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Merge pull request #17982 from galaxybot/dev_auto_update_dependencies

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Update Python dependencies
This commit is contained in:
Marius van den Beek
2024-04-17 10:34:30 +02:00
committed by GitHub
parent 8e900c55b4 edf06c5e35
commit bc248efe2a
8 changed files with 169 additions and 50 deletions
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client/src/api/schema/schema.ts
+125
View File
@@ -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";
/**
lib/galaxy/dependencies/dev-requirements.txt
+14 -24
View File
@@ -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"
lib/galaxy/dependencies/pinned-lint-requirements.txt
+1 -1
View File
@@ -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
lib/galaxy/dependencies/pinned-requirements.txt
+20 -20
View File
@@ -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"
lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+2 -2
View File
@@ -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"
lib/galaxy_test/conftest.py
+2
View File
@@ -11,6 +11,8 @@ from galaxy.web import statsd_client as statsd
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():
pyproject.toml
+1 -2
View File
@@ -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 = "*"
test/integration/conftest.py
+4 -1
View File
@@ -2,7 +2,10 @@ import tempfile
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")