try:
             return self.implied_attributes
         except AttributeError:

diff --git a/peppy/utils.py b/peppy/utils.py
@@ -15,7 +15,6 @@
     from collections import Sized
 else:
     from collections.abc import Sized
-import warnings
 import yaml
 from .const import SAMPLE_INDEPENDENT_PROJECT_SECTIONS
 from ubiquerg import is_collection_like
@@ -398,16 +397,6 @@ def standard_stream_redirector(stream):
         sys.stdout, sys.stderr = genuine_stdout, genuine_stderr
 
 
-def warn_derived_cols():
-    """ Produce deprecation warning about derived columns. """
-    _warn_cols_to_attrs("derived")
-
-
-def warn_implied_cols():
-    """ Produce deprecation warning about implied columns. """
-    _warn_cols_to_attrs("implied")
-
-
 def get_name_depr_msg(old, new, cls=None):
     """
     Warn of an attribute name deprecation.
@@ -420,12 +409,6 @@ def get_name_depr_msg(old, new, cls=None):
     return msg if cls is None else "On {} ".format(cls.__name__) + msg
 
 
-def _warn_cols_to_attrs(prefix):
-    """ Produce deprecation warning about 'columns' rather than 'attributes' """
-    warnings.warn("{pfx}_columns should be encoded and referenced "
-                  "as {pfx}_attributes".format(pfx=prefix), DeprecationWarning)
-
-
 class CommandChecker(object):
     """
     Validate PATH availability of executables referenced by a config file.