diff --git a/doc/source/releases/16.10.rst b/doc/source/releases/16.10.rst new file mode 100644 index 00000000000..20a18f6aacd --- /dev/null +++ b/doc/source/releases/16.10.rst @@ -0,0 +1,679 @@ + +.. to_doc + +16.10 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + +* Introduce Galaxy Webhooks - plugins for the web UI + (including work from `@bgruening `__, + and `@anatskiy `__). + `Pull Request 3040`_, `Pull Request 3102`_ +* The workflow run form has been replaced by one backed by the new tool form and the API. + `Pull Request 2669`_, `Pull Request 2720`_, `Pull Request 2766`_, + `Pull Request 2776`_, `Pull Request 2770`_, `Pull Request 2895`_, + `Pull Request 2935`_, `Pull Request 3007`_, `Pull Request 2969`_, + `Pull Request 2799`_, `Pull Request 3082`_, `Pull Request 2672`_, + `Pull Request 2920`_, `Pull Request 2777`_, `Pull Request 2902`_ +* Overhaul of charts visualization - more visualizations, more options, and better user interface. + `Pull Request 2875`_, `Pull Request 2820`_ +* Paginate contents of large histories. + `Pull Request 2588`_ +* Reload tools automatically without restarting Galaxy during tool shed installs + (thanks to `@mvdbeek `__). + `Pull Request 2840`_, `Pull Request 3025`_ +* Implement a collection operation tool for merging collections + (thanks to `@Takadonet `__). + `Pull Request 2771`_ +* Add a password strength evaluation bar + (thanks to `@benfulton `__). + `Pull Request 2687`_ +* Implement a GoDocker job runner + (thanks to `@varunshankar `__). + `Pull Request 2791`_, `Pull Request 2653`_ +* Support for API batch requests. + `Pull Request 1768`_ +* Allow JSONP to be returned from API endpoints. + `Pull Request 2937`_ +* Add "Save as" as an option in the workflow editor + (thanks to `@tmcgowan `__). + `Pull Request 3035`_ +* Replace `reference documentation `__ + for tool XML files with automatically generated + documentation from a now official Galaxy XSD documentation (with help from many). + `Pull Request 2923`_, `Pull Request 2936`_, `Pull Request 3086`_, + `Pull Request 2932`_, `Pull Request 2903`_, `Pull Request 3020`_, + `Pull Request 3072`_ +* Allow naming input datasets and collections during workflow extraction. + `Pull Request 2943`_ +* Various enhancements for API driven installation of tool shed repositories. + `Pull Request 2769`_ +* Implement beta support for discovering biocontainer Docker containers automatically for tool dependencies. + `Pull Request 2986`_ +* Improved API support for downloading datasets and relevant files. + `Pull Request 2741`_, `Pull Request 2885`_ +* Make tool search field stay at top of window when tool list scrolls. + (thanks to `@sszakony `__). + `Pull Request 2730`_, `Issue 2375`_ +* Scratchbook enhancement to include info and view details links for datasets. + `Pull Request 2733`_ +* Add implicit conversions target extension to HDA name when listed as + selection option in the tool form. + `Pull Request 2734`_ +* Add column names to BED datatype so that column names are displayed in + the dataset viewer. + `Pull Request 2784`_ +* Add "All" and "None" buttons to copy dataset view. + `Pull Request 2957`_ +* Lazy load workflow invocation steps to vastly improve scheduling performance of large + collection workflows + (thanks to `@nsoranzo `__). + `Pull Request 2978`_ +* Allow '.' and '_' for public names + (thanks to `@nsoranzo `__). + `Pull Request 2947`_ +* Add CEL datatype + (thanks to `@nturaga `__). + `Pull Request 3073`_ +* Add a netcdf datatype for metabolomics spectre data + (thanks to `@lecorguille `__). + `Pull Request 2706`_ +* Returning Blast datatypes to Galaxy core + (thanks to `@peterjc `__). + `Pull Request 2696`_ +* Add HDT format (with turtle format sniffer improvements) + (thanks to `@jjkoehorst `__). + `Pull Request 2787`_ +* Allow more configurability for containerized jobs. + `Pull Request 2790`_ +* Functionality to allow admins to switch on/off the line endings conversion + on library dataset import + (thanks to `@SANBI-SA `__). + `Pull Request 2819`_ +* Fix dataset selector update when deleting history items. + `Pull Request 2677`_ +* Add a tutorial on building job runners to the documentation + (thanks to `@varunshankar `__). + `Pull Request 2700`_ +* Allow viewing tool help from history datasets + (thanks to `@tmcgowan `__). + `Pull Request 3051`_ +* Prevent TS from creating sessions for repository status checks. + `Pull Request 2732`_ +* Shorten Conda environment names + (thanks to `@bgruening `__). + `Pull Request 2794`_ +* Various release process improvements (including an enhancement from + `@nsoranzo `__). + `Pull Request 2857`_, `Pull Request 2858`_, `Pull Request 2689`_, + `Pull Request 2865`_, `Pull Request 2952`_, `Pull Request 2695`_, + `Pull Request 2991`_, `Pull Request 3232`_ +* Various datatypes fixes and enhancements + (thanks to `@nsoranzo `__). + `Pull Request 2690`_ +* Various fixes and improvements for galaxy.json. + `Pull Request 2697`_ +* Improve samtools usage with ``--version-only`` check + (thanks to `@remimarenco `__). + `Pull Request 2705`_ +* All-around improvements to toolbox loading/reloading + (thanks to `@mvdbeek `__). + `Pull Request 2901`_ +* Refactor shed tool lineage registration + (thanks to `@mvdbeek `__). + `Pull Request 2909`_ +* Log the resolved dependency type + (thanks to `@mvdbeek `__). + `Pull Request 2917`_, `Pull Request 3036`_ +* Fixes for Python 3 and new import linting for dozens of packages + (largely thanks to `@nsoranzo `__). + `Pull Request 2731`_, `Pull Request 3177`_, `Pull Request 2983`_, + `Pull Request 2889`_, `Pull Request 3031`_, `Pull Request 3170`_, + `Pull Request 3154`_ +* Change every occurrence in the code of ``__all__`` from list to a tuple + (thanks to `@nsoranzo `__). + `Pull Request 3041`_, `Pull Request 3071`_ +* Docstring linting and fixes. + `Pull Request 3003`_, `Pull Request 3004`_ +* Update python-ldap module + (thanks to `@abretaud `__). + `Pull Request 2738`_ +* Update sqlalchemy to 1.0.15 (from 1.0.8). + `Pull Request 2979`_ +* Slightly revise auto configuration of loggers. + `Pull Request 2735`_ +* Various ``Makefile`` improvements and fixes. + `Pull Request 2757`_, `Pull Request 2688`_, `Pull Request 3167`_ +* Improve startup scripts + (thanks to `@nsoranzo `__). + `Pull Request 2765`_ +* Remove ``enable_beta_tool_command_isolation`` config option + (thanks to `@nsoranzo `__). + `Pull Request 2830`_ +* Regularize comments configuration samples. + `Pull Request 2824`_, `Pull Request 2841`_, `Pull Request 2814`_ +* Skip whoami check for LDAP servers not supporting it + (thanks to `@nsoranzo `__). + `Pull Request 2832`_ +* Filter disposable mail blacklist on the first domain level only. + `Pull Request 2839`_ +* Fix link target in admin view of tool lineages. + `Pull Request 2862`_ +* Refactor duplicated back-end code to create a new ``trans`` method for + getting the most recently touched history. + `Pull Request 2870`_ +* Document setting column names in Galaxy tool XSD. + `Pull Request 2965`_ +* Functional test case for testing column names as meta-data + (thanks to `@yhoogstrate `__). + `Pull Request 2970`_ +* Improve ``version_command`` tag. + `Pull Request 2961`_ +* Add ``rgb`` option for color picker tool parameter. + `Pull Request 3006`_ +* Improved docs and testing for color parameters. + `Pull Request 3016`_ +* Add documentation on optional ``multiple="true"`` data parameters. + `Pull Request 3024`_ +* Fix tool XSD to accept a help attribute for ``section``s + (thanks to `@joachimwolff `__). + `Pull Request 3131`_ +* In Trackster, read numerical data directly from bigWig files. + `Pull Request 2880`_ +* Improve wording of tool installation forms + (thanks to `@nturaga `__). + `Pull Request 2893`_ +* Add `database/dependencies` to `.gitignore` + (thanks to `@nturaga `__). + `Pull Request 2904`_ +* Allow admin to serialize/deserialize dataset permissions via the API. + `Pull Request 2912`_ +* Allow API access to genome fasta index and sequence + (thanks to `@jj-umn `__). + `Pull Request 2939`_ +* Extend ``PUT /api/workflows/{id}`` with additional workflow properties + (thanks to `@tmcgowan `__). + `Pull Request 3080`_ +* Update the copyright year in the LICENSE.txt. + `Pull Request 2926`_ +* Remove unnecessary use of binascii + (thanks to `@nsoranzo `__). + `Pull Request 2946`_ +* Change wording to be more clear about how workflow output cleanup works. + `Pull Request 2966`_ +* Optimized workflow invocation step update. + `Pull Request 2973`_ +* Update issues.rst to bring inline with actual usage on Github. + `Pull Request 2976`_ +* Improve Conda FAQ documentation. + `Pull Request 2998`_, `Pull Request 2891`_, `Pull Request 2871`_ +* Add documentation for ``conda_copy_dependencies`` option + (thanks to `@abretaud `__). + `Pull Request 3105`_ +* Slight clarification of run.sh messaging when using Conda. + `Pull Request 3188`_ +* Display tool requirements for conda-only tools + (thanks to `@mvdbeek `__). + `Pull Request 3262`_ +* Pass dependency shell command errors to log + (thanks to `@mvdbeek `__). + `Pull Request 3129`_ +* Fix for bioconda recipes depending on conda-forge. + `Pull Request 3023`_ +* Increase min number of columns for pileup sniffing to 5 + (thanks to `@nsoranzo `__). + `Pull Request 3033`_ +* Remove outdated warning on ID_SECRET + (thanks to `@erasche `__). + `Pull Request 3046`_ +* Always display text + `Pull Request 3052`_ +* Add Galaxy architecture slides documentation to project. + `Pull Request 3060`_, `Pull Request 3091`_ +* Add tool XML reload to tool run page - for admins only + (thanks to `@tmcgowan `__). + `Pull Request 3070`_, `Issue 943 `__ +* Move thumbnail list view to shared UI elements, revise tabs, add test cases + `Pull Request 3079`_ +* Include filenames in .loc file DEBUG lines + (thanks to `@peterjc `__). + `Pull Request 3095`_ +* Log loading of resources from .loc files + (thanks to `@peterjc `__). + `Pull Request 3099`_ +* Eager load tags and annotations in history display. + `Pull Request 3110`_ +* Display an error message when toolbox filtering fails. + `Pull Request 3123`_ +* Bring in various updates from galaxy-lib. + `Pull Request 3169`_, `Pull Request 2888`_ +* Add links to local tours to sample welcome. + `Pull Request 3176`_ +* Fix history deletion bug when using impersonation. + `Pull Request 2654`_ +* Refactor upload dialog to use local CSS classes and avoid model listeners. + `Pull Request 2711`_ +* Rework tool shed middleware + `Pull Request 2782`_, `Pull Request 2753`_ +* Refactor - move filelock.py to galaxy.util. + `Pull Request 2879`_ +* Use requests in driver_util for better proxy handling + (thanks to `@mvdbeek `__). + `Pull Request 3013`_ +* Fix workflow extraction API tests on PostgreSQL + (thanks to `@nsoranzo `__). + `Pull Request 3039`_ +* Avoid pointless lambda function + (thanks to `@peterjc `__). + `Pull Request 3097`_ +* Remove unnecessary ``set_output_history`` parameter + (thanks to `@nsoranzo `__). + `Pull Request 3155`_ +* Various code fixes for object store and docs + (thanks to `@nsoranzo `__). + `Pull Request 3119`_ +* Fix BLAST database *.loc files inconsistency + (thanks to `@peterjc `__). + `Pull Request 3098`_ +* Add ``download_to_file`` function to ``galaxy.util`` + (thanks to `@nsoranzo `__). + `Pull Request 3100`_ +* Log invalid XML filename + (thanks to `@mvdbeek `__). + `Pull Request 3124`_ +* Quote all paths in converter tool XML files + (thanks to `@mvdbeek `__). + `Pull Request 3165`_ + +Fixes +------------------------------- + +* Use default job history on ``build_for_rerun`` if current history is unavailable. + `Pull Request 2668`_ +* Fixing button width on composite upload dialog + (thanks to `@sszakony `__). + `Pull Request 2703`_, `Issue 2591 `__ +* Fix for splitting dataset collections + (thanks to `@gregvonkuster `__). + `Pull Request 2708`_ +* Fix tours pasting content into text area. + `Pull Request 2715`_ +* Slight styling tweak to prevent overflow on the right edge in composite upload dialog. + `Pull Request 2716`_ +* Workflow toolbox style updates. + `Pull Request 2740`_ +* Fix docker command_list + (thanks to `@manabuishii `__). + `Pull Request 2748`_ +* Fix ``list:list`` history display in the GUI. + `Pull Request 2758`_ +* Parse internal parameters such as job resource selections when data + converter tools are executed implicitly. + `Pull Request 2761`_ +* Fix broken check when creating Docker volumes default for jobs + (thanks to `@manabuishii `__). + `Pull Request 2763`_ +* Fix to prevent login form from appearing in scratchbook window + (thanks to `@sszakony `__). + `Pull Request 2808`_ +* Allow NodeJS proxy to do reverse proxying + (thanks to `@erasche `__). + `Pull Request 2817`_ +* Fixes for the RStudio interactive environment + (thanks to `@erasche `__). + `Pull Request 2818`_ +* Acquire lock before attempting to install conda + (thanks to `@mvdbeek `__). + `Pull Request 2826`_ +* Fix Galaxy for if pyuwsgi is install in Galaxy's virtual environment. + `Pull Request 2836`_ +* Fix tabular renderer display when ``total_cols > line_cols > 1``. + `Pull Request 2845`_ +* Remove empty file in toolbox module. + `Pull Request 2877`_ +* Fix for workflow execution when using collections. + `Pull Request 2898`_, `Issue 2806 `__ +* Implement ``split`` on a validator. + `Pull Request 2921`_ +* Catch failure to import grp in util (for Pulsar on Windows) + `Pull Request 2928`_ +* Bump pysam, remove ``already_compressed`` usage due to new wheel. + `Pull Request 2953`_ +* Re-build DOM on render for modal in the front-end. + `Pull Request 2955`_ +* Fix optional column form values when editing dataset properties. + `Pull Request 2960`_ +* Fix optional flag for library datasets in legacy library UI. + `Pull Request 2962`_ +* Reload metadata and lib tools on toolbox reload + (thanks to `@mvdbeek `__). + `Pull Request 2992`_ +* Update some old information in API guideline docs. + `Pull Request 3011`_ +* Fix for rerunning tool with workflow resume that is part of a collection. + `Pull Request 3019`_ +* Missing double quotation in tool XSD example + (thanks to `@ramezrawas `__). + `Pull Request 3027`_ +* Include base classes when searching datatypes by name. + `Pull Request 3028`_ +* Image detection fixes. + `Pull Request 3042`_ +* Fix tabular filtering tool broken in `#2983 + `__ + `Pull Request 3043`_ +* Fix GFF attribute filtering tool broken in `#2983 + `__ + `Pull Request 3044`_ +* Fix for displaying parameters to the user that have a ``False`` value. + `Pull Request 3045`_ +* Fix downloading tool tarball with boolean test input values. + `Pull Request 3047`_ +* Sort bedtools output in ``bam_to_bigwig`` conversion + (thanks to `@lparsons `__). + `Pull Request 3049`_ +* Remove incorrect communication server check. + `Pull Request 3053`_ +* Fix import orders for updates to flake8_import_order. + `Pull Request 3059`_ +* Dataset metadata should not be cached when building chart visualizations. + `Pull Request 3062`_ +* Fix libraries prefix. + `Pull Request 3074`_ +* Fix qunit local testing install -- now runs on modern node (v6.9.1). + `Pull Request 3089`_ +* Add routes to get genomes indexes and sequences + (thanks to `@jj-umn `__). + `Pull Request 3109`_ +* Escape section name when writing to XML + (thanks to `@mvdbeek `__). + `Pull Request 3122`_ +* Fix tools placed outside of panel section + (thanks to `@mvdbeek `__). + `Pull Request 3125`_ +* Fix XSD for ``exclude_min`` and ``exclude_max`` + (thanks to `@gregvonkuster `__). + `Pull Request 3108`_ +* Update galaxy.xsd + (thanks to `@lecorguille `__). + `Pull Request 3132`_ +* Fix to treat the value of ``message_box_visible`` in ``galaxy.ini`` as a boolean. + `Pull Request 3139`_ +* Ensure a From: address is set for user activation emails. + `Pull Request 3140`_ +* Explicitly specify attributes which should be copied to converted datasets. + `Pull Request 3149`_ +* Prefer existing .venv over conda, when both are available. + `Pull Request 3180`_ +* Validate cycles and step size before building model for workflow execution. + `Pull Request 3183`_ +* Fix a typo in the intro tour. + `Pull Request 3184`_ +* Make SAM to bam converter tool compatible with samtools >= 1.3 + (thanks to `@mvdbeek `__). + `Pull Request 3187`_ +* Remove unused (and unintended) config override. + `Pull Request 3198`_ +* Fixes for deleting histories. + `Pull Request 3203`_ +* Change 'History Actions' to 'Current History' in history options menu. + `Pull Request 3205`_ +* Preserve custom event handler for form inputs. + `Pull Request 3210`_ +* Admin installation UX wording fixes. + `Pull Request 3226`_ +* Backport `#3106 `__ and + `#3222 `__: Cached + conda environments and API to manage them + (thanks to `@mvdbeek `__). + `Pull Request 3227`_ + +.. _Issue 2375: https://github.com/galaxyproject/galaxy/issues/2375 +.. github_links +.. _Pull Request 1768: https://github.com/galaxyproject/galaxy/pull/1768 +.. _Pull Request 2588: https://github.com/galaxyproject/galaxy/pull/2588 +.. _Pull Request 2653: https://github.com/galaxyproject/galaxy/pull/2653 +.. _Pull Request 2654: https://github.com/galaxyproject/galaxy/pull/2654 +.. _Pull Request 2668: https://github.com/galaxyproject/galaxy/pull/2668 +.. _Pull Request 2669: https://github.com/galaxyproject/galaxy/pull/2669 +.. _Pull Request 2672: https://github.com/galaxyproject/galaxy/pull/2672 +.. _Pull Request 2674: https://github.com/galaxyproject/galaxy/pull/2674 +.. _Pull Request 2677: https://github.com/galaxyproject/galaxy/pull/2677 +.. _Pull Request 2686: https://github.com/galaxyproject/galaxy/pull/2686 +.. _Pull Request 2687: https://github.com/galaxyproject/galaxy/pull/2687 +.. _Pull Request 2688: https://github.com/galaxyproject/galaxy/pull/2688 +.. _Pull Request 2689: https://github.com/galaxyproject/galaxy/pull/2689 +.. _Pull Request 2690: https://github.com/galaxyproject/galaxy/pull/2690 +.. _Pull Request 2695: https://github.com/galaxyproject/galaxy/pull/2695 +.. _Pull Request 2696: https://github.com/galaxyproject/galaxy/pull/2696 +.. _Pull Request 2697: https://github.com/galaxyproject/galaxy/pull/2697 +.. _Pull Request 2700: https://github.com/galaxyproject/galaxy/pull/2700 +.. _Pull Request 2703: https://github.com/galaxyproject/galaxy/pull/2703 +.. _Pull Request 2705: https://github.com/galaxyproject/galaxy/pull/2705 +.. _Pull Request 2706: https://github.com/galaxyproject/galaxy/pull/2706 +.. _Pull Request 2708: https://github.com/galaxyproject/galaxy/pull/2708 +.. _Pull Request 2711: https://github.com/galaxyproject/galaxy/pull/2711 +.. _Pull Request 2715: https://github.com/galaxyproject/galaxy/pull/2715 +.. _Pull Request 2716: https://github.com/galaxyproject/galaxy/pull/2716 +.. _Pull Request 2720: https://github.com/galaxyproject/galaxy/pull/2720 +.. _Pull Request 2730: https://github.com/galaxyproject/galaxy/pull/2730 +.. _Pull Request 2731: https://github.com/galaxyproject/galaxy/pull/2731 +.. _Pull Request 2732: https://github.com/galaxyproject/galaxy/pull/2732 +.. _Pull Request 2733: https://github.com/galaxyproject/galaxy/pull/2733 +.. _Pull Request 2734: https://github.com/galaxyproject/galaxy/pull/2734 +.. _Pull Request 2735: https://github.com/galaxyproject/galaxy/pull/2735 +.. _Pull Request 2738: https://github.com/galaxyproject/galaxy/pull/2738 +.. _Pull Request 2740: https://github.com/galaxyproject/galaxy/pull/2740 +.. _Pull Request 2741: https://github.com/galaxyproject/galaxy/pull/2741 +.. _Pull Request 2748: https://github.com/galaxyproject/galaxy/pull/2748 +.. _Pull Request 2753: https://github.com/galaxyproject/galaxy/pull/2753 +.. _Pull Request 2757: https://github.com/galaxyproject/galaxy/pull/2757 +.. _Pull Request 2758: https://github.com/galaxyproject/galaxy/pull/2758 +.. _Pull Request 2761: https://github.com/galaxyproject/galaxy/pull/2761 +.. _Pull Request 2762: https://github.com/galaxyproject/galaxy/pull/2762 +.. _Pull Request 2763: https://github.com/galaxyproject/galaxy/pull/2763 +.. _Pull Request 2765: https://github.com/galaxyproject/galaxy/pull/2765 +.. _Pull Request 2766: https://github.com/galaxyproject/galaxy/pull/2766 +.. _Pull Request 2769: https://github.com/galaxyproject/galaxy/pull/2769 +.. _Pull Request 2770: https://github.com/galaxyproject/galaxy/pull/2770 +.. _Pull Request 2771: https://github.com/galaxyproject/galaxy/pull/2771 +.. _Pull Request 2776: https://github.com/galaxyproject/galaxy/pull/2776 +.. _Pull Request 2777: https://github.com/galaxyproject/galaxy/pull/2777 +.. _Pull Request 2782: https://github.com/galaxyproject/galaxy/pull/2782 +.. _Pull Request 2784: https://github.com/galaxyproject/galaxy/pull/2784 +.. _Pull Request 2787: https://github.com/galaxyproject/galaxy/pull/2787 +.. _Pull Request 2790: https://github.com/galaxyproject/galaxy/pull/2790 +.. _Pull Request 2791: https://github.com/galaxyproject/galaxy/pull/2791 +.. _Pull Request 2794: https://github.com/galaxyproject/galaxy/pull/2794 +.. _Pull Request 2799: https://github.com/galaxyproject/galaxy/pull/2799 +.. _Pull Request 2808: https://github.com/galaxyproject/galaxy/pull/2808 +.. _Pull Request 2814: https://github.com/galaxyproject/galaxy/pull/2814 +.. _Pull Request 2816: https://github.com/galaxyproject/galaxy/pull/2816 +.. _Pull Request 2817: https://github.com/galaxyproject/galaxy/pull/2817 +.. _Pull Request 2818: https://github.com/galaxyproject/galaxy/pull/2818 +.. _Pull Request 2819: https://github.com/galaxyproject/galaxy/pull/2819 +.. _Pull Request 2820: https://github.com/galaxyproject/galaxy/pull/2820 +.. _Pull Request 2824: https://github.com/galaxyproject/galaxy/pull/2824 +.. _Pull Request 2826: https://github.com/galaxyproject/galaxy/pull/2826 +.. _Pull Request 2830: https://github.com/galaxyproject/galaxy/pull/2830 +.. _Pull Request 2832: https://github.com/galaxyproject/galaxy/pull/2832 +.. _Pull Request 2836: https://github.com/galaxyproject/galaxy/pull/2836 +.. _Pull Request 2839: https://github.com/galaxyproject/galaxy/pull/2839 +.. _Pull Request 2840: https://github.com/galaxyproject/galaxy/pull/2840 +.. _Pull Request 2841: https://github.com/galaxyproject/galaxy/pull/2841 +.. _Pull Request 2845: https://github.com/galaxyproject/galaxy/pull/2845 +.. _Pull Request 2848: https://github.com/galaxyproject/galaxy/pull/2848 +.. _Pull Request 2857: https://github.com/galaxyproject/galaxy/pull/2857 +.. _Pull Request 2858: https://github.com/galaxyproject/galaxy/pull/2858 +.. _Pull Request 2862: https://github.com/galaxyproject/galaxy/pull/2862 +.. _Pull Request 2865: https://github.com/galaxyproject/galaxy/pull/2865 +.. _Pull Request 2870: https://github.com/galaxyproject/galaxy/pull/2870 +.. _Pull Request 2871: https://github.com/galaxyproject/galaxy/pull/2871 +.. _Pull Request 2872: https://github.com/galaxyproject/galaxy/pull/2872 +.. _Pull Request 2875: https://github.com/galaxyproject/galaxy/pull/2875 +.. _Pull Request 2877: https://github.com/galaxyproject/galaxy/pull/2877 +.. _Pull Request 2879: https://github.com/galaxyproject/galaxy/pull/2879 +.. _Pull Request 2880: https://github.com/galaxyproject/galaxy/pull/2880 +.. _Pull Request 2885: https://github.com/galaxyproject/galaxy/pull/2885 +.. _Pull Request 2887: https://github.com/galaxyproject/galaxy/pull/2887 +.. _Pull Request 2888: https://github.com/galaxyproject/galaxy/pull/2888 +.. _Pull Request 2889: https://github.com/galaxyproject/galaxy/pull/2889 +.. _Pull Request 2891: https://github.com/galaxyproject/galaxy/pull/2891 +.. _Pull Request 2893: https://github.com/galaxyproject/galaxy/pull/2893 +.. _Pull Request 2894: https://github.com/galaxyproject/galaxy/pull/2894 +.. _Pull Request 2895: https://github.com/galaxyproject/galaxy/pull/2895 +.. _Pull Request 2898: https://github.com/galaxyproject/galaxy/pull/2898 +.. _Pull Request 2901: https://github.com/galaxyproject/galaxy/pull/2901 +.. _Pull Request 2902: https://github.com/galaxyproject/galaxy/pull/2902 +.. _Pull Request 2903: https://github.com/galaxyproject/galaxy/pull/2903 +.. _Pull Request 2904: https://github.com/galaxyproject/galaxy/pull/2904 +.. _Pull Request 2905: https://github.com/galaxyproject/galaxy/pull/2905 +.. _Pull Request 2909: https://github.com/galaxyproject/galaxy/pull/2909 +.. _Pull Request 2912: https://github.com/galaxyproject/galaxy/pull/2912 +.. _Pull Request 2917: https://github.com/galaxyproject/galaxy/pull/2917 +.. _Pull Request 2920: https://github.com/galaxyproject/galaxy/pull/2920 +.. _Pull Request 2921: https://github.com/galaxyproject/galaxy/pull/2921 +.. _Pull Request 2923: https://github.com/galaxyproject/galaxy/pull/2923 +.. _Pull Request 2926: https://github.com/galaxyproject/galaxy/pull/2926 +.. _Pull Request 2928: https://github.com/galaxyproject/galaxy/pull/2928 +.. _Pull Request 2932: https://github.com/galaxyproject/galaxy/pull/2932 +.. _Pull Request 2935: https://github.com/galaxyproject/galaxy/pull/2935 +.. _Pull Request 2936: https://github.com/galaxyproject/galaxy/pull/2936 +.. _Pull Request 2937: https://github.com/galaxyproject/galaxy/pull/2937 +.. _Pull Request 2939: https://github.com/galaxyproject/galaxy/pull/2939 +.. _Pull Request 2943: https://github.com/galaxyproject/galaxy/pull/2943 +.. _Pull Request 2946: https://github.com/galaxyproject/galaxy/pull/2946 +.. _Pull Request 2947: https://github.com/galaxyproject/galaxy/pull/2947 +.. _Pull Request 2952: https://github.com/galaxyproject/galaxy/pull/2952 +.. _Pull Request 2953: https://github.com/galaxyproject/galaxy/pull/2953 +.. _Pull Request 2955: https://github.com/galaxyproject/galaxy/pull/2955 +.. _Pull Request 2957: https://github.com/galaxyproject/galaxy/pull/2957 +.. _Pull Request 2960: https://github.com/galaxyproject/galaxy/pull/2960 +.. _Pull Request 2961: https://github.com/galaxyproject/galaxy/pull/2961 +.. _Pull Request 2962: https://github.com/galaxyproject/galaxy/pull/2962 +.. _Pull Request 2965: https://github.com/galaxyproject/galaxy/pull/2965 +.. _Pull Request 2966: https://github.com/galaxyproject/galaxy/pull/2966 +.. _Pull Request 2969: https://github.com/galaxyproject/galaxy/pull/2969 +.. _Pull Request 2970: https://github.com/galaxyproject/galaxy/pull/2970 +.. _Pull Request 2971: https://github.com/galaxyproject/galaxy/pull/2971 +.. _Pull Request 2972: https://github.com/galaxyproject/galaxy/pull/2972 +.. _Pull Request 2973: https://github.com/galaxyproject/galaxy/pull/2973 +.. _Pull Request 2974: https://github.com/galaxyproject/galaxy/pull/2974 +.. _Pull Request 2975: https://github.com/galaxyproject/galaxy/pull/2975 +.. _Pull Request 2976: https://github.com/galaxyproject/galaxy/pull/2976 +.. _Pull Request 2978: https://github.com/galaxyproject/galaxy/pull/2978 +.. _Pull Request 2979: https://github.com/galaxyproject/galaxy/pull/2979 +.. _Pull Request 2983: https://github.com/galaxyproject/galaxy/pull/2983 +.. _Pull Request 2986: https://github.com/galaxyproject/galaxy/pull/2986 +.. _Pull Request 2990: https://github.com/galaxyproject/galaxy/pull/2990 +.. _Pull Request 2991: https://github.com/galaxyproject/galaxy/pull/2991 +.. _Pull Request 2992: https://github.com/galaxyproject/galaxy/pull/2992 +.. _Pull Request 2998: https://github.com/galaxyproject/galaxy/pull/2998 +.. _Pull Request 3003: https://github.com/galaxyproject/galaxy/pull/3003 +.. _Pull Request 3004: https://github.com/galaxyproject/galaxy/pull/3004 +.. _Pull Request 3005: https://github.com/galaxyproject/galaxy/pull/3005 +.. _Pull Request 3006: https://github.com/galaxyproject/galaxy/pull/3006 +.. _Pull Request 3007: https://github.com/galaxyproject/galaxy/pull/3007 +.. _Pull Request 3010: https://github.com/galaxyproject/galaxy/pull/3010 +.. _Pull Request 3011: https://github.com/galaxyproject/galaxy/pull/3011 +.. _Pull Request 3013: https://github.com/galaxyproject/galaxy/pull/3013 +.. _Pull Request 3016: https://github.com/galaxyproject/galaxy/pull/3016 +.. _Pull Request 3019: https://github.com/galaxyproject/galaxy/pull/3019 +.. _Pull Request 3020: https://github.com/galaxyproject/galaxy/pull/3020 +.. _Pull Request 3023: https://github.com/galaxyproject/galaxy/pull/3023 +.. _Pull Request 3024: https://github.com/galaxyproject/galaxy/pull/3024 +.. _Pull Request 3025: https://github.com/galaxyproject/galaxy/pull/3025 +.. _Pull Request 3027: https://github.com/galaxyproject/galaxy/pull/3027 +.. _Pull Request 3028: https://github.com/galaxyproject/galaxy/pull/3028 +.. _Pull Request 3031: https://github.com/galaxyproject/galaxy/pull/3031 +.. _Pull Request 3032: https://github.com/galaxyproject/galaxy/pull/3032 +.. _Pull Request 3033: https://github.com/galaxyproject/galaxy/pull/3033 +.. _Pull Request 3035: https://github.com/galaxyproject/galaxy/pull/3035 +.. _Pull Request 3036: https://github.com/galaxyproject/galaxy/pull/3036 +.. _Pull Request 3037: https://github.com/galaxyproject/galaxy/pull/3037 +.. _Pull Request 3039: https://github.com/galaxyproject/galaxy/pull/3039 +.. _Pull Request 3040: https://github.com/galaxyproject/galaxy/pull/3040 +.. _Pull Request 3041: https://github.com/galaxyproject/galaxy/pull/3041 +.. _Pull Request 3042: https://github.com/galaxyproject/galaxy/pull/3042 +.. _Pull Request 3043: https://github.com/galaxyproject/galaxy/pull/3043 +.. _Pull Request 3044: https://github.com/galaxyproject/galaxy/pull/3044 +.. _Pull Request 3045: https://github.com/galaxyproject/galaxy/pull/3045 +.. _Pull Request 3046: https://github.com/galaxyproject/galaxy/pull/3046 +.. _Pull Request 3047: https://github.com/galaxyproject/galaxy/pull/3047 +.. _Pull Request 3049: https://github.com/galaxyproject/galaxy/pull/3049 +.. _Pull Request 3051: https://github.com/galaxyproject/galaxy/pull/3051 +.. _Pull Request 3052: https://github.com/galaxyproject/galaxy/pull/3052 +.. _Pull Request 3053: https://github.com/galaxyproject/galaxy/pull/3053 +.. _Pull Request 3056: https://github.com/galaxyproject/galaxy/pull/3056 +.. _Pull Request 3059: https://github.com/galaxyproject/galaxy/pull/3059 +.. _Pull Request 3060: https://github.com/galaxyproject/galaxy/pull/3060 +.. _Pull Request 3062: https://github.com/galaxyproject/galaxy/pull/3062 +.. _Pull Request 3070: https://github.com/galaxyproject/galaxy/pull/3070 +.. _Pull Request 3071: https://github.com/galaxyproject/galaxy/pull/3071 +.. _Pull Request 3072: https://github.com/galaxyproject/galaxy/pull/3072 +.. _Pull Request 3073: https://github.com/galaxyproject/galaxy/pull/3073 +.. _Pull Request 3074: https://github.com/galaxyproject/galaxy/pull/3074 +.. _Pull Request 3077: https://github.com/galaxyproject/galaxy/pull/3077 +.. _Pull Request 3079: https://github.com/galaxyproject/galaxy/pull/3079 +.. _Pull Request 3080: https://github.com/galaxyproject/galaxy/pull/3080 +.. _Pull Request 3082: https://github.com/galaxyproject/galaxy/pull/3082 +.. _Pull Request 3086: https://github.com/galaxyproject/galaxy/pull/3086 +.. _Pull Request 3087: https://github.com/galaxyproject/galaxy/pull/3087 +.. _Pull Request 3089: https://github.com/galaxyproject/galaxy/pull/3089 +.. _Pull Request 3091: https://github.com/galaxyproject/galaxy/pull/3091 +.. _Pull Request 3095: https://github.com/galaxyproject/galaxy/pull/3095 +.. _Pull Request 3097: https://github.com/galaxyproject/galaxy/pull/3097 +.. _Pull Request 3098: https://github.com/galaxyproject/galaxy/pull/3098 +.. _Pull Request 3099: https://github.com/galaxyproject/galaxy/pull/3099 +.. _Pull Request 3100: https://github.com/galaxyproject/galaxy/pull/3100 +.. _Pull Request 3102: https://github.com/galaxyproject/galaxy/pull/3102 +.. _Pull Request 3103: https://github.com/galaxyproject/galaxy/pull/3103 +.. _Pull Request 3105: https://github.com/galaxyproject/galaxy/pull/3105 +.. _Pull Request 3108: https://github.com/galaxyproject/galaxy/pull/3108 +.. _Pull Request 3109: https://github.com/galaxyproject/galaxy/pull/3109 +.. _Pull Request 3110: https://github.com/galaxyproject/galaxy/pull/3110 +.. _Pull Request 3113: https://github.com/galaxyproject/galaxy/pull/3113 +.. _Pull Request 3116: https://github.com/galaxyproject/galaxy/pull/3116 +.. _Pull Request 3119: https://github.com/galaxyproject/galaxy/pull/3119 +.. _Pull Request 3122: https://github.com/galaxyproject/galaxy/pull/3122 +.. _Pull Request 3123: https://github.com/galaxyproject/galaxy/pull/3123 +.. _Pull Request 3124: https://github.com/galaxyproject/galaxy/pull/3124 +.. _Pull Request 3125: https://github.com/galaxyproject/galaxy/pull/3125 +.. _Pull Request 3129: https://github.com/galaxyproject/galaxy/pull/3129 +.. _Pull Request 3130: https://github.com/galaxyproject/galaxy/pull/3130 +.. _Pull Request 3131: https://github.com/galaxyproject/galaxy/pull/3131 +.. _Pull Request 3132: https://github.com/galaxyproject/galaxy/pull/3132 +.. _Pull Request 3135: https://github.com/galaxyproject/galaxy/pull/3135 +.. _Pull Request 3139: https://github.com/galaxyproject/galaxy/pull/3139 +.. _Pull Request 3140: https://github.com/galaxyproject/galaxy/pull/3140 +.. _Pull Request 3141: https://github.com/galaxyproject/galaxy/pull/3141 +.. _Pull Request 3149: https://github.com/galaxyproject/galaxy/pull/3149 +.. _Pull Request 3154: https://github.com/galaxyproject/galaxy/pull/3154 +.. _Pull Request 3155: https://github.com/galaxyproject/galaxy/pull/3155 +.. _Pull Request 3165: https://github.com/galaxyproject/galaxy/pull/3165 +.. _Pull Request 3167: https://github.com/galaxyproject/galaxy/pull/3167 +.. _Pull Request 3169: https://github.com/galaxyproject/galaxy/pull/3169 +.. _Pull Request 3170: https://github.com/galaxyproject/galaxy/pull/3170 +.. _Pull Request 3176: https://github.com/galaxyproject/galaxy/pull/3176 +.. _Pull Request 3177: https://github.com/galaxyproject/galaxy/pull/3177 +.. _Pull Request 3180: https://github.com/galaxyproject/galaxy/pull/3180 +.. _Pull Request 3183: https://github.com/galaxyproject/galaxy/pull/3183 +.. _Pull Request 3184: https://github.com/galaxyproject/galaxy/pull/3184 +.. _Pull Request 3187: https://github.com/galaxyproject/galaxy/pull/3187 +.. _Pull Request 3188: https://github.com/galaxyproject/galaxy/pull/3188 +.. _Pull Request 3191: https://github.com/galaxyproject/galaxy/pull/3191 +.. _Pull Request 3198: https://github.com/galaxyproject/galaxy/pull/3198 +.. _Pull Request 3203: https://github.com/galaxyproject/galaxy/pull/3203 +.. _Pull Request 3205: https://github.com/galaxyproject/galaxy/pull/3205 +.. _Pull Request 3210: https://github.com/galaxyproject/galaxy/pull/3210 +.. _Pull Request 3226: https://github.com/galaxyproject/galaxy/pull/3226 +.. _Pull Request 3227: https://github.com/galaxyproject/galaxy/pull/3227 +.. _Pull Request 3232: https://github.com/galaxyproject/galaxy/pull/3232 +.. _Pull Request 3262: https://github.com/galaxyproject/galaxy/pull/3262 + diff --git a/doc/source/releases/16.10_announce.rst b/doc/source/releases/16.10_announce.rst index 758c47f2b80..97552d63251 100644 --- a/doc/source/releases/16.10_announce.rst +++ b/doc/source/releases/16.10_announce.rst @@ -3,8 +3,39 @@ October 2016 Galaxy Release (v 16.10) =========================================================== +.. include:: _header.rst -Schedule +Highlights =========================================================== - * Planned Freeze Date: 2016-10-03 - * Planned Release Date: 2016-10-24 + +**Feature1** + Feature description. + +**Feature2** + Feature description. + +**Feature3** + Feature description. + +`Github `__ +=========================================================== + +New Galaxy repository + .. code-block:: shell + + $ git clone -b release_16.10 https://github.com/galaxyproject/galaxy.git + +Update of existing Galaxy repository + .. code-block:: shell + + $ git checkout release_16.10 && git pull --ff-only origin release_16.10 + +See `our wiki `__ for additional details regarding the source code locations. + +Release Notes +=========================================================== + +.. include:: 16.10.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/17.01_announce.rst b/doc/source/releases/17.01_announce.rst new file mode 100644 index 00000000000..943de5860de --- /dev/null +++ b/doc/source/releases/17.01_announce.rst @@ -0,0 +1,10 @@ + +=========================================================== +January 2017 Galaxy Release (v 17.01) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2017-01-02 + * Planned Release Date: 2017-01-23 diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py index fdc74493332..8f4ad47891b 100644 --- a/scripts/bootstrap_history.py +++ b/scripts/bootstrap_history.py @@ -105,12 +105,12 @@ Highlights New Galaxy repository .. code-block:: shell - $ git clone -b release_${release} https://github.com/galaxyproject/galaxy.git + $$ git clone -b release_${release} https://github.com/galaxyproject/galaxy.git Update of existing Galaxy repository .. code-block:: shell - $ git checkout release_${release} && git pull --ff-only origin release_${release} + $$ git checkout release_${release} && git pull --ff-only origin release_${release} See `our wiki `__ for additional details regarding the source code locations. @@ -491,7 +491,7 @@ def main(argv): text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL) history = extend(".. github_links", text) if owner: - to_doc += "\n(thanks to `@%s `__.)" % ( + to_doc += "\n(thanks to `@%s `__)." % ( owner, owner, ) to_doc += "\n`Pull Request {0}`_".format(pull_request)