Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3e511292afe6dcdbb3bf533ef6b6e2520c2c652 https://github.com/galaxyproject/galaxy/commit/a3e511292afe6dcdbb3bf533ef6b6... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/form/form-select-content.js M lib/galaxy/auth/providers/ldap_ad.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/tool_shed/api/repositories.py M static/maps/mvc/form/form-select-content.js.map M static/scripts/mvc/form/form-select-content.js Log Message: ----------- Merge branch 'release_15.05' Commit: a8a1a150c6ec1a474753052b96b25aec8a22813e https://github.com/galaxyproject/galaxy/commit/a8a1a150c6ec1a474753052b96b25... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge branch 'release_15.05' Commit: 130004feb10f1fe3a26908401146b8e47c1202ff https://github.com/galaxyproject/galaxy/commit/130004feb10f1fe3a26908401146b... Author: Nate Coraor <nate@bx.psu.edu> Date: 2015-08-12 (Wed, 12 Aug 2015) Changed paths: M .ci/flake8_wrapper.sh M .ci/pep8_sources.txt M .gitignore M CONTRIBUTING.md A CONTRIBUTORS.md M LICENSE.txt M README.rst M client/GruntFile.js M client/README.md M client/bower.json R client/galaxy/scripts/galaxy.workflow_editor.canvas.js R client/galaxy/scripts/galaxy.workflows.js M client/galaxy/scripts/libs/d3.js M client/galaxy/scripts/libs/jquery/jquery.js M client/galaxy/scripts/libs/raven.js M client/galaxy/scripts/libs/require.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/form/form-data.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/library/library-folderlist-view.js M 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client/toolshed/scripts/toolshed.groups.js M config/auth_conf.xml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced M config/object_store_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/config/ipython.xml M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/ipython/templates/notebook.ipynb A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample A config/plugins/interactive_environments/rstudio/config/rstudio.xml A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js A 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tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/gff/gff_filter_by_feature_count.xml M tools/filters/gff/gtf_filter_by_attribute_values_list.xml M tools/filters/headWrapper.xml M tools/filters/joiner2.xml M tools/filters/lav_to_bed.py M tools/filters/lav_to_bed.xml M tools/filters/lav_to_bed_code.py M tools/filters/pasteWrapper.xml M tools/filters/remove_beginning.xml M tools/filters/tailWrapper.xml M tools/filters/ucsc_gene_table_to_intervals.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.py M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_reverse_complement.py M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_to_fasta.xml M tools/plotting/bar_chart.xml M tools/plotting/boxplot.xml M tools/solid_tools/maq_cs_wrapper_code.py M tools/stats/filtering.xml M tools/stats/grouping.py M tools/stats/gsummary.py M tools/stats/gsummary.xml M tools/stats/gsummary.xml.groups M tools/visualization/LAJ.xml M tools/visualization/LAJ_code.py Log Message: ----------- Merge branch 'release_15.07' Commit: 737248d41d4e1d682361b85d48ea65574367e59d https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea6... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: b8fd98979c775daf46a768572fb30f4467fd7458 https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb30... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-20 (Thu, 20 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: 083789526105abda87a701835b8ff44e0ec89405 https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8ff... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge pull request #625 from dannon/release_15.07 [release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers. Commit: b29e81014979d2e72d704a22560a278cfec42927 https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a2... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix for valid height/width definitions in workflow rendering code. Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa917... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings. Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231 https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf8... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.01' into release_15.03 Commit: c569f7856d41fe9b51808302569283c800a4eb93 https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b5180830256928... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'release_15.03' into release_15.05 Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5 https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5f... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Log Message: ----------- Merge branch 'release_15.05' into release_15.07 Commit: d055102596d85b5a3d6da90e8397016f6daf2271 https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e83970... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/render.py M lib/tool_shed/metadata/repository_metadata_manager.py M scripts/cleanup_datasets/cleanup_datasets.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/mvc/workflow/workflow-terminals.js M test/unit/test_galaxy_mapping.py Log Message: ----------- Merge branch 'release_15.07' Commit: 950f471c2326cc8d90c7efe372c063f47ed7f3e4 https://github.com/galaxyproject/galaxy/commit/950f471c2326cc8d90c7efe372c06... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2015-08-21 (Fri, 21 Aug 2015) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/795e30171149...950f471c2326