Merge remote-tracking branch 'origin/dev' into api.batch

.ci/check_controller.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+MAX_LINE_COUNT=19900
+project_dir=`dirname $0`/..
+cd $project_dir
+bash -c "[ `find lib/galaxy/webapps/galaxy/controllers/ -name '*.py' | xargs wc -l | tail -n 1 | awk '{ printf \$1; }'` -lt $MAX_LINE_COUNT ]"

.ci/check_mako.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+MAX_MAKO_COUNT=330
+project_dir=`dirname $0`/..
+cd $project_dir
+bash -c "[ `find templates -iname '*.mako'  | wc -l | cut -f1 -d' '` -lt $MAX_MAKO_COUNT ]"

.ci/flake8_blacklist.txt

@@ -1,16 +1,9 @@
 .venv/
-contrib/
 client/
 database/
 doc/patch.py
 doc/source/conf.py
-lib/galaxy/model/migrate/versions/
-lib/galaxy/model/tool_shed_install/migrate/versions/
-lib/galaxy/util/pastescript/serve.py
-lib/galaxy/webapps/tool_shed/model/migrate/versions/
-lib/galaxy_utils/
-lib/pkg_resources.py
-lib/tool_shed/
+lib/galaxy/util/jstree.py
 scripts/api/
 scripts/data_libraries/
 scripts/loc_files/
@@ -20,8 +13,15 @@ scripts/scramble/
 scripts/tool_shed/
 scripts/tools/
 scripts/transfer.py
-test/base/
-test/casperjs/
-test/install_and_test_tool_shed_repositories/
-test/tool_shed/
-tools/
+tools/data_source/
+tools/filters/
+tools/genomespace/
+tools/meme/
+tools/metag_tools/
+tools/phenotype_association/
+tools/plotting/
+tools/solid_tools/
+tools/sr_assembly/
+tools/sr_mapping/
+tools/validation/
+tools/visualization/

.ci/flake8_py3_wrapper.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -e
+
+flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` `paste -s .ci/py3_sources.txt`

.ci/flake8_wrapper.sh

@@ -4,5 +4,5 @@ set -e
 
 flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
 
-# Look for obviously broken stuff lots more places.
-flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py,lib/pkg_resources.py lib/ test/{api,unit}
+# Apply stricter rules for the directories shared with Pulsar
+flake8 --ignore= --max-line-length=150 lib/galaxy/jobs/runners/util/ lib/pulsar/

.ci/py3_sources.txt

@@ -0,0 +1,14 @@
+lib/galaxy/util/
+lib/galaxy/jobs/runners/util/
+lib/pulsar/
+lib/galaxy/tools/parser/
+lib/galaxy/tools/lint.py
+lib/galaxy/tools/lint_util.py
+lib/galaxy/tools/loader.py
+lib/galaxy/tools/loader_directory.py
+lib/galaxy/tools/linters/
+lib/galaxy/tools/deps/
+lib/galaxy/tools/toolbox/
+lib/galaxy/tools/parser/
+lib/galaxy/jobs/metrics/
+lib/galaxy/objectstore/

.gitignore

@@ -43,6 +43,7 @@ reports_webapp.pid
 # Config files
 universe_wsgi.ini
 reports_wsgi.ini
+reports.ini
 tool_shed_wsgi.ini
 
 # Config files.
@@ -76,15 +77,20 @@ tool-data/shared/igv/igv_build_sites.txt
 tool-data/shared/rviewer/rviewer_build_sites.txt
 tool-data/shared/ncbi/builds.txt
 tool-data/shared/ucsc/builds.txt
+tool-data/shared/ucsc/manual_builds.txt
 tool-data/shared/ensembl/builds.txt
 tool-data/shared/ucsc/publicbuilds.txt
 tool-data/shared/ucsc/ucsc_build_sites.txt
 tool-data/*.loc
 tool-data/genome/*
 tool-data/*.sample
+tool-data/testtoolshed.g2.bx.psu.edu/
+tool-data/toolshed.g2.bx.psu.edu/
+
 
 # Test output
 test-data-cache
+run_framework_tests.html
 run_functional_tests.html
 run_api_tests.html
 test/tool_shed/tmp/*
@@ -106,7 +112,8 @@ tool-data/shared/jars/
 # CSS build artifacts.
 sprite-*.less
 
-# Local node_modules and bower_components directories
+# JS, Local node_modules, and bower_components directories
+static/scripts/bundled
 node_modules
 bower_components
 
@@ -118,4 +125,3 @@ doc/build
 .DS_Store
 *.rej
 *~
-

CODE_OF_CONDUCT.md

@@ -0,0 +1,99 @@
+Galaxy Project 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
+committed to providing a welcoming and inspiring community for all and expect
+our code of conduct to be honored. Anyone who violates this code of conduct may
+be banned from the community.
+
+Our open source community strives to:
+
+* **Be friendly and patient.**
+
+* **Be welcoming**: We strive to be a community that welcomes and
+  supports people of all backgrounds and identities. This includes, but is not
+  limited to members of any race, ethnicity, culture, national origin, colour,
+  immigration status, social and economic class, educational level, sex, sexual
+  orientation, gender identity and expression, age, size, family status,
+  political belief, religion, and mental and physical ability.
+
+* **Be considerate**: Your work will be used by other people, and you in turn
+  will depend on the work of others. Any decision you take will affect users
+  and colleagues, and you should take those consequences into account when
+  making decisions. Remember that we're a world-wide community, so you might
+  not be communicating in someone else's primary language.
+
+* **Be respectful**: Not all of us will agree all the time, but disagreement is
+  no excuse for poor behavior and poor manners. We might all experience some
+  frustration now and then, but we cannot allow that frustration to turn into a
+  personal attack. It’s important to remember that a community where people
+  feel uncomfortable or threatened is not a productive one.
+
+* **Be careful in the words that we choose**: We are a community of
+  professionals, and we conduct ourselves professionally. Be kind to others. Do
+  not insult or put down other participants. Harassment and other exclusionary
+  behavior aren't acceptable. This includes, but is not limited to: Violent
+  threats or language directed against another person, Discriminatory jokes and
+  language, Posting sexually explicit or violent material, Posting (or
+  threatening to post) other people’s personally identifying information
+  (“doxing”), Personal insults, especially those using racist or sexist terms,
+  Unwelcome sexual attention, Advocating for, or encouraging, any of the above
+  behavior, Repeated harassment of others. In general, if someone asks you to
+  stop, then stop.
+
+* **Try to understand why we disagree**: Disagreements, both social and
+  technical, happen all the time. It is important that we resolve disagreements
+  and differing views constructively. Remember that we’re different. Diversity
+  contributes to the strength of our community, which is composed of people
+  from a wide range of backgrounds. Different people have different
+  perspectives on issues. Being unable to understand why someone holds a
+  viewpoint doesn’t mean that they’re wrong. Don’t forget that it is human to
+  err and blaming each other doesn’t get us anywhere. Instead, focus on helping
+  to resolve issues and learning from mistakes.
+
+### Diversity Statement
+
+We encourage everyone to participate and are committed to building a community
+for all. Although we will fail at times, we seek to treat everyone both as
+fairly and equally as possible. Whenever a participant has made a mistake, we
+expect them to take responsibility for it. If someone has been harmed or
+offended, it is our responsibility to listen carefully and respectfully, and do
+our best to right the wrong.
+
+Although this list cannot be exhaustive, we explicitly honor diversity in age,
+gender, gender identity or expression, culture, ethnicity, language, national
+origin, political beliefs, profession, race, religion, sexual orientation,
+socioeconomic status, and technical ability. We will not tolerate
+discrimination based on any of the protected characteristics above, including
+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:
+
+- Your contact information.
+
+- Names (real, nicknames, or pseudonyms) of any individuals involved. If there
+  are additional witnesses, please include them as well. Your account of what
+  occurred, and if you believe the incident is ongoing. If there is a publicly
+  available record (e.g. a mailing list archive or a public IRC logger), please
+  include a link.
+
+- Any additional information that may be helpful.
+
+After filing a report, a representative will contact you personally, review the
+incident, follow up with any additional questions, and make a decision as to
+how to respond. If the person who is harassing you is part of the response
+team, they will recuse themselves from handling your incident. If the complaint
+originates from a member of the response team, it will be handled by a
+different member of the response team. We will respect confidentiality requests
+for the purpose of protecting victims of abuse.
+
+### Attribution & Acknowledgements
+
+This code of conduct is based on the Open Code of Conduct from the TODOGroup.