Merge branch 'dev' of https://github.com/galaxyproject/galaxy into jupytool

.ci/autopep8.sh

@@ -1,2 +1,2 @@
-exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -s -d ',' - )
+exclude=$(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_ignorelist.txt | paste -s -d ',' - )
 autopep8 -i -r --exclude $exclude --select E11,E101,E127,E201,E202,E22,E301,E302,E303,E304,E306,E711,W291,W292,W293,W391 ./lib/ ./test/

.ci/first_startup.sh

@@ -1,16 +1,45 @@
 #!/bin/sh
+case "$1" in
+    galaxy|"")
+        SCRIPT=./run.sh
+        PORT=8080
+        LOGFILE=galaxy.log
+        GRAVITY_LOGFILE=database/gravity/log/gunicorn.log
+        SUPERVISORD_LOGFILE=database/gravity/supervisor/supervisord.log
+        ;;
+    reports)
+        SCRIPT=./run_reports.sh
+        PORT=9001
+        LOGFILE=reports_webapp.log
+        ;;
+    *)
+        echo "ERROR: Unrecognized app"
+        exit 1
+        ;;
+esac
 TRIES=120
-URL=http://localhost:8080
+URL=http://localhost:$PORT
 EXIT_CODE=1
 i=0
 echo "Testing for correct startup:"
-bash run.sh --daemon && \
+$SCRIPT --daemon && \
     while [ "$i" -le $TRIES ]; do
-        curl "$URL" && EXIT_CODE=0 && break
+        curl --max-time 1 "$URL" && EXIT_CODE=0 && break
         sleep 1
         i=$((i + 1))
     done
-kill -9 "$(cat galaxy.pid)"
+$SCRIPT --skip-wheels --stop-daemon
 echo "exit code:$EXIT_CODE, showing startup log:"
-cat galaxy.log
+if [ -f "$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_blacklist.txt

@@ -1,19 +0,0 @@
-.git
-.tox
-.venv
-.venv3
-packages/*/.venv
-packages/*/build
-packages/*/dist
-packages/venv
-node_modules
-database
-doc/build
-doc/source/conf.py
-eggs
-lib/galaxy/util/jstree.py
-lib/galaxy/web/proxy/js/node_modules
-static/maps
-static/scripts
-build
-dist

.ci/flake8_ignorelist.txt

@@ -0,0 +1,20 @@
+.git
+.tox
+.venv
+.venv3
+packages/*/.venv
+packages/*/build
+packages/*/dist
+packages/venv
+node_modules
+database
+doc/build
+doc/source/conf.py
+eggs
+lib/galaxy/util/jstree.py
+lib/galaxy/web/proxy/js/node_modules
+static/maps
+static/scripts
+test/functional/tools/cwl_tools/v1.?/
+build
+dist

.ci/flake8_wrapper.sh

@@ -2,7 +2,7 @@
 
 set -e
 
-flake8 --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
+flake8 --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore=D --max-line-length=150 lib/galaxy/jobs/runners/util/
+flake8 --ignore=E203,D --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/flake8_wrapper_docstrings.sh

@@ -17,5 +17,5 @@ if [ "$1" = "--include" ];
 then
     flake8 $args $(paste -sd' ' .ci/flake8_docstrings_include_list.txt)
 else
-    flake8 $args --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
+    flake8 $args --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
 fi

.ci/jenkins/api-py3

@@ -1 +0,0 @@
-api

.ci/jenkins/api/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --db postgres --clean_pyc --skip_flakey_fails -api "$@"

.ci/jenkins/framework-py3

@@ -1 +0,0 @@
-framework

.ci/jenkins/framework/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --db postgres --clean_pyc --framework "$@"

.ci/jenkins/integration-py3

@@ -1 +0,0 @@
-integration

.ci/jenkins/integration/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --db postgres --clean_pyc --integration "$@"

.ci/jenkins/main-tools-py3

@@ -1 +0,0 @@
-main-tools

.ci/jenkins/main-tools/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --db postgres --clean_pyc -main "$@"

.ci/jenkins/selenium-compose/Dockerfile

@@ -1,24 +0,0 @@
-FROM toolshed/requirements
-LABEL maintainer="John Chilton <jmchilton@gmail.com>"
-
-RUN apt-get -qq update && \
-    apt-get install --no-install-recommends -y postgresql-client python-pip libffi-dev python-cffi && \
-    apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-
-ENV GALAXY_ROOT=/galaxy \
-    GALAXY_CONFIG_OVERRIDE_ADMIN_USERS=admin@galaxy.org,test@bx.psu.edu \
-    GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DATASET_PURGE=true \
-    GALAXY_CONFIG_OVERRIDE_ALLOW_LIBRARY_PATH_PASTE=true \
-    GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_WORKFLOW_MODULES=true \
-    GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DELETION=true \
-    GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres@postgres/galaxy \
-    GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53 \
-    GALAXY_CONFIG_OVERRIDE_JOB_CONFIG_FILE=/galaxy/config/job_conf.xml.sample_basic \
-    GALAXY_CONFIG_OVERRIDE_DATATYPES_CONFIG_FILE=/galaxy/test/functional/tools/sample_datatypes_conf.xml \
-    GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE=/galaxy/test/functional/tools/samples_tool_conf.xml \
-    GALAXY_CONFIG_FILE=/galaxy/.ci/jenkins/selenium/galaxy.ini \
-    GALAXY_VIRTUAL_ENV=/galaxy_env
-
-ADD run_galaxy.bash /run_galaxy.bash
-EXPOSE 8080
-CMD /run_galaxy.bash

.ci/jenkins/selenium-compose/docker-compose.yml

@@ -1,21 +0,0 @@
-version: '2'
-services:
-  postgres:
-    image: postgres
-  galaxy:
-    build: .
-    image: ubuntu
-    volumes:
-      - "${TARGET_ROOT}:${TARGET_PATH}"
-    links:
-      - postgres
-    ports:
-      - "${GALAXY_PORT}:8080"
-    environment:
-      GALAXY_TEST_UID: "${MY_UID}"
-  selenium:
-    image: selenium/standalone-chrome:3.5.2
-    ports:
-      - "${SELENIUM_PORT}:4444"
-    links:
-      - galaxy

.ci/jenkins/selenium-compose/galaxy.ini

@@ -1,17 +0,0 @@
-[server:main]
-
-use = egg:Paste#http
-port = 8080
-host = 0.0.0.0
-use_threadpool = True
-threadpool_kill_thread_limit = 10800
-
-[filter:proxy-prefix]
-use = egg:PasteDeploy#prefix
-prefix = /galaxypf
-
-[app:main]
-
-paste.app_factory = galaxy.web.buildapp:app_factory
-
-filter-with = proxy-prefix

.ci/jenkins/selenium-compose/run_galaxy.bash

@@ -1,39 +0,0 @@
-#!/bin/bash
-
-set -e
-
-# Same hacks to setup a Galaxy user as used in test/docker/base/run_test_wrapper.sh
-# We want to make sure Galaxy runs as the same user as the external user so the files have the correct permission.
-echo "Deleting galaxy user - it may not exist and this is fine."
-deluser galaxy | true
-
-: ${GALAXY_TEST_UID:-"1"}
-
-echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
-groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
-echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
-useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
-echo "Setting galaxy user password - the operation may fail."
-echo "galaxy:galaxy" | chpasswd | true
-
-virtualenv "$GALAXY_VIRTUAL_ENV"
-chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
-
-cd /galaxy
-sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
-
-echo "Waiting for postgres to become available"
-while ! nc -z postgres 5432;
-do
-    sleep 1
-    printf "."
-done
-
-echo "Creating postgres database for Galaxy"
-createdb -w -U postgres -h postgres galaxy
-
-echo "Starting and waiting for Galaxy daemon(s)"
-sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
-
-echo "Galaxy daemon ready, monitoring Galaxy logs"
-tail -f "$GALAXY_ROOT/main.log"

.ci/jenkins/selenium-compose/run_tests.sh

@@ -1,124 +0,0 @@
-#!/bin/bash
-
-TEST_DIRECTORY=`dirname $0`
-
-DEFAULT_COMPOSE_PROJECT_NAME=`basename $TEST_DIRECTORY`
-COMPOSE_PROJECT_NAME=${COMPOSE_PROJECT_NAME:-$DEFAULT_COMPOSE_PROJECT_NAME}
-# If in Jenkins environment, append ${BUILD_NUMBER} to project so builds don't interfer.
-if [ ! -z "$BUILD_NUMBER" ];
-then
-    COMPOSE_PROJECT_NAME="${COMPOSE_PROJECT_NAME}${BUILD_NUMBER}"
-fi
-export COMPOSE_PROJECT_NAME
-
-echo "Running Jenkins test from $TEST_DIRECTORY with compose project name $COMPOSE_PROJECT_NAME"
-
-find lib -iname '*pyc' -exec rm -rf {} \;
-find test -iname '*pyc' -exec rm -rf {} \;
-
-./scripts/common_startup.sh --dev-wheels
-
-. .venv/bin/activate
-
-pip install docker-compose
-
-# TODO: Let docker-compose pick these at random.
-export GALAXY_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
-export SELENIUM_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
-
-export TARGET_ROOT=`pwd`
-export TARGET_PATH=/galaxy
-export MY_UID=$(id -u)
-
-cd $TEST_DIRECTORY
-
-echo "Cleaning up previous executions if needed."
-docker-compose down | true
-docker-compose build galaxy
-docker-compose up -d
-
-function tear_down {
-    docker-compose down
-}
-
-trap tear_down EXIT
-
-for service_name in postgres galaxy selenium
-do
-    echo "Waiting on service ${service_name}"
-    while true
-    do
-        if docker ps | grep -q "${COMPOSE_PROJECT_NAME}_${service_name}"
-        then
-            container_id=`docker ps | grep "${COMPOSE_PROJECT_NAME}_${service_name}" | cut -d " " -f 1`
-            eval "${service_name}_container_id=${container_id}"
-            echo "Service ${service_name} ready - with container ID ${container_id}"
-            break
-        fi
-        printf "."
-        sleep 1;
-    done
-done
-
-
-if [ "$1" = "--debug-running-containers" ];
-then
-    env
-    exit 0
-fi
-
-export GALAXY_TEST_EXTERNAL="http://localhost:$GALAXY_PORT/"
-
-echo "Waiting on docker-compose managed Galaxy server - $GALAXY_TEST_EXTERNAL."
-while ! curl -s "$GALAXY_TEST_EXTERNAL";
-do
-    for service_name in postgres galaxy selenium
-    do
-        if ! docker ps | grep -q "${COMPOSE_PROJECT_NAME}_${service_name}"
-        then
-            echo "Service ${service_name} stopped before Galaxy came up, exiting and halting containers."
-            for service_name in postgres galaxy selenium
-            do
-                container_id_var="${service_name}_container_id"
-                container_id="${!container_id_var}"
-                echo "Dumping logs for $service_name container (${container_id})..."
-                echo "---"
-                docker logs "${container_id}"
-                echo "---"
-            done
-            exit 1
-        fi
-    done
-
-    printf "."
-    sleep 4;
-done;
-
-# Access Selenium on localhost via port $SELENIUM_PORT
-export GALAXY_TEST_SELENIUM_REMOTE=1
-export GALAXY_TEST_SELENIUM_REMOTE_PORT="${SELENIUM_PORT}"
-
-# Retry all failed Selenium tests a second time to deal
-# with transiently failing tests. Failure information for
-# first tests is still populated in database/test_errors
-# and available at the top of the Jenkins test report.
-export GALAXY_TEST_SELENIUM_RETRIES=1
-
-# Access Galaxy on localhost via port $GALAXY_PORT
-export GALAXY_TEST_PORT="${GALAXY_PORT}"
-
-# Have Selenium access Galaxy at this URL
-export GALAXY_TEST_EXTERNAL_FROM_SELENIUM="http://galaxy:8080/galaxypf"
-export GALAXY_TEST_EXTERNAL="http://localhost:${GALAXY_TEST_PORT}/galaxypf"
-
-# Point tests at the Master API Key configured in the Dockerfile.
-export GALAXY_CONFIG_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53
-
-cd ../../..
-
-./run_tests.sh --selenium "$@"
-exit_code=$?
-
-cd $TEST_DIRECTORY
-
-exit $exit_code

.ci/jenkins/selenium-py3

@@ -1 +0,0 @@
-selenium

.ci/jenkins/selenium/run_tests.sh

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-# Enable retries on tests to reduce chances of transient failures.
-: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
-
-# If in Jenkins environment, use it for artifacts.
-if [ -n "$BUILD_NUMBER" ];
-then
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
-else
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
-fi
-
-mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
-mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
-
-mkdir -p ~/.jenkins-yarn-cache
-YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
-
-# Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
-export DOCKER_RUN_EXTRA_ARGS
-
-./run_tests.sh --dockerize --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"

.ci/jenkins/toolshed/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --db postgres --clean_pyc --toolshed "$@"

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

@@ -0,0 +1,32 @@
+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:12
+        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

@@ -0,0 +1,12 @@
+#!/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

.circleci/config.yml

@@ -17,6 +17,8 @@ variables:
         - ~/.cache/yarn
   install_tox: &install_tox
     run: sudo pip install tox
+  install_deb_reqs: &install_deb_reqs
+    run: sudo apt-get update && sudo apt-get install ffmpeg nodejs -y
   set_workdir: &set_workdir
     working_directory: ~/repo
   requires_get_code: &requires_get_code
@@ -25,7 +27,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -81,44 +83,9 @@ jobs:
           key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
           paths:
             - ~/repo
-  py35_docstring:
-    docker:
-      - image: circleci/python:3.5
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py35-lint_docstring_include_list
-  py35_lint:
-    docker:
-      - image: circleci/python:3.5
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py35-lint
-  py35_unit:
-    docker:
-      - image: circleci/python:3.5
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py35-unit
-  py35_first_startup:
-    docker:
-      - image: circleci/python:3.5
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      # Use this job to test the latest migrations
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
-      - run: mv db_gx_rev_0141.sqlite database/universe.sqlite
-      - *install_tox
-      - run: tox -e py35-first_startup
   validate_test_tools:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -128,29 +95,16 @@ jobs:
       - run: tox -e validate_test_tools
   test_galaxy_packages:
     docker:
-      - image: circleci/python:3.5
+      - image: circleci/python:3.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
+      - *install_deb_reqs
       - run: tox -e test_galaxy_packages
-  js_unit:
-    docker:
-      - image: circleci/node:12-browsers
-    <<: *set_workdir
-    steps:
-      - *restore_yarn_cache
-      - run: cd client && yarn install --frozen-lockfile
-      - *save_yarn_cache
-      - run:
-          name: Build client
-          command: cd client && yarn run build
-          environment:
-              NODE_OPTIONS: --max_old_space_size=4096
-      - run: cd client && yarn run test
   js_lint:
     docker:
-      - image: circleci/node:12-browsers
+      - image: cimg/node:16.13.2
     <<: *set_workdir
     steps:
       - *restore_yarn_cache
@@ -163,19 +117,9 @@ workflows:
   get_code_and_test:
     jobs:
       - get_code
-      - py35_docstring:
-          <<: *requires_get_code
-      - py35_lint:
-          <<: *requires_get_code
-      - py35_unit:
-          <<: *requires_get_code
-      - py35_first_startup:
-          <<: *requires_get_code
       - test_galaxy_packages:
           <<: *requires_get_code
       - validate_test_tools:
           <<: *requires_get_code
-      - js_unit:
-          <<: *requires_get_code
       - js_lint:
           <<: *requires_get_code

.dockerignore

@@ -0,0 +1,4 @@
+.k8s_ci.Dockerfile
+.venv
+database
+node_modules

.git-blame-ignore-revs

@@ -0,0 +1,7 @@
+# Migrate code style to Black and Apply isort
+623a5e165ad79e15321b19b2a2afbf2f9224cc90
+# Application of black styling to /tools/
+03351d2a9f81b938d650e2a955c65c18526ee7f0
+# Migrate code style to Prettier
+5b2928f851bd5ea3b9c2a04abf2cee9ff0bc54cc
+87873c5e2f4e6b97fe0f2084bfca0295fcd471de

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+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)
+
+**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

@@ -0,0 +1 @@
+comment: false

.github/labeler.yml

@@ -0,0 +1,68 @@
+---
+area/admin:
+  - client/src/components/admin/**/*
+  - doc/source/admin/**/*
+area/API:
+  - lib/galaxy/webapps/galaxy/api/**/*
+area/client:
+  - client/*
+area/datatypes:
+  - lib/galaxy/datatypes/**/*
+  - lib/galaxy/config/sample/datatypes_conf.xml.sample
+area/dependencies:
+  - lib/galaxy/dependencies/**/*
+area/documentation:
+  - doc/**/*
+area/jobs:
+  - lib/galaxy/jobs/**/*
+area/libraries:
+  - client/src/components/LibraryFolder/**/*
+  - lib/galaxy/webapps/galaxy/api/libraries.py
+area/objectstore:
+  - lib/galaxy/objectstore/**/*
+area/packaging:
+  - packages/**/*
+area/reports:
+  - client/src/reports/**/*
+  - lib/galaxy/webapps/reports/**/*
+  - templates/webapps/reports/**/*
+area/scripts:
+  - scripts/**/*
+area/security:
+  - lib/galaxy/security/**/*
+area/testing:
+  - lib/galaxy_test/**/*
+  - run_tests.sh
+  - test/**/*
+  - test-data/**/*
+area/testing/api:
+  - lib/galaxy_test/api/**/*
+area/testing/integration:
+  - test/integration/**/*
+  - test/integration_selenium/**/*
+area/testing/selenium:
+  - lib/galaxy/selenium/**/*
+  - lib/galaxy_test/selenium/**/*
+area/tool-dependencies:
+  - lib/galaxy/tool_util/deps/**/*
+area/tool-framework:
+  - lib/galaxy/tools/**/*
+  - lib/galaxy/tool_util/**/*
+  - lib/galaxy/webapps/galaxy/api/tools.py
+area/tools:
+  - tools/**/*
+  - tool-data/**/*
+area/toolshed:
+  - client/src/toolshed/**/*
+  - lib/galaxy/webapps/galaxy/api/toolshed.py
+  - lib/toolshed/**/*
+  - templates/webapps/tool_shed/**/*
+area/UI-UX:
+  - client/src/**/*
+  - templates/**/*
+area/util:
+  - lib/galaxy/util/**/*
+area/visualizations:
+  - config/plugins/visualizations/**/*
+area/workflows:
+  - lib/galaxy/workflow/**/*

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+(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 contributions under [Galaxy's current license](https://github.com/galaxyproject/galaxy/blob/dev/LICENSE.txt).
+- [x] I agree to allow the Galaxy committers to license these and all my past contributions to the core galaxy codebase under the [MIT license](https://opensource.org/licenses/MIT). If this condition is an issue, uncheck and just let us know why with an e-mail to galaxy-committers@lists.galaxyproject.org.

.github/workflows/api.yaml

@@ -0,0 +1,76 @@
+name: API tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  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'
+concurrency:
+  group: api-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    services:
+      postgres:
+        image: postgres:13
+        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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-api
+      - name: Run tests
+        run: ./run_tests.sh --coverage --skip_flakey_fails -api
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: api
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: API test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_api_tests.html'

.github/workflows/build_container_image.yaml

@@ -0,0 +1,50 @@
+name: Build Container Image
+on:
+  push:
+    branches:
+      - 'release*'
+      - dev
+concurrency:
+  group: docker-build-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build:
+    name: Build container image
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'galaxyproject'
+    steps:
+      - uses: actions/checkout@v2
+      # https://stackoverflow.com/questions/59810838/how-to-get-the-short-sha-for-the-github-workflow
+      - name: Set outputs
+        id: commit
+        run: echo "::set-output name=sha_short::$(git rev-parse --short HEAD)"
+      - name: Set branch name
+        id: branch
+        run: echo "::set-output name=name::$(BRANCH_NAME=${GITHUB_REF##*/}; echo ${BRANCH_NAME/release_/})"
+      - name: Build container image
+        run: docker build . --build-arg GIT_COMMIT=$(git rev-parse HEAD) --build-arg BUILD_DATE=$(date -u +'%Y-%m-%dT%H:%M:%SZ') --build-arg IMAGE_TAG=${{ steps.branch.outputs.name }} -t galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} -t quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }} -f .k8s_ci.Dockerfile
+      - name: Create auto-expiring one for per-commit auto repository
+        run: echo "FROM galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}" | docker build --label "quay.expires-after"="90d" -t "quay.io/galaxyproject/galaxy-k8s-auto:${{ steps.commit.outputs.sha_short }}" -
+      - name: Login to quay.io
+        uses: actions-hub/docker/login@master
+        env:
+          DOCKER_USERNAME: ${{ secrets.QUAY_USERNAME }}
+          DOCKER_PASSWORD: ${{ secrets.QUAY_PASSWORD }}
+          DOCKER_REGISTRY_URL: quay.io
+      - name: Push to quay.io with branch name
+        uses: actions-hub/docker@master
+        with:
+          args: push quay.io/galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}
+      - name: Push to quay.io with commit hash
+        uses: actions-hub/docker@master
+        with:
+          args: push quay.io/galaxyproject/galaxy-k8s-auto:${{ steps.commit.outputs.sha_short }}
+      - name: Login to DockerHub
+        uses: actions-hub/docker/login@master
+        env:
+          DOCKER_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
+          DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_PASSWORD }}
+      - name: Push to DockerHub with branch name
+        uses: actions-hub/docker@master
+        with:
+          args: push galaxyproject/galaxy-min:${{ steps.branch.outputs.name }}

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,70 @@
+# 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'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['javascript', 'python']
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      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.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # 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@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and 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@v1

.github/workflows/converter_tests.yaml

@@ -1,14 +1,33 @@
 name: Converter tests
-on: [push, pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
+env:
+  GALAXY_TEST_RAISE_EXCEPTION_ON_HISTORYLESS_HDA: '1'
+concurrency:
+  group: converter-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
-
   test:
     name: Test
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
     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" >> $GITHUB_ENV
     - uses: actions/checkout@v2
       with:
         path: 'galaxy root'
@@ -30,5 +49,37 @@ jobs:
       run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
     - name: Install planemo
       run: pip install planemo
+    - name: Install jq
+      run: sudo apt-get install jq
+    - name: Determine converters to check
+      run: |
+        ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -v -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip > tool_list.txt
+        echo "Skipping checks for the following converters:"
+        ls 'galaxy root'/lib/galaxy/datatypes/converters/*xml | grep -f 'galaxy root'/lib/galaxy/datatypes/converters/.tt_skip
+        echo "Checking only the following converters:"
+        cat tool_list.txt
+    - name: Lint converters
+      run: |
+        mapfile -t TOOL_ARRAY < tool_list.txt
+        for CONVERTER in "${TOOL_ARRAY[@]}"; do
+          planemo lint --skip citations,stdio,help --report_level warn "$CONVERTER"
+        done
     - name: Run tests
-      run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' 'galaxy root'/lib/galaxy/datatypes/converters/*xml
+      run: |
+        mkdir -p json_output
+        mapfile -t TOOL_ARRAY < tool_list.txt
+        for CONVERTER in "${TOOL_ARRAY[@]}"; do
+          json=$(mktemp -u -p json_output --suff .json)
+          planemo test --test_output_json "$json" --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' "$CONVERTER" || true
+        done
+        planemo merge_test_reports json_output/*.json tool_test_output.json
+        planemo test_reports tool_test_output.json --test_output tool_test_output.html
+        if jq '.["tests"][]["data"]["status"]' tool_test_output.json | grep -v "success"; then
+          echo "Unsuccessful tests found, inspect the 'Converter test results' artifact for details."
+          exit 1
+        fi
+    - uses: actions/upload-artifact@v2
+      if: failure()
+      with:
+        name: Converter test results (${{ matrix.python-version }})
+        path: tool_test_output.html

.github/workflows/cwl_conformance.yaml

@@ -0,0 +1,69 @@
+name: CWL conformance
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+concurrency:
+  group: cwl-conformance-${{ 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: ['3.7']
+        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:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Run tests
+        run: ./run_tests.sh --coverage --skip_flakey_fails -cwl lib/galaxy_test/api/cwl -- -m "${{ matrix.marker }} and ${{ matrix.conformance-version }}"
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: cwl-conformance
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: CWL conformance test results (${{ matrix.python-version }}, ${{ matrix.marker }}, ${{ matrix.conformance-version }})
+          path: 'galaxy root/run_cwl_tests.html'

.github/workflows/db_indexes.yaml

@@ -0,0 +1,71 @@
+name: Database indexes
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: database-${{ github.ref }}
+  cancel-in-progress: true
+defaults:
+  run:
+    working-directory: 'galaxy root'
+jobs:
+  check:
+    name: Check database indexes
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+        db: ['postgresql', 'sqlite']
+        postgresql-version: ['13']
+        include:
+          - db: postgresql
+            postgresql-version: '9.6'
+    services:
+      postgres:
+        image: postgres:${{ matrix.postgresql-version }}
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Cache tox env
+      uses: actions/cache@v2
+      with:
+        path: .tox
+        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-check-indexes
+    - name: Install tox
+      run: pip install tox
+    - name: Check indexes on postgresql
+      if: matrix.db == 'postgresql'
+      env:
+        GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION: 'postgresql://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+      run: tox -e check_indexes
+    - name: Check indexes on sqlite
+      if: matrix.db == 'sqlite'
+      run: tox -e check_indexes

.github/workflows/dependencies.yaml

@@ -0,0 +1,38 @@
+name: Update dependencies
+on:
+  schedule:
+    - cron: '0 3 * * 6'  # Run every saturday at 3 am.
+jobs:
+  update_dependencies:
+    name: Update dependencies
+    if: github.repository_owner == 'galaxyproject'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+      - name: Update dependencies
+        run: | 
+          python -m venv .venv
+          make update-dependencies
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          author: galaxybot <galaxybot@users.noreply.github.com>
+          token: ${{ secrets.GALAXYBOT_PAT }}
+          commit-message: Update Python dependencies
+          branch: dev_auto_update_dependencies
+          delete-branch: true
+          push-to-fork: galaxybot/galaxy
+          title: Update Python dependencies
+          body: Run `make update-dependencies`.
+          labels: area/dependencies

.github/workflows/docs.yaml

@@ -0,0 +1,77 @@
+name: Build docs
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    steps:
+      - name: Get target branch name (push)
+        if: github.event_name == 'push'
+        run: echo "TARGET_BRANCH=${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@v2
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
+      - name: Install Python dependencies
+        run: pip install -r requirements.txt -r lib/galaxy/dependencies/dev-requirements.txt sphinxcontrib-simpleversioning
+      - name: Add Google Analytics to doc/source/conf.py
+        run: |
+          sed -i -e "/html_theme_options = {/a\
+          \    'analytics_id': 'UA-45719423-17'," -e "s#https://docs.galaxyproject.org/en/[^/]*/#https://docs.galaxyproject.org/en/$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:]]|master)
+                  UPLOAD_DIR=$TARGET_BRANCH
+                  ;;
+              dev)
+                  UPLOAD_DIR=latest
+                  ;;
+              *)
+                  echo "Not deploying documentation for branch $TARGET_BRANCH"
+                  exit 0
+                  ;;
+          esac
+          pip install awscli
+          aws s3 sync doc/build/html/ "s3://galaxy-docs/en/$UPLOAD_DIR" --region us-east-2 --size-only --delete

.github/workflows/first_startup.yaml

@@ -0,0 +1,58 @@
+name: first startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+env:
+  YARN_INSTALL_OPTS: --frozen-lockfile
+concurrency:
+  group: first-startup-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+
+  test:
+    name: Startup test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.10']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Cache tox env
+      uses: actions/cache@v2
+      with:
+        path: .tox
+        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-first-startup
+    - uses: mvdbeek/gha-yarn-cache@master
+      with:
+        yarn-lock-file: 'galaxy root/client/yarn.lock'
+    - name: Install tox
+      run: pip install tox
+    - name: run tests
+      run: tox -e first_startup
+      working-directory: 'galaxy root'

.github/workflows/framework.yaml

@@ -0,0 +1,74 @@
+name: Framework tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  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: framework-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    services:
+      postgres:
+        image: postgres:13
+        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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-framework
+      - name: Run tests
+        run: ./run_tests.sh --coverage --framework
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: framework
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Framework test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_framework_tests.html'

.github/workflows/integration.yaml

@@ -1,19 +1,38 @@
 name: Integration
-on: [push, pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
 env:
-  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
   GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
+  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'
+concurrency:
+  group: integration-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: [3.7]
-        subset: ['upload_datatype', 'extended_metadata', 'kubernetes', 'not (upload_datatype or extended_metadata or kubernetes)']
+        python-version: ['3.7']
+        chunk: ['0', '1', '2', '3']
     services:
       postgres:
-        image: postgres:11
+        image: postgres:13
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
@@ -25,36 +44,59 @@ jobs:
         ports:
           - 5672:5672
     steps:
-    - name: Prune unused docker image, volumes and containers
-      run: docker system prune -a -f
-    - name: Clean dotnet folder for space
-      if: matrix.subset == 'kubernetes'
-      run: rm -Rf /usr/share/dotnet
-    - name: Setup Minikube
-      if: matrix.subset == 'kubernetes'
-      id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.3
-      with:
-        minikube-version: "1.9.0-0_amd64"
-    - name: Launch Minikube
-      if: matrix.subset == 'kubernetes'
-      run: eval ${{ steps.minikube.outputs.launcher }}
-    - name: Check pods
-      if: matrix.subset == 'kubernetes'
-      run: |
-        kubectl get pods
-    - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip dir
-      uses: actions/cache@v1
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Run tests
-      run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
-      working-directory: 'galaxy root'
+      - 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: Setup Minikube
+        id: minikube
+        uses: CodingNagger/minikube-setup-action@v1.0.3
+        with:
+          minikube-version: "1.9.0-0_amd64"
+      - name: Launch Minikube
+        run: eval ${{ steps.minikube.outputs.launcher }}
+      - name: Check pods
+        run: |
+          kubectl get pods
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v1
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Run tests
+        run: |
+          . .ci/minikube-test-setup/start_services.sh
+          ./run_tests.sh --coverage -integration test/integration -- --num-shards=4 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Integration test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_integration_tests.html'

.github/workflows/integration_selenium.yaml

@@ -1,45 +1,86 @@
 name: Integration Selenium
-on: [push, pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+  schedule:
+    # Run at midnight UTC every Tuesday
+    - cron: '0 0 * * 2'
 env:
-  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
-  GALAXY_TEST_SELENIUM_REMOTE: '1'
-  GALAXY_TEST_SELENIUM_REMOTE_PORT: "4444"
   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: integration-selenium-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
     services:
       postgres:
-        image: postgres:11
+        image: postgres:13
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
           POSTGRES_DB: postgres
         ports:
           - 5432:5432
-      selenium:
-        image: selenium/standalone-chrome:3.141.59
-        ports:
-          - 4444:4444
     steps:
-    - name: Prune unused docker image, volumes and containers
-      run: docker system prune -a -f
-    - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip dir
-      uses: actions/cache@v1
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Run tests
-      run: './run_tests.sh -integration test/integration_selenium'
-      working-directory: 'galaxy root'
+      - 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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-integration-selenium
+      - uses: mvdbeek/gha-yarn-cache@master
+        with:
+          yarn-lock-file: 'galaxy root/client/yarn.lock'
+      - uses: nanasess/setup-chromedriver@master
+      - name: Run tests
+        run: ./run_tests.sh --coverage -integration test/integration_selenium
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: integration-selenium
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Integration Selenium test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_integration_tests.html'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Integration Selenium debug info (${{ matrix.python-version }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/jest.yaml

@@ -0,0 +1,37 @@
+name: Client Unit Testing
+on:
+  push:
+    paths:
+      - 'client/**'
+      - '.github/workflows/jest.yaml'
+  pull_request:
+    paths:
+      - 'client/**'
+      - '.github/workflows/jest.yaml'
+concurrency:
+  group: client-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  client-unit-test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node: [16]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Setup node
+      uses: actions/setup-node@v2
+      with:
+        node-version: ${{ matrix.node}}
+        cache: 'yarn'
+        cache-dependency-path: 'client/yarn.lock'
+    - run: yarn install --frozen-lockfile
+      working-directory: client
+    - name: Stage client libs (Gulp)
+      run: yarn run gulp client
+      working-directory: client
+    - name: Run Unit Tests
+      run: yarn run qunit
+      working-directory: client
+    - run: yarn jest
+      working-directory: client

.github/workflows/labels-verifier.yaml

@@ -0,0 +1,25 @@
+name: Labels Verifier
+on:
+  pull_request_target:
+    types: [closed]
+jobs:
+  onMerged:
+    name: "Check Labels on merge"
+    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@v3
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            github.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

@@ -0,0 +1,47 @@
+name: Python linting
+on:
+  push:
+    paths:
+      - '**.py'
+  pull_request:
+    paths:
+      - '**.py'
+concurrency:
+  group: py-lint-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.10']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('lib/galaxy/dependencies/pinned-lint-requirements.txt') }}
+      - name: Cache tox env
+        uses: actions/cache@v2
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('lib/galaxy/dependencies/pinned-lint-requirements.txt') }}-lint
+      - name: Install tox
+        run: pip install tox
+      - 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
+      - uses: psf/black@stable
+      - uses: jamescurtin/isort-action@master

.github/workflows/maintenance_bot.yaml

@@ -0,0 +1,47 @@
+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'
+    runs-on: ubuntu-latest
+    env:
+      MILESTONE_NUMBER: 22
+    steps:
+      - name: Get latest pull request labels
+        id: get_pr_labels
+        uses: actions/github-script@v3
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const response = await github.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: ${{ ! contains(join(fromJSON(steps.get_pr_labels.outputs.result).*.name, ', '), 'area/') }}
+        uses: actions/labeler@main
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+      - 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@v3
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            github.issues.update({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: context.issue.number,
+              milestone: ${{ env.MILESTONE_NUMBER }},
+            });

.github/workflows/mulled.yaml

@@ -1,28 +1,54 @@
 name: Mulled Unit Tests
-on: [push, pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: mulled-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
-
   test:
     name: Test
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
     steps:
-    - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip dir
-      uses: actions/cache@v1
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Install tox
-      run: pip install tox
-    - name: run tests
-      run: tox -e mulled
-      working-directory: 'galaxy root'
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v1
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache tox env
+        uses: actions/cache@v2
+        with:
+          path: .tox
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-mulled
+      - name: Install tox
+        run: pip install tox
+      - name: run tests
+        run: tox -e mulled
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Mulled unit test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_unit_tests.html'

.github/workflows/osx_startup.yaml

@@ -1,28 +1,49 @@
-name: OSX
-on: [push, pull_request]
+name: macOS startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: osx-first-startup-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
-
   test:
     name: Startup test
     runs-on: macos-latest
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v2
       with:
         path: 'galaxy root'
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
     - name: Cache pip dir
       uses: actions/cache@v1
       id: pip-cache
       with:
         path: ~/Library/Caches/pip
-        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6
-        key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Install tox
-      run: pip install tox
+        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.7
+        key: pip-cache-3.7-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Cache tox env
+      uses: actions/cache@v2
+      with:
+        path: .tox
+        key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-osx
     - name: Install and activate miniconda  # use this job to test using Python from a conda environment
-      uses: goanpeca/setup-miniconda@v1
+      uses: conda-incubator/setup-miniconda@v2
       with:
         activate-environment: ''
+    - name: Install tox
+      run: pip install tox
     - name: run tests
       run: tox -e first_startup
-      shell: bash -l {0}  # need this to have CONDA_EXE set
       working-directory: 'galaxy root'

.github/workflows/performance.yaml

@@ -0,0 +1,73 @@
+name: Performance tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  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: performance-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7']
+    services:
+      postgres:
+        image: postgres:13
+        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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        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@v2
+        if: failure()
+        with:
+          name: API test results
+          path: 'galaxy root/run_api_tests.html'
+      - uses: actions/upload-artifact@v2
+        with:
+          name: Performance Metrics
+          path: 'galaxy root/test.html'

.github/workflows/reports_startup.yaml

@@ -0,0 +1,55 @@
+name: Reports startup
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+env:
+  YARN_INSTALL_OPTS: --frozen-lockfile
+concurrency:
+  group: reports-startup-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Reports startup test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.10']
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Cache galaxy venv
+      uses: actions/cache@v2
+      with:
+        path: 'galaxy root/.venv'
+        key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-reports-startup
+    - uses: mvdbeek/gha-yarn-cache@master
+      with:
+        yarn-lock-file: 'galaxy root/client/yarn.lock'
+    - name: Install tox
+      run: pip install tox
+    - name: Run tests
+      run: tox -e reports_startup
+      working-directory: 'galaxy root'

.github/workflows/selenium.yaml

@@ -0,0 +1,86 @@
+name: Selenium tests
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+  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: selenium-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7']
+        chunk: [0, 1, 2]
+    services:
+      postgres:
+        image: postgres:13
+        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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium
+      - uses: mvdbeek/gha-yarn-cache@master
+        with:
+          yarn-lock-file: 'galaxy root/client/yarn.lock'
+      - uses: nanasess/setup-chromedriver@master
+      - name: Run tests
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Selenium test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_selenium_tests.html'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Selenium debug info (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/selenium_beta.yaml

@@ -0,0 +1,87 @@
+name: Selenium tests (beta history panel)
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+  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_SELENIUM_BETA_HISTORY: 1
+  GALAXY_TEST_SKIP_FLAKEY_TESTS_ON_ERROR: 1
+  YARN_INSTALL_OPTS: --frozen-lockfile
+  GALAXY_CONFIG_SQLALCHEMY_WARN_20: '1'
+concurrency:
+  group: selenium-beta-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7']
+        chunk: [0, 1, 2]
+    services:
+      postgres:
+        image: postgres:13
+        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@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-selenium-beta
+      - uses: mvdbeek/gha-yarn-cache@master
+        with:
+          yarn-lock-file: 'galaxy root/client/yarn.lock'
+      - uses: nanasess/setup-chromedriver@master
+      - name: Run tests
+        run: ./run_tests.sh --coverage -selenium lib/galaxy_test/selenium -- --num-shards=3 --shard-id=${{ matrix.chunk }}
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: selenium-beta-history
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Selenium beta history panel test results (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/run_selenium_tests.html'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Selenium beta history panel debug info (${{ matrix.python-version }}, ${{ matrix.chunk }})
+          path: 'galaxy root/database/test_errors'

.github/workflows/test_galaxy_release.yaml

@@ -0,0 +1,25 @@
+name: Test Galaxy release script
+on:
+  push:
+    paths:
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+  pull_request:
+    paths:
+      - lib/galaxy/version.py
+      - scripts/release.sh
+      - test/release.sh
+concurrency:
+  group: test-galaxy-release-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - name: Run tests
+        run: ./test/release.sh

.github/workflows/toolshed.yaml

@@ -1,18 +1,29 @@
-name: Toolshed
-on: [push, pull_request]
+name: Toolshed tests
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
 env:
-  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
-  TOOL_SHED_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
+  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: toolshed-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   test:
     name: Test
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: ['3.7']
     services:
       postgres:
-        image: postgres:11
+        image: postgres:13
         env:
           POSTGRES_USER: postgres
           POSTGRES_PASSWORD: postgres
@@ -20,18 +31,32 @@ jobs:
         ports:
           - 5432:5432
     steps:
-    - uses: actions/checkout@v2
-      with:
-        path: 'galaxy root'
-    - uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Cache pip dir
-      uses: actions/cache@v1
-      id: pip-cache
-      with:
-        path: ~/.cache/pip
-        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
-    - name: Run tests
-      run: './run_tests.sh -toolshed'
-      working-directory: 'galaxy root'
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v1
+        id: pip-cache
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-toolshed
+      - name: Run tests
+        run: './run_tests.sh -toolshed'
+        working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Toolshed test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_toolshed_tests.html'

.github/workflows/unit-postgres.yaml

@@ -0,0 +1,58 @@
+name: Unit w/postgres tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+env:
+  GALAXY_TEST_DBURI: 'postgresql://postgres:postgres@localhost:5432/postgres?client_encoding=utf8'  # using postgres as the db
+concurrency:
+  group: py-unit-postgres-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7']
+    services:
+      postgres:
+        image: postgres:13
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        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'

.github/workflows/unit.yaml

@@ -0,0 +1,58 @@
+name: Unit tests
+on:
+  push:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+  pull_request:
+    paths-ignore:
+      - 'client/**'
+      - 'doc/**'
+      - 'lib/galaxy_test/selenium/**'
+concurrency:
+  group: py-unit-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.7', '3.10']
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          path: 'galaxy root'
+      - uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get full Python version
+        id: full-python-version
+        shell: bash
+        run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+      - name: Cache pip dir
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+      - name: Cache galaxy venv
+        uses: actions/cache@v2
+        with:
+          path: 'galaxy root/.venv'
+          key: gxy-venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('galaxy root/requirements.txt') }}-unit
+      - name: Install ffmpeg
+        run: sudo apt-get update && sudo apt-get -y install ffmpeg
+      - name: Run tests
+        run: ./run_tests.sh --coverage -u
+        working-directory: 'galaxy root'
+      - uses: codecov/codecov-action@v2
+        with:
+          flags: py-unit
+          working-directory: 'galaxy root'
+      - uses: actions/upload-artifact@v2
+        if: failure()
+        with:
+          name: Unit test results (${{ matrix.python-version }})
+          path: 'galaxy root/run_unit_tests.html'

.gitignore

@@ -1,4 +1,5 @@
 .hg*
+
 # Downloaded and locally built eggs
 eggs
 scripts/scramble/build
@@ -21,25 +22,7 @@ lib/galaxy/web/framework/static/scripts
 lib/galaxy/web/framework/static/style
 
 # Database stuff
-database/*.sqlite
-database/beaker_sessions
-database/citations
-database/community_files
-database/compiled_templates
-database/dependencies
-database/files
-database/job_working_directory
-database/jobs_directory
-database/mulled
-database/object_store_cache
-database/objects
-database/openid_consumer_cache
-database/pbs
-database/shed_tools
-database/test_errors
-database/tmp
-database/tool_cache
-database/tool_search_index
+/database/
 
 
 # Python bytecode
@@ -49,6 +32,10 @@ database/tool_search_index
 *.lock
 *.log
 *.pid
+celerybeat-schedule
+
+# Celery state files
+celerybeat-schedule.*
 
 # Tool Shed Runtime Files
 tool_shed_webapp.lock
@@ -95,6 +82,7 @@ config/plugins/**/.cache
 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
@@ -121,12 +109,13 @@ tool-data/**/*.fa
 .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_selenium_tests.html
 run_toolshed_tests.html
-run_api_tests.html
 test/tool_shed/tmp/*
 .coverage
 htmlcov
@@ -139,7 +128,7 @@ test/unit/**.log
 .idea
 .vscode
 client/**/jsconfig.json
-
+vetur.config.js
 
 # Chrom len files
 *.len
@@ -153,18 +142,16 @@ static/plugins
 static/scripts
 node_modules
 bower_components
-client/galaxy/scripts/libs/*
-client/galaxy/style/less/*
+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/api/api.rst
-doc/source/api/ts_api.rst
 doc/source/dev/schema.md
-doc/source/dev/schema.rst
-client/styleguide
+client/docs/dist
 
 # webpack stats
 client/webpack-stats.json
@@ -181,7 +168,16 @@ packages/*/*.egg-info
 *~
 
 # standalone script + main, or build into dist.
-config/plugins/visualizations/**/static/dist
-config/plugins/visualizations/**/static/script.js
-config/plugins/visualizations/**/static/main.css
-config/plugins/visualizations/**/static/plugin_build_hash.txt
+config/plugins/**/static/dist
+config/plugins/**/static/script.js
+config/plugins/**/static/main.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
+
+# CWL conformance tests
+lib/galaxy_test/api/cwl/test_cwl_conformance_v1_?.py
+test/functional/tools/cwl_tools/v1.?/

.gitpod.yml

@@ -0,0 +1,34 @@
+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:
+  - init: >
+      cp .vscode/settings_gitpod.json .vscode/settings.json &&
+      cp .vscode/launch_gitpod.json .vscode/launch.json &&
+      pip install psycopg2 &&
+      pip install -r lib/galaxy/dependencies/dev-requirements.txt &&
+      createdb galaxy &&
+      make client
+  - command: cp config/galaxy.yml.sample config/galaxy.yml
+  - command: make client-watch
+# Ports to expose on workspace startup (optional)
+ports:
+  - port: 8000
+vscode:
+  extensions:
+    - ms-python.python
+    - ms-python.vscode-pylance

.isort.cfg

@@ -0,0 +1,14 @@
+[settings]
+extend_skip=doc/source/conf.py,lib/galaxy/util/jstree.py
+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/*
+src_paths=lib

.k8s_ci.Dockerfile

@@ -0,0 +1,194 @@
+# Stage 1:
+# - base: ubuntu (default) OR prebuilt image0
+# - install build tools
+# - clone playbook
+# Stage 2: build galaxy client and server in parallel
+# Stage 2.1:
+# - run playbook with server build steps only
+# - remove build artifacts + files not needed in container
+# Stage 2.2:
+# - run playbook with client build steps only
+# - remove build artifacts + files not needed in container
+# Stage 3:
+# - 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=$ROOT_DIR/server
+
+ARG STAGE1_BASE=python:3.7-slim
+ARG FINAL_STAGE_BASE=$STAGE1_BASE
+ARG GALAXY_USER=galaxy
+ARG GALAXY_PLAYBOOK_REPO=https://github.com/galaxyproject/galaxy-docker-k8s
+ARG GALAXY_PLAYBOOK_BRANCH=v2.0.0
+
+ARG GIT_COMMIT=unspecified
+ARG BUILD_DATE=unspecified
+ARG IMAGE_TAG=unspecified
+
+#======================================================
+# Stage 1 - Setup common requirements for build
+#======================================================
+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<2.10' \
+    && 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 *
+ENV LC_ALL en_US.UTF-8
+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
+
+# Add Galaxy source code
+COPY . $SERVER_DIR/
+
+#======================================================
+# Stage 2.1 - Build galaxy server
+#======================================================
+FROM stage1 AS server_build
+ARG SERVER_DIR
+
+RUN ansible-playbook -i localhost, playbook.yml -v -e galaxy_build_client=False -e galaxy_virtualenv_command=virtualenv
+
+RUN cat /galaxy/server/lib/galaxy/dependencies/conditional-requirements.txt | grep psycopg2-binary | xargs /galaxy/server/.venv/bin/pip install
+
+# 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* \
+        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 '{}' +
+
+#======================================================
+# Stage 2.2 - Build galaxy client
+#======================================================
+FROM stage1 AS client_build
+ARG SERVER_DIR
+
+RUN ansible-playbook -i localhost, playbook.yml -v --tags "galaxy_build_client" -e galaxy_virtualenv_command=virtualenv
+
+WORKDIR $SERVER_DIR
+RUN rm -rf \
+        .ci \
+        .git \
+        .venv/include/node \
+        .venv/src/node* \
+        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 '{}' +
+
+#======================================================
+# Stage 3 - Build final image based on previous stages
+#======================================================
+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 \
+        curl \
+        procps \
+        less \
+        bzip2 \
+        tini \
+    && 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 \
+    && 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 $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=server_build $ROOT_DIR .
+COPY --chown=$GALAXY_USER:$GALAXY_USER --from=client_build $SERVER_DIR/static ./server/static
+
+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
+
+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

.vscode/.test.env

@@ -0,0 +1 @@
+GALAXY_TEST_TOOL_CONF="lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"

.vscode/launch_gitpod.json

@@ -0,0 +1,46 @@
+{
+    "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": "${workspaceFolder}/config/galaxy.yml",
+                "GALAXY_CONDA_AUTO_INIT": "false",
+                "GALAXY_CONFIG_TOOL_CONFIG_FILE": "lib/galaxy/config/sample/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml",
+                "GALAXY_CONFIG_DATABASE_CONNECTION": "postgresql://localhost/galaxy"
+            }
+        },
+        {
+            "name": "Tool test framework",
+            "type": "python",
+            "request": "launch",
+            "program": "${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

@@ -0,0 +1,13 @@
+{
+    "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"
+}
+

CODE_OF_CONDUCT.md

@@ -1,5 +1,16 @@
-Galaxy Project Code of Conduct
-==============================
+# Galaxy Project Code of Conduct
+
+## Note: Change is Coming
+
+Since 2015 the Galaxy Project Code of Conduct has resided here, and updates to it have been coordinated by the Committers Group for this repo.
+
+This code of conduct has served us reasonably well over the years, but it is time for a refresh.  Since 2015 the world has become much more aware of the need for codes of conduct, and best practices for creating and enforcing them have moved forward significantly.
+
+**As a result it is past time to update both our code of conduct and our process for maintaining it.**  The Galaxy Outreach and Training [Working Group](https://galaxyproject.org/community/wg/) is currently working on a first draft of a new code and new processes.  The final code and processes we adopt will be [implemented](https://galaxyproject.org/community/coc/) only after it has been discussed, revised, and approved by the community.
+
+Until that happens this will remain the Galaxy Project Code of Conduct.
+
+# Code of Conduct
 
 This code of conduct outlines our expectations for participants within the
 Galaxy community, as well as steps to reporting unacceptable behavior. We are
@@ -71,10 +82,18 @@ participants with disabilities.
 ### Reporting Issues
 
 If you experience or witness unacceptable behavior, or have any other concerns,
-please report it by contacting Dave Clements (clementsgalaxy@gmail.com). To
-report an issue involving Dave Clements please email James Taylor
-(james@taylorlab.org). All reports will be handled with discretion. In your
-report please include:
+please report it to any combination of the following people that makes you feel
+the most comfortable:
+
+- Dave Clements (clementsgalaxy@gmail.com). Dave is the Galaxy Project community
+  outreach manager and has experience handling Code of Conduct related issues.
+- Dr. Mike Schatz (mschatz@cs.jhu.edu). Mike is Dave Clements' direct manager
+  and issues related to Dave in some way should be reported to Mike.
+- Helena Rasche (helena.rasche@gmail.com). Helena is a well-known, trusted
+  community member, is LGBT+, and has completely separate funding and
+  institutional affiliation from Dave and Mike.
+
+All reports will be handled with discretion. In your report please include:
 
 - Your contact information.
 

CONTRIBUTING.md

@@ -41,7 +41,10 @@ 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.
+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
@@ -88,10 +91,23 @@ https://help.github.com/en/github/getting-started-with-github/git-and-github-lea
    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. Commit and push your changes to your
+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 external references
+   (e.g. GitHub issue fixed) using full URLs, and errors or tracebacks the
+   commit is supposed 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).
 
-7. Open a [pull
+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:
 
@@ -101,10 +117,10 @@ https://help.github.com/en/github/getting-started-with-github/git-and-github-lea
 
    * How to test the changes, if you haven't included specific tests already.
 
-8. The pull request should pass all the continuous integration tests which are
+9. The pull request should pass all the continuous integration tests which are
    automatically started by GitHub using e.g. Travis CI.
 
-9. Your pull request will be handled according to [some
+10. Your pull request will be handled according to [some
    rules](doc/source/project/organization.rst#handling-pull-requests).
 
 ## Style guidelines
@@ -114,11 +130,13 @@ https://help.github.com/en/github/getting-started-with-github/git-and-github-lea
 - 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 `setup.cfg`
-  file.
-- Python imports should be ordered following the
-  [smarkets](https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py)
-  style.
+  - divergences from PEP-8 are listed in the `[flake8]` section of the
+    `setup.cfg` 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).

CONTRIBUTORS.md

@@ -132,6 +132,7 @@ The following individuals have contributed code to Galaxy:
 * 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>

Makefile

@@ -1,15 +1,10 @@
 # Location of virtualenv used for development.
 VENV?=.venv
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
-IN_VENV=if [ -f $(VENV)/bin/activate ]; then . $(VENV)/bin/activate; fi;
-RELEASE_CURR:=16.01
-RELEASE_CURR_MINOR_NEXT:=$(shell $(IN_VENV) python scripts/bootstrap_history.py --print-next-minor-version)
-RELEASE_NEXT:=16.04
-# TODO: This needs to be updated with create_release_rc
-#RELEASE_NEXT_BRANCH:=release_$(RELEASE_NEXT)
-RELEASE_NEXT_BRANCH:=dev
+IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
+RELEASE_CURR:=22.05
 RELEASE_UPSTREAM:=upstream
-MY_UPSTREAM:=origin
+TARGET_BRANCH=$(RELEASE_UPSTREAM)/dev
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
 DOCS_DIR=doc
@@ -18,6 +13,13 @@ SLIDESHOW_DIR=$(DOC_SOURCE_DIR)/slideshow
 OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
 SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
 YARN := $(shell command -v yarn 2> /dev/null)
+YARN_INSTALL_OPTS=--network-timeout 300000 --check-files
+CWL_TARGETS := test/functional/tools/cwl_tools/v1.0/conformance_tests.yaml \
+	test/functional/tools/cwl_tools/v1.1/conformance_tests.yaml \
+	test/functional/tools/cwl_tools/v1.2/conformance_tests.yaml \
+	lib/galaxy_test/api/cwl/test_cwl_conformance_v1_0.py \
+	lib/galaxy_test/api/cwl/test_cwl_conformance_v1_1.py \
+	lib/galaxy_test/api/cwl/test_cwl_conformance_v1_2.py
 
 all: help
 	@echo "This makefile is used for building Galaxy's JS client, documentation, and drive the release process. A sensible all target is not implemented."
@@ -30,9 +32,19 @@ docs: ## Generate HTML documentation.
 	$(IN_VENV) $(MAKE) -C doc clean
 	$(IN_VENV) $(MAKE) -C doc html
 
+docs-develop: ## Fast doc generation and more warnings (for development)
+	$(IN_VENV) GALAXY_DOCS_SKIP_VIEW_CODE=1 SPHINXOPTS='-j 4' $(MAKE) -C doc html
+
 setup-venv:
 	if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
 
+diff-format:  ## Format Python code changes since last commit
+	$(IN_VENV) darker .
+
+format:  ## Format Python code base
+	$(IN_VENV) isort .
+	$(IN_VENV) black .
+
 list-dependency-updates: setup-venv
 	$(IN_VENV) pip list --outdated --format=columns
 
@@ -52,12 +64,6 @@ open-docs: docs _open-docs ## generate Sphinx HTML documentation and open in bro
 open-project: ## open project on github
 	$(OPEN_RESOURCE) $(PROJECT_URL)
 
-lint: ## check style using tox and flake8 for Python 2 and Python 3
-	$(IN_VENV) tox -e py27-lint && tox -e py34-lint
-
-uwsgi-rebuild-validation: ## rebuild uwsgi_config.yml kwalify schema against latest uwsgi master.
-	$(CONFIG_MANAGE) build_uwsgi_yaml
-
 tool-shed-config-validate: ## validate tool shed YAML configuration file
 	$(CONFIG_MANAGE) validate tool_shed
 
@@ -129,21 +135,36 @@ release-check-blocking-prs: ## Check github for release blocking PRs
 release-bootstrap-history: ## bootstrap history for a new release
 	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
 
-build-dependencies-docker: ## Builds the docker container used for dependency updates
-	$(MAKE) -C lib/galaxy/dependencies/pipfiles/docker
+update-lint-requirements:
+	./lib/galaxy/dependencies/update_lint_requirements.sh
 
-update-dependencies:  build-dependencies-docker ## update linting + dev dependencies
-	sh lib/galaxy/dependencies/pipfiles/update.sh -d
+update-dependencies: update-lint-requirements ## update pinned and dev dependencies
+	$(IN_VENV) ./lib/galaxy/dependencies/update.sh
 
-update-and-commit-dependencies: build-dependencies-docker ## update and commit linting + dev dependencies
-	sh lib/galaxy/dependencies/pipfiles/update.sh -d -c
+$(CWL_TARGETS):
+	./scripts/update_cwl_conformance_tests.sh
+
+generate-cwl-conformance-tests: $(CWL_TARGETS)  ## Initialise CWL conformance tests
+
+clean-cwl-conformance-tests:  ## Clean CWL conformance tests
+	for f in $(CWL_TARGETS); do \
+		if [ $$(basename "$$f") = conformance_tests.yaml ]; then \
+			rm -rf $$(dirname "$$f"); \
+		else \
+			rm -f "$$f"; \
+		fi \
+	done
+
+update-cwl-conformance-tests: ## update CWL conformance tests
+	$(MAKE) clean-cwl-conformance-tests
+	$(MAKE) generate-cwl-conformance-tests
 
 node-deps: ## Install NodeJS dependencies.
 ifndef YARN
 	@echo "Could not find yarn, which is required to build the Galaxy client.\nTo install yarn, please visit \033[0;34mhttps://yarnpkg.com/en/docs/install\033[0m for instructions, and package information for all platforms.\n"
 	false;
 else
-	cd client && yarn install --network-timeout 300000 --check-files
+	cd client && yarn install $(YARN_INSTALL_OPTS)
 endif
 	
 
@@ -163,9 +184,9 @@ client-watch: node-deps ## A useful target for parallel development building.  S
 	cd client && yarn run watch
 
 client-dev-server: node-deps ## Starts a webpack dev server for client development (HMR enabled)
-	cd client && yarn run webpack-dev-server
+	cd client && yarn run serve
 
-client-test: node-deps  ## Run JS unit tests via Karma
+client-test: node-deps  ## Run JS unit tests
 	cd client && yarn run test
 
 client-eslint: node-deps # Run client linting
@@ -176,101 +197,20 @@ client-format-check: node-deps # Run client formatting check
 
 client-lint: client-eslint client-format-check ## ES lint and check format of client
 
-client-test-watch: client ## Watch and run qunit tests on changes via Karma
-	cd client && yarn run test-watch
+client-test-watch: client ## Watch and run all client unit tests on changes
+	cd client && yarn run jest-watch
+
+serve-selenium-notebooks: ## Serve testing notebooks for Jupyter
+	cd lib && export PYTHONPATH=`pwd`; jupyter notebook --notebook-dir=galaxy_test/selenium/jupyter
 
 # Release Targets
-release-create-rc: release-ensure-upstream ## Create a release-candidate branch
-	git checkout dev
-	git pull --ff-only $(RELEASE_UPSTREAM) dev
-	git push $(MY_UPSTREAM) dev
-	git checkout -b release_$(RELEASE_CURR)
-	git push $(MY_UPSTREAM) release_$(RELEASE_CURR)
-	git push $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
-	git checkout -b version-$(RELEASE_CURR)
-	sed -i.bak -e "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_CURR)\"/" lib/galaxy/version.py
-	sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = \"rc1\"/" lib/galaxy/version.py
-	rm -f lib/galaxy/version.py.bak
-	git add lib/galaxy/version.py
-	git commit -m "Update version to $(RELEASE_CURR).rc1"
-	git checkout dev
+release-create-rc: ## Create a release-candidate branch or new release-candidate version
+	$(IN_VENV) ./scripts/release.sh -c
 
-	git checkout -b version-$(RELEASE_NEXT).dev
-	sed -i.bak -e "s/^VERSION_MAJOR = .*/VERSION_MAJOR = \"$(RELEASE_NEXT)\"/" lib/galaxy/version.py
-	rm -f lib/galaxy/version.py.bak
-	git add lib/galaxy/version.py
-	git commit -m "Update version to $(RELEASE_NEXT).dev"
+release-create: ## Create a release branch
+	$(IN_VENV) ./scripts/release.sh
 
-	-git merge version-$(RELEASE_CURR)
-	git checkout --ours lib/galaxy/version.py
-	git add lib/galaxy/version.py
-	git commit -m "Merge branch 'version-$(RELEASE_CURR)' into version-$(RELEASE_NEXT).dev"
-	git push $(MY_UPSTREAM) version-$(RELEASE_CURR):version-$(RELEASE_CURR)
-	git push $(MY_UPSTREAM) version-$(RELEASE_NEXT).dev:version-$(RELEASE_NEXT).dev
-	git checkout dev
-	# TODO: Use hub to automate these PR creations or push directly.
-	@echo "Open a PR from version-$(RELEASE_CURR) of your fork to release_$(RELEASE_CURR)"
-	@echo "Open a PR from version-$(RELEASE_NEXT).dev of your fork to dev"
-
-release-create: release-ensure-upstream ## Create a release branch
-	git checkout master
-	git pull --ff-only $(RELEASE_UPSTREAM) master
-	git push $(MY_UPSTREAM) master
-	git checkout release_$(RELEASE_CURR)
-	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
-	#git push $(MY_UPSTREAM) release_$(RELEASE_CURR)
-	git checkout dev
-	git pull --ff-only $(RELEASE_UPSTREAM) dev
-	#git push $(MY_UPSTREAM) dev
-	# Test run of merging. If there are conflicts, it will fail here.
-	git merge release_$(RELEASE_CURR)
-	git checkout release_$(RELEASE_CURR)
-	sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = None/" lib/galaxy/version.py
-	rm -f lib/galaxy/version.py.bak
-	git add lib/galaxy/version.py
-	git commit -m "Update version to $(RELEASE_CURR)"
-	git tag -m "Tag version $(RELEASE_CURR)" v$(RELEASE_CURR)
-
-	git checkout dev
-	-git merge release_$(RELEASE_CURR)
-	git checkout --ours lib/galaxy/version.py
-	git add lib/galaxy/version.py
-	git commit -m "Merge branch 'release_$(RELEASE_CURR)' into dev"
-	git checkout master
-	git merge release_$(RELEASE_CURR)
-	git push $(RELEASE_UPSTREAM) release_$(RELEASE_CURR):release_$(RELEASE_CURR)
-	git push $(RELEASE_UPSTREAM) dev:dev
-	git push $(RELEASE_UPSTREAM) master:master
-	git push $(RELEASE_UPSTREAM) --tags
-
-release-create-point: ## Create a point release
-	git pull --ff-only $(RELEASE_UPSTREAM) master
-	git push $(MY_UPSTREAM) master
-	git checkout release_$(RELEASE_CURR)
-	git pull --ff-only $(RELEASE_UPSTREAM) release_$(RELEASE_CURR)
-	#git push $(MY_UPSTREAM) release_$(RELEASE_CURR)
-	git checkout $(RELEASE_NEXT_BRANCH)
-	git pull --ff-only $(RELEASE_UPSTREAM) $(RELEASE_NEXT_BRANCH)
-	#git push $(MY_UPSTREAM) $(RELEASE_NEXT_BRANCH)
-	git merge release_$(RELEASE_CURR)
-	git checkout release_$(RELEASE_CURR)
-	sed -i.bak -e "s/^VERSION_MINOR = .*/VERSION_MINOR = \"$(RELEASE_CURR_MINOR_NEXT)\"/" lib/galaxy/version.py
-	rm -f lib/galaxy/version.py.bak
-	git add lib/galaxy/version.py
-	git commit -m "Update version to $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)"
-	git tag -m "Tag version $(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)" v$(RELEASE_CURR).$(RELEASE_CURR_MINOR_NEXT)
-	git checkout $(RELEASE_NEXT_BRANCH)
-	-git merge release_$(RELEASE_CURR)
-	git checkout --ours lib/galaxy/version.py
-	git add lib/galaxy/version.py
-	git commit -m "Merge branch 'release_$(RELEASE_CURR)' into $(RELEASE_NEXT_BRANCH)"
-	git checkout master
-	git merge release_$(RELEASE_CURR)
-	#git push origin release_$(RELEASE_CURR):release_$(RELEASE_CURR)
-	#git push origin $(RELEASE_NEXT_BRANCH):release_$(RELEASE_NEXT_BRANCH)
-	#git push origin master:master
-	#git push origin --tags
-	git checkout release_$(RELEASE_CURR)
+release-create-point: release-create ## Create a point release
 
 .PHONY: help
 

README.rst

@@ -24,12 +24,12 @@ Community support is available at `Galaxy Help <https://help.galaxyproject.org/>
 Galaxy Quickstart
 =================
 
-Galaxy requires Python 3.5 or 3.6 . To check your Python version, run:
+Galaxy requires Python 3.7 . To check your Python version, run:
 
 .. code:: console
 
     $ python -V
-    Python 3.6.10
+    Python 3.7.6
 
 Start Galaxy:
 

check_model.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+cd "$(dirname "$0")"
+
+. ./scripts/common_startup_functions.sh
+
+setup_python
+
+python ./scripts/check_model.py "$@"
+
+[ $? -ne 0 ] && exit 1;
+exit 0;

client/.eslintignore

@@ -1,6 +0,0 @@
-*.test.js
-galaxy/scripts/qunit
-galaxy/scripts/mocha
-galaxy/scripts/libs
-galaxy/scripts/nls
-galaxy/scripts/legacy

client/.eslintrc.js

@@ -1,47 +0,0 @@
-module.exports = {
-    extends: [
-        "eslint:recommended",
-        "plugin:vue/strongly-recommended"
-        //"airbnb-base", eventually
-    ],
-    env: {
-        browser: true,
-        commonjs: true,
-        es6: true,
-        node: true,
-        mocha: true
-    },
-    parserOptions: {
-        parser: "babel-eslint",
-        sourceType: "module"
-    },
-    rules: {
-        // Standard rules
-        "no-console": "off",
-        "no-unused-vars": ["error", { args: "none" }],
-        "prefer-const": "error",
-        "one-var": ["error", "never"],
-
-        "vue/valid-v-slot": "error",
-        "vue/v-slot-style": ["error", { atComponent: "v-slot", default: "v-slot", named: "longform" }],
-
-        // Vue TODO (enable these)
-        "vue/require-default-prop": "warn",
-        "vue/require-prop-types": "warn",
-        "vue/prop-name-casing": "warn",
-
-        // Prettier compromises/workarounds -- mostly #wontfix?
-        "vue/html-indent": "off",
-        "vue/max-attributes-per-line": "off",
-        "vue/html-self-closing": "off",
-        "vue/singleline-html-element-content-newline": "off",
-        "vue/multiline-html-element-content-newline": "off",
-        "vue/html-closing-bracket-newline": "off",
-        "vue/html-closing-bracket-spacing": "off"
-    },
-    globals: {
-        // chai tests
-        assert: true,
-        expect: true
-    }
-};

client/.eslintrc.json

@@ -0,0 +1,45 @@
+{
+    "extends": [
+        "eslint:recommended",
+        "plugin:vue/strongly-recommended"
+        //"airbnb-base", eventually
+    ],
+    "env": {
+        "browser": true,
+        "commonjs": true,
+        "es6": true,
+        "node": true,
+        "jest": true
+    },
+    "parserOptions": {
+        "parser": "@babel/eslint-parser",
+        "sourceType": "module"
+    },
+    "rules": {
+        // Standard rules
+        "no-console": "off",
+        "no-unused-vars": ["error", { "args": "none" }],
+        "prefer-const": "error",
+        "one-var": ["error", "never"],
+        "curly": "error",
+
+        "vue/valid-v-slot": "error",
+        "vue/v-slot-style": ["error", { "atComponent": "v-slot", "default": "v-slot", "named": "longform" }],
+
+        // Vue TODO (enable these)
+        "vue/require-default-prop": "warn",
+        "vue/require-prop-types": "warn",
+        "vue/prop-name-casing": "warn",
+        "vue/multi-word-component-names": "warn",
+
+        // Prettier compromises/workarounds -- mostly #wontfix?
+        "vue/html-indent": "off",
+        "vue/max-attributes-per-line": "off",
+        "vue/html-self-closing": "off",
+        "vue/singleline-html-element-content-newline": "off",
+        "vue/multiline-html-element-content-newline": "off",
+        "vue/html-closing-bracket-newline": "off",
+        "vue/html-closing-bracket-spacing": "off"
+    },
+    "ignorePatterns": ["src/qunit", "src/mocha", "src/libs", "src/nls", "src/legacy"]
+}

client/.node_version

@@ -1 +1 @@
-12.16.3
+16.13.2

client/README.md

@@ -1,36 +1,35 @@
-Client Build System
-===================
+# Client Build System
 
 Installs, stages, and builds the client-side scripts necessary for running the
 Galaxy webapp. When started through `run.sh` or any other method that utilizes
-`scripts/common_startup.sh`, Galaxy will (since 18.09) *automatically* build
+`scripts/common_startup.sh`, Galaxy will (since 18.09) _automatically_ build
 the client as a part of server startup, when it detects changes, unless that
 functionality is explicitly disabled.
 
-The base dependencies used are Node.js and Yarn.  Galaxy now includes these in
+The base dependencies used are Node.js and Yarn. Galaxy now includes these in
 the virtual environment, and they can be accessed by activating that with `.
 .venv/bin/activate` from the Galaxy root directory.
 
 If you'd like to install your own dependencies, on OSX the easiest way to get
-set up is using `homebrew` and the command `brew install nodejs yarn`.  More
+set up is using `homebrew` and the command `brew install nodejs yarn`. More
 information, including instructions for other platforms, is available at
-https://nodejs.org/ and https://yarnpkg.com/ .
+[https://nodejs.org](https://nodejs.org) and
+[https://yarnpkg.com/](https://yarnpkg.com).
 
 The Galaxy client build has necessarily grown more complex in the past several
 years, but we are still trying to keep things as simple as possible for
-everyone.  If you're having any trouble with building the client after
-following the instructions below, please create an issue on GitHub or reach out
-for help directly on Gitter at https://gitter.im/galaxyproject/Lobby .
+everyone. If you're having any trouble with building the client after following
+the instructions below, please create an issue on GitHub or reach out for help
+directly on Gitter at
+[https://gitter.im/galaxyproject/Lobby](https://gitter.im/galaxyproject/Lobby).
 
-
-Complete Client Build
-=====================
+## Complete Client Build
 
 There are many moving parts to the client build system, but the entry point for
 most people is the 'client' rule in the Makefile at the root of the Galaxy
-repository.  Execute the following to perform a complete build suitable for
+repository. Execute the following to perform a complete build suitable for
 local development, including dependency staging, style building, script
-processing, and bundling.  This is a development-specific build which includes
+processing, and bundling. This is a development-specific build which includes
 extra debugging features, and excludes several production optimizations made
 during the build process.
 
@@ -49,276 +48,120 @@ for inspection of live javascript to facilitate debugging, use:
 Important Note: The Galaxy repository does not include client script artifacts,
 and these should not be committed.
 
+## Automatic Rebuilding
 
-Automatic Rebuilding (Watch Mode)
-=================================
-
-When you're actively developing, it is sometimes convenient to have the client
-automatically rebuild every time you save a file.  You can do this using:
+When you're actively developing, it is convenient to have the client
+automatically rebuild every time you save a file. You can do this using:
 
     make client-watch
 
-This will first stage any dependencies (yarn-installed packages like jquery,
-etc), and then will watch for changes in any of the galaxy client source files.
-When a file is changed, the client will automatically rebuild, after which you
-can usually force refresh your browser to see changes.  Note that it is still
-recommended to run `make client` after you are finished actively developing
-using `make client-watch`.  
+This will first stage client dependencies, initiate a build, and then will
+watch for changes in any of the galaxy client source files.  When a file is
+changed, the client will automatically rebuild, after which you can refresh
+your browser to see changes.
 
-Note that there's a new, better option described in the next section.  This
-method of building will likely be deprecated as HMR is more widely tested.
+For even more rapid development you can use the webpack development server,
+which takes advantage of hot module replacement (HMR). This technique allows
+swapping out of javascript modules while the application is running without
+requiring a full page reload most of the time, at least in the more modern
+parts of the application.
 
-
-Even Better Automatic Rebuilding (HMR)
-======================================
-
-For even more rapid development you can use the webpack development server for
-Hot Module Replacement (HMR).  This technique allows swapping out of modules
-while the application is running without requiring a full page reload most of
-the time.
-
-Setting this up is a little more involved, but it is the fastest possible way
-to iterate when developing the client.  You'll need to start two separate
-processes here.  The first command below starts a special webpack dev server
-after a client build, and the second starts a Galaxy server like usual, but
-with extra mappings that redirect client artifact requests to the mentioned
-webpack dev server.
+The command below starts a special webpack dev server after a client
+build.
 
     make client-dev-server
-    GALAXY_CLIENT_DEV_SERVER=1 sh run.sh
 
-Note that this only works under uWSGI due to the extra internal routing rules
-employed.  If you're using the older Paste-based galaxy webserver you'll need
-to swap it over to take advantage of this functionality.
+This will start up an extra client development server running on port 8081.
+Open your browser to http://localhost:8081 (instead of the default 8080 that
+Galaxy would run on), and you should see Galaxy like normal.  Except now, when
+you change client code it'll automatically rebuild *and* reload the relevant
+portion of the application for you.  Note that unlike previous versions of this
+functionality, it is no longer required to use uWSGI for this.  Lastly, if you
+are running Galaxy at a location other than the default, you can specify a
+different proxy target (in this example, port 8000) using the GALAXY_URL
+environment variable:
 
+    GALAXY_URL="http://localhost:8000" make client-dev-server
 
-Changing Styles/CSS
-===================
+Sometimes you want to run your local UI against a remote Galaxy server. This is also possible, if you enable `CHANGE_ORIGIN` flag 
+
+    CHANGE_ORIGIN=true GALAXY_URL="https://usegalaxy.org/" make client-dev-server
+
+## Changing Styles/CSS
 
 Galaxy uses Sass for its styling, which is a superset of CSS that compiles down
-to regular CSS.  Most Galaxy styling source (.scss) files are kept in
-`client/galaxy/style/scss.  There are additionally style blocks alongside some
-Vue components -- styles that are particular to that individual component and
-do not apply site-wide.
+to regular CSS. Most Galaxy styling source (.scss) files are kept in
+`client/src/style/scss. There are additionally style blocks alongside some Vue
+components -- styles that are particular to that individual component and do
+not apply site-wide.
 
 On build, the compiled css bundle is served at `/static/style/base.css`.
 
 As mentioned above, `make client` will rebuild styles, as a part of the webpack
-build.  For iterative development, "Watch Mode" rebuilds as described above do
+build. For iterative development, "Watch Mode" rebuilds as described above do
 include style changes.
 
-
-# Client-Side Unit Testing
+## Client-Side Unit Testing
 
 Galaxy's client is undergoing an extensive refactoring and modernizing process.
 As part of this initiative, we would like to request that all new client-side
 code submissions come with accompanying javascript unit-tests for the
 developer-facing API of your new code.
 
-## Testing Technologies
+### Testing Technologies
 
-[Galaxy uses Mocha](https://mochajs.org/) for its client-side unit testing
-framework with [Chai as its assertion library](https://www.chaijs.com/) and
-[karma as a test runner](https://karma-runner.github.io/latest/index.html).
-The karma configs are contained in the client/karma folder. Unit tests are run
-using Chrome headless by default.
+[Galaxy uses Jest](https://jestjs.io/) for its client-side unit testing
+framework.
 
 For testing Vue components, we use the [Vue testing
 utils](https://vue-test-utils.vuejs.org/) to mount individual components in a
-test bed and check them for rendered features.
+test bed and check them for rendered features.  Please use jest-based mocking
+for isolating test functionality.
 
-We use the [babel plugin
-Rewire](https://github.com/speedskater/babel-plugin-rewire) to mock imported
-ES6 dependencies during unit-testing. [Sinon](https://sinonjs.org/) is also
-available for more robust stubbing, mocking and spying utilities.
+A set of older qUnit tests also exist which will be phased-out as the code they
+support is replaced with modern component-based implementations. In the
+meantime, we still run the qunit tests in sequence.
 
-A set of older qUnit tests also exist which will likely be phased-out as the
-code they support is replaced with modern component-based implementations. In
-the meantime, karma runs both the mocha and qunit tests in sequence.
+### Running the tests
 
+#### At Build-Time
 
-## Running the tests
-
-### At Build-Time
 To simply run all the javascript unit tests, you can use make from the root
 directory. This is what happens during a complete client build.
 
      make client-test
 
-
-### During Development
+#### During Development
 
 During client-side development, it is more convenient to have granular testing
 options. The various testing scripts are defined inside package.json within the
-client folder, and are called either with `yarn` as demonstrated in the 
+client folder, and are called with `yarn` as demonstrated in the
 following commands.
 
-#### Run all tests (mocha and qunit):
+This is what CI is going to run, and also what 'make client-test' invokes,
+executing all the client tests:
 
      yarn run test
 
-#### Watch and rerun all client-side unit-tests every time a source file changes:
+You can also bypass qunit and single-run all of the jest tests like so:
 
-     yarn run test-watch
+     yarn run jest
 
-#### Run only specified test files when a source file changes:
+Or, if you really want to run just the qunit tests:
 
-    yarn run test-watch watch-only="Tags/*.test.js"
+    yarn run qunit
 
-(The above watch-only parameter will be mapped to the following glob expression "**/Tags/*.test.js")
+##### Watch and rerun jest unit tests every time a source file changes
 
-#### Run qunit legacy tests
+This is incredibly handy, and there are a host of options in the interactive
+terminal this starts for executing Jest tests.
 
-    yarn run test-qunit
+     yarn run jest-watch
 
+##### Run only specified test files when a source file changes
 
-## Writing a test file
+    yarn run jest-watch MyModule
 
-The karma configs are setup to look at any file ending in "*.test.js". Please
-place your test files inside client/galaxy/scripts folders right next to
-whatever files that they are testing.
+    yarn run jest-watch Dialog
 
-```javascript
-// yourtestfile.test.js
-
-import { things } from "./yourtestfile.js";
-
-describe("some module you wrote", () => {
-
-    let transientVariables, serviceInstances, testData;
-
-    beforeEach(() => {
-        // setup your code (if necessary)
-    })
-
-    afterEach(() => {
-        // teardown your code (so it doesn't ruin the next test)
-    })
-
-    it("should do something or other", () => {
-        assert(somethingThatShouldTrue, "explain what went wrong");
-        expect(something).to.eq(true);
-    })
-})
-```
-
-
-## Testing ~~Suggestions~~ Obligations
-
-
-### Clearly document the intent of your test
-
-Please remember that these tests are not *for* you. They're for the people who
-come after you. It will be a lot easier to modify, repair and upgrade your code
-if they can figure out what you were originally hoping to accomplish.
-
-Add a couple of comments. Use variable names that mean something. Use the
-assertion failure description parameters when possible. Nobody's code is as
-self-documenting as they believe it to be.
-
-```javascript
-
-// NOT AWESOME
-// this test forces the next victim to have to
-// read every single line of source code you wrote
-it("should work", async () => {
-    let thing = await svc.loadHistories();
-    assert(thing);
-})
-
-// BETTER
-// With this test, you can just read at the errors on the mocha 
-// test output to have a pretty good idea of what went sour.
-it("should have resolved to an array of integer IDs", async () => {
-    let historyIds = await historyService.loadHistories();
-    assert(historyIds, "History service should have had a result");
-    assert(historyIds instanceof Array, "History results should have been an array");
-    assert(historyIds.length == 4, "History call should have returned 4 ids");
-})
-
-```
-
-
-### Only test the public API that you define (carefully!)
-
-Internal implementations come and go with library upgrades and new tech. But
-the point of the unit test is to make sure your units work as designed....
-which means you need to... you know... design your code to work in units.
-
-Separate your concerns and identify the developer-facing methods and functions
-you expect them to use. Test THOSE. Everything else should probably be
-considered an implementation detail.
-
-Assume nobody cares *how* your code works, we just need to know that the public
-API you designed *does* work. If performance problems or new tech necessitate a
-re-write, these tests become a guide for the next implementation.
-
-
-### Wrap native browser resources in a function so they can be easily mocked
-
-If your javascript needs to talk to the window object, or navigator, etc. wrap
-that in a function call so that it can be easily mocked during testing.
-
-```javascript
-
-// myModule.js
-
-// ... other code
-
-export function redirectTo(url) {
-    window.location = url;
-}
-
-
-// myModule.test.js
-
-import { __RewireAPI__ as myModuleRewire} from "./myModule";
-
-function fakeRedirect(url) {
-    console.log(`I would have gone to: ${url}`);
-}
-
-describe("some module", () => {
-
-    beforeEach(() => {
-        myModuleRewire.__Rewire__("redirectTo", fakeRedirect);
-    })
-
-    // ....
-})
-```
-
-### Implement logic in pure functions when possible
-
-The more of your logic that is written in deterministic functions (i.e. no
-side-effects, same inputs always result in same outputs) the easier it is to
-test. Just load up the functions and supply suitable test inputs.
-
-There is almost definitely no such thing as a well-written 1000 line function.
-Most of whatever happened in that thing was probably deterministic and can be
-broken up into easily testable chunks.
-
-
-## Specific test scenarios & examples
-
-[Mocking an imported dependency](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
-
-[Testing async operations](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
-
-[Testing a Vue component for expected rendering output](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
-
-[Firing an event against a shallow mounted vue component](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
-
-
-## The dirty secret about testing
-
-It's good to have tests, but testing code isn't really about testing at all,
-it's actually about software design. 
-
-Maintainable software is testable software. If you can run a unit test on your
-code, then that means you must have necessarily separated your code into
-testable units and you will have almost definitely written better, more
-modular, more easily manipulated code, and nobody will ever contemplate using
-git-blame to figure out what went wrong.
-
-Probably.
+    yarn run jest-watch workflow/run

client/babel.config.json

@@ -0,0 +1,8 @@
+{
+    "presets": ["@babel/preset-env"],
+    "env": {
+        "test": {
+            "plugins": ["@babel/plugin-transform-runtime"]
+        }
+    }
+}

client/bower.json

@@ -1,22 +0,0 @@
-{
-  "name": "galaxy-client-libs",
-  "version": "0.0.0",
-  "description": "External client-side libraries used by Galaxy",
-  "keywords": [
-    "galaxy",
-    "galaxyproject"
-  ],
-  "homepage": "usegalaxy.org",
-  "dependencies": {
-    "farbtastic": "~2.0.0-alpha.1",
-    "jquery-form": "~3.46.0",
-    "jquery-autocomplete": "git://github.com/dyve/jquery-autocomplete",
-    "select2": "~3.5.2",
-    "jStorage": "~0.4.12",
-    "dynatree": "~1.2.5",
-    "wymeditor": "~1.0.0-rc.1",
-    "jstree": "~3.0.9",
-    "jquery-ui": "git://github.com/jquery/jquery-ui.git#~1.11.2",
-     "threedubmedia.jquery.event": "*"
-  }
-}

client/docs/avoid-using-global-Galaxy.md

@@ -0,0 +1,73 @@
+Without a doubt. The most problematic part of the old client is the way every important piece of
+information was hung on a global variable whose initialization is completely unregulated.
+
+### Don't directly reference window.Galaxy in Vue components
+
+Components take props. Please pass in any values you might need from window.Galaxy as props and
+avoid referencing global Galaxy inside your components. I've even created basic providers which give
+you access to the Galaxy.config, current user, and current user histories. Please use them to
+retrieve your values, and bypass importing Galaxy altogether.
+
+#### Sometimes you still need to update Vue from backbone as the legacy environment changes
+There are definitely use-cases where the Backbone models update over time and we need to update some
+value inside Vue. Instead of importing backbone models directly into Vue components, try building a
+backbone event listener that updates some relevant Vuex store.
+
+* [Keeping Vuex in Sync with
+  Galaxy](https://github.com/galaxyproject/galaxy/blob/dev/client/src/store/syncVuexToGalaxy.js)
+
+These issues should disappear over time as the all of the old client is rebuilt in the new
+ecosystem.
+
+
+## Mount Functions
+
+In what most people think of as a "standard" Vue application there would be only one place that Vue
+is mounted to the HTML environment, and that would be in a main.j or an app.js. Most modern
+single-page applications only have one starting point like that.
+
+However, we are incrementally replacing old Backbone views, so in its current state, Galaxy may have
+several mounting functions for various components depending on where that component is intended to
+fit into the existing Backbone layouts.
+
+
+### Using the standard mount to pass in Galaxy variables as props
+
+A standard mount function has been provided in src/utils. This mount function accepts a component
+definition, and then allows you to start up your Vue component with our standard load-out of plugins
+including localization, Vuex, and a couple other utilities. This is the preferred way to mount your
+component inside the old Backbone layout until the application is fully converted.
+
+```js static
+// src/mvc/OldBackboneView.js
+
+import { getGalaxyInstance } from "app";
+import MyComponent from "components/MyComponent";
+import { mountVueComponent } from "utils/mountVueComponent";
+
+const OldBackboneView = {
+
+    someInitMethodYouMake() {
+        const Galaxy = getGalaxyInstance();
+        const mounter = mountVueComponent(MyComponent);
+
+        // pass in required props
+        const props = { 
+
+            // Something peeled off the global galaxy
+            somePropVal: Galaxy.someDealie, 
+
+            // ...or the current history
+            name: Galaxy.currentHistory.name,
+
+            // or maybe from the backbone model for this view
+            shoeSize: this.model.shoeSize
+        };
+
+        // VM is a Vue instance.
+        // this.$el is some jquery selection, first item is the actual DOM object
+        const container = this.$el[0];
+        const vm = mounter(props, container);
+    }
+}
+```

client/docs/never-use-jquery.md

@@ -0,0 +1,18 @@
+Did you know, jQuery is old enough to drive? It's old enough to get a driver's license. jQuery is a
+tool that was built to deal with inconsistencies in browsers that NO LONGER EXIST. In a couple
+years, jQuery will be voting, drinking, and capable of being tried as an adult. 
+
+If you think you need jQuery, you are mistaken. Please seek help from somebody in the wg-ui-ux
+workgroup. There is nothing jQuery can provide you that isn't already part of vanilla javascript or
+a standard well-tested 3rd party modern npm module.
+
+But that's not even the main problem. jQuery injects global initializations into every page on the
+site whether you want it or not. jQuery leverages an outdated initialization paradigm which is
+hugely problematic when it comes to unit testing and module building.
+
+One of our most important goals in redesigning Galaxy is the complete elimination of this library
+from our source, along with all its invasive plugins.
+
+### References
+* [You Don't Need jQuery](https://github.com/nefe/You-Dont-Need-jQuery)
+* [document.querySelector](https://developer.mozilla.org/en-US/docs/Web/API/Document/querySelector)

client/docs/providers-and-renderers.md

@@ -0,0 +1,164 @@
+We are using components in two very distinct ways. The first, "normal", kind of component will
+probably look familiar to anybody whis is already passingly familiar with Vue. Here the relevant
+information comes in as properties, any internal variables get defined in "data", changes go out as
+events.
+
+### Composition Example
+
+```html static
+<!-- Use of a renderless component with a display component -->
+<DoodadProvider v-slot="{ doodad, saveDoodad }">
+    <DoodadEditor :doodad="doodad" @update:doodad="saveDoodad" />
+</DoodadProvider>
+```
+
+In this example, we've created a component whose job is to deal with loading and updating the doodad
+object. Notice that there is no markup inside the DoodadProvider other than the explicit renderless
+component we previously made, but you are free to putput whatever you want in there, accessing the
+doodad and saveDoddad properties as desired, as well as any other local data with the only
+restriction that Vue needs a single root element in which to render.
+
+
+## The Renderer
+
+```html static
+<!-- DoodadEditor.vue, a simple "rendering" component -->
+
+<template>
+    <AutoComplete
+        :options="options"
+        :value="doodad.category"  
+        @select="saveCategory"
+    />
+</template>
+
+<script>
+
+export default {
+    props: { 
+        doodad: { type: Object, required: true },
+        options: { type: Array, required: true },
+    },
+    methods: {
+        saveCategory(newCategory) {
+            this.$emit('update:doodad', { ...this.doodad, category: newCategory });
+        }
+    }
+}
+
+</script>
+```
+
+This component accepts a mandatory input object (doodad), lets the user play with a category prop,
+then emits a fresh object after it's done. So what, what's the big deal? The important part to walk
+away from this dumb example is the things that are NOT in this sample component. 
+
+This component doesn't save the data. This component doesn't make ajax calls, and this component
+doesn't mutate its props. What it does do is to allow the user to edit some object named "doodad"
+and emits a new fresh version of that doodad when it's done. (Note also that we are using the
+update:propname event syntax whenever possible [to facilitate .sync
+binds](https://vuejs.org/v2/guide/components-custom-events.html#sync-Modifier)).
+
+Whatever happens to that new object is somebody else's job. As soon as you tie the data management
+to the rendering, the re-usability of your components craters.
+
+
+## The Provider
+
+As the opposite of the rendering component, a provider or renderless component, is pure logic. It
+should not know or care what your renderer is going to do with the data it provides. It is simply a
+fancy way of configuring some data manipulation methods. This is one of the many ways of reusing
+functionality available in Vue. Some others are [Mixins](https://vuejs.org/v2/guide/mixins.html),
+[Provide/Inject](https://v3.vuejs.org/guide/component-provide-inject.html) and (in Vue3) [the
+composition API](https://v3.vuejs.org/guide/composition-api-introduction.html).
+
+
+```js static
+// DoodadProvider.js
+
+import { loadDoodad, saveDoodad } from "./someAjaxQueryModule";
+
+export default {
+    data() {
+        return {
+            loaded: false,
+            doodad: null
+        }
+    },
+    methods: {
+        async saveDoodad(newVal) {
+            this.loaded = false;
+            const newVal = await saveDoodad(newVal);
+            this.doodad = newVal;
+            this.loaded = true;
+        },
+        async loadDoodad(newVal) {
+            this.loaded = false;
+            const newVal = await loadDoodad(newVal);
+            this.loaded = true;
+            return newVal;
+        }
+    },
+    async created() {
+        this.doodad = await loadDoodad();
+    },
+    render() {
+        return return this.$scopedSlots.default({
+            loaded: this.loaded,
+            doodad: this.doodad,
+            saveDoodad: this.saveDoodad
+        });
+    }
+}
+```
+
+Here is an example of a simple possible renderless provider. The important part about this is the
+render() function which simply renders [one big default
+slot](https://vuejs.org/v2/guide/components-slots.html) and binds some of its own properties to that
+slot for use by downstream components.
+
+## Unit Testing a renderless component
+
+Testing of a component like our editor is pretty straightforward and follows the standard Vue
+guidelines. If you did a clean-enough job you won't even need to mock anything since all your data
+dependencies should be delivered via props.
+
+But it's not so obvious how to unit-test a renderless provider. What do you check for? There's no
+mandatory markup, just one big empty slot.
+
+```js static
+// Testing a renderless component
+
+import { shallowMount } from "@vue/test-utils";
+import { getLocalVue, waitForLifecyleEvent } from "jest/helpers";
+import DoodadProvider from "./DoodadProvider";
+
+describe("A renderless component", () => {
+    const localVue = getLocalVue();
+    let wrapper;
+    let slotProps;
+
+    beforeEach(async () => {
+        wrapper = shallowMount(DoodadProvider, {
+            localVue,
+            // The mount fn allows you to hook into a slot for this very reason
+            scopedSlots: {
+                default(props) {
+                    slotProps = props;
+                },
+            },
+        });
+
+        // waits for "updated" Vue lifecycle hook to fire on the renderless 
+        // component. This is often good enough for waiting for 
+        // an initial ajax load to finish, for example
+        await waitForLifecyleEvent(wrapper.vm, "updated");
+    })
+
+    test("someProp", () => {
+        const { someProp } = slotProps;
+        expect(someProp).toExist();
+        // ...more tests
+    })
+})
+```

client/docs/readme.md

@@ -0,0 +1,71 @@
+### A component is really just a fancy function
+
+I'm not talking about how webpack turns it into a rendering function. That's obvious.
+
+I mean conceptually, props come in (like arguments) and events go out (like the return statements).
+A component is a fancy kind of function that can keep emitting results and accept changing inputs
+over time. In truth it more closely resembles an Observable, but an observable is ALSO a slightly
+fancier kind of function. 
+
+If you just think of a component as thing that takes input props and emits output events you're well
+on your way to using them well.
+
+The worst components are ones that might as well just be a big single page script. That's zero
+percent better than the spaghetti we're working so hard to replace. That's just repackaging all the
+problems of the old imperative class-based legacy code.
+
+### Get comfortable with events, limit your dependence on Vuex
+
+New vue programmers are ok at handing props to components, but they rarely use events effectively
+(at first). As a result they end up using a lot of global state, a million little data props and
+relying on imperfect globalized tools like Vuex or other imported dependencies for every little
+variable. 
+
+Vuex definitely has its uses, but not as many as you might expect given the way it is
+overly-emphasized in common tutorials. It's easy to walk away from an "Intro to Vue" video with the
+idea that all data must live in Vuex all the time. That's a really undesirable situation. 
+
+Although vuex is a well-organized (many would say over-organized) state machine, it is important
+to remember that it is still a kind of global injection and deserves to be considered as such.
+
+* [Should I Store This Data in
+  Vuex](https://markus.oberlehner.net/blog/should-i-store-this-data-in-vuex/)
+* [Vuex getters are great, but don’t overuse
+  them](https://codeburst.io/vuex-getters-are-great-but-dont-overuse-them-9c946689b414)
+
+Data persistence should be something that happens near the top of your component tree, not down in
+the guts. 
+
+Your first thought with a component should be: "How can I offload the handling of the results of
+this component to my caller?" The answer is usually going to be events. A component that simply
+accepts props and emits events can be re-used in more contexts than one that relies on an external
+global state to operate.
+
+#### Read up on .sync and v-model
+
+They're just fancy shorthands for a prop / event handler combination. They are fundamentally no
+different from props and events, but the syntax is important to understand.
+
+
+### Think carefully about what should really be in "data".
+
+Most of good component design boils down to answering the following question: What do I want to put
+in data, computed, and props?
+
+Data is the place where temp data goes that is not sensible to persist in Vuex or other
+application-wide global state, usually because its use is very specific to the operation of this
+particular component. There really should only be a few variables in data.
+
+#### Break down your own internal dependencies
+
+Most components only need one or two variables in data. If you have a large amount of data
+variables, it's worth taking a little time to stop and build a mini-dependency tree for yourself.
+You will probably find that almost everything can be written in terms of computed transformations on
+a small number of data and properties.
+
+Defining your values using computes will lead to a lot less "oh I forgot to update that
+variable"-style bugs.
+
+If you have more than a few data variables you probably (a) aren't leveraging computeds and
+properties, or (b) are trying to implement too many features for just one component. It is important
+separate your concerns in components just like you do in any other kind of programming.

client/docs/unit-testing/debugging-unit-tests.md

@@ -0,0 +1,76 @@
+### ...in VSCode
+
+There's a bunch of "how to debug javascript in vscode" cookbooks out there for the googling, but
+most of them don't bother explaining all the gotchas and what each of the cryptic configuration
+parameters actually does.
+
+I've gone ahead and annotated all the options, hopefully this will save some time, at least until VS
+code updates its test extensions again.
+
+#### To debug a single Jest test:
+
+1. Open a jest test (a file that ends with *.test.js)
+
+1. Make sure the test file is selected, especially if you have multiple files open. This process
+   will fail confusingly and without obvious error if you have not launched the debugger with the
+   actual Jest test file selected, and it's easy to accidentally click into another file if you've
+   got a dozen open.
+
+1. Place a breakpoint in the margin of the file. You can place breakpoints anywhere in your source,
+   but you must launch the debugger while the jest file is selected because that is where jest and
+   webpack will start compiling. Alternatively, you can manually override the selected file in the
+   configuration definition, like if you're testing the same file over and over again and don't want
+   to worry about selecting it.
+
+1. Update your .vscode/launch.json file to include the following launch configuration. If you don't
+   have a .vscode folder, you can just make one, but my experience is this all works better if you
+   have explicitly saved your VSCode project into a workspace rather than just using "code ." from a
+   terminal. Doing so will have initialized the .vscode folder already.
+
+1. Click on the "Run and Debug" tab from the vscode icons on the left and choose the sample launch
+   configuration (defined below) from the dropdown "run and debug". Or just hit F5.
+
+1. Wait a bit, for webpack to compile everything, eventually you should be able to hover over
+   variables near your breakpoint and see their values in the "Variables" section of the Run and
+   Debug pane.
+
+
+
+```json
+// sample launch.json
+{
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "type": "node",
+            "name": "debug selected jest test",
+            "request": "launch",
+            
+            // launches version of jest from inside the node_modules
+            // this means you need to have run yarn first
+            "program": "${workspaceFolder}/client/node_modules/jest/bin/jest",
+            "args": [
+                // Alias -i. 
+                // Normally jest opens up a bunch of workers to run all your tests faster
+                // but we don't want that right now.
+                "--runInBand",
+                
+                // finds jest config
+                "--config",
+                "${workspaceFolder}/client/tests/jest/jest.config.js",
+
+                // This is how vscode references the currently selected file
+                "${file}"
+            ],
+            "cwd": "${workspaceFolder}/client",
+
+            // opens jest output in integrated terminal
+            "console": "integratedTerminal",
+
+            // allows you to place breakpoints right in vscode's gutter
+            "disableOptimisticBPs": true,
+        },
+        
+    ]
+}
+```

client/docs/unit-testing/readme.md

@@ -0,0 +1,20 @@
+
+[Galaxy uses Jest](https://jestjs.io/) for its client-side unit testing
+framework.
+
+For testing Vue components, we use the [Vue testing
+utils](https://vue-test-utils.vuejs.org/) to mount individual components in a
+test bed and check them for rendered features.  Please use jest-based mocking
+for isolating test functionality.
+
+
+### Specific test scenarios & examples
+
+* [Mocking an imported
+dependency](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/tagService.test.js)
+* [Testing async
+operations](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/tagService.test.js)
+* [Testing a Vue component for expected rendering
+output](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/StatelessTags.test.js)
+* [Firing an event against a shallow mounted vue
+component](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/StatelessTags.test.js)

client/docs/unit-testing/strategies.md

@@ -0,0 +1,59 @@
+Part of making good code is making that code easy to test. 
+
+### Implement logic in pure functions when possible
+
+The more of your logic that is written in deterministic functions (i.e. no
+side-effects, same inputs always result in same outputs) the easier it is to
+test. Just load up the functions and supply suitable test inputs.
+
+There is almost definitely no such thing as a well-written 1000 line function.
+Most of whatever happened in that thing was probably deterministic and can be
+broken up into easily testable chunks.
+
+
+### Wrap native browser resources in a function so they can be easily mocked
+
+If your javascript needs to talk to the window object, or navigator, etc. wrap
+that in a function call so that it can be easily mocked during testing.
+
+
+#### Your Module
+```js static
+// myModule.js
+
+// ... other code
+
+export function redirectTo(url) {
+    window.location = url;
+}
+
+export function theThingYouReallyCareAbout() {
+    .....
+    redirectTo(somePlace);
+    ....
+}
+```
+
+#### Your test file
+```js static
+// myModule.test.js
+import { theThingYouReallyCareAbout, redirectTo } from "./myModule";
+
+// calling jest.mock on the appropriate import path wraps the exports and gives
+// access to new testing methods like mockImplementation
+jest.mock("./myModule");
+redirectTo.mockImplementation((url) => {
+    console.log(`I would have gone to: ${url}`);
+});
+
+// You are testing theThingYouReallyCareAbout, but that function needs
+// to call a window.relocate, By wrapping redirectTo as a function it was easy to mock
+// and avoid errors in your test, because native browser objects do not even exist
+// in the unit-testing environment.
+describe("theThingYouReallyCareAbout", () => {
+    it("Performs a redirect when Foo is clicked"){
+        const result = theThingYouReallyCareAbout(abc123);
+        expect(result).toBe(1);
+    }
+});
+```

client/docs/unit-testing/writing-tests.md

@@ -0,0 +1,73 @@
+### Clearly document the intent of your test
+
+Please remember that these tests are not _for_ you. They're for the people who
+come after you. It will be a lot easier to modify, repair and upgrade your code
+if they can figure out what you were originally hoping to accomplish.  Try to
+use as detailed 'expect' statements as possible -- overuse of 'toBeTruthy()'
+for example, can hide the intent of your test.
+
+Add a couple of comments. Use variable names that mean something.  Nobody's
+code is as self-documenting as they believe it to be.
+
+
+### Only test the public API that you define
+
+Internal implementations come and go with library upgrades and new tech. But
+the point of the unit test is to make sure your units work as designed....
+which means you need to... you know... design your code to work in units.
+
+Separate your concerns and identify the developer-facing methods and functions
+you expect them to use. Test THOSE. Everything else should probably be
+considered an implementation detail.
+
+The other side of the same coin is to test *only* the unit in question.  If your
+component has a model that uses a service that touches Vuex, which then uses
+Axios to fetch some data -- don't test all that at once.  Break things apart and
+mock functionality to isolate testing to units.  End to end testing is a
+separate thing that shouldn't be attempted using spec tests in Jest.
+
+Assume nobody cares _how_ your code works, we just need to know that the public
+API you designed _does_ work. If performance problems or new tech necessitate a
+re-write, these tests become a guide for the next implementation.
+
+
+### Writing a test file
+
+Jest will try to test any file ending in "\*.test.js". Please place your test
+files inside client/src folders right next to whatever files that they are
+testing.
+
+Jest has extensive documentation on the expect API, mocking, and more on the
+[official docs page](https://jestjs.io/docs/en/getting-started.html), which will
+be your best resource here.
+
+```js static
+// yourcode.test.js
+
+import { things } from "./yourcode.js";
+
+describe("some module you wrote", () => {
+    let transientVariables;
+    let serviceInstances;
+    let testData;
+
+    beforeEach(() => {
+        // setup your code (if necessary)
+    });
+
+    afterEach(() => {
+        // teardown your code (so it doesn't ruin the next test)
+    });
+
+    it("should do something or other", () => {
+        expect(workflowNodeCount()).toBe(5);
+    });
+});
+```
+
+
+### Check out the Jest helper functions
+
+We have created some [common helpers for common testing
+scenarios](https://github.com/galaxyproject/galaxy/blob/dev/client/tests/jest/helpers.js). 
+

client/galaxy/config/development.js

@@ -1,3 +0,0 @@
-export default {
-    name: "development configs"
-}

client/galaxy/config/production.js

@@ -1,3 +0,0 @@
-export default {
-    name: "production configs"
-}

client/galaxy/config/testing.js

@@ -1,4 +0,0 @@
-export default {
-    name: "unit testing configs",
-    testBuild: true,
-};

client/galaxy/docs/README.md

@@ -1,5 +0,0 @@
-The \*.md files in this directory are rendered as a style guide generated when
-running ```yarn run styleguide```.
-
-For more details see [Vue
-Styleguidist](https://github.com/vue-styleguidist/vue-styleguidist).

client/galaxy/docs/bootstrap.md

@@ -1,379 +0,0 @@
-## Buttons
-
-Regular buttons
-
-```vue
-<div>
-   <button type="button" class="btn btn-primary">Primary</button>
-   <button type="button" class="btn btn-secondary">Secondary</button>
-   <button type="button" class="btn btn-success">Success</button>
-   <button type="button" class="btn btn-info">Info</button>
-   <button type="button" class="btn btn-warning">Warning</button>
-   <button type="button" class="btn btn-danger">Danger</button>
-   <button type="button" class="btn btn-link">Link</button>
-</div>
-```
-
-Disabled
-
-```vue
-<div>
-   <button type="button" class="btn btn-primary disabled">Primary</button>
-   <button type="button" class="btn btn-secondary disabled">Secondary</button>
-   <button type="button" class="btn btn-success disabled">Success</button>
-   <button type="button" class="btn btn-info disabled">Info</button>
-   <button type="button" class="btn btn-warning disabled">Warning</button>
-   <button type="button" class="btn btn-danger disabled">Danger</button>
-   <button type="button" class="btn btn-link disabled">Link</button>
-</div>
-```
-
-```vue
-<div>
-   <button type="button" class="btn btn-outline-primary">Primary</button>
-   <button type="button" class="btn btn-outline-secondary">Secondary</button>
-   <button type="button" class="btn btn-outline-success">Success</button>
-   <button type="button" class="btn btn-outline-info">Info</button>
-   <button type="button" class="btn btn-outline-warning">Warning</button>
-   <button type="button" class="btn btn-outline-danger">Danger</button>
-</div>
-```
-
-```vue
- <div class="btn-group" role="group" aria-label="Button group with nested dropdown">
-   <button type="button" class="btn btn-primary">Primary</button>
-   <div class="btn-group" role="group">
-     <button id="btnGroupDrop1" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"></button>
-     <div class="dropdown-menu" aria-labelledby="btnGroupDrop1">
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-     </div>
-   </div>
- </div>
-```
-
-```vue
- <div class="btn-group" role="group" aria-label="Button group with nested dropdown">
-   <button type="button" class="btn btn-success">Success</button>
-   <div class="btn-group" role="group">
-     <button id="btnGroupDrop2" type="button" class="btn btn-success dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"></button>
-     <div class="dropdown-menu" aria-labelledby="btnGroupDrop2">
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-     </div>
-   </div>
- </div>
-```
-
-```vue
- <div class="btn-group" role="group" aria-label="Button group with nested dropdown">
-   <button type="button" class="btn btn-info">Info</button>
-   <div class="btn-group" role="group">
-     <button id="btnGroupDrop3" type="button" class="btn btn-info dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"></button>
-     <div class="dropdown-menu" aria-labelledby="btnGroupDrop3">
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-       <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-     </div>
-   </div>
- </div>
-```
-
-```vue
-   <div class="btn-group" role="group" aria-label="Button group with nested dropdown">
-     <button type="button" class="btn btn-danger">Danger</button>
-     <div class="btn-group" role="group">
-       <button id="btnGroupDrop4" type="button" class="btn btn-danger dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"></button>
-       <div class="dropdown-menu" aria-labelledby="btnGroupDrop4">
-         <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-         <a class="dropdown-item" href="javascript:void(0)">Dropdown link</a>
-       </div>
-     </div>
-   </div>
-```
-
-```vue
- <div>
-   <button type="button" class="btn btn-primary btn-lg">Large button</button>
-   <button type="button" class="btn btn-primary">Default button</button>
-   <button type="button" class="btn btn-primary btn-sm">Small button</button>
- </div>
-```
-
-## Alerts
-
-```vue
-<div class="alert alert-dismissable alert-warning">
-  <button type="button" class="close" data-dismiss="alert">&times;</button>
-  <h4>Warning!</h4>
-  <p>Best check yo self, you're not looking too good. Nulla vitae elit libero, a pharetra augue. Praesent commodo cursus magna, <a href="javascript:void(0)" class="alert-link">vel scelerisque nisl consectetur et</a>.</p>
-</div>
-```
-
-```vue
-<div class="alert alert-dismissable alert-danger">
-  <button type="button" class="close" data-dismiss="alert">&times;</button>
-  <strong>Oh snap!</strong> <a href="javascript:void(0)" class="alert-link">Change a few things up</a> and try submitting again.
-</div>
-```
-
-```vue
-<div class="alert alert-dismissable alert-success">
-  <button type="button" class="close" data-dismiss="alert">&times;</button>
-  <strong>Well done!</strong> You successfully read <a href="javascript:void(0)" class="alert-link">this important alert message</a>.
-</div>
-```
-
-```vue
-<div class="alert alert-dismissable alert-info">
-  <button type="button" class="close" data-dismiss="alert">&times;</button>
-  <strong>Heads up!</strong> This <a href="javascript:void(0)" class="alert-link">alert needs your attention</a>, but it's not super important.
-</div>
-```
-
-## Badges
-
-```vue
-<div>
-  <span class="badge badge-primary">Primary</span>
-  <span class="badge badge-secondary">Secondary</span>
-  <span class="badge badge-success">Success</span>
-  <span class="badge badge-warning">Warning</span>
-  <span class="badge badge-danger">Danger</span>
-  <span class="badge badge-info">Info</span>
-</div>
-```
-
-```vue
-<div class="">
-  <ul class="nav nav-pills">
-    <li class="active"><a href="javascript:void(0)">Home <span class="badge">42</span></a></li>
-    <li><a href="javascript:void(0)">Profile <span class="badge-pill"></span></a></li>
-    <li><a href="javascript:void(0)">Messages <span class="badge-pill">3</span></a></li>
-  </ul>
-</div>
-```
-
-## Tables
-
-```vue
-<div class="">
-  <table class="table table-striped table-bordered table-hover">
-    <thead>
-      <tr>
-        <th>#</th>
-        <th>Column heading</th>
-        <th>Column heading</th>
-        <th>Column heading</th>
-      </tr>
-    </thead>
-    <tbody>
-      <tr>
-        <td>1</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr>
-        <td>2</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr>
-        <td>3</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr class="table-success">
-        <td>4</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr class="table-danger">
-        <td>5</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr class="table-warning">
-        <td>6</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-      <tr class="table-active">
-        <td>7</td>
-        <td>Column content</td>
-        <td>Column content</td>
-        <td>Column content</td>
-      </tr>
-    </tbody>
-  </table>
-</div>
-```
-
-## Cards
-
-```vue
-<div class="row">
-  <div class="col-lg-4">
-    <div class="bs-component">
-      <div class="card text-white bg-primary mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Primary card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-secondary mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Secondary card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-success mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Success card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-danger mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Danger card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-warning mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Warning card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-info mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Info card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card bg-light mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Light card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card text-white bg-dark mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Dark card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-    </div>
-  </div>
-  <div class="col-lg-4">
-    <div class="bs-component">
-      <div class="card border-primary mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Primary card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-secondary mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Secondary card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-success mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Success card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-danger mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Danger card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-warning mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Warning card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-info mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Info card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-light mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Light card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-      <div class="card border-dark mb-3" style="max-width: 20rem;">
-        <div class="card-header">Header</div>
-        <div class="card-body">
-          <h4 class="card-title">Dark card title</h4>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-      </div>
-    </div>
-  </div>
-
-  <div class="col-lg-4">
-    <div class="bs-component">
-      <div class="card mb-3">
-        <h3 class="card-header">Card header</h3>
-        <div class="card-body">
-          <h5 class="card-title">Special title treatment</h5>
-          <h6 class="card-subtitle text-muted">Support card subtitle</h6>
-        </div>
-        <img style="height: 200px; width: 100%; display: block;" src="data:image/svg+xml;charset=UTF-8,%3Csvg%20width%3D%22318%22%20height%3D%22180%22%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20viewBox%3D%220%200%20318%20180%22%20preserveAspectRatio%3D%22none%22%3E%3Cdefs%3E%3Cstyle%20type%3D%22text%2Fcss%22%3E%23holder_158bd1d28ef%20text%20%7B%20fill%3Argba(255%2C255%2C255%2C.75)%3Bfont-weight%3Anormal%3Bfont-family%3AHelvetica%2C%20monospace%3Bfont-size%3A16pt%20%7D%20%3C%2Fstyle%3E%3C%2Fdefs%3E%3Cg%20id%3D%22holder_158bd1d28ef%22%3E%3Crect%20width%3D%22318%22%20height%3D%22180%22%20fill%3D%22%23777%22%3E%3C%2Frect%3E%3Cg%3E%3Ctext%20x%3D%22129.359375%22%20y%3D%2297.35%22%3EImage%3C%2Ftext%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E" alt="Card image">
-        <div class="card-body">
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-        </div>
-        <ul class="list-group list-group-flush">
-          <li class="list-group-item">Cras justo odio</li>
-          <li class="list-group-item">Dapibus ac facilisis in</li>
-          <li class="list-group-item">Vestibulum at eros</li>
-        </ul>
-        <div class="card-body">
-          <a href="javascript:void(0)" class="card-link">Card link</a>
-          <a href="javascript:void(0)" class="card-link">Another link</a>
-        </div>
-        <div class="card-footer text-muted">
-          2 days ago
-        </div>
-      </div>
-      <div class="card">
-        <div class="card-body">
-          <h4 class="card-title">Card title</h4>
-          <h6 class="card-subtitle mb-2 text-muted">Card subtitle</h6>
-          <p class="card-text">Some quick example text to build on the card title and make up the bulk of the card's content.</p>
-          <a href="javascript:void(0)" class="card-link">Card link</a>
-          <a href="javascript:void(0)" class="card-link">Another link</a>
-        </div>
-      </div>
-    </div>
-  </div>
-</div>
-```

client/galaxy/docs/galaxy-buttons.md

@@ -1,49 +0,0 @@
-## Buttons
-
-```vue
-<button>Just a default button</button>
-```
-
-```vue
-<a href="javascript:void(0)" class="action-button">An anchor with .action-button</a>
-```
-
-All the crazy permutations of menu button...
-
-```vue
-<a href="javascript:void(0)" class="menubutton">An anchor with .menu-button</a>
-```
-
-```vue
-<a href="javascript:void(0)" class="menubutton popup">An anchor with .menu-button.popup</a>
-```
-
-```vue
-<a href="javascript:void(0)" class="menubutton popup split">
-  <a class="menubutton-label">An anchor with .menu-button.popup.split</a>
-</a>
-```
-
-## Radio Buttons
-
-As generated by mvc.ui.ui-options
-
-```vue
-<div class="btn-group btn-group-toggle" data-toggle="buttons">
-  <label class="btn btn-secondary active">
-    <input type="radio" name="options" id="option1" autocomplete="off" checked> Active
-  </label>
-  <label class="btn btn-secondary">
-    <input type="radio" name="options" id="option2" autocomplete="off"> Radio
-  </label>
-  <label class="btn btn-secondary">
-    <input type="radio" name="options" id="option3" autocomplete="off"> Radio
-  </label>
-</div>
-```
-
-## Pagination
-
-```vue
-<ul class="pagination"><li class="page-item disabled"><a class="page-link" href="#page/1"><span class="fa fa-angle-double-left"></span></a></li><li class="page-item disabled"><a class="page-link" href="#page/1">0</a></li><li class="page-item active"><a class="page-link" href="#page/1">1</a></li><li class="page-item"><a class="page-link" href="#page/2">2</a></li><li class="page-item"><a class="page-link" href="#page/4"><span class="fa fa-angle-double-right"></span></a></li></ul>
-```

client/galaxy/docs/galaxy-forms.md

@@ -1,55 +0,0 @@
-## Forms
-
-Manually crafted "tool" form class, this is broken in the BS4 branch I think.
-
-```vue
-<div class="tool-form">
-  <form name="foo">
-     <div class="form-row">
-       <label>Label Input 1</label>
-       <input id="input1" type="text" name="input1" size="40" />
-     </div>
-     <div class="form-row">
-       <input type="submit" id="send" name="submit" value="submit" />
-     </div>
-  </form>
-</div>
-```
-
-Portlet variant generated by mvc.form.form-view
-
-```vue
-<div class="ui-portlet-limited" id="uid-8">
-  <div class="portlet-header">
-  <div class="portlet-operations"></div>
-  <div class="portlet-title">
-    <i class="portlet-title-icon fa fa-unlock-alt" style="display: inline;"></i>
-    <span class="portlet-title-text">Portlet Title</span></div>
-  </div>
-  <div class="portlet-content">
-    <div class="portlet-body">
-	  <div class="ui-message alert alert-info"></div>
-	  <div>
-	    <div class="ui-form-element section-row">
-		  <div class="ui-form-error ui-error"><span class="fa fa-arrow-down"></span><span class="ui-form-error-text"></span></div>
-		  <div class="ui-form-title">
-		  	<div class="ui-form-collapsible" style="display: none;">
-		  	  <i class="ui-form-collapsible-icon"></i>
-		  	  <span class="ui-form-collapsible-text"></span>
-		  	</div>
-		  	<span class="ui-form-title-text">Text Field 1</span>
-		  </div>
-		  <div class="ui-form-field">
-		  	<input class="ui-input" id="field-uid-4" type="text">
-		  	<span class="ui-form-info"></span>
-		  	<div class="ui-form-backdrop" style="display: none;"></div>
-		  </div>
-		  <div class="ui-form-preview" style="display: none;"></div>
-		</div>
-		<div class="ui-form-element section-row">
-		  <div class="ui-form-error ui-error" style="display: none;"><span class="fa fa-arrow-down"></span><span class="ui-form-error-text"></span></div>
-		  <div class="ui-form-title"><div class="ui-form-collapsible" style="display: none;"><i class="ui-form-collapsible-icon"></i><span class="ui-form-collapsible-text"></span></div><span class="ui-form-title-text" style="display: inline;">Password</span></div>
-		  <div class="ui-form-field">
-		  	<input class="ui-input" type="password"><span class="ui-form-info"></span><div class="ui-form-backdrop" style="display: none;"></div></div><div class="ui-form-preview" style="display: none;"></div></div>
-		<div class="ui-form-element section-row" id="uid-7" style="display: none;"><div class="ui-form-error ui-error" style="display: none;"><span class="fa fa-arrow-down"></span><span class="ui-form-error-text"></span></div><div class="ui-form-title"><div class="ui-form-collapsible" style="display: none;"><i class="ui-form-collapsible-icon"></i><span class="ui-form-collapsible-text"></span></div><span class="ui-form-title-text" style="display: inline;">token</span></div><div class="ui-form-field"><div id="field-uid-7"><div style="display: none;"></div><div></div></div><span class="ui-form-info"></span><div class="ui-form-backdrop" style="display: none;"></div></div><div class="ui-form-preview" style="display: none;"></div></div></div></div><div class="portlet-buttons"><button type="button" class="ui-button-default btn btn-primary ui-clear-float" id="submit" data-original-title="" title=""><i class="icon fa fa-save ui-margin-right"></i><span class="title">Submit</span><div class="progress" style="display: none;"><div class="progress-bar" style="width: 0%;"></div></div></button></div></div><div class="portlet-backdrop"></div></div>
-```

client/galaxy/docs/galaxy-masthead.md

@@ -1,69 +0,0 @@
-## Masthead
-
-As generated by layout.masthead.js
-
-Default height:
-
-```vue
-<nav id="masthead" class="navbar navbar-expand justify-content-center navbar-dark bg-dark">
-  <a class="navbar-brand">
-    <img class="navbar-brand-image"/>
-    <span class="navbar-brand-title">Title</span>
-  </a>
-  <ul class="navbar-nav">
-    <li class="nav-item">
-      <a class="nav-link">Header 1</a>
-    </li>
-    <li class="nav-item dropdown">
-      <a class="nav-link dropdown-toggle">Header 2</a>
-    </li>
-    <li class="nav-item active">
-      <a class="nav-link">Active Header</a>
-    </li>
-  </ul>
-</nav>
-```
-
-Override height with "height: 80px;"
-
-```vue
-<nav id="masthead" class="navbar navbar-expand justify-content-center navbar-dark bg-dark" style="height: 80px;">
-  <a class="navbar-brand">
-    <img class="navbar-brand-image"/>
-    <span class="navbar-brand-title">Title</span>
-  </a>
-  <ul class="navbar-nav">
-    <li class="nav-item">
-      <a class="nav-link">Header 1</a>
-    </li>
-    <li class="nav-item dropdown">
-      <a class="nav-link dropdown-toggle">Header 2</a>
-    </li>
-    <li class="nav-item active">
-      <a class="nav-link">Active Header</a>
-    </li>
-  </ul>
-</nav>
-```
-
-Override height with "height: 4rem;"
-
-```vue
-<nav id="masthead" class="navbar navbar-expand justify-content-center navbar-dark bg-dark" style="height: 4rem;">
-  <a class="navbar-brand">
-    <img class="navbar-brand-image"/>
-    <span class="navbar-brand-title">Title</span>
-  </a>
-  <ul class="navbar-nav">
-    <li class="nav-item">
-      <a class="nav-link">Header 1</a>
-    </li>
-    <li class="nav-item dropdown">
-      <a class="nav-link dropdown-toggle">Header 2</a>
-    </li>
-    <li class="nav-item active">
-      <a class="nav-link">Active Header</a>
-    </li>
-  </ul>
-</nav>
-```

client/galaxy/docs/galaxy-menus.md

@@ -1,19 +0,0 @@
-## Popup menus
-
-These are the classes for the menu itself, normally floating, so placed inside
-a relative element.
-
-```vue
-<div style="position: relative; height: 12rem;">
-  <div class="popmenu-wrapper" style="top: 0;">
-    <ul class="dropdown-menu">
-      <li class="head"><a>Heading one</a></li>
-      <li><a>An item</a></li>
-      <li><a>Another item</a></li>
-      <li class="head"><a>Heading two</a></li>
-      <li><a>Third item</a></li>
-      <li><a>Last item</a></li>
-    </ul>
-  </div>
-</div>
-```

client/galaxy/docs/galaxy-messages.md

@@ -1,33 +0,0 @@
-### Panel Messages
-
-Messages that appear across the top of the panel view below the masthead.
-
-```vue
-<div>
-  <div v-for="type in ['done', 'info', 'warning', 'error']">
-    <div v-bind:class="'panel-' + type + '-message'">I'm a panel-{{type}}-message</div>
-  </div>
-</div>
-```
-
-### Large Messages
-
-Used for providing feedback inline.
-
-```vue
-<div>
-  <div v-for="type in ['done', 'info', 'warning', 'error']">
-    <div v-bind:class="type + 'messagelarge'">I'm a {{type}}messagelarge</div>
-  </div>
-</div>
-```
-
-### Small Messages
-
-```vue
-<div>
-  <div v-for="type in ['done', 'info', 'warning', 'error']">
-    <div v-bind:class="type + 'message'">I'm a {{type}}message</div>
-  </div>
-</div>
-```

client/galaxy/docs/galaxy-panels.md

@@ -1,20 +0,0 @@
-## Panel (toolMenuContainer)
-
-```vue
-<div style="height: 200px;">
-  <div style="position: absolute; width: 250px; height: 200px; border: dotted gray 1px">
-    <div class="unified-panel-header">
-      <div class="unified-panel-header-inner">
-        Header
-      </div>
-    </div>
-    <div class="unified-panel-body">
-      <div class="toolMenuContainer">
-      one<br>
-      two<br>
-      three<br>
-      </div>
-    </div>
-  </div>
-</div>
-```

client/galaxy/docs/galaxy-tables.md

@@ -1,14 +0,0 @@
-## Tables
-
-Tables using the .grid class
-
-```vue
-<table class="grid">
-  <thead class="grid-table-header">
-    <tr><th>One</th><th>Two</th></tr>
-  </thead>
-  <tbody class="grid-table-body">
-    <tr><td>Value 1</td><td>Value 2</td></tr>
-  </tbody>
-</table>
-```

client/galaxy/docs/galaxy-tabs.md

@@ -1,32 +0,0 @@
-## Tabs
-
-Tabs as generated by mvc.ui.ui-tabs
-
-```vue
-<ul style="display: flex;" class="tab-navigation nav nav-tabs">
-	<li class="tab-element nav-item" id="tab-attribute" style="display: list-item;" data-original-title="" title="">
-		<a class="nav-link active" id="tab-title-link-attribute">
-			<i class="tab-icon fa fa-bars"></i>
-			<span id="tab-title-text-attribute" class="tab-title-text">Attributes</span>
-		</a>
-	</li>
-	<li class="tab-element nav-item" id="tab-convert" style="display: list-item;" data-original-title="" title="">
-		<a class="nav-link" id="tab-title-link-convert">
-			<i class="tab-icon fa fa-gear"></i>
-			<span id="tab-title-text-convert" class="tab-title-text">Convert</span>
-		</a>
-	</li>
-	<li class="tab-element nav-item" id="tab-datatype" style="display: list-item;" data-original-title="" title="">
-		<a class="nav-link" id="tab-title-link-datatype">
-			<i class="tab-icon fa fa-database"></i>
-			<span id="tab-title-text-datatype" class="tab-title-text">Datatypes</span>
-		</a>
-	</li>
-	<li class="tab-element nav-item" id="tab-permissions" style="display: list-item;" data-original-title="" title="">
-		<a class="nav-link" id="tab-title-link-permissions">
-			<i class="tab-icon fa fa-user"></i>
-			<span id="tab-title-text-permissions" class="tab-title-text">Permissions</span>
-		</a>
-	</li>
-</ul>
-```

client/galaxy/jsconfig.json

@@ -1,5 +0,0 @@
-{
-    "compilerOptions": {
-        "baseUrl": "./scripts/"
-    }
-}

client/galaxy/scripts/components/Citations.vue

@@ -1,140 +0,0 @@
-<template>
-    <div>
-        <b-card class="citation-card" v-if="!simple" header-tag="nav">
-            <template v-slot:header>
-                <b-nav card-header tabs>
-                    <b-nav-item
-                        :active="outputFormat === outputFormats.CITATION"
-                        @click="outputFormat = outputFormats.CITATION"
-                        >Citations (APA)</b-nav-item
-                    >
-                    <b-nav-item
-                        :active="outputFormat === outputFormats.BIBTEX"
-                        @click="outputFormat = outputFormats.BIBTEX"
-                        >BibTeX</b-nav-item
-                    >
-                </b-nav>
-            </template>
-            <div v-if="source === 'histories'" class="infomessage">
-                When writing up your analysis, remember to include all references that should be cited in order to
-                completely describe your work. Also, please remember to
-                <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
-            </div>
-            <div class="citations-formatted">
-                <template v-for="citation in formattedCitations">
-                    <div :key="citation" class="formatted-reference" v-html="citation"></div>
-                </template>
-            </div>
-        </b-card>
-        <div v-else-if="formattedCitations.length">
-            <b-btn v-b-toggle="id" variant="primary">Citations</b-btn>
-            <b-collapse
-                :id="id.replace(/ /g, '_')"
-                class="mt-2"
-                @show="$emit('show')"
-                @shown="$emit('shown')"
-                @hide="$emit('hide')"
-                @hidden="$emit('hidden')"
-            >
-                <b-card>
-                    <template v-for="citation in formattedCitations">
-                        <div :key="citation" class="formatted-reference" v-html="citation"></div>
-                    </template>
-                </b-card>
-            </b-collapse>
-        </div>
-    </div>
-</template>
-<script>
-import Vue from "vue";
-import BootstrapVue from "bootstrap-vue";
-import axios from "axios";
-import Cite from "citation-js";
-import { getAppRoot } from "onload/loadConfig";
-
-Vue.use(BootstrapVue);
-
-const outputFormats = Object.freeze({
-    CITATION: "bibliography",
-    BIBTEX: "bibtex",
-    RAW: "raw",
-});
-
-export default {
-    props: {
-        source: {
-            type: String,
-            required: true,
-        },
-        id: {
-            type: String,
-            required: true,
-        },
-        simple: {
-            type: Boolean,
-            required: false,
-            default: false,
-        },
-    },
-    data() {
-        return {
-            citations: [],
-            errors: [],
-            showCollapse: false,
-            outputFormats,
-            outputFormat: outputFormats.CITATION,
-        };
-    },
-    computed: {
-        formattedCitations() {
-            const processed = [];
-            if (this.citations.length !== 0) {
-                for (const c of this.citations) {
-                    let link = "";
-                    if (c.cite.data && c.cite.data[0] && c.cite.data[0].URL) {
-                        link = `&nbsp<a href="${c.cite.data[0].URL}" target="_blank">[Link]</a>`;
-                    }
-                    const formattedCitation = c.cite.format(this.outputFormat, {
-                        format: "html",
-                        template: "apa",
-                        lang: "en-US",
-                        append: link,
-                    });
-                    processed.push(formattedCitation);
-                }
-            }
-            return processed;
-        },
-    },
-    updated() {
-        this.$nextTick(() => {
-            this.$emit("rendered");
-        });
-    },
-    created() {
-        axios
-            .get(`${getAppRoot()}api/${this.source}/${this.id}/citations`)
-            .then((response) => {
-                response.data.forEach((rawCitation) => {
-                    try {
-                        const cite = new Cite(rawCitation.content);
-                        this.citations.push({ raw: rawCitation.content, cite: cite });
-                    } catch (err) {
-                        console.warn(`Error parsing bibtex: ${err}`);
-                    }
-                });
-            })
-            .catch((e) => {
-                console.error(e);
-            });
-    },
-};
-</script>
-<style>
-.citation-card .card-header .nav-tabs {
-    margin-bottom: -0.75rem !important;
-}
-.formatted-reference {
-    margin-bottom: 0.5rem;
-}
-</style>