Only force files to be included when run from CLI

Previously we added support so users can do:

    $ flake8 bin/executable

But this broke the fact that git hooks shouldn't check things like
reStructuredText doc files. This commit restores that functionality but
will cause bin/executable to be ignored in the git hook. This seems fair
since folks can amend their filename patterns to include it explicitly.

Closes #268

docs/source/release-notes/3.3.0.rst

@@ -3,7 +3,11 @@
 
 You can view the `3.3.0 milestone`_ on GitLab for more details.
 
+- Fix problem where hooks should only check \*.py files. (See also
+  `GitLab#268`_)
 
 .. links
 .. _3.3.0 milestone:
     https://gitlab.com/pycqa/flake8/milestones/16
+.. _GitLab#268:
+    https://gitlab.com/pycqa/flake8/issues/268

src/flake8/checker.py

@@ -257,24 +257,17 @@ class Manager(object):
             paths = ['.']
 
         filename_patterns = self.options.filename
+        running_from_vcs = self.options._running_from_vcs
 
         # NOTE(sigmavirus24): Yes this is a little unsightly, but it's our
         # best solution right now.
-        def should_create_file_checker(filename):
+        def should_create_file_checker(filename, argument):
             """Determine if we should create a file checker."""
             matches_filename_patterns = utils.fnmatch(
                 filename, filename_patterns
             )
             is_stdin = filename == '-'
             file_exists = os.path.exists(filename)
-            return (file_exists and matches_filename_patterns) or is_stdin
-
-        checks = self.checks.to_dictionary()
-        self.checkers = [
-            FileChecker(filename, checks, self.options)
-            for argument in paths
-            for filename in utils.filenames_from(argument,
-                                                 self.is_path_excluded)
             # NOTE(sigmavirus24): If a user explicitly specifies something,
             # e.g, ``flake8 bin/script`` then we should run Flake8 against
             # that. Since should_create_file_checker looks to see if the
@@ -282,7 +275,19 @@ class Manager(object):
             # the event that the argument and the filename are identical.
             # If it was specified explicitly, the user intended for it to be
             # checked.
-            if argument == filename or should_create_file_checker(filename)
+            explicitly_provided = (not running_from_vcs and
+                                   (argument == filename))
+            return ((file_exists and
+                     (explicitly_provided or matches_filename_patterns)) or
+                    is_stdin)
+
+        checks = self.checks.to_dictionary()
+        self.checkers = [
+            FileChecker(filename, checks, self.options)
+            for argument in paths
+            for filename in utils.filenames_from(argument,
+                                                 self.is_path_excluded)
+            if should_create_file_checker(filename, argument)
         ]
         LOG.info('Checking %d files', len(self.checkers))
 

src/flake8/main/application.py

@@ -174,6 +174,8 @@ class Application(object):
             if not self.parsed_diff:
                 self.exit()
 
+        self.options._running_from_vcs = False
+
         self.check_plugins.provide_options(self.option_manager, self.options,
                                            self.args)
         self.listening_plugins.provide_options(self.option_manager,
@@ -300,16 +302,20 @@ class Application(object):
         self.make_guide()
         self.make_file_checker_manager()
 
-    def _run(self, argv):
+    def report(self):
-        # type: (Union[NoneType, List[str]]) -> NoneType
+        """Report errors, statistics, and benchmarks."""
-        self.initialize(argv)
-        self.run_checks()
         self.formatter.start()
         self.report_errors()
         self.report_statistics()
         self.report_benchmarks()
         self.formatter.stop()
 
+    def _run(self, argv):
+        # type: (Union[NoneType, List[str]]) -> NoneType
+        self.initialize(argv)
+        self.run_checks()
+        self.report()
+
     def run(self, argv=None):
         # type: (Union[NoneType, List[str]]) -> NoneType
         """Run our application.

src/flake8/main/git.py

@@ -43,6 +43,7 @@ def hook(lazy=False, strict=False):
         filepaths = list(copy_indexed_files_to(tempdir, lazy))
         app.initialize(['.'])
         app.options.exclude = update_excludes(app.options.exclude, tempdir)
+        app.options._running_from_vcs = True
         app.run_checks(filepaths)
 
     app.report_errors()

src/flake8/main/mercurial.py

@@ -35,7 +35,10 @@ def hook(ui, repo, **kwargs):
     filenames = list(get_filenames_from(repo, kwargs))
 
     app = application.Application()
-    app.run(filenames)
+    app.initialize(filenames)
+    app.options._running_from_vcs = True
+    app.run_checks()
+    app.report()
 
     if strict:
         return app.result_count