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Merge pull request #8037 from jmchilton/release_19.05_notes
[19.05] 19.05 Release Notes
This commit is contained in:
Martin Cech
@@ -41,13 +41,13 @@ There's a new discussion forum to replace Biostars. It is accessible under the '
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:alt: Galaxy's new help forum which replaces biostars
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New Visualisations
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New Visualizations
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===========================================================
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`Aequatus visualisation plugin <https://docs.google.com/presentation/d/1_KdwjbIyjUhdb_huAzOuI34693mciw_vXDCGLctKs9A/edit#slide=id.p2>`__ has been released which allows visualisation of gene alignments and gene family aggregations.
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.. figure:: https://lh3.googleusercontent.com/wgNqZT2idSR4AkvUZ55ZQGXOfOPlAxFimO9795WvrQwP1ZMxxdYwNmRZErf-n5hZMGa1SulFry321vgHPoc11wsmJlmVPrmyxG8buV6P=s1600
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:alt: The Aequatus visualisation allows analysing gene family alignments
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:alt: The Aequatus visualization allows analyzing gene family alignments
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New Datatypes
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===========================================================
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@@ -0,0 +1,721 @@
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.. to_doc
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19.05
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===============================
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.. announce_start
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Enhancements
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-------------------------------
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* Implement the ability to favorite tools.
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`Pull Request 7209`_
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* Add data dialog option to tool form data selector.
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`Pull Request 7553`_, `Pull Request 7460`_
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* Many workflow editor connection fixes and enhancements making
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them more correct, accessible, and transparent
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(with huge thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7466`_, `Pull Request 7435`_, `Pull Request 7972`_,
|
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`Pull Request 7979`_, `Pull Request 7642`_, `Pull Request 7989`_,
|
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`Pull Request 7254`_
|
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* Add a Galaxy IE for cellxgene.
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`Pull Request 7268`_
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* Implement expression tools and non-data tool outputs
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(with thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7556`_, `Pull Request 7796`_, `Pull Request 7797`_,
|
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`Pull Request 7944`_
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* Add Galaxy cloud runner support
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(thanks to `@nuwang <https://github.com/nuwang>`__).
|
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`Pull Request 7226`_
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* More robust task messaging
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7548`_
|
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* Allow implicit conversion for input collection parameters
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(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7683`_
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* Allow import of "Format 2" workflows by default.
|
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`Pull Request 7659`_
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* Decompose Galaxy into Python libraries in-tree.
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`Pull Request 7524`_
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* Rewrite and generalize History import and export - dozens of fixes, support for collections,
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Python library support, etc..
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`Pull Request 7367`_, `Pull Request 7214`_, `Pull Request 7366`_,
|
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`Pull Request 7369`_, `Pull Request 7370`_, `Pull Request 7358`_,
|
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`Pull Request 7505`_, `Pull Request 7507`_, `Pull Request 7363`_,
|
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`Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_,
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`Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_
|
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* User facing release notes
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(thanks to `@erasche <https://github.com/erasche>`__).
|
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`Pull Request 7527`_
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* Implement dataset source and hash tracking.
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`Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_
|
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* Custos integration for AuthNZ
|
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(thanks to `@machristie <https://github.com/machristie>`__).
|
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`Pull Request 7195`_
|
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* Flush out API support for AuthNZ and CloudAuthz
|
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`Pull Request 7598`_, `Pull Request 7609`_,
|
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`Pull Request 7592`_, `Pull Request 7597`_,
|
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`Pull Request 7639`_
|
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* Update to PSA 3.1 and support login with Globus identity.
|
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`Pull Request 7463`_
|
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* Swap from 'slug.js' to 'slugify.js' - saving 10 MB in client bundles.
|
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`Pull Request 7538`_
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* Update all client dependencies - including to Backbone 1.4, Bootstrap 4.2, Vue 2.6.
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`Pull Request 7544`_, `Pull Request 7637`_
|
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* Allow admins to import dynamic JSON-based tools.
|
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`Pull Request 7545`_
|
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* Implement environment modules mapping files
|
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(thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
|
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`Pull Request 7398`_
|
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* Allow tool testing of multiple files within a zip output
|
||||
(thanks to `@thermokarst <https://github.com/thermokarst>`__).
|
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`Pull Request 7400`_
|
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* Add datatype converters between tabular and CSV.
|
||||
`Pull Request 7246`_
|
||||
* Add Azure and GCP support for ObjectStore Cloud backend.
|
||||
`Pull Request 7272`_
|
||||
* Add a validator that ensure metadata value is on a range.
|
||||
(thanks to `@fmareuil <https://github.com/fmareuil>`__).
|
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`Pull Request 7288`_
|
||||
* Fix post job actions for "Database Operation" tools, implement ``change_datatype``
|
||||
for collection output
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7480`_
|
||||
* Implement and enforce ESLint linting of the entire client code base.
|
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`Pull Request 7202`_, `Pull Request 7860`_
|
||||
* Multiple enhancements to the LSF cli-plugin job runner - support
|
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out of memory handling, project specification, and Spectrum LSF.
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__ and
|
||||
`@selten <https://github.com/selten>`__).
|
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`Pull Request 6866`_, `Pull Request 7581`_, `Pull Request 7486`_
|
||||
* Drop support for Python 3.4 and officially support Python 3.5 or greater.
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7291`_
|
||||
* Batch bulk hide and delete operations when multiple selected.
|
||||
`Pull Request 5495`_
|
||||
* Implement client initialization pipeline.
|
||||
`Pull Request 7117`_
|
||||
* Allow storing objects in the object store by UUID.
|
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`Pull Request 7154`_, `Pull Request 7650`_
|
||||
* Replace login and registration mako templates with VueJS components.
|
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`Pull Request 6621`_, `Pull Request 7047`_, `Pull Request 7329`_,
|
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`Pull Request 7442`_, `Pull Request 7756`_, `Pull Request 7347`_
|
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* Track messages generated tool stdio tags in the database instead of just appending them
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to tool standard error. Structured UI in reporting also.
|
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(with help from `@bernt-matthias <https://github.com/bernt-matthias>`__)
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`Pull Request 7095`_
|
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* Track job script stdout and stderr separately from the tool's stdout and stderr in the database.
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`Pull Request 7095`_
|
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* Support loading/using tools that are not in the install database
|
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(with help from `@mvdbeek <https://github.com/mvdbeek>`__).
|
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`Pull Request 7316`_, `Pull Request 8021`_
|
||||
* Git providers error reporting plugins
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 7485`_
|
||||
* Rename ``_future_expose_api`` to ``expose_api`` and ``expose_api`` to ``legacy_expose_api``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7743`_
|
||||
* Add ``mtx`` datatype
|
||||
(thanks to `@bebatut <https://github.com/bebatut>`__ and
|
||||
`@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_
|
||||
* Add ``geojson`` datatype
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 7773`_
|
||||
* Add shapefile (``shp``) datatype
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 7819`_
|
||||
* Add ``imgt.json`` datatype for IMGT immune system libraries
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 7587`_
|
||||
* Add microarrays data types ``gpr`` and ``gal``
|
||||
(thanks to `@bensellak <https://github.com/bensellak>`__).
|
||||
`Pull Request 7457`_
|
||||
* Add ``spaln`` database type
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 7718`_
|
||||
* Redefine ``cel`` datatype
|
||||
(thanks to `@bensellak <https://github.com/bensellak>`__).
|
||||
`Pull Request 7514`_
|
||||
* Run most tests formerly ran on Travis on CircleCI
|
||||
(with help from `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7424`_, `Pull Request 7573`_, `Pull Request 7451`_,
|
||||
`Pull Request 7207`_, `Pull Request 7539`_, `Pull Request 7574`_
|
||||
* Toolshed API enhancements.
|
||||
`Pull Request 6652`_
|
||||
* Kubernetes job runner integration test and enhancements
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 6958`_
|
||||
* Implement sniffing of datatypes for library datasets.
|
||||
`Pull Request 7379`_
|
||||
* Rewrite tool output metadata collection - now portable and more correct, tested,
|
||||
and documented.
|
||||
`Pull Request 7470`_, `Pull Request 7459`_, `Pull Request 7156`_
|
||||
`Pull Request 7483`_, `Pull Request 7158`_, `Pull Request 7213`_,
|
||||
`Pull Request 7694`_, `Pull Request 7596`_, `Pull Request 7186`_,
|
||||
`Pull Request 7471`_
|
||||
* Add ``python`` to ``Count1`` tool requirements
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7185`_
|
||||
* Fixes and enhancements for the grouping1 tool - including not removing empty cells
|
||||
at the begin/start of lines
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__ and
|
||||
`@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7205`_, `Pull Request 7844`_
|
||||
* Workflow editor accessibility fixes.
|
||||
`Pull Request 7750`_
|
||||
* Python dependency updates and documentation fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7215`_, `Pull Request 7247`_, `Pull Request 7285`_,
|
||||
`Pull Request 7740`_
|
||||
* Remove requirement pin on specific Sphinx version
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7365`_
|
||||
* Drop conditional pygmentz requirement (autoinstalled as necessary), minor
|
||||
formatting in conditional-reqs
|
||||
`Pull Request 7219`_
|
||||
* Fix spacing between checkbox and buttons in history sharing view.
|
||||
`Pull Request 7222`_
|
||||
* Use regular font-size and styling in uploader.
|
||||
`Pull Request 7232`_
|
||||
* Remove underline from history datasets.
|
||||
`Pull Request 7235`_
|
||||
* Add headless testing option for Selenium tests.
|
||||
`Pull Request 7287`_
|
||||
* Build tool XML schema docs using ``sphinx_markdown_tables``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7313`_
|
||||
* Refactor dataset controller to reuse input validation checks between get/set.
|
||||
`Pull Request 7322`_
|
||||
* Add web server documentation notes about ``Range`` support
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__ and
|
||||
`@nsoranzo <https://github.com/nsoranzo>`_).
|
||||
`Pull Request 7323`_, `Pull Request 7334`_
|
||||
* Fall back to binary comparison if BAM conversion fails during tool tests
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7342`_
|
||||
* Update ``area`` issue/PR labels
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7344`_
|
||||
* Remove deprecated ``collect_outputs_from`` configuration option.
|
||||
`Pull Request 7144`_
|
||||
* Remove ``ToolsController._rerun_tool()`` API method
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7345`_
|
||||
* Refactor ``item_attrs.py`` for reuse without mixin inheritance.
|
||||
`Pull Request 7346`_
|
||||
* Add ``--force_path_paste`` argument to tool test verify script.
|
||||
`Pull Request 7356`_
|
||||
* Separate client node version requirement into individual dotfile for reuse.
|
||||
`Pull Request 7357`_
|
||||
* Improve tool testing for counting datasets in paired collections
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7359`_
|
||||
* Do not default to ``DEV_WHEELS=1`` if no ``git`` is found
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
`Pull Request 7371`_
|
||||
* Restore gray scale difference between panel vs portlet background color for
|
||||
contrast.
|
||||
`Pull Request 7387`_
|
||||
* Specify exceptions more precisely in user API controller.
|
||||
`Pull Request 7397`_
|
||||
* Automatically set ``cookie_path`` using ``url_for()``.
|
||||
`Pull Request 7404`_
|
||||
* Allow configuration location of user preferences extra configuration
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7428`_
|
||||
* Add hover styling to target tool in tool panel
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7437`_
|
||||
* Update Docker testing image
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7439`_, `Pull Request 7187`_
|
||||
* Remove unused code
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7445`_
|
||||
* Note `cannot import name _remove_dead_weakref` error and solution
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 7461`_
|
||||
* Add option to pass in individual globs to client unit test watcher
|
||||
`Pull Request 7477`_
|
||||
* Update of tours overview according to `#5860
|
||||
<https://github.com/galaxyproject/galaxy/issues/5860>`__
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 7478`_
|
||||
* Add new metadata and data table tool validators
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7500`_
|
||||
* Updated documentation in ``admin/scaling.md`` for Systemd
|
||||
(thanks to `@ooobik <https://github.com/ooobik>`__).
|
||||
`Pull Request 7515`_
|
||||
* Replace backbone tagging views with VueJs components.
|
||||
`Pull Request 7516`_
|
||||
* Eliminate import dependency of datatypes on galaxy.web (``url_for``).
|
||||
`Pull Request 7521`_
|
||||
* Static plugin staging as a part of client build instead of startup.
|
||||
`Pull Request 7532`_
|
||||
* Implement dockerized variant of ``update.sh`` for project Python dependencies.
|
||||
`Pull Request 7546`_
|
||||
* Refactor XSD output elements to share common output attributes.
|
||||
`Pull Request 7555`_
|
||||
* Improve linking between job conf handler assignment and documentation
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7558`_
|
||||
* Refactor ``galaxy.web.security`` into ``galaxy.security.idencoding``.
|
||||
`Pull Request 7560`_
|
||||
* Move the 'create new history' out of the history context menu
|
||||
`Pull Request 7565`_, `Pull Request 7606`_
|
||||
* Improve workflow cog menu user interface.
|
||||
`Pull Request 7594`_, `Pull Request 7858`_
|
||||
* Make ``galaxy.model.dataset_collections`` more usable outside manager context.
|
||||
`Pull Request 7595`_
|
||||
* Webpack bundle overhaul and initial dynamic loading.
|
||||
`Pull Request 7605`_
|
||||
* Don't un-hide mapped-over outputs when job fails
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7630`_
|
||||
* Continue gracefully in set_meta if unable to count number of dataset lines.
|
||||
`Pull Request 7641`_
|
||||
* Implement functional dict-ifiable tool outputs and error detection.
|
||||
`Pull Request 7651`_
|
||||
* Refactor ``IntegrationTestCase`` to allow integration test functions.
|
||||
`Pull Request 7657`_
|
||||
* Drop .pyc files before attempting to migrate
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7677`_
|
||||
* Add docs to OIDC backends configuration file.
|
||||
`Pull Request 7691`_
|
||||
* Update ``CITATION`` to latest Galaxy update paper
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7698`_
|
||||
* Update pull request procedures to exempt notes, changelogs, and
|
||||
packages from mandatory review.
|
||||
`Pull Request 7706`_
|
||||
* Update procedures to relax the vote requirement for fixing bugs in releases
|
||||
`Pull Request 7707`_
|
||||
* Improve error message if GFF file is missing attribute col
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7708`_
|
||||
* Add hostname to task message queues
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7712`_
|
||||
* OIDC login buttons based on configuration
|
||||
(thanks to `@machristie <https://github.com/machristie>`__).
|
||||
`Pull Request 7720`_
|
||||
* Enable the selection of library datasets in the tool form
|
||||
`Pull Request 7746`_
|
||||
* Replace ``enable_beta_export_format2_default`` with
|
||||
``default_workflow_export_format``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7748`_
|
||||
* Report a couple common errors in dataset/job report.
|
||||
`Pull Request 7755`_
|
||||
* Add singularity to valid types, allow customization of test history name
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7760`_
|
||||
* Update parameter_input type when changing parameter type
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7780`_
|
||||
* Don't clean up jobs when running tests if `$GALAXY_TEST_NO_CLEANUP` is set
|
||||
`Pull Request 7798`_
|
||||
* Add option to wait for the database to become available
|
||||
(thanks to `@ic4f <https://github.com/ic4f>`__).
|
||||
`Pull Request 7827`_
|
||||
* Remove recursion from ``expand_nested_tokens()``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7834`_
|
||||
* Allow composite upload if all non-optional files are selected
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7872`_
|
||||
* Cleanup integration test configuration code.
|
||||
`Pull Request 7874`_
|
||||
* Add "Reset" button to composite upload interface
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7875`_
|
||||
* Add local namespaced resolver to default container resolvers
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7896`_
|
||||
* Use node-watch instead of fs.watch to watch for db changes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7967`_
|
||||
* Remove reset handler from ruler input element.
|
||||
`Pull Request 6321`_
|
||||
* Declutter the history 'cog' menu.
|
||||
`Pull Request 6437`_
|
||||
* Remove deprecated OpenID features.
|
||||
`Pull Request 7028`_, `Pull Request 7395`_
|
||||
* Restores OpenID post authentication protocols.
|
||||
`Pull Request 7676`_
|
||||
* Replace custom UI colors with equivalent theme colors, consolidate color
|
||||
handling.
|
||||
`Pull Request 7203`_
|
||||
* Modernize library toolbar client code.
|
||||
`Pull Request 7234`_
|
||||
* Large refactoring of model migrations
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7621`_, `Pull Request 7248`_,
|
||||
`Pull Request 7737`_, `Pull Request 7695`_
|
||||
* Implement a general purpose tagging component in the Galaxy client code.
|
||||
`Pull Request 7270`_
|
||||
* Define doctype method on XMLParser target
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7303`_
|
||||
* Refactor ``galaxy.util.handlers`` -> ``galaxy.web.stack.handlers``.
|
||||
`Pull Request 7339`_
|
||||
* Move ``create_history_template`` out of ``galaxy.util``.
|
||||
`Pull Request 7522`_
|
||||
* Refactor ``galaxy.web.form_builder`` into ``galaxy.util.form_builder``.
|
||||
`Pull Request 7529`_
|
||||
* Drop unused install keyword and load TS workflows with utf-8 encoding
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7423`_
|
||||
* Remove biostar integrations.
|
||||
(with help from `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7443`_, `Pull Request 7510`_
|
||||
* Refactor TagManager (back) to TagHandler.
|
||||
`Pull Request 7530`_
|
||||
* Refactor ``output_collect.py`` toward a database session-less modality.
|
||||
`Pull Request 7541`_
|
||||
* Drop D3 from publicly provided libs
|
||||
`Pull Request 7542`_
|
||||
* Fix dependency cycle between ``galaxy.security`` and ``galaxy.model``.
|
||||
`Pull Request 7554`_
|
||||
* Refactor ``galaxy.dataset_collections`` into ``galaxy.model.dataset_collections``.
|
||||
`Pull Request 7588`_
|
||||
* Toastr debowerization and refactoring.
|
||||
`Pull Request 7640`_
|
||||
* Tweak ``popup-menu.js`` error handling.
|
||||
`Pull Request 7643`_
|
||||
* Update Conda version that new Galaxies will install
|
||||
`Pull Request 8048`_
|
||||
|
||||
Fixes
|
||||
-------------------------------
|
||||
|
||||
* Fix client styleguide asset handling.
|
||||
`Pull Request 7664`_
|
||||
* Handle subworkflows in view workflow mako
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7276`_
|
||||
* Fix removing tags from a dataset previously only the first tag could be removed
|
||||
(thanks to `@gtrack <https://github.com/gtrack>`__).
|
||||
`Pull Request 7674`_, `Pull Request 7680`_
|
||||
* Fix displaying and editing SelectTagParameters in workflow editor
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7534`_
|
||||
* Fix workflow output rectification.
|
||||
`Pull Request 7101`_
|
||||
* Interactive Environment Fixes
|
||||
`Pull Request 7917`_
|
||||
* Make job script actually return tool exit code
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7147`_
|
||||
* Fix client galaxy object instance access in visualizations.
|
||||
`Pull Request 7198`_
|
||||
* Assorted component bugfixes.
|
||||
`Pull Request 7200`_
|
||||
* Update IE proxy dependencies.
|
||||
`Pull Request 7208`_
|
||||
* Cleanup code for univa job runner
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7210`_
|
||||
* Verify and update .venv's node version.
|
||||
`Pull Request 7220`_
|
||||
* Update ``use_interactive`` default in docs
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7221`_
|
||||
* Fix hotdata method access.
|
||||
`Pull Request 7256`_
|
||||
* Fix saving imported subworkflows
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7262`_
|
||||
* Fix "occured" typo everywhere
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7266`_
|
||||
* Fix flakey history import metadata test
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7279`_
|
||||
* Do not skip the client build in dockerized selenium tests
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7280`_
|
||||
* Fixes for the cluster documentation
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7281`_
|
||||
* Fix ``ObjectNotFound`` exception when exporting an history
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 7286`_
|
||||
* Do not remove tools from other installed revisions when uninstalling TS
|
||||
repo
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7300`_
|
||||
* Remove unused keyword in resend email helper.
|
||||
`Pull Request 7315`_
|
||||
* Fix popupmenu creation.
|
||||
`Pull Request 7318`_
|
||||
* Fix trackster toolbox filter for logged-in users
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7319`_
|
||||
* Remove overlapping tooltip from dropdown button in library toolbar.
|
||||
`Pull Request 7321`_
|
||||
* UI fixes for libraries.
|
||||
`Pull Request 7337`_
|
||||
* Fix ``test_import_metadata_regeneration`` API test
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7340`_
|
||||
* Possible fix for fasta file never getting filesize
|
||||
(thanks to `@Slugger70 <https://github.com/Slugger70>`__).
|
||||
`Pull Request 7374`_
|
||||
* Fix upload button style.
|
||||
`Pull Request 7381`_
|
||||
* Fix link doc syntax
|
||||
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
|
||||
`Pull Request 7388`_
|
||||
* Update application documentation
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7391`_
|
||||
* Fix pie chart and portlet height in flexboxes.
|
||||
`Pull Request 7396`_
|
||||
* Fix ``LocalShellRunner``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7438`_
|
||||
* Use a lock on cleanup, expire_tool and cache_tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7446`_
|
||||
* Fix loading workflows with steps without default label
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7448`_
|
||||
* Remove broken configuration option tool_submission_burst
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7449`_
|
||||
* Restore ``get_filename`` to ``galaxy.tools.verify:verify()``
|
||||
`Pull Request 7452`_
|
||||
* Fix documentation for statsd and uwsgi
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 7453`_
|
||||
* Fix hidden parameter use in workflows
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7458`_
|
||||
* Fix syntax of XSD tool schema.
|
||||
`Pull Request 7462`_
|
||||
* Fix workflow building typo
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7472`_
|
||||
* Correct ``virtualenv`` download with no ``wget``/``curl``
|
||||
(thanks to `@hmenager <https://github.com/hmenager>`__).
|
||||
`Pull Request 7476`_
|
||||
* Use a relative ``output.publicPath`` to avoid 404 errors when serving with a url
|
||||
prefix
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 7481`_
|
||||
* Restrict loading of JSON files on the server via the workflow API to Galaxy
|
||||
admins
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7499`_
|
||||
* Fix warning message formatting in sharing controller
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7504`_
|
||||
* Make sure ``temp_output_dir`` path is absolute
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7517`_
|
||||
* Create directory before copying file there
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 7519`_
|
||||
* Fix routing when serving Galaxy at a prefix.
|
||||
`Pull Request 7523`_
|
||||
* Small object store fixes.
|
||||
`Pull Request 7536`_
|
||||
* Fix entering workflow parameter in workflow run form
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7543`_
|
||||
* Extend reload test case logging
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7547`_
|
||||
* Correct db-self handler assignment method
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7561`_
|
||||
* Fix database config doctests when env vars are in use for dburi
|
||||
`Pull Request 7562`_
|
||||
* Fix help warnings style.
|
||||
`Pull Request 7566`_
|
||||
* Fix to run ``bootstrap_history.py`` inside Galaxy's virtualenv
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7584`_
|
||||
* Update cloud imports to adhere with cloudbridge interface changes.
|
||||
`Pull Request 7586`_
|
||||
* Fix RStudio GIE
|
||||
(thanks to `@erasche <https://github.com/erasche>`__).
|
||||
`Pull Request 7590`_, `Pull Request 7925`_
|
||||
* Fix styleguide.
|
||||
`Pull Request 7602`_
|
||||
* Fix history options menu href navigation
|
||||
`Pull Request 7612`_
|
||||
* Minor cli and metadata fixes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7614`_
|
||||
* Improve string escaping and changeset validation on toolshed.
|
||||
`Pull Request 7616`_
|
||||
* Delay workflow step execution for discovered & mapped-over input
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7633`_
|
||||
* Fix float to int casting
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7634`_
|
||||
* Adjust ``test_run_with_numeric_input_connection`` to extra line
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7645`_
|
||||
* Fix incorrect LDDAs being used as collection members.
|
||||
`Pull Request 7646`_
|
||||
* Fix GenomeSpace tools.
|
||||
`Pull Request 7647`_, `Pull Request 7697`_
|
||||
* Bugfix for input selection with tag representation in ``ui-select-default``.
|
||||
`Pull Request 7658`_
|
||||
* Drop now unused import endpoint from workflow controller.
|
||||
`Pull Request 7660`_
|
||||
* Fix for ``trans.redirect`` not setting cookies/headers.
|
||||
`Pull Request 7663`_
|
||||
* Fix shutdown for Pulsar MQ Runner.
|
||||
`Pull Request 7667`_
|
||||
* Fix "Run workflow" jumps when clicking
|
||||
(thanks to `@gtrack <https://github.com/gtrack>`__).
|
||||
`Pull Request 7675`_
|
||||
* Detect errors using exit code for sort tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7679`_
|
||||
* Fix ``format_source`` for implicit conversion inputs and ``fasta.gz`` upload
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7682`_
|
||||
* Plugin static staging fix.
|
||||
`Pull Request 7689`_
|
||||
* Fix side panel styling, adjust appearance in reports.
|
||||
`Pull Request 7690`_
|
||||
* Patch for metadata setting of minimal BIOM1 files
|
||||
(thanks to `@bebatut <https://github.com/bebatut>`__).
|
||||
`Pull Request 7696`_
|
||||
* Only check for exit code on actual sort command
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7699`_
|
||||
* Update ``pytest-posgresql`` to 1.4.0, which removes a hard dependency on
|
||||
``psycopg2``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7703`_
|
||||
* Fix runner param validation in the DRMAA runner.
|
||||
`Pull Request 7709`_
|
||||
* Restrict workflow invocation index to current user
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7711`_
|
||||
* Copy ``tools_by_id`` before collecting dependency status
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7713`_
|
||||
* Fix uWSGI startup with separate ini file under Python 3
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7716`_
|
||||
* Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait``
|
||||
under macOS
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7722`_
|
||||
* Fix check on links in ``CompressedFile.safemembers()``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7723`_
|
||||
* Unpause dependent jobs when resuming jobs
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7724`_
|
||||
* Commented-out cloudbridge requirement for the cloud/send tool.
|
||||
`Pull Request 7727`_
|
||||
* Fix comments
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7738`_
|
||||
* Upgrade to latest Pulsar release for various remote job running fixes.
|
||||
`Pull Request 7744`_, `Pull Request 7865`_
|
||||
* Fix automatic user registration.
|
||||
`Pull Request 7749`_
|
||||
* Sanitize HTML in messages using ``galaxy.util.sanitize_html``.
|
||||
`Pull Request 7751`_
|
||||
* Fix Kubernetes integration tests for Docker on Mac.
|
||||
`Pull Request 7754`_
|
||||
* Fix BootstrapVue component specification in Citations.
|
||||
`Pull Request 7778`_
|
||||
* Symlink two more images that are accessed via non-webpack'd applications.
|
||||
`Pull Request 7779`_
|
||||
* Make ``url_get`` return unicode
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7782`_
|
||||
* Disable flexible spreading of radio buttons by default.
|
||||
`Pull Request 7788`_
|
||||
* Fix default value handling of color parameter.
|
||||
`Pull Request 7475`_
|
||||
* Fix various Python deprecations
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7800`_
|
||||
* Return HTTP 400 for `GET /api/datasets/nonexistent_id`
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7806`_
|
||||
* Encode email messages using UTF-8
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7812`_
|
||||
* Fix nested macro/token expansion on Python 3
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7823`_
|
||||
* Possible fix for WSGI process issue `#7758
|
||||
<https://github.com/galaxyproject/galaxy/issues/7758>`__
|
||||
(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
|
||||
`Pull Request 7824`_
|
||||
* Fix ``InputValueWrapper`` gt/ge/lt/le comparisons
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7826`_
|
||||
* Fix trackster issue with constraining (``overflow:non-visible``) containers.
|
||||
`Pull Request 7845`_
|
||||
* Improve upload accessibility.
|
||||
`Pull Request 7848`_
|
||||
* Adjust appearance of user creation form in admin panel.
|
||||
`Pull Request 7851`_
|
||||
* Use just the env name when checking ``CONDA_DEFAULT_ENV``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7853`_
|
||||
* Fix workflow extraction for jobs whose JobToDatasetOutputAssociation
|
||||
references a discovered dataset
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7855`_
|
||||
* Fix flag for library dataset option in data selector.
|
||||
`Pull Request 7859`_
|
||||
* Fix bug preventing handler runner plugin handling.
|
||||
`Pull Request 7870`_
|
||||
* Fix click targeting for quota usage details
|
||||
`Pull Request 7877`_
|
||||
* Allow typing e in float param field.
|
||||
`Pull Request 7880`_
|
||||
* Update Cheetah dependency, fixes ``AssertionError``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7887`_
|
||||
* Fix application of history default permissions to anonymous histories
|
||||
carried over upon login.
|
||||
`Pull Request 7904`_
|
||||
* Fix multi-history copying of collections.
|
||||
`Pull Request 7906`_
|
||||
* Remove GFF headers during conversion and test fix
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7916`_
|
||||
* Fix community tags showing JSON file.
|
||||
`Pull Request 7923`_
|
||||
* Fix upload of gzipped VCF files
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7933`_
|
||||
* Fix documentation building
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7934`_
|
||||
* Listen to history changes in tool form until job has been submitted.
|
||||
`Pull Request 7943`_
|
||||
* Fixed wrong example for ``amqp_ack_republish_time`` in
|
||||
``job_conf.xml.sample_advanced``
|
||||
(thanks to `@AndreasSko <https://github.com/AndreasSko>`__).
|
||||
`Pull Request 7983`_
|
||||
* Backport various upload encoding fixes from `#7995 <https://github.com/galaxyproject/galaxy/issues/7995>`__
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 8000`_, `Pull Request 8004`_
|
||||
* Disable create user button while request is being processed
|
||||
`Pull Request 8029`_
|
||||
* Fix multipanel history search
|
||||
`Pull Request 8085`_
|
||||
|
||||
.. include:: 19.05_prs.rst
|
||||
|
||||
@@ -3,8 +3,60 @@
|
||||
May 2019 Galaxy Release (v 19.05)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Schedule
|
||||
Highlights
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2019-05-06
|
||||
* Planned Release Date: 2019-05-27
|
||||
|
||||
**User Facing Release Notes**
|
||||
Galaxy releases now include "user facing" release notes, you are reading
|
||||
the traditional release notes which have always been relatively admin and developer
|
||||
oriented but will likely be even more so now. Features such as favoriting tools,
|
||||
improved workflow editor feedback, and an exciting new cellxgene GIE may have
|
||||
been featured in these release notes in the past but are now featured in the
|
||||
user release notes instead. A huge thanks to `@erasche <https://github.com/erasche>`__
|
||||
for getting the ball rolling on this initiative.
|
||||
|
||||
Checkout the 19.05 user release notes at https://docs.galaxyproject.org/en/release_19.05/releases/19.05_announce_user.htm.
|
||||
|
||||
**Login and Registration Rewrite**
|
||||
The march toward replacing templated backend generated HTML with modern, reactive
|
||||
components accelerated in Galaxy 19.05. Galaxy's login, logout, and registration pages
|
||||
were replaced with VueJS components. Support for OIDC login options was added and
|
||||
certain deprecated OpenID login options were removed. This release contains many other
|
||||
client code enhancements including a new client initialization pipeline, ESLint based
|
||||
linting, and greatly optimized initial dynamic loading of bundles.
|
||||
|
||||
**Improvements to Workflow Expressivity**
|
||||
In 19.01, non-data connections were added to the workflow editor in the form of
|
||||
explicit, typed, non-data inputs to workflows. This idea has been generalized in 19.05
|
||||
and tool can now produce non-data outputs and a new class of tools called "Expression"
|
||||
tools has been added to make this especially easy. The Format 2 workflow format is now
|
||||
importable by default and admin-only extensions even allow embedding tool definitions
|
||||
directly into workflows. Many thanks to `@mvdbeek <https://github.com/mvdbeek>`__ for
|
||||
pushing this effort.
|
||||
|
||||
Get Galaxy
|
||||
==========
|
||||
|
||||
The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
|
||||
|
||||
To get a new Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git clone -b release_19.05 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
To update an existing Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git fetch origin && git checkout release_19.05 && git pull --ff-only origin release_19.05
|
||||
|
||||
See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
.. include:: 19.05.rst
|
||||
:start-after: announce_start
|
||||
|
||||
.. include:: _thanks.rst
|
||||
|
||||
@@ -0,0 +1,97 @@
|
||||
|
||||
===========================================================
|
||||
May 2019 Galaxy Release (v 19.05)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
**Tool Favorites**
|
||||
|
||||
|
||||
Tools can now be marked as favorites, and then they'll be easily accessible from the star button in your tool panel.
|
||||
|
||||
.. figure:: images/19.05-favs.gif
|
||||
:alt: Adding a favorite tool.
|
||||
|
||||
**Workflow Editor Connection Feedback**
|
||||
|
||||
The editor now provides feedback on why connections are invalid, so you aren't left wondering why two tools won't connect. For complex data pipelines this should greatly simplify your life!
|
||||
|
||||
.. figure:: images/19.05-wf-hints.gif
|
||||
:alt: Workflow editor connections provide feedback on why they won't connect.
|
||||
|
||||
**Data Dialog for Tool Form**
|
||||
|
||||
There is a new way to select datasets when running tools! It is a very simple method to select any number of files from both your History and Data Libraries.
|
||||
|
||||
.. figure:: images/19.05-inputs.gif
|
||||
:alt: Data dialog for selecting dataset in the tool form.
|
||||
|
||||
Additionally the selector implements a highly requested feature, the ability to run tools on arbitrary datasets from a collection
|
||||
|
||||
.. figure:: images/19.05-input-collection.gif
|
||||
:alt: Selecting datasets from within a collection.
|
||||
|
||||
**History Export/Import Reworked**
|
||||
|
||||
These features used to be clumsy in the past but do not despair since in this release they got a revamp and their reliability skyrocketed! Moving historic object across Galaxies should now be easier than ever. Rocketfuel included.
|
||||
|
||||
New Visualizations
|
||||
===========================================================
|
||||
|
||||
.. visualizations
|
||||
|
||||
`@jxtx <https://github.com/jxtx>`__ has implemented a Galaxy Interactive
|
||||
Environment for `cellxgene <https://github.com/chanzuckerberg/cellxgene>`__, an
|
||||
interactive explorer for single-cell transcriptomics data. `Pull Request 7268`_
|
||||
|
||||
.. figure:: https://user-images.githubusercontent.com/79973/51766184-f5faea80-20a7-11e9-86c8-a3127d501076.gif
|
||||
:alt: cellxgene demo
|
||||
|
||||
|
||||
New Datatypes
|
||||
===========================================================
|
||||
|
||||
* Add the single-cell datatype ``mtx``
|
||||
(thanks to `@bebatut <https://github.com/bebatut>`__ and
|
||||
`@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_
|
||||
* Add ``geojson`` and shapefile (``shp``) datatypes for better GIS data support
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 7773`_, `Pull Request 7819`_
|
||||
* Add ``imgt.json`` datatype for IMGT immune system libraries
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 7587`_
|
||||
* Add microarrays data types ``gpr`` and ``gal``
|
||||
(thanks to `@bensellak <https://github.com/bensellak>`__).
|
||||
`Pull Request 7457`_
|
||||
* Add ``spaln`` (space-efficient spliced alignment) database type
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 7718`_
|
||||
* Redefine ``cel`` datatype
|
||||
(thanks to `@bensellak <https://github.com/bensellak>`__).
|
||||
`Pull Request 7514`_
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
|
||||
* Update grouping tool to not remove empty cells at the begin/start of lines
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 7205`_
|
||||
* Add general purpose expression tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 7796`_
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
Please see the `full release notes <19.05_announce.html>`_ for more details.
|
||||
|
||||
.. include:: 19.05_prs.rst
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,370 @@
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 4659: https://github.com/galaxyproject/galaxy/pull/4659
|
||||
.. _Pull Request 5495: https://github.com/galaxyproject/galaxy/pull/5495
|
||||
.. _Pull Request 6321: https://github.com/galaxyproject/galaxy/pull/6321
|
||||
.. _Pull Request 6437: https://github.com/galaxyproject/galaxy/pull/6437
|
||||
.. _Pull Request 6621: https://github.com/galaxyproject/galaxy/pull/6621
|
||||
.. _Pull Request 6652: https://github.com/galaxyproject/galaxy/pull/6652
|
||||
.. _Pull Request 6866: https://github.com/galaxyproject/galaxy/pull/6866
|
||||
.. _Pull Request 6958: https://github.com/galaxyproject/galaxy/pull/6958
|
||||
.. _Pull Request 7028: https://github.com/galaxyproject/galaxy/pull/7028
|
||||
.. _Pull Request 7047: https://github.com/galaxyproject/galaxy/pull/7047
|
||||
.. _Pull Request 7095: https://github.com/galaxyproject/galaxy/pull/7095
|
||||
.. _Pull Request 7101: https://github.com/galaxyproject/galaxy/pull/7101
|
||||
.. _Pull Request 7117: https://github.com/galaxyproject/galaxy/pull/7117
|
||||
.. _Pull Request 7144: https://github.com/galaxyproject/galaxy/pull/7144
|
||||
.. _Pull Request 7147: https://github.com/galaxyproject/galaxy/pull/7147
|
||||
.. _Pull Request 7154: https://github.com/galaxyproject/galaxy/pull/7154
|
||||
.. _Pull Request 7156: https://github.com/galaxyproject/galaxy/pull/7156
|
||||
.. _Pull Request 7158: https://github.com/galaxyproject/galaxy/pull/7158
|
||||
.. _Pull Request 7177: https://github.com/galaxyproject/galaxy/pull/7177
|
||||
.. _Pull Request 7185: https://github.com/galaxyproject/galaxy/pull/7185
|
||||
.. _Pull Request 7186: https://github.com/galaxyproject/galaxy/pull/7186
|
||||
.. _Pull Request 7187: https://github.com/galaxyproject/galaxy/pull/7187
|
||||
.. _Pull Request 7192: https://github.com/galaxyproject/galaxy/pull/7192
|
||||
.. _Pull Request 7193: https://github.com/galaxyproject/galaxy/pull/7193
|
||||
.. _Pull Request 7195: https://github.com/galaxyproject/galaxy/pull/7195
|
||||
.. _Pull Request 7198: https://github.com/galaxyproject/galaxy/pull/7198
|
||||
.. _Pull Request 7200: https://github.com/galaxyproject/galaxy/pull/7200
|
||||
.. _Pull Request 7202: https://github.com/galaxyproject/galaxy/pull/7202
|
||||
.. _Pull Request 7203: https://github.com/galaxyproject/galaxy/pull/7203
|
||||
.. _Pull Request 7205: https://github.com/galaxyproject/galaxy/pull/7205
|
||||
.. _Pull Request 7207: https://github.com/galaxyproject/galaxy/pull/7207
|
||||
.. _Pull Request 7208: https://github.com/galaxyproject/galaxy/pull/7208
|
||||
.. _Pull Request 7209: https://github.com/galaxyproject/galaxy/pull/7209
|
||||
.. _Pull Request 7210: https://github.com/galaxyproject/galaxy/pull/7210
|
||||
.. _Pull Request 7213: https://github.com/galaxyproject/galaxy/pull/7213
|
||||
.. _Pull Request 7214: https://github.com/galaxyproject/galaxy/pull/7214
|
||||
.. _Pull Request 7215: https://github.com/galaxyproject/galaxy/pull/7215
|
||||
.. _Pull Request 7219: https://github.com/galaxyproject/galaxy/pull/7219
|
||||
.. _Pull Request 7220: https://github.com/galaxyproject/galaxy/pull/7220
|
||||
.. _Pull Request 7221: https://github.com/galaxyproject/galaxy/pull/7221
|
||||
.. _Pull Request 7222: https://github.com/galaxyproject/galaxy/pull/7222
|
||||
.. _Pull Request 7226: https://github.com/galaxyproject/galaxy/pull/7226
|
||||
.. _Pull Request 7232: https://github.com/galaxyproject/galaxy/pull/7232
|
||||
.. _Pull Request 7234: https://github.com/galaxyproject/galaxy/pull/7234
|
||||
.. _Pull Request 7235: https://github.com/galaxyproject/galaxy/pull/7235
|
||||
.. _Pull Request 7246: https://github.com/galaxyproject/galaxy/pull/7246
|
||||
.. _Pull Request 7247: https://github.com/galaxyproject/galaxy/pull/7247
|
||||
.. _Pull Request 7248: https://github.com/galaxyproject/galaxy/pull/7248
|
||||
.. _Pull Request 7254: https://github.com/galaxyproject/galaxy/pull/7254
|
||||
.. _Pull Request 7255: https://github.com/galaxyproject/galaxy/pull/7255
|
||||
.. _Pull Request 7256: https://github.com/galaxyproject/galaxy/pull/7256
|
||||
.. _Pull Request 7262: https://github.com/galaxyproject/galaxy/pull/7262
|
||||
.. _Pull Request 7266: https://github.com/galaxyproject/galaxy/pull/7266
|
||||
.. _Pull Request 7268: https://github.com/galaxyproject/galaxy/pull/7268
|
||||
.. _Pull Request 7270: https://github.com/galaxyproject/galaxy/pull/7270
|
||||
.. _Pull Request 7272: https://github.com/galaxyproject/galaxy/pull/7272
|
||||
.. _Pull Request 7276: https://github.com/galaxyproject/galaxy/pull/7276
|
||||
.. _Pull Request 7279: https://github.com/galaxyproject/galaxy/pull/7279
|
||||
.. _Pull Request 7280: https://github.com/galaxyproject/galaxy/pull/7280
|
||||
.. _Pull Request 7281: https://github.com/galaxyproject/galaxy/pull/7281
|
||||
.. _Pull Request 7285: https://github.com/galaxyproject/galaxy/pull/7285
|
||||
.. _Pull Request 7286: https://github.com/galaxyproject/galaxy/pull/7286
|
||||
.. _Pull Request 7287: https://github.com/galaxyproject/galaxy/pull/7287
|
||||
.. _Pull Request 7288: https://github.com/galaxyproject/galaxy/pull/7288
|
||||
.. _Pull Request 7291: https://github.com/galaxyproject/galaxy/pull/7291
|
||||
.. _Pull Request 7300: https://github.com/galaxyproject/galaxy/pull/7300
|
||||
.. _Pull Request 7303: https://github.com/galaxyproject/galaxy/pull/7303
|
||||
.. _Pull Request 7313: https://github.com/galaxyproject/galaxy/pull/7313
|
||||
.. _Pull Request 7315: https://github.com/galaxyproject/galaxy/pull/7315
|
||||
.. _Pull Request 7316: https://github.com/galaxyproject/galaxy/pull/7316
|
||||
.. _Pull Request 7318: https://github.com/galaxyproject/galaxy/pull/7318
|
||||
.. _Pull Request 7319: https://github.com/galaxyproject/galaxy/pull/7319
|
||||
.. _Pull Request 7321: https://github.com/galaxyproject/galaxy/pull/7321
|
||||
.. _Pull Request 7322: https://github.com/galaxyproject/galaxy/pull/7322
|
||||
.. _Pull Request 7323: https://github.com/galaxyproject/galaxy/pull/7323
|
||||
.. _Pull Request 7329: https://github.com/galaxyproject/galaxy/pull/7329
|
||||
.. _Pull Request 7334: https://github.com/galaxyproject/galaxy/pull/7334
|
||||
.. _Pull Request 7337: https://github.com/galaxyproject/galaxy/pull/7337
|
||||
.. _Pull Request 7339: https://github.com/galaxyproject/galaxy/pull/7339
|
||||
.. _Pull Request 7340: https://github.com/galaxyproject/galaxy/pull/7340
|
||||
.. _Pull Request 7342: https://github.com/galaxyproject/galaxy/pull/7342
|
||||
.. _Pull Request 7344: https://github.com/galaxyproject/galaxy/pull/7344
|
||||
.. _Pull Request 7345: https://github.com/galaxyproject/galaxy/pull/7345
|
||||
.. _Pull Request 7346: https://github.com/galaxyproject/galaxy/pull/7346
|
||||
.. _Pull Request 7347: https://github.com/galaxyproject/galaxy/pull/7347
|
||||
.. _Pull Request 7350: https://github.com/galaxyproject/galaxy/pull/7350
|
||||
.. _Pull Request 7356: https://github.com/galaxyproject/galaxy/pull/7356
|
||||
.. _Pull Request 7357: https://github.com/galaxyproject/galaxy/pull/7357
|
||||
.. _Pull Request 7358: https://github.com/galaxyproject/galaxy/pull/7358
|
||||
.. _Pull Request 7359: https://github.com/galaxyproject/galaxy/pull/7359
|
||||
.. _Pull Request 7363: https://github.com/galaxyproject/galaxy/pull/7363
|
||||
.. _Pull Request 7365: https://github.com/galaxyproject/galaxy/pull/7365
|
||||
.. _Pull Request 7366: https://github.com/galaxyproject/galaxy/pull/7366
|
||||
.. _Pull Request 7367: https://github.com/galaxyproject/galaxy/pull/7367
|
||||
.. _Pull Request 7369: https://github.com/galaxyproject/galaxy/pull/7369
|
||||
.. _Pull Request 7370: https://github.com/galaxyproject/galaxy/pull/7370
|
||||
.. _Pull Request 7371: https://github.com/galaxyproject/galaxy/pull/7371
|
||||
.. _Pull Request 7374: https://github.com/galaxyproject/galaxy/pull/7374
|
||||
.. _Pull Request 7379: https://github.com/galaxyproject/galaxy/pull/7379
|
||||
.. _Pull Request 7381: https://github.com/galaxyproject/galaxy/pull/7381
|
||||
.. _Pull Request 7387: https://github.com/galaxyproject/galaxy/pull/7387
|
||||
.. _Pull Request 7388: https://github.com/galaxyproject/galaxy/pull/7388
|
||||
.. _Pull Request 7391: https://github.com/galaxyproject/galaxy/pull/7391
|
||||
.. _Pull Request 7395: https://github.com/galaxyproject/galaxy/pull/7395
|
||||
.. _Pull Request 7396: https://github.com/galaxyproject/galaxy/pull/7396
|
||||
.. _Pull Request 7397: https://github.com/galaxyproject/galaxy/pull/7397
|
||||
.. _Pull Request 7398: https://github.com/galaxyproject/galaxy/pull/7398
|
||||
.. _Pull Request 7400: https://github.com/galaxyproject/galaxy/pull/7400
|
||||
.. _Pull Request 7404: https://github.com/galaxyproject/galaxy/pull/7404
|
||||
.. _Pull Request 7423: https://github.com/galaxyproject/galaxy/pull/7423
|
||||
.. _Pull Request 7424: https://github.com/galaxyproject/galaxy/pull/7424
|
||||
.. _Pull Request 7428: https://github.com/galaxyproject/galaxy/pull/7428
|
||||
.. _Pull Request 7435: https://github.com/galaxyproject/galaxy/pull/7435
|
||||
.. _Pull Request 7437: https://github.com/galaxyproject/galaxy/pull/7437
|
||||
.. _Pull Request 7438: https://github.com/galaxyproject/galaxy/pull/7438
|
||||
.. _Pull Request 7439: https://github.com/galaxyproject/galaxy/pull/7439
|
||||
.. _Pull Request 7442: https://github.com/galaxyproject/galaxy/pull/7442
|
||||
.. _Pull Request 7443: https://github.com/galaxyproject/galaxy/pull/7443
|
||||
.. _Pull Request 7445: https://github.com/galaxyproject/galaxy/pull/7445
|
||||
.. _Pull Request 7446: https://github.com/galaxyproject/galaxy/pull/7446
|
||||
.. _Pull Request 7448: https://github.com/galaxyproject/galaxy/pull/7448
|
||||
.. _Pull Request 7449: https://github.com/galaxyproject/galaxy/pull/7449
|
||||
.. _Pull Request 7451: https://github.com/galaxyproject/galaxy/pull/7451
|
||||
.. _Pull Request 7452: https://github.com/galaxyproject/galaxy/pull/7452
|
||||
.. _Pull Request 7453: https://github.com/galaxyproject/galaxy/pull/7453
|
||||
.. _Pull Request 7457: https://github.com/galaxyproject/galaxy/pull/7457
|
||||
.. _Pull Request 7458: https://github.com/galaxyproject/galaxy/pull/7458
|
||||
.. _Pull Request 7459: https://github.com/galaxyproject/galaxy/pull/7459
|
||||
.. _Pull Request 7460: https://github.com/galaxyproject/galaxy/pull/7460
|
||||
.. _Pull Request 7461: https://github.com/galaxyproject/galaxy/pull/7461
|
||||
.. _Pull Request 7462: https://github.com/galaxyproject/galaxy/pull/7462
|
||||
.. _Pull Request 7463: https://github.com/galaxyproject/galaxy/pull/7463
|
||||
.. _Pull Request 7466: https://github.com/galaxyproject/galaxy/pull/7466
|
||||
.. _Pull Request 7470: https://github.com/galaxyproject/galaxy/pull/7470
|
||||
.. _Pull Request 7471: https://github.com/galaxyproject/galaxy/pull/7471
|
||||
.. _Pull Request 7472: https://github.com/galaxyproject/galaxy/pull/7472
|
||||
.. _Pull Request 7475: https://github.com/galaxyproject/galaxy/pull/7475
|
||||
.. _Pull Request 7476: https://github.com/galaxyproject/galaxy/pull/7476
|
||||
.. _Pull Request 7477: https://github.com/galaxyproject/galaxy/pull/7477
|
||||
.. _Pull Request 7478: https://github.com/galaxyproject/galaxy/pull/7478
|
||||
.. _Pull Request 7480: https://github.com/galaxyproject/galaxy/pull/7480
|
||||
.. _Pull Request 7481: https://github.com/galaxyproject/galaxy/pull/7481
|
||||
.. _Pull Request 7483: https://github.com/galaxyproject/galaxy/pull/7483
|
||||
.. _Pull Request 7485: https://github.com/galaxyproject/galaxy/pull/7485
|
||||
.. _Pull Request 7486: https://github.com/galaxyproject/galaxy/pull/7486
|
||||
.. _Pull Request 7487: https://github.com/galaxyproject/galaxy/pull/7487
|
||||
.. _Pull Request 7499: https://github.com/galaxyproject/galaxy/pull/7499
|
||||
.. _Pull Request 7500: https://github.com/galaxyproject/galaxy/pull/7500
|
||||
.. _Pull Request 7504: https://github.com/galaxyproject/galaxy/pull/7504
|
||||
.. _Pull Request 7505: https://github.com/galaxyproject/galaxy/pull/7505
|
||||
.. _Pull Request 7507: https://github.com/galaxyproject/galaxy/pull/7507
|
||||
.. _Pull Request 7510: https://github.com/galaxyproject/galaxy/pull/7510
|
||||
.. _Pull Request 7514: https://github.com/galaxyproject/galaxy/pull/7514
|
||||
.. _Pull Request 7515: https://github.com/galaxyproject/galaxy/pull/7515
|
||||
.. _Pull Request 7516: https://github.com/galaxyproject/galaxy/pull/7516
|
||||
.. _Pull Request 7517: https://github.com/galaxyproject/galaxy/pull/7517
|
||||
.. _Pull Request 7518: https://github.com/galaxyproject/galaxy/pull/7518
|
||||
.. _Pull Request 7519: https://github.com/galaxyproject/galaxy/pull/7519
|
||||
.. _Pull Request 7521: https://github.com/galaxyproject/galaxy/pull/7521
|
||||
.. _Pull Request 7522: https://github.com/galaxyproject/galaxy/pull/7522
|
||||
.. _Pull Request 7523: https://github.com/galaxyproject/galaxy/pull/7523
|
||||
.. _Pull Request 7524: https://github.com/galaxyproject/galaxy/pull/7524
|
||||
.. _Pull Request 7527: https://github.com/galaxyproject/galaxy/pull/7527
|
||||
.. _Pull Request 7529: https://github.com/galaxyproject/galaxy/pull/7529
|
||||
.. _Pull Request 7530: https://github.com/galaxyproject/galaxy/pull/7530
|
||||
.. _Pull Request 7532: https://github.com/galaxyproject/galaxy/pull/7532
|
||||
.. _Pull Request 7534: https://github.com/galaxyproject/galaxy/pull/7534
|
||||
.. _Pull Request 7536: https://github.com/galaxyproject/galaxy/pull/7536
|
||||
.. _Pull Request 7537: https://github.com/galaxyproject/galaxy/pull/7537
|
||||
.. _Pull Request 7538: https://github.com/galaxyproject/galaxy/pull/7538
|
||||
.. _Pull Request 7539: https://github.com/galaxyproject/galaxy/pull/7539
|
||||
.. _Pull Request 7540: https://github.com/galaxyproject/galaxy/pull/7540
|
||||
.. _Pull Request 7541: https://github.com/galaxyproject/galaxy/pull/7541
|
||||
.. _Pull Request 7542: https://github.com/galaxyproject/galaxy/pull/7542
|
||||
.. _Pull Request 7543: https://github.com/galaxyproject/galaxy/pull/7543
|
||||
.. _Pull Request 7544: https://github.com/galaxyproject/galaxy/pull/7544
|
||||
.. _Pull Request 7545: https://github.com/galaxyproject/galaxy/pull/7545
|
||||
.. _Pull Request 7546: https://github.com/galaxyproject/galaxy/pull/7546
|
||||
.. _Pull Request 7547: https://github.com/galaxyproject/galaxy/pull/7547
|
||||
.. _Pull Request 7548: https://github.com/galaxyproject/galaxy/pull/7548
|
||||
.. _Pull Request 7549: https://github.com/galaxyproject/galaxy/pull/7549
|
||||
.. _Pull Request 7553: https://github.com/galaxyproject/galaxy/pull/7553
|
||||
.. _Pull Request 7554: https://github.com/galaxyproject/galaxy/pull/7554
|
||||
.. _Pull Request 7555: https://github.com/galaxyproject/galaxy/pull/7555
|
||||
.. _Pull Request 7556: https://github.com/galaxyproject/galaxy/pull/7556
|
||||
.. _Pull Request 7558: https://github.com/galaxyproject/galaxy/pull/7558
|
||||
.. _Pull Request 7560: https://github.com/galaxyproject/galaxy/pull/7560
|
||||
.. _Pull Request 7561: https://github.com/galaxyproject/galaxy/pull/7561
|
||||
.. _Pull Request 7562: https://github.com/galaxyproject/galaxy/pull/7562
|
||||
.. _Pull Request 7565: https://github.com/galaxyproject/galaxy/pull/7565
|
||||
.. _Pull Request 7566: https://github.com/galaxyproject/galaxy/pull/7566
|
||||
.. _Pull Request 7569: https://github.com/galaxyproject/galaxy/pull/7569
|
||||
.. _Pull Request 7570: https://github.com/galaxyproject/galaxy/pull/7570
|
||||
.. _Pull Request 7571: https://github.com/galaxyproject/galaxy/pull/7571
|
||||
.. _Pull Request 7572: https://github.com/galaxyproject/galaxy/pull/7572
|
||||
.. _Pull Request 7573: https://github.com/galaxyproject/galaxy/pull/7573
|
||||
.. _Pull Request 7574: https://github.com/galaxyproject/galaxy/pull/7574
|
||||
.. _Pull Request 7575: https://github.com/galaxyproject/galaxy/pull/7575
|
||||
.. _Pull Request 7581: https://github.com/galaxyproject/galaxy/pull/7581
|
||||
.. _Pull Request 7584: https://github.com/galaxyproject/galaxy/pull/7584
|
||||
.. _Pull Request 7586: https://github.com/galaxyproject/galaxy/pull/7586
|
||||
.. _Pull Request 7587: https://github.com/galaxyproject/galaxy/pull/7587
|
||||
.. _Pull Request 7588: https://github.com/galaxyproject/galaxy/pull/7588
|
||||
.. _Pull Request 7589: https://github.com/galaxyproject/galaxy/pull/7589
|
||||
.. _Pull Request 7590: https://github.com/galaxyproject/galaxy/pull/7590
|
||||
.. _Pull Request 7592: https://github.com/galaxyproject/galaxy/pull/7592
|
||||
.. _Pull Request 7594: https://github.com/galaxyproject/galaxy/pull/7594
|
||||
.. _Pull Request 7595: https://github.com/galaxyproject/galaxy/pull/7595
|
||||
.. _Pull Request 7596: https://github.com/galaxyproject/galaxy/pull/7596
|
||||
.. _Pull Request 7597: https://github.com/galaxyproject/galaxy/pull/7597
|
||||
.. _Pull Request 7598: https://github.com/galaxyproject/galaxy/pull/7598
|
||||
.. _Pull Request 7601: https://github.com/galaxyproject/galaxy/pull/7601
|
||||
.. _Pull Request 7602: https://github.com/galaxyproject/galaxy/pull/7602
|
||||
.. _Pull Request 7605: https://github.com/galaxyproject/galaxy/pull/7605
|
||||
.. _Pull Request 7606: https://github.com/galaxyproject/galaxy/pull/7606
|
||||
.. _Pull Request 7609: https://github.com/galaxyproject/galaxy/pull/7609
|
||||
.. _Pull Request 7612: https://github.com/galaxyproject/galaxy/pull/7612
|
||||
.. _Pull Request 7614: https://github.com/galaxyproject/galaxy/pull/7614
|
||||
.. _Pull Request 7616: https://github.com/galaxyproject/galaxy/pull/7616
|
||||
.. _Pull Request 7621: https://github.com/galaxyproject/galaxy/pull/7621
|
||||
.. _Pull Request 7630: https://github.com/galaxyproject/galaxy/pull/7630
|
||||
.. _Pull Request 7633: https://github.com/galaxyproject/galaxy/pull/7633
|
||||
.. _Pull Request 7634: https://github.com/galaxyproject/galaxy/pull/7634
|
||||
.. _Pull Request 7637: https://github.com/galaxyproject/galaxy/pull/7637
|
||||
.. _Pull Request 7639: https://github.com/galaxyproject/galaxy/pull/7639
|
||||
.. _Pull Request 7640: https://github.com/galaxyproject/galaxy/pull/7640
|
||||
.. _Pull Request 7641: https://github.com/galaxyproject/galaxy/pull/7641
|
||||
.. _Pull Request 7642: https://github.com/galaxyproject/galaxy/pull/7642
|
||||
.. _Pull Request 7643: https://github.com/galaxyproject/galaxy/pull/7643
|
||||
.. _Pull Request 7645: https://github.com/galaxyproject/galaxy/pull/7645
|
||||
.. _Pull Request 7646: https://github.com/galaxyproject/galaxy/pull/7646
|
||||
.. _Pull Request 7647: https://github.com/galaxyproject/galaxy/pull/7647
|
||||
.. _Pull Request 7650: https://github.com/galaxyproject/galaxy/pull/7650
|
||||
.. _Pull Request 7651: https://github.com/galaxyproject/galaxy/pull/7651
|
||||
.. _Pull Request 7652: https://github.com/galaxyproject/galaxy/pull/7652
|
||||
.. _Pull Request 7655: https://github.com/galaxyproject/galaxy/pull/7655
|
||||
.. _Pull Request 7656: https://github.com/galaxyproject/galaxy/pull/7656
|
||||
.. _Pull Request 7657: https://github.com/galaxyproject/galaxy/pull/7657
|
||||
.. _Pull Request 7658: https://github.com/galaxyproject/galaxy/pull/7658
|
||||
.. _Pull Request 7659: https://github.com/galaxyproject/galaxy/pull/7659
|
||||
.. _Pull Request 7660: https://github.com/galaxyproject/galaxy/pull/7660
|
||||
.. _Pull Request 7663: https://github.com/galaxyproject/galaxy/pull/7663
|
||||
.. _Pull Request 7664: https://github.com/galaxyproject/galaxy/pull/7664
|
||||
.. _Pull Request 7666: https://github.com/galaxyproject/galaxy/pull/7666
|
||||
.. _Pull Request 7667: https://github.com/galaxyproject/galaxy/pull/7667
|
||||
.. _Pull Request 7674: https://github.com/galaxyproject/galaxy/pull/7674
|
||||
.. _Pull Request 7675: https://github.com/galaxyproject/galaxy/pull/7675
|
||||
.. _Pull Request 7676: https://github.com/galaxyproject/galaxy/pull/7676
|
||||
.. _Pull Request 7677: https://github.com/galaxyproject/galaxy/pull/7677
|
||||
.. _Pull Request 7678: https://github.com/galaxyproject/galaxy/pull/7678
|
||||
.. _Pull Request 7679: https://github.com/galaxyproject/galaxy/pull/7679
|
||||
.. _Pull Request 7680: https://github.com/galaxyproject/galaxy/pull/7680
|
||||
.. _Pull Request 7681: https://github.com/galaxyproject/galaxy/pull/7681
|
||||
.. _Pull Request 7682: https://github.com/galaxyproject/galaxy/pull/7682
|
||||
.. _Pull Request 7683: https://github.com/galaxyproject/galaxy/pull/7683
|
||||
.. _Pull Request 7684: https://github.com/galaxyproject/galaxy/pull/7684
|
||||
.. _Pull Request 7689: https://github.com/galaxyproject/galaxy/pull/7689
|
||||
.. _Pull Request 7690: https://github.com/galaxyproject/galaxy/pull/7690
|
||||
.. _Pull Request 7691: https://github.com/galaxyproject/galaxy/pull/7691
|
||||
.. _Pull Request 7693: https://github.com/galaxyproject/galaxy/pull/7693
|
||||
.. _Pull Request 7694: https://github.com/galaxyproject/galaxy/pull/7694
|
||||
.. _Pull Request 7695: https://github.com/galaxyproject/galaxy/pull/7695
|
||||
.. _Pull Request 7696: https://github.com/galaxyproject/galaxy/pull/7696
|
||||
.. _Pull Request 7697: https://github.com/galaxyproject/galaxy/pull/7697
|
||||
.. _Pull Request 7698: https://github.com/galaxyproject/galaxy/pull/7698
|
||||
.. _Pull Request 7699: https://github.com/galaxyproject/galaxy/pull/7699
|
||||
.. _Pull Request 7702: https://github.com/galaxyproject/galaxy/pull/7702
|
||||
.. _Pull Request 7703: https://github.com/galaxyproject/galaxy/pull/7703
|
||||
.. _Pull Request 7704: https://github.com/galaxyproject/galaxy/pull/7704
|
||||
.. _Pull Request 7706: https://github.com/galaxyproject/galaxy/pull/7706
|
||||
.. _Pull Request 7707: https://github.com/galaxyproject/galaxy/pull/7707
|
||||
.. _Pull Request 7708: https://github.com/galaxyproject/galaxy/pull/7708
|
||||
.. _Pull Request 7709: https://github.com/galaxyproject/galaxy/pull/7709
|
||||
.. _Pull Request 7711: https://github.com/galaxyproject/galaxy/pull/7711
|
||||
.. _Pull Request 7712: https://github.com/galaxyproject/galaxy/pull/7712
|
||||
.. _Pull Request 7713: https://github.com/galaxyproject/galaxy/pull/7713
|
||||
.. _Pull Request 7716: https://github.com/galaxyproject/galaxy/pull/7716
|
||||
.. _Pull Request 7717: https://github.com/galaxyproject/galaxy/pull/7717
|
||||
.. _Pull Request 7718: https://github.com/galaxyproject/galaxy/pull/7718
|
||||
.. _Pull Request 7719: https://github.com/galaxyproject/galaxy/pull/7719
|
||||
.. _Pull Request 7720: https://github.com/galaxyproject/galaxy/pull/7720
|
||||
.. _Pull Request 7722: https://github.com/galaxyproject/galaxy/pull/7722
|
||||
.. _Pull Request 7723: https://github.com/galaxyproject/galaxy/pull/7723
|
||||
.. _Pull Request 7724: https://github.com/galaxyproject/galaxy/pull/7724
|
||||
.. _Pull Request 7727: https://github.com/galaxyproject/galaxy/pull/7727
|
||||
.. _Pull Request 7737: https://github.com/galaxyproject/galaxy/pull/7737
|
||||
.. _Pull Request 7738: https://github.com/galaxyproject/galaxy/pull/7738
|
||||
.. _Pull Request 7740: https://github.com/galaxyproject/galaxy/pull/7740
|
||||
.. _Pull Request 7743: https://github.com/galaxyproject/galaxy/pull/7743
|
||||
.. _Pull Request 7744: https://github.com/galaxyproject/galaxy/pull/7744
|
||||
.. _Pull Request 7746: https://github.com/galaxyproject/galaxy/pull/7746
|
||||
.. _Pull Request 7748: https://github.com/galaxyproject/galaxy/pull/7748
|
||||
.. _Pull Request 7749: https://github.com/galaxyproject/galaxy/pull/7749
|
||||
.. _Pull Request 7750: https://github.com/galaxyproject/galaxy/pull/7750
|
||||
.. _Pull Request 7751: https://github.com/galaxyproject/galaxy/pull/7751
|
||||
.. _Pull Request 7754: https://github.com/galaxyproject/galaxy/pull/7754
|
||||
.. _Pull Request 7755: https://github.com/galaxyproject/galaxy/pull/7755
|
||||
.. _Pull Request 7756: https://github.com/galaxyproject/galaxy/pull/7756
|
||||
.. _Pull Request 7760: https://github.com/galaxyproject/galaxy/pull/7760
|
||||
.. _Pull Request 7773: https://github.com/galaxyproject/galaxy/pull/7773
|
||||
.. _Pull Request 7777: https://github.com/galaxyproject/galaxy/pull/7777
|
||||
.. _Pull Request 7778: https://github.com/galaxyproject/galaxy/pull/7778
|
||||
.. _Pull Request 7779: https://github.com/galaxyproject/galaxy/pull/7779
|
||||
.. _Pull Request 7780: https://github.com/galaxyproject/galaxy/pull/7780
|
||||
.. _Pull Request 7782: https://github.com/galaxyproject/galaxy/pull/7782
|
||||
.. _Pull Request 7785: https://github.com/galaxyproject/galaxy/pull/7785
|
||||
.. _Pull Request 7788: https://github.com/galaxyproject/galaxy/pull/7788
|
||||
.. _Pull Request 7789: https://github.com/galaxyproject/galaxy/pull/7789
|
||||
.. _Pull Request 7796: https://github.com/galaxyproject/galaxy/pull/7796
|
||||
.. _Pull Request 7797: https://github.com/galaxyproject/galaxy/pull/7797
|
||||
.. _Pull Request 7798: https://github.com/galaxyproject/galaxy/pull/7798
|
||||
.. _Pull Request 7800: https://github.com/galaxyproject/galaxy/pull/7800
|
||||
.. _Pull Request 7806: https://github.com/galaxyproject/galaxy/pull/7806
|
||||
.. _Pull Request 7812: https://github.com/galaxyproject/galaxy/pull/7812
|
||||
.. _Pull Request 7815: https://github.com/galaxyproject/galaxy/pull/7815
|
||||
.. _Pull Request 7819: https://github.com/galaxyproject/galaxy/pull/7819
|
||||
.. _Pull Request 7823: https://github.com/galaxyproject/galaxy/pull/7823
|
||||
.. _Pull Request 7824: https://github.com/galaxyproject/galaxy/pull/7824
|
||||
.. _Pull Request 7826: https://github.com/galaxyproject/galaxy/pull/7826
|
||||
.. _Pull Request 7827: https://github.com/galaxyproject/galaxy/pull/7827
|
||||
.. _Pull Request 7834: https://github.com/galaxyproject/galaxy/pull/7834
|
||||
.. _Pull Request 7839: https://github.com/galaxyproject/galaxy/pull/7839
|
||||
.. _Pull Request 7840: https://github.com/galaxyproject/galaxy/pull/7840
|
||||
.. _Pull Request 7844: https://github.com/galaxyproject/galaxy/pull/7844
|
||||
.. _Pull Request 7845: https://github.com/galaxyproject/galaxy/pull/7845
|
||||
.. _Pull Request 7848: https://github.com/galaxyproject/galaxy/pull/7848
|
||||
.. _Pull Request 7851: https://github.com/galaxyproject/galaxy/pull/7851
|
||||
.. _Pull Request 7853: https://github.com/galaxyproject/galaxy/pull/7853
|
||||
.. _Pull Request 7855: https://github.com/galaxyproject/galaxy/pull/7855
|
||||
.. _Pull Request 7856: https://github.com/galaxyproject/galaxy/pull/7856
|
||||
.. _Pull Request 7858: https://github.com/galaxyproject/galaxy/pull/7858
|
||||
.. _Pull Request 7859: https://github.com/galaxyproject/galaxy/pull/7859
|
||||
.. _Pull Request 7860: https://github.com/galaxyproject/galaxy/pull/7860
|
||||
.. _Pull Request 7864: https://github.com/galaxyproject/galaxy/pull/7864
|
||||
.. _Pull Request 7865: https://github.com/galaxyproject/galaxy/pull/7865
|
||||
.. _Pull Request 7866: https://github.com/galaxyproject/galaxy/pull/7866
|
||||
.. _Pull Request 7870: https://github.com/galaxyproject/galaxy/pull/7870
|
||||
.. _Pull Request 7872: https://github.com/galaxyproject/galaxy/pull/7872
|
||||
.. _Pull Request 7874: https://github.com/galaxyproject/galaxy/pull/7874
|
||||
.. _Pull Request 7875: https://github.com/galaxyproject/galaxy/pull/7875
|
||||
.. _Pull Request 7877: https://github.com/galaxyproject/galaxy/pull/7877
|
||||
.. _Pull Request 7880: https://github.com/galaxyproject/galaxy/pull/7880
|
||||
.. _Pull Request 7887: https://github.com/galaxyproject/galaxy/pull/7887
|
||||
.. _Pull Request 7896: https://github.com/galaxyproject/galaxy/pull/7896
|
||||
.. _Pull Request 7904: https://github.com/galaxyproject/galaxy/pull/7904
|
||||
.. _Pull Request 7906: https://github.com/galaxyproject/galaxy/pull/7906
|
||||
.. _Pull Request 7916: https://github.com/galaxyproject/galaxy/pull/7916
|
||||
.. _Pull Request 7917: https://github.com/galaxyproject/galaxy/pull/7917
|
||||
.. _Pull Request 7923: https://github.com/galaxyproject/galaxy/pull/7923
|
||||
.. _Pull Request 7925: https://github.com/galaxyproject/galaxy/pull/7925
|
||||
.. _Pull Request 7933: https://github.com/galaxyproject/galaxy/pull/7933
|
||||
.. _Pull Request 7934: https://github.com/galaxyproject/galaxy/pull/7934
|
||||
.. _Pull Request 7943: https://github.com/galaxyproject/galaxy/pull/7943
|
||||
.. _Pull Request 7944: https://github.com/galaxyproject/galaxy/pull/7944
|
||||
.. _Pull Request 7954: https://github.com/galaxyproject/galaxy/pull/7954
|
||||
.. _Pull Request 7956: https://github.com/galaxyproject/galaxy/pull/7956
|
||||
.. _Pull Request 7967: https://github.com/galaxyproject/galaxy/pull/7967
|
||||
.. _Pull Request 7969: https://github.com/galaxyproject/galaxy/pull/7969
|
||||
.. _Pull Request 7972: https://github.com/galaxyproject/galaxy/pull/7972
|
||||
.. _Pull Request 7979: https://github.com/galaxyproject/galaxy/pull/7979
|
||||
.. _Pull Request 7983: https://github.com/galaxyproject/galaxy/pull/7983
|
||||
.. _Pull Request 7989: https://github.com/galaxyproject/galaxy/pull/7989
|
||||
.. _Pull Request 8000: https://github.com/galaxyproject/galaxy/pull/8000
|
||||
.. _Pull Request 8004: https://github.com/galaxyproject/galaxy/pull/8004
|
||||
.. _Pull Request 8021: https://github.com/galaxyproject/galaxy/pull/8021
|
||||
.. _Pull Request 8029: https://github.com/galaxyproject/galaxy/pull/8029
|
||||
.. _Pull Request 8048: https://github.com/galaxyproject/galaxy/pull/8048
|
||||
.. _Pull Request 8085: https://github.com/galaxyproject/galaxy/pull/8085
|
||||
@@ -0,0 +1,10 @@
|
||||
|
||||
===========================================================
|
||||
September 2019 Galaxy Release (v 19.09)
|
||||
===========================================================
|
||||
|
||||
|
||||
Schedule
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2019-09-02
|
||||
* Planned Release Date: 2019-09-23
|
||||
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|
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|
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|
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|
After Width: | Height: | Size: 281 KiB |
@@ -38,7 +38,7 @@ DEVTEAM = [
|
||||
"davebx", "martenson", "jmchilton",
|
||||
"tnabtaf", "natefoo", "jgoecks",
|
||||
"guerler", "jennaj", "nekrut", "jxtx",
|
||||
"VJalili"
|
||||
"VJalili", "WilliamHolden", "Nerdinacan"
|
||||
]
|
||||
|
||||
TEMPLATE = string.Template("""
|
||||
@@ -143,15 +143,21 @@ Highlights
|
||||
Feature description.
|
||||
|
||||
|
||||
New Visualisations
|
||||
New Visualizations
|
||||
===========================================================
|
||||
|
||||
.. visualizations
|
||||
|
||||
New Datatypes
|
||||
===========================================================
|
||||
|
||||
.. datatypes
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
@@ -174,6 +180,9 @@ Schedule
|
||||
* Planned Release Date: ${release_date}
|
||||
""")
|
||||
|
||||
PRS_TEMPLATE = """
|
||||
.. github_links
|
||||
"""
|
||||
|
||||
RELEASE_ISSUE_TEMPLATE = string.Template("""
|
||||
|
||||
@@ -337,7 +346,7 @@ def do_release(argv):
|
||||
release=release_name
|
||||
)
|
||||
announce_file = _release_file(release_name + "_announce.rst")
|
||||
open(announce_file, "w").write(announce_info.encode("utf-8"))
|
||||
_write_file(announce_file, announce_info)
|
||||
|
||||
announce_user_info = ANNOUNCE_USER_TEMPLATE.substitute(
|
||||
month_name=month_name,
|
||||
@@ -345,7 +354,10 @@ def do_release(argv):
|
||||
release=release_name
|
||||
)
|
||||
announce_user_file = _release_file(release_name + "_announce_user.rst")
|
||||
open(announce_user_file, "w").write(announce_user_info.encode("utf-8"))
|
||||
_write_file(announce_user_file, announce_user_info)
|
||||
|
||||
prs_file = _release_file(release_name + "_prs.rst")
|
||||
_write_file(prs_file, PRS_TEMPLATE)
|
||||
|
||||
next_version_params = _next_version_params(release_name)
|
||||
next_version = next_version_params["version"]
|
||||
@@ -354,10 +366,9 @@ def do_release(argv):
|
||||
next_announce = NEXT_TEMPLATE.substitute(**next_version_params)
|
||||
open(next_release_file, "w").write(next_announce.encode("utf-8"))
|
||||
releases_index = _release_file("index.rst")
|
||||
releases_index_contents = open(releases_index, "r").read()
|
||||
releases_index_contents = _read_file(releases_index)
|
||||
releases_index_contents = releases_index_contents.replace(".. announcements\n", ".. announcements\n " + next_version + "_announce\n")
|
||||
with open(releases_index, "w") as f:
|
||||
f.write(releases_index_contents)
|
||||
_write_file(releases_index, releases_index_contents)
|
||||
|
||||
for pr in _get_prs(release_name):
|
||||
# 2015-06-29 18:32:13 2015-04-22 19:11:53 2015-08-12 21:15:45
|
||||
@@ -365,15 +376,16 @@ def do_release(argv):
|
||||
"title": pr.title,
|
||||
"number": pr.number,
|
||||
"head": pr.head,
|
||||
"labels": _pr_to_labels(pr),
|
||||
}
|
||||
main([argv[0], "--release_file", "%s_prs.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)])
|
||||
main([argv[0], "--release_file", "%s.rst" % release_name, "--request", as_dict, "pr" + str(pr.number)])
|
||||
|
||||
|
||||
def check_release(argv):
|
||||
github = _github_client()
|
||||
release_name = argv[2]
|
||||
for pr in _get_prs(release_name):
|
||||
_text_target(github, pr)
|
||||
_text_target(github, pr, labels=_pr_to_labels(pr))
|
||||
|
||||
|
||||
def check_blocking_prs(argv):
|
||||
@@ -451,8 +463,16 @@ def _get_prs(release_name, state="closed"):
|
||||
user=PROJECT_OWNER,
|
||||
repo=PROJECT_NAME,
|
||||
)
|
||||
reached_old_prs = False
|
||||
|
||||
for page in pull_requests:
|
||||
if reached_old_prs:
|
||||
break
|
||||
|
||||
for pr in page:
|
||||
if pr.created_at < datetime.datetime(2016, 11, 1, 0, 0):
|
||||
reached_old_prs = True
|
||||
pass
|
||||
merged_at = pr.merged_at
|
||||
milestone = pr.milestone
|
||||
proper_state = state != "closed" or merged_at
|
||||
@@ -504,10 +524,15 @@ def main(argv):
|
||||
if newest_release is None:
|
||||
newest_release = sorted(os.listdir(RELEASES_PATH))[-1]
|
||||
history_path = os.path.join(RELEASES_PATH, newest_release)
|
||||
history = open(history_path, "r").read().decode("utf-8")
|
||||
user_announce_path = history_path[0:-len(".rst")] + "_announce_user.rst"
|
||||
prs_path = history_path[0:-len(".rst")] + "_prs.rst"
|
||||
|
||||
def extend(from_str, line, source=history):
|
||||
from_str += "\n"
|
||||
history = _read_file(history_path)
|
||||
user_announce = _read_file(user_announce_path)
|
||||
prs_content = _read_file(prs_path)
|
||||
|
||||
def extend_target(target, line, source=history):
|
||||
from_str = ".. %s\n" % target
|
||||
return source.replace(from_str, from_str + line + "\n")
|
||||
|
||||
ident = argv[1]
|
||||
@@ -548,48 +573,72 @@ def main(argv):
|
||||
if owner in DEVTEAM:
|
||||
owner = None
|
||||
text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
|
||||
history = extend(".. github_links", text)
|
||||
prs_content = extend_target("github_links", text, prs_content)
|
||||
if owner:
|
||||
to_doc += "\n(thanks to `@%s <https://github.com/%s>`__)." % (
|
||||
owner, owner,
|
||||
)
|
||||
to_doc += "\n`Pull Request {0}`_".format(pull_request)
|
||||
if github:
|
||||
text_target = _text_target(github, pull_request)
|
||||
labels = None
|
||||
if req and 'labels' in req:
|
||||
labels = req['labels']
|
||||
text_target = _text_target(github, pull_request, labels=labels)
|
||||
elif ident.startswith("issue"):
|
||||
issue = ident[len("issue"):]
|
||||
text = ".. _Issue {0}: {1}/issues/{0}".format(issue, PROJECT_URL)
|
||||
history = extend(".. github_links", text)
|
||||
prs_content = extend_target("github_links", text, prs_content)
|
||||
to_doc += "`Issue {0}`_".format(issue)
|
||||
else:
|
||||
short_rev = ident[:7]
|
||||
text = ".. _{0}: {1}/commit/{0}".format(short_rev, PROJECT_URL)
|
||||
history = extend(".. github_links", text)
|
||||
prs_content = extend_target("github_links", text, prs_content)
|
||||
to_doc += "{0}_".format(short_rev)
|
||||
|
||||
to_doc = wrap(to_doc)
|
||||
history = extend(".. %s\n" % text_target, to_doc, history)
|
||||
open(history_path, "w").write(history.encode("utf-8"))
|
||||
history = extend_target(text_target, to_doc, history)
|
||||
if req and 'labels' in req:
|
||||
labels = req['labels']
|
||||
if 'area/datatypes' in labels:
|
||||
user_announce = extend_target("datatypes", to_doc, user_announce)
|
||||
if 'area/visualizations' in labels:
|
||||
user_announce = extend_target("visualizations", to_doc, user_announce)
|
||||
if 'area/tools' in labels:
|
||||
user_announce = extend_target("tools", to_doc, user_announce)
|
||||
_write_file(history_path, history)
|
||||
_write_file(prs_path, prs_content)
|
||||
_write_file(user_announce_path, user_announce)
|
||||
|
||||
|
||||
def _text_target(github, pull_request):
|
||||
labels = []
|
||||
def _read_file(path):
|
||||
with open(path, "r") as f:
|
||||
return f.read().decode("utf-8")
|
||||
|
||||
|
||||
def _write_file(path, contents):
|
||||
with open(path, "w") as f:
|
||||
f.write(contents.encode("utf-8"))
|
||||
|
||||
|
||||
def _text_target(github, pull_request, labels=None):
|
||||
pr_number = None
|
||||
if isinstance(pull_request, string_types):
|
||||
pr_number = pull_request
|
||||
else:
|
||||
pr_number = pull_request.number
|
||||
|
||||
try:
|
||||
labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
|
||||
except Exception as e:
|
||||
print(e)
|
||||
if labels is None:
|
||||
labels = []
|
||||
try:
|
||||
labels = github.issues.labels.list_by_issue(int(pr_number), user=PROJECT_OWNER, repo=PROJECT_NAME)
|
||||
labels = [l.name.lower() for l in labels]
|
||||
except Exception as e:
|
||||
print(e)
|
||||
is_bug = is_enhancement = is_feature = is_minor = is_major = is_merge = is_small_enhancement = False
|
||||
if len(labels) == 0:
|
||||
print('No labels found for %s' % pr_number)
|
||||
return None
|
||||
for label in labels:
|
||||
label_name = label.name.lower()
|
||||
for label_name in labels:
|
||||
if label_name == "minor":
|
||||
is_minor = True
|
||||
elif label_name == "major":
|
||||
@@ -604,11 +653,14 @@ def _text_target(github, pull_request):
|
||||
is_enhancement = True
|
||||
elif label_name in ["kind/testing", "kind/refactoring"]:
|
||||
is_small_enhancement = True
|
||||
elif label_name == "procedures":
|
||||
# Treat procedures as an implicit enhancement.
|
||||
is_enhancement = True
|
||||
|
||||
is_some_kind_of_enhancement = is_enhancement or is_feature or is_small_enhancement
|
||||
|
||||
if not(is_bug or is_some_kind_of_enhancement or is_minor or is_merge):
|
||||
print("No kind/ or minor or merge label found for %s" % _pr_to_str(pull_request))
|
||||
print("No 'kind/*' or 'minor' or 'merge' or 'procedures' label found for %s" % _pr_to_str(pull_request))
|
||||
text_target = None
|
||||
|
||||
if is_minor or is_merge:
|
||||
@@ -632,6 +684,11 @@ def _text_target(github, pull_request):
|
||||
return text_target
|
||||
|
||||
|
||||
def _pr_to_labels(pr):
|
||||
labels = [l["name"].lower() for l in pr.labels]
|
||||
return labels
|
||||
|
||||
|
||||
def _previous_release(to):
|
||||
previous_release = None
|
||||
for release in _releases():
|
||||
|
||||
Reference in New Issue
Block a user