Code cleanups from pyupgrade

Found by running:

```
ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py37-plus
```

lib/galaxy/datatypes/molecules.py

@@ -1382,7 +1382,7 @@ class ExtendedXYZ(XYZ):
             if properties is None:  # re.search returned None
                 raise ValueError(f"Could not find column properties in line: {comment}")
             properties = [s.split(":") for s in re.findall(r"[a-zA-Z]+:[SIRL]:[0-9]+", properties.group(1))]
-            total_columns = sum([int(s[2]) for s in properties])
+            total_columns = sum(int(s[2]) for s in properties)
 
             for _ in range(n_atoms):
                 atom_dict = {}

lib/galaxy/files/sources/__init__.py

@@ -1,9 +1,10 @@
 import abc
 import os
 import time
-from typing import Set
-
-from typing_extensions import ClassVar
+from typing import (
+    ClassVar,
+    Set,
+)
 
 from galaxy.exceptions import (
     ConfigurationError,

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -4,6 +4,7 @@ import logging
 import os
 from typing import (
     Any,
+    ClassVar,
     Dict,
     List,
     Optional,
@@ -12,7 +13,6 @@ from typing import (
 
 import fs
 from fs.base import FS
-from typing_extensions import ClassVar
 
 from ..sources import BaseFilesSource
 

lib/galaxy/files/uris.py

@@ -36,7 +36,7 @@ def stream_url_to_str(
 ) -> str:
     tmp_file = stream_url_to_file(path, file_sources=file_sources, prefix=prefix)
     try:
-        with open(tmp_file, "r") as f:
+        with open(tmp_file) as f:
             return f.read()
     finally:
         os.remove(tmp_file)

lib/galaxy/managers/workflows.py

@@ -146,7 +146,7 @@ class WorkflowsManager(sharable.SharableModelManager):
             filters.append(model.StoredWorkflowUserShareAssociation.user == user)
 
         if show_published or user is None and show_published is None:
-            filters.append((model.StoredWorkflow.published == true()))
+            filters.append(model.StoredWorkflow.published == true())
 
         query = trans.sa_session.query(model.StoredWorkflow)
         if show_shared:

lib/galaxy/model/store/__init__.py

@@ -2257,7 +2257,7 @@ def source_to_import_store(
             delete = True
         target_path = source_uri
         if target_path.endswith(".json"):
-            with open(target_path, "r") as f:
+            with open(target_path) as f:
                 store_dict = load(f)
             assert isinstance(store_dict, dict)
             model_import_store = get_import_model_store_for_dict(

lib/galaxy/model/store/load_objects.py

@@ -50,7 +50,7 @@ def main(argv=None):
 
     data: Dict[str, Any] = {}
     if is_json:
-        with open(store_path, "r") as f:
+        with open(store_path) as f:
             store_dict = yaml.safe_load(f)
         data["store_dict"] = store_dict
     else:

lib/galaxy/web/short_term_storage/__init__.py

@@ -244,7 +244,7 @@ class ShortTermStorageManager(ShortTermStorageAllocator, ShortTermStorageMonitor
 
     def _load_metadata(self, target_directory: Path, meta_name: str):
         meta_path = target_directory / f"{meta_name}.json"
-        with open(meta_path, "r") as f:
+        with open(meta_path) as f:
             return json.load(f)
 
     def _directory(self, target: Union[str, ShortTermStorageTarget]) -> Path:

lib/galaxy/web_stack/gunicorn_config.py

@@ -32,7 +32,7 @@ def _next_worker_id(server):
     if server._worker_id_overload:
         return server._worker_id_overload.pop()
 
-    in_use = set(w._worker_id for w in tuple(server.WORKERS.values()) if w.alive)
+    in_use = {w._worker_id for w in tuple(server.WORKERS.values()) if w.alive}
     free = set(range(1, server._worker_id_current_workers + 1)) - in_use
 
     return free.pop()

test/integration/test_job_files.py

@@ -85,13 +85,13 @@ class JobFilesIntegerationTestCase(integration_util.IntegrationTestCase):
         post_url = self._api_url(f"jobs/{job_id}/files", use_key=False)
         response = requests.post(post_url, data=data, files=files())
         api_asserts.assert_status_code_is_ok(response)
-        assert open(path, "r").read() == "some initial text data"
+        assert open(path).read() == "some initial text data"
 
         work_dir_file = os.path.join(working_directory, "work")
         data = {"path": work_dir_file, "job_key": job_key}
         response = requests.post(post_url, data=data, files=files())
         api_asserts.assert_status_code_is_ok(response)
-        assert open(work_dir_file, "r").read() == "some initial text data"
+        assert open(work_dir_file).read() == "some initial text data"
 
         # set job state to finished and ensure the file is no longer
         # readable

test/unit/data/test_dataset_materialization.py

@@ -337,6 +337,6 @@ def _assert_2_bed_metadata(hda: HistoryDatasetAssociation) -> None:
 
 
 def _assert_path_contains_2_bed(path) -> None:
-    with open(path, "r") as f:
+    with open(path) as f:
         contents = f.read()
     assert contents == CONTENTS_2_BED