Merge branch 'dev' into fix_string_datetime_validator

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Add Data.set_data_io(), which allows for setting a `DataIO` to a data object after-the-fact. @bendichter and @CodyCBakerPhD [#1013](https://github.com/hdmf-dev/hdmf/pull/1013)
 - Added `add_ref_termset`, updated helper methods for `HERD`, revised `add_ref` to support validations prior to populating the tables
   and added `add_ref_container`.  @mavaylon1 [#968](https://github.com/hdmf-dev/hdmf/pull/968)
+- Use `stacklevel` in most warnings. @rly [#1027](https://github.com/hdmf-dev/hdmf/pull/1027)
 
 ### Minor Improvements
 - Updated `__gather_columns` to ignore the order of bases when generating columns from the super class. @mavaylon1 [#991](https://github.com/hdmf-dev/hdmf/pull/991)

src/hdmf/backends/hdf5/h5_utils.py

@@ -499,7 +499,7 @@ def __init__(self, **kwargs):
         # Check for possible collision with other parameters
         if not isinstance(getargs('data', kwargs), Dataset) and self.__link_data:
             self.__link_data = False
-            warnings.warn('link_data parameter in H5DataIO will be ignored')
+            warnings.warn('link_data parameter in H5DataIO will be ignored', stacklevel=2)
         # Call the super constructor and consume the data parameter
         super().__init__(**kwargs)
         # Construct the dict with the io args, ignoring all options that were set to None
@@ -523,7 +523,7 @@ def __init__(self, **kwargs):
                 self.__iosettings.pop('compression', None)
                 if 'compression_opts' in self.__iosettings:
                     warnings.warn('Compression disabled by compression=False setting. ' +
-                                  'compression_opts parameter will, therefore, be ignored.')
+                                  'compression_opts parameter will, therefore, be ignored.', stacklevel=2)
                     self.__iosettings.pop('compression_opts', None)
         # Validate the compression options used
         self._check_compression_options()
@@ -537,7 +537,8 @@ def __init__(self, **kwargs):
         # Check possible parameter collisions
         if isinstance(self.data, Dataset):
             for k in self.__iosettings.keys():
-                warnings.warn("%s in H5DataIO will be ignored with H5DataIO.data being an HDF5 dataset" % k)
+                warnings.warn("%s in H5DataIO will be ignored with H5DataIO.data being an HDF5 dataset" % k,
+                              stacklevel=2)
 
         self.__dataset = None
 
@@ -594,7 +595,7 @@ def _check_compression_options(self):
             if self.__iosettings['compression'] not in ['gzip', h5py_filters.h5z.FILTER_DEFLATE]:
                 warnings.warn(str(self.__iosettings['compression']) + " compression may not be available "
                               "on all installations of HDF5. Use of gzip is recommended to ensure portability of "
-                              "the generated HDF5 files.")
+                              "the generated HDF5 files.", stacklevel=3)
 
     @staticmethod
     def filter_available(filter, allow_plugin_filters):

src/hdmf/backends/hdf5/h5tools.py

@@ -324,7 +324,9 @@ def copy_file(self, **kwargs):
         """
 
         warnings.warn("The copy_file class method is no longer supported and may be removed in a future version of "
-                      "HDMF. Please use the export method or h5py.File.copy method instead.", DeprecationWarning)
+                      "HDMF. Please use the export method or h5py.File.copy method instead.",
+                      category=DeprecationWarning,
+                      stacklevel=2)
 
         source_filename, dest_filename, expand_external, expand_refs, expand_soft = getargs('source_filename',
                                                                                             'dest_filename',

src/hdmf/build/map.py

@@ -4,4 +4,4 @@
 
 import warnings
 warnings.warn('Classes in map.py should be imported from hdmf.build. Importing from hdmf.build.map will be removed '
-              'in HDMF 3.0.', DeprecationWarning)
+              'in HDMF 3.0.', DeprecationWarning, stacklevel=2)

src/hdmf/common/resources.py

@@ -628,7 +628,7 @@ def add_ref(self, **kwargs):
             if entity_uri is not None:
                 entity_uri = entity.entity_uri
                 msg = 'This entity already exists. Ignoring new entity uri'
-                warn(msg)
+                warn(msg, stacklevel=2)
 
         #################
         # Validate Object

src/hdmf/common/table.py

@@ -503,7 +503,7 @@ def __set_table_attr(self, col):
             msg = ("An attribute '%s' already exists on %s '%s' so this column cannot be accessed as an attribute, "
                    "e.g., table.%s; it can only be accessed using other methods, e.g., table['%s']."
                    % (col.name, self.__class__.__name__, self.name, col.name, col.name))
-            warn(msg)
+            warn(msg, stacklevel=2)
         else:
             setattr(self, col.name, col)
 
@@ -764,7 +764,7 @@ def add_column(self, **kwargs):  # noqa: C901
 
         if isinstance(index, VectorIndex):
             warn("Passing a VectorIndex in for index may lead to unexpected behavior. This functionality will be "
-                 "deprecated in a future version of HDMF.", FutureWarning)
+                 "deprecated in a future version of HDMF.", category=FutureWarning, stacklevel=2)
 
         if name in self.__colids:  # column has already been added
             msg = "column '%s' already exists in %s '%s'" % (name, self.__class__.__name__, self.name)
@@ -781,7 +781,7 @@ def add_column(self, **kwargs):  # noqa: C901
                        "Please ensure the new column complies with the spec. "
                        "This will raise an error in a future version of HDMF."
                        % (name, self.__class__.__name__, spec_table))
-                warn(msg)
+                warn(msg, stacklevel=2)
 
             index_bool = index or not isinstance(index, bool)
             spec_index = self.__uninit_cols[name].get('index', False)
@@ -791,7 +791,7 @@ def add_column(self, **kwargs):  # noqa: C901
                        "Please ensure the new column complies with the spec. "
                        "This will raise an error in a future version of HDMF."
                        % (name, self.__class__.__name__, spec_index))
-                warn(msg)
+                warn(msg, stacklevel=2)
 
             spec_col_cls = self.__uninit_cols[name].get('class', VectorData)
             if col_cls != spec_col_cls:
@@ -800,7 +800,7 @@ def add_column(self, **kwargs):  # noqa: C901
                        "Please ensure the new column complies with the spec. "
                        "This will raise an error in a future version of HDMF."
                        % (name, self.__class__.__name__, spec_col_cls))
-                warn(msg)
+                warn(msg, stacklevel=2)
 
         ckwargs = dict(kwargs)
 
@@ -1517,7 +1517,7 @@ def _validate_on_set_parent(self):
         if set(table_ancestor_ids).isdisjoint(self_ancestor_ids):
             msg = (f"The linked table for DynamicTableRegion '{self.name}' does not share an ancestor with the "
                    "DynamicTableRegion.")
-            warn(msg)
+            warn(msg, stacklevel=2)
         return super()._validate_on_set_parent()
 
 

src/hdmf/spec/namespace.py

@@ -50,13 +50,13 @@ def __init__(self, **kwargs):
             self['full_name'] = full_name
         if version == str(SpecNamespace.UNVERSIONED):
             # the unversioned version may be written to file as a string and read from file as a string
-            warn("Loaded namespace '%s' is unversioned. Please notify the extension author." % name)
+            warn("Loaded namespace '%s' is unversioned. Please notify the extension author." % name, stacklevel=2)
             version = SpecNamespace.UNVERSIONED
         if version is None:
             # version is required on write -- see YAMLSpecWriter.write_namespace -- but can be None on read in order to
             # be able to read older files with extensions that are missing the version key.
             warn(("Loaded namespace '%s' is missing the required key 'version'. Version will be set to '%s'. "
-                  "Please notify the extension author.") % (name, SpecNamespace.UNVERSIONED))
+                  "Please notify the extension author.") % (name, SpecNamespace.UNVERSIONED), stacklevel=2)
             version = SpecNamespace.UNVERSIONED
         self['version'] = version
         if date is not None:
@@ -529,7 +529,7 @@ def load_namespaces(self, **kwargs):
                 if ns['version'] != self.__namespaces.get(ns['name'])['version']:
                     # warn if the cached namespace differs from the already loaded namespace
                     warn("Ignoring cached namespace '%s' version %s because version %s is already loaded."
-                         % (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']))
+                         % (ns['name'], ns['version'], self.__namespaces.get(ns['name'])['version']), stacklevel=2)
             else:
                 to_load.append(ns)
         # now load specs into namespace

src/hdmf/spec/spec.py

@@ -318,7 +318,7 @@ def __init__(self, **kwargs):
         default_name = getargs('default_name', kwargs)
         if default_name:
             if name is not None:
-                warn("found 'default_name' with 'name' - ignoring 'default_name'")
+                warn("found 'default_name' with 'name' - ignoring 'default_name'", stacklevel=2)
             else:
                 self['default_name'] = default_name
         self.__attributes = dict()

src/hdmf/spec/write.py

@@ -247,7 +247,7 @@ def export_spec(ns_builder, new_data_types, output_dir):
     """
 
     if len(new_data_types) == 0:
-        warnings.warn('No data types specified. Exiting.')
+        warnings.warn('No data types specified. Exiting.', stacklevel=2)
         return
 
     ns_path = ns_builder.name + '.namespace.yaml'

src/hdmf/utils.py

@@ -434,7 +434,7 @@ def fmt_docval_args(func, kwargs):
                   "removes all arguments not accepted by the function's docval, so if you are passing kwargs that "
                   "includes extra arguments and the function's docval does not allow extra arguments (allow_extra=True "
                   "is set), then you will need to pop the extra arguments out of kwargs before calling the function.",
-                  PendingDeprecationWarning)
+                  PendingDeprecationWarning, stacklevel=2)
     func_docval = getattr(func, docval_attr_name, None)
     ret_args = list()
     ret_kwargs = dict()
@@ -488,7 +488,7 @@ def call_docval_func(func, kwargs):
                   "removes all arguments not accepted by the function's docval, so if you are passing kwargs that "
                   "includes extra arguments and the function's docval does not allow extra arguments (allow_extra=True "
                   "is set), then you will need to pop the extra arguments out of kwargs before calling the function.",
-                  PendingDeprecationWarning)
+                  PendingDeprecationWarning, stacklevel=2)
     with warnings.catch_warnings(record=True):
         # catch and ignore only PendingDeprecationWarnings from fmt_docval_args so that two
         # PendingDeprecationWarnings saying the same thing are not raised
@@ -645,7 +645,7 @@ def _check_args(args, kwargs):
             parse_warnings = parsed.get('future_warnings')
             if parse_warnings:
                 msg = '%s: %s' % (func.__qualname__, ', '.join(parse_warnings))
-                warnings.warn(msg, FutureWarning)
+                warnings.warn(msg, category=FutureWarning, stacklevel=3)
 
             for error_type, ExceptionType in (('type_errors', TypeError),
                                               ('value_errors', ValueError),