Merge branch 'dev' into topic/libmamba

.ci/eslint_wrapper.sh

@@ -5,4 +5,4 @@ set -e
 # Setting NODE_PATH and config appropriately, using dependencies from
 # client/node_modules, run eslint against args passed to this script.
 # Primary use case here is for a pre-commit check.
-NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.json "$@"
+NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.js "$@"

.ci/flake8_ignorelist.txt

@@ -1,7 +1,6 @@
 .git
 .tox
-.venv
-.venv3
+.venv*
 packages/*/.venv
 packages/*/build
 packages/*/dist
@@ -11,6 +10,7 @@ database
 doc/build
 eggs
 lib/galaxy/web/proxy/js/node_modules
+lib/tool_shed/test/test_data/repos
 static/maps
 static/scripts
 test/functional/tools/cwl_tools/v1.?/

.ci/ignore-spelling.txt

@@ -1 +1,3 @@
 hda
+implementors
+purgable

.ci/validate_test_tools.sh

@@ -7,5 +7,7 @@ xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
 xmllint --noout "$xsd_path"
 
 test_tools_path='test/functional/tools'
-tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$')
+# test all test tools except upload.xml which uses a non-standard conditional
+# (without param) which does not survive xsd validation
+tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$' | grep -v upload.xml)
 sh scripts/validate_tools.sh $tool_files_list

.circleci/config.yml

@@ -15,7 +15,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -73,7 +73,7 @@ jobs:
             - ~/repo
   validate_test_tools:
     docker:
-      - image: cimg/python:3.7
+      - image: cimg/python:3.8
     <<: *set_workdir
     steps:
       - *restore_repo_cache

.flake8

@@ -4,6 +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/ISSUE_TEMPLATE/bug_report.md

@@ -14,6 +14,10 @@ A clear and concise description of what the bug is.
 Galaxy Version: (check <galaxy_url>/api/version if you don't know)
 Commit: (run `git rev-parse HEAD` if you run this Galaxy server)
 
+**Browser and Operating System**
+Operating System: Windows, Linux, macOS
+Browser: Firefox, Chrome, Chrome-based, Safari
+
 **To Reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'

.github/codeql/codeql-config.yml

@@ -0,0 +1,2 @@
+paths-ignore:
+  - 'lib/galaxy/datatypes/test/*.bcsl.ts'

.github/labeler.yml

@@ -1,73 +1,130 @@
 ---
 area/admin:
-  - client/src/components/admin/**/*
-  - doc/source/admin/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/admin/**/*
+      - doc/source/admin/**/*
 area/API:
-  - lib/galaxy/webapps/galaxy/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/webapps/galaxy/api/**/*
 area/auth:
-  - lib/galaxy/auth/**/*
-  - lib/galaxy/authnz/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/auth/**/*
+      - lib/galaxy/authnz/**/*
 area/client:
-  - client/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/*
 area/database:
-  - lib/galaxy/model/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/model/**/*
 area/datatypes:
-  - lib/galaxy/datatypes/**/*
-  - lib/galaxy/config/sample/datatypes_conf.xml.sample
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/datatypes/**/*
+      - lib/galaxy/config/sample/datatypes_conf.xml.sample
 area/dependencies:
-  - lib/galaxy/dependencies/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/dependencies/**/*
 area/documentation:
-  - doc/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - doc/**/*
 area/jobs:
-  - lib/galaxy/jobs/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/jobs/**/*
 area/libraries:
-  - client/src/components/LibraryFolder/**/*
-  - lib/galaxy/webapps/galaxy/api/libraries.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/components/LibraryFolder/**/*
+      - lib/galaxy/webapps/galaxy/api/libraries.py
 area/objectstore:
-  - lib/galaxy/objectstore/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/objectstore/**/*
 area/packaging:
-  - packages/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - packages/**/*
 area/reports:
-  - client/src/reports/**/*
-  - lib/galaxy/webapps/reports/**/*
-  - templates/webapps/reports/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/reports/**/*
+      - lib/galaxy/webapps/reports/**/*
+      - templates/webapps/reports/**/*
 area/scripts:
-  - scripts/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - scripts/**/*
 area/security:
-  - lib/galaxy/security/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/security/**/*
 area/testing:
-  - lib/galaxy_test/**/*
-  - run_tests.sh
-  - test/**/*
-  - test-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/**/*
+      - run_tests.sh
+      - test/**/*
+      - test-data/**/*
 area/testing/api:
-  - lib/galaxy_test/api/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy_test/api/**/*
 area/testing/integration:
-  - test/integration/**/*
-  - test/integration_selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - test/integration/**/*
+      - test/integration_selenium/**/*
 area/testing/selenium:
-  - lib/galaxy/selenium/**/*
-  - lib/galaxy_test/selenium/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/selenium/**/*
+      - lib/galaxy_test/selenium/**/*
 area/tool-dependencies:
-  - lib/galaxy/tool_util/deps/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tool_util/deps/**/*
 area/tool-framework:
-  - lib/galaxy/tools/**/*
-  - lib/galaxy/tool_util/**/*
-  - lib/galaxy/webapps/galaxy/api/tools.py
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/tools/**/*
+      - lib/galaxy/tool_util/**/*
+      - lib/galaxy/webapps/galaxy/api/tools.py
 area/tools:
-  - tools/**/*
-  - tool-data/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - tools/**/*
+      - tool-data/**/*
 area/toolshed:
-  - client/src/toolshed/**/*
-  - lib/galaxy/webapps/galaxy/api/toolshed.py
-  - lib/toolshed/**/*
-  - templates/webapps/tool_shed/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - client/src/toolshed/**/*
+      - lib/galaxy/webapps/galaxy/api/toolshed.py
+      - lib/toolshed/**/*
+      - templates/webapps/tool_shed/**/*
 area/UI-UX:
-  - client/src/**/*
-  - templates/**/*
+  - all:
+    - changed-files:
+      - any-glob-to-any-file:
+        - client/src/**/*
+        - templates/**/*
+      - all-globs-to-all-files:
+        - '!client/src/api/schema/schema.ts'
 area/util:
-  - lib/galaxy/util/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/util/**/*
 area/visualizations:
-  - config/plugins/visualizations/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - config/plugins/visualizations/**/*
 area/workflows:
-  - lib/galaxy/workflow/**/*
+  - changed-files:
+    - any-glob-to-any-file:
+      - lib/galaxy/workflow/**/*

.github/workflows/api.yaml

@@ -28,7 +28,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.7']
+        python-version: ['3.8']
         chunk: [0, 1]
     services:
       postgres:
@@ -44,23 +44,28 @@ jobs:
         run: |
           echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
           echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           path: 'galaxy root'
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get full Python version
         id: full-python-version
         shell: bash
         run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
       - name: Cache pip dir
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
       - name: Cache galaxy venv
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: 'galaxy root/.venv'
           key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
@@ -71,7 +76,7 @@ jobs:
         with:
           flags: api
           working-directory: 'galaxy root'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})

.github/workflows/build_client.yaml

@@ -0,0 +1,38 @@
+name: Build client for selenium tests
+on:
+  workflow_call:
+    outputs:
+      commit-id:
+        description: Commit ID
+        value: ${{ jobs.build-client.outputs.commit-id }}
+jobs:
+  build-client:
+    runs-on: ubuntu-latest
+    outputs:
+      commit-id: ${{ steps.client-commit.outputs.commit }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '18.12.1'
+          cache: 'yarn'
+          cache-dependency-path: 'galaxy root/client/yarn.lock'
+      - name: get client commit
+        id: client-commit
+        shell: bash
+        run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
+        working-directory: 'galaxy root'
+      - name: cache client build
+        uses: actions/cache@v4
+        id: cache
+        with:
+          key: galaxy-static-${{ steps.client-commit.outputs.commit }}
+          path: 'galaxy root/static'
+      - name: Build client
+        if: steps.cache.outputs.cache-hit != 'true'
+        env:
+          GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR: 1
+        run: make client
+        working-directory: 'galaxy root'

.github/workflows/build_container_image.yaml

@@ -2,8 +2,10 @@ name: Build Container Image
 on:
   push:
     branches:
-      - 'release*'
       - dev
+      - release_*
+    tags:
+      - v*
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -13,14 +15,22 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository_owner == 'galaxyproject'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
       - name: Set outputs
         id: commit
         run: echo "sha_short=$(git rev-parse --short HEAD)" >> $GITHUB_OUTPUT
       - name: Set branch name
         id: branch
-        run: echo "name=$(BRANCH_NAME=${GITHUB_REF##*/}; echo ${BRANCH_NAME/release_/})" >> $GITHUB_OUTPUT
+        run: |
+          if [[ "$GITHUB_REF" == "refs/tags/"* ]]; then
+            echo "name=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/dev" ]]; then
+            echo "name=dev" >> $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF" == "refs/heads/release_"* ]]; then
+            echo "name=${GITHUB_REF#refs/heads/release_}-auto" >> $GITHUB_OUTPUT
+          fi
+        shell: bash
       - name: Build container image
         run: docker build . --build-arg GIT_COMMIT=$(git rev-parse HEAD) --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg IMAGE_TAG=${{ steps.branch.outputs.name }} -t galaxy/galaxy-min:${{ steps.branch.outputs.name }} -t quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} -f .k8s_ci.Dockerfile
       - name: Create auto-expiring one for per-commit auto repository