diff --git a/doc/source/releases/19.01.rst b/doc/source/releases/19.01.rst index d23ae82795f..99cf8df2d26 100644 --- a/doc/source/releases/19.01.rst +++ b/doc/source/releases/19.01.rst @@ -11,74 +11,73 @@ Enhancements .. major_feature -* Initial work on updating styles - `Pull Request 6422`_ -* Unified webpack4 - `Pull Request 6917`_ - -.. feature - -* Feature/isa data type - (thanks to `@phnmnl `__). - `Pull Request 5787`_ -* Cloud Authorization - `Pull Request 5903`_ -* Adds Aequatus visualisation plugin - (thanks to `@anilthanki `__). - `Pull Request 6484`_ -* Send data to cloud - `Pull Request 6583`_ -* Add utility function to create history entries - `Pull Request 6693`_ -* Give all model objects with an id a __repr__ that includes the id - `Pull Request 6757`_ -* Allow API import/export of format 2 workflows. - `Pull Request 6776`_ -* adding itp and mdp datatypes (for gromacs) - (thanks to `@simonbray `__). - `Pull Request 6812`_ -* Datatype pqr - (thanks to `@jj-umn `__). - `Pull Request 6816`_ -* nmrML data type. - (thanks to `@phnmnl `__). - `Pull Request 6903`_ -* Quick 'make all datasets private' implementation. - `Pull Request 6952`_ -* add RMA6 data type (MEGAN6 read-match archive) - (thanks to `@bernt-matthias `__). - `Pull Request 6962`_ -* datatype_fastg - (thanks to `@jj-umn `__). - `Pull Request 6987`_ -* Added support for chaining dynamic destinations - (thanks to `@nuwang `__). - `Pull Request 7006`_ -* Add styled loader vue component - (thanks to `@inkuzmin `__). - `Pull Request 7052`_ -* Add datatype for Mash Sketch files. - (thanks to `@dfornika `__). - `Pull Request 7087`_ -* Configurable job/workflow handler assignment methods - `Pull Request 7091`_ * Use singularity build / exec with biocontainers (thanks to `@mvdbeek `__). `Pull Request 7125`_ -* Perform job assignment using DB serialization techniques - `Pull Request 7129`_ - -.. enhancement - +* Adds Aequatus visualisation plugin + (thanks to `@anilthanki `__). + `Pull Request 6484`_ +* Integrate framework code for interfacing with cloud authorization providers. + `Pull Request 5903`_ +* Added support for chaining dynamic destinations + (thanks to `@nuwang `__). + `Pull Request 7006`_ +* Upgrade web client building to use `webpack `__ 4 + `Pull Request 6917`_ +* Implement 'make all datasets private' functionality. + `Pull Request 6952`_ +* Add datatype sniff button to edit dataset attributes page + (thanks to `@qiagu `__). + `Pull Request 7018`_ +* Overhaul handler assignment methods. + `Pull Request 7129`_, `Pull Request 7091`_ +* Add tool for sending dataset to the cloud. + `Pull Request 6583`_ +* Infrastructure/API Support for composite uploads/downloads. + `Pull Request 6844`_ +* Improvements to tool testing including aloowing tests without admin API keys. + (thanks to `@mvdbeek `__). + `Pull Request 7160`_, + `Pull Request 7199`_, `Pull Request 7167 `__ +* Add ISA-TAB datatype + (thanks to `@phnmnl `__). + `Pull Request 5787`_ +* Adding itp and mdp datatypes (for gromacs) + (thanks to `@simonbray `__). + `Pull Request 6812`_ +* Add pqr datatype + (thanks to `@jj-umn `__). + `Pull Request 6816`_ +* Add nmrML datatype + (thanks to `@phnmnl `__). + `Pull Request 6903`_ +* Add RMA6 datatype (MEGAN6 read-match archive) + (thanks to `@bernt-matthias `__). + `Pull Request 6962`_ +* Add fastg datatype + (thanks to `@jj-umn `__). + `Pull Request 6987`_ +* Add datatype for Mash Sketch files. + (thanks to `@dfornika `__). + `Pull Request 7087`_ +* Add JavaScript client library utility function to create history entries. + `Pull Request 6693`_ +* Give all model objects with an id a __repr__ that includes the id + `Pull Request 6757`_ +* Add styled loader vue component + (thanks to `@inkuzmin `__). + `Pull Request 7052`_ * Restore the ability to track jobs for a WF invocation step. `Pull Request 6559`_ -* improved grouping tool +* Improvements to the grouping tool (thanks to `@bernt-matthias `__). `Pull Request 6577`_ * Trim whitespace from data manager conf paths (thanks to `@pvanheus `__). `Pull Request 6682`_ -* Deprecate `size` attribute of `` and remove it from tools +* Track workflow step input definitions in our model. + `Pull Request 6850`_, `Pull Request 7103`_ +* Deprecate `size` attribute of `` and remove it from tools (thanks to `@nsoranzo `__). `Pull Request 6684`_ * Create container_resolvers_conf.xml.sample @@ -86,48 +85,32 @@ Enhancements `Pull Request 6700`_ * Update to latest galaxy-lib. `Pull Request 6709`_ -* Updates to OIDC backends default config +* Updates to OIDC backends default config. `Pull Request 6727`_ * Vue rewrite of admin data manager (local data) in steps (thanks to `@scrathat `__). `Pull Request 6729`_ -* Look up collection_type if collection_type_source is set - (thanks to `@mvdbeek `__). - `Pull Request 6732`_ -* pgcleanup.py enhancements - `Pull Request 6736`_ * Small local testing improvements (thanks to `@nsoranzo `__). `Pull Request 6738`_ -* Fill in needed state defaults when importing manually crafted workflows. - `Pull Request 6746`_ -* Add backrefs to mapped objects pointing at Dataset +* Add backrefs to mapped objects pointing at `Dataset`. `Pull Request 6754`_ -* Fixes for the upload row template +* Fixes for the upload row template. `Pull Request 6758`_ -* Disable file name text field after upload +* Disable file name text field after upload. `Pull Request 6762`_ -* Remove empty log messages - (thanks to `@galaxyproject `__). +* Remove empty log messages. `Pull Request 6763`_ -* Display input and output tool labels in the workflow editor - (thanks to `@mvdbeek `__). - `Pull Request 6770`_ -* Release issue scaffold tweaks +* Release issue scaffold tweaks. `Pull Request 6778`_ -* Warn job runner plugin writers not to emulate condor.py. +* Warn job runner plugin writers not to emulate `condor.py`. `Pull Request 6783`_ -* Add PB and EB to util.size_to_bytes +* Add `PB` and `EB` to `util.size_to_bytes` `Pull Request 6786`_ -* CLI plugin for LSF - (thanks to `@pcm32 `__). - `Pull Request 6788`_ -* Add a pgcleanup action to purge HDAs of purged histories +* Add a `pgcleanup.py` action to purge HDAs of purged histories. `Pull Request 6801`_ -* Support for Enhancements to gxformat2. - `Pull Request 6807`_ -* Support for Enhancements to gxformat2 (part II) - `Pull Request 6811`_ +* Various `pgcleanup.py` enhancements. + `Pull Request 6736`_, `Pull Request 6877`_ * Fix typos on "reserve_memory" / "reserve_cpu" (thanks to `@pvanheus `__). `Pull Request 6817`_ @@ -137,50 +120,39 @@ Enhancements * Add docs about running jobs in containers (thanks to `@pvanheus `__). `Pull Request 6820`_ -* Remove `trans` from OIDC-related types +* Remove `trans` from OIDC-related types. `Pull Request 6826`_ * Clarify code used in output tags (thanks to `@pvanheus `__). `Pull Request 6827`_ -* Convert user_is_admin and user_can_do_run_as to properties +* Convert `user_is_admin` and `user_can_do_run_as` to properties. `Pull Request 6835`_ -* Don't create jobs for inactive users +* Don't create jobs for inactive users. `Pull Request 6837`_ -* Replace deprecated assertEquals() method +* Replace deprecated `assertEquals()` method (thanks to `@nsoranzo `__). `Pull Request 6841`_ -* Infrastructure/API Support for Composite Uploads/Downloads - `Pull Request 6844`_ -* Updated GIE docs +* Improvements to GIE docs (thanks to `@thobalose `__). `Pull Request 6846`_ -* Indicate language in client docs to enable syntax highlighting. - (thanks to `@ic4f `__). +* Indicate language in client docs to enable syntax highlighting.. `Pull Request 6848`_ -* Track workflow step input definitions in our model. - `Pull Request 6850`_ * Fix panel header margins in history and tool panel `Pull Request 6854`_ * Small fixes (thanks to `@nsoranzo `__). `Pull Request 6861`_ -* Use card-styles for display applications, job manager and other admin views - `Pull Request 6868`_ * Datatype upload integration test and fixes (thanks to `@mvdbeek `__). `Pull Request 6869`_ -* Refactor pgcleanup.py and add new routines - `Pull Request 6877`_ * Use small button for editable text fields in history annotation `Pull Request 6878`_ * Improve k8s job error handling (thanks to `@ilveroluca `__). `Pull Request 6886`_ -* Catered for shlex.split(command_inject) and updated Neo4j IE to v3.1.9 +* Fixes and updates to the Neo4j GIE (thanks to `@thobalose `__). `Pull Request 6897`_ -* Fix style for legacy toolshed selection page - `Pull Request 6910`_ * Allow ``remove_value`` filter on data tables (thanks to `@nsoranzo `__). `Pull Request 6914`_ @@ -188,28 +160,25 @@ Enhancements (thanks to `@nsoranzo `__). `Pull Request 6921`_ * Be more precise with the job runner worker thread join timeout and improve - documentation + documentation. `Pull Request 6924`_ -* Add workflow step parameters to workflow editor (try 3) - `Pull Request 6925`_ -* Allocate more memory for selenium Python 3 client. - `Pull Request 6927`_ +* Selenium test enhancements and fixes. + `Pull Request 6927`_, `Pull Request 6982`_ * Small testing tweaks from the CWL branch. `Pull Request 6929`_ -* tests need to count data sets and collections +* Tests need to count data sets and collections (thanks to `@bernt-matthias `__). `Pull Request 6931`_ -* Eliminate some mutable defaults in populators.py. +* Eliminate some mutable defaults in `populators.py`. `Pull Request 6933`_ -* Default shed tool installation to database/shed_tools +* Default shed tool installation to `database/shed_tools`. `Pull Request 6937`_ -* Collection builder: add option to strip url prefix from pair names +* Add option to strip url prefix from pair names to collection builder (thanks to `@shiltemann `__). `Pull Request 6943`_ -* Small API Workflow Test Improvements. +* Small API workflow test improvements. `Pull Request 6954`_ -* Switch from PhantomJS to Chrome Headless for unit tests - (thanks to `@Nerdinacan `__). +* Switch from PhantomJS to Chrome Headless for unit tests. `Pull Request 6959`_ * Added a metadata element to the biom1 datatype (thanks to `@Slugger70 `__). @@ -217,81 +186,67 @@ Enhancements * Update locale.js (thanks to `@istevenshen `__). `Pull Request 6974`_ -* Use virtualenv when conda is on PATH +* Use `virtualenv` when `conda` is on `PATH` (thanks to `@mvdbeek `__). `Pull Request 6975`_ -* changed exit code and regex parsing +* Improvements to exit code and regex parsing (thanks to `@bernt-matthias `__). `Pull Request 6977`_ -* optimize images with optipng +* Optimize images with optipng (thanks to `@bgruening `__). `Pull Request 6980`_ -* List tags as attribute of TestCollection +* Fix tool XSD to list tags as attribute of `TestCollection` (thanks to `@mvdbeek `__). `Pull Request 6983`_ -* Apply new styling theme to workflow editor - `Pull Request 6985`_ * Use ``detect_errors="exit_code"`` in ``__SET_METADATA__`` tool (thanks to `@nsoranzo `__). `Pull Request 6989`_ -* Don't mount external /tmp for tests. +* Don't mount external `/tmp` for tests. `Pull Request 6990`_ -* Upgrade nodeenv's nodejs to 10.13.0 LTS +* Upgrade nodeenv's nodejs to 10.13.0 LTS. `Pull Request 6991`_ -* Fix broken links on Job Configuration page (documentation) - (thanks to `@ic4f `__). +* Fix broken links on Job Configuration page. `Pull Request 6992`_ * Allow rules module override and refactor submodule imports (thanks to `@nuwang `__). `Pull Request 6993`_ -* external_runner: load json template first +* Fix external_runner to load json template first (thanks to `@bernt-matthias `__). `Pull Request 6995`_ -* drmaa: soft catch of external runner fails +* CLI plugin for `LSF `__ + (thanks to `@pcm32 `__), `Pull Request 7007`_ + `Pull Request 6788`_ +* A new UNIVA extension to the DRMAA job runner + (thanks to `@bernt-matthias `__). + `Pull Request 7004`_, `Pull Request 7161`_ +* DRMAA fix to soft catch of external runner fails (thanks to `@bernt-matthias `__). `Pull Request 6997`_ -* A new runner for DRMAA (currently UNIVA) - (thanks to `@bernt-matthias `__). - `Pull Request 7004`_ -* Replace global Galaxy references with galaxy singleton accessor/setter - (thanks to `@Nerdinacan `__). +* Replace global Galaxy references with galaxy singleton accessor/setter. `Pull Request 7005`_ * Workflow test case - test marking inputs as outputs. `Pull Request 7016`_ -* Fix login and registration form appearance - `Pull Request 7017`_ -* Add datatype sniff button to edit dataset attributes page - (thanks to `@qiagu `__). - `Pull Request 7018`_ -* File-based Workflow Editor - `Pull Request 7019`_ * Expose published workflows through API (thanks to `@frederikcoppens `__). `Pull Request 7020`_ * Pass a ``JobWrapper`` instead of a ``Job`` to ``stop_job()`` methods (thanks to `@nsoranzo `__). `Pull Request 7023`_ -* Provide element_identifier attribute in DatsetCollectionWrapper +* Fix `element_identifier` access (thanks to `@mvdbeek `__). `Pull Request 7031`_ * Avoid replacing data-referenced input values with default values `Pull Request 7043`_ -* doc: updated error parsing docs +* Udate error parsing docs (thanks to `@bernt-matthias `__). `Pull Request 7049`_ -* Added resubmit handlers on Pulsar connection failures +* Add resubmit handlers on Pulsar connection failures (thanks to `@nuwang `__). `Pull Request 7053`_ -* add new item to the help menu +* Add new "Help" item to the help menu. `Pull Request 7054`_ -* Eliminate dependency on make for automatic client build +* Eliminate dependency on make for automatic client build. `Pull Request 7060`_ -* Make tags more colourful - (thanks to `@erasche `__). - `Pull Request 7072`_ -* Follow-up on `#7070 `__ - (thanks to `@nsoranzo `__). - `Pull Request 7079`_ * Remove legacy job handling hacks. `Pull Request 7082`_ * De-couple objectstore abstraction from XML. @@ -303,18 +258,17 @@ Enhancements * Run singularity in silent mode (thanks to `@mvdbeek `__). `Pull Request 7104`_ -* Eliminate unused code block in output_collect. +* Eliminate unused code block in `output_collect`. `Pull Request 7109`_ -* Add to_dict() to ObjectStores. +* Add `to_dict()` to ObjectStores. `Pull Request 7110`_ -* Enable tagging+annotation of jobs regardless of state - (thanks to `@ic4f `__). +* Enable tagginga and annotation of jobs regardless of state. `Pull Request 7115`_ -* Remove unused __collected_datasets__ from tool hook dict. +* Remove unused `__collected_datasets__` from tool hook dict. `Pull Request 7123`_ -* Adds a vue component to display tool errors in the admin panel +* Add a vue component to display tool errors in the admin panel. `Pull Request 7124`_ -* Update help text as per suggestion from CWunder +* Update help text in `filter_from_file` tool. (thanks to `@pvanheus `__). `Pull Request 7127`_ * Remove unneeded session flushes and adds when discovering outputs. @@ -322,61 +276,32 @@ Enhancements * Drop tools without installable dependencies (thanks to `@mvdbeek `__). `Pull Request 7136`_ -* Small de-duplication cleanups to galaxy.jobs +* Small de-duplication cleanups to `galaxy.jobs` `Pull Request 7155`_ -* Unprivileged remote tool tests - (thanks to `@mvdbeek `__). - `Pull Request 7160`_ -* doc: added missing docs for new UNIVA runner - (thanks to `@bernt-matthias `__). - `Pull Request 7161`_ -* Add error listener for input elements - `Pull Request 7183`_ -* Backport `#7167 `__ - - interactor improvements - (thanks to `@mvdbeek `__). - `Pull Request 7199`_ -* Properly deal with missing tools in workflows - (thanks to `@mvdbeek `__). - `Pull Request 7227`_ -* Backport `#7183 `__ - input element listener - (thanks to `@mvdbeek `__). - `Pull Request 7229`_ -* Stop tool migrations checking by default... +* Improve tool form client to add error listener for input elements. + `Pull Request 7183`_, `Pull Request 7229`_ +* Stop tool migrations checking by default (was broken in some cases). `Pull Request 7275`_ - -.. small_enhancement - -* Remove legacy tool form styles from structure history view and admin tables - `Pull Request 6790`_ -* Replace trans with session and request in psa Storage +* Replace `trans` with `session` and `request` in PSA Storage. `Pull Request 6838`_ * Share ssh key generation across tests (thanks to `@mvdbeek `__). `Pull Request 6865`_ -* Specify POST and GET actions for cloudauthz API actions +* Specify `POST` and `GET` actions for cloudauthz API actions. `Pull Request 6876`_ -* prevent sanitized history names being saved in database +* Prevent sanitized history names being saved in database. `Pull Request 6898`_ -* Refactor cloud "Upload" > "Get" +* Rework language in cloud data fetch tool from "Upload" to "Get" `Pull Request 6899`_ * Refactor collection mapping workflows toward independence from tools. `Pull Request 6911`_ -* Refactor workflow editor styles and move from mako to css - `Pull Request 6967`_ -* Normalized jquery bundle - (thanks to `@Nerdinacan `__). +* Normalized jquery bundle. `Pull Request 6970`_ -* Replaced jStorage with store - (thanks to `@Nerdinacan `__). +* Replaced jStorage with store. `Pull Request 6994`_ -* Fix handling of forgotten LSF jobs in cli - (thanks to `@pcm32 `__). - `Pull Request 7007`_ * Remove ``sudo: false`` from .travis.yml, it will stop being supported soon `Pull Request 7035`_ -* Fixes state-change animations causing 'block' display +* Fixes state-change animations causing 'block' display. `Pull Request 7122`_ @@ -388,10 +313,10 @@ Fixes .. bug -* Allow schema to validate +* Fixes to allow config schema to validate (thanks to `@erasche `__). `Pull Request 5919`_ -* Patch update.sh to address dependency update issues on a macOS. +* Patch `update.sh` to address dependency update issues on a macOS. `Pull Request 6694`_ * Fix wrong version being returned if requested version doesn't exist (thanks to `@mvdbeek `__). @@ -414,27 +339,20 @@ Fixes `Pull Request 6843`_ * Revert selective metadata flushing - breaks multiple uploads/outputs. `Pull Request 6858`_ -* Use fluid container for slider to get full width - `Pull Request 6870`_ * prevent double sanitizing history name when renaming (thanks to `@almahmoud `__). `Pull Request 6871`_ -* Fix rule editor element alignment +* Fix rule editor element alignment. `Pull Request 6874`_ * Fix styleguide; change permissions on jstree.scss. - (thanks to `@ic4f `__). `Pull Request 6879`_ -* Fix selenium test selectors for alert messages - `Pull Request 6881`_ -* Username filtering for published workflows +* Fix username filtering for published workflows (thanks to `@almahmoud `__). `Pull Request 6882`_ -* Align toolshed makos used in the admin panel, fix slider height +* Align toolshed makos used in the admin panel, fix slider height. `Pull Request 6883`_ -* Improve resilience on handling sharing attributes +* Improve resilience on handling sharing attributes. `Pull Request 6884`_ -* Fixes for built-in Scatterplot plugin - `Pull Request 6905`_ * Update Bug Reports docs to use YAML syntax (thanks to `@nsoranzo `__). `Pull Request 6909`_ @@ -469,9 +387,6 @@ Fixes * Fix traceback when starting under Python3 with ``galaxy.ini`` (thanks to `@nsoranzo `__). `Pull Request 6978`_ -* Update test/selenium_tests/test_library_contents.py - (thanks to `@Nerdinacan `__). - `Pull Request 6982`_ * Fix charts entrypoint for compatibility with newer chunk changes. `Pull Request 6984`_ * reclaim ownership for failed jobs @@ -513,14 +428,13 @@ Fixes * Update ``galaxy.yml.sample`` and ``galaxy_options.rst`` (thanks to `@nsoranzo `__). `Pull Request 7064`_ -* Fix link to requirements.txt - (thanks to `@ic4f `__). +* Fix link to requirements.txt. `Pull Request 7065`_ * Improved parsing of sizes (bytes) (thanks to `@bernt-matthias `__). `Pull Request 7067`_ -* downgrade bdbag, 1.5.0 requires python:>=2.7.9 - `Pull Request 7070`_ +* Downgrade bdbag - 1.5.0 requires python:>=2.7.9 + `Pull Request 7070`_, `Pull Request 7079`_ * Fix process key (thanks to `@mvdbeek `__). `Pull Request 7071`_ @@ -532,9 +446,6 @@ Fixes * Fix toolshed repository error display (thanks to `@jvanbraekel `__). `Pull Request 7080`_ -* Fix hashing, AND was not the right operation - (thanks to `@erasche `__). - `Pull Request 7081`_ * Fix via refactor set_metadata so more output metadata pruned properly. `Pull Request 7084`_ * Replace `credentials` with `authz_id` @@ -546,13 +457,11 @@ Fixes `Pull Request 7096`_ * Client readme updates. `Pull Request 7102`_ -* Fix migration 0146 column selection on downgrade - `Pull Request 7103`_ * Don't write outputs to object store twice. `Pull Request 7111`_ * Fix `make client-watch` extra error message. `Pull Request 7113`_ -* Properly escape history names in scratchbook titles +* Properly escape history names in scratchbook titles. `Pull Request 7114`_ * Fix activation of ``_galaxy_`` conda env (thanks to `@nsoranzo `__). @@ -561,27 +470,20 @@ Fixes `Pull Request 7120`_ * Fixes and tests for collecting extra files for discovered datasets. `Pull Request 7131`_ -* Address CORS issue in toolshed iframe handlers - (thanks to `@Nerdinacan `__). +* Address CORS issue in toolshed iframe handlers. `Pull Request 7135`_ * Use regular js-event handling instead of jquery for uploader `Pull Request 7145`_ * Fixes toolshed and reports styling that was previously applied at the… `Pull Request 7146`_ -* Correct code error in 'build job runner' tutorial - (thanks to `@ic4f `__). +* Correct code error in 'build job runner' tutorial. `Pull Request 7148`_ -* added store library to exported libs in bundleEntries - (thanks to `@Nerdinacan `__). +* Added store library to exported libs in bundleEntries. `Pull Request 7149`_ -* Follow-up on handling connectable and collapsible parameters in workflows - `Pull Request 7150`_ * Fix dataset discovery for YAML/dictified tools. `Pull Request 7152`_ * Fix for parsing collection outputs for YAML/dictified tools. `Pull Request 7153`_ -* Do not use default values for runtime values in workflow execution form - `Pull Request 7157`_ * Lower provider name (thanks to `@machristie `__). `Pull Request 7166`_ @@ -599,16 +501,16 @@ Fixes `Pull Request 7174`_ * Prevent XSS on toolshed when browsing repo changeset `Pull Request 7180`_ -* Fix hda accessibility check in Page's renderForSave name fetching +* Fix HDA accessibility check in Page's renderForSave name fetching `Pull Request 7181`_ -* Fix workflow parameter test case? +* Fix for workflow parameter test case. `Pull Request 7188`_ -* fix library dataset permission API +* Fixes for library dataset permission API. `Pull Request 7190`_ * Properly document handler assignment method configuration and fix logging - configuration docs + configuration docs. `Pull Request 7191`_ -* Re-enable script staging +* Re-enable script staging. `Pull Request 7196`_ * Fix error in view_tool_metadata (thanks to `@mvdbeek `__). @@ -616,7 +518,7 @@ Fixes * Data library: fix tag_using_filenames not properly converted to bool (thanks to `@abretaud `__). `Pull Request 7204`_ -* Swap to normal event bindings for multipanel drag/drop. +* Fix GUI wap to normal event bindings for multipanel drag/drop. `Pull Request 7218`_ * Fix displaying tool help images on python 3 (thanks to `@mvdbeek `__). @@ -627,24 +529,21 @@ Fixes * Interval datatype fixes (thanks to `@mvdbeek `__). `Pull Request 7237`_ -* strip() text when parsing xml +* `strip()` text when parsing xml (thanks to `@mvdbeek `__). `Pull Request 7252`_ -* Fix install operation in installed_repository_grid +* Fix install operation in `installed_repository_grid` (thanks to `@mvdbeek `__). `Pull Request 7253`_ -* Not all workflow outputs have a UUID - (thanks to `@mvdbeek `__). - `Pull Request 7258`_ * Update sqlalchemy-migrate requirement to 0.12.0 (thanks to `@nsoranzo `__). `Pull Request 7265`_ -* Fix _.escape typo in toolshed group detail view +* Fix `_.escape` typo in toolshed group detail view. `Pull Request 7267`_ * Fix installing tools via tool_id (thanks to `@mvdbeek `__). `Pull Request 7277`_ -* Remove errant space in intermine_simple_display.loc.sample +* Remove errant space in `intermine_simple_display.loc.sample`. `Pull Request 7298`_ .. github_links diff --git a/doc/source/releases/19.01_announce.rst b/doc/source/releases/19.01_announce.rst index 260fcc121d6..638b10acc55 100644 --- a/doc/source/releases/19.01_announce.rst +++ b/doc/source/releases/19.01_announce.rst @@ -8,14 +8,44 @@ January 2019 Galaxy Release (v 19.01) Highlights =========================================================== -**Feature1** - Feature description. +**Revised UI Style** + The Galaxy stylesheet has been substantially reworked resulting in the largest visual + refresh to Galaxy in years. -**Feature2** - Feature description. + `Pull Request 6422`_, `Pull Request 6910`_, `Pull Request 6881`_, + `Pull Request 6967`_, `Pull Request 6790`_, `Pull Request 6868`_, + `Pull Request 7017`_, `Pull Request 6985`_, `Pull Request 6870`_, + `Pull Request 6905`_ + +**More Colorful Tags** + Use consistently hashed randomized colors for history dataset name tags to allow increase visual + distinction between tags making it easier to track data flow in complex histories. + Thanks to `@erasche `__. + `Pull Request 7072`_, `Pull Request 7081`_ + +**Extensive Workflow Enhancements (continued)** + 18.09 featured a bunch of important and diverse fixes and enhancements to workflows on + both the frontend and backend. That progress continues in 19.01. + + The workflow editor now features explicit step parameter nodes for non-file data (integers, + strings, booleans, etc) and the ability to connect these to all tool inputs - not just files + (`Pull Request 6925`_, `Pull Request 7150`_). + The YAML-based Galaxy Format 2 workflow language is now included in Galaxy as a beta option + and allows import and export of human readable workflows (`Pull Request 6776`_, `Pull Request 6811`_, + `Pull Request 6807`_, `Pull Request 6746`_) as well as extensions to allow Galaxy + to serve as a file editor for such workflows (`Pull Request 7019`_). The workflow editor features + more helpful labels on inputs and outputs (`Pull Request 6770`_) and important fixes including + logic for connecting collections (`Pull Request 6732`_) and dealing with missing tools + (`Pull Request 7227`_, `Pull Request 7258`_). The workflow run form now deals with default + values more correctly (`Pull Request 7157`_). + +**Support for Singularity Biocontainers** + Galaxy can now be configured to fetch `Biocontainers `__ automatically + for `Singularity `__ enabled job destinations. Previously this + would happen automatically for Docker containers but not Singularity containers. Thanks to + `@mvdbeek `__. + `Pull Request 7125`_ -**Feature3** - Feature description. Get Galaxy ========== diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst index d23874192ab..1a59eb20ee8 100644 --- a/doc/source/releases/index.rst +++ b/doc/source/releases/index.rst @@ -4,6 +4,7 @@ Releases .. toctree:: :maxdepth: 1 + 19.01_announce 18.09_announce 18.05_announce 18.01_announce