initial commit

.ci/check_controller.sh

+#!/bin/bash
+set -e
+MAX_LINE_COUNT=19900
+project_dir=`dirname $0`/..
+cd $project_dir
+bash -c "[ `find lib/galaxy/webapps/galaxy/controllers/ -name '*.py' | xargs wc -l | tail -n 1 | awk '{ printf \$1; }'` -lt $MAX_LINE_COUNT ]"

.ci/check_mako.sh

+#!/bin/bash
+set -e
+MAX_MAKO_COUNT=330
+project_dir=`dirname $0`/..
+cd $project_dir
+bash -c "[ `find templates -iname '*.mako'  | wc -l | cut -f1 -d' '` -lt $MAX_MAKO_COUNT ]"

.ci/check_test_class_names.sh

+#!/bin/sh
+TEST=$(mktemp)
+TEST_EXTRA_CLASSES=$(mktemp)
+
+pytest --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST"
+pytest -o python_classes='Test* *Test *TestCase' --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST_EXTRA_CLASSES"
+
+n_tests=$(grep 'tests collected' "$TEST" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+n_tests_extra_classes=$(grep 'tests collected' "$TEST_EXTRA_CLASSES" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+
+if [ "$n_tests_extra_classes" -gt "$n_tests" ]; then
+    echo "New test class with name not starting with Test introduced, change it to have tests collected by pytest"
+    diff "$TEST" "$TEST_EXTRA_CLASSES"
+    exit 1
+fi

.ci/eslint_wrapper.sh

+#!/bin/bash
+
+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.js "$@"

.ci/first_startup.sh

+#!/bin/sh
+case "$1" in
+    galaxy|"")
+        SCRIPT=./run.sh
+        PORT=8080
+        LOGFILE=galaxy.log
+        GRAVITY_LOGFILE=database/gravity/log/gunicorn.log
+        SUPERVISORD_LOGFILE=database/gravity/supervisor/supervisord.log
+        ;;
+    reports)
+        SCRIPT=./run_reports.sh
+        PORT=9001
+        LOGFILE=reports_webapp.log
+        ;;
+    *)
+        echo "ERROR: Unrecognized app"
+        exit 1
+        ;;
+esac
+TRIES=120
+URL=http://localhost:$PORT
+EXIT_CODE=1
+i=0
+echo "Testing for correct startup:"
+$SCRIPT --daemon && \
+    while [ "$i" -le $TRIES ]; do
+        curl --max-time 1 "$URL" && EXIT_CODE=0 && break
+        sleep 1
+        i=$((i + 1))
+    done
+$SCRIPT --skip-wheels --stop-daemon
+echo "exit code:$EXIT_CODE, showing startup log:"
+if [ -f "$LOGFILE" ]; then
+    cat "$LOGFILE"
+elif [ ! -f "$LOGFILE" -a -f "$GRAVITY_LOGFILE" ]; then
+    echo "Warning: $LOGFILE does not exist, showing gravity startup log instead"
+    cat "$GRAVITY_LOGFILE"
+elif [ ! -f "$LOGFILE" -a ! -f "$GRAVITY_LOGFILE" -a -f "$SUPERVISORD_LOGFILE" ]; then
+    echo "Warning: $LOGFILE and $GRAVITY_LOGFILE do not exist, showing supervisord startup log instead"
+    cat "$SUPERVISORD_LOGFILE"
+else
+    echo "ERROR: No log files found!"
+    ls -lR database/gravity
+fi
+exit $EXIT_CODE

.ci/flake8_docstrings_include_list.txt

+lib/galaxy/jobs/metrics
+lib/galaxy/exceptions
+lib/galaxy/containers

.ci/flake8_ignorelist.txt

+.git
+.tox
+.venv*
+packages/*/.venv
+packages/*/build
+packages/*/dist
+packages/venv
+node_modules
+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.?/
+build
+dist

.ci/flake8_wrapper.sh

+#!/bin/bash
+
+set -e
+
+flake8 --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
+
+# Apply stricter rules for the directories shared with Pulsar
+flake8 --ignore=E203,D --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/flake8_wrapper_docstrings.sh

+#!/bin/bash
+
+set -e
+
+# D100 - Missing docstring in public module.
+# D2XX - Whitespace issues.
+# D3XX - Quoting issues.
+# D401 - First line should be in imperative mood 
+# D403 - First word of the first line should be properly capitalized
+args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
+
+# If the first argument is --include, lint the modules expected to pass. If
+# the first argument is --exclude, lint all modules the full Galaxy linter lints
+# (this will fail).
+
+if [ "$1" = "--include" ];
+then
+    flake8 $args $(paste -sd' ' .ci/flake8_docstrings_include_list.txt)
+else
+    flake8 $args --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
+fi

.ci/ignore-spelling.txt

+hda
+implementors
+purgable

.ci/minikube-test-setup/deployment.yaml

+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  labels:
+    app.kubernetes.io/name: testing
+  name: testing
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app.kubernetes.io/name: test
+  template:
+    metadata:
+      labels:
+        app.kubernetes.io/name: test
+    spec:
+      containers:
+      - image: postgres:17
+        name: postgres
+        ports:
+        - containerPort: 5432
+        env:
+          - name: POSTGRES_DB
+            value: postgres
+          - name: POSTGRES_USER
+            value:  postgres
+          - name: POSTGRES_PASSWORD
+            value: postgres
+      - image: rabbitmq
+        name: rabbitmq
+        ports:
+        - containerPort: 5672

.ci/minikube-test-setup/start_services.sh

+#!/usr/bin/env bash
+set -ex
+
+SCRIPTDIR=$(dirname "${BASH_SOURCE[0]}")
+kubectl apply -f "$SCRIPTDIR/deployment.yaml"
+kubectl expose deployment testing --type=LoadBalancer --name=testing-service
+
+CLUSTER_IP=$(kubectl get service testing-service -o jsonpath='{.spec.clusterIP}')
+GALAXY_TEST_DBURI="postgresql://postgres:postgres@${CLUSTER_IP}:5432/galaxy?client_encoding=utf-8"
+GALAXY_TEST_AMQP_URL="amqp://${CLUSTER_IP}:5672//"
+export GALAXY_TEST_DBURI
+export GALAXY_TEST_AMQP_URL

.ci/validate_test_tools.sh

+#!/bin/sh
+
+cd "$(dirname "$0")"/..
+
+xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
+# Lint the XSD
+xmllint --noout "$xsd_path"
+
+test_tools_path='test/functional/tools'
+# 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

+# Python CircleCI 2.0 configuration file
+version: 2
+variables:
+  restore_repo_cache: &restore_repo_cache
+    restore_cache:
+      keys:
+        - v1-repo-{{ .Environment.CIRCLE_SHA1 }}
+  install_tox: &install_tox
+    run: pip install tox
+  set_workdir: &set_workdir
+    working_directory: ~/repo
+  requires_get_code: &requires_get_code
+    requires:
+      - get_code
+jobs:
+  get_code:
+    docker:
+      - image: cimg/python:3.10
+    <<: *set_workdir
+    steps:
+      # Replace standard code checkout with shallow clone to speed things up.
+      - run:
+          name: Checkout code
+          command: |-
+              # Add github.com to known hosts
+              mkdir -p ~/.ssh
+              echo 'github.com ssh-rsa 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
+              ' >> ~/.ssh/known_hosts
+
+              # Add the user ssh key and set correct perms
+              (umask 077; touch ~/.ssh/id_rsa)
+              chmod 0600 ~/.ssh/id_rsa
+              echo "$CHECKOUT_KEY" > ~/.ssh/id_rsa
+
+              # Use git+ssh instead of https
+              git config --global url."ssh://git@github.com".insteadOf "https://github.com" || true
+              git config --global gc.auto 0 || true
+
+              # Shallow clone
+              git clone --depth=1 "${CIRCLE_REPOSITORY_URL}" .
+
+              if [[ -n "${CIRCLE_PR_NUMBER}" ]]; then
+                  # Update PR refs for testing.
+                  FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/head:pr/${CIRCLE_PR_NUMBER}/head"
+                  FETCH_REFS="${FETCH_REFS} +refs/pull/${CIRCLE_PR_NUMBER}/merge:pr/${CIRCLE_PR_NUMBER}/merge"
+
+                  # Retrieve the refs
+                  git fetch --force origin ${FETCH_REFS}
+
+                  # Checkout PR merge ref.
+                  git checkout -f "pr/${CIRCLE_PR_NUMBER}/merge"
+
+                  # Test for *some* merge conflicts.
+                  git branch --merged | grep "pr/${CIRCLE_PR_NUMBER}/head" > /dev/null
+              else
+                  if [ -n "$CIRCLE_TAG" ]; then
+                      git fetch --depth=1 --force origin "refs/tags/${CIRCLE_TAG}"
+                  else
+                      git fetch --depth=1 --force origin "$CIRCLE_BRANCH:remotes/origin/$CIRCLE_BRANCH"
+                  fi
+                  if [ -n "$CIRCLE_TAG" ]; then
+                      git reset --hard "$CIRCLE_SHA1"
+                      git checkout "$CIRCLE_TAG"
+                  elif [ -n "$CIRCLE_BRANCH" ]; then
+                      git reset --hard "$CIRCLE_SHA1"
+                      git checkout -B "$CIRCLE_BRANCH"
+                  fi
+                  git reset --hard "${CIRCLE_SHA1}"
+              fi
+      - save_cache:
+          key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
+          paths:
+            - ~/repo
+  validate_test_tools:
+    docker:
+      - image: cimg/python:3.10
+    <<: *set_workdir
+    steps:
+      - *restore_repo_cache
+      - run: sudo apt-get update
+      - run: sudo apt-get install -y libxml2-utils
+      - *install_tox
+      - run: tox -e validate_test_tools
+workflows:
+  version: 2
+  get_code_and_test:
+    jobs:
+      - get_code
+      - validate_test_tools:
+          <<: *requires_get_code

.claude/commands/triage-bug.md

+Persona: You are a senior engineer responsible for maintaining the Galaxy project.
+
+Arguments:
+
+- $ARGUMENTS - Github issue number and optional work level (low/medium/high, default: medium)
+  Examples: "21536", "21536 low", "21536 high"
+
+Parse the issue number and work level from $ARGUMENTS. Work levels control triage depth:
+
+- **low**: Research and understand only, skip fix planning
+- **medium**: Research + single plan for most probable cause
+- **high**: Research + plans for all theories + plan assessment
+
+You will be supplied a Github issue number to triage. A Galaxy developer will be assigned the issue but your job is to structure the conversation around the issue.
+
+Fetch the issue using "gh issue view <number>" and write the issue contents to `ISSUE_<#>.md`.
+
+Write all triage artifacts to the current working directory.
+
+Galaxy versions look like 24.1, 26.2, etc.. and these correspond to branches such as release_24.1, release_26.2, etc.. Be sure you're on the target branch before continuing.
+
+Launch subagents to perform actions to help in the triage process. Run independent tasks in parallel where possible (e.g., code research and importance assessment can run concurrently since they only need the original issue), but tasks that depend on artifacts from earlier subagents must wait (e.g., history research and planning need to read the code research document first). As the agent responsible for the triage process - please read the artifacts generated from subagents and direct the process as it makes sense. Your job is to direct the process though - do not try to fix the issue or do research yourself.
+
+When to launch subagents and what they should do are as follows:
+
+- When: Always (all levels)
+  What: Launch a subagent to research the issue. This subagent should create a document called `ISSUE_<#>_CODE_RESEARCH.md` where `<#>` is the issue number. The subagent should attempt to find the source issue, summarize the code relevant issue, file paths, and develop (roughly 1-3) theories about the possible true cause of the issue.
+- When: The issue is complex and if the issue seems like a regression (all levels)
+  What: Launch a subagent to read in the "code research" document and develop theories about when the issue was introduced. Create a document called `ISSUE_<#>_HISTORY.md` where `<#>` is the issue number. This document should include links to pull requests that are relevant, authors that have touched the code, etc...
+- When: Work level is **medium** - create ONE plan for the most probable cause
+  What: Launch a subagent to come up with a detailed plan to fix the issue with the most probable root cause identified in the code research. Create a document called `ISSUE_<#>_PLAN.md`.
+- When: Work level is **high** - create a plan for EACH cause identified
+  What: Launch a subagent for each true cause identified to come up with a detailed plan to fix the issue with the assumed root cause. Create a document called `ISSUE_<#>_PLAN_<cause>.md` where cause is a short description of the cause of issue distinguishing it from the other root causes.
+- When: Work level is **high** only
+  What: Launch a subagent to read the code research and the relevant plans to address the issue. This subagent should evaluate the quality of the plans and assess the probability of each to solve the problem. This subagent should create a document called `ISSUE_<#>_PLAN_ASSESSMENT.md`.
+- When: Always (all levels)
+  What: Launch a subagent to assess bug importance. Create a document called `ISSUE_<#>_IMPORTANCE.md`. Assess:
+    - Severity (critical/high/medium/low): data loss/security > crash/hang > functional breakage > cosmetic/minor
+    - Blast radius: all users, specific configurations, edge cases only
+    - Workaround existence: none / painful / acceptable
+    - Regression status: new regression (which version) vs long-standing
+    - User impact signals: issue reactions, duplicate reports, support requests
+    - Recommendation: hotfix / next release / backlog / wontfix with rationale
+
+Once all of the subagents are done - please write a new document called `ISSUE_<#>_SUMMARY.md`.
+
+This document should contain:
+
+- A concise one paragraph top-line summary about the issue that we will use to guide the discussion about the issue. Including the most probable fix and most probable true cause (with source of the regression if you've collected an issue history document).
+- Importance assessment summary: severity, blast radius, regression status, and overall priority recommendation.
+- Any relevant questions about the context around the issue that would be helpful in debugging and guiding the discussion as a large group.
+- A complexity assessment (low/medium/high) for the fix, and how difficult it is to recreate and test the issue.
+
+Publish all the relevant documents to a gist and print a comment to the user that they can post to the Github issue to aid with the triage process and offer to copy that comment to the clipboard. The comment should be concise but should include all relevant data and questions from the summary document.

.claude/commands/triage-feature.md

+Persona: You are a senior engineer responsible for maintaining the Galaxy project.
+
+Arguments:
+
+- $ARGUMENTS - Github issue number and optional work level (low/medium/high, default: medium)
+  Examples: "21474", "21474 low", "21474 high"
+
+Parse the issue number and work level from $ARGUMENTS. Work levels control triage depth:
+
+- **low**: Research and understand only, skip implementation planning
+- **medium**: Research + single recommended approach with focused plan
+- **high**: Research + multiple approaches + comprehensive plan
+
+You will be supplied a Github issue number for a feature request to triage. A Galaxy developer will be assigned the issue but your job is to structure the conversation around the feature.
+
+Fetch the issue using "gh issue view <number>" and write the issue contents to `FEATURE_<#>.md`.
+
+Write all triage artifacts to the current working directory.
+
+Launch subagents to perform actions to help in the triage process. Run independent tasks in parallel where possible (e.g., demand research and code research can run concurrently since they only need the original issue), but tasks that depend on artifacts from earlier subagents must wait (e.g., implementation planning needs to read the research documents first). As the agent responsible for the triage process - please read the artifacts generated from subagents and direct the process as it makes sense. Your job is to direct the process though - do not try to implement the feature or do research yourself.
+
+When to launch subagents and what they should do are as follows:
+
+- When: Always (all levels)
+  What: Launch a subagent to research user demand signals. This subagent should create a document called `FEATURE_<#>_DEMAND.md`. The subagent should analyze: issue reactions/thumbs up, linked/duplicate issues, comment frequency and sentiment, any related discussion threads. Quantify demand where possible.
+- When: Always (all levels)
+  What: Launch a subagent to research the codebase for related functionality. This subagent should create a document called `FEATURE_<#>_CODE_RESEARCH.md`. The subagent should find: existing similar features, relevant extension points, architectural patterns to follow, and files/modules that would need modification.
+- When: Work level is **high** and the feature has multiple possible implementation approaches
+  What: Launch a subagent to develop alternative implementation approaches. Create a document called `FEATURE_<#>_APPROACHES.md`. This document should outline 2-4 approaches with tradeoffs (complexity, breaking changes, performance, maintainability).
+- When: Always (all levels)
+  What: Launch a subagent to assess importance. Create a document called `FEATURE_<#>_IMPORTANCE.md`. Assess:
+    - User demand (high/medium/low) based on reactions, comments, linked issues
+    - Strategic value (high/medium/low) - does it align with project direction, enable other features, improve UX significantly
+    - Complexity (low/medium/high) based on code research — do not estimate time or duration
+    - Risk assessment (breaking changes, migration needs, security considerations)
+    - Recommendation: prioritize now / backlog / defer / decline with rationale
+- When: Work level is **medium** - create a focused implementation plan
+  What: Launch a subagent to read the research documents and create an implementation plan for the single recommended approach. Create a document called `FEATURE_<#>_PLAN.md`. Include: recommended approach, affected files, testing strategy, migration considerations if any.
+- When: Work level is **high** - create a comprehensive implementation plan
+  What: Launch a subagent to read all research documents (including approaches) and create a detailed implementation plan. Create a document called `FEATURE_<#>_PLAN.md`. Include: recommended approach with rationale for choosing it over alternatives, affected files, testing strategy, migration considerations if any.
+
+Once all of the subagents are done - please write a new document called `FEATURE_<#>_SUMMARY.md`.
+
+This document should contain:
+
+- A concise one paragraph top-line summary about the feature request and recommended approach.
+- Importance assessment summary: demand level, strategic value, effort, and overall priority recommendation.
+- Key questions for the group discussion that would help refine requirements or approach.
+- Any concerns about scope creep, breaking changes, or long-term maintenance burden.
+
+Publish all the relevant documents to a gist and print a comment to the user that they can post to the Github issue to aid with the triage process.

.claude/commands/triage-issue.md

+Persona: You are a senior engineer responsible for maintaining the Galaxy project.
+
+Arguments:
+- $ARGUMENTS - Github issue number and optional work level (low/medium/high, default: medium)
+  Examples: "21536", "21536 low", "21536 high"
+
+Parse the issue number and work level from $ARGUMENTS.
+
+Fetch the issue using "gh issue view <number>" and analyze its content to determine if it is:
+- **Bug**: A report of something broken, not working as expected, an error, regression, or malfunction
+- **Feature**: A request for new functionality, enhancement, improvement, or capability that doesn't exist
+
+Classification signals:
+- Bug indicators: "error", "crash", "broken", "doesn't work", "regression", "fails", "exception", stack traces, reproduction steps describing unexpected behavior
+- Feature indicators: "would be nice", "please add", "feature request", "enhancement", "suggestion", "support for", "ability to", describing desired new behavior
+
+Once classified, inform the user of your classification and reasoning in one sentence.
+
+Then read the appropriate command file and execute its instructions:
+- For bugs: Read `.claude/commands/triage-bug.md` and follow those instructions
+- For features: Read `.claude/commands/triage-feature.md` and follow those instructions
+
+Pass through the original issue number and work level to the triage workflow.
+
+If the classification is ambiguous, ask the user which triage path to follow before proceeding.

.claude/commands/weekly-triage.md

+Persona: You are the lead engineer running the weekly Galaxy triage meeting.
+
+Arguments:
+
+- $ARGUMENTS - Optional: `[project_number] [column_name] [work_level]`
+  Defaults: project 26, column "Triage/Discuss", work level "medium"
+  Examples: "" (all defaults), "26", "26 Triage/Discuss low", "26 Triage/Discuss high"
+
+Parse arguments from $ARGUMENTS. If fewer than 3 are provided, use defaults for the missing ones. Work levels: low (research only), medium (research + single plan), high (research + all theories + assessment).
+
+## Step 1: Fetch project board issues
+
+Run `gh project item-list <project_number> --owner galaxyproject --format json --limit 500` to get all items.
+
+Filter the JSON results to only items where `status` matches the target column name. Extract issue numbers and titles. Print the count of issues found in the column.
+
+## Step 2: Filter to uncommented issues
+
+For each issue, run `gh issue view <number> --repo galaxyproject/galaxy --json comments,assignees` to check the comment count and assignees. Skip an issue if:
+
+- It has 1+ comments (already being discussed)
+- It has any assignees (already claimed by someone)
+
+Print how many issues need triage out of the total, noting how many were skipped for each reason. If zero issues remain, print a summary and stop.
+
+## Step 3: Launch triage agents in parallel batches
+
+Process uncommented issues in batches of up to 5 parallel Task agents. Each agent receives:
+
+- The issue number and work level
+- Instructions to read `.claude/commands/triage-issue.md` and follow its full workflow (which classifies the issue and dispatches to triage-bug.md or triage-feature.md)
+- The triage-issue skill already handles: classification, launching research/planning subagents, writing artifact files, creating a gist, and drafting a comment
+
+**Important override for batch mode:** Tell each agent to NOT ask the user for classification confirmation if ambiguous — default to bug. Also tell each agent to post the triage comment directly to the issue using `gh issue comment NUM --repo galaxyproject/galaxy` instead of printing it for the user to copy. The comment should include the gist link.
+
+## Step 4: Collect results and print summary
+
+As each agent completes, collect its findings. Print a final markdown summary table:
+
+| Issue | Title | Type | Recommendation | Complexity | Gist |
+| ----- | ----- | ---- | -------------- | ---------- | ---- |
+
+Include a row for each triaged issue. For skipped issues (already had comments or assignees), note them below the table.
+
+Print total counts: issues in column, skipped (had comments), skipped (assigned), triaged, failed.

.coveragerc

+[run]
+branch = True
+include = lib/galaxy/*
+disable_warnings = include-ignored

.dockerignore

+.k8s_ci.Dockerfile
+.venv
+database
+**/node_modules

.flake8

+[flake8]
+# These are exceptions allowed by Galaxy style guidelines:
+# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
+# B042 Seems to unnecessarily complicate exception classes
+# 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,B042,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

.git-blame-ignore-revs

+# Migrate code style to Black and Apply isort
+623a5e165ad79e15321b19b2a2afbf2f9224cc90
+# Application of black styling to /tools/
+03351d2a9f81b938d650e2a955c65c18526ee7f0
+# Migrate code style to Prettier
+5b2928f851bd5ea3b9c2a04abf2cee9ff0bc54cc
+87873c5e2f4e6b97fe0f2084bfca0295fcd471de
+# vue/recommended standardization (attribute and property order)
+3bea88e761473b5d67d215d2faf732c86abd2091
+44ac26da4c53dedad3499cfef6d9d4cb61364a05

.gitattributes

+* text=auto
+lib/galaxy/datatypes/test/dosimzml eol=crlf

.github/ISSUE_TEMPLATE/bug_report.md

+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Galaxy Version and/or server at which you observed the bug**
+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 '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here.

.github/codecov.yml

+comment: false

.github/codeql/codeql-config.yml

+paths-ignore:
+  - 'lib/galaxy/datatypes/test/*.bcsl.ts'

.github/dependabot.yml

+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/labeler.yml

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

.github/pull_request_template.md

+(Please replace this header with a description of your pull request. Please include *BOTH* what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
+(If fixing a bug, please add any relevant error or traceback)
+(For UI components, it is recommended to include screenshots or screencasts)
+
+## How to test the changes?
+(Select all options that apply)
+- [ ] I've included appropriate [automated tests](https://docs.galaxyproject.org/en/latest/dev/writing_tests.html).
+- [ ] This is a refactoring of components with existing test coverage.
+- [ ] Instructions for manual testing are as follows:
+  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]
+
+## License
+- [x] I agree to license these and all my past contributions to the core galaxy codebase under the [MIT license](https://opensource.org/licenses/MIT).

.github/release.yml

+changelog:
+  exclude:
+    labels:
+      - merge
+      - procedures
+      - planning
+      - status/needs feedback
+      - status/planning
+    authors:
+      - dependabot[bot]
+      - github-actions[bot]
+      - galaxybot
+  categories:
+    - title: 🎉 Major Changes
+      labels:
+        - highlight
+        - highlight/admin
+        - highlight/dev
+        - highlight/power-user
+    - title: 🚀 New Features
+      labels:
+        - kind/feature
+      exclude:
+        labels:
+          - area/documentation
+    - title: 🔧 Enhancements
+      labels:
+        - kind/enhancement
+    - title: 🐛 Bug Fixes
+      labels:
+        - kind/bug
+    - title: '🔒 Security Updates'
+      labels:
+        - 'area/security'
+    - title: '⚡ Performance'
+      labels:
+        - 'area/performance'
+    - title: '🧰 Refactoring'
+      labels:
+        - 'kind/refactoring'
+    - title: '📚 Documentation'
+      labels:
+        - 'area/documentation'
+    - title: '🔧 Admin & Configuration'
+      labels:
+        - 'area/admin'
+        - 'area/configuration'
+    - title: '🛠️ API Changes'
+      labels:
+        - 'area/API'
+    - title: '🧪 Testing'
+      labels:
+        - 'area/testing'
+        - 'area/testing/api'
+        - 'area/testing/integration'
+        - 'area/testing/selenium'
+    - title: '🏗️ Infrastructure & Dependencies'
+      labels:
+        - 'area/dependencies'
+        - 'area/client-build'
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/api.yaml

+name: API tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_TEST_REQUIRE_ALL_NEEDED_TOOLS: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+        chunk: [0, 1]
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
+      - name: Run tests
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api lib/galaxy_test/api -- --num-shards=2 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: api
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: API test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_api_tests.html'

.github/workflows/bioblend.yaml

+name: BioBlend Tests
+on:
+  pull_request:
+    paths:
+      - .github/workflows/bioblend.yaml
+      - lib/galaxy/schema/**
+      - lib/galaxy/webapps/galaxy/api/**
+      - lib/galaxy/webapps/galaxy/services/**
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      postgres:
+        image: postgres:17
+        # Provide the password for postgres
+        env:
+          POSTGRES_PASSWORD: postgres
+        # Set health checks to wait until postgres has started
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    strategy:
+      fail-fast: false
+      matrix:
+        tox_env: [py314]
+        galaxy_python_version: ['3.10']
+    steps:
+      - name: Checkout Galaxy
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 1
+          path: galaxy
+          persist-credentials: false
+      - name: Checkout Bioblend
+        uses: actions/checkout@v6
+        with:
+          repository: galaxyproject/bioblend
+          path: bioblend
+          persist-credentials: false
+      - name: Calculate Python version for BioBlend from tox_env
+        id: get_bioblend_python_version
+        run: echo "bioblend_python_version=$(echo "${{ matrix.tox_env }}" | sed -e 's/^py\([3-9]\)\([0-9]\+\)/\1.\2/')" >> $GITHUB_OUTPUT
+      - name: Set up Python for BioBlend
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ steps.get_bioblend_python_version.outputs.bioblend_python_version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Set up Python for Galaxy
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.galaxy_python_version }}
+      - name: Run tests
+        env:
+          PGPASSWORD: postgres
+          PGPORT: 5432
+          PGHOST: localhost
+        run: |
+          # Create a PostgreSQL database for Galaxy. The default SQLite3 database makes test fail randomly because of "database locked" error.
+          createdb -U postgres galaxy
+          export DATABASE_CONNECTION=postgresql://postgres:@localhost/galaxy
+          ./bioblend/run_bioblend_tests.sh -g galaxy -v python${{ matrix.galaxy_python_version }} -e ${{ matrix.tox_env }}
+      - name: The job has failed
+        if: ${{ failure() }}
+        run: |
+          cat galaxy/*.log

.github/workflows/build_client.yaml

+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: ${{ steps.client-commit.outputs.commit }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - name: Read Node.js version
+        id: node-version
+        run: echo "version=$(cat 'galaxy root/client/.node_version')" >> $GITHUB_OUTPUT
+      - uses: actions/setup-node@v6
+        with:
+          node-version: ${{ steps.node-version.outputs.version }}
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          package_json_file: 'galaxy root/package.json'
+      - name: get client commit
+        id: client-commit
+        shell: bash
+        run: echo "commit=$(git rev-parse HEAD 2>/dev/null)" >> $GITHUB_OUTPUT
+        working-directory: 'galaxy root'
+      - name: cache client build
+        uses: actions/cache@v5
+        id: cache
+        with:
+          key: galaxy-static-${{ 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
+          NODE_OPTIONS: --max-old-space-size=4096
+        run: make client
+        working-directory: 'galaxy root'

.github/workflows/check_test_class_names.yaml

+name: Check test class names
+on:
+  pull_request:
+    paths:
+      - '.ci/check_test_class_names.sh'
+      - 'lib/galaxy_test/**'
+      - 'test/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Python dependencies
+        run: uv pip install --system -r requirements.txt -r lib/galaxy/dependencies/pinned-test-requirements.txt
+      - name: Run tests
+        run: .ci/check_test_class_names.sh

.github/workflows/client-unit.yaml

+name: Client Unit Testing
+on:
+  push:
+    paths:
+      - 'client/**'
+      - '.github/workflows/client-unit.yaml'
+  pull_request:
+    paths:
+      - 'client/**'
+      - '.github/workflows/client-unit.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  client-unit-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - name: Read Node.js version
+        id: node-version
+        run: echo "version=$(cat 'client/.node_version')" >> $GITHUB_OUTPUT
+      - name: Setup node
+        uses: actions/setup-node@v6
+        with:
+          node-version: ${{ steps.node-version.outputs.version }}
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+      - run: pnpm install --frozen-lockfile
+        working-directory: client
+      - name: Pre-build (icons and plugins)
+        run: node scripts/build.mjs
+        working-directory: client
+      - name: Run Vitest Unit Tests
+        run: pnpm test
+        working-directory: client

.github/workflows/codeql-analysis.yml

+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ dev ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ dev ]
+  schedule:
+    - cron: '16 6 * * 0'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['javascript-typescript', 'python']
+        # CodeQL supports [ 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v4
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+          # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+          config-file: ./.github/codeql/codeql-config.yml
+
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v4
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+      #   If the Autobuild fails above, remove it and uncomment the following three lines
+      #   modify them (or add more) to build your code if your project
+      #   uses a compiled language
+
+      #- run: |
+      #   make bootstrap
+      #   make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v4

.github/workflows/converter_tests.yaml

+name: Converter tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - name: Clone galaxyproject/galaxy-test-data
+        uses: actions/checkout@v6
+        with:
+          repository: galaxyproject/galaxy-test-data
+          path: galaxy-test-data
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Move test data
+        run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
+      - name: Install planemo
+        run: uv tool install planemo
+      - name: Determine converters to check
+        run: |
+          ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
+          echo "Skipping checks for the following converters:"
+          ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
+          echo "Checking only the following converters:"
+          cat tool_list.txt
+      - name: Lint converters
+        run: |
+          mapfile -t TOOL_ARRAY < tool_list.txt
+          planemo lint --skip CitationsMissing,HelpEmpty,HelpMissing --report_level warn "${TOOL_ARRAY[@]}"
+      - name: Run tests
+        run: |
+          mapfile -t TOOL_ARRAY < tool_list.txt
+          planemo test --biocontainers --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "${TOOL_ARRAY[@]}"
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Converter test results (${{ matrix.python-version }})
+          path: tool_test_output.html

.github/workflows/cwl_conformance.yaml

+name: CWL conformance
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    if: ${{ false }}
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ startsWith(matrix.marker, 'red') }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+        marker: ['green', 'red and required', 'red and not required']
+        conformance-version: ['cwl_conformance_v1_0'] #, 'cwl_conformance_v1_1', 'cwl_conformance_v1_2']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
+      - name: Run tests
+        run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: cwl-conformance
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})
+          path: 'galaxy root/run_cwl_tests.html'

.github/workflows/db_indexes.yaml

+name: Database indexes
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+defaults:
+  run:
+    working-directory: 'galaxy root'
+jobs:
+  check:
+    name: Check database indexes
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        db: ['postgresql', 'sqlite']
+        postgresql-version: ['17']
+        python-version: ['3.10']
+        include:
+          - db: postgresql
+            postgresql-version: '9.6'
+            python-version: '3.10'
+    services:
+      postgres:
+        image: postgres:${{ matrix.postgresql-version }}
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Set database connection on PostgreSQL
+        if: matrix.db == 'postgresql'
+        run: echo 'GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8' >> $GITHUB_ENV
+      - name: Check indexes
+        run: tox -e check_indexes

.github/workflows/dependencies.yaml

+name: Update dependencies
+on:
+  schedule:
+    - cron: '0 3 * * 6'  # Run every saturday at 3 am.
+  workflow_dispatch:
+jobs:
+  update_dependencies:
+    name: Update dependencies
+    if: github.repository_owner == 'galaxyproject'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Update dependencies
+        run: make update-dependencies
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v8
+        with:
+          author: galaxybot <galaxybot@users.noreply.github.com>
+          token: ${{ secrets.GALAXYBOT_PAT }}
+          commit-message: |
+            Update Python dependencies
+
+            by running `make update-dependencies`.
+          branch: dev_auto_update_dependencies
+          delete-branch: true
+          push-to-fork: galaxybot/galaxy
+          title: Update Python dependencies
+          body: by running `make update-dependencies`.
+          labels: |
+            area/dependencies
+            kind/enhancement

.github/workflows/deployment.yaml

+name: Deployment Tests
+on:
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Galaxy Deployment to target'
+        required: true
+        default: 'usegalaxymain'
+        type: choice
+        options:
+        - usegalaxytest
+        - usegalaxymain
+        - usegalaxyeu
+      type:
+        description: 'Test type'
+        required: true
+        default: 'all'
+        type: choice
+        options:
+        - all
+        - api
+        - selenium
+      debug:
+        required: true
+        description: 'Run deployment tests with debug mode on'
+        type: boolean
+jobs:
+  testdeployment:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - uses: nanasess/setup-chromedriver@v2
+      - name: Run tests
+        run: bash ./test/deployment/usegalaxystar.bash
+        env:
+          GALAXY_TEST_DEPLOYMENT_TARGET: ${{ inputs.target }}
+          GALAXY_TEST_DEPLOYMENT_DEBUG: ${{ inputs.debug }}
+          GALAXY_TEST_DEPLOYMENT_TEST_TYPE: ${{ inputs.type }}
+          GALAXY_TEST_USEGALAXYMAIN_USER_EMAIL: "jmchilton+test@gmail.com"
+          GALAXY_TEST_USEGALAXYMAIN_USER_PASSWORD: ${{ secrets.USEGALAXYMAIN_USER_PASSWORD }}
+          GALAXY_TEST_USEGALAXYMAIN_USER_KEY: ${{ secrets.USEGALAXYMAIN_USER_KEY }}
+          GALAXY_TEST_USEGALAXYTEST_USER_EMAIL: "jmchilton+test@gmail.com"
+          GALAXY_TEST_USEGALAXYTEST_USER_PASSWORD: ${{ secrets.USEGALAXYTEST_USER_PASSWORD }}
+          GALAXY_TEST_USEGALAXYTEST_USER_KEY: ${{ secrets.USEGALAXYTEST_USER_KEY }}
+          GALAXY_TEST_USEGALAXYEU_USER_EMAIL: "jmchilton+test@gmail.com"
+          GALAXY_TEST_USEGALAXYEU_USER_PASSWORD: ${{ secrets.USEGALAXYEU_USER_PASSWORD }}
+          GALAXY_TEST_USEGALAXYEU_USER_KEY: ${{ secrets.USEGALAXYEU_USER_KEY }}
+          GALAXY_TEST_TIMEOUT_MULTIPLIER: 10
+      - uses: actions/upload-artifact@v7
+        if: always()
+        with:
+          name: Deployment test results (${{ inputs.target }}, ${{ inputs.type }}, ${{ inputs.debug }}, ${{ matrix.python-version }})
+          path: 'deployment_tests.html'

.github/workflows/docs.yaml

+name: Build docs
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - name: Get target branch name (push)
+        if: github.event_name == 'push'
+        run: echo "TARGET_BRANCH=${GITHUB_REF##*/}" >> $GITHUB_ENV
+      - name: Get target branch name (pull request)
+        if: github.event_name == 'pull_request'
+        run: echo "TARGET_BRANCH=$GITHUB_BASE_REF" >> $GITHUB_ENV
+      - name: Show target branch name
+        run: echo $TARGET_BRANCH
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Python dependencies
+        run: uv pip install --system -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
+      - name: Add Google Analytics to doc/source/conf.py
+        run: |
+          sed -i -e "/html_theme_options = {/a\
+          \    'analytics_id': 'UA-45719423-17'," -e "s#https://docs.galaxyproject.org/en/[^/]*/#https://docs.galaxyproject.org/en/$TARGET_BRANCH/#" doc/source/conf.py
+      - name: Checkout the latest doc/source/conf.versioning.py
+        if: github.event_name != 'push' || github.ref != 'refs/heads/dev'
+        run: |
+          # We cannot just download the latest version from dev, because it may be newer in this branch/PR
+          git fetch origin dev:dev
+          if [ ! -f doc/source/conf.versioning.py ] || [ "$(git log -1 --pretty="format:%ct" dev -- doc/source/conf.versioning.py)" -gt "$(git log -1 --pretty="format:%ct" -- doc/source/conf.versioning.py)" ]; then
+              git checkout dev -- doc/source/conf.versioning.py
+          fi
+      - name: Append doc/source/conf.versioning.py
+        run: cat doc/source/conf.versioning.py >> doc/source/conf.py
+      - name: Build docs
+        run: make docs
+      - name: Deploy docs
+        if: github.event_name == 'push' && github.repository_owner == 'galaxyproject'
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        run: |
+          case "$TARGET_BRANCH" in
+              release_[[:digit:]][[:digit:]].[[:digit:]][[:digit:]] | release_[[:digit:]][[:digit:]].[[:digit:]] | master)
+                  UPLOAD_DIR=$TARGET_BRANCH
+                  ;;
+              dev)
+                  UPLOAD_DIR=latest
+                  ;;
+              *)
+                  echo "Not deploying documentation for branch $TARGET_BRANCH"
+                  exit 0
+                  ;;
+          esac
+          uv tool install awscli
+          aws s3 sync doc/build/html/ "s3://galaxy-docs/en/$UPLOAD_DIR" --region us-east-2 --size-only --delete

.github/workflows/first_startup.yaml

+name: first startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+env:
+  YARN_INSTALL_OPTS: --frozen-lockfile
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build-client:
+    uses: ./.github/workflows/build_client.yaml
+  test:
+    name: Startup test
+    needs: build-client
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Restore client cache
+        uses: actions/cache@v5
+        with:
+          fail-on-cache-miss: true
+          key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
+          path: 'galaxy root/static'
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: run tests
+        run: tox -e first_startup
+        working-directory: 'galaxy root'

.github/workflows/framework_tools.yaml

+name: Tool framework tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+        use-legacy-api: ['if_needed', 'always']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+      - name: Run tests
+        run: GALAXY_TEST_USE_LEGACY_TOOL_API="${{ matrix.use-legacy-api }}" ./run_tests.sh --coverage --framework-tools
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Tool framework test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_tests.html'

.github/workflows/framework_workflows.yaml

+name: Workflow framework tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_WORKFLOW_AFTER_RERUN: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+      - name: Run tests
+        run: ./run_tests.sh --coverage --framework-workflows
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: framework-workflows
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Workflow framework test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_workflows_tests.html'

.github/workflows/integration.yaml

+name: Integration
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+        chunk: ['0', '1', '2', '3']
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          # Skip outputs_to_working_directory: true in integration tests, doesn't work with pulsar
+          # echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - name: Prune unused docker image, volumes and containers
+        run: docker system prune -a -f
+      - name: Clean dotnet folder for space
+        run: rm -Rf /usr/share/dotnet
+      - name: Install packages
+        # ffmpeg: ffprobe needed by media datatypes
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Setup Minikube
+        uses: medyagh/setup-minikube@latest
+        with:
+          driver: none
+          kubernetes-version: '1.28.0'
+      - name: Check pods
+        run: kubectl get pods -A
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
+      - name: Install Apptainer's singularity
+        uses: eWaterCycle/setup-apptainer@v2
+      - name: Run tests
+        run: |
+          . .ci/minikube-test-setup/start_services.sh
+          ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: integration
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_integration_tests.html'

.github/workflows/integration_selenium.yaml

+name: Integration Selenium
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_SKIP_CLIENT_BUILD: '0'
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_SELENIUM_RETRIES: 1
+  YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+  GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  setup-selenium:
+    uses: ./.github/workflows/setup_selenium.yaml
+  build-client:
+    uses: ./.github/workflows/build_client.yaml
+  test:
+    name: Test
+    needs: [setup-selenium, build-client]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - name: Prune unused docker image, volumes and containers
+        run: docker system prune -a -f
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration-selenium
+      - name: Restore client cache
+        uses: actions/cache@v5
+        with:
+          fail-on-cache-miss: true
+          key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
+          path: 'galaxy root/static'
+      - name: Run tests
+        run: ./run_tests.sh --coverage -integration test/integration_selenium
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: integration-selenium
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Integration Selenium test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_integration_tests.html'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Integration Selenium debug info (${{ matrix.python-version }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/js_lint.yaml

+name: Client linting
+on:
+  push:
+    paths:
+      - 'client/**'
+      - '.github/workflows/js_lint.yaml'
+  pull_request:
+    paths:
+      - 'client/**'
+      - '.github/workflows/js_lint.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  client-unit-test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - name: Read Node.js version
+        id: node-version
+        run: echo "version=$(cat 'client/.node_version')" >> $GITHUB_OUTPUT
+      - name: Setup node
+        uses: actions/setup-node@v6
+        with:
+          node-version: ${{ steps.node-version.outputs.version }}
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+      - run: pnpm install --frozen-lockfile
+        working-directory: client
+      - name: Run ESLint
+        run: pnpm run eslint
+        working-directory: client
+      - name: Run prettier checks
+        run: pnpm run format-check
+        working-directory: client
+      - name: Run vue-tsc
+        working-directory: client
+        run: pnpm type-check

.github/workflows/labels-verifier.yaml

+name: Labels Verifier
+on:
+  pull_request_target:
+    types: [closed]
+jobs:
+  onMerged:
+    name: "Check Labels on merge"
+    permissions:
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check Labels on merge
+        if: |
+          github.event.pull_request.merged == true &&
+          ! contains(join(github.event.pull_request.labels.*.name, ', '), 'kind/') &&
+          ! contains(github.event.pull_request.labels.*.name, 'merge') &&
+          ! contains(github.event.pull_request.labels.*.name, 'minor')
+        uses: actions/github-script@v8
+        with:
+          script: |
+            github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              body: 'This PR was merged without a "kind/" label, please correct.',
+            })

.github/workflows/lint.yaml

+name: Python linting
+on:
+  push:
+    paths:
+      - '**.py'
+      - '.github/workflows/lint.yaml'
+      - .flake8
+      - .isort.cfg
+      - lib/galaxy/dependencies/**
+      - mypy.ini
+      - pyproject.toml
+      - tox.ini
+  pull_request:
+    paths:
+      - '**.py'
+      - '.github/workflows/lint.yaml'
+      - .flake8
+      - .isort.cfg
+      - lib/galaxy/dependencies/**
+      - mypy.ini
+      - pyproject.toml
+      - tox.ini
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    env:
+      LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
+      TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
+      CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run linting
+        run: tox -e lint
+      - name: Run docstring linting
+        run: tox -e lint_docstring_include_list
+      - name: Run mypy checks
+        run: tox -e mypy
+      - name: Run format checks
+        run: tox -e format

.github/workflows/lint_openapi_schema.yml

+name: OpenAPI linting
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  validate-schema:
+    name: Validate OpenAPI schema
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - name: Read Node.js version
+        id: node-version
+        run: echo "version=$(cat 'galaxy root/client/.node_version')" >> $GITHUB_OUTPUT
+      - uses: actions/setup-node@v6
+        with:
+          node-version: ${{ steps.node-version.outputs.version }}
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          package_json_file: 'galaxy root/package.json'
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
+      - name: Install dependencies
+        run: ./scripts/common_startup.sh --dev-wheels --skip-client-build
+        working-directory: 'galaxy root'
+      - name: Lint schema
+        run: make lint-api-schema
+        working-directory: 'galaxy root'
+      - name: Build typescript schema
+        run: make update-client-api-schema
+        working-directory: 'galaxy root'
+      - name: Diff...
+        run: git diff
+        working-directory: 'galaxy root'
+      - name: Check for changes
+        run: |
+          if [[ `git status --porcelain` ]]; then
+            echo "Rebuilding client/src/api/schema/schema.ts resulted in changes, run 'make update-client-api-schema' and commit results"
+            exit 1
+          fi
+        working-directory: 'galaxy root'

.github/workflows/main_tools.yaml

+name: Main tool tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+      - name: Run tests
+        run: ./run_tests.sh --coverage --main_tools
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: main-tools
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Main tool test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_tests.html'

.github/workflows/maintenance_bot.yaml

+name: Maintenance Bot
+on:
+  pull_request_target:
+    types: [opened, reopened, edited, ready_for_review, unlabeled]
+jobs:
+  labeler:
+    name: Assign labels and milestone
+    if: github.repository_owner == 'galaxyproject'
+    permissions:
+      contents: read
+      issues: write
+      pull-requests: write
+    runs-on: ubuntu-latest
+    env:
+      MILESTONE_NUMBER: 33
+    steps:
+      - name: Get latest pull request labels
+        id: get_pr_labels
+        uses: actions/github-script@v8
+        with:
+          script: |
+            const response = await github.rest.issues.listLabelsOnIssue({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+            });
+            console.log(response);
+            return response.data;
+      - name: Add area labels
+        if: ${{ ! contains(join(fromJSON(steps.get_pr_labels.outputs.result).*.name, ', '), 'area/') }}
+        uses: actions/labeler@v6
+      - name: Assign milestone
+        if: |
+          ! github.event.pull_request.milestone &&
+          ! contains(github.event.pull_request.labels.*.name, 'merge') &&
+          ! contains(github.event.pull_request.labels.*.name, 'status/WIP') &&
+          ! contains(github.event.pull_request.title, 'WIP') &&
+          ! github.event.pull_request.draft
+        uses: actions/github-script@v8
+        with:
+          script: |
+            github.rest.issues.update({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              milestone: ${{ env.MILESTONE_NUMBER }},
+            });

.github/workflows/mulled.yaml

+name: Mulled Unit Tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Install Apptainer's singularity
+        uses: eWaterCycle/setup-apptainer@v2
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run tests
+        run: tox -e mulled
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Mulled unit test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_unit_tests.html'

.github/workflows/osx_startup.yaml

+name: macOS startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build-client:
+    uses: ./.github/workflows/build_client.yaml
+  test:
+    name: Startup test
+    runs-on: macos-latest
+    needs: build-client
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - name: Install miniforge  # use this job to test using Python from a conda environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          activate-environment: ''
+      - name: Restore client cache
+        uses: actions/cache@v5
+        with:
+          fail-on-cache-miss: true
+          key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
+          path: 'galaxy root/static'
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run tests
+        run: tox -e first_startup
+        working-directory: 'galaxy root'
+        env:
+          GALAXY_CONDA_PYTHON_VERSION: "${{ matrix.python-version }}"

.github/workflows/performance.yaml

+name: Performance tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-performance
+      - name: Run tests
+        run: ./run_tests.sh --ci_test_metrics --structured_data_html --structured_data_report_file "test.json" --skip_flakey_fails -api lib/galaxy_test/performance
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: API test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_api_tests.html'
+      - uses: actions/upload-artifact@v7
+        with:
+          name: Performance Metrics (${{ matrix.python-version }})
+          path: 'galaxy root/test.html'

.github/workflows/playwright.yaml

+name: Playwright tests
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_CONFIG_GALAXY_URL_PREFIX: '/galaxypf'
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_SELENIUM_RETRIES: 1
+  GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 1
+  GALAXY_TEST_SELENIUM_HEADLESS: 1
+  YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build-client:
+    uses: ./.github/workflows/build_client.yaml
+  test:
+    name: Test
+    needs: [build-client]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+        chunk: [0, 1, 2]
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-playwright
+      - name: Restore client cache
+        uses: actions/cache@v5
+        with:
+          fail-on-cache-miss: true
+          key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
+          path: 'galaxy root/static'
+      - name: Run tests
+        run: ./run_tests.sh --coverage -playwright lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: playwright
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Playwright test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_playwright_tests.html'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Playwright debug info (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/pr-title-update.yml

+name: Update PR title
+
+on:
+  pull_request_target:
+    types: [opened, edited, reopened]
+
+jobs:
+  update-title:
+    if: github.event.action != 'edited' || github.event.changes.base.ref.from != ''
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+    steps:
+      - name: Update PR title
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
+          TARGET_BRANCH: "${{ github.base_ref }}"
+          PR_TITLE: "${{ github.event.pull_request.title }}"
+          REPO: "${{ github.repository }}"
+        run: |
+          VERSION=$(echo $TARGET_BRANCH | grep -oP '^release_\K\d+.\d+$' || true)
+          NEW_TITLE=$(echo "$PR_TITLE" | sed -E "s/\[[0-9]+\.[0-9]+\] //")
+          if [[ -n "$VERSION" ]]; then
+            NEW_TITLE="[$VERSION] $NEW_TITLE"
+          fi
+          if [[ "$NEW_TITLE" != "$PR_TITLE" ]]; then
+            gh pr edit $PR_NUMBER --repo "$REPO" --title "$NEW_TITLE"
+          fi

.github/workflows/publish_artifacts.yaml

+name: Publish release artifacts
+on:
+  release:
+    types: [released, prereleased]
+  workflow_dispatch:
+    inputs:
+      release_type:
+        description: 'create release or prerelease artifact ?'
+        required: true
+        default: 'prerelease'
+        type: choice
+        options:
+        - release
+        - prerelease
+      release_tag:
+        description: 'Specify tag to build for'
+        required: true
+        type: string
+jobs:
+  check-permissions:
+    if: github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if user can create releases
+        run: |
+          PERMISSION=$(gh api repos/${{ github.repository }}/collaborators/${{ github.actor }}/permission --jq '.permission')
+          if [[ "$PERMISSION" != "admin" ]]; then
+            echo "Error: Only repository admins can manually trigger release artifacts"
+            exit 1
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  build-and-publish-pypi:
+    if: |
+      github.repository_owner == 'galaxyproject' &&
+      (github.event_name == 'release' ||
+       (github.event_name == 'workflow_dispatch' && !cancelled() && !failure()))
+    needs: [check-permissions]
+    name: Build and Publish to PyPI
+    runs-on: ubuntu-latest
+    strategy:
+        matrix:
+            python-version: ['3.10']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install script dependencies
+        run: uv tool install galaxy-release-util
+      - name: Build and publish to PyPI
+        run: |
+          galaxy-release-util build-and-upload --no-confirm
+        env:
+            TWINE_USERNAME: __token__
+            TWINE_PASSWORD: ${{ (github.event_name == 'workflow_dispatch' && inputs.release_type == 'prerelease') || (github.event_name == 'release' && github.event.release.prerelease) && secrets.PYPI_TEST_TOKEN || secrets.PYPI_MAIN_TOKEN }}
+            TWINE_REPOSITORY_URL: ${{ (github.event_name == 'workflow_dispatch' && inputs.release_type == 'prerelease') || (github.event_name == 'release' && github.event.release.prerelease) && 'https://test.pypi.org/legacy/' || 'https://upload.pypi.org/legacy/' }}
+
+  build-and-publish-npm:
+    if: |
+      github.repository_owner == 'galaxyproject' &&
+      (github.event_name == 'release' ||
+       (github.event_name == 'workflow_dispatch' && !cancelled() && !failure()))
+    needs: [check-permissions]
+    name: Build and Publish to NPM
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event_name == 'workflow_dispatch' && inputs.release_tag || '' }}
+          persist-credentials: false
+      - name: Read Node.js version
+        id: node-version
+        run: echo "version=$(cat client/.node_version)" >> $GITHUB_OUTPUT
+      - uses: actions/setup-node@v6
+        with:
+          node-version: ${{ steps.node-version.outputs.version }}
+          registry-url: 'https://registry.npmjs.org'
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+      - name: build client
+        run: pnpm install && pnpm build-production
+        working-directory: 'client'
+      # Ensure npm 11.5.1 or later for trusted publishing
+      - run: npm install -g npm@latest
+        working-directory: 'client'
+      - name: publish client
+        if: (github.event_name == 'workflow_dispatch' && inputs.release_type == 'release') || (github.event_name == 'release' && !github.event.release.prerelease)
+        run: npm publish --provenance --access public
+        working-directory: 'client'
+      - name: sync client-api version
+        run: npm run sync-version
+        working-directory: 'client-api'
+      - name: build client-api
+        run: npm install && npm run build
+        working-directory: 'client-api'
+      - name: publish client-api
+        if: (github.event_name == 'workflow_dispatch' && inputs.release_type == 'release') || (github.event_name == 'release' && !github.event.release.prerelease)
+        run: npm publish --provenance --access public
+        working-directory: 'client-api'

.github/workflows/selenium.yaml

+name: Selenium tests
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'packages/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_CONFIG_GALAXY_URL_PREFIX: '/galaxypf'
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+  GALAXY_TEST_SELENIUM_RETRIES: 1
+  GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 1
+  YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  setup-selenium:
+    uses: ./.github/workflows/setup_selenium.yaml
+  build-client:
+    uses: ./.github/workflows/build_client.yaml
+  test:
+    name: Test
+    needs: [setup-selenium, build-client]
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+        chunk: [0, 1, 2]
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - if: github.event_name == 'schedule'
+        run: |
+          echo "GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY=extended" >> $GITHUB_ENV
+          echo "GALAXY_CONFIG_OVERRIDE_OUTPUTS_TO_WORKING_DIRECTORY=true" >> $GITHUB_ENV
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
+      - name: Restore client cache
+        uses: actions/cache@v5
+        with:
+          fail-on-cache-miss: true
+          key: galaxy-static-${{ needs.build-client.outputs.commit-id }}
+          path: 'galaxy root/static'
+      - name: Run tests
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: selenium
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Selenium test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_selenium_tests.html'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Selenium debug info (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/setup_selenium.yaml

+on:
+  workflow_call:
+jobs:
+  setup_chromedriver:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install chromedriver
+        uses: nanasess/setup-chromedriver@v2

.github/workflows/test_galaxy_packages.yaml

+name: Test Galaxy packages
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run tests
+        run: tox -e test_galaxy_packages
+        working-directory: 'galaxy root'

.github/workflows/test_galaxy_packages_for_pulsar.yaml

+name: Test Galaxy packages for Pulsar
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8']  # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Apptainer's singularity
+        uses: eWaterCycle/setup-apptainer@v2
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run tests
+        run: tox -e test_galaxy_packages_for_pulsar
+        working-directory: 'galaxy root'

.github/workflows/test_galaxy_release.yaml

+name: Test Galaxy release script
+on:
+  push:
+    paths:
+      - '.github/workflows/test_galaxy_release.yaml'
+      - lib/galaxy/dependencies/**
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+  pull_request:
+    paths:
+      - '.github/workflows/test_galaxy_release.yaml'
+      - lib/galaxy/dependencies/**
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Run tests
+        run: ./test/release.sh

.github/workflows/toolshed.yaml

+name: Toolshed tests
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  TOOL_SHED_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+        test-install-client: ['galaxy_api', 'standalone']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
+      - name: Install dependencies
+        run: ./scripts/common_startup.sh --dev-wheels --skip-client-build
+        working-directory: 'galaxy root'
+      - name: Setup pnpm
+        uses: pnpm/action-setup@v4
+        with:
+          package_json_file: 'galaxy root/lib/tool_shed/webapp/frontend/package.json'
+      - name: Build Frontend
+        run: |
+          . .venv/bin/activate
+          cd lib/tool_shed/webapp/frontend
+          pnpm install --frozen-lockfile
+          make client
+        working-directory: 'galaxy root'
+      - name: Install playwright
+        run: |
+          . .venv/bin/activate
+          playwright install
+        working-directory: 'galaxy root'
+      - name: Run tests
+        run: ./run_tests.sh -toolshed
+        env:
+          TOOL_SHED_TEST_INSTALL_CLIENT: ${{ matrix.test-install-client }}
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Toolshed test results (${{ matrix.python-version }}, ${{ matrix.test-install-client }})
+          path: 'galaxy root/run_toolshed_tests.html'

.github/workflows/unit-postgres.yaml

+name: Unit w/postgres tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/postgres?client_encoding=utf8'  # using postgres as the db
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10']
+    services:
+      postgres:
+        image: postgres:17
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Cache galaxy venv
+        uses: actions/cache@v5
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit-postgres
+      - name: Run migration tests
+        run: ./run_tests.sh -unit test/unit/data/model/migrations/test_migrations.py
+        working-directory: 'galaxy root'
+      - name: Run test migrate database
+        run: ./run_tests.sh -unit test/unit/app/test_migrate_database.py
+        working-directory: 'galaxy root'

.github/workflows/unit.yaml

+name: Unit tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+      - 'packages/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.10', '3.14']
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          path: 'galaxy root'
+          persist-credentials: false
+      - uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo "version=$(python -c 'import sys; print("-".join(str(v) for v in sys.version_info))')" >> $GITHUB_OUTPUT
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Install tox
+        run: uv tool install tox --with tox-uv
+      - name: Run tests
+        run: tox -e unit-coverage
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v5
+        with:
+          flags: py-unit
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v7
+        if: failure()
+        with:
+          name: Unit test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_unit_tests.html'

.gitignore

+.hg*
+
+# Downloaded and locally built eggs
+eggs
+scripts/scramble/build
+scripts/scramble/lib
+scripts/scramble/archives
+
+# Python virtualenv
+.venv*/
+
+# Python build artifacts
+build
+dist
+lib/galaxy.egg-info
+.eggs
+
+# Generated static content
+lib/galaxy/web/framework/static/maps
+lib/galaxy/web/framework/static/scripts
+lib/galaxy/web/framework/static/style
+lib/galaxy/web/framework/meta.json
+
+# Misc. data, config, cache files
+/database/
+
+# Python bytecode
+*.pyc
+
+# Galaxy runtime files
+*.lock
+*.log
+*.pid
+celerybeat-schedule
+
+# Celery state files
+celerybeat-schedule.*
+
+# Tool Shed runtime files
+tool_shed_webapp.lock
+tool_shed_webapp.log
+tool_shed_webapp.pid
+hgweb.config*
+lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml
+
+# Reports runtime files
+reports_webapp.lock
+reports_webapp.log
+reports_webapp.pid
+
+# Jupyter runtime files
+.ipynb_checkpoints
+
+# Config files
+universe_wsgi.ini
+reports_wsgi.ini
+reports.ini
+tool_shed_wsgi.ini
+datatypes_conf.xml
+tool_conf.xml
+external_service_types_conf.xml
+migrated_tools_conf.xml
+shed_tool_conf.xml
+tool_data_table_conf.xml
+tool_sheds_conf.xml
+integrated_tool_panel.xml
+openid_conf.xml
+shed_tool_data_table_conf.xml
+job_conf.xml
+data_manager_conf.xml
+shed_data_manager_conf.xml
+object_store_conf.xml
+job_metrics_conf.xml
+workflow_schedulers_conf.xml
+config/*
+config/plugins/interactive_environments/**/*.ini
+config/plugins/**/.cache
+config/plugins/**/.parcel-cache
+config/plugins/visualizations
+!config/plugins
+static/welcome.html.*
+static/welcome.html
+static/client_build_hash.txt
+lib/galaxy_test/selenium/jupyter/galaxy_selenium_context.yml
+
+# Tool data
+tool-data/annotation_profiler_options.xml
+tool-data/annotation_profiler_valid_builds.txt
+tool-data/gatk_annotations.txt
+tool-data/gd.restriction_enzymes.txt
+tool-data/gd.species.txt
+tool-data/shared/igv/igv_build_sites.txt
+tool-data/shared/rviewer/rviewer_build_sites.txt
+tool-data/shared/ncbi/builds.txt
+tool-data/shared/ucsc/builds.txt
+tool-data/shared/ucsc/manual_builds.txt
+tool-data/shared/ensembl/builds.txt
+tool-data/shared/ucsc/publicbuilds.txt
+tool-data/shared/ucsc/ucsc_build_sites.txt
+tool-data/*.loc
+tool-data/genome/*
+tool-data/*.sample
+tool-data/testtoolshed.g2.bx.psu.edu/
+tool-data/toolshed.g2.bx.psu.edu/
+tool-data/**/*.fa
+
+# Test output
+.pytest_cache/
+assets/
+test-data-cache
+run_api_tests.html
+run_cwl_tests.html
+run_framework_tests.html
+run_functional_tests.html
+run_integration_tests.html
+run_playwright_tests.html
+run_selenium_tests.html
+run_toolshed_tests.html
+test/tool_shed/tmp/*
+.coverage
+htmlcov
+run_unit_tests.html
+test/unit/**.log
+.tox
+tool_test_output.html
+tool_test_output.json
+
+# Project files
+*.kpf
+.idea
+.vscode
+client/**/jsconfig.json
+vetur.config.js
+.pre-commit-config.yaml
+galaxy.code-workspace
+
+# Chrom len files
+*.len
+
+# JARs
+tool-data/shared/jars/
+
+# JS, Local node_modules, and bower_components directories
+static/maps
+static/plugins
+static/scripts
+node_modules
+bower_components
+client/src/libs/*
+
+# Old galaxy client location
+client/galaxy
+
+# Documentation build files
+doc/build
+doc/schema.md
+doc/source/admin/config_logging_default_yaml.rst
+doc/source/dev/schema.md
+doc/source/dev/plantuml.jar
+client/docs/dist
+
+# Webpack stats
+client/webpack-stats.json
+
+# Packages
+packages/*/build
+packages/*/dist
+packages/*/*.egg-info
+packages/meta/requirements.txt
+
+# Standalone script + main, or build into dist
+config/plugins/**/static/dist
+config/plugins/**/static/script.js
+config/plugins/**/static/main.css
+config/plugins/**/static/script.css
+config/plugins/**/static/plugin_build_hash.txt
+config/plugins/**/static/*.map
+
+# Viz-specific build artifacts to ignore (until these are removed from codebase)
+config/plugins/visualizations/annotate_image/static/jquery.contextMenu.css
+config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
+config/plugins/visualizations/scatterplot/static/scatterplot.js
+config/plugins/visualizations/tiffviewer/static/
+
+# CWL conformance tests
+lib/galaxy_test/api/cwl/test_cwl_conformance_v1_?.py
+test/functional/tools/cwl_tools/v1.?/
+
+# Involucro tool
+involucro
+
+# Misc
+*.orig
+.DS_Store
+*.rej
+*~

.gitpod.yml

+github:
+  prebuilds:
+    # enable for the master/default branch (defaults to true)
+    master: true
+    # enable for all branches in this repo (defaults to false)
+    branches: true
+    # enable for pull requests coming from this repo (defaults to true)
+    pullRequests: true
+    # enable for pull requests coming from forks (defaults to false)
+    pullRequestsFromForks: true
+    # add a "Review in Gitpod" button as a comment to pull requests (defaults to true)
+    addComment: false
+    # add a "Review in Gitpod" button to pull requests (defaults to false)
+    addBadge: false
+    # add a label once the prebuild is ready to pull requests (defaults to false)
+    addLabel: false
+image: gitpod/workspace-postgres
+tasks:
+  - name: Setup Development Environment
+    init: >
+      cp .vscode/settings_gitpod.json .vscode/settings.json &&
+      cp .vscode/launch_gitpod.json .vscode/launch.json &&
+      python3 -m venv .venv &&
+      . .venv/bin/activate &&
+      pip install psycopg2 &&
+      pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt &&
+      pip install tox &&
+      gp sync-done setup
+    command: createdb galaxy
+  - name: Setup Galaxy Configuration
+    command: cp config/galaxy.yml.sample config/galaxy.yml
+  - name: Watch Client with Webpack
+    init: gp sync-await setup
+    command: make client-watch
+# Ports to expose on workspace startup (optional)
+ports:
+  - port: 8000
+vscode:
+  extensions:
+    - ms-python.python
+    # No longer seems to work.
+    # - ms-python.vscode-pylance

.isort.cfg

+[settings]
+combine_as_imports=true
+force_alphabetical_sort_within_sections=true
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap=2
+# Same line length as for black
+line_length=120
+no_lines_before=LOCALFOLDER
+profile=black
+reverse_relative=true
+skip_gitignore=true
+# Make isort run faster by skipping database
+skip_glob=database/*,lib/tool_shed/test/test_data/repos/*
+src_paths=lib

.k8s_ci.Dockerfile

+# Stage 1:
+# - base: ubuntu (default) OR prebuilt image0
+# - install build tools
+# - clone playbook
+# - run playbook
+# - remove build artifacts + files not needed in container
+# Stage 2:
+# - create galaxy user + group + directory
+# - copy galaxy files from stage 2.1 and 2.2
+# - finalize container (set path, user...)
+
+# Init ARGs
+ARG ROOT_DIR=/galaxy
+ARG SERVER_DIR=$ROOT_DIR/server
+
+ARG STAGE1_BASE=python:3.12-slim
+ARG FINAL_STAGE_BASE=$STAGE1_BASE
+ARG GALAXY_USER=galaxy
+ARG GALAXY_PLAYBOOK_REPO=https://github.com/galaxyproject/galaxy-docker-k8s
+ARG GALAXY_PLAYBOOK_BRANCH=v4.2.0
+
+ARG GIT_COMMIT=unspecified
+ARG BUILD_DATE=unspecified
+ARG IMAGE_TAG=unspecified
+
+#======================================================
+# Stage 1 - Run playbook
+#======================================================
+FROM $STAGE1_BASE AS stage1
+ARG DEBIAN_FRONTEND=noninteractive
+ARG SERVER_DIR
+ARG GALAXY_PLAYBOOK_REPO
+ARG GALAXY_PLAYBOOK_BRANCH
+
+# Init Env
+ENV LC_ALL=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+# Install build dependencies + ansible
+RUN set -xe; \
+    echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
+    && apt-get -qq update && apt-get install -y --no-install-recommends \
+        locales locales-all \
+        git \
+        make \
+        libc-dev \
+        bzip2 \
+        gcc \
+    && pip install --no-cache virtualenv ansible==11.11.0 \
+    && apt-get autoremove -y && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/*
+
+# Remove context from previous build; copy current context; run playbook
+WORKDIR /tmp/ansible
+RUN rm -rf *
+
+# Add Galaxy source code
+COPY . $SERVER_DIR/
+
+RUN git clone --depth 1 --branch $GALAXY_PLAYBOOK_BRANCH $GALAXY_PLAYBOOK_REPO galaxy-docker
+WORKDIR /tmp/ansible/galaxy-docker
+RUN ansible-galaxy install -r requirements.yml -p roles --force-with-deps
+RUN ansible-playbook -i localhost, playbook.yml -v -e galaxy_virtualenv_command=virtualenv
+
+# Remove build artifacts + files not needed in container
+WORKDIR $SERVER_DIR
+# Save commit hash of HEAD before zapping git folder
+RUN git rev-parse HEAD > GITREVISION
+RUN rm -rf \
+        .ci \
+        .git \
+        .venv/include/node \
+        .venv/src/node* \
+        client/dist \
+        doc \
+        test \
+        test-data
+# Clean up *all* node_modules, including plugins.  Everything is already built+staged.
+RUN find . -name "node_modules" -type d -prune -exec rm -rf '{}' +
+# Remove pre-built visualization plugin static files (not present in base image, ~220MB)
+RUN find config/plugins/visualizations -mindepth 2 -maxdepth 2 -name "static" -type d -exec rm -rf '{}' +
+
+#======================================================
+# Stage 2 - Build final image based on previous stage
+#======================================================
+FROM $FINAL_STAGE_BASE
+ARG DEBIAN_FRONTEND=noninteractive
+ARG ROOT_DIR
+ARG SERVER_DIR
+ARG GALAXY_USER
+
+ARG GIT_COMMIT
+ARG BUILD_DATE
+ARG IMAGE_TAG
+
+LABEL org.opencontainers.image.title="Galaxy Minimal Image" \
+      org.opencontainers.image.description="A size optimized image for Galaxy targeting k8s and ci applications" \
+      org.opencontainers.image.authors="galaxyproject.org" \
+      org.opencontainers.image.vendor="Galaxy Project" \
+      org.opencontainers.image.documentation="https://github.com/galaxyproject/galaxy-docker-k8s" \
+      org.opencontainers.image.licenses="MIT" \
+      org.opencontainers.image.version="$IMAGE_TAG" \
+      org.opencontainers.image.url="https://github.com/galaxyproject/galaxy-docker-k8s" \
+      org.opencontainers.image.source="https://github.com/galaxyproject/galaxy.git" \
+      org.opencontainers.image.revision=$GIT_COMMIT \
+      org.opencontainers.image.created=$BUILD_DATE
+
+# Init Env
+ENV LC_ALL=en_US.UTF-8
+ENV LANG=en_US.UTF-8
+
+# Install procps (contains kill, ps etc.), less, curl, vim-tiny and nano-tiny
+# for convenience and debugging purposes. Nano and vim commands are aliased
+# to their tiny variants using the debian alternatives system.
+# Bzip2 and virtualenv are installed for backwards compatibility with older
+# versions of this image which was based on Ubuntu and contained these
+# utilities.
+RUN set -xe; \
+    echo "Acquire::http {No-Cache=True;};" > /etc/apt/apt.conf.d/no-cache \
+    && apt-get -qq update && apt-get install -y --no-install-recommends \
+        locales \
+        vim-tiny \
+        nano-tiny \
+        netcat-openbsd \
+        curl \
+        procps \
+        less \
+        bzip2 \
+        tini \
+        wget \
+    && update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 0 \
+    && update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 0 \
+    && echo "set nocompatible\nset backspace=indent,eol,start" >> /usr/share/vim/vimrc.tiny \
+    && echo "$LANG UTF-8" > /etc/locale.gen \
+    && locale-gen $LANG && update-locale LANG=$LANG \
+    && curl -L https://github.com/galaxyproject/gxadmin/releases/latest/download/gxadmin > /usr/bin/gxadmin \
+    && chmod +x /usr/bin/gxadmin \
+    && apt-get autoremove -y && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* /tmp/*
+
+# Create Galaxy user, group, directory; chown
+RUN set -xe; \
+      adduser --system --group --uid 10001 $GALAXY_USER \
+      && mkdir -p $SERVER_DIR \
+      && chown $GALAXY_USER:$GALAXY_USER $ROOT_DIR -R
+
+WORKDIR $ROOT_DIR
+# Copy galaxy files to final image
+# The chown value MUST be hardcoded (see https://github.com/moby/moby/issues/35018)
+COPY --chown=$GALAXY_USER:$GALAXY_USER --from=stage1 $ROOT_DIR .
+
+WORKDIR $SERVER_DIR
+
+# The data in version.json will be displayed in Galaxy's /api/version endpoint
+RUN printf "{\n  \"git_commit\": \"$(cat GITREVISION)\",\n  \"build_date\": \"$BUILD_DATE\",\n  \"image_tag\": \"$IMAGE_TAG\"\n}\n" > version.json \
+    && chown $GALAXY_USER:$GALAXY_USER version.json
+
+EXPOSE 8080
+USER $GALAXY_USER
+
+ENV PATH="$SERVER_DIR/.venv/bin:${PATH}"
+ENV GALAXY_CONFIG_CONDA_AUTO_INIT=False
+
+ENTRYPOINT ["tini", "--"]
+
+# [optional] to run:
+CMD ["galaxy"]

.pre-commit-config.yaml.sample

+repos:
+  - repo: https://github.com/psf/black
+    rev: 26.1.0
+    hooks:
+    - id: black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.8
+    hooks:
+      - id: ruff
+        args: [--fix]
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+    - id: flake8
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.1.0
+    hooks:
+    - id: prettier
+      additional_dependencies:
+        - prettier@3.6.2 # SEE: https://github.com/pre-commit/pre-commit/issues/3133
+      exclude_types:  # .prettierignore ignored apparently ...
+        - yaml
+        - json
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0  # Use the ref you want to point at
+    hooks:
+      - id: trailing-whitespace
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: name-tests-test
+  - repo: https://github.com/detailyang/pre-commit-shell
+    rev: 1.0.5
+    hooks:
+    - id: shell-lint
+      args: [--format=json]
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.27.4
+    hooks:
+      - id: check-github-workflows
+  - repo: local
+    hooks:
+    -   id: eslint
+        name: client eslint
+        language: system
+        files: ^client/
+        entry: .ci/eslint_wrapper.sh
+        types: [file]
+        types_or: [javascript, jsx, ts, tsx, vue]
+#  - repo: https://github.com/pycqa/isort
+#    rev: 5.10.1
+#    hooks:
+#      - id: isort
+#        name: isort (python)

.redocly.lint-ignore.yaml

+# This file instructs Redocly's linter to ignore the rules contained for specific parts of your API.
+# See https://redoc.ly/docs/cli/ for more information.
+_schema.yaml:
+  no-empty-servers:
+    - '#/openapi'
+  no-ambiguous-paths:
+    - >-
+      #/paths/~1api~1histories~1{history_id}~1contents~1{dataset_id}~1permissions
+    - >-
+      #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1display
+    - >-
+      #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1extra_files
+    - >-
+      #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1metadata_file
+    - >-
+      #/paths/~1api~1histories~1{history_id}~1contents~1{history_content_id}~1tags
+    - '#/paths/~1api~1histories~1{history_id}~1contents~1{id}~1validate'
+    - '#/paths/~1api~1histories~1{history_id}~1contents~1{type}s~1{id}'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1biocompute'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1jobs_summary'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1prepare_store_download'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1report'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1report.pdf'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1step_jobs_summary'
+    - '#/paths/~1api~1invocations~1{invocation_id}~1write_store'
+    - '#/paths/~1api~1quotas~1{id}~1purge'
+    - '#/paths/~1api~1users~1{user_id}~1api_key'
+    - '#/paths/~1api~1users~1{user_id}~1beacon'
+    - '#/paths/~1api~1users~1{user_id}~1custom_builds'
+    - '#/paths/~1api~1users~1{user_id}~1recalculate_disk_usage'
+    - '#/paths/~1api~1users~1{user_id}~1send_activation_email'
+    - '#/paths/~1api~1users~1{user_id}~1usage'
+  no-unused-components:
+    - '#/components/schemas/FetchDataPayload'
+  security-defined:
+    - '#/paths/~1api~1authenticate~1baseauth/get'
+_shed_schema.yaml:
+  no-empty-servers:
+    - '#/openapi'
+  operation-2xx-response:
+    - '#/paths/~1repository~1status_for_installed_repository/get'
+  security-defined:
+    - '#/paths/~1api~1authenticate~1baseauth/get'
+    - '#/paths/~1api~1categories~1{encoded_category_id}/get'
+    - '#/paths/~1api~1ga4gh~1trs~1v2~1service-info/get'
+    - '#/paths/~1api~1ga4gh~1trs~1v2~1toolClasses/get'
+    - '#/paths/~1api~1ga4gh~1trs~1v2~1tools/get'
+    - '#/paths/~1api~1repositories~1get_ordered_installable_revisions/get'
+    - '#/paths/~1api~1repositories~1updates/get'
+    - '#/paths/~1api~1repositories~1{encoded_repository_id}/get'
+    - '#/paths/~1api~1repositories~1{encoded_repository_id}~1metadata/get'
+    - >-
+      #/paths/~1api~1repositories~1{encoded_repository_id}~1revisions~1{changeset_revision}~1readmes/get
+    - '#/paths/~1api~1version/get'
+    - >-
+      #/paths/~1api_internal~1repositories~1{encoded_repository_id}~1metadata/get
+    - '#/paths/~1repository~1get_changeset_revision_and_ctx_rev/get'
+    - '#/paths/~1repository~1get_ctx_rev/get'
+    - '#/paths/~1repository~1get_repository_type/get'
+    - '#/paths/~1repository~1get_required_repo_info_dict/get'
+    - '#/paths/~1repository~1get_tool_dependencies/get'
+    - '#/paths/~1repository~1next_installable_changeset_revision/get'
+    - '#/paths/~1repository~1previous_changeset_revisions/get'
+    - '#/paths/~1repository~1static~1images~1{repository_id}~1{image_file}/get'
+    - '#/paths/~1repository~1status_for_installed_repository/get'
+    - '#/paths/~1repository~1updated_changeset_revisions/get'

.redocly.yaml

+organization: galaxyproject.org
+extends:
+  - recommended
+rules:
+  operation-4xx-response: off

.vscode/.test.env

+GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml"

.vscode/launch_gitpod.json

+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "GalaxyFastAPI uvicorn",
+            "type": "python",
+            "request": "launch",
+            "module": "uvicorn",
+            "args": ["--app-dir", "lib", "--factory", "galaxy.webapps.galaxy.fast_factory:factory"],
+            "env": {
+                "GALAXY_CONFIG_FILE": "${workspaceFolder}/config/galaxy.yml",
+                "GALAXY_CONDA_AUTO_INIT": "false",
+                "GALAXY_CONFIG_TOOL_CONFIG_FILE": "lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/sample_tool_conf.xml",
+                "GALAXY_CONFIG_DATABASE_CONNECTION": "postgresql://localhost/galaxy"
+            }
+        },
+        {
+            "name": "Tool test framework",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/.venv/bin/pytest",
+            "args": [
+                "test/functional/test_toolbox_pytest.py",
+                "-m",
+                "tool",
+                "-k",
+                "job_properties_test_2"
+            ]
+        },
+        {
+            "type": "node",
+            "name": "debug selected jest unit test",
+            "request": "launch",
+            "program": "${workspaceFolder}/client/node_modules/jest/bin/jest",
+            "args": [
+                "--runInBand",
+                "--config",
+                "${workspaceFolder}/client/tests/jest/jest.config.js",
+                "${file}"
+            ],
+            "cwd": "${workspaceFolder}/client",
+            "console": "integratedTerminal",
+            "disableOptimisticBPs": true
+        }
+    ]
+}

.vscode/settings_gitpod.json

+{
+    "python.testing.pytestArgs": [
+        "--doctest-modules",
+        "lib/galaxy_test/api/",
+        "lib/galaxy/datatypes",
+        "test/unit",
+        "test/integration",
+        "lib/galaxy_test/selenium/"
+    ],
+    "python.testing.pytestEnabled": true,
+    "python.envFile": "${workspaceFolder}/.vscode/.test.env"
+}
+

.vscode/shed.code-snippets

+{
+    "shedcomp": {
+        "prefix": "shed_component",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "\t$0",
+            "</script>",
+            "<template>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed component"
+    },
+    "shedpage": {
+        "prefix": "shed_page",
+        "body": [
+            "<script setup lang=\"ts\">",
+            "import PageContainer from \"@/components/PageContainer.vue\"",
+            "</script>",
+            "<template>",
+            "    <page-container>",
+            "        $0",
+            "    </page-container>",
+            "</template>"
+        ],
+       "description": "outline of a tool shed page"
+    },
+    "shedfetcher": {
+        "prefix": "shed_fetcher",
+        "body": [
+            "import { fetcher } from \"@/schema\"",
+            "const fetcher = fetcher.path(\"$1\").method(\"get\").create()"
+        ],
+        "description": "Import shed fetcher and instantiate with a path"
+    },
+    "shedrouter": {
+        "prefix": "shed_router",
+        "body": [
+            "import router from \"@/router\""
+        ]
+    }
+}
\ No newline at end of file

CITATION

+If you use or extend Galaxy in your published work, please cite this
+publication:
+
+- The Galaxy Community. "The Galaxy platform for accessible, reproducible, and
+  collaborative data analyses: 2024 update"
+  Nucleic Acids Res. (2024) 52(W1):W83-W94 doi:10.1093/nar/gkae410
+
+BibTeX format:
+
+@article{10.1093/nar/gkae410,
+  title = {The {Galaxy} platform for accessible, reproducible, and collaborative data analyses: 2024 update},
+  author = {The Galaxy Community},
+  journal = {Nucleic Acids Res.},
+  doi = {10.1093/nar/gkae410},
+  volume = {52},
+  number = {W1},
+  pages = {W83-W94},
+  year = {2024},
+  url = {https://doi.org/10.1093/nar/gkae410},
+  publisher = {Oxford University Press}
+}
+
+
+More publications
+-----------------
+
+To cite specific Galaxy components/features or other Galaxy project
+publications, see
+
+https://galaxyproject.org/citing-galaxy

CODE_OF_CONDUCT.md

+# Galaxy Project Code of Conduct
+
+This project is committed to providing a welcoming and harassment-free
+experience for everyone. We therefore expect participants to abide by our Code
+of Conduct, which can be found at:
+
+https://galaxyproject.org/community/coc/

CONTRIBUTING.md

+# Contributing
+
+Galaxy welcomes new development!  This document briefly describes how to
+contribute to the [core galaxy repository](https://github.com/galaxyproject/galaxy).
+For general information on the Galaxy ecosystem, please see the
+[Galaxy Community Hub](https://galaxyproject.org).
+For a description of how the Galaxy code is structured, see the
+[Galaxy Code Architecture slides](https://training.galaxyproject.org/training-material/topics/dev/tutorials/architecture/slides.html)
+that are part of the [Galaxy Training Materials](https://training.galaxyproject.org/).
+
+## Before you Begin
+
+If you have an idea for a feature to add or an approach for a bugfix, it is
+best to communicate with Galaxy developers early. The primary venue for this is
+the [GitHub issue tracker](https://github.com/galaxyproject/galaxy/issues).
+Browse through existing GitHub issues and if one seems related, comment on it.
+For more direct communication, Galaxy developers are generally available on
+the [Galaxy Matrix space](https://matrix.to/#/#galaxyproject:matrix.org), in
+particular on the [galaxyprojec/dev channel](https://matrix.to/#/#galaxyproject_dev:gitter.im)
+and in the various [Working Group](https://galaxyproject.org/community/wg/)
+channels.
+
+If you're looking to help but aren't sure where to start, we also maintain a
+[tag](https://github.com/galaxyproject/galaxy/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22)
+on GitHub for smaller issues we believe would make the best entry points for
+new developers.
+
+## Reporting a new issue
+
+If no existing Galaxy issue seems appropriate, a new issue can be opened using
+[this form](https://github.com/galaxyproject/galaxy/issues/new).
+
+## How to Contribute
+
+All changes to the [core galaxy
+repository](https://github.com/galaxyproject/galaxy) should be made through pull
+requests (with just two exceptions outlined below).
+
+If you are new to Git, the Software Carpentry's [Version Control with
+Git](https://swcarpentry.github.io/git-novice/) tutorial is a good place to
+start.  More learning resources are listed at
+https://help.github.com/en/github/getting-started-with-github/git-and-github-learning-resources
+
+1. Make sure you have a free [GitHub](https://github.com/) account. To increase
+   the security of your account, we strongly recommend that you configure
+   [two-factor authentication](https://docs.github.com/en/github/authenticating-to-github/securing-your-account-with-two-factor-authentication-2fa).
+   Additionally, you may want to [sign your commits](https://docs.github.com/en/github/authenticating-to-github/managing-commit-signature-verification).
+
+2. Fork the [galaxy repository](https://github.com/galaxyproject/galaxy) on
+   GitHub to make your changes.  To keep your copy up to date with respect to
+   the main repository, you need to frequently [sync your
+   fork](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/syncing-a-fork):
+
+   ```
+   $ git remote add upstream https://github.com/galaxyproject/galaxy
+   $ git fetch upstream
+   $ git checkout dev
+   $ git merge upstream/dev
+   ```
+
+3. Choose the correct branch to develop your changes against.
+
+   * The `master` branch is kept in sync with the latest tagged release, but
+     should **not** be used as the base (i.e. target) branch of a pull request.
+
+   * Additions of new features to the codebase should be based off the `dev`
+     branch (`git checkout -b feature_branch dev`), with few
+     [exceptions](doc/source/project/organization.rst#handling-pull-requests).
+
+   * Most bug fixes should target the oldest supported release exhibiting the
+     issue (`git checkout -b bugfix_branch release_XX.XX`).
+
+   * Serious security problems should not be fixed via pull request - please see
+     [the Galaxy security policies](SECURITY.md) for information about
+     responsibly disclosing security issues.
+
+4. If your changes modify code please ensure the resulting files conform to
+   the [style guidelines](#style-guidelines) below.
+
+   If you are working on the Galaxy user interface (i.e. JavaScript,
+   styles, etc.), see more information in the [client README](client/README.md).
+
+5. Galaxy contains hundreds of tests of different types and complexity and
+   running each is difficult and probably not reasonable on your workstation. So
+   please review the [running tests documentation](test/TESTING.md) and run any
+   that seem relevant.
+
+   If possible, also try to add new tests for the features added or bugs fixed
+   by your pull request.
+
+   Developers reviewing your pull request will be happy to help you add or run
+   the relevant tests as part of the pull request review process.
+
+6. Write a useful and properly formatted commit message.
+   Follow [these guidelines and template](https://git-scm.com/book/en/v2/Distributed-Git-Contributing-to-a-Project#_commit_guidelines),
+   in particular start your message with a short imperative sentence on a single
+   line, possibly followed by a blank line and a more detailed explanation.
+
+   In the detailed explanation it's good to include relevant references (e.g.
+   any GitHub issue being fixed) using full URLs, and errors or tracebacks the
+   commit is meant to fix.
+   You can use the Markdown syntax for lists and code highlighting, wrapping the
+   explanation text at 72 characters when possible.
+
+   Example of a good commit message: https://github.com/galaxyproject/galaxy/commit/0429c4d515536f9cca6b70b2abeb019de807c955
+
+7. Commit and push your changes to your
+   [fork](https://help.github.com/en/github/using-git/pushing-commits-to-a-remote-repository).
+
+8. Open a [pull
+   request](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request)
+   with these changes. Your pull request message ideally should include:
+
+   * Why you made the changes (e.g. references to GitHub issues being fixed).
+
+   * A description of the implementation of the changes.
+
+   * How to test the changes, if you haven't included specific tests already.
+
+9. The pull request should pass all the continuous integration tests which are
+   automatically started by GitHub.
+
+10. Your pull request will be handled according to [some
+    rules](doc/source/project/organization.rst#handling-pull-requests).
+
+11. If, before your pull request is merged, conflicts arise between your branch
+    and the target branch (because other commits were pushed to the target
+    branch), you need to either:
+
+    1) [rebase your branch](https://git-scm.com/docs/git-rebase) on top of the
+       target branch, or
+    2) merge the target branch into your branch.
+
+    We recommend the first approach (i.e. rebasing) because it produces cleaner
+    git histories, which are easier to bisect. If your branch is called
+    `feature_branch` and your target branch is `dev`, you can rebase your branch
+    with the following commands:
+
+    ```
+    $ git checkout feature_branch
+    $ git pull
+    $ git fetch upstream
+    $ git rebase upstream/dev
+    ```
+
+    Once you have resolved the conflicts in all commits of your branch, you can
+    force-push the rebased branch to update the pull request:
+
+    ```
+    $ git push --force
+    ```
+
+## Style guidelines
+
+### Python
+
+- Galaxy follows [PEP-8](https://www.python.org/dev/peps/pep-0008/), with
+  particular emphasis on readability being the ultimate goal:
+  - 4 spaces (not tabs!) per indentation level
+  - divergences from PEP-8 are listed in the `[flake8]` section of the `.flake8`
+    file and in the `[tool.ruff]` section of the `pyproject.toml` file.
+  - The Python code base is automatically formatted using
+    [isort](https://pycqa.github.io/isort/) (for imports) and
+    [black](https://black.readthedocs.io). To easily format your Python code
+    before submitting your contribution, please either use `make diff-format`
+    or run `isort FILE; black FILE` for each FILE you modify.
+- Python [docstrings](http://www.python.org/dev/peps/pep-0257/) need to be in
+  [reStructured Text (RST)](https://docutils.sourceforge.io/rst.html) format and
+  compatible with [Sphinx](https://www.sphinx-doc.org).
+- String formatting should normally be done using
+  [formatted string literals (f-strings)](https://docs.python.org/3/tutorial/inputoutput.html#formatted-string-literals),
+  except:
+  - when the format string is kept in a separate variable, in which case the
+    [string ``format()`` method](https://docs.python.org/3/tutorial/inputoutput.html#the-string-format-method)
+    should be used;
+  - when [formatting a log message](https://docs.python.org/3/library/logging.html#logging.Logger.debug),
+    in which case it's better to use a
+    [`printf`-style](https://docs.python.org/3/library/stdtypes.html#old-string-formatting)
+    message format string and pass its arguments to the logging method
+    separately. This is a bit more efficient than using f-strings and allows for
+    better log aggregation. For more information, see this
+    [blog post](https://dev.to/izabelakowal/what-is-the-best-string-formatting-technique-for-logging-in-python-d1d).
+
+## Documentation
+
+General documentation (e.g. admin, development, release notes) is found in the
+``doc/source/`` directory.
+The documentation source files need to be written in one of these markup
+languages:
+- [reStructuredText](https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html)
+  (with Sphinx extensions)
+- [Markdown](https://myst-parser.readthedocs.io/en/latest/syntax/typography.html)
+  (with MyST-Parser extensions).
+These source files are then built into HTML documentation with
+[Sphinx](https://www.sphinx-doc.org/) by running ``make docs`` and published on
+the [Galaxy Documentation website](https://docs.galaxyproject.org/).
+
+## A Quick Note about Tools
+
+For the most part, Galaxy tools should be published to a [Tool
+Shed](https://galaxyproject.org/toolshed) and not in this repository directly.
+More information about tool development can be found [on the community
+hub](https://galaxyproject.org/develop).

CONTRIBUTORS.md

+# Contributors
+
+The following individuals have contributed code to Galaxy:
+
+* Enis Afgan <afgane@gmail.com>
+* Istvan Albert <istvan.albert@gmail.com>
+* Renato Alves <alves.rjc@gmail.com> <rjalves@igc.gulbenkian.pt>
+* Guruprasad Ananda <gua110@bx.psu.edu>
+* Evgeny Anatskiy <evgeny.anatskiy@gmail.com>
+* Florent Angly <florent.angly@gmail.com>
+* Patrick Austin <patrick.austin@stfc.ac.uk>
+* Raj Ayyampalayam <raj76@uga.edu>
+* Abdulrahman Azab <eng.azab@gmail.com>
+* Finn Bacall <finn.bacall@manchester.ac.uk>
+* Dannon Baker <dannon.baker@gmail.com>
+* balto <balto_59@hotmail.fr>
+* Christopher Bare <christopherbare@gmail.com>
+* Bérénice Batut <berenice.batut@gmail.com>
+* Marius van den Beek <m.vandenbeek@gmail.com>
+* Maria Bernard <maria.bernard@jouy.inra.fr>
+* Jean-Frédéric Berthelot <jean-frederic.berthelot@lifl.fr>
+* Léo Biscassi <leo.biscassi@gmail.com>
+* Dan Blanchard <dan.blanchard@gmail.com>
+* Clemens Blank <blankclemens@gmail.com>
+* Daniel Blankenberg <dan.blankenberg@gmail.com> <dan@bx.psu.edu>
+* Jorrit Boekel <jorrit.boekel@scilifelab.se>
+* James Boocock <sfk2001@gmail.com>
+* Carlos Borroto <carlos.borroto@gmail.com>
+* Daniel Bouchard <dbouchard@corefacility.ca> <daniel.bouchard@phac-aspc.gc.ca>
+* Dave Bouvier <dave@bx.psu.edu>
+* Adam Brenner <aebrenne@uci.edu>
+* Anthony Bretaudeau <anthony.bretaudeau@rennes.inra.fr> <abretaud@irisa.fr>
+* Christian Y. Brenninkmeijer <christian.brenninkmeijer@manchester.ac.uk>
+* Freek de Bruijn <freek.de.bruijn@nbic.nl>
+* Richard Burhans <burhans@bx.psu.edu>
+* Jennifer Cabral <jencabral@gmail.com>
+* Martin Čech <marten@bx.psu.edu>
+* Eli Chadwick <eli.chadwick@manchester.ac.uk>
+* Ramkrishna Chakrabarty <rc@bx.psu.edu>
+* Matt Chambers <matt.chambers42@gmail.com>
+* Brad Chapman <chapmanb@50mail.com>
+* John Chilton <jmchilton@gmail.com>
+* Saket Choudhary <saketkc@gmail.com>
+* Wen-Yu Chung <wychung@bx.psu.edu>
+* Dave Clements <clements@galaxyproject.org>
+* Peter Cock <p.j.a.cock@googlemail.com> <peter.cock@hutton.ac.uk>
+* Ira Cooke <iracooke@gmail.com>
+* Nate Coraor <nate@bx.psu.edu>
+* Michael Cotterell <mepcotterell@gmail.com>
+* Michael R. Crusoe <crusoe@ucdavis.edu>
+* Gianmauro Cuccuru <gmauro@crs4.it>
+* Frederik Delaere <frederik.delaere@gmail.com>
+* Matthias Desmet <matthias.desmet@ugent.be>
+* Matthew Ryan Dillon <matthewrdillon@gmail.com>
+* Olivia Doppelt <olivia.doppelt@pasteur.fr>
+* Shane Dowling <shane@shanedowling.com>
+* John Duddy <jduddy@illumina.com>
+* Carl Eberhard <carlfeberhard@gmail.com>
+* Ignacio Eguinoa <ignacio.eguinoa@gmail.com>
+* Mark Einon <mark.einon@gmail.com>
+* Kyle Ellrott <kellrott@gmail.com> <kellrott@soe.ucsc.edu>
+* Eric Enns <eric.enns@gmail.com>
+* fescudie <fescudie@toulouse.inra.fr>
+* Anne Fouilloux <annefou@uio.no>
+* Dorine Francheteau <dorine@bx.psu.edu>
+* Jean-Frédéric (@JeanFred on Github)
+* Maximilian Friedersdorff <max@friedersdorff.com>
+* Jaime Frey <jfrey@cs.wisc.edu>
+* Ben Fulton <benmarkfulton@gmail.com>
+* Carrie Ganote <cganote@iu.edu>
+* Ryan Golhar <ngsbioinformatics@gmail.com>
+* Jeremy Goecks <jeremy.goecks@moffitt.org>
+* Nuwan Goonasekera <nuwan.goonasekera@gmail.com>
+* Björn Grüning <bjoern.gruening@gmail.com> <bjoern@gruenings.eu>
+* Aysam Guerler <aysam.guerler@gmail.com>
+* Simon Guest <simon.guest@agresearch.co.nz>
+* Nalin Gupta <nalin.gupta@stfc.ac.uk>
+* Jianbin He <jbhe@bx.psu.edu>
+* Peter van Heusden <pvh@sanbi.ac.za>
+* Morita Hideyuki <h-morita@esm.co.jp>
+* Saskia Hiltemann <zazkia@gmail.com>
+* Rob Hooft <rob.hooft@nbic.nl>
+* Y. Hoogstrate <y.hoogstrate@erasmusmc.nl>
+* Hans-Rudolf Hotz <hrhotz@gmail.com>
+* Jian-Long Huang <jlh@pyhub.org>
+* Gert Hulselmans <gert.hulselmans@med.kuleuven.be>
+* Manabu Ishii <manabu.ishii.rb@gmail.com>
+* Jennifer Jackson <jen@bx.psu.edu>
+* Joachim Jacob <joachim.jacob@gmail.com>
+* Xiaoqian Jiang <jxq198409@hotmail.com>
+* Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
+* Kaivan Kamali <kxk302@gmail.com>
+* Radhesh Kamath <radhesh@bx.psu.edu>
+* Iyad Kandalaft <ik@iyadk.com>
+* Jan Kanis <jan.code@jankanis.nl>
+* David King <dcking@bx.psu.edu>
+* Rory Kirchner <roryk@mit.edu>
+* Edward Kirton <eskirton@lbl.gov>
+* Jasper Koehorst <jasperkoehorst@gmail.com>
+* Anup Kumar <anup.rulez@gmail.com>
+* Brad Langhorst <langhorst@neb.com>
+* Delphine Lariviere <lariviere.delphine@gmail.com>
+* Ross Lazarus <ross.lazarus@gmail.com> <rossl@bx.psu.edu>
+* Yvan Le Bras <yvan.le_bras@irisa.fr>
+* Gildas Le Corguillé @lecorguille
+* Alexander Lenail <alexander.lenail@tufts.edu>
+* Simone Leo <simone.leo@gmail.com>
+* Kanwei Li <kanwei@gmail.com>
+* Michael Li <michael.li@uwaterloo.ca>
+* Pierre Lindenbaum <plindenbaum@yahoo.fr>
+* Mikael Loaec <mikael.loaec@versailles.inra.fr>
+* Thoba Lose <lose.thoba@gmail.com>
+* Philip Mabon <philipmabon@gmail.com>
+* Remi Marenco <remi.marenco@gmail.com> <remimarenco@gmail.com>
+* Zipho Mashologu <zipho@trustpay.biz>
+* Thomas McGowan <mcgo0092@msi.umn.edu>
+* Scott McManus <scottmcmanus@emory.edu> <scottmcmanus@gatech.edu>
+* Hervé Ménager <herve.menager@pasteur.fr>
+* Pablo Moreno <pablo.a.moreno@gmail.com>
+* Hunter Moseley <hunter.moseley@louisville.edu>
+* Takao Nakaguchi <takao.nakaguchi@gmail.com>
+* Arjun Nath <arjun@bx.psu.edu>
+* Anton Nekrutenko <anton@bx.psu.edu> <anton@nekrut.org>
+* Eric Paniagua <paniagua.cshl@gmail.com>
+* Richard Park <rpark@bu.edu>
+* Lance Parsons <lparsons@princeton.edu>
+* Balthazar Pavot <balthazar.pavot@hotmail.fr>
+* Chinmay Rao <chinmay@bx.psu.edu>
+* Matt Ralston <mrals89@gmail.com>
+* ramezrawas <ramezrawas@gmail.com>
+* Helena Rasche <helena.rasche@gmail.com>
+* Athos Ribeiro <athoscr@fedoraproject.org>
+* Andrew Robinson <Andrew.Robinson@latrobe.edu.au>
+* Devon Ryan <dpryan79@gmail.com>
+* Michael Sauria <crockopotamus@gmail.com>
+* Andrea Sbardellati <andrea.sbardellati@crs4.it>
+* Ian Schenck <ian@bx.psu.edu>
+* Jelle Scholtalbers <j.scholtalbers@gmail.com>
+* Nick Semenkovich <semenko@alum.mit.edu>
+* Varun Shankar <varunshankar55@gmail.com>
+* Matthew Shirley <mdshw5@gmail.com>
+* Timur Shtatland <shtatland@neb.com>
+* Sourav Singh <ssouravsingh12@gmail.com>
+* Clare Sloggett <sloc@unimelb.edu.au>
+* Eteri Sokhoyan @Sokhoyan
+* Nicola Soranzo <nicola.soranzo@earlham.ac.uk> <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
+* Nick Stoler <nick@nstoler.com>
+* Roy Storey <kiwiroy@gmail.com>
+* Hanfei Sun <ad9075@gmail.com>
+* Ilya Sytchev <hackdna@gmail.com>
+* Scott Szakonyi <sszakony@nd.edu>
+* James Taylor <james@jamestaylor.org>
+* Tomithy Too <tomithy.too@gmail.com>
+* David Trudgian <dave@trudgian.net> <david.trudgian@utsouthwestern.edu>
+* Nitesh Turaga <nitesh.turaga@gmail.com>
+* Clayton Turner <clayclay911@gmail.com>
+* Jesse c j van Dam <jesse.vandam@wur.nl>
+* Ashok Varadharajan <ashvark@gmail.com>
+* Marek Vavruša <marek@vavrusa.com>
+* Martijn Vermaat <m.vermaat.hg@lumc.nl>
+* Kelly Vincent <kpvincent@bx.psu.edu>
+* Jeremy Volkening <jdv@base2bio.com>
+* Greg Von Kuster <greg@bx.psu.edu>
+* Pavan Videm <videmp@informatik.uni-freiburg.de>
+* Hiral Vora <hvora1@uncc.edu>
+* Junzhou Wang <junzhouwang@gmail.com>
+* Andrew Warren <anwarren@vbi.vt.edu>
+* Trevor Wennblom <trevor@well.com>
+* Joachim Wolff <wolffj@informatik.uni-freiburg.de>
+* Thomas Wollmann <thomas.s.wollmann@gmail.com> <thomas.wollmann@bioquant.uni-heidelberg.de>
+* Jay Young <xiaojay@gmail.com>
+* Yi Zhang <yizhang@bx.psu.edu>
+
+# Institutional sponsors
+
+Galaxy development began at The Pennsylvania State University in 2006.
+In 2009 all contributions to that point were licensed by The
+Pennsylvania State University under the terms of the Academic Free
+License 3.0 (see LICENSE.txt). This license applies to all subsequent
+contributions - including but not limited to development at The
+Pennsylvania State University, Emory University, Johns Hopkins
+University, and George Washington University as part of the following
+NIH and NSF grants:
+
+* NSF DBI 0543285, “Tailoring genomic data to the needs of experimental
+  biologists and educators”
+* NIH R21 HG005133, “A turnkey solution for next generation sequence
+  data analysis”
+* NIH R01 HG004909, “An efficient lightweight environment for biomedical
+  computation”
+* NSF DBI 0850103, “Cyberinfrastructure for accessible and reproducible
+  research in life sciences”
+* NIH RC2 HG005542, “Dynamically scalable accessible analysis for next
+  generation sequence data”
+* NIH U41 HG006620, “Democratization of data analysis in life sciences
+  through Galaxy”

LICENSE.txt

+Copyright (c) 2005-2026 Galaxy Contributors (see CONTRIBUTORS.md)
+
+Galaxy is provided from 2026-02-25 onwards entirely under the MIT License.
+
+Some icons found in Galaxy are from the Silk Icons set, available under
+the Creative Commons Attribution 2.5 License, from:
+
+http://www.famfamfam.com/lab/icons/silk/
+
+
+Other images and documentation are licensed under the Creative Commons
+Attribution 3.0 (CC BY 3.0) License. See:
+
+http://creativecommons.org/licenses/by/3.0/
+
+
+--------------------------------------------------------------------------------
+
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

+.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
+   :alt: Galaxy Logo
+
+The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
+
+Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
+
+.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
+    :target: https://gitter.im/galaxyproject/Lobby
+    :alt: Chat on gitter
+
+.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
+    :target: https://webchat.freenode.net/?channels=galaxyproject
+    :alt: Chat on irc
+
+.. image:: https://img.shields.io/badge/release-documentation-blue.svg
+    :target: https://docs.galaxyproject.org/en/master/
+    :alt: Release Documentation
+
+.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
+    :target: https://travis-ci.org/galaxyproject/galaxy
+    :alt: Inspect the test results
+
+Galaxy Quickstart
+=================
+
+Galaxy requires Python 3.10 or higher. To check your Python version, run:
+
+.. code:: console
+
+    $ python -V
+    Python 3.10.12
+
+Start Galaxy:
+
+.. code:: console
+
+    $ sh run.sh
+
+Once Galaxy completes startup, you should be able to view Galaxy in your
+browser at: http://localhost:8080
+
+For more installation details please see: https://getgalaxy.org/
+
+Documentation is available at: https://docs.galaxyproject.org/
+
+Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
+
+Tools
+=====
+
+Tools can be either installed from the Tool Shed or added manually.
+For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
+Note that not all dependencies for the tools provided in the
+``tool_conf.xml.sample`` are included. To install them please visit
+"Manage dependencies" in the admin interface.
+
+Issues and Galaxy Development
+=============================
+
+Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .

README.rst

+.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
+   :alt: Galaxy Logo
+
+The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
+
+Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
+
+.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
+    :target: https://gitter.im/galaxyproject/Lobby
+    :alt: Chat on gitter
+
+.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
+    :target: https://webchat.freenode.net/?channels=galaxyproject
+    :alt: Chat on irc
+
+.. image:: https://img.shields.io/badge/release-documentation-blue.svg
+    :target: https://docs.galaxyproject.org/en/master/
+    :alt: Release Documentation
+
+.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
+    :target: https://travis-ci.org/galaxyproject/galaxy
+    :alt: Inspect the test results
+
+Galaxy Quickstart
+=================
+
+Galaxy requires Python 3.10 or higher. To check your Python version, run:
+
+.. code:: console
+
+    $ python -V
+    Python 3.10.12
+
+Start Galaxy:
+
+.. code:: console
+
+    $ sh run.sh
+
+Once Galaxy completes startup, you should be able to view Galaxy in your
+browser at: http://localhost:8080
+
+For more installation details please see: https://getgalaxy.org/
+
+Documentation is available at: https://docs.galaxyproject.org/
+
+Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
+
+Tools
+=====
+
+Tools can be either installed from the Tool Shed or added manually.
+For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
+Note that not all dependencies for the tools provided in the
+``tool_conf.xml.sample`` are included. To install them please visit
+"Manage dependencies" in the admin interface.
+
+Issues and Galaxy Development
+=============================
+
+Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .

SECURITY.md

+# Security
+
+The Galaxy project is strongly committed to security and responsible disclosure. We have adopted and published a set of policies specifying how we will act in response to reported security issues, in order to ensure timely updates are made available to all affected parties.
+
+## Reporting Security Issues
+
+If you believe you have discovered a security issue, please email [galaxy-committers@lists.galaxyproject.org](galaxy-committers@lists.galaxyproject.org). Please use `[SECURITY]` in the email title. Alternatively you can report a security vulnerability using GitHub [private reporting](https://github.com/galaxyproject/galaxy/security/advisories/new). In either case one of the maintainers will acknowledge your report within 2 US business days.
+
+We ask that you not disclose the issues publicly. We will provide you credit for the discovery when publicly disclosing the issue.
+
+Security issues which *only* affect a pre-release version of Galaxy (i.e. the `dev` branch in GitHub) do not need to go through this process, so you may open issues and pull requests publicly.
+
+## Supported versions
+
+The following branches or releases receive security support:
+
+- Development on the `dev` branch, hosted on GitHub, which will become the next release of Galaxy
+- Releases within the past 12 months.
+  - E.g. 24.0 will receive support for a full year, at which point 25.0 will be available.
+
+For unsupported branches:
+
+- Older versions of Galaxy may be affected by security issues.
+- Security patches *may* apply
+- The security team does not commit to investigating issues that pertain to unsupported releases.
+- The security team does not commit to issuing patches or new releases of unsupported versions.
+
+## Issue Severity
+
+Galaxy takes a very conservative stance on issue severity as individual Galaxy instances often install tools and make customizations that might increase their risk in the face of otherwise less-serious vulnerabilities. As a result, issues that would be considered less-severe in other projects may be treated as higher risk here.
+
+### Issue Classification
+
+Severity     | Examples
+------------ | ---------
+High         | Remote code execution (RCE), SQL Injection, Cross-site scripting (XSS), and *any issue allowing user impersonation*.
+Medium / Low | Unvalidated redirects/forwards, Issues due to uncommon configuration options.
+
+These are only examples. The security team will provide a severity classification based on its impact on the average Galaxy instance. However, Galaxy administrators should take it upon themselves to evaluate the impact for their instance(s).
+
+## Notification of Vulnerabilities
+
+For high severity issues, we will notify [the list of public Galaxy owners](https://lists.galaxyproject.org/lists/galaxy-public-servers.lists.galaxyproject.org/) with:
+
+- A description of the issue
+- List of supported versions that are affected
+- Steps to update or patch your Galaxy
+
+The issue will then be embargoed for three (3) days. For medium and low
+severity issues, or for publicly announcing high severity issues after the
+embargo, we will:
+
+- Patch the oldest release within the 12 month support window, and merge that fix forward.
+  - Updates will be available on the `release_XX.YY` branches.
+- Update each release branch
+- Publish a repository security advisory on GitHub containing:
+  - A description of the issue
+  - List of supported versions that are affected
+  - Steps to update or patch your Galaxy
+  - A CVE identifier (if applicable)
+
+If an issue is deemed to be time-sensitive – e.g. due to active and ongoing exploits in the wild – the embargo may be shortened considerably.
+
+If we believe that the reported issue affects other Galaxy Project components or projects outside of the Galaxy ecosystem, we may discuss the issue with those projects and coordinate disclosure and resolution with them.

check_model.sh

+#!/bin/sh
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+setup_python
+
+python ./scripts/check_model.py "$@"
+
+[ $? -ne 0 ] && exit 1;
+exit 0;

client-api/.npmignore

+# Development files
+node_modules/
+coverage/
+.vscode/
+.idea/
+.git/
+.github/
+.DS_Store
+
+# Source and test files (only dist is published)
+src/examples/
+src/**/*.test.ts
+vitest.config.ts
+tsconfig.json
+tsconfig.*.json
+tsup.config.ts
+
+# CI/CD
+*.yml
+*.yaml
+
+# Logs
+*.log
+npm-debug.log*
+pnpm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Lock files
+package-lock.json
+pnpm-lock.yaml
+yarn.lock
+
+# Not ignoring src directory since we're including it for source maps and debugging
\ No newline at end of file

client-api/src/api

+../../client/src/api
\ No newline at end of file