Merge remote-tracking branch 'newgene/master' into 0.12.x

.flake8

@@ -1,3 +1,14 @@
 [flake8]
-# ignore=E226,E265,E302,E402,E731,F821,W503
-max-line-length=160
+# Let Black handle all the formatting.
+ignore = E,B008,W503
+max-line-length=120
+exclude =
+  biothings/utils/jsondiff.py,     # 3rd party code, don't touch
+  biothings/utils/jsonpatch.py,    # 3rd party code, don't touch
+  biothings/utils/parallel.py,     # deprecated code, don't touch
+  biothings/utils/parallel_mp.py,  # deprecated code, don't touch
+  biothings/utils/shelve.py,       # deprecated code, don't touch
+  biothings/hub/dataload/sync.py,  # deprecated code, don't touch
+  biothings/hub/dataload/validator.py, # deprecated code, don't touch
+  tests/snapshots,
+  .svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.eggs,*.egg

.gitignore

@@ -35,6 +35,7 @@ config.py
 !/tests/hub/hubdb/config.py
 .hubdb
 .hubdb.*
+*.biothings_hub*
 
 # other local files
 .notes/

biothings/__init__.py

@@ -8,13 +8,15 @@ class _version_info(NamedTuple):
     micro: int
 
 
-version_info = _version_info(0, 12, 'dev')
-__version__ = '.'.join(map(str, version_info))
+version_info = _version_info(0, 12, "dev")
+__version__ = ".".join(map(str, version_info))
 
 
 def config_for_app(config):
     import warnings
-    warnings.warn((
-        "It is safe to remove this function call now. "
-        "import biothings.hub will take care of it."
-    ), DeprecationWarning)
+
+    warnings.warn(
+        'It is safe to remove this function call now, just "import biothings.hub" will take care of it.',
+        DeprecationWarning,
+        stacklevel=2,
+    )