Merge pull request #16267 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

client/src/schema/schema.ts

@@ -13175,7 +13175,7 @@ export interface operations {
     index_api_jobs_get: {
         /** Index */
         parameters?: {
-            /** @description If true, and requestor is an admin, will return external job id and user email. This is only available to admins. */
+            /** @description If true, and requester is an admin, will return external job id and user email. This is only available to admins. */
             /** @description an encoded user id to restrict query to, must be own id if not admin user */
             /** @description Determines columns to return. Defaults to 'collection'. */
             /** @description Limit listing of jobs to those that are updated after specified date (e.g. '2014-01-01') */

lib/galaxy/dependencies/dev-requirements.txt

@@ -22,10 +22,10 @@ cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
 charset-normalizer==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
-click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12"
+click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
-codespell==2.2.4 ; python_version >= "3.7" and python_version < "3.12"
-colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (os_name == "nt" or sys_platform == "win32" or platform_system == "Windows")
+codespell==2.2.5 ; python_version >= "3.7" and python_version < "3.12"
+colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 coverage[toml]==7.2.7 ; python_version >= "3.7" and python_version < "3.12"
 cryptography==41.0.1 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "linux"
 cwltest==2.3.20230527113600 ; python_version >= "3.7" and python_version < "3.12"
@@ -35,7 +35,7 @@ defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12"
 deprecated==1.2.14 ; python_version >= "3.7" and python_version < "3.12"
 docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12"
 exceptiongroup==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
-filelock==3.12.1 ; python_version >= "3.7" and python_version < "3.12"
+filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
 fluent-logger==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
@@ -74,16 +74,17 @@ multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12"
 mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 myst-parser==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
-numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.12"
+numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.9"
+numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
 pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"
-platformdirs==3.5.3 ; python_version >= "3.7" and python_version < "3.12"
+platformdirs==3.6.0 ; python_version >= "3.7" and python_version < "3.12"
 pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
-port-for==0.6.3 ; python_version >= "3.7" and python_version < "3.12"
+port-for==0.7.0 ; python_version >= "3.7" and python_version < "3.12"
 prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
 prompt-toolkit==3.0.38 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin"
@@ -103,7 +104,7 @@ pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.12"
 pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12"
-pytest-mock==3.10.0 ; python_version >= "3.7" and python_version < "3.12"
+pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12"
 pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 pytest==7.3.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -118,7 +119,7 @@ requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
 responses==0.23.1 ; python_version >= "3.7" and python_version < "3.12"
 rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12"
-rich==13.4.1 ; python_version >= "3.7" and python_version < "3.12"
+rich==13.4.2 ; python_version >= "3.7" and python_version < "3.12"
 ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
 ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12"
 schema-salad==8.4.20230606143604 ; python_version >= "3.7" and python_version < "3.12"
@@ -143,7 +144,7 @@ sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12
 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12"
 statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12"
 testfixtures==7.1.0 ; python_version >= "3.7" and python_version < "3.12"
-tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
+tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
 toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12"
 tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11"
 trio-websocket==0.10.3 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -13,7 +13,7 @@ anyio==3.7.0 ; python_version >= "3.7" and python_version < "3.12"
 apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12"
 appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12"
 arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
-argcomplete==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
+argcomplete==3.1.1 ; python_version >= "3.7" and python_version < "3.12"
 async-timeout==4.0.2 ; python_version >= "3.7" and python_version < "3.12"
 asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8"
 attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12"
@@ -41,7 +41,7 @@ cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12"
 circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12"
-click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12"
+click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 click==8.1.3 ; python_version >= "3.7" and python_version < "3.12"
 cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12"
 cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -65,8 +65,8 @@ edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12"
 email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12"
 exceptiongroup==1.1.1 ; python_version >= "3.7" and python_version < "3.11"
 fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12"
-fastapi==0.96.1 ; python_version >= "3.7" and python_version < "3.12"
-filelock==3.12.1 ; python_version >= "3.7" and python_version < "3.12"
+fastapi==0.97.0 ; python_version >= "3.7" and python_version < "3.12"
+filelock==3.12.2 ; python_version >= "3.7" and python_version < "3.12"
 frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12"
 fs==2.4.16 ; python_version >= "3.7" and python_version < "3.12"
 fsspec==2023.1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -107,7 +107,8 @@ mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 networkx==2.5 ; python_version >= "3.7" and python_version < "3.12"
 nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8"
-numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.12"
+numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.9"
+numpy==1.25.0 ; python_version >= "3.9" and python_version < "3.12"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
 orjson==3.9.1 ; python_version >= "3.7" and python_version < "3.12"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -156,7 +157,7 @@ requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12"
 requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
 requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
 requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12"
-rich==13.4.1 ; python_version >= "3.7" and python_version < "3.12"
+rich==13.4.2 ; python_version >= "3.7" and python_version < "3.12"
 rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12"
 routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12"
 rsa==4.9 ; python_version >= "3.7" and python_version < "3.12"
@@ -180,7 +181,7 @@ supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12"
 svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
 tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12"
 tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12"
-tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.12"
+tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12"
 tornado==6.2 ; python_version >= "3.7" and python_version < "3.12"
 tqdm==4.65.0 ; python_version >= "3.7" and python_version < "3.12"
 tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -197,7 +198,7 @@ webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12"
 webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12"
 whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12"
 wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12"
-yacman==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
+yacman==0.9.1 ; python_version >= "3.7" and python_version < "3.12"
 yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12"
 zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12"
 zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -79,7 +79,7 @@
 UserDetailsQueryParam: bool = Query(
     default=False,
     title="Include user details",
-    description="If true, and requestor is an admin, will return external job id and user email. This is only available to admins.",
+    description="If true, and requester is an admin, will return external job id and user email. This is only available to admins.",
 )
 
 UserIdQueryParam: Optional[DecodedDatabaseIdField] = Query(