April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f6c00e: improve ux of various builder elements
by GitHub 21 Apr '18

21 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6c00e79217501b7622c151bac119726f8004a64 https://github.com/galaxyproject/galaxy/commit/f6c00e79217501b7622c151bac11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- improve ux of various builder elements Commit: f0e0b5c9fc88119ee5f2d380d38b0aa3e89079e1 https://github.com/galaxyproject/galaxy/commit/f0e0b5c9fc88119ee5f2d380d38b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix rule source edit cancel button. Commit: c4ad1f55e49c374eac8724d7ffbb787e5ac37c15 https://github.com/galaxyproject/galaxy/commit/c4ad1f55e49c374eac8724d7ffbb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Disable reorient button. Commit: 1df00bfb51afbbf5969429aae274a88315e40d51 https://github.com/galaxyproject/galaxy/commit/1df00bfb51afbbf5969429aae274… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/package.json M client/webpack.config.js Log Message: ----------- Add bootstrap vue as a dependency. Commit: 847695a16248986b8f2d798f420f887f127b6d6a https://github.com/galaxyproject/galaxy/commit/847695a16248986b8f2d798f420f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Use bootstrap-vue to add many new tooltips to rule builder. Commit: 798d7d86795fd9dbee51f3551a051245111129ab https://github.com/galaxyproject/galaxy/commit/798d7d86795fd9dbee51f3551a05… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- bootstrap-vue popover describing regex. Commit: 5e78c00824b6ba2e97cd46b671133de9cec43ad1 https://github.com/galaxyproject/galaxy/commit/5e78c00824b6ba2e97cd46b67113… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- various UX and style improvements Commit: 34689c7629d7c1a2c00afb5d43ca22a62e76b4c9 https://github.com/galaxyproject/galaxy/commit/34689c7629d7c1a2c00afb5d43ca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Merge branch 'ux-stylechanges' of github.com:jmchilton/galaxy into ux-stylechanges Commit: 909075c67839830207bda14c455139eecaf979b8 https://github.com/galaxyproject/galaxy/commit/909075c67839830207bda14c4551… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - tweak tooltip placement so it doesn't overlap menu. Fixes test cases. Commit: d94cd0a9c20b497e17b7bfe3a5d059513d367e16 https://github.com/galaxyproject/galaxy/commit/d94cd0a9c20b497e17b7bfe3a5d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder Another tweak to fix test cases. Commit: d51812b832dbd1268e6ac76a1c22af05880d4525 https://github.com/galaxyproject/galaxy/commit/d51812b832dbd1268e6ac76a1c22… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/package.json M client/webpack.config.js Log Message: ----------- Merge pull request #5940 from jmchilton/ux-stylechanges More Rule Builder Style Changes Compare: https://github.com/galaxyproject/galaxy/compare/13661adcad91...d51812b832db

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[galaxyproject/galaxy] f6066d: RuleBuilder style fixes - bs4 branch fallout.
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6066d34fa403cf10cabdcaa58e420d6b7cc83b6 https://github.com/galaxyproject/galaxy/commit/f6066d34fa403cf10cabdcaa58e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder style fixes - bs4 branch fallout. Commit: 5bd45837dd3f044e72e8abbe90ea701be4627e80 https://github.com/galaxyproject/galaxy/commit/5bd45837dd3f044e72e8abbe90ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - Set a minimum width for column selectors. Commit: 63620ba4007e81799606e91ef0549f32905fe791 https://github.com/galaxyproject/galaxy/commit/63620ba4007e81799606e91ef054… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js Log Message: ----------- Improve styling, validation of Build button in rule upload table. Commit: 20c8260108e3829425cd2b7dfb75ca8ddc1d1356 https://github.com/galaxyproject/galaxy/commit/20c8260108e3829425cd2b7dfb75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Redo footer inputs for rule builder. Gives more space for name and genome - dynamically resizes to space given with some reasonable minimum and maximum widths for widgets. Commit: f2d6a2d6b43ae32ce1302c7b2e0d5e0c9296ef94 https://github.com/galaxyproject/galaxy/commit/f2d6a2d6b43ae32ce1302c7b2e0d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- RuleBuilder - fix click handler for BS4 changes. Commit: b59ea1633f4ec9724acf133ad8095bf9e8e6c99f https://github.com/galaxyproject/galaxy/commit/b59ea1633f4ec9724acf133ad809… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Proper bootstrap 4 dropdown menus in the RuleBuilder. Commit: 13661adcad91e99a9fc029fab7324194a63db605 https://github.com/galaxyproject/galaxy/commit/13661adcad91e99a9fc029fab732… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_uploads.py Log Message: ----------- Merge pull request #5909 from jmchilton/rule_builder_styling Rule builder styling fixes. Compare: https://github.com/galaxyproject/galaxy/compare/c2467f27ae54...13661adcad91

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[galaxyproject/galaxy] 313a0f: check that source before trying to move
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 313a0ff2973c8f528b88013d17761df449fd174b https://github.com/galaxyproject/galaxy/commit/313a0ff2973c8f528b88013d1776… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- check that source before trying to move Commit: aecbdac334a18ff1f82494fc6c0b58de90ad610c https://github.com/galaxyproject/galaxy/commit/aecbdac334a18ff1f82494fc6c0b… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py M lib/galaxy/util/__init__.py Log Message: ----------- move the dir existance check out of move_merge Commit: c2467f27ae547b05513f011868c0d4a2d456c606 https://github.com/galaxyproject/galaxy/commit/c2467f27ae547b05513f011868c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5922 from abretaud/movemerge Fix error with data managers when trying to move_merge inexistant extra_files dir Compare: https://github.com/galaxyproject/galaxy/compare/33a28b8b8b6d...c2467f27ae54

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[galaxyproject/galaxy] c5e19d: Improves handling of existing k8s jobs on restart, ...
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c5e19d4a532be11d695a12d3b3dca42d877057a8 https://github.com/galaxyproject/galaxy/commit/c5e19d4a532be11d695a12d3b3dc… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improves handling of existing k8s jobs on restart, and avoids clashes with jobs of previous instances, establishing an optional trust mechanism. Commit: 46b51944c68f65f8da5151ace54d2bcaeed353cd https://github.com/galaxyproject/galaxy/commit/46b51944c68f65f8da5151ace54d… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-03-22 (Thu, 22 Mar 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- PEP style fixes k8s runner. Commit: dc563eae75cc4394aafdeef5ae9cd04213326225 https://github.com/galaxyproject/galaxy/commit/dc563eae75cc4394aafdeef5ae9c… Author: Pablo Moreno <pablo.a.moreno(a)gmail.com> Date: 2018-04-15 (Sun, 15 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Adds timeout behaviour for k8s existing job deletion Commit: 33a28b8b8b6d36e7ab972c9f3241ce92bd4fbc2b https://github.com/galaxyproject/galaxy/commit/33a28b8b8b6d36e7ab972c9f3241… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #5761 from phnmnl/galaxy-prs/k8s-improves-job-handling-existing-jobs Kubernetes: Improves handling of existing jobs on Galaxy restart. Compare: https://github.com/galaxyproject/galaxy/compare/09fcf13aafb5...33a28b8b8b6d

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[galaxyproject/galaxy] de5ac4: more tolerant sanitizing
by GitHub 20 Apr '18

20 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: de5ac42fa9672d6bcf1b7e0c958c13adff2dafa8 https://github.com/galaxyproject/galaxy/commit/de5ac42fa9672d6bcf1b7e0c958c… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- more tolerant sanitizing Commit: 16f9e58af5cceb9eb7f969a581bbf66316a99986 https://github.com/galaxyproject/galaxy/commit/16f9e58af5cceb9eb7f969a581bb… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- quotes Commit: bb9963dddce6e1287785ae4452f3883229ed7a6c https://github.com/galaxyproject/galaxy/commit/bb9963dddce6e1287785ae4452f3… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-10 (Tue, 10 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- fix quote escaping Commit: 0b191abaf18271b9a51f21a13808e2b74c6cf0b1 https://github.com/galaxyproject/galaxy/commit/0b191abaf18271b9a51f21a13808… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- pass the condition by a json file instead of arg Commit: dc4902353f3254aa962f8efe1ea4e2af5f7499ab https://github.com/galaxyproject/galaxy/commit/dc4902353f3254aa962f8efe1ea4… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.xml Log Message: ----------- add test case for fixed bug Commit: dadb4fcda723ab14421b07cb4b1747aa3e8b325d https://github.com/galaxyproject/galaxy/commit/dadb4fcda723ab14421b07cb4b17… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M tools/stats/filtering.xml Log Message: ----------- change back version Commit: 09fcf13aafb5dd6aa1f3b31446af91c7ca2ea3a6 https://github.com/galaxyproject/galaxy/commit/09fcf13aafb5dd6aa1f3b31446af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: A test-data/filter1_in6.bed A test-data/filter1_test6.bed M tools/stats/filtering.py M tools/stats/filtering.xml Log Message: ----------- Merge pull request #5872 from abretaud/filter_sanitize Filter tool: fix too strict sanitizing Compare: https://github.com/galaxyproject/galaxy/compare/b9fe69fb8b46...09fcf13aafb5

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[galaxyproject/galaxy] fce2dd: Eliminate compressed datatype boiler plate.
by GitHub 19 Apr '18

19 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fce2dd3ae801cd13a542388746b84f9cca2a4c48 https://github.com/galaxyproject/galaxy/commit/fce2dd3ae801cd13a542388746b8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Eliminate compressed datatype boiler plate. Just annotate auto_compressed_types="gz|bz2|gz,bz2" in datatypes_conf.xml and get for free: - The compressed datatype with correct extension, no need to have a class definition. - Converters from the compressed datatype to the uncompressed datatype. - A sniffer in the correct order. Additionally, the hacky way we were controlling whether types would be sniffed or not has been improved. This can now be set in the datatypes_conf.xml file or read from a global Galaxy configuration option for options that haven't been explicitly set on a per-datatype basis in the configuration (sniff_compressed_dynamic_datatypes_default). This should simplify all future datatypes moving in this direction and introduces the possibility of also just loading them in dynamically as needed based on what the tools in the tool panel annotate for inputs and outputs. See a tool with an input of type "genbank.gz" should be enough to trigger this someday I hope. Commit: 379714e5beace2ca7b31eab064f22862902b1831 https://github.com/galaxyproject/galaxy/commit/379714e5beace2ca7b31eab064f2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- remove sniffers that no longer exist from sample config Commit: b9fe69fb8b46ffc2c9842d672c547413439f12d8 https://github.com/galaxyproject/galaxy/commit/b9fe69fb8b46ffc2c9842d672c54… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/config.py R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M lib/galaxy/webapps/galaxy/api/datatypes.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5794 from jmchilton/dynamic_compressed_types Infrastructure for dynamic compressed datatypes Compare: https://github.com/galaxyproject/galaxy/compare/21c10e960b21...b9fe69fb8b46

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[galaxyproject/galaxy] 7d0a49: sort with header: fix syntax
by GitHub 19 Apr '18

19 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7d0a49c34de6c628e9716bbe45f26e6fb2c976da https://github.com/galaxyproject/galaxy/commit/7d0a49c34de6c628e9716bbe45f2… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/sorter.xml Log Message: ----------- sort with header: fix syntax Commit: de9a5a526b56e8b8223ac8ad0ffe93fdab783998 https://github.com/galaxyproject/galaxy/commit/de9a5a526b56e8b8223ac8ad0ffe… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab M tools/filters/sorter.xml Log Message: ----------- sort with header: add test-data for the state of art Commit: 47437d054077d55b21e6cafab429dce85ba54fd0 https://github.com/galaxyproject/galaxy/commit/47437d054077d55b21e6cafab429… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/sort_out4.sam M tools/filters/sorter.py M tools/filters/sorter.xml Log Message: ----------- sort with header: done Commit: d4faabae95a898771df579ad649a9501fa17c353 https://github.com/galaxyproject/galaxy/commit/d4faabae95a898771df579ad649a… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M tools/filters/sorter.xml Log Message: ----------- add requirements Commit: 376aa79825248ac7944b4183baa21fd4df0960bc https://github.com/galaxyproject/galaxy/commit/376aa79825248ac7944b4183baa2… Author: lecorguille <lecorguille(a)users.noreply.github.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M tools/filters/sorter.py M tools/filters/sorter.xml Log Message: ----------- subprocess Commit: 89ac586fff3e768f6f8c1f4bce30ab4958e35ab3 https://github.com/galaxyproject/galaxy/commit/89ac586fff3e768f6f8c1f4bce30… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M tools/filters/sorter.py Log Message: ----------- flake8 fixes Commit: 145903eae313a238830aab279a1070a007facee5 https://github.com/galaxyproject/galaxy/commit/145903eae313a238830aab279a10… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: A .ci/autopep8.sh A .ci/check_py3_compatibility.sh M .ci/first_startup.sh M .ci/flake8_blacklist.txt R .ci/flake8_lint_include_list.txt R .ci/flake8_py3_wrapper.sh M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh R .ci/flake8_wrapper_imports.sh M .ci/jenkins/api/run_tests.sh A .ci/jenkins/selenium-compose/Dockerfile A .ci/jenkins/selenium-compose/docker-compose.yml A .ci/jenkins/selenium-compose/galaxy.ini A .ci/jenkins/selenium-compose/run_galaxy.bash A .ci/jenkins/selenium-compose/run_tests.sh R .ci/jenkins/selenium/Dockerfile R .ci/jenkins/selenium/docker-compose.yml R .ci/jenkins/selenium/galaxy.ini R .ci/jenkins/selenium/run_galaxy.bash M .ci/jenkins/selenium/run_tests.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M Makefile M README.rst A SECURITY_POLICY.md A client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-styles.md M client/galaxy/scripts/admin.toolshed.js M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js A client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/login.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 A client/galaxy/scripts/components/Citations.vue A client/galaxy/scripts/components/DisplayStructured.vue A client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/HistoryView.vue A client/galaxy/scripts/components/Message.vue A client/galaxy/scripts/components/PluginList.vue A client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/WorkflowImport.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/i18n.js A client/galaxy/scripts/layout/communication-server-view.js R client/galaxy/scripts/layout/generic-nav-view.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/modal.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js A 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client/galaxy/scripts/mocha/tests/rules_dsl_spec.yml A client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/annotation.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js R client/galaxy/scripts/mvc/citation/citation-model.js R client/galaxy/scripts/mvc/citation/citation-view.js M client/galaxy/scripts/mvc/collection/base-creator.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-view-edit.js M client/galaxy/scripts/mvc/collection/collection-view.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/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/data.js M 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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 R templates/webapps/tool_shed/repository/grid.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 A test-data/1.csv M test-data/1.fastqsanger M test-data/1.fastqsolexa A test-data/1.sam.gz A test-data/5_Ig-like.gff A test-data/bad.html.gz A test-data/bam_native_from_sam.bam A test-data/example-bag.zip A test-data/joiner_header_in1.tab A test-data/joiner_header_in2.tab A test-data/joiner_out1.bed A test-data/joiner_out2.bed A test-data/joiner_out3.bed A test-data/joiner_out4.bed A test-data/joiner_out5.tab A test-data/joiner_out6.tab A test-data/joiner_out7.tab M test-data/neostore.zip A test-data/new_element_sort_order.txt A test-data/new_tags_1.txt A test-data/qname_sorted.bam A test-data/random-file A test-data/rules/PRJDA60709.tsv A test-data/rules/PRJDB3920.tsv A test-data/rules/PRJNA355367.tsv A test-data/rules/uniprot.json A test-data/rules/uniprot.tsv M test-data/sam_with_header.sam A test-data/selenium-test-notebook.ipynb M test-data/simple_line_alternative.txt M test-data/simple_lines_interleaved.txt A test-data/test.vcf.gz A test-data/testdir1.zip M 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test/base/integration_util.py M test/base/interactor.py M test/base/nose_util.py M test/base/populators.py R test/base/test_db_util.py A test/base/testcase.py R test/base/tool_shed_util.py R test/base/twilltestcase.py A test/base/workflow_fixtures.py M test/base/workflows_format_2/converter.py M test/base/workflows_format_2/main.py R test/casperjs/README.txt R test/casperjs/api-anon-history-permission-tests.js R test/casperjs/api-anon-history-tests.js R test/casperjs/api-hda-tests.js R test/casperjs/api-history-permission-tests.js R test/casperjs/casperjs_runner.py R test/casperjs/modules/api.js R test/casperjs/modules/historyoptions.js R test/casperjs/modules/historypanel.js R test/casperjs/modules/tools.js R test/casperjs/modules/user.js R test/casperjs/page-data/selectors.json R test/casperjs/server_env.py R test/casperjs/spaceghost.js R test/casperjs/test-data/simple_test.ga R test/casperjs/utils/simple-galaxy.js M test/docker/base/Dockerfile M test/docker/base/ansible_vars.yml M 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test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml A test/integration/sets_tmp_dir_expression_job_conf.xml A test/integration/sets_tmp_dir_to_true_job_conf.xml A test/integration/simple_job_conf.xml A test/integration/test_config_options_users.py A test/integration/test_data_manager_table_reload.py A test/integration/test_dockerized_jobs.py A test/integration/test_job_environments.py M test/integration/test_job_resubmission.py A test/integration/test_local_job_cancellation.py R test/integration/test_maximum_worklfow_invocation_duration.py A test/integration/test_mules_as_job_handlers.py M test/integration/test_resolvers.py A test/integration/test_scripts.py A test/integration/test_shed_tool_tests.py A test/integration/test_upload_configuration_options.py M test/integration/test_workflow_handler_configuration.py A test/integration/test_workflow_scheduling_options.py A test/integration/tool_sheds_conf.xml A test/integration/uses_shed.py M test/manual/launch_and_run.sh M test/manual/workflows_scaling.py R test/qunit/Gruntfile.js R test/qunit/README.txt R test/qunit/package.json R test/qunit/scripts R test/qunit/test-app.js R test/qunit/test-common.js R test/qunit/test-data/bootstrapped.js R test/qunit/test-data/fakeserver.js R test/qunit/test-data/job-dag-1.js R test/qunit/test-data/paired-collection-creator.data.js R test/qunit/test-libs/qunit-1.23.1.css R test/qunit/test-libs/qunit-1.23.1.js R test/qunit/test-libs/sinon-1.17.3.js R test/qunit/test-libs/sinon-qunit-1.0.0.js R test/qunit/tests/form_tests.html R test/qunit/tests/form_tests.js R test/qunit/tests/galaxy-app-base.html R test/qunit/tests/galaxy-app-base.js R test/qunit/tests/graph.html R test/qunit/tests/graph.js R test/qunit/tests/hda-base.html R test/qunit/tests/hda-base.js R test/qunit/tests/history_contents_model_tests.html R test/qunit/tests/history_contents_model_tests.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into sort_header Commit: d11f76b0315f6f29d6232e3a440d50fd1481bb55 https://github.com/galaxyproject/galaxy/commit/d11f76b0315f6f29d6232e3a440d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M tools/filters/sorter.py Log Message: ----------- More flake8 fixes for sorter.py. Commit: 21c10e960b21c35776812cca53427425f4ff5667 https://github.com/galaxyproject/galaxy/commit/21c10e960b21c35776812cca5342… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: A test-data/sort_out1.bed A test-data/sort_out2.bed A test-data/sort_out3.tab A test-data/sort_out4.sam M tools/filters/sorter.py M tools/filters/sorter.xml Log Message: ----------- Merge pull request #4235 from lecorguille/sort_header Sort header Compare: https://github.com/galaxyproject/galaxy/compare/6178863d3cb6...21c10e960b21

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[galaxyproject/galaxy] fe0a48: forgot to document github bug reporter
by GitHub 19 Apr '18

19 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fe0a4853b96ddc163ebfb09f961885b88c5577dd https://github.com/galaxyproject/galaxy/commit/fe0a4853b96ddc163ebfb09f9618… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- forgot to document github bug reporter Commit: 393f055a2307f090f71dc2c7750b8487cfafcd96 https://github.com/galaxyproject/galaxy/commit/393f055a2307f090f71dc2c7750b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Merge pull request #5928 from erasche/document-gh-reporter [18.01] forgot to document github bug reporter Compare: https://github.com/galaxyproject/galaxy/compare/c85f07cf5fa2...393f055a2307

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[galaxyproject/galaxy] 6a541a: This forces the panel control sizing correctly, in...
by GitHub 19 Apr '18

19 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a541af4dcdfe537b5ee216b022f36ba0c78d920 https://github.com/galaxyproject/galaxy/commit/6a541af4dcdfe537b5ee216b022f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- This forces the panel control sizing correctly, instead of being smushed up in the flex column (issue was on Chrome, worked fine in Firefox) Commit: 6178863d3cb617b283d5c15e27ad65a699abb649 https://github.com/galaxyproject/galaxy/commit/6178863d3cb617b283d5c15e27ad… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge pull request #5914 from dannon/fix-multipanel-height Multiview history panel-control fix. Compare: https://github.com/galaxyproject/galaxy/compare/43c418053c65...6178863d3cb6

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[galaxyproject/galaxy] 3182df: correct signal num
by GitHub 19 Apr '18

19 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 3182dfa70e4220621fe5eb85a05b2f5430a31d3d https://github.com/galaxyproject/galaxy/commit/3182dfa70e4220621fe5eb85a05b… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- correct signal num Commit: c85f07cf5fa2452122487cb66c3955fc88c6ea45 https://github.com/galaxyproject/galaxy/commit/c85f07cf5fa2452122487cb66c39… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5921 from erasche/fix-docs [18.01] correct signal num in docs Compare: https://github.com/galaxyproject/galaxy/compare/c4e124231270...c85f07cf5fa2

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