Merge branch 'release_19.09' into add_k8s_job_ttl

Author: nuwang

.ci/flake8_blacklist.txt

@@ -2,6 +2,10 @@
 .tox
 .venv
 .venv3
+packages/*/.venv
+packages/*/build
+packages/*/dist
+packages/venv
 node_modules
 database
 doc/build
@@ -11,3 +15,5 @@ lib/galaxy/util/jstree.py
 lib/galaxy/web/proxy/js/node_modules
 static/maps
 static/scripts
+build
+dist

.ci/jenkins/selenium-compose/Dockerfile

@@ -1,5 +1,5 @@
 FROM toolshed/requirements
-MAINTAINER John Chilton, jmchilton@gmail.com
+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 && \

.ci/validate_test_tools.sh

@@ -1,11 +1,11 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
 xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
 # Lint the XSD
 xmllint --noout "$xsd_path"
 
 test_tools_path='test/functional/tools'
-tool_files_list=$(ls "$test_tools_path"/*xml | grep -v '_conf.xml$')
+tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$')
 sh scripts/validate_tools.sh $tool_files_list

.circleci/config.yml

@@ -25,7 +25,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -83,31 +83,31 @@ jobs:
             - ~/repo
   py27_lint:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py27-lint
   py27_unit:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py27-unit
   py27_docstring:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py27-lint_docstring_include_list
   py27_first_startup:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -140,23 +140,28 @@ jobs:
     steps:
       - *restore_repo_cache
       - *install_tox
-      - run: sudo apt-get update
-      # For uwsgi
-      - run: sudo apt-get install -y libpython3.5-dev
       - run: tox -e py35-first_startup
   validate_test_tools:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - run: sudo apt-get update
       - run: sudo apt-get install -y libxml2-utils
       - *install_tox
       - run: tox -e validate_test_tools
+  test_galaxy_packages:
+    docker:
+      - image: circleci/python:3.5
+    <<: *set_workdir
+    steps:
+      - *restore_repo_cache
+      - *install_tox
+      - run: tox -e test_galaxy_packages
   check_py3_compatibility:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -202,6 +207,8 @@ workflows:
           <<: *requires_get_code
       - py35_first_startup:
           <<: *requires_get_code
+      - test_galaxy_packages:
+          <<: *requires_get_code
       - validate_test_tools:
           <<: *requires_get_code
       - check_py3_compatibility:

.gitignore

@@ -9,6 +9,17 @@ scripts/scramble/archives
 .venv
 .venv3
 
+# Python build artifacts
+build
+dist
+lib/galaxy.egg-info
+.eggs
+
+# Generated static content
+lib/galaxy/web/framework/static/maps
+lib/galaxy/web/framework/static/scripts
+lib/galaxy/web/framework/static/style
+
 # Database stuff
 database/beaker_sessions
 database/citations
@@ -18,6 +29,7 @@ database/files
 database/jobs_directory
 database/job_working_directory
 database/pbs
+database/shed_tools
 database/test_errors
 database/tmp
 database/*.sqlite
@@ -72,6 +84,7 @@ job_metrics_conf.xml
 workflow_schedulers_conf.xml
 config/*
 config/plugins/interactive_environments/**/*.ini
+config/plugins/**/.cache
 !config/plugins
 static/welcome.html.*
 static/welcome.html
@@ -160,3 +173,6 @@ packages/*/*.egg-info
 .DS_Store
 *.rej
 *~
+
+# Plugin build artifacts -- TODO make this more generic as a part of the standard plugin interface
+config/plugins/visualizations/**/static/script.js

.travis.yml

@@ -14,7 +14,7 @@ install:
         sh scripts/common_startup.sh
         wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
         mv db_gx_rev_0127.sqlite database/universe.sqlite
-        sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
+        sh manage_db.sh upgrade
     elif [ "$TOX_ENV" == "py35-first_startup" ]; then
         MINICONDA_URL="https://repo.anaconda.com/miniconda"
         MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"

CONTRIBUTING.md

@@ -112,5 +112,5 @@ If no existing Galaxy issue seems appropriate, a new issue can be opened using
   this repository - please checkout the
   [tools-iuc](https://github.com/galaxyproject/tools-iuc) repository on GitHub.
 
-  More information about tool development can be found [on the comunity
+  More information about tool development can be found [on the community
   hub](https://galaxyproject.org/develop).

Makefile

@@ -10,7 +10,7 @@ RELEASE_NEXT:=16.04
 RELEASE_NEXT_BRANCH:=dev
 RELEASE_UPSTREAM:=upstream
 MY_UPSTREAM:=origin
-CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/webapps/config_manage.py
+CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
 PROJECT_URL?=https://github.com/galaxyproject/galaxy
 DOCS_DIR=doc
 DOC_SOURCE_DIR=$(DOCS_DIR)/source

client/.node_version

@@ -1 +1 @@
-10.13.0
+10.15.3

client/galaxy/docs/bootstrap.md

@@ -45,8 +45,8 @@ Disabled
    <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="#">Dropdown link</a>
-       <a class="dropdown-item" href="#">Dropdown link</a>
+       <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>
@@ -58,8 +58,8 @@ Disabled
    <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="#">Dropdown link</a>
-       <a class="dropdown-item" href="#">Dropdown link</a>
+       <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>
@@ -71,8 +71,8 @@ Disabled
    <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="#">Dropdown link</a>
-       <a class="dropdown-item" href="#">Dropdown link</a>
+       <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>
@@ -84,12 +84,11 @@ Disabled
      <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="#">Dropdown link</a>
-         <a class="dropdown-item" href="#">Dropdown link</a>
+         <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>
- </div>
 ```
 
 ```vue
@@ -106,28 +105,28 @@ Disabled
 <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="#" class="alert-link">vel scelerisque nisl consectetur et</a>.</p>
+  <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="#" class="alert-link">Change a few things up</a> and try submitting again.
+  <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="#" class="alert-link">this important alert message</a>.
+  <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="#" class="alert-link">alert needs your attention</a>, but it's not super important.
+  <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>
 ```
 
@@ -147,9 +146,9 @@ Disabled
 ```vue
 <div class="">
   <ul class="nav nav-pills">
-    <li class="active"><a href="#">Home <span class="badge">42</span></a></li>
-    <li><a href="#">Profile <span class="badge-pill"></span></a></li>
-    <li><a href="#">Messages <span class="badge-pill">3</span></a></li>
+    <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>
 ```
@@ -358,8 +357,8 @@ Disabled
           <li class="list-group-item">Vestibulum at eros</li>
         </ul>
         <div class="card-body">
-          <a href="#" class="card-link">Card link</a>
-          <a href="#" class="card-link">Another link</a>
+          <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
@@ -370,8 +369,8 @@ Disabled
           <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="#" class="card-link">Card link</a>
-          <a href="#" class="card-link">Another link</a>
+          <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>