diff --git a/doc/source/releases/19.01_announce_user.rst b/doc/source/releases/19.01_announce_user.rst index 7381c4d9049..d486d8bf735 100644 --- a/doc/source/releases/19.01_announce_user.rst +++ b/doc/source/releases/19.01_announce_user.rst @@ -41,13 +41,13 @@ There's a new discussion forum to replace Biostars. It is accessible under the ' :alt: Galaxy's new help forum which replaces biostars -New Visualisations +New Visualizations =========================================================== `Aequatus visualisation plugin `__ has been released which allows visualisation of gene alignments and gene family aggregations. .. figure:: https://lh3.googleusercontent.com/wgNqZT2idSR4AkvUZ55ZQGXOfOPlAxFimO9795WvrQwP1ZMxxdYwNmRZErf-n5hZMGa1SulFry321vgHPoc11wsmJlmVPrmyxG8buV6P=s1600 - :alt: The Aequatus visualisation allows analysing gene family alignments + :alt: The Aequatus visualization allows analyzing gene family alignments New Datatypes =========================================================== diff --git a/doc/source/releases/19.05.rst b/doc/source/releases/19.05.rst new file mode 100644 index 00000000000..7166c497f17 --- /dev/null +++ b/doc/source/releases/19.05.rst @@ -0,0 +1,721 @@ + +.. to_doc + +19.05 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +* Implement the ability to favorite tools. + `Pull Request 7209`_ +* Add data dialog option to tool form data selector. + `Pull Request 7553`_, `Pull Request 7460`_ +* Many workflow editor connection fixes and enhancements making + them more correct, accessible, and transparent + (with huge thanks to `@mvdbeek `__). + `Pull Request 7466`_, `Pull Request 7435`_, `Pull Request 7972`_, + `Pull Request 7979`_, `Pull Request 7642`_, `Pull Request 7989`_, + `Pull Request 7254`_ +* Add a Galaxy IE for cellxgene. + `Pull Request 7268`_ +* Implement expression tools and non-data tool outputs + (with thanks to `@mvdbeek `__). + `Pull Request 7556`_, `Pull Request 7796`_, `Pull Request 7797`_, + `Pull Request 7944`_ +* Add Galaxy cloud runner support + (thanks to `@nuwang `__). + `Pull Request 7226`_ +* More robust task messaging + (thanks to `@mvdbeek `__). + `Pull Request 7548`_ +* Allow implicit conversion for input collection parameters + (thanks to `@mvdbeek `__). + `Pull Request 7683`_ +* Allow import of "Format 2" workflows by default. + `Pull Request 7659`_ +* Decompose Galaxy into Python libraries in-tree. + `Pull Request 7524`_ +* Rewrite and generalize History import and export - dozens of fixes, support for collections, + Python library support, etc.. + `Pull Request 7367`_, `Pull Request 7214`_, `Pull Request 7366`_, + `Pull Request 7369`_, `Pull Request 7370`_, `Pull Request 7358`_, + `Pull Request 7505`_, `Pull Request 7507`_, `Pull Request 7363`_, + `Pull Request 7193`_, `Pull Request 7192`_, `Pull Request 7537`_, + `Pull Request 7540`_, `Pull Request 7684`_, `Pull Request 7704`_ +* User facing release notes + (thanks to `@erasche `__). + `Pull Request 7527`_ +* Implement dataset source and hash tracking. + `Pull Request 7487`_, `Pull Request 4659`_, `Pull Request 7549`_ +* Custos integration for AuthNZ + (thanks to `@machristie `__). + `Pull Request 7195`_ +* Flush out API support for AuthNZ and CloudAuthz + `Pull Request 7598`_, `Pull Request 7609`_, + `Pull Request 7592`_, `Pull Request 7597`_, + `Pull Request 7639`_ +* Update to PSA 3.1 and support login with Globus identity. + `Pull Request 7463`_ +* Swap from 'slug.js' to 'slugify.js' - saving 10 MB in client bundles. + `Pull Request 7538`_ +* Update all client dependencies - including to Backbone 1.4, Bootstrap 4.2, Vue 2.6. + `Pull Request 7544`_, `Pull Request 7637`_ +* Allow admins to import dynamic JSON-based tools. + `Pull Request 7545`_ +* Implement environment modules mapping files + (thanks to `@FredericBGA `__). + `Pull Request 7398`_ +* Allow tool testing of multiple files within a zip output + (thanks to `@thermokarst `__). + `Pull Request 7400`_ +* 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 `__). + `Pull Request 7288`_ +* Fix post job actions for "Database Operation" tools, implement ``change_datatype`` + for collection output + (thanks to `@mvdbeek `__). + `Pull Request 7480`_ +* Implement and enforce ESLint linting of the entire client code base. + `Pull Request 7202`_, `Pull Request 7860`_ +* Multiple enhancements to the LSF cli-plugin job runner - support + out of memory handling, project specification, and Spectrum LSF. + (thanks to `@pcm32 `__ and + `@selten `__). + `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 `__). + `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. + `Pull Request 7154`_, `Pull Request 7650`_ +* Replace login and registration mako templates with VueJS components. + `Pull Request 6621`_, `Pull Request 7047`_, `Pull Request 7329`_, + `Pull Request 7442`_, `Pull Request 7756`_, `Pull Request 7347`_ +* Track messages generated tool stdio tags in the database instead of just appending them + to tool standard error. Structured UI in reporting also. + (with help from `@bernt-matthias `__) + `Pull Request 7095`_ +* Track job script stdout and stderr separately from the tool's stdout and stderr in the database. + `Pull Request 7095`_ +* Support loading/using tools that are not in the install database + (with help from `@mvdbeek `__). + `Pull Request 7316`_, `Pull Request 8021`_ +* Git providers error reporting plugins + (thanks to `@selten `__). + `Pull Request 7485`_ +* Rename ``_future_expose_api`` to ``expose_api`` and ``expose_api`` to ``legacy_expose_api`` + (thanks to `@mvdbeek `__). + `Pull Request 7743`_ +* Add ``mtx`` datatype + (thanks to `@bebatut `__ and + `@nsoranzo `__). + `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_ +* Add ``geojson`` datatype + (thanks to `@bgruening `__). + `Pull Request 7773`_ +* Add shapefile (``shp``) datatype + (thanks to `@bgruening `__). + `Pull Request 7819`_ +* Add ``imgt.json`` datatype for IMGT immune system libraries + (thanks to `@jj-umn `__). + `Pull Request 7587`_ +* Add microarrays data types ``gpr`` and ``gal`` + (thanks to `@bensellak `__). + `Pull Request 7457`_ +* Add ``spaln`` database type + (thanks to `@pvanheus `__). + `Pull Request 7718`_ +* Redefine ``cel`` datatype + (thanks to `@bensellak `__). + `Pull Request 7514`_ +* Run most tests formerly ran on Travis on CircleCI + (with help from `@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 `__). + `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 `__). + `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 `__ and + `@mvdbeek `__). + `Pull Request 7205`_, `Pull Request 7844`_ +* Workflow editor accessibility fixes. + `Pull Request 7750`_ +* Python dependency updates and documentation fixes + (thanks to `@nsoranzo `__). + `Pull Request 7215`_, `Pull Request 7247`_, `Pull Request 7285`_, + `Pull Request 7740`_ +* Remove requirement pin on specific Sphinx version + (thanks to `@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 `__). + `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 `__ and + `@nsoranzo `_). + `Pull Request 7323`_, `Pull Request 7334`_ +* Fall back to binary comparison if BAM conversion fails during tool tests + (thanks to `@bernt-matthias `__). + `Pull Request 7342`_ +* Update ``area`` issue/PR labels + (thanks to `@nsoranzo `__). + `Pull Request 7344`_ +* Remove deprecated ``collect_outputs_from`` configuration option. + `Pull Request 7144`_ +* Remove ``ToolsController._rerun_tool()`` API method + (thanks to `@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 `__). + `Pull Request 7359`_ +* Do not default to ``DEV_WHEELS=1`` if no ``git`` is found + (thanks to `@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 `__). + `Pull Request 7428`_ +* Add hover styling to target tool in tool panel + (thanks to `@erasche `__). + `Pull Request 7437`_ +* Update Docker testing image + (thanks to `@mvdbeek `__). + `Pull Request 7439`_, `Pull Request 7187`_ +* Remove unused code + (thanks to `@nsoranzo `__). + `Pull Request 7445`_ +* Note `cannot import name _remove_dead_weakref` error and solution + (thanks to `@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 + `__ + (thanks to `@selten `__). + `Pull Request 7478`_ +* Add new metadata and data table tool validators + (thanks to `@bernt-matthias `__). + `Pull Request 7500`_ +* Updated documentation in ``admin/scaling.md`` for Systemd + (thanks to `@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 `__). + `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 `__). + `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 `__). + `Pull Request 7677`_ +* Add docs to OIDC backends configuration file. + `Pull Request 7691`_ +* Update ``CITATION`` to latest Galaxy update paper + (thanks to `@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 `__). + `Pull Request 7708`_ +* Add hostname to task message queues + (thanks to `@mvdbeek `__). + `Pull Request 7712`_ +* OIDC login buttons based on configuration + (thanks to `@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 `__). + `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 `__). + `Pull Request 7760`_ +* Update parameter_input type when changing parameter type + (thanks to `@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 `__). + `Pull Request 7827`_ +* Remove recursion from ``expand_nested_tokens()`` + (thanks to `@nsoranzo `__). + `Pull Request 7834`_ +* Allow composite upload if all non-optional files are selected + (thanks to `@mvdbeek `__). + `Pull Request 7872`_ +* Cleanup integration test configuration code. + `Pull Request 7874`_ +* Add "Reset" button to composite upload interface + (thanks to `@mvdbeek `__). + `Pull Request 7875`_ +* Add local namespaced resolver to default container resolvers + (thanks to `@mvdbeek `__). + `Pull Request 7896`_ +* Use node-watch instead of fs.watch to watch for db changes + (thanks to `@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 `__). + `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 `__). + `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 `__). + `Pull Request 7423`_ +* Remove biostar integrations. + (with help from `@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 `__). + `Pull Request 7276`_ +* Fix removing tags from a dataset previously only the first tag could be removed + (thanks to `@gtrack `__). + `Pull Request 7674`_, `Pull Request 7680`_ +* Fix displaying and editing SelectTagParameters in workflow editor + (thanks to `@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 `__). + `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 `__). + `Pull Request 7210`_ +* Verify and update .venv's node version. + `Pull Request 7220`_ +* Update ``use_interactive`` default in docs + (thanks to `@nsoranzo `__). + `Pull Request 7221`_ +* Fix hotdata method access. + `Pull Request 7256`_ +* Fix saving imported subworkflows + (thanks to `@mvdbeek `__). + `Pull Request 7262`_ +* Fix "occured" typo everywhere + (thanks to `@nsoranzo `__). + `Pull Request 7266`_ +* Fix flakey history import metadata test + (thanks to `@mvdbeek `__). + `Pull Request 7279`_ +* Do not skip the client build in dockerized selenium tests + (thanks to `@nsoranzo `__). + `Pull Request 7280`_ +* Fixes for the cluster documentation + (thanks to `@nsoranzo `__). + `Pull Request 7281`_ +* Fix ``ObjectNotFound`` exception when exporting an history + (thanks to `@abretaud `__). + `Pull Request 7286`_ +* Do not remove tools from other installed revisions when uninstalling TS + repo + (thanks to `@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 `__). + `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 `__). + `Pull Request 7340`_ +* Possible fix for fasta file never getting filesize + (thanks to `@Slugger70 `__). + `Pull Request 7374`_ +* Fix upload button style. + `Pull Request 7381`_ +* Fix link doc syntax + (thanks to `@galaxyproject `__). + `Pull Request 7388`_ +* Update application documentation + (thanks to `@nsoranzo `__). + `Pull Request 7391`_ +* Fix pie chart and portlet height in flexboxes. + `Pull Request 7396`_ +* Fix ``LocalShellRunner`` + (thanks to `@mvdbeek `__). + `Pull Request 7438`_ +* Use a lock on cleanup, expire_tool and cache_tool + (thanks to `@mvdbeek `__). + `Pull Request 7446`_ +* Fix loading workflows with steps without default label + (thanks to `@mvdbeek `__). + `Pull Request 7448`_ +* Remove broken configuration option tool_submission_burst + (thanks to `@mvdbeek `__). + `Pull Request 7449`_ +* Restore ``get_filename`` to ``galaxy.tools.verify:verify()`` + `Pull Request 7452`_ +* Fix documentation for statsd and uwsgi + (thanks to `@abretaud `__). + `Pull Request 7453`_ +* Fix hidden parameter use in workflows + (thanks to `@mvdbeek `__). + `Pull Request 7458`_ +* Fix syntax of XSD tool schema. + `Pull Request 7462`_ +* Fix workflow building typo + (thanks to `@mvdbeek `__). + `Pull Request 7472`_ +* Correct ``virtualenv`` download with no ``wget``/``curl`` + (thanks to `@hmenager `__). + `Pull Request 7476`_ +* Use a relative ``output.publicPath`` to avoid 404 errors when serving with a url + prefix + (thanks to `@abretaud `__). + `Pull Request 7481`_ +* Restrict loading of JSON files on the server via the workflow API to Galaxy + admins + (thanks to `@nsoranzo `__). + `Pull Request 7499`_ +* Fix warning message formatting in sharing controller + (thanks to `@mvdbeek `__). + `Pull Request 7504`_ +* Make sure ``temp_output_dir`` path is absolute + (thanks to `@nsoranzo `__). + `Pull Request 7517`_ +* Create directory before copying file there + (thanks to `@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 `__). + `Pull Request 7543`_ +* Extend reload test case logging + (thanks to `@mvdbeek `__). + `Pull Request 7547`_ +* Correct db-self handler assignment method + (thanks to `@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 `__). + `Pull Request 7584`_ +* Update cloud imports to adhere with cloudbridge interface changes. + `Pull Request 7586`_ +* Fix RStudio GIE + (thanks to `@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 `__). + `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 `__). + `Pull Request 7633`_ +* Fix float to int casting + (thanks to `@mvdbeek `__). + `Pull Request 7634`_ +* Adjust ``test_run_with_numeric_input_connection`` to extra line + (thanks to `@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 `__). + `Pull Request 7675`_ +* Detect errors using exit code for sort tool + (thanks to `@mvdbeek `__). + `Pull Request 7679`_ +* Fix ``format_source`` for implicit conversion inputs and ``fasta.gz`` upload + (thanks to `@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 `__). + `Pull Request 7696`_ +* Only check for exit code on actual sort command + (thanks to `@mvdbeek `__). + `Pull Request 7699`_ +* Update ``pytest-posgresql`` to 1.4.0, which removes a hard dependency on + ``psycopg2`` + (thanks to `@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 `__). + `Pull Request 7711`_ +* Copy ``tools_by_id`` before collecting dependency status + (thanks to `@mvdbeek `__). + `Pull Request 7713`_ +* Fix uWSGI startup with separate ini file under Python 3 + (thanks to `@nsoranzo `__). + `Pull Request 7716`_ +* Fix (re)starting Galaxy using paste, ``GALAXY_RUN_ALL=1`` and ``--wait`` + under macOS + (thanks to `@nsoranzo `__). + `Pull Request 7722`_ +* Fix check on links in ``CompressedFile.safemembers()`` + (thanks to `@nsoranzo `__). + `Pull Request 7723`_ +* Unpause dependent jobs when resuming jobs + (thanks to `@mvdbeek `__). + `Pull Request 7724`_ +* Commented-out cloudbridge requirement for the cloud/send tool. + `Pull Request 7727`_ +* Fix comments + (thanks to `@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 `__). + `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 `__). + `Pull Request 7800`_ +* Return HTTP 400 for `GET /api/datasets/nonexistent_id` + (thanks to `@nsoranzo `__). + `Pull Request 7806`_ +* Encode email messages using UTF-8 + (thanks to `@nsoranzo `__). + `Pull Request 7812`_ +* Fix nested macro/token expansion on Python 3 + (thanks to `@mvdbeek `__). + `Pull Request 7823`_ +* Possible fix for WSGI process issue `#7758 + `__ + (thanks to `@tmcgowan `__). + `Pull Request 7824`_ +* Fix ``InputValueWrapper`` gt/ge/lt/le comparisons + (thanks to `@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 `__). + `Pull Request 7853`_ +* Fix workflow extraction for jobs whose JobToDatasetOutputAssociation + references a discovered dataset + (thanks to `@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 `__). + `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 `__). + `Pull Request 7916`_ +* Fix community tags showing JSON file. + `Pull Request 7923`_ +* Fix upload of gzipped VCF files + (thanks to `@nsoranzo `__). + `Pull Request 7933`_ +* Fix documentation building + (thanks to `@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 `__). + `Pull Request 7983`_ +* Backport various upload encoding fixes from `#7995 `__ + (thanks to `@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 + diff --git a/doc/source/releases/19.05_announce.rst b/doc/source/releases/19.05_announce.rst index feb23a84dc9..7a2d1e9d979 100644 --- a/doc/source/releases/19.05_announce.rst +++ b/doc/source/releases/19.05_announce.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 `__ + 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 `__ for + pushing this effort. + +Get Galaxy +========== + +The code lives at `GitHub `__ and you should have `Git `__ 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 `__ for additional details regarding the source code locations. + +Release Notes +=========================================================== + +.. include:: 19.05.rst + :start-after: announce_start + +.. include:: _thanks.rst diff --git a/doc/source/releases/19.05_announce_user.rst b/doc/source/releases/19.05_announce_user.rst new file mode 100644 index 00000000000..dc4dfa1c960 --- /dev/null +++ b/doc/source/releases/19.05_announce_user.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 `__ has implemented a Galaxy Interactive +Environment for `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 `__ and + `@nsoranzo `__). + `Pull Request 7569`_, `Pull Request 7702`_, `Pull Request 7717`_ +* Add ``geojson`` and shapefile (``shp``) datatypes for better GIS data support + (thanks to `@bgruening `__). + `Pull Request 7773`_, `Pull Request 7819`_ +* Add ``imgt.json`` datatype for IMGT immune system libraries + (thanks to `@jj-umn `__). + `Pull Request 7587`_ +* Add microarrays data types ``gpr`` and ``gal`` + (thanks to `@bensellak `__). + `Pull Request 7457`_ +* Add ``spaln`` (space-efficient spliced alignment) database type + (thanks to `@pvanheus `__). + `Pull Request 7718`_ +* Redefine ``cel`` datatype + (thanks to `@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 `__). + `Pull Request 7205`_ +* Add general purpose expression tool + (thanks to `@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 diff --git a/doc/source/releases/19.05_prs.rst b/doc/source/releases/19.05_prs.rst new file mode 100644 index 00000000000..59ca8a5b131 --- /dev/null +++ b/doc/source/releases/19.05_prs.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 diff --git a/doc/source/releases/19.09_announce.rst b/doc/source/releases/19.09_announce.rst new file mode 100644 index 00000000000..7a051006b08 --- /dev/null +++ b/doc/source/releases/19.09_announce.rst @@ -0,0 +1,10 @@ + +=========================================================== +September 2019 Galaxy Release (v 19.09) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2019-09-02 + * Planned Release Date: 2019-09-23 diff --git a/doc/source/releases/images/19.05-favs.gif b/doc/source/releases/images/19.05-favs.gif new file mode 100644 index 00000000000..b0b4218da3d Binary files /dev/null and b/doc/source/releases/images/19.05-favs.gif differ diff --git a/doc/source/releases/images/19.05-input-collection.gif b/doc/source/releases/images/19.05-input-collection.gif new file mode 100644 index 00000000000..08073613628 Binary files /dev/null and b/doc/source/releases/images/19.05-input-collection.gif differ diff --git a/doc/source/releases/images/19.05-inputs.gif b/doc/source/releases/images/19.05-inputs.gif new file mode 100644 index 00000000000..3c4122e5162 Binary files /dev/null and b/doc/source/releases/images/19.05-inputs.gif differ diff --git a/doc/source/releases/images/19.05-wf-hints.gif b/doc/source/releases/images/19.05-wf-hints.gif new file mode 100644 index 00000000000..69fa3e69778 Binary files /dev/null and b/doc/source/releases/images/19.05-wf-hints.gif differ diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py index 901c50aeb66..154b4e34de5 100644 --- a/scripts/bootstrap_history.py +++ b/scripts/bootstrap_history.py @@ -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 `__)." % ( 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():