tighten type ignores

galaxyproject · Nov 23, 2021 · 90145da · 90145da
1 parent 286add3
commit 90145da
Show file tree

Hide file tree

Showing 56 changed files with 265 additions and 263 deletions.
diff --git a/lib/galaxy/__init__.py b/lib/galaxy/__init__.py
@@ -3,4 +3,4 @@
 """
 
 from pkgutil import extend_path
-__path__ = extend_path(__path__, __name__)  # type: ignore
+__path__ = extend_path(__path__, __name__)  # type: ignore[has-type]
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -291,7 +291,7 @@ def __init__(self, **kwargs) -> None:
         # Tours registry
         tour_registry = build_tours_registry(self.config.tour_config_dir)
         self.tour_registry = tour_registry
-        self[ToursRegistry] = tour_registry  # type: ignore
+        self[ToursRegistry] = tour_registry  # type: ignore[misc]
         # Webhooks registry
         self.webhooks_registry = self._register_singleton(WebhooksRegistry, WebhooksRegistry(self.config.webhooks_dir))
         # Load security policy.

diff --git a/lib/galaxy/config/script.py b/lib/galaxy/config/script.py
@@ -8,7 +8,7 @@
 try:
     import pip
 except ImportError:
-    pip = None  # type: ignore
+    pip = None  # type: ignore[assignment]
 
 
 CONFIGURE_URL = "https://docs.galaxyproject.org/en/master/admin/"

diff --git a/lib/galaxy/containers/docker.py b/lib/galaxy/containers/docker.py
@@ -13,13 +13,13 @@
 try:
     import docker
 except ImportError:
-    docker = None  # type: ignore
+    docker = None  # type: ignore[assignment]
 
 try:
     from requests.exceptions import ConnectionError, ReadTimeout
 except ImportError:
-    ConnectionError = None  # type: ignore
-    ReadTimeout = None  # type: ignore
+    ConnectionError = None  # type: ignore[assignment,misc]
+    ReadTimeout = None  # type: ignore[assignment,misc]
 
 from galaxy.containers import Container, ContainerInterface
 from galaxy.containers.docker_decorators import (

diff --git a/lib/galaxy/datatypes/constructive_solid_geometry.py b/lib/galaxy/datatypes/constructive_solid_geometry.py
@@ -1,11 +1,11 @@
 # TODO: revisit ignoring type and write some tests for this, the multi-inheritance in this
 # this file is challenging, it should be broken into true mixins.
-# type: ignore
 """
 Constructive Solid Geometry file formats.
 """
 
 import abc
+from typing import List
 
 from galaxy import util
 from galaxy.datatypes import data
@@ -122,15 +122,15 @@ def display_peek(self, dataset):
             return f"Ply file ({nice_size(dataset.get_size())})"
 
 
-class PlyAscii(Ply, data.Text):
+class PlyAscii(Ply, data.Text):  # type: ignore[misc]
     file_ext = "plyascii"
     subtype = 'ascii'
 
     def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
 
 
-class PlyBinary(Ply, Binary):
+class PlyBinary(Ply, Binary):  # type: ignore[misc]
     file_ext = "plybinary"
     subtype = 'binary'
 
@@ -313,7 +313,7 @@ def set_meta(self, dataset, **kwd):
                                 # FIELD FieldData 2
                                 processing_field_section = True
                                 num_fields = int(items[-1])
-                                fields_processed = []
+                                fields_processed: List[str] = []
                             elif processing_field_section:
                                 if len(fields_processed) == num_fields:
                                     processing_field_section = False
@@ -445,15 +445,15 @@ def display_peek(self, dataset):
             return f"Vtk file ({nice_size(dataset.get_size())})"
 
 
-class VtkAscii(Vtk, data.Text):
+class VtkAscii(Vtk, data.Text):  # type: ignore[misc]
     file_ext = "vtkascii"
     subtype = 'ASCII'
 
     def __init__(self, **kwd):
         data.Text.__init__(self, **kwd)
 
 
-class VtkBinary(Vtk, Binary):
+class VtkBinary(Vtk, Binary):   # type: ignore[misc]
     file_ext = "vtkbinary"
     subtype = 'BINARY'
 

diff --git a/lib/galaxy/files/sources/ftp.py b/lib/galaxy/files/sources/ftp.py
@@ -1,7 +1,7 @@
 try:
     from fs.ftpfs import FTPFS
 except ImportError:
-    FTPFS = None  # type: ignore
+    FTPFS = None  # type: ignore[misc,assignment]
 
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 

diff --git a/lib/galaxy/jobs/runners/util/cli/factory.py b/lib/galaxy/jobs/runners/util/cli/factory.py
@@ -5,7 +5,7 @@
     )
     code_dir = 'lib'
 except ImportError:
-    from pulsar.managers.util.cli import (  # type: ignore
+    from pulsar.managers.util.cli import (  # type: ignore[no-redef]
         CliInterface,
         split_params
     )

diff --git a/lib/galaxy/jobs/runners/util/cli/job/__init__.py b/lib/galaxy/jobs/runners/util/cli/job/__init__.py
@@ -13,7 +13,7 @@
 except ImportError:
 
     # Not in Galaxy, map Galaxy job states to Pulsar ones.
-    class job_states(str, Enum):  # type: ignore
+    class job_states(str, Enum):  # type: ignore[no-redef]
         RUNNING = 'running'
         OK = 'complete'
         QUEUED = 'queued'

diff --git a/lib/galaxy/managers/tags.py b/lib/galaxy/managers/tags.py
@@ -16,8 +16,8 @@
 
 taggable_item_names = {item: item for item in ItemTagAssociation.associated_item_names}
 # This Enum is generated dynamically and mypy can not statically infer it's real type
-# so it should be ignored. See:https://github.com/python/mypy/issues/4865#issuecomment-592560696
-TaggableItemClass = Enum('TaggableItemClass', taggable_item_names)  # type: ignore
+# so it should be ignored. See: https://github.com/python/mypy/issues/4865#issuecomment-592560696
+TaggableItemClass = Enum('TaggableItemClass', taggable_item_names)  # type: ignore[misc]
 
 
 class ItemTagsPayload(BaseModel):