Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1debb7c63d9b61d7391bb8abbf474d6272be662 https://github.com/galaxyproject/galaxy/commit/c1debb7c63d9b61d7391bb8abbf47... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M config/galaxy.ini.sample
Log Message: ----------- Refactor galaxy.ini.sample config comments toward per-option docs.
Commit: 025f92bb73c7347536bf23f2adcff833c3c7284c https://github.com/galaxyproject/galaxy/commit/025f92bb73c7347536bf23f2adcff... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py
Log Message: ----------- Random fix for tool filters.
Commit: cd30a3424f3e564f3729b083e6abbd642c0122fa https://github.com/galaxyproject/galaxy/commit/cd30a3424f3e564f3729b083e6abb... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/reports/config.py
Log Message: ----------- Don't read global configuration for reports - it doesn't use it.
Commit: 6dd0684be3f8825676a7854b6f36faf874f03176 https://github.com/galaxyproject/galaxy/commit/6dd0684be3f8825676a7854b6f36f... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/util/path/__init__.py
Log Message: ----------- Fix ignoring ".sample" in newish path module.
Required to correctly detect the extension of sample configuration files.
Commit: 4a2a7e79459f65f1686c8814ca1a4a59bf829be5 https://github.com/galaxyproject/galaxy/commit/4a2a7e79459f65f1686c8814ca1a4... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- config_manage.py - allow printing comment header on sample description files.
Generated from the desc field in the app schema.
Commit: 87ace980d73ba7130dd29015145a09bd10f6dd68 https://github.com/galaxyproject/galaxy/commit/87ace980d73ba7130dd29015145a0... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- config_manage.py - fix sample file generation for large default values.
The various messages in the Galaxy config were being split across lines and generating invalid YAML.
Commit: 146dfd21143774d5451b4417eb223d73cdc23573 https://github.com/galaxyproject/galaxy/commit/146dfd21143774d5451b4417eb223... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- config_manage.py - hack uWSGI section of sample file generation.
Because uWSGI seems really bad at parsing fairly simple, entirely valid YAML.
Commit: 72466136d148848b560827ac5b34945d308216ed https://github.com/galaxyproject/galaxy/commit/72466136d148848b560827ac5b349... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- config_manage.py - improve default value formatting in RST.
Commit: 1b58157d003db7a663aa102994aea2873e2f7a7b https://github.com/galaxyproject/galaxy/commit/1b58157d003db7a663aa102994aea... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- config_manage.py - fix to generate YAML booleans in RST docs.
The new default - might as well use that representation.
Commit: 0ae21925b7c08c82a8daf4887e78ca66b06f38e9 https://github.com/galaxyproject/galaxy/commit/0ae21925b7c08c82a8daf4887e78c... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: A tmp_config_convert/convert.py
Log Message: ----------- convert_yaml - script to convert galaxy.ini.sample to config_schema.yml.
Commit: 44341ba5c1ca11bf94eb97c9644d3ac11f1b0268 https://github.com/galaxyproject/galaxy/commit/44341ba5c1ca11bf94eb97c9644d3... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: A tmp_config_convert/galaxy.ini.sample
Log Message: ----------- convert_yaml - setup copy of galaxy.ini.sample for conversion to work on.
Commit: 3703f05c33b702bf4c27e14619bb6965f1d4e38f https://github.com/galaxyproject/galaxy/commit/3703f05c33b702bf4c27e14619bb6... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M tmp_config_convert/galaxy.ini.sample
Log Message: ----------- convert_yaml - cleanup noise in conversion's copy of galaxy.ini.sample before conversion.
Commit: f058370a98fa84f3b7bdf5286c4e16cd3b811947 https://github.com/galaxyproject/galaxy/commit/f058370a98fa84f3b7bdf5286c4e1... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M config/galaxy.ini.sample
Log Message: ----------- convert_yaml - run conversion to YAML.
Commit: 2b12d0b605732f918e075ae52ea3518e15e61598 https://github.com/galaxyproject/galaxy/commit/2b12d0b605732f918e075ae52ea35... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: R config/galaxy.ini.sample A lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- convert_yaml - make sample a schema.
Commit: 6901fa9371be28584957fe14a06c73c221ed223b https://github.com/galaxyproject/galaxy/commit/6901fa9371be28584957fe14a06c7... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: R tmp_config_convert/convert.py R tmp_config_convert/galaxy.ini.sample
Log Message: ----------- convert_yaml - remove tmp directory for converting yaml.
Commit: 8a9dc5907d377819989d9c0165929c0f378d0559 https://github.com/galaxyproject/galaxy/commit/8a9dc5907d377819989d9c0165929... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M Makefile A lib/galaxy/webapps/galaxy/uwsgi_schema.yml
Log Message: ----------- yaml_config - Add entry points (e.g. Makefile) for dealing with Galaxy YAML configs.
Commit: d08dc05d9588e24a31de3a4a1ba9a07b42ae2e2e https://github.com/galaxyproject/galaxy/commit/d08dc05d9588e24a31de3a4a1ba9a... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: A config/galaxy.yml.sample
Log Message: ----------- yaml_config - Generate Galaxy yaml sample.
Commit: 4f4928b38677475fd3d70b0435bc9910154ccaba https://github.com/galaxyproject/galaxy/commit/4f4928b38677475fd3d70b0435bc9... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst A doc/source/admin/options.rst M lib/galaxy/webapps/config_manage.py
Log Message: ----------- yaml_config - Add RST docs for Galaxy options.
Automatically generated from the new specification.
Commit: 7bae23e105a46378b6042b6d00b1c61778349c0f https://github.com/galaxyproject/galaxy/commit/7bae23e105a46378b6042b6d00b1c... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M .travis.yml M scripts/common_startup.sh M scripts/galaxy-main M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh
Log Message: ----------- yaml_config - update code base for converting galaxy.ini.sample to YAML.
Commit: ba35d474a012d2ef60a6191fbfe3ee03ed04e09c https://github.com/galaxyproject/galaxy/commit/ba35d474a012d2ef60a6191fbfe3e... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M doc/source/admin/authentication.md M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M doc/source/admin/reports.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/interactive_environments.rst
Log Message: ----------- yaml_config - update admin docs for switch to YAML config.
Commit: 14f0185b217fad83009f2f8822a75774af42ae42 https://github.com/galaxyproject/galaxy/commit/14f0185b217fad83009f2f8822a75... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M test/docker/base/run_test_wrapper.sh
Log Message: ----------- yaml_config - change test wrapper to work with either ini or yml in container.
Commit: f06860a8fb200f01154e4822b3931f32c882a706 https://github.com/galaxyproject/galaxy/commit/f06860a8fb200f01154e4822b3931... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/config.py M lib/galaxy/webapps/tool_shed/config.py
Log Message: ----------- yaml_config - Don't parse YAML configurations as ini files.
Commit: 60cbcfd1eeb07a8b93e96ce148e911f1dfddb22b https://github.com/galaxyproject/galaxy/commit/60cbcfd1eeb07a8b93e96ce148e91... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M .ci/first_startup.sh
Log Message: ----------- yaml_config - Try to fix first startup CI job for uWSGI default.
Commit: bce21ab3f3ef7948a53c251c45f36b386928a29e https://github.com/galaxyproject/galaxy/commit/bce21ab3f3ef7948a53c251c45f36... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/config.py
Log Message: ----------- Axe special amqp config handling not used by modern messaging stuff.
It wasn't compatible with YAML config and looks unused as far as I can tell.
xref https://github.com/galaxyproject/galaxy/commit/6b92bf6eb8ca8a5114fc2ecf7fda6...
Commit: 8f69d17e8612dd8f33355a4bfd7a46ba635f1403 https://github.com/galaxyproject/galaxy/commit/8f69d17e8612dd8f33355a4bfd7a4... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M scripts/get_uwsgi_args.py
Log Message: ----------- Don't use uWSGI master mode by default. Fixes Ctrl+C on macOS and is really only important in production configs where you should be using a config file anyway.
Commit: cec42d1656f9e6ea5f28b3fd02dbe3eb3f1bf078 https://github.com/galaxyproject/galaxy/commit/cec42d1656f9e6ea5f28b3fd02dbe... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M doc/source/admin/conda_faq.rst
Log Message: ----------- yaml_config - Update Conda FAQ to link out to last .ini variant of docs for those who need them.
Commit: 33abb94252544686b313e7c238e19882bdcbc2af https://github.com/galaxyproject/galaxy/commit/33abb94252544686b313e7c238e19... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M scripts/common_startup_functions.sh
Log Message: ----------- Drop missing --safe-pidfile uWSGI arg until it is released.
Commit: f5aa17df1893ed9901de629e602fa052c169fa25 https://github.com/galaxyproject/galaxy/commit/f5aa17df1893ed9901de629e602fa... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Fix the use of --set galaxy_config_file with uWSGI where the app name is the PasteDeploy default `app:main`.
Commit: 8cd23970fbb1f6250a65f570c288579777464cbf https://github.com/galaxyproject/galaxy/commit/8cd23970fbb1f6250a65f570c2885... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Fix for None config_file in web stack stuff.
Commit: c99b4ece5bfb0b2d30049796cc9e415e05ef2092 https://github.com/galaxyproject/galaxy/commit/c99b4ece5bfb0b2d30049796cc9e4... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/job_metrics.md M doc/source/admin/special_topics/nginx.md
Log Message: ----------- [17.09] Deployer doc fixes.
Commit: 0585efaaa7d7d63d54088e120e3d5a7cd7e6ef33 https://github.com/galaxyproject/galaxy/commit/0585efaaa7d7d63d54088e120e3d5... Author: John Chilton jmchilton@gmail.com Date: 2017-12-06 (Wed, 06 Dec 2017)
Changed paths: M doc/source/admin/cluster.md M doc/source/admin/jobs.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst
Log Message: ----------- Update newer deployer config docs for switch to YAML config.
Commit: 70ee8d00cc3708b866723de9fe784c9c6a2cda3c https://github.com/galaxyproject/galaxy/commit/70ee8d00cc3708b866723de9fe784... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths: M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- Begin config schema for Galaxy (just the new not-in-galaxy.ini logging option for now, the rest will be autogenerated from the sample)
Commit: 0664921e00ba5dac623c19f1f5344a7f367aaa62 https://github.com/galaxyproject/galaxy/commit/0664921e00ba5dac623c19f1f5344... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths: A doc/source/admin/application_server.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst
Log Message: ----------- WIP admin documentation updates
Commit: 8cf649b33186838f1de2364b696d36f962bc99bf https://github.com/galaxyproject/galaxy/commit/8cf649b33186838f1de2364b696d3... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-07 (Thu, 07 Dec 2017)
Changed paths: R doc/source/admin/application_server.rst M doc/source/admin/config.rst M doc/source/admin/index.rst M doc/source/admin/reports.rst M doc/source/admin/scaling.md
Log Message: ----------- WIP admin docs updates for 18.01
Commit: 5ae0c323ec1ef374a24e18efb59df423424aa80c https://github.com/galaxyproject/galaxy/commit/5ae0c323ec1ef374a24e18efb59df... Author: John Chilton jmchilton@gmail.com Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths: M lib/galaxy/webapps/config_manage.py A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py
Log Message: ----------- Expand number of parameters with custom conversion/linting for Galaxy.
Add functionality and test case for converting parameter names (e.g. from allow_library_path_paste to allow_path_pate) during conversion.
Commit: e8a9cc27ff9e7de6aa70aedc7005773d34d3d59d https://github.com/galaxyproject/galaxy/commit/e8a9cc27ff9e7de6aa70aedc70057... Author: Nate Coraor nate@bx.psu.edu Date: 2017-12-08 (Fri, 08 Dec 2017)
Changed paths: M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Locate the Galaxy config file when multiple uWSGI --yaml/--json arguments are used.
Commit: 542aa95fa40288b7b754d3908d87967a7ce92e34 https://github.com/galaxyproject/galaxy/commit/542aa95fa40288b7b754d3908d879... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-08 (Mon, 08 Jan 2018)
Changed paths: M scripts/common_startup_functions.sh
Log Message: ----------- uWSGI: Use --master when daemonizing (required when using http server w/ daemonization) and fix `run.sh --stop-daemon`
Commit: 36ecca47e7c859a980c4e775db0ebedbb1c02cef https://github.com/galaxyproject/galaxy/commit/36ecca47e7c859a980c4e775db0eb... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-09 (Tue, 09 Jan 2018)
Changed paths: M doc/source/admin/scaling.md
Log Message: ----------- Major updates to the scaling doc for uWSGI
Commit: 18b3599207b12ff3019d7d1032101b6bdb99eb75 https://github.com/galaxyproject/galaxy/commit/18b3599207b12ff3019d7d1032101... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M doc/source/admin/scaling.md
Log Message: ----------- Remove emperor mode reference
Commit: daa7845580c08f7ded43af2aa1ff183fc95c5a05 https://github.com/galaxyproject/galaxy/commit/daa7845580c08f7ded43af2aa1ff1... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M lib/galaxy/config.py
Log Message: ----------- Add docstring to LOGGING_CONFIG_DEFAULT so that it is part of the autodoc generated docs, so that it can be linked from statically written docs.
Commit: 9204916ac8ffbfb5dad3734275fa3d4843300d20 https://github.com/galaxyproject/galaxy/commit/9204916ac8ffbfb5dad3734275fa3... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M doc/source/admin/config.rst
Log Message: ----------- Galaxy config doc corrections
Commit: e0891cac355d062711b645e5e4859cddd6f14cdd https://github.com/galaxyproject/galaxy/commit/e0891cac355d062711b645e5e4859... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M doc/source/conf.py
Log Message: ----------- Add intersphinx mapping to the Python 2.7 documentation
Commit: db00f97175c2870300617a8de8a5adac16e7b0d5 https://github.com/galaxyproject/galaxy/commit/db00f97175c2870300617a8de8a5a... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M .gitignore M doc/Makefile M doc/source/admin/config_logging.rst
Log Message: ----------- Finish Galaxy logging configuration documentation
Commit: adcf2138ae2f2013bed9386356b2b7c5d2d53648 https://github.com/galaxyproject/galaxy/commit/adcf2138ae2f2013bed9386356b2b... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M .gitignore
Log Message: ----------- Add missing generated docs to .gitignore
Commit: 1e275e84f8d1ce2d1afb5974d62d988ccc0e2bfe https://github.com/galaxyproject/galaxy/commit/1e275e84f8d1ce2d1afb5974d62d9... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M doc/source/admin/index.rst
Log Message: ----------- Add loggging configuration to admin docs TOC and move the cluster docs after the scaling docs
Commit: 35b1e2c9e7ce349f8cc37d363bb637b96a37266b https://github.com/galaxyproject/galaxy/commit/35b1e2c9e7ce349f8cc37d363bb63... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-10 (Wed, 10 Jan 2018)
Changed paths: M doc/source/admin/jobs.md M doc/source/admin/scaling.md
Log Message: ----------- Correct the handlers section of the job conf documentation.
Commit: 1daa2ae6e5b11843912e2c42af2a0040a32d6030 https://github.com/galaxyproject/galaxy/commit/1daa2ae6e5b11843912e2c42af2a0... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-11 (Thu, 11 Jan 2018)
Changed paths: M scripts/get_uwsgi_args.py
Log Message: ----------- Fix support for proxy prefix under uWSGI.
Commit: 1b583fb851ebfc476f53daff7447b37ee8477561 https://github.com/galaxyproject/galaxy/commit/1b583fb851ebfc476f53daff7447b... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-11 (Thu, 11 Jan 2018)
Changed paths: M doc/source/admin/index.rst A doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md M doc/source/admin/special_topics/index.rst R doc/source/admin/special_topics/nginx.md
Log Message: ----------- Update nginx documentation for uWSGI
Commit: 5a0d60537cdf9417c347921f06ae9b22e577274c https://github.com/galaxyproject/galaxy/commit/5a0d60537cdf9417c347921f06ae9... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-11 (Thu, 11 Jan 2018)
Changed paths: A doc/source/admin/apache.md M doc/source/admin/index.rst M doc/source/admin/nginx.md M doc/source/admin/production.md M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/index.rst M lib/galaxy/webapps/galaxy/api/configuration.py
Log Message: ----------- Update Apache documentation for uWSGI
Commit: 78992968ecd0de1f95b99352b53ea2ecd246f954 https://github.com/galaxyproject/galaxy/commit/78992968ecd0de1f95b99352b53ea... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-11 (Thu, 11 Jan 2018)
Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md
Log Message: ----------- Correct documentation line endings
Commit: f4131b8d2bcf75c1724e19265cf4ca93dfaefa73 https://github.com/galaxyproject/galaxy/commit/f4131b8d2bcf75c1724e19265cf4c... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-12 (Fri, 12 Jan 2018)
Changed paths: M doc/source/admin/apache.md M doc/source/admin/nginx.md
Log Message: ----------- Correct doc typos caught by @nsoranzo
Commit: 5fcefe404f7d5cd5d2dbbf0628b265e9d24138f5 https://github.com/galaxyproject/galaxy/commit/5fcefe404f7d5cd5d2dbbf0628b26... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-12 (Fri, 12 Jan 2018)
Changed paths: A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst M doc/source/admin/apache.md M doc/source/admin/nginx.md A doc/source/admin/proxy_package_layout.rst
Log Message: ----------- Attempt to reduce duplication in the proxy documentation through the use of includes, move the multi-config-file discussion to a common page.
Commit: efb061d4d4a88b491e77b52b670d18c1f28a81de https://github.com/galaxyproject/galaxy/commit/efb061d4d4a88b491e77b52b670d1... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-12 (Fri, 12 Jan 2018)
Changed paths: M doc/source/admin/scaling.md
Log Message: ----------- Add a tiny bit about uwsgitop
Commit: cdc6657bda6a70ecc036f53cf265f1815dc2badc https://github.com/galaxyproject/galaxy/commit/cdc6657bda6a70ecc036f53cf265f... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-15 (Mon, 15 Jan 2018)
Changed paths: M config/galaxy.yml.sample M lib/galaxy/webapps/config_manage.py
Log Message: ----------- Update galaxy.yml.sample uwsgi section from defaults in get_uwsgi_args.py
Commit: 44c291bc663a94635d0b2b1f8e04529dcf307f9d https://github.com/galaxyproject/galaxy/commit/44c291bc663a94635d0b2b1f8e045... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: A .ci/check_py3_compatibility.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/history-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/router.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/legacy/grid/grid-model.js A client/galaxy/scripts/legacy/grid/grid-template.js A client/galaxy/scripts/legacy/grid/grid-view.js M client/galaxy/scripts/libs/jquery/jquery.wymeditor.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-error.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hdca-li.js M client/galaxy/scripts/mvc/history/history-item-li.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/library/library-dataset-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-library-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/toolshed/repo-status-view.js M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js M client/galaxy/scripts/mvc/toolshed/repository-view.js M client/galaxy/scripts/mvc/toolshed/shed-list-view.js M client/galaxy/scripts/mvc/toolshed/workflows-view.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/mvc/ui/ui-frames.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js M client/galaxy/scripts/mvc/ui/ui-select-library.js M client/galaxy/scripts/mvc/upload/collection/collection-row.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M client/galaxy/scripts/mvc/upload/composite/composite-row.js M client/galaxy/scripts/mvc/upload/composite/composite-view.js M client/galaxy/scripts/mvc/upload/default/default-row.js M client/galaxy/scripts/mvc/upload/default/default-view.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/upload/upload-view.js M client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow-manager.js M client/galaxy/scripts/mvc/workflow/workflow-node.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/nls/zh/locale.js M client/galaxy/scripts/onload.js A client/galaxy/scripts/reports/run_stats.js R client/galaxy/scripts/reports_webapp/run_stats.js A client/galaxy/scripts/toolshed/groups/group-detail-view.js A client/galaxy/scripts/toolshed/groups/group-list-view.js A client/galaxy/scripts/toolshed/groups/group-listrow-view.js A client/galaxy/scripts/toolshed/groups/group-model.js A client/galaxy/scripts/toolshed/toolshed.groups.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/sweepster.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js M client/galaxy/style/less/history.less M client/galaxy/style/less/library.less R client/grunt-tasks/install-libs.js R client/grunt-tasks/scripts.js M client/gulpfile.js M client/package.json R client/toolshed/scripts/mvc/groups/group-detail-view.js R client/toolshed/scripts/mvc/groups/group-list-view.js R client/toolshed/scripts/mvc/groups/group-listrow-view.js R client/toolshed/scripts/mvc/groups/group-model.js R client/toolshed/scripts/toolshed.groups.js M client/webpack.config.js M client/yarn.lock M config/datatypes_conf.xml.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample M config/plugins/visualizations/charts/templates/charts.mako M config/plugins/webhooks/demo/tour_generator/helper/__init__.py M config/plugins/webhooks/demo/tour_generator/static/script.js M config/user_preferences_extra_conf.yml.sample M contrib/galaxy.fedora-init M contrib/nagios/check_galaxy.py M doc/source/admin/production.md M doc/source/api/quickstart.rst M lib/galaxy/actions/library.py M lib/galaxy/config.py M lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/cram_to_bam.py M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py A lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/datatypes/plant_tribes.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/set_metadata_tool.xml M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/test/1.bam A lib/galaxy/datatypes/test/1.vcf 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lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/profile.py M lib/galaxy/web/framework/middleware/remoteuser.py M lib/galaxy/web/framework/middleware/translogger.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/web/security/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/web/stack/transport.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/authenticate.py M lib/galaxy/webapps/galaxy/api/configuration.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/library_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/toolshed.py M lib/galaxy/webapps/galaxy/api/users.py 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lib/galaxy/webapps/reports/controllers/workflows.py A lib/galaxy/webapps/reports/framework/__init__.py A lib/galaxy/webapps/reports/framework/grids.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/api/tools.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/controllers/repository_review.py M lib/galaxy/webapps/tool_shed/controllers/upload.py M lib/galaxy/webapps/tool_shed/security/__init__.py M lib/galaxy/webapps/tool_shed/util/hgweb_config.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M lib/tool_shed/grids/util.py M lib/tool_shed/metadata/metadata_generator.py M lib/tool_shed/metadata/repository_metadata_manager.py M lib/tool_shed/tools/data_table_manager.py M lib/tool_shed/tools/tool_validator.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/hg_util.py M lib/tool_shed/util/repository_util.py M lib/tool_shed/util/tool_dependency_util.py M lib/tool_shed/util/tool_util.py M lib/tool_shed/util/workflow_util.py R openid/yahoo.xml R scripts/api/form_create_from_xml.py R scripts/api/request_type_create_from_xml.py R scripts/api/requests_update_state.py R scripts/api/sample_configurations/sample_tracking/request_form.xml R scripts/api/sample_configurations/sample_tracking/request_type.xml R scripts/api/sample_configurations/sample_tracking/sample_form.xml R scripts/api/sample_dataset_update_status.py R scripts/api/sample_update_state.py R 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M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/scripts/bundled/admin.bundled.js R static/scripts/bundled/adminToolshed.bundled.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js R static/scripts/bundled/library.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/login.bundled.js R static/scripts/bundled/masthead.bundled.js R static/scripts/bundled/viz.bundled.js R static/scripts/bundled/workflow.bundled.js M static/scripts/galaxy.js M static/scripts/galaxy.library.js M static/scripts/galaxy.pages.js M static/scripts/layout/generic-nav-view.js M static/scripts/layout/router.js M static/scripts/layout/scratchbook.js A static/scripts/legacy/grid/grid-model.js A static/scripts/legacy/grid/grid-template.js A static/scripts/legacy/grid/grid-view.js M static/scripts/libs/jquery/jquery.wymeditor.js R static/scripts/libs/vue.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-error.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/grid/grid-model.js M static/scripts/mvc/grid/grid-shared.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/grid/grid-view.js M static/scripts/mvc/history/history-item-li.js M static/scripts/mvc/history/history-list.js M static/scripts/mvc/library/library-dataset-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M 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templates/webapps/reports/index.mako R templates/webapps/reports/requests_per_month_all.mako R templates/webapps/reports/requests_per_user.mako R templates/webapps/reports/requests_user_per_month.mako M templates/webapps/reports/run_stats.mako M templates/webapps/tool_shed/admin/dataset_security/group/group_create.mako M templates/webapps/tool_shed/admin/dataset_security/role/role_create.mako M templates/webapps/tool_shed/category/grid.mako M templates/webapps/tool_shed/category/valid_grid.mako M templates/webapps/tool_shed/common/common.mako M templates/webapps/tool_shed/common/grid_common.mako M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako M templates/webapps/tool_shed/group/index.mako M templates/webapps/tool_shed/repository/common.mako M templates/webapps/tool_shed/repository/find_tools.mako M templates/webapps/tool_shed/repository/find_workflows.mako M templates/webapps/tool_shed/repository/manage_repository.mako M templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako M templates/webapps/tool_shed/repository/tool_form.mako M templates/webapps/tool_shed/repository/view_repository.mako M templates/webapps/tool_shed/repository_review/browse_review.mako M templates/webapps/tool_shed/repository_review/edit_review.mako M templates/webapps/tool_shed/repository_review/grid.mako M templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako M templates/webapps/tool_shed/user/manage_email_alerts.mako M test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml A test/functional/tools/multi_output_recurse.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_dynamic_job_conf.xml M test/integration/resubmission_rules/rules.py A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py A test/shed_functional/test_data/bowtie2_loc_sample/bowtie2_indices.loc.sample A test/unit/datatypes/converters/__init__.py A test/unit/datatypes/converters/test_interval_to_tabix.py A test/unit/datatypes/test_bam.py A test/unit/datatypes/test_bcf.py A test/unit/datatypes/test_cram.py A test/unit/datatypes/test_vcf.py A test/unit/datatypes/util.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_parsing.py A test/unit/tools/test_tool_validation.py M tools/data_source/microbial_import_code.py M tools/data_source/upload.py M tools/data_source/upload.xml M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini
Log Message: ----------- Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config
Commit: 3fdbaa3dec07078388ce63bdb1a6f9251ffeb3f1 https://github.com/galaxyproject/galaxy/commit/3fdbaa3dec07078388ce63bdb1a6f... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: M config/galaxy.yml.sample M doc/source/admin/galaxy_options.rst
Log Message: ----------- Regenerate galaxy.yml.sample and documentation for newly added/documented config options.
Commit: dd0aeec50013e172a0f49c1e5681cc73ed635213 https://github.com/galaxyproject/galaxy/commit/dd0aeec50013e172a0f49c1e5681c... Author: Nate Coraor nate@bx.psu.edu Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- Fix lint error
Commit: 7659efc68c92948e5e8e00404e537752158061cb https://github.com/galaxyproject/galaxy/commit/7659efc68c92948e5e8e00404e537... Author: Martin Cech marten@bx.psu.edu Date: 2018-01-18 (Thu, 18 Jan 2018)
Changed paths: M .gitignore M .travis.yml M Makefile R config/galaxy.ini.sample A config/galaxy.yml.sample M doc/Makefile A doc/source/admin/_inc_proxy_prereq.rst A doc/source/admin/_inc_proxy_serving_root.rst A doc/source/admin/_inc_proxy_ssl.rst A doc/source/admin/apache.md M doc/source/admin/authentication.md M doc/source/admin/cluster.md M doc/source/admin/conda_faq.rst A doc/source/admin/config.rst A doc/source/admin/config_logging.rst M doc/source/admin/dependency_resolvers.rst A doc/source/admin/galaxy_options.rst M doc/source/admin/index.rst M doc/source/admin/jobs.md A doc/source/admin/nginx.md A doc/source/admin/options.rst M doc/source/admin/production.md A doc/source/admin/proxy_package_layout.rst M doc/source/admin/reports.md M doc/source/admin/reports.rst M doc/source/admin/scaling.md R doc/source/admin/special_topics/apache.md M doc/source/admin/special_topics/bug_reports.rst M doc/source/admin/special_topics/chat.rst M doc/source/admin/special_topics/ftp.md M doc/source/admin/special_topics/index.rst M doc/source/admin/special_topics/interactive_environments.rst R doc/source/admin/special_topics/nginx.md M doc/source/admin/special_topics/performance_tracking.rst M doc/source/admin/special_topics/webhooks.rst M doc/source/admin/tool_panel.rst M doc/source/conf.py M lib/galaxy/config.py M lib/galaxy/tools/toolbox/filters/__init__.py M lib/galaxy/util/path/__init__.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/configuration.py A lib/galaxy/webapps/galaxy/config_schema.yml A lib/galaxy/webapps/galaxy/uwsgi_schema.yml M lib/galaxy/webapps/reports/config.py M lib/galaxy/webapps/tool_shed/config.py M scripts/common_startup.sh M scripts/common_startup_functions.sh M scripts/galaxy-main M scripts/get_uwsgi_args.py M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py M test/base/driver_util.py M test/docker/base/run_test_wrapper.sh A test/unit/config/1705_allow_path_paste/config/galaxy.ini A test/unit/config/__init__.py M test/unit/config/test_config_manage.py
Log Message: ----------- Merge pull request #5105 from jmchilton/ini_to_yaml_config
Convert options file to YAML and use uWSGI by default
Compare: https://github.com/galaxyproject/galaxy/compare/b174dafa36f0...7659efc68c92