From f47ea88c236be2414d40ef933dd3ee3c5aa2cbcb Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 19 Aug 2016 13:05:05 -0400 Subject: [PATCH] initial curated release notes for 16.07 --- doc/source/releases/16.07.rst | 843 +++++++++++++++++++++++++ doc/source/releases/16.07_announce.rst | 51 +- doc/source/releases/16.10_announce.rst | 10 + 3 files changed, 901 insertions(+), 3 deletions(-) create mode 100644 doc/source/releases/16.07.rst create mode 100644 doc/source/releases/16.10_announce.rst diff --git a/doc/source/releases/16.07.rst b/doc/source/releases/16.07.rst new file mode 100644 index 00000000000..971550f2397 --- /dev/null +++ b/doc/source/releases/16.07.rst @@ -0,0 +1,843 @@ + +.. to_doc + +------------------------------- +16.07 +------------------------------- + +Conda +------------------------------- + +* Install via conda + (thanks to `@mvdbeek `__ + and `@bwlang `__.) + `Pull Request 2554`_ +* install Conda at startup; enable conda_auto_init in sample conf + `Pull Request 2759`_ + +API +------------------------------- + +* TS API: add endpoint to check current user + `Pull Request 2243`_ +* Users API: add the update endpoint + `Pull Request 2595`_ + +Collections +------------------------------- + +* Collection Operations (Limited) + `Pull Request 2434`_ +* Implement UI to display list of lists dataset collections + `Pull Request 2613`_ + +Datatypes +------------------------------- + +* Add support to PDBQT molecule datatype + (thanks to `@leobiscassi `__.) + `Pull Request 2452`_ +* Add the trackhub composite datatype + (thanks to `@remimarenco `__.) + `Pull Request 2348`_ +* Import mothur datatypes + (thanks to `@shiltemann `__.) + `Pull Request 2038`_ + +Highlighted Enhancements +------------------------------- + +* Galactic Radio Telescope + (thanks to `@erasche `__.) + `Pull Request 2455`_ +* Galaxy Communication Server + (thanks to `@anuprulez `__ + and `@bgruening `__.) + `Pull Request 2515`_ +* Add DTD to Galaxy + (thanks to `@ericenns `__.) + `Pull Request 2579`_ +* Azure blob objectstore + (thanks to `@zfrenchee `__.) + `Pull Request 2621`_ +* HTCondor Docker Integration + (thanks to `@bgruening `__.) + `Pull Request 2278`_ +* Kubernetes job runner + (thanks to `@pcm32 `__.) + `Pull Request 2314`_ +* improvements to toolbox search + `Pull Request 2273`_ +* Generate metadata in separate conda environment + (thanks to `@mvdbeek `__.) + `Pull Request 2253`_ +* Reports: new pages and improvements + (thanks to `@BalthazarPavot `__.) + `Pull Request 2664`_ +* Nicer bug report emails + (thanks to `@erasche `__.) + `Pull Request 2143`_ +* Tools with auto_format='true' connectable in workflow editor + (thanks to `@yhoogstrate `__.) + `Pull Request 2144`_ +* Drop "Galaxy pip" in favor of manylinux1 wheels (which are supported in pip + >= 8.1) + `Pull Request 2383`_ +* Allow tool form to listen to history + (thanks to `@nturaga `__.) + `Pull Request 2476`_ +* Add EDAM operations to tools and expose in API + (thanks to `@mvdbeek `__.) + `Pull Request 2379`_ + +Enhancements +------------------------------- + +* Add filter_failed_datasets_from_collection.py script + (thanks to `@chambm `__.) + `Pull Request 2358`_ +* Run workflow form revision + `Pull Request 2077`_ +* galaxy-lib tweaks + `Pull Request 2110`_ +* Automate and clarify more of the release process. + `Pull Request 2117`_ +* API: add server_starttime to api/configuration + `Pull Request 2124`_ +* This should fix bug `#1892 + `__ in toolshed + (thanks to `@nturaga `__.) + `Pull Request 2142`_ +* Use "$NCPUS" if defined to set GALAXY_SLOTS + (thanks to `@mvdbeek `__.) + `Pull Request 2145`_ +* Replacing the _getIndex method by UnderscoreJS method _.findIndex() + (thanks to `@anuprulez `__.) + `Pull Request 2157`_ +* activation config touch + `Pull Request 2158`_ +* Implement ``single_user = `` config option. + `Pull Request 2165`_ +* More documentation and flexibility for FTP imports. + `Pull Request 2168`_ +* Stats prefix configurability and conditional wheel req. + `Pull Request 2171`_ +* Fix running tool tests if remote user middleware is enabled. + `Pull Request 2173`_ +* Improve handling of a missing R environment. + `Pull Request 2215`_ +* Quote some parameters in Trim tool command + (thanks to `@nsoranzo `__.) + `Pull Request 2248`_ +* Tool execution dependency resolution already contains the relevant + `Pull Request 2254`_ +* add Saskia to contributors + `Pull Request 2256`_ +* A pass adding new contributors from 15.10->16.04(ish). + `Pull Request 2257`_ +* Sort contributors by surname ASC. + `Pull Request 2258`_ +* Add grunt watcher on the .less files + (thanks to `@remimarenco `__.) + `Pull Request 2274`_ +* requirements updates (end of custom Whoosh) + `Pull Request 2276`_ +* Enhance library functions for tools. + `Pull Request 2279`_ +* Shift asbool handling in datatypes api so that an appropriate error m… + `Pull Request 2286`_ +* More small fixes from downstream projects. + `Pull Request 2292`_ +* For published workflow display, Provide a better error when the workf… + `Pull Request 2302`_ +* Bump sqlite3 version + (thanks to `@matthdsm `__.) + `Pull Request 2307`_ +* Show DCE count in collection and HDCA views + `Pull Request 2326`_ +* Client library updates + `Pull Request 2328`_ +* Revise form data visitor + `Pull Request 2330`_ +* UI, history: update using xhr date header + `Pull Request 2335`_ +* History/Sharable model user sharing API + `Pull Request 2340`_ +* Update to latest galaxy-lib. + `Pull Request 2354`_ +* Revise portlet view, integrate collapsible option + `Pull Request 2360`_ +* Fix issue with lowercasing in datatypes/registry.py + (thanks to `@remimarenco `__.) + `Pull Request 2361`_ +* Improve composite output tool test. + `Pull Request 2363`_ +* Fix release notes generator + `Pull Request 2366`_ +* Upgrade shared ui libraries, add test cases + `Pull Request 2368`_ +* Python3: use open() instead of file() + (thanks to `@nsoranzo `__.) + `Pull Request 2370`_ +* More clarification of release process. + `Pull Request 2372`_ +* Update template to include the release of the Docker container + (thanks to `@galaxyproject `__.) + `Pull Request 2378`_ +* Remove backported importlib and ordereddict + `Pull Request 2380`_ +* Note on updating tool testing + (thanks to `@erasche `__.) + `Pull Request 2381`_ +* Docker swarm support for interactive environments + `Pull Request 2386`_ +* Add support for EDAM data annotations to datatypes + (thanks to `@nsoranzo `__.) + `Pull Request 2387`_ +* Ever more informative, explicit, and complete release checklist. + `Pull Request 2388`_ +* Add a new workflow building mode variation which does access the history + `Pull Request 2390`_ +* Fixes pep8 issues from `#2386 + `__ + (thanks to `@galaxyproject `__.) + `Pull Request 2392`_ +* Add conda search function + (thanks to `@bgruening `__.) + `Pull Request 2395`_ +* Add history navigation options for dataset frames to scratch book + `Pull Request 2396`_ +* Add EDAM topics to tools and expose in API + (thanks to `@nsoranzo `__.) + `Pull Request 2397`_ +* SLURM: when scontrol fails, try to get job state with sacct + (thanks to `@nsoranzo `__.) + `Pull Request 2403`_ +* Enhancements to tool test output verification. + `Pull Request 2409`_ +* UI, datasets: show hid in 'view details' page + `Pull Request 2411`_ +* Update galaxy-lib related modules to latest in that project. + `Pull Request 2414`_ +* Updates and fixes for the run workflow ui elements + `Pull Request 2416`_ +* Raise Exception if watch_tools has an unrecognized value + (thanks to `@nsoranzo `__.) + `Pull Request 2418`_ +* Python3: use log.warning() instead of deprecated log.warn() + (thanks to `@nsoranzo `__.) + `Pull Request 2420`_ +* minor docs touch + `Pull Request 2427`_ +* Correct various EDAM data/format annotations in datatypes + (thanks to `@hmenager `__.) + `Pull Request 2428`_ +* small updates to Mothur datatypes + (thanks to `@shiltemann `__.) + `Pull Request 2429`_ +* Update Galaxy testing to target latest galaxy-lib. + `Pull Request 2436`_ +* fixed $defaults according to `#2430 + `__ + (thanks to `@ThomasWollmann `__.) + `Pull Request 2438`_ +* Properly list subworkflows in run workflow form + `Pull Request 2440`_ +* Python3: Make some files compatible with Python3 + (thanks to `@nsoranzo `__.) + `Pull Request 2453`_ +* Add parameter expansion caller and test cases as preparation for workflow + api extension + `Pull Request 2464`_ +* Set a default for tool_dependencies_dir. + `Pull Request 2480`_ +* Add a password expiration config option (resolves `#2485 + `__) + (thanks to `@benfulton `__.) + `Pull Request 2486`_ +* Update against latest galaxy-lib. + `Pull Request 2494`_ +* display TIFF in upload + (thanks to `@bgruening `__.) + `Pull Request 2516`_ +* Use self.decode_id instead of trans.security.decode_id + (thanks to `@nsoranzo `__.) + `Pull Request 2529`_ +* Charts revision + `Pull Request 2531`_ +* Add Makefile target for fetching updated bower dependencies. + `Pull Request 2534`_ +* Make conda autoinstall of packages safer: + (thanks to `@pvanheus `__.) + `Pull Request 2538`_ +* Updates to Interactive Environment docs + (thanks to `@pvanheus `__.) + `Pull Request 2543`_ +* bigWig files displayed in IGV + (thanks to `@dpryan79 `__.) + `Pull Request 2545`_ +* Allow users to purge datasets by default + `Pull Request 2553`_ +* Kubernetes runner: improves handling of failed jobs + (thanks to `@phnmnl `__.) + `Pull Request 2559`_ +* Fixes `#2442 `__ + (thanks to `@erasche `__.) + `Pull Request 2572`_ +* Python3: port 215 files + (thanks to `@bxlab `__.) + `Pull Request 2574`_ +* Add python-ldap module to conditional requirements + (thanks to `@abretaud `__.) + `Pull Request 2576`_ +* Kubernetes runner: authenticate through service account + (thanks to `@phnmnl `__.) + `Pull Request 2578`_ +* Update gsummary.xml + (thanks to `@lecorguille `__.) + `Pull Request 2590`_ +* Add Warning when Conda is installed + (thanks to `@remimarenco `__.) + `Pull Request 2596`_ +* Added the neostore (neo4j db) for noe4jdb dataset + (thanks to `@zipho `__.) + `Pull Request 2605`_ +* Fix smart_str for Python 3. Add doctests + (thanks to `@nsoranzo `__.) + `Pull Request 2608`_ +* Added Neo4j IE + (thanks to `@thobalose `__.) + `Pull Request 2610`_ +* Committing format changes to the user impersonation dropdown. + (thanks to `@sszakony `__.) + `Pull Request 2612`_ +* Use pagination and filtering for select2 fields + `Pull Request 2615`_ +* Update workflow share dropdown width + (thanks to `@sszakony `__.) + `Pull Request 2617`_ +* Graph visualization: add parsers, change datatypes + `Pull Request 2620`_ +* Fix certain combos of dynamic deeply nested collections in workflows. + `Pull Request 2634`_ +* add tar to datatypes_conf.xml + (thanks to `@mariabernard `__.) + `Pull Request 2636`_ +* Optimize get_file_peek() + (thanks to `@nsoranzo `__.) + `Pull Request 2637`_ +* Move workflow run and history options to top, add loading indicator + `Pull Request 2643`_ +* Enhance workflow run button to indicate workflow loading progress, keep + header fixed + `Pull Request 2647`_ +* Allow uploading strict BED datatypes. + `Pull Request 2648`_ +* Reduce server sided refresh requests to changes in data associated input + fields + `Pull Request 2652`_ +* Add import order linting using tox and flake8-import-order. + `Pull Request 2661`_ +* Add hg38 to main for ucsc_build_sites.txt.sample + `Pull Request 2670`_ +* Extend the list of files tested with flake8-import-order to all files + already passing + (thanks to `@nsoranzo `__.) + `Pull Request 2682`_ +* List resolver toolshed packages + (thanks to `@mvdbeek `__.) + `Pull Request 2750`_ + + +.. small_enhancement + +* remove buildbot remnants + `Pull Request 2125`_ +* try pushing again when we get unexpected exception... + `Pull Request 2130`_ +* Refactor checking tool files toward reuse with workflows in planemo. + `Pull Request 2183`_ +* Rename/refactor Utils.validate() to Utils.isEmpty() + `Pull Request 2239`_ +* Cleanup of the install and test framework. + `Pull Request 2249`_ +* cleanup TS and Reports configs + (thanks to `@galaxyproject `__.) + `Pull Request 2267`_ +* Move specific methods from shed_util_common.py to specific_util.py + `Pull Request 2269`_ +* Revise selection, options and drilldown wrappers, add tests + `Pull Request 2305`_ +* Visualizations: remove graphview + `Pull Request 2329`_ +* Update qunit and sinon + `Pull Request 2338`_ +* Build job success messages within tool form view + `Pull Request 2355`_ +* Cleanup of E203 primarily, and some other misc formatting encountered… + `Pull Request 2364`_ +* isolate the data libraries css to affect only the libraries app + `Pull Request 2444`_ +* Re-add get_updated_changeset_revisions_from_tool_shed() method + (thanks to `@nsoranzo `__.) + `Pull Request 2472`_ +* Workaround for circular import. Refactor. + `Pull Request 2477`_ +* run_tests.sh: Clarify when/where the report file is created. + (thanks to `@NickSto `__.) + `Pull Request 2564`_ +* Reroute consistent workflow endpoint to internal api + `Pull Request 2622`_ +* Add tool test for what happens when output filter throws exception. + `Pull Request 2631`_ +* Ignore .tox directory. Used to be ignored by default w/ flake8 appar… + `Pull Request 2650`_ +* Reorder base templates meta tags + `Pull Request 2651`_ +* Import pyparsing in testing so twill's older version doesn't get loaded. + `Pull Request 2656`_ +* Change default refresh mode for form views + `Pull Request 2667`_ +* Fix unit tests + (thanks to `@nsoranzo `__.) + `Pull Request 2691`_ +* Create a uWSGI postfork function registry and start the tool conf watcher + thread post-fork + `Pull Request 2774`_ + + +Fixes +------------------------------- + +.. major_bug + +* Do not encode dict items that start with 'metadata_' in return value of + api/tools/create. + `Pull Request 2459`_ + +.. bug + +* fix blocking issue check + `Pull Request 2113`_ +* Correctly check set_environment declarations when updating repository. + `Pull Request 2116`_ +* Hide hidden data parameters in workflow editor + `Pull Request 2120`_ +* Place $headers before integrity_check + (thanks to `@mvdbeek `__.) + `Pull Request 2146`_ +* Fix bug when determining locale + (thanks to `@xiaojay `__.) + `Pull Request 2213`_ +* Add pyparsing dependency of svgwrite. Unpin mercurial. + (thanks to `@nsoranzo `__.) + `Pull Request 2223`_ +* Fixes `#2230 `__ + (thanks to `@erasche `__.) + `Pull Request 2231`_ +* Multi-data collection reductions in repeat blocks are broken. + `Pull Request 2233`_ +* Encode collection reduce in serializable fashion + `Pull Request 2241`_ +* Cast everything to a string + (thanks to `@erasche `__.) + `Pull Request 2252`_ +* Use standard model.orm.now for toolshed's password reset token dateti… + `Pull Request 2261`_ +* fixed ui bugs in tours + (thanks to `@ThomasWollmann `__.) + `Pull Request 2262`_ +* Preliminary fix for displaying raw text/html + `Pull Request 2263`_ +* Correctly use defaults specified in galaxy.ini.sample for statsd. + `Pull Request 2268`_ +* Fix encoding issues in test/unit/test_objectstore.py. + `Pull Request 2280`_ +* Workflow sharing slug edit fix. + `Pull Request 2293`_ +* Always remove the working directory after creating the capsule archive. + `Pull Request 2294`_ +* update check for Conda env. + (thanks to `@matthdsm `__.) + `Pull Request 2295`_ +* Make grunt watch (for scripts) work again, settings were being overwr… + `Pull Request 2296`_ +* Monkeypatch Whoosh to use mkdtemp rather than a fixed temporary directory + `Pull Request 2310`_ +* Build: remove redundant webpack step in makefile + `Pull Request 2327`_ +* Unicodify has different semantics to str, causing bug reporter bug + (thanks to `@erasche `__.) + `Pull Request 2336`_ +* Wrap statsd timing middleware more closely around the core applicatio… + `Pull Request 2342`_ +* UI & API: fix display of inaccessible datasets + `Pull Request 2351`_ +* Update README to remove 2.6 + (thanks to `@remimarenco `__.) + `Pull Request 2367`_ +* Revise asserts triggering false exceptions for dynamic parameters + `Pull Request 2374`_ +* Fix the installed conda version to 3.19.3. + (thanks to `@bgruening `__.) + `Pull Request 2394`_ +* Check variable's presence before calling str methods + (thanks to `@erasche `__.) + `Pull Request 2408`_ +* UI, history: correctly handle index API defaults + `Pull Request 2413`_ +* Fix to 4a61a4c: add hids for dataset inputs + `Pull Request 2415`_ +* wrap bare str raises with generic Exception() + `Pull Request 2421`_ +* Fix raven.js import order in galaxy.panels.mako + `Pull Request 2445`_ +* Fix usage of super() in the mothur datatypes. + (thanks to `@bgruening `__.) + `Pull Request 2457`_ +* Make pykube an optional dependency since we don't have wheels for it. + `Pull Request 2468`_ +* fix markup for button links on sharing template + `Pull Request 2481`_ +* fix image generation for workflows with missing tools + `Pull Request 2488`_ +* mothur datatypes: don't generate error for pairwise distance matrices + (thanks to `@shiltemann `__.) + `Pull Request 2489`_ +* Kubernetes runner: fixes result files from work directory not being + recovered issue + (thanks to `@phnmnl `__.) + `Pull Request 2498`_ +* Toolbox filter fixes + `Pull Request 2499`_ +* This is an extra hammer swing at `#1531 + `__ / `#1542 + `__ + `Pull Request 2505`_ +* Copy PJAs when importing a workflow. + `Pull Request 2508`_ +* Fix two errors in sff_extract.py detected by flake8 + `Pull Request 2509`_ +* Fix HTML errors on 2 templates + (thanks to `@nsoranzo `__.) + `Pull Request 2524`_ +* Fix tabular display chunking + `Pull Request 2527`_ +* Writes Kubernetes logs files in UTF-8 + (thanks to `@phnmnl `__.) + `Pull Request 2528`_ +* Fix dataset matcher when no tool available. + (thanks to `@zipho `__.) + `Pull Request 2540`_ +* Initialize objectstore for fix_set_dataset_sizes script + `Pull Request 2544`_ +* Fix old bug in non-allowed_images.yml GIEs + (thanks to `@erasche `__.) + `Pull Request 2548`_ +* More defensive GIE Proxying + (thanks to `@erasche `__.) + `Pull Request 2552`_ +* Fixes for showing min/max labels in Trackster. + `Pull Request 2555`_ +* Fix tag_autocomplete issue in workflow editor. + `Pull Request 2569`_ +* Fix element_identifier unavailable with data_collection input param + (thanks to `@abretaud `__.) + `Pull Request 2570`_ +* Ignore W503 (line break before binary operator) as PEP 8 has reversed its + position on this. + `Pull Request 2594`_ +* Fix hex vs float parsing in request body + `Pull Request 2597`_ +* Kubernetes runner corrects working directory not passed to container + (thanks to `@phnmnl `__.) + `Pull Request 2616`_ +* Fixes for workflow extraction of mapping collection jobs. + `Pull Request 2625`_ +* Workflow SVG generation fix + `Pull Request 2628`_ +* Smart string handling on the wsgi response -- this fixes uwsgi blanki… + `Pull Request 2630`_ +* Properly initialize datasets when workflow is loaded for execution + `Pull Request 2632`_ +* typo in summary statistics tool + (thanks to `@nturaga `__.) + `Pull Request 2639`_ +* Set allow_duplicate_entries="False" for built-in Tool Data Tables. + `Pull Request 2644`_ +* Ensure Galaxy's python binary is used for metadata generation. + `Pull Request 2660`_ +* Fix an error with getting the size of an object from Azure. Attempte… + `Pull Request 2678`_ +* Limit creation of multitudes of default, empty histories. + `Pull Request 2684`_ +* Fix the sanitization of None values in utils. This had previously no… + `Pull Request 2693`_ +* Fix: Remove the old HubAssembly class + (thanks to `@remimarenco `__.) + `Pull Request 2701`_ +* Fix metadata collection on workdir outputs for Pulsar. + `Pull Request 2721`_ +* Allow link buttons to trigger regular click events + `Pull Request 2743`_ +* Fix unused href parameter when adding scratchbook frames + `Pull Request 2744`_ +* Update common_startup.sh to require python2.7 in .venv + (thanks to `@BenjaminHCCarr `__.) + `Pull Request 2756`_ +* separate styles of new and old libraries fixing various ui bugs + `Pull Request 2780`_ +* Make conda install and resolver status more robust + (thanks to `@mvdbeek `__.) + `Pull Request 2789`_ +* Do not instantiate the raven (sentry) client or tool conf watchdog threads + until uWSGI postfork + `Pull Request 2792`_ +* API, history contents: allow 'source' in payload + `Pull Request 2809`_ + +.. github_links +.. _Pull Request 2038: https://github.com/galaxyproject/galaxy/pull/2038 +.. _Pull Request 2077: https://github.com/galaxyproject/galaxy/pull/2077 +.. _Pull Request 2079: https://github.com/galaxyproject/galaxy/pull/2079 +.. _Pull Request 2110: https://github.com/galaxyproject/galaxy/pull/2110 +.. _Pull Request 2113: https://github.com/galaxyproject/galaxy/pull/2113 +.. _Pull Request 2116: https://github.com/galaxyproject/galaxy/pull/2116 +.. _Pull Request 2117: https://github.com/galaxyproject/galaxy/pull/2117 +.. _Pull Request 2119: https://github.com/galaxyproject/galaxy/pull/2119 +.. _Pull Request 2120: https://github.com/galaxyproject/galaxy/pull/2120 +.. _Pull Request 2121: https://github.com/galaxyproject/galaxy/pull/2121 +.. _Pull Request 2124: https://github.com/galaxyproject/galaxy/pull/2124 +.. _Pull Request 2125: https://github.com/galaxyproject/galaxy/pull/2125 +.. _Pull Request 2130: https://github.com/galaxyproject/galaxy/pull/2130 +.. _Pull Request 2142: https://github.com/galaxyproject/galaxy/pull/2142 +.. _Pull Request 2143: https://github.com/galaxyproject/galaxy/pull/2143 +.. _Pull Request 2144: https://github.com/galaxyproject/galaxy/pull/2144 +.. _Pull Request 2145: https://github.com/galaxyproject/galaxy/pull/2145 +.. _Pull Request 2146: https://github.com/galaxyproject/galaxy/pull/2146 +.. _Pull Request 2157: https://github.com/galaxyproject/galaxy/pull/2157 +.. _Pull Request 2158: https://github.com/galaxyproject/galaxy/pull/2158 +.. _Pull Request 2165: https://github.com/galaxyproject/galaxy/pull/2165 +.. _Pull Request 2168: https://github.com/galaxyproject/galaxy/pull/2168 +.. _Pull Request 2171: https://github.com/galaxyproject/galaxy/pull/2171 +.. _Pull Request 2173: https://github.com/galaxyproject/galaxy/pull/2173 +.. _Pull Request 2183: https://github.com/galaxyproject/galaxy/pull/2183 +.. _Pull Request 2213: https://github.com/galaxyproject/galaxy/pull/2213 +.. _Pull Request 2215: https://github.com/galaxyproject/galaxy/pull/2215 +.. _Pull Request 2223: https://github.com/galaxyproject/galaxy/pull/2223 +.. _Pull Request 2231: https://github.com/galaxyproject/galaxy/pull/2231 +.. _Pull Request 2233: https://github.com/galaxyproject/galaxy/pull/2233 +.. _Pull Request 2239: https://github.com/galaxyproject/galaxy/pull/2239 +.. _Pull Request 2241: https://github.com/galaxyproject/galaxy/pull/2241 +.. _Pull Request 2243: https://github.com/galaxyproject/galaxy/pull/2243 +.. _Pull Request 2248: https://github.com/galaxyproject/galaxy/pull/2248 +.. _Pull Request 2249: https://github.com/galaxyproject/galaxy/pull/2249 +.. _Pull Request 2252: https://github.com/galaxyproject/galaxy/pull/2252 +.. _Pull Request 2253: https://github.com/galaxyproject/galaxy/pull/2253 +.. _Pull Request 2254: https://github.com/galaxyproject/galaxy/pull/2254 +.. _Pull Request 2256: https://github.com/galaxyproject/galaxy/pull/2256 +.. _Pull Request 2257: https://github.com/galaxyproject/galaxy/pull/2257 +.. _Pull Request 2258: https://github.com/galaxyproject/galaxy/pull/2258 +.. _Pull Request 2261: https://github.com/galaxyproject/galaxy/pull/2261 +.. _Pull Request 2262: https://github.com/galaxyproject/galaxy/pull/2262 +.. _Pull Request 2263: https://github.com/galaxyproject/galaxy/pull/2263 +.. _Pull Request 2267: https://github.com/galaxyproject/galaxy/pull/2267 +.. _Pull Request 2268: https://github.com/galaxyproject/galaxy/pull/2268 +.. _Pull Request 2269: https://github.com/galaxyproject/galaxy/pull/2269 +.. _Pull Request 2271: https://github.com/galaxyproject/galaxy/pull/2271 +.. _Pull Request 2273: https://github.com/galaxyproject/galaxy/pull/2273 +.. _Pull Request 2274: https://github.com/galaxyproject/galaxy/pull/2274 +.. _Pull Request 2276: https://github.com/galaxyproject/galaxy/pull/2276 +.. _Pull Request 2278: https://github.com/galaxyproject/galaxy/pull/2278 +.. _Pull Request 2279: https://github.com/galaxyproject/galaxy/pull/2279 +.. _Pull Request 2280: https://github.com/galaxyproject/galaxy/pull/2280 +.. _Pull Request 2286: https://github.com/galaxyproject/galaxy/pull/2286 +.. _Pull Request 2289: https://github.com/galaxyproject/galaxy/pull/2289 +.. _Pull Request 2292: https://github.com/galaxyproject/galaxy/pull/2292 +.. _Pull Request 2293: https://github.com/galaxyproject/galaxy/pull/2293 +.. _Pull Request 2294: https://github.com/galaxyproject/galaxy/pull/2294 +.. _Pull Request 2295: https://github.com/galaxyproject/galaxy/pull/2295 +.. _Pull Request 2296: https://github.com/galaxyproject/galaxy/pull/2296 +.. _Pull Request 2302: https://github.com/galaxyproject/galaxy/pull/2302 +.. _Pull Request 2305: https://github.com/galaxyproject/galaxy/pull/2305 +.. _Pull Request 2307: https://github.com/galaxyproject/galaxy/pull/2307 +.. _Pull Request 2308: https://github.com/galaxyproject/galaxy/pull/2308 +.. _Pull Request 2310: https://github.com/galaxyproject/galaxy/pull/2310 +.. _Pull Request 2314: https://github.com/galaxyproject/galaxy/pull/2314 +.. _Pull Request 2326: https://github.com/galaxyproject/galaxy/pull/2326 +.. _Pull Request 2327: https://github.com/galaxyproject/galaxy/pull/2327 +.. _Pull Request 2328: https://github.com/galaxyproject/galaxy/pull/2328 +.. _Pull Request 2329: https://github.com/galaxyproject/galaxy/pull/2329 +.. _Pull Request 2330: https://github.com/galaxyproject/galaxy/pull/2330 +.. _Pull Request 2335: https://github.com/galaxyproject/galaxy/pull/2335 +.. _Pull Request 2336: https://github.com/galaxyproject/galaxy/pull/2336 +.. _Pull Request 2338: https://github.com/galaxyproject/galaxy/pull/2338 +.. _Pull Request 2340: https://github.com/galaxyproject/galaxy/pull/2340 +.. _Pull Request 2342: https://github.com/galaxyproject/galaxy/pull/2342 +.. _Pull Request 2348: https://github.com/galaxyproject/galaxy/pull/2348 +.. _Pull Request 2351: https://github.com/galaxyproject/galaxy/pull/2351 +.. _Pull Request 2354: 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https://github.com/galaxyproject/galaxy/pull/2420 +.. _Pull Request 2421: https://github.com/galaxyproject/galaxy/pull/2421 +.. _Pull Request 2427: https://github.com/galaxyproject/galaxy/pull/2427 +.. _Pull Request 2428: https://github.com/galaxyproject/galaxy/pull/2428 +.. _Pull Request 2429: https://github.com/galaxyproject/galaxy/pull/2429 +.. _Pull Request 2434: https://github.com/galaxyproject/galaxy/pull/2434 +.. _Pull Request 2436: https://github.com/galaxyproject/galaxy/pull/2436 +.. _Pull Request 2438: https://github.com/galaxyproject/galaxy/pull/2438 +.. _Pull Request 2440: https://github.com/galaxyproject/galaxy/pull/2440 +.. _Pull Request 2444: https://github.com/galaxyproject/galaxy/pull/2444 +.. _Pull Request 2445: https://github.com/galaxyproject/galaxy/pull/2445 +.. _Pull Request 2452: https://github.com/galaxyproject/galaxy/pull/2452 +.. _Pull Request 2453: https://github.com/galaxyproject/galaxy/pull/2453 +.. _Pull Request 2455: https://github.com/galaxyproject/galaxy/pull/2455 +.. _Pull Request 2457: https://github.com/galaxyproject/galaxy/pull/2457 +.. _Pull Request 2459: https://github.com/galaxyproject/galaxy/pull/2459 +.. _Pull Request 2464: https://github.com/galaxyproject/galaxy/pull/2464 +.. _Pull Request 2468: https://github.com/galaxyproject/galaxy/pull/2468 +.. _Pull Request 2469: https://github.com/galaxyproject/galaxy/pull/2469 +.. _Pull Request 2472: https://github.com/galaxyproject/galaxy/pull/2472 +.. _Pull Request 2476: https://github.com/galaxyproject/galaxy/pull/2476 +.. _Pull Request 2477: https://github.com/galaxyproject/galaxy/pull/2477 +.. _Pull Request 2480: https://github.com/galaxyproject/galaxy/pull/2480 +.. _Pull Request 2481: https://github.com/galaxyproject/galaxy/pull/2481 +.. _Pull Request 2486: https://github.com/galaxyproject/galaxy/pull/2486 +.. _Pull Request 2488: https://github.com/galaxyproject/galaxy/pull/2488 +.. _Pull Request 2489: https://github.com/galaxyproject/galaxy/pull/2489 +.. _Pull Request 2494: https://github.com/galaxyproject/galaxy/pull/2494 +.. _Pull Request 2498: https://github.com/galaxyproject/galaxy/pull/2498 +.. _Pull Request 2499: https://github.com/galaxyproject/galaxy/pull/2499 +.. _Pull Request 2505: https://github.com/galaxyproject/galaxy/pull/2505 +.. _Pull Request 2508: https://github.com/galaxyproject/galaxy/pull/2508 +.. _Pull Request 2509: https://github.com/galaxyproject/galaxy/pull/2509 +.. _Pull Request 2515: https://github.com/galaxyproject/galaxy/pull/2515 +.. _Pull Request 2516: https://github.com/galaxyproject/galaxy/pull/2516 +.. _Pull Request 2524: https://github.com/galaxyproject/galaxy/pull/2524 +.. _Pull Request 2527: https://github.com/galaxyproject/galaxy/pull/2527 +.. _Pull Request 2528: https://github.com/galaxyproject/galaxy/pull/2528 +.. _Pull Request 2529: https://github.com/galaxyproject/galaxy/pull/2529 +.. _Pull Request 2531: https://github.com/galaxyproject/galaxy/pull/2531 +.. _Pull Request 2534: https://github.com/galaxyproject/galaxy/pull/2534 +.. _Pull Request 2538: https://github.com/galaxyproject/galaxy/pull/2538 +.. _Pull Request 2540: https://github.com/galaxyproject/galaxy/pull/2540 +.. _Pull Request 2543: https://github.com/galaxyproject/galaxy/pull/2543 +.. _Pull Request 2544: https://github.com/galaxyproject/galaxy/pull/2544 +.. _Pull Request 2545: https://github.com/galaxyproject/galaxy/pull/2545 +.. _Pull Request 2548: https://github.com/galaxyproject/galaxy/pull/2548 +.. _Pull Request 2552: https://github.com/galaxyproject/galaxy/pull/2552 +.. _Pull Request 2553: https://github.com/galaxyproject/galaxy/pull/2553 +.. _Pull Request 2554: https://github.com/galaxyproject/galaxy/pull/2554 +.. _Pull Request 2555: https://github.com/galaxyproject/galaxy/pull/2555 +.. _Pull Request 2559: https://github.com/galaxyproject/galaxy/pull/2559 +.. _Pull Request 2564: https://github.com/galaxyproject/galaxy/pull/2564 +.. _Pull Request 2569: https://github.com/galaxyproject/galaxy/pull/2569 +.. _Pull Request 2570: https://github.com/galaxyproject/galaxy/pull/2570 +.. _Pull Request 2572: https://github.com/galaxyproject/galaxy/pull/2572 +.. _Pull Request 2574: https://github.com/galaxyproject/galaxy/pull/2574 +.. _Pull Request 2576: https://github.com/galaxyproject/galaxy/pull/2576 +.. _Pull Request 2578: https://github.com/galaxyproject/galaxy/pull/2578 +.. _Pull Request 2579: https://github.com/galaxyproject/galaxy/pull/2579 +.. _Pull Request 2590: https://github.com/galaxyproject/galaxy/pull/2590 +.. _Pull Request 2594: https://github.com/galaxyproject/galaxy/pull/2594 +.. _Pull Request 2595: https://github.com/galaxyproject/galaxy/pull/2595 +.. _Pull Request 2596: https://github.com/galaxyproject/galaxy/pull/2596 +.. _Pull Request 2597: https://github.com/galaxyproject/galaxy/pull/2597 +.. _Pull Request 2599: https://github.com/galaxyproject/galaxy/pull/2599 +.. _Pull Request 2605: https://github.com/galaxyproject/galaxy/pull/2605 +.. _Pull Request 2608: https://github.com/galaxyproject/galaxy/pull/2608 +.. _Pull Request 2610: https://github.com/galaxyproject/galaxy/pull/2610 +.. _Pull Request 2612: https://github.com/galaxyproject/galaxy/pull/2612 +.. _Pull Request 2613: https://github.com/galaxyproject/galaxy/pull/2613 +.. _Pull Request 2615: https://github.com/galaxyproject/galaxy/pull/2615 +.. _Pull Request 2616: https://github.com/galaxyproject/galaxy/pull/2616 +.. _Pull Request 2617: https://github.com/galaxyproject/galaxy/pull/2617 +.. _Pull Request 2620: https://github.com/galaxyproject/galaxy/pull/2620 +.. _Pull Request 2621: https://github.com/galaxyproject/galaxy/pull/2621 +.. _Pull Request 2622: https://github.com/galaxyproject/galaxy/pull/2622 +.. _Pull Request 2625: https://github.com/galaxyproject/galaxy/pull/2625 +.. _Pull Request 2628: https://github.com/galaxyproject/galaxy/pull/2628 +.. _Pull Request 2630: https://github.com/galaxyproject/galaxy/pull/2630 +.. _Pull Request 2631: https://github.com/galaxyproject/galaxy/pull/2631 +.. _Pull Request 2632: https://github.com/galaxyproject/galaxy/pull/2632 +.. _Pull Request 2634: https://github.com/galaxyproject/galaxy/pull/2634 +.. _Pull Request 2636: https://github.com/galaxyproject/galaxy/pull/2636 +.. _Pull Request 2637: https://github.com/galaxyproject/galaxy/pull/2637 +.. _Pull Request 2639: https://github.com/galaxyproject/galaxy/pull/2639 +.. _Pull Request 2643: https://github.com/galaxyproject/galaxy/pull/2643 +.. _Pull Request 2644: https://github.com/galaxyproject/galaxy/pull/2644 +.. _Pull Request 2646: https://github.com/galaxyproject/galaxy/pull/2646 +.. _Pull Request 2647: https://github.com/galaxyproject/galaxy/pull/2647 +.. _Pull Request 2648: https://github.com/galaxyproject/galaxy/pull/2648 +.. _Pull Request 2650: https://github.com/galaxyproject/galaxy/pull/2650 +.. _Pull Request 2651: https://github.com/galaxyproject/galaxy/pull/2651 +.. _Pull Request 2652: https://github.com/galaxyproject/galaxy/pull/2652 +.. _Pull Request 2656: https://github.com/galaxyproject/galaxy/pull/2656 +.. _Pull Request 2660: https://github.com/galaxyproject/galaxy/pull/2660 +.. _Pull Request 2661: https://github.com/galaxyproject/galaxy/pull/2661 +.. _Pull Request 2664: https://github.com/galaxyproject/galaxy/pull/2664 +.. _Pull Request 2667: https://github.com/galaxyproject/galaxy/pull/2667 +.. _Pull Request 2670: https://github.com/galaxyproject/galaxy/pull/2670 +.. _Pull Request 2678: https://github.com/galaxyproject/galaxy/pull/2678 +.. _Pull Request 2680: https://github.com/galaxyproject/galaxy/pull/2680 +.. _Pull Request 2681: https://github.com/galaxyproject/galaxy/pull/2681 +.. _Pull Request 2682: https://github.com/galaxyproject/galaxy/pull/2682 +.. _Pull Request 2684: https://github.com/galaxyproject/galaxy/pull/2684 +.. _Pull Request 2685: https://github.com/galaxyproject/galaxy/pull/2685 +.. _Pull Request 2691: https://github.com/galaxyproject/galaxy/pull/2691 +.. _Pull Request 2693: https://github.com/galaxyproject/galaxy/pull/2693 +.. _Pull Request 2701: https://github.com/galaxyproject/galaxy/pull/2701 +.. _Pull Request 2721: https://github.com/galaxyproject/galaxy/pull/2721 +.. _Pull Request 2723: https://github.com/galaxyproject/galaxy/pull/2723 +.. _Pull Request 2737: https://github.com/galaxyproject/galaxy/pull/2737 +.. _Pull Request 2743: https://github.com/galaxyproject/galaxy/pull/2743 +.. _Pull Request 2744: https://github.com/galaxyproject/galaxy/pull/2744 +.. _Pull Request 2749: https://github.com/galaxyproject/galaxy/pull/2749 +.. _Pull Request 2750: https://github.com/galaxyproject/galaxy/pull/2750 +.. _Pull Request 2756: https://github.com/galaxyproject/galaxy/pull/2756 +.. _Pull Request 2759: https://github.com/galaxyproject/galaxy/pull/2759 +.. _Pull Request 2773: https://github.com/galaxyproject/galaxy/pull/2773 +.. _Pull Request 2774: https://github.com/galaxyproject/galaxy/pull/2774 +.. _Pull Request 2780: https://github.com/galaxyproject/galaxy/pull/2780 +.. _Pull Request 2789: https://github.com/galaxyproject/galaxy/pull/2789 +.. _Pull Request 2792: https://github.com/galaxyproject/galaxy/pull/2792 +.. _Pull Request 2809: https://github.com/galaxyproject/galaxy/pull/2809 +.. _Pull Request 2810: https://github.com/galaxyproject/galaxy/pull/2810 + diff --git a/doc/source/releases/16.07_announce.rst b/doc/source/releases/16.07_announce.rst index d1d926ddc8d..a52623c2922 100644 --- a/doc/source/releases/16.07_announce.rst +++ b/doc/source/releases/16.07_announce.rst @@ -3,8 +3,53 @@ July 2016 Galaxy Release (v 16.07) =========================================================== +.. include:: _header.rst -Schedule +Highlights =========================================================== - * Planned Freeze Date: 2016-07-04 - * Planned Release Date: 2016-07-25 + +**Shift of Galaxy tool dependencies to Conda** + Galaxy admins obtained the ability to install Galaxy tool's + dependencies using the Conda package manager. Also starting + with this release Galaxy will automatically install + Conda at startup. + See `PR #2554 `__ + and `PR #2759 `__ + +**Feature2** + Feature description. + +**Galaxy chat** + Admins can now plug in the included communication server to enable + users of their instance to use real-time chat within the Galaxy interface. + See `PR #2515 `__ + +`Github `__ +=========================================================== + +New installs + .. code-block:: shell + + % git clone -b release_16.07 https://github.com/galaxyproject/galaxy.git + +Optionally update to latest stable release + .. code-block:: shell + + % git checkout master && pull --ff-only origin master + +See `our wiki `__ for additional details regarding the source code locations. + +Deprecation Notices +=========================================================== + +The following URLs will be removed and should be considered deprecated: + * ``\history\as_xml`` + * ``\history\list_as_xml`` + +Release Notes +=========================================================== + +.. include:: 16.07.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/16.10_announce.rst b/doc/source/releases/16.10_announce.rst new file mode 100644 index 00000000000..758c47f2b80 --- /dev/null +++ b/doc/source/releases/16.10_announce.rst @@ -0,0 +1,10 @@ + +=========================================================== +October 2016 Galaxy Release (v 16.10) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2016-10-03 + * Planned Release Date: 2016-10-24