Add stacklevel parameter to warnings.warn() call

31 files changed, 71 insertions, 67 deletions

diff --git a/sphinx/application.py b/sphinx/application.py
index d2fd776ff..4014a2efa 100644
--- a/sphinx/application.py
+++ b/sphinx/application.py
@@ -990,7 +990,7 @@ class Sphinx:
         if isinstance(lexer, Lexer):
             warnings.warn('app.add_lexer() API changed; '
                           'Please give lexer class instead instance',
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
             lexers[alias] = lexer
         else:
             lexer_classes[alias] = lexer
diff --git a/sphinx/builders/_epub_base.py b/sphinx/builders/_epub_base.py
index b2d8413a8..f26a1ba9f 100644
--- a/sphinx/builders/_epub_base.py
+++ b/sphinx/builders/_epub_base.py
@@ -173,7 +173,7 @@ class EpubBuilder(StandaloneHTMLBuilder):
         """Replace all characters not allowed in text an attribute values."""
         warnings.warn(
             '%s.esc() is deprecated. Use html.escape() instead.' % self.__class__.__name__,
-            RemovedInSphinx40Warning)
+            RemovedInSphinx40Warning, stacklevel=2)
         name = name.replace('&', '&')
         name = name.replace('<', '&lt;')
         name = name.replace('>', '&gt;')
diff --git a/sphinx/builders/applehelp.py b/sphinx/builders/applehelp.py
index f081f9fe5..759ba66da 100644
--- a/sphinx/builders/applehelp.py
+++ b/sphinx/builders/applehelp.py
@@ -32,7 +32,7 @@ deprecated_alias('sphinx.builders.applehelp',
 
 def setup(app: Sphinx) -> Dict[str, Any]:
     warnings.warn('sphinx.builders.applehelp has been moved to sphinxcontrib-applehelp.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     app.setup_extension('sphinxcontrib.applehelp')
 
     return {
diff --git a/sphinx/builders/html/__init__.py b/sphinx/builders/html/__init__.py
index 320c7feb6..85767b14e 100644
--- a/sphinx/builders/html/__init__.py
+++ b/sphinx/builders/html/__init__.py
@@ -882,7 +882,7 @@ class StandaloneHTMLBuilder(Builder):
                     'The %s.feed() method signature is deprecated. Update to '
                     '%s.feed(docname, filename, title, doctree).' % (
                         indexer_name, indexer_name),
-                    RemovedInSphinx40Warning)
+                    RemovedInSphinx40Warning, stacklevel=2)
 
     def _get_local_toctree(self, docname: str, collapse: bool = True, **kwargs: Any) -> str:
         if 'includehidden' not in kwargs:
diff --git a/sphinx/builders/htmlhelp.py b/sphinx/builders/htmlhelp.py
index 8732de7fd..1d6304d38 100644
--- a/sphinx/builders/htmlhelp.py
+++ b/sphinx/builders/htmlhelp.py
@@ -32,7 +32,7 @@ deprecated_alias('sphinx.builders.htmlhelp',
 
 def setup(app: Sphinx) -> Dict[str, Any]:
     warnings.warn('sphinx.builders.htmlhelp has been moved to sphinxcontrib-htmlhelp.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     app.setup_extension('sphinxcontrib.htmlhelp')
 
     return {
diff --git a/sphinx/builders/latex/__init__.py b/sphinx/builders/latex/__init__.py
index b1fe4b73e..225975c20 100644
--- a/sphinx/builders/latex/__init__.py
+++ b/sphinx/builders/latex/__init__.py
@@ -363,7 +363,7 @@ class LaTeXBuilder(Builder):
 
     def apply_transforms(self, doctree: nodes.document) -> None:
         warnings.warn('LaTeXBuilder.apply_transforms() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
     def finish(self) -> None:
         self.copy_image_files()
diff --git a/sphinx/cmd/quickstart.py b/sphinx/cmd/quickstart.py
index 8f8ae58a1..29d2e8187 100644
--- a/sphinx/cmd/quickstart.py
+++ b/sphinx/cmd/quickstart.py
@@ -187,7 +187,7 @@ def do_prompt(text: str, default: str = None, validator: Callable[[str], Any] =
 def convert_python_source(source: str, rex: Pattern = re.compile(r"[uU]('.*?')")) -> str:
     # remove Unicode literal prefixes
     warnings.warn('convert_python_source() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     return rex.sub('\\1', source)
 
 
diff --git a/sphinx/config.py b/sphinx/config.py
index 19a8f6c4f..6e6c256c5 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -444,7 +444,7 @@ def check_unicode(config: Config) -> None:
     since that can result in UnicodeErrors all over the place
     """
     warnings.warn('sphinx.config.check_unicode() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
 
     nonascii_re = re.compile(br'[\x80-\xff]')
 
diff --git a/sphinx/domains/math.py b/sphinx/domains/math.py
index 88b6e4eb8..e77bd0ed7 100644
--- a/sphinx/domains/math.py
+++ b/sphinx/domains/math.py
@@ -142,7 +142,7 @@ class MathDomain(Domain):
 
     def add_equation(self, env: BuildEnvironment, docname: str, labelid: str) -> int:
         warnings.warn('MathDomain.add_equation() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         if labelid in self.equations:
             path = env.doc2path(self.equations[labelid][0])
             msg = __('duplicate label of equation %s, other instance in %s') % (labelid, path)
@@ -154,7 +154,7 @@ class MathDomain(Domain):
 
     def get_next_equation_number(self, docname: str) -> int:
         warnings.warn('MathDomain.get_next_equation_number() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         targets = [eq for eq in self.equations.values() if eq[0] == docname]
         return len(targets) + 1
 
diff --git a/sphinx/domains/python.py b/sphinx/domains/python.py
index 99339ccbd..39c7de142 100644
--- a/sphinx/domains/python.py
+++ b/sphinx/domains/python.py
@@ -530,10 +530,11 @@ class PyModulelevel(PyObject):
             if cls.__name__ != 'DirectiveAdapter':
                 warnings.warn('PyModulelevel is deprecated. '
                               'Please check the implementation of %s' % cls,
-                              RemovedInSphinx40Warning)
+                              RemovedInSphinx40Warning, stacklevel=2)
                 break
         else:
-            warnings.warn('PyModulelevel is deprecated', RemovedInSphinx40Warning)
+            warnings.warn('PyModulelevel is deprecated',
+                          RemovedInSphinx40Warning, stacklevel=2)
 
         return super().run()
 
@@ -675,10 +676,11 @@ class PyClassmember(PyObject):
             if cls.__name__ != 'DirectiveAdapter':
                 warnings.warn('PyClassmember is deprecated. '
                               'Please check the implementation of %s' % cls,
-                              RemovedInSphinx40Warning)
+                              RemovedInSphinx40Warning, stacklevel=2)
                 break
         else:
-            warnings.warn('PyClassmember is deprecated', RemovedInSphinx40Warning)
+            warnings.warn('PyClassmember is deprecated',
+                          RemovedInSphinx40Warning, stacklevel=2)
 
         return super().run()
 
@@ -896,10 +898,11 @@ class PyDecoratorMixin:
             if cls.__name__ != 'DirectiveAdapter':
                 warnings.warn('PyDecoratorMixin is deprecated. '
                               'Please check the implementation of %s' % cls,
-                              RemovedInSphinx50Warning)
+                              RemovedInSphinx50Warning, stacklevel=2)
                 break
         else:
-            warnings.warn('PyDecoratorMixin is deprecated', RemovedInSphinx50Warning)
+            warnings.warn('PyDecoratorMixin is deprecated',
+                          RemovedInSphinx50Warning, stacklevel=2)
 
         ret = super().handle_signature(sig, signode)  # type: ignore
         signode.insert(0, addnodes.desc_addname('@', '@'))
diff --git a/sphinx/domains/std.py b/sphinx/domains/std.py
index 74e901779..6dc597022 100644
--- a/sphinx/domains/std.py
+++ b/sphinx/domains/std.py
@@ -292,7 +292,7 @@ def make_glossary_term(env: "BuildEnvironment", textnodes: Iterable[Node], index
         document.note_explicit_target(term)
     else:
         warnings.warn('make_glossary_term() expects document is passed as an argument.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         gloss_entries = env.temp_data.setdefault('gloss_entries', set())
         node_id = nodes.make_id('term-' + termtext)
         if node_id == 'term':
@@ -660,7 +660,7 @@ class StandardDomain(Domain):
 
     def add_object(self, objtype: str, name: str, docname: str, labelid: str) -> None:
         warnings.warn('StandardDomain.add_object() is deprecated.',
-                      RemovedInSphinx50Warning)
+                      RemovedInSphinx50Warning, stacklevel=2)
         self.objects[objtype, name] = (docname, labelid)
 
     @property
@@ -786,7 +786,7 @@ class StandardDomain(Domain):
             resolver = self._resolve_option_xref
         elif typ == 'citation':
             warnings.warn('pending_xref(domain=std, type=citation) is deprecated: %r' % node,
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
             domain = env.get_domain('citation')
             return domain.resolve_xref(env, fromdocname, builder, typ, target, node, contnode)
         elif typ == 'term':
@@ -1082,15 +1082,15 @@ class StandardDomain(Domain):
 
     def note_citations(self, env: "BuildEnvironment", docname: str, document: nodes.document) -> None:  # NOQA
         warnings.warn('StandardDomain.note_citations() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
     def note_citation_refs(self, env: "BuildEnvironment", docname: str, document: nodes.document) -> None:  # NOQA
         warnings.warn('StandardDomain.note_citation_refs() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
     def note_labels(self, env: "BuildEnvironment", docname: str, document: nodes.document) -> None:  # NOQA
         warnings.warn('StandardDomain.note_labels() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
 
 def setup(app: "Sphinx") -> Dict[str, Any]:
diff --git a/sphinx/environment/__init__.py b/sphinx/environment/__init__.py
index c8735461d..6584ac6d8 100644
--- a/sphinx/environment/__init__.py
+++ b/sphinx/environment/__init__.py
@@ -331,10 +331,10 @@ class BuildEnvironment:
         """
         if suffix:
             warnings.warn('The suffix argument for doc2path() is deprecated.',
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
         if base not in (True, False, None):
             warnings.warn('The string style base argument for doc2path() is deprecated.',
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
 
         pathname = self.project.doc2path(docname, base is True)
         if suffix:
diff --git a/sphinx/environment/collectors/indexentries.py b/sphinx/environment/collectors/indexentries.py
index 2ef59909b..a4c0450d2 100644
--- a/sphinx/environment/collectors/indexentries.py
+++ b/sphinx/environment/collectors/indexentries.py
@@ -29,7 +29,7 @@ class IndexEntriesCollector(EnvironmentCollector):
 
     def __init__(self) -> None:
         warnings.warn('IndexEntriesCollector is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
     def clear_doc(self, app: Sphinx, env: BuildEnvironment, docname: str) -> None:
         env.indexentries.pop(docname, None)
diff --git a/sphinx/ext/apidoc.py b/sphinx/ext/apidoc.py
index 23be0a00a..b01604617 100644
--- a/sphinx/ext/apidoc.py
+++ b/sphinx/ext/apidoc.py
@@ -54,7 +54,7 @@ template_dir = path.join(package_dir, 'templates', 'apidoc')
 def makename(package: str, module: str) -> str:
     """Join package and module with a dot."""
     warnings.warn('makename() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     # Both package and module can be None/empty.
     if package:
         name = package
@@ -112,7 +112,7 @@ def write_file(name: str, text: str, opts: Any) -> None:
 def format_heading(level: int, text: str, escape: bool = True) -> str:
     """Create a heading of <level> [1, 2 or 3 supported]."""
     warnings.warn('format_warning() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     if escape:
         text = rst.escape(text)
     underlining = ['=', '-', '~', ][level - 1] * len(text)
@@ -122,7 +122,7 @@ def format_heading(level: int, text: str, escape: bool = True) -> str:
 def format_directive(module: str, package: str = None) -> str:
     """Create the automodule directive and add the options."""
     warnings.warn('format_directive() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     directive = '.. automodule:: %s\n' % module_join(package, module)
     for option in OPTIONS:
         directive += '    :%s:\n' % option
@@ -209,7 +209,7 @@ def create_modules_toc_file(modules: List[str], opts: Any, name: str = 'modules'
 def shall_skip(module: str, opts: Any, excludes: List[str] = []) -> bool:
     """Check if we want to skip this module."""
     warnings.warn('shall_skip() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     # skip if the file doesn't exist and not using implicit namespaces
     if not opts.implicit_namespaces and not path.exists(module):
         return True
diff --git a/sphinx/ext/autodoc/__init__.py b/sphinx/ext/autodoc/__init__.py
index 609928422..36e0b6455 100644
--- a/sphinx/ext/autodoc/__init__.py
+++ b/sphinx/ext/autodoc/__init__.py
@@ -434,7 +434,7 @@ class Documenter:
         if encoding is not None:
             warnings.warn("The 'encoding' argument to autodoc.%s.get_doc() is deprecated."
                           % self.__class__.__name__,
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
         if ignore is not None:
             warnings.warn("The 'ignore' argument to autodoc.%s.get_doc() is deprecated."
                           % self.__class__.__name__,
@@ -953,7 +953,7 @@ class DocstringSignatureMixin:
         if encoding is not None:
             warnings.warn("The 'encoding' argument to autodoc.%s._find_signature() is "
                           "deprecated." % self.__class__.__name__,
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
         docstrings = self.get_doc()
         self._new_docstrings = docstrings[:]
         result = None
@@ -987,7 +987,7 @@ class DocstringSignatureMixin:
         if encoding is not None:
             warnings.warn("The 'encoding' argument to autodoc.%s.get_doc() is deprecated."
                           % self.__class__.__name__,
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
         lines = getattr(self, '_new_docstrings', None)
         if lines is not None:
             return lines
@@ -1247,7 +1247,7 @@ class ClassDocumenter(DocstringSignatureMixin, ModuleLevelDocumenter):  # type:
         if encoding is not None:
             warnings.warn("The 'encoding' argument to autodoc.%s.get_doc() is deprecated."
                           % self.__class__.__name__,
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
         lines = getattr(self, '_new_docstrings', None)
         if lines is not None:
             return lines
@@ -1757,7 +1757,7 @@ class SlotsAttributeDocumenter(AttributeDocumenter):
 
 def get_documenters(app: Sphinx) -> Dict[str, "Type[Documenter]"]:
     """Returns registered Documenter classes"""
-    warnings.warn("get_documenters() is deprecated.", RemovedInSphinx50Warning)
+    warnings.warn("get_documenters() is deprecated.", RemovedInSphinx50Warning, stacklevel=2)
     return app.registry.documenters
 
 
diff --git a/sphinx/ext/autodoc/directive.py b/sphinx/ext/autodoc/directive.py
index 3be19f089..9a3428f5d 100644
--- a/sphinx/ext/autodoc/directive.py
+++ b/sphinx/ext/autodoc/directive.py
@@ -66,7 +66,7 @@ class DocumenterBridge:
         else:
             # create fake object for self.state.document.settings.tab_width
             warnings.warn('DocumenterBridge requires a state object on instantiation.',
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
             settings = Struct(tab_width=8)
             document = Struct(settings=settings)
             self.state = Struct(document=document)
diff --git a/sphinx/ext/autosummary/__init__.py b/sphinx/ext/autosummary/__init__.py
index 57f775272..ed49c56df 100644
--- a/sphinx/ext/autosummary/__init__.py
+++ b/sphinx/ext/autosummary/__init__.py
@@ -659,7 +659,7 @@ def autolink_role(typ: str, rawtext: str, etext: str, lineno: int, inliner: Inli
     Expands to ':obj:`text`' if `text` is an object that can be imported;
     otherwise expands to '*text*'.
     """
-    warnings.warn('autolink_role() is deprecated.', RemovedInSphinx40Warning)
+    warnings.warn('autolink_role() is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
     env = inliner.document.settings.env
     pyobj_role = env.get_domain('py').role('obj')
     objects, msg = pyobj_role('obj', rawtext, etext, lineno, inliner, options, content)
diff --git a/sphinx/ext/autosummary/generate.py b/sphinx/ext/autosummary/generate.py
index 693f0e5b0..e5bdc0e30 100644
--- a/sphinx/ext/autosummary/generate.py
+++ b/sphinx/ext/autosummary/generate.py
@@ -126,7 +126,7 @@ class AutosummaryRenderer:
                           RemovedInSphinx50Warning, stacklevel=2)
         if template_dir:
             warnings.warn('template_dir argument for AutosummaryRenderer is deprecated.',
-                          RemovedInSphinx50Warning)
+                          RemovedInSphinx50Warning, stacklevel=2)
 
         system_templates_path = [os.path.join(package_dir, 'ext', 'autosummary', 'templates')]
         loader = SphinxTemplateLoader(app.srcdir, app.config.templates_path,
@@ -279,25 +279,25 @@ def generate_autosummary_docs(sources: List[str], output_dir: str = None,
                               overwrite: bool = True) -> None:
     if info:
         warnings.warn('info argument for generate_autosummary_docs() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         _info = info
     else:
         _info = logger.info
 
     if warn:
         warnings.warn('warn argument for generate_autosummary_docs() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         _warn = warn
     else:
         _warn = logger.warning
 
     if builder:
         warnings.warn('builder argument for generate_autosummary_docs() is deprecated.',
-                      RemovedInSphinx50Warning)
+                      RemovedInSphinx50Warning, stacklevel=2)
 
     if template_dir:
         warnings.warn('template_dir argument for generate_autosummary_docs() is deprecated.',
-                      RemovedInSphinx50Warning)
+                      RemovedInSphinx50Warning, stacklevel=2)
 
     showed_sources = list(sorted(sources))
     if len(showed_sources) > 20:
@@ -390,7 +390,7 @@ def find_autosummary_in_docstring(name: str, module: str = None, filename: str =
     """
     if module:
         warnings.warn('module argument for find_autosummary_in_docstring() is deprecated.',
-                      RemovedInSphinx50Warning)
+                      RemovedInSphinx50Warning, stacklevel=2)
 
     try:
         real_name, obj, parent, modname = import_by_name(name)
diff --git a/sphinx/ext/doctest.py b/sphinx/ext/doctest.py
index 645521f9b..26966016d 100644
--- a/sphinx/ext/doctest.py
+++ b/sphinx/ext/doctest.py
@@ -47,7 +47,7 @@ doctestopt_re = re.compile(r'#\s*doctest:.+$', re.MULTILINE)
 
 def doctest_encode(text: str, encoding: str) -> str:
     warnings.warn('doctest_encode() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     return text
 
 
diff --git a/sphinx/ext/todo.py b/sphinx/ext/todo.py
index c5cacc437..bfb46903f 100644
--- a/sphinx/ext/todo.py
+++ b/sphinx/ext/todo.py
@@ -105,7 +105,7 @@ class TodoDomain(Domain):
 
 
 def process_todos(app: Sphinx, doctree: nodes.document) -> None:
-    warnings.warn('process_todos() is deprecated.', RemovedInSphinx40Warning)
+    warnings.warn('process_todos() is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
     # collect all todos in the environment
     # this is not done in the directive itself because it some transformations
     # must have already been run, e.g. substitutions
@@ -221,7 +221,8 @@ def process_todo_nodes(app: Sphinx, doctree: nodes.document, fromdocname: str) -
     """Replace all todolist nodes with a list of the collected todos.
     Augment each todo with a backlink to the original location.
     """
-    warnings.warn('process_todo_nodes() is deprecated.', RemovedInSphinx40Warning)
+    warnings.warn('process_todo_nodes() is deprecated.',
+                  RemovedInSphinx40Warning, stacklevel=2)
 
     domain = cast(TodoDomain, app.env.get_domain('todo'))
     todos = sum(domain.todos.values(), [])  # type: List[todo_node]
@@ -273,7 +274,7 @@ def process_todo_nodes(app: Sphinx, doctree: nodes.document, fromdocname: str) -
 
 
 def purge_todos(app: Sphinx, env: BuildEnvironment, docname: str) -> None:
-    warnings.warn('purge_todos() is deprecated.', RemovedInSphinx40Warning)
+    warnings.warn('purge_todos() is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
     if not hasattr(env, 'todo_all_todos'):
         return
     env.todo_all_todos = [todo for todo in env.todo_all_todos  # type: ignore
@@ -282,7 +283,7 @@ def purge_todos(app: Sphinx, env: BuildEnvironment, docname: str) -> None:
 
 def merge_info(app: Sphinx, env: BuildEnvironment, docnames: Iterable[str],
                other: BuildEnvironment) -> None:
-    warnings.warn('merge_info() is deprecated.', RemovedInSphinx40Warning)
+    warnings.warn('merge_info() is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
     if not hasattr(other, 'todo_all_todos'):
         return
     if not hasattr(env, 'todo_all_todos'):
diff --git a/sphinx/parsers.py b/sphinx/parsers.py
index 3974d1c66..6a07d1801 100644
--- a/sphinx/parsers.py
+++ b/sphinx/parsers.py
@@ -64,7 +64,7 @@ class Parser(docutils.parsers.Parser):
 
     @property
     def app(self) -> "Sphinx":
-        warnings.warn('parser.app is deprecated.', RemovedInSphinx50Warning)
+        warnings.warn('parser.app is deprecated.', RemovedInSphinx50Warning, stacklevel=2)
         return self._app
 
 
diff --git a/sphinx/pycode/__init__.py b/sphinx/pycode/__init__.py
index 0a6ff5214..4879fb349 100644
--- a/sphinx/pycode/__init__.py
+++ b/sphinx/pycode/__init__.py
@@ -133,7 +133,7 @@ class ModuleAnalyzer:
         pos = source.tell()
         if not decoded:
             warnings.warn('decode option for ModuleAnalyzer is deprecated.',
-                          RemovedInSphinx40Warning)
+                          RemovedInSphinx40Warning, stacklevel=2)
             self._encoding, _ = tokenize.detect_encoding(source.readline)
             source.seek(pos)
             self.code = source.read().decode(self._encoding)
@@ -185,5 +185,5 @@ class ModuleAnalyzer:
     @property
     def encoding(self) -> str:
         warnings.warn('ModuleAnalyzer.encoding is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         return self._encoding
diff --git a/sphinx/roles.py b/sphinx/roles.py
index ff24fcf55..57d11c269 100644
--- a/sphinx/roles.py
+++ b/sphinx/roles.py
@@ -574,7 +574,7 @@ def index_role(typ: str, rawtext: str, text: str, lineno: int, inliner: Inliner,
 
 class Index(ReferenceRole):
     def run(self) -> Tuple[List[Node], List[system_message]]:
-        warnings.warn('Index role is deprecated.', RemovedInSphinx40Warning)
+        warnings.warn('Index role is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
         target_id = 'index-%s' % self.env.new_serialno('index')
         if self.has_explicit_title:
             # if an explicit target is given, process it as a full entry
diff --git a/sphinx/search/__init__.py b/sphinx/search/__init__.py
index d9853ff06..f9bbe0590 100644
--- a/sphinx/search/__init__.py
+++ b/sphinx/search/__init__.py
@@ -203,7 +203,7 @@ class WordCollector(nodes.NodeVisitor):
     def is_meta_keywords(self, node: addnodes.meta, nodetype: Any = None) -> bool:
         if nodetype is not None:
             warnings.warn('"nodetype" argument for WordCollector.is_meta_keywords() '
-                          'is deprecated.', RemovedInSphinx40Warning)
+                          'is deprecated.', RemovedInSphinx40Warning, stacklevel=2)
 
         if isinstance(node, addnodes.meta) and node.get('name') == 'keywords':
             meta_lang = node.get('lang')
diff --git a/sphinx/util/__init__.py b/sphinx/util/__init__.py
index 12ae051f1..73d25a8f6 100644
--- a/sphinx/util/__init__.py
+++ b/sphinx/util/__init__.py
@@ -110,7 +110,7 @@ def get_matching_docs(dirname: str, suffixes: List[str],
     Exclude files and dirs matching a pattern in *exclude_patterns*.
     """
     warnings.warn('get_matching_docs() is now deprecated. Use get_matching_files() instead.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     suffixpatterns = ['*' + s for s in suffixes]
     for filename in get_matching_files(dirname, exclude_matchers):
         for suffixpattern in suffixpatterns:
@@ -315,7 +315,7 @@ _coding_re = re.compile(r'coding[:=]\s*([-\w.]+)')
 def detect_encoding(readline: Callable[[], bytes]) -> str:
     """Like tokenize.detect_encoding() from Py3k, but a bit simplified."""
     warnings.warn('sphinx.util.detect_encoding() is deprecated',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
 
     def read_or_stop() -> bytes:
         try:
diff --git a/sphinx/util/compat.py b/sphinx/util/compat.py
index 0135899eb..4923343ae 100644
--- a/sphinx/util/compat.py
+++ b/sphinx/util/compat.py
@@ -46,7 +46,7 @@ class IndexEntriesMigrator(SphinxTransform):
                 if len(entries) == 4:
                     source, line = get_source_line(node)
                     warnings.warn('An old styled index node found: %r at (%s:%s)' %
-                                  (node, source, line), RemovedInSphinx40Warning)
+                                  (node, source, line), RemovedInSphinx40Warning, stacklevel=2)
                     node['entries'][i] = entries + (None,)
 
 
diff --git a/sphinx/util/docfields.py b/sphinx/util/docfields.py
index 699738888..c07bc7f66 100644
--- a/sphinx/util/docfields.py
+++ b/sphinx/util/docfields.py
@@ -224,12 +224,12 @@ class DocFieldTransformer:
         except Exception:
             # for 3rd party extensions directly calls this transformer.
             warnings.warn('DocFieldTransformer expects given directive object is a subclass '
-                          'of ObjectDescription.', RemovedInSphinx40Warning)
+                          'of ObjectDescription.', RemovedInSphinx40Warning, stacklevel=2)
             self.typemap = self.preprocess_fieldtypes(directive.__class__.doc_field_types)
 
     def preprocess_fieldtypes(self, types: List[Field]) -> Dict[str, Tuple[Field, bool]]:
         warnings.warn('DocFieldTransformer.preprocess_fieldtypes() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         typemap = {}
         for fieldtype in types:
             for name in fieldtype.names:
diff --git a/sphinx/util/inspect.py b/sphinx/util/inspect.py
index 9eb05b29b..c81edc949 100644
--- a/sphinx/util/inspect.py
+++ b/sphinx/util/inspect.py
@@ -58,7 +58,7 @@ def getargspec(func: Callable) -> Any:
     """Like inspect.getfullargspec but supports bound methods, and wrapped
     methods."""
     warnings.warn('sphinx.ext.inspect.getargspec() is deprecated',
-                  RemovedInSphinx50Warning)
+                  RemovedInSphinx50Warning, stacklevel=2)
     # On 3.5+, signature(int) or similar raises ValueError. On 3.4, it
     # succeeds with a bogus signature. We want a TypeError uniformly, to
     # match historical behavior.
@@ -329,7 +329,7 @@ def safe_getattr(obj: Any, name: str, *defargs: Any) -> Any:
 def safe_getmembers(object: Any, predicate: Callable[[str], bool] = None,
                     attr_getter: Callable = safe_getattr) -> List[Tuple[str, Any]]:
     """A version of inspect.getmembers() that uses safe_getattr()."""
-    warnings.warn('safe_getmembers() is deprecated', RemovedInSphinx40Warning)
+    warnings.warn('safe_getmembers() is deprecated', RemovedInSphinx40Warning, stacklevel=2)
 
     results = []  # type: List[Tuple[str, Any]]
     for key in dir(object):
@@ -555,7 +555,7 @@ class Signature:
     def __init__(self, subject: Callable, bound_method: bool = False,
                  has_retval: bool = True) -> None:
         warnings.warn('sphinx.util.inspect.Signature() is deprecated',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
         # check subject is not a built-in class (ex. int, str)
         if (isinstance(subject, type) and
diff --git a/sphinx/util/nodes.py b/sphinx/util/nodes.py
index bca6e0bfc..33ce8e4a9 100644
--- a/sphinx/util/nodes.py
+++ b/sphinx/util/nodes.py
@@ -280,7 +280,7 @@ def extract_messages(doctree: Element) -> Iterable[Tuple[Element, str]]:
 
 def find_source_node(node: Element) -> str:
     warnings.warn('find_source_node() is deprecated.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     return get_node_source(node)
 
 
diff --git a/sphinx/util/osutil.py b/sphinx/util/osutil.py
index 248abd0e7..23f5b0137 100644
--- a/sphinx/util/osutil.py
+++ b/sphinx/util/osutil.py
@@ -86,7 +86,7 @@ def ensuredir(path: str) -> None:
 def walk(top: str, topdown: bool = True, followlinks: bool = False) -> Iterator[Tuple[str, List[str], List[str]]]:  # NOQA
     warnings.warn('sphinx.util.osutil.walk() is deprecated for removal. '
                   'Please use os.walk() instead.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     return os.walk(top, topdown=topdown, followlinks=followlinks)
 
 
@@ -178,7 +178,7 @@ def abspath(pathdir: str) -> str:
 def getcwd() -> str:
     warnings.warn('sphinx.util.osutil.getcwd() is deprecated. '
                   'Please use os.getcwd() instead.',
-                  RemovedInSphinx40Warning)
+                  RemovedInSphinx40Warning, stacklevel=2)
     return os.getcwd()
 
 
diff --git a/sphinx/writers/latex.py b/sphinx/writers/latex.py
index 9390ba5de..e3ddedccf 100644
--- a/sphinx/writers/latex.py
+++ b/sphinx/writers/latex.py
@@ -96,7 +96,7 @@ class LaTeXWriter(writers.Writer):
             visitor = self.builder.create_translator(self.document, self.builder, self.theme)
         except TypeError:
             warnings.warn('LaTeXTranslator now takes 3rd argument; "theme".',
-                          RemovedInSphinx50Warning)
+                          RemovedInSphinx50Warning, stacklevel=2)
             visitor = self.builder.create_translator(self.document, self.builder)
 
         self.document.walkabout(visitor)
@@ -292,7 +292,7 @@ class LaTeXTranslator(SphinxTranslator):
 
         if theme is None:
             warnings.warn('LaTeXTranslator now takes 3rd argument; "theme".',
-                          RemovedInSphinx50Warning)
+                          RemovedInSphinx50Warning, stacklevel=2)
 
         # flags
         self.in_title = 0
@@ -2072,7 +2072,7 @@ class LaTeXTranslator(SphinxTranslator):
 
     def babel_defmacro(self, name: str, definition: str) -> str:
         warnings.warn('babel_defmacro() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
 
         if self.elements['babel']:
             prefix = '\\addto\\extras%s{' % self.babel.get_language()
@@ -2085,7 +2085,7 @@ class LaTeXTranslator(SphinxTranslator):
 
     def generate_numfig_format(self, builder: "LaTeXBuilder") -> str:
         warnings.warn('generate_numfig_format() is deprecated.',
-                      RemovedInSphinx40Warning)
+                      RemovedInSphinx40Warning, stacklevel=2)
         ret = []  # type: List[str]
         figure = self.builder.config.numfig_format['figure'].split('%s', 1)
         if len(figure) == 1: