- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 47ed81: Remove unreachable print statement
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47ed81feb95c092587c68deb07e247c3a4d29bff https://github.com/galaxyproject/galaxy/commit/47ed81feb95c092587c68deb07e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M tools/data_source/upload.py Log Message: ----------- Remove unreachable print statement I don't think an exception could ever occur here. Commit: ed375993ebc43112e03f58779d7c8c104e67956a https://github.com/galaxyproject/galaxy/commit/ed375993ebc43112e03f58779d7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix analyze75 hdr file upload when convert newlines is on Commit: bd25ff919c2f94dea446e656a757c61f8237db89 https://github.com/galaxyproject/galaxy/commit/bd25ff919c2f94dea446e656a757… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #7414 from mvdbeek/fix_analyze_75 [19.01] Fix analyze 75 datatype upload Commit: 14f3ce3b5092467e3d9dde9bd94fdab5f6b604b2 https://github.com/galaxyproject/galaxy/commit/14f3ce3b5092467e3d9dde9bd94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix workflow interface drop to import Commit: 1583eecfdb338aae17fbb199160f7937e3b0ec01 https://github.com/galaxyproject/galaxy/commit/1583eecfdb338aae17fbb199160f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Client formatting sync for 19.01 Commit: 7553326ba1af32e50c3695cbb67795fc11f0ecdc https://github.com/galaxyproject/galaxy/commit/7553326ba1af32e50c3695cbb677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7415 from dannon/fix-workflow-drop-hack [19.01] Fix workflow list drop-to-upload Commit: 574cc22a08d6c109abf12bad02cbb6e47c512df6 https://github.com/galaxyproject/galaxy/commit/574cc22a08d6c109abf12bad02cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_19.01' into dev Commit: fdb18045b76220b847163857e6e58acc19cef347 https://github.com/galaxyproject/galaxy/commit/fdb18045b76220b847163857e6e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 19.01 Commit: 68c835e8ac2c68a3ddc2d02ec7e39e5b78c08485 https://github.com/galaxyproject/galaxy/commit/68c835e8ac2c68a3ddc2d02ec7e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: Log Message: ----------- Merge branch 'release_19.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ccdf4fb0b60e...68c835e8ac2c

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[galaxyproject/galaxy] fdb180: Update version to 19.01
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: fdb18045b76220b847163857e6e58acc19cef347 https://github.com/galaxyproject/galaxy/commit/fdb18045b76220b847163857e6e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 19.01

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[galaxyproject/galaxy] 14f3ce: Fix workflow interface drop to import
by John Chilton 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 14f3ce3b5092467e3d9dde9bd94fdab5f6b604b2 https://github.com/galaxyproject/galaxy/commit/14f3ce3b5092467e3d9dde9bd94f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js Log Message: ----------- Fix workflow interface drop to import Commit: 1583eecfdb338aae17fbb199160f7937e3b0ec01 https://github.com/galaxyproject/galaxy/commit/1583eecfdb338aae17fbb199160f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Client formatting sync for 19.01 Commit: 7553326ba1af32e50c3695cbb67795fc11f0ecdc https://github.com/galaxyproject/galaxy/commit/7553326ba1af32e50c3695cbb677… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/components/admin/ErrorStack.vue M client/galaxy/scripts/galaxy.interactive_environments.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/scss/base.scss Log Message: ----------- Merge pull request #7415 from dannon/fix-workflow-drop-hack [19.01] Fix workflow list drop-to-upload Compare: https://github.com/galaxyproject/galaxy/compare/bd25ff919c2f...7553326ba1af

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[galaxyproject/galaxy] 47ed81: Remove unreachable print statement
by Martin Cech 26 Feb '19

26 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: 47ed81feb95c092587c68deb07e247c3a4d29bff https://github.com/galaxyproject/galaxy/commit/47ed81feb95c092587c68deb07e2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M tools/data_source/upload.py Log Message: ----------- Remove unreachable print statement I don't think an exception could ever occur here. Commit: ed375993ebc43112e03f58779d7c8c104e67956a https://github.com/galaxyproject/galaxy/commit/ed375993ebc43112e03f58779d7c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Fix analyze75 hdr file upload when convert newlines is on Commit: bd25ff919c2f94dea446e656a757c61f8237db89 https://github.com/galaxyproject/galaxy/commit/bd25ff919c2f94dea446e656a757… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M lib/galaxy/datatypes/proteomics.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #7414 from mvdbeek/fix_analyze_75 [19.01] Fix analyze 75 datatype upload Compare: https://github.com/galaxyproject/galaxy/compare/808aa5bef7fb...bd25ff919c2f

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[galaxyproject/galaxy] f7a3c0: Fix settings of pie charts
by Dannon 26 Feb '19

26 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f7a3c0b6fef1e55b0012b1287931644e5afd6e8e https://github.com/galaxyproject/galaxy/commit/f7a3c0b6fef1e55b0012b1287931… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix settings of pie charts Commit: 402fd2896bf8e9556db5322e13e3485303d166d2 https://github.com/galaxyproject/galaxy/commit/402fd2896bf8e9556db5322e13e3… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M client/galaxy/style/scss/ui.scss Log Message: ----------- Set portlet height to auto Commit: 96b4d1efc23c22c2085a7810f1b62d8bdd2c5cc8 https://github.com/galaxyproject/galaxy/commit/96b4d1efc23c22c2085a7810f1b6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Fix setting remaining setting for label column placement Commit: ccdf4fb0b60eb1af6131ab20ce827d4549a75c97 https://github.com/galaxyproject/galaxy/commit/ccdf4fb0b60eb1af6131ab20ce82… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-26 (Tue, 26 Feb 2019) Changed paths: M client/galaxy/style/scss/ui.scss M config/plugins/visualizations/nvd3/nvd3_bar/package.json M config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css M config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml Log Message: ----------- Merge pull request #7396 from guerler/fix_pie_chart Fix pie chart and portlet height in flexboxes Compare: https://github.com/galaxyproject/galaxy/compare/9d5e532df2d5...ccdf4fb0b60e

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[galaxyproject/infrastructure-playbook] 82c4d3: Certbot support for the Mailman server
by Nate Coraor 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 82c4d3bc724b85cfef9aa5b7d682ec4a6bec991b https://github.com/galaxyproject/infrastructure-playbook/commit/82c4d3bc724… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/mailman/TODO.txt M env/mailman/group_vars/listservers.yml R env/mailman/templates/nginx/anvil-lists.j2 R env/mailman/templates/nginx/galaxy-lists.j2 M env/mailman/templates/nginx/mailman.j2 A env/mailman/templates/nginx/mailman_ssl.j2 M env/mailman/webservers.yml Log Message: ----------- Certbot support for the Mailman server

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[galaxyproject/usegalaxy-playbook] 55f1d4: Installed column_maker 1.2.0
by Dave B. 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 55f1d464eb2bdbcce25accc72ddae3e49cfba539 https://github.com/galaxyproject/usegalaxy-playbook/commit/55f1d464eb2bdbcc… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Installed column_maker 1.2.0

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[galaxyproject/usegalaxy-playbook] 9f32b1: Update Main shed_tool_conf
by Martin Cech 25 Feb '19

25 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9f32b1951135d95f8bf25cd6487a0b5f4b4d2ee9 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f32b1951135d95f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main shed_tool_conf

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[galaxyproject/galaxy] 4372b4: Simplify tag handling in history export.
by Dannon 25 Feb '19

25 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4372b493aa3781857c30926933e0324ac30f8517 https://github.com/galaxyproject/galaxy/commit/4372b493aa3781857c30926933e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2019-02-22 (Fri, 22 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Simplify tag handling in history export. Not yet used in import so we might as well simplify our lives and synchronize this with API exports before we actually start using them. Commit: 9d5e532df2d5c7ec976a28e4f7591694baaf3077 https://github.com/galaxyproject/galaxy/commit/9d5e532df2d5c7ec976a28e4f759… Author: Dannon <dannon.baker(a)gmail.com> Date: 2019-02-25 (Mon, 25 Feb 2019) Changed paths: M lib/galaxy/tools/imp_exp/__init__.py Log Message: ----------- Merge pull request #7369 from jmchilton/imp_exp_simple_3 Simplify tag handling in history export. Compare: https://github.com/galaxyproject/galaxy/compare/67bb91348bb2...9d5e532df2d5

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[galaxyproject/galaxy] 73fc69: specify generic exceptions more precisely
by Nicola Soranzo 24 Feb '19

24 Feb '19

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 73fc69d7899984446d52091ea179320dd08da0f2 https://github.com/galaxyproject/galaxy/commit/73fc69d7899984446d52091ea179… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- specify generic exceptions more precisely Commit: 564d0d7f9584f09c2ebf1af1f24c61c4226132c5 https://github.com/galaxyproject/galaxy/commit/564d0d7f9584f09c2ebf1af1f24c… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: c459d9a98ac1101438bc0b3cf747b84958b69e0c https://github.com/galaxyproject/galaxy/commit/c459d9a98ac1101438bc0b3cf747… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: 09a3802602c512ed51e02c243447db0776921f56 https://github.com/galaxyproject/galaxy/commit/09a3802602c512ed51e02c243447… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- choose better exceptions class Co-Authored-By: martenson <marten(a)bx.psu.edu> Commit: b197fedf60b8e82f68bdb61e05d2f6d2bad33a7b https://github.com/galaxyproject/galaxy/commit/b197fedf60b8e82f68bdb61e05d2… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-21 (Thu, 21 Feb 2019) Changed paths: M lib/galaxy/exceptions/error_codes.json Log Message: ----------- improve exception message per @nsoranzo Commit: 67bb91348bb26584b83592542424d329714d6b47 https://github.com/galaxyproject/galaxy/commit/67bb91348bb26584b83592542424… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2019-02-24 (Sun, 24 Feb 2019) Changed paths: M lib/galaxy/exceptions/error_codes.json M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Merge pull request #7397 from martenson/focus-exceptions specify generic exceptions more precisely Compare: https://github.com/galaxyproject/galaxy/compare/7324db1273da...67bb91348bb2

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