diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index 6fcbdcf3520d..190abb1ad1ea 100644 --- a/client/src/api/schema/schema.ts +++ b/client/src/api/schema/schema.ts @@ -2134,6 +2134,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "add_input"; /** Collection Type */ @@ -2169,6 +2170,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "add_step"; /** @@ -2276,6 +2278,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "History"; /** @@ -2392,6 +2395,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "History"; /** @@ -2556,6 +2560,7 @@ export interface components { * Category * @default broadcast * @constant + * @enum {string} */ category?: "broadcast"; /** @@ -2578,6 +2583,7 @@ export interface components { * Category * @default broadcast * @constant + * @enum {string} */ category?: "broadcast"; /** @@ -2620,6 +2626,7 @@ export interface components { * Category * @default broadcast * @constant + * @enum {string} */ category?: "broadcast"; content: components["schemas"]["BroadcastNotificationContent"]; @@ -2668,6 +2675,7 @@ export interface components { /** * Browsable * @constant + * @enum {boolean} */ browsable: true; /** @@ -2725,6 +2733,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "change_datatype"; }; @@ -2735,6 +2744,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "change_dbkey"; }; @@ -2948,6 +2958,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "composite"; /** Tags */ @@ -3048,6 +3059,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "connect"; /** Input */ @@ -3441,6 +3453,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Quota"; /** @@ -3507,6 +3520,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "User"; /** @@ -3780,6 +3794,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "DatasetCollectionElement"; /** @@ -3829,6 +3844,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "DatasetCollection"; /** @@ -3934,6 +3950,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "HistoryDatasetCollectionAssociation"; tags: components["schemas"]["TagCollection"]; @@ -3996,6 +4013,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "DatasetHash"; }; @@ -4335,6 +4353,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "DefaultQuotaAssociation"; /** @@ -4562,6 +4581,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "disconnect"; /** Input */ @@ -4748,6 +4768,7 @@ export interface components { * Source * @description The source of this dataset, which in the case of the model can only be `hdca`. * @constant + * @enum {string} */ src: "hdca"; }; @@ -4834,6 +4855,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Job"; /** @@ -5032,6 +5054,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "extract_input"; /** Input */ @@ -5045,6 +5068,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "extract_untyped_parameter"; /** Label */ @@ -5064,6 +5088,7 @@ export interface components { /** * FavoriteObjectType * @constant + * @enum {string} */ FavoriteObjectType: "tools"; /** FavoriteObjectsSummary */ @@ -5136,6 +5161,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "files"; /** Tags */ @@ -5151,6 +5177,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "fill_defaults"; }; @@ -5204,6 +5231,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "file"; /** @@ -5269,6 +5297,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "fill_step_defaults"; /** Step */ @@ -5304,6 +5333,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "folder"; /** @@ -5360,6 +5390,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "ftp_import"; /** Tags */ @@ -5389,6 +5420,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "ftp_import"; /** Tags */ @@ -5432,6 +5464,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Group"; /** @@ -5451,6 +5484,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "GroupQuotaAssociation"; }; @@ -5468,6 +5502,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Group"; /** name of the group */ @@ -5791,6 +5826,7 @@ export interface components { * @description TODO * @default file * @constant + * @enum {string} */ api_type?: "file"; /** Copied From Ldda Id */ @@ -5892,6 +5928,7 @@ export interface components { * History Content Type * @description This is always `dataset` for datasets. * @constant + * @enum {string} */ history_content_type: "dataset"; /** @@ -5928,6 +5965,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "HistoryDatasetAssociation"; /** @@ -5976,6 +6014,7 @@ export interface components { * @description This is always `file` for datasets. * @default file * @constant + * @enum {string} */ type?: "file"; /** @@ -6043,6 +6082,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "HistoryDatasetAssociation"; /** @@ -6097,6 +6137,7 @@ export interface components { * History Content Type * @description This is always `dataset` for datasets. * @constant + * @enum {string} */ history_content_type: "dataset"; /** @@ -6207,6 +6248,7 @@ export interface components { * History Content Type * @description This is always `dataset_collection` for dataset collections. * @constant + * @enum {string} */ history_content_type: "dataset_collection"; /** @@ -6243,6 +6285,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "HistoryDatasetCollectionAssociation"; /** @@ -6271,6 +6314,7 @@ export interface components { * @description This is always `collection` for dataset collections. * @default collection * @constant + * @enum {string} */ type?: "collection"; /** @@ -6339,6 +6383,7 @@ export interface components { * History Content Type * @description This is always `dataset_collection` for dataset collections. * @constant + * @enum {string} */ history_content_type: "dataset_collection"; /** @@ -6370,6 +6415,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "HistoryDatasetCollectionAssociation"; /** @@ -6393,6 +6439,7 @@ export interface components { * @description This is always `collection` for dataset collections. * @default collection * @constant + * @enum {string} */ type?: "collection"; /** @@ -6529,6 +6576,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "hdas"; }; @@ -6592,6 +6640,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "hdca"; }; @@ -7024,6 +7073,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "History"; /** @@ -7138,6 +7188,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "History"; /** @@ -7206,6 +7257,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model: "ImplicitCollectionJobs"; /** @@ -7249,6 +7301,7 @@ export interface components { * src * @description Indicates that the tool data should be resolved by a URI. * @constant + * @enum {string} */ src: "uri"; /** @@ -7321,6 +7374,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "data_collection_input"; /** When */ @@ -7363,6 +7417,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "data_input"; /** When */ @@ -7405,6 +7460,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "parameter_input"; /** When */ @@ -7502,6 +7558,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "ToolShedRepository"; /** @@ -7537,6 +7594,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "history_deleted"; }; @@ -7545,6 +7603,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "cancelled_on_review"; /** @@ -7558,6 +7617,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "user_request"; }; @@ -7571,6 +7631,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "workflow_output_not_found"; /** Workflow step id of step that caused a warning. */ @@ -7592,6 +7653,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "collection_failed"; /** @@ -7616,6 +7678,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "dataset_failed"; /** @@ -7634,6 +7697,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "expression_evaluation_failed"; /** @@ -7658,6 +7722,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "job_failed"; /** @@ -7678,6 +7743,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "output_not_found"; /** @@ -7696,6 +7762,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "when_not_boolean"; /** @@ -7758,6 +7825,7 @@ export interface components { /** * Model * @constant + * @enum {string} */ model: "WorkflowInvocation"; /** @@ -7784,6 +7852,7 @@ export interface components { * Source * @description Source model of the output dataset. * @constant + * @enum {string} */ src: "hda"; /** @@ -7804,6 +7873,7 @@ export interface components { * Source * @description Source model of the output dataset collection. * @constant + * @enum {string} */ src: "hdca"; /** @@ -7878,6 +7948,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Report"; /** @@ -7885,6 +7956,7 @@ export interface components { * @description Format of the invocation report. * @default markdown * @constant + * @enum {string} */ render_format?: "markdown"; /** @@ -7945,6 +8017,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "WorkflowInvocationStep"; /** @@ -8010,6 +8083,7 @@ export interface components { * @description The source model of the output. * @default hdca * @constant + * @enum {string} */ src?: "hdca"; }; @@ -8024,6 +8098,7 @@ export interface components { /** * Model * @constant + * @enum {string} */ model: "ImplicitCollectionJobs"; /** @@ -8050,6 +8125,7 @@ export interface components { /** * Model * @constant + * @enum {string} */ model: "Job"; /** @@ -8076,6 +8152,7 @@ export interface components { /** * Model * @constant + * @enum {string} */ model: "WorkflowInvocationStep"; /** @@ -8104,6 +8181,7 @@ export interface components { * @description The source model of the output. * @default hda * @constant + * @enum {string} */ src?: "hda"; /** @@ -8127,6 +8205,7 @@ export interface components { /** * Reason * @constant + * @enum {string} */ reason: "unexpected_failure"; /** @@ -8361,6 +8440,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Job"; /** @@ -8524,6 +8604,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Job"; /** @@ -8722,6 +8803,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model: "Job"; /** @@ -8793,6 +8875,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Job"; /** @@ -8926,6 +9009,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "library"; }; @@ -8966,6 +9050,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "library_folder"; }; @@ -9009,6 +9094,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "LibraryFolder"; /** @@ -9057,6 +9143,7 @@ export interface components { /** * LibraryFolderPermissionAction * @constant + * @enum {string} */ LibraryFolderPermissionAction: "set_permissions"; /** LibraryFolderPermissionsPayload */ @@ -9114,6 +9201,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Library"; /** @@ -9224,6 +9312,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Library"; /** @@ -9351,6 +9440,7 @@ export interface components { * * The user will always receive notifications from these categories. * @constant + * @enum {string} */ MandatoryNotificationCategory: "broadcast"; /** MaterializeDatasetInstanceAPIRequest */ @@ -9376,6 +9466,7 @@ export interface components { * Category * @default message * @constant + * @enum {string} */ category?: "message"; /** @@ -9503,6 +9594,7 @@ export interface components { * Category * @default new_shared_item * @constant + * @enum {string} */ category?: "new_shared_item"; /** @@ -9922,6 +10014,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Page"; /** @@ -9997,6 +10090,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Page"; /** @@ -10087,6 +10181,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "pasted"; /** Tags */ @@ -10146,6 +10241,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "path"; /** Tags */ @@ -10193,6 +10289,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "pause"; /** When */ @@ -10363,6 +10460,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Quota"; /** @@ -10415,6 +10513,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Quota"; /** @@ -10593,6 +10692,7 @@ export interface components { /** * Class * @constant + * @enum {string} */ class: "Directory"; /** @@ -10616,6 +10716,7 @@ export interface components { /** * Class * @constant + * @enum {string} */ class: "File"; /** @@ -10667,6 +10768,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "remove_unlabeled_workflow_outputs"; }; @@ -10753,6 +10855,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Role"; /** @@ -10844,6 +10947,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "server_dir"; /** Tags */ @@ -11275,6 +11379,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "Job"; /** @@ -11505,6 +11610,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "StoredWorkflow"; /** @@ -11615,6 +11721,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "subworkflow"; /** When */ @@ -11806,6 +11913,7 @@ export interface components { /** * Type * @constant + * @enum {string} */ type: "tool"; /** When */ @@ -11928,6 +12036,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_annotation"; /** Annotation */ @@ -11966,6 +12075,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_creator"; /** Creator */ @@ -12064,6 +12174,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_license"; /** License */ @@ -12074,6 +12185,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_name"; /** Name */ @@ -12092,6 +12204,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_output_label"; /** Output */ @@ -12145,6 +12258,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_report"; report: components["schemas"]["Report"]; @@ -12154,6 +12268,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_step_label"; /** @@ -12172,6 +12287,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "update_step_position"; position_shift: components["schemas"]["Position"]; @@ -12199,6 +12315,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "upgrade_all_steps"; }; @@ -12207,6 +12324,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "upgrade_subworkflow"; /** Content Id */ @@ -12222,6 +12340,7 @@ export interface components { /** * Action Type * @constant + * @enum {string} */ action_type: "upgrade_tool"; /** @@ -12277,6 +12396,7 @@ export interface components { /** * Src * @constant + * @enum {string} */ src: "url"; /** Tags */ @@ -12372,6 +12492,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "User"; /** @@ -12511,6 +12632,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "UserQuotaAssociation"; /** @@ -12655,6 +12777,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "WorkflowInvocation"; /** @@ -12735,6 +12858,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model_class: "WorkflowInvocation"; /** @@ -12799,6 +12923,7 @@ export interface components { * Model class * @description The name of the database model class. * @constant + * @enum {string} */ model: "WorkflowInvocation"; /** diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index ac0461e41e4f..83e06b46e4a7 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,26 +1,20 @@ -aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13" -amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13" babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13" +backports-tarfile==1.1.0 ; python_version >= "3.8" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" -backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" -billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" -black==24.3.0 ; python_version >= "3.8" and python_version < "3.13" +black==24.4.0 ; python_version >= "3.8" and python_version < "3.13" build==1.2.1 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" -celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" -click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13" -click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13" -click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13" click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") @@ -29,23 +23,23 @@ coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" -darker==2.1.0 ; python_version >= "3.8" and python_version < "3.13" -darkgraylib==1.1.1 ; python_version >= "3.8" and python_version < "3.13" +darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13" +darkgraylib==1.2.0 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13" docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" -filelock==3.13.3 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13" fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13" -graylint==1.0.1 ; python_version >= "3.8" and python_version < "3.13" +graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13" greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13" httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13" -idna==3.6 ; python_version >= "3.8" and python_version < "3.13" +idna==3.7 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10" @@ -53,14 +47,13 @@ iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13" jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13" -jaraco-context==5.1.0 ; python_version >= "3.8" and python_version < "3.13" +jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13" jaraco-functools==4.0.0 ; python_version >= "3.8" and python_version < "3.13" jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13" junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13" keyring==25.1.0 ; python_version >= "3.8" and python_version < "3.13" kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13" -kombu==5.3.6 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13" @@ -86,15 +79,14 @@ pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13" platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13" -playwright==1.42.0 ; python_version >= "3.8" and python_version < "3.13" +playwright==1.43.0 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13" -prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13" psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" -pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13" +pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13" pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13" pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13" pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -104,7 +96,6 @@ pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" pytest-asyncio==0.23.6 ; python_version >= "3.8" and python_version < "3.13" pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13" @@ -130,13 +121,13 @@ rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" selenium==4.19.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.2.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -162,10 +153,9 @@ tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13" twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13" -tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" +tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" werkzeug==3.0.2 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index d45d101010d4..730194ff2389 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.2.6 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.3.5 +ruff==0.3.7 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 5181edef346e..8bc4c310b5d9 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -2,10 +2,10 @@ a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.12.2 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.12.3 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13" -aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.4 ; python_version >= "3.8" and python_version < "3.13" aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13" @@ -16,7 +16,7 @@ anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" apispec==6.6.0 ; python_version >= "3.8" and python_version < "3.13" appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13" arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13" -argcomplete==3.2.3 ; python_version >= "3.8" and python_version < "3.13" +argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -27,13 +27,13 @@ bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13" bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13" bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.13" bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13" -beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.13" +beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.51 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.69 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -53,8 +53,8 @@ coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13" cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13" -cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.13" -cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13" +cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13" +cwltool==3.1.20240404144621 ; python_version >= "3.8" and python_version < "3.13" decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13" @@ -67,7 +67,7 @@ edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13" email-validator==2.1.1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" fastapi==0.110.1 ; python_version >= "3.8" and python_version < "3.13" -filelock==3.13.3 ; python_version >= "3.8" and python_version < "3.13" +filelock==3.13.4 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13" fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" @@ -84,9 +84,9 @@ gunicorn==21.2.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" h5grove==2.1.0 ; python_version >= "3.8" and python_version < "3.13" -h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13" +h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" -idna==3.6 ; python_version >= "3.8" and python_version < "3.13" +idna==3.7 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9" isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" @@ -97,10 +97,10 @@ jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13" jsonschema==4.21.1 ; python_version >= "3.8" and python_version < "3.13" -kombu==5.3.6 ; python_version >= "3.8" and python_version < "3.13" +kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" -mako==1.3.2 ; python_version >= "3.8" and python_version < "3.13" +mako==1.3.3 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.6 ; python_version >= "3.8" and python_version < "3.13" markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" @@ -117,7 +117,7 @@ nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" -orjson==3.10.0 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.10.1 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -134,10 +134,10 @@ psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.5.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.7.0 ; python_version >= "3.8" and python_version < "3.13" pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13" pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13" pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -156,7 +156,7 @@ python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13" python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13" pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" -pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.13" +pyzmq==26.0.0 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" @@ -173,9 +173,9 @@ rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.2.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -184,7 +184,7 @@ sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" -sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.13" +sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index a39a18f06f07..191ee946583f 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -5,8 +5,8 @@ lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" -pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.18.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.7.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13" types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy_test/conftest.py b/lib/galaxy_test/conftest.py index 64f69aee6f57..74dd381288af 100644 --- a/lib/galaxy_test/conftest.py +++ b/lib/galaxy_test/conftest.py @@ -11,6 +11,8 @@ from galaxy_test.api._framework import ApiTestCase from galaxy_test.driver.driver_util import GalaxyTestDriver +pytest_plugins = ("celery.contrib.pytest",) + @pytest.fixture(scope="session", autouse=True) def celery_includes(): diff --git a/pyproject.toml b/pyproject.toml index 155bcbc30cdf..2fdd4b314297 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -89,7 +89,7 @@ pillow = "*" psutil = "*" pulsar-galaxy-lib = ">=0.15.0.dev0" pycryptodome = "*" -pydantic = {version = ">=2, !=2.6.0, !=2.6.1, !=2.6.2, !=2.6.3, !=2.6.4", extras = ["email"]} # https://github.com/pydantic/pydantic/issues/8760 +pydantic = {version = ">=2.7.0", extras = ["email"]} # https://github.com/pydantic/pydantic/issues/8760 PyJWT = "*" pykwalify = "*" pylibmagic = "*" @@ -143,7 +143,6 @@ pkce = "*" playwright = "*" pytest = "*" pytest-asyncio = "*" -pytest-celery = "*" pytest-cov = "*" pytest-html = "*" pytest-httpserver = "*" diff --git a/test/integration/conftest.py b/test/integration/conftest.py index 3a0619d076cf..afe729466aaa 100644 --- a/test/integration/conftest.py +++ b/test/integration/conftest.py @@ -2,7 +2,10 @@ import pytest -from galaxy_test.conftest import pytest_configure # noqa: F401 +from galaxy_test.conftest import ( # noqa: F401 + pytest_configure, + pytest_plugins, +) @pytest.fixture(scope="session")