Merge branch 'dev' into page_permissions

.ci/flake8_ignorelist.txt

@@ -1,7 +1,6 @@
 .git
 .tox
-.venv
-.venv3
+.venv*
 packages/*/.venv
 packages/*/build
 packages/*/dist

.flake8

@@ -4,7 +4,8 @@
 # E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length (delegated to black)
+# E701,E704 are multiple statements on one line; we follow black's formatting here. See https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#configuration
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E203,E402,E501,E701,E704,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/tool_shed/test/test_data/repos

.github/workflows/docs.yaml

@@ -62,7 +62,7 @@ jobs:
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
         run: |
           case "$TARGET_BRANCH" in
-              release_[[:digit:]][[:digit:]].[[:digit:]][[:digit:]]|master)
+              release_[[:digit:]][[:digit:]].[[:digit:]][[:digit:]] | release_[[:digit:]][[:digit:]].[[:digit:]] | master)
                   UPLOAD_DIR=$TARGET_BRANCH
                   ;;
               dev)

.github/workflows/first_startup.yaml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/lint.yaml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     env:
       LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
       TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
@@ -55,6 +55,4 @@ jobs:
       - name: Run mypy checks
         run: tox -e mypy
       - uses: psf/black@stable
-        with:
-          version: "23.3.0"
       - uses: isort/isort-action@master

.github/workflows/lint_openapi_schema.yml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/osx_startup.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/reports_startup.yaml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     defaults:
       run:
         shell: bash -l {0}

.github/workflows/test_galaxy_packages.yaml

@@ -18,11 +18,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
       - uses: actions/checkout@v3
         with:
           path: 'galaxy root'
+      - uses: actions/setup-node@v3
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}

.github/workflows/toolshed.yaml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
         shed-api: ['v1', 'v2']
         test-install-client: ['galaxy_api', 'standalone']
     services:

.github/workflows/unit.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
     steps:
       - uses: actions/checkout@v3
         with:

.gitignore

@@ -7,8 +7,7 @@ scripts/scramble/lib
 scripts/scramble/archives
 
 # Python virtualenv
-.venv
-.venv3
+.venv*/
 
 # Python build artifacts
 build

Makefile

@@ -2,7 +2,7 @@
 VENV?=.venv
 # Source virtualenv to execute command (darker, sphinx, twine, etc...)
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
-RELEASE_CURR:=23.3
+RELEASE_CURR:=24.0
 RELEASE_UPSTREAM:=upstream
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy

client/docs/readme.md

@@ -16,6 +16,8 @@ problems of the old imperative class-based legacy code.
 
 ### Get comfortable with events, limit your dependence on Vuex
 
+**Note**: We are not using Vuex in Galaxy anymore, but the advice still applies.
+
 New vue programmers are ok at handing props to components, but they rarely use events effectively
 (at first). As a result they end up using a lot of global state, a million little data props and
 relying on imperfect globalized tools like Vuex or other imported dependencies for every little

client/package.json

@@ -72,7 +72,6 @@
     "jspdf": "^2.5.1",
     "linkify-html": "^4.1.1",
     "linkifyjs": "^4.1.1",
-    "localforage": "^1.10.0",
     "lodash.isequal": "^4.5.0",
     "markdown-it": "^13.0.2",
     "markdown-it-regexp": "^0.4.0",
@@ -106,9 +105,6 @@
     "vue-rx": "^6.2.0",
     "vue-virtual-scroll-list": "^2.3.5",
     "vuedraggable": "^2.24.3",
-    "vuex": "^3.6.2",
-    "vuex-cache": "^3.4.0",
-    "vuex-persist": "2.3",
     "winbox": "^0.2.82",
     "xml-beautifier": "^0.5.0"
   },

client/src/api/histories.ts

@@ -3,7 +3,10 @@ import { fetcher } from "@/api/schema";
 export const historiesFetcher = fetcher.path("/api/histories").method("get").create();
 export const archivedHistoriesFetcher = fetcher.path("/api/histories/archived").method("get").create();
 export const deleteHistory = fetcher.path("/api/histories/{history_id}").method("delete").create();
+export const deleteHistories = fetcher.path("/api/histories/batch/delete").method("put").create();
 export const undeleteHistory = fetcher.path("/api/histories/deleted/{history_id}/undelete").method("post").create();
 export const historiesQuery = fetcher.path("/api/histories/query").method("get").create();
 export const sharing = fetcher.path("/api/histories/{history_id}/sharing").method("get").create();
 export const enableLink = fetcher.path("/api/histories/{history_id}/enable_link_access").method("put").create();
+export const undeleteHistories = fetcher.path("/api/histories/batch/undelete").method("put").create();
+export const publishedHistoriesFetcher = fetcher.path("/api/histories/published").method("get").create();

client/src/api/invocations.ts

@@ -2,7 +2,9 @@ import axios from "axios";
 
 import { getAppRoot } from "@/onload";
 
-import { ApiResponse } from "./schema";
+import { ApiResponse, fetcher } from "./schema";
+
+export const invocationsFetcher = fetcher.path("/api/invocations").method("get").create();
 
 // TODO: Replace these interfaces with real schema models after https://github.com/galaxyproject/galaxy/pull/16707 is merged
 export interface WorkflowInvocation {

client/src/api/jobs.ts

@@ -8,3 +8,5 @@ export const jobLockStatus = fetcher.path("/api/job_lock").method("get").create(
 export const jobLockUpdate = fetcher.path("/api/job_lock").method("put").create();
 
 export const fetchJobDestinationParams = fetcher.path("/api/jobs/{job_id}/destination_params").method("get").create();
+
+export const jobsFetcher = fetcher.path("/api/jobs").method("get").create();