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Embellish 18.09 release notes

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Nicola Soranzo
2018-10-11 17:51:07 +01:00
parent d33006cf33
commit d42b899b78
2 changed files with 68 additions and 66 deletions
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doc/source/releases/18.09.rst
+66 -64
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@@ -23,7 +23,7 @@ Enhancements
`Pull Request 6201`_
* Enable automatic reload of dynamic job rules on change
`Pull Request 6215`_
* added daa (diamond alignment) datatype
* Added daa (diamond alignment) datatype
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 6313`_
* Allows DatasetMatcher to use multiple filters
@@ -42,13 +42,13 @@ Enhancements
.. enhancement
* Add a FilterEmptyDatasetsTool and allow filtering tools to apply to
* Add a ``FilterEmptyDatasetsTool`` and allow filtering tools to apply to
arbitrary collection structures
(thanks to `@Mataivic <https://github.com/Mataivic>`__).
`Pull Request 5640`_
* Minor enhancements for cgroup metrics
`Pull Request 5993`_
* Optimize safe_walk to call realpath a lot less for typical calls...
* Optimize ``safe_walk`` to call ``realpath`` a lot less for typical calls
`Pull Request 5995`_
* Documentation and typo fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -75,10 +75,10 @@ Enhancements
`Pull Request 6122`_
* Sharing.vue bootstrapping and a bugfix
`Pull Request 6132`_
* Use from_work_dir in CONVERTER_fasta_to_fai
* Use ``from_work_dir`` in ``CONVERTER_fasta_to_fai``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6135`_
* Make workflow editor toolTitle link include the tools description
* Make workflow editor ``toolTitle`` link include the tools description
(thanks to `@scrathat <https://github.com/scrathat>`__).
`Pull Request 6142`_
* Small fixes and small refactorings toward reuse in CWL branch (retry)
@@ -95,7 +95,7 @@ Enhancements
`Pull Request 6206`_
* Some more upload/sniff tests.
`Pull Request 6212`_
* Test element_identifier usage with single data parameters, in repeat/cond.
* Test ``element_identifier`` usage with single data parameters, in repeat/cond.
`Pull Request 6213`_
* Charts filename download fix
`Pull Request 6216`_
@@ -112,10 +112,10 @@ Enhancements
* Fix collection mapping to allow subcollection mapping over multi-data
inputs.
`Pull Request 6255`_
* Use Mercurial CLI instead of API for archive_repository_revision()
* Use Mercurial CLI instead of API for ``archive_repository_revision()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6273`_
* Consolidate use of get_repo_for_repository() and clone_repository()
* Consolidate use of ``get_repo_for_repository()`` and ``clone_repository()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6277`_
* Index select2 field values
@@ -140,7 +140,7 @@ Enhancements
* Replace unmaintained pycrypto dependency with pycryptodome
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6324`_
* Add py34-first_startup to Travis and default tox tests
* Add py34-first_startup to Travis and default tox tests
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6325`_
* Visualization static staging
@@ -158,7 +158,7 @@ Enhancements
* Create client build hash on toplevel concurrent watch in addition to
individual builds.
`Pull Request 6381`_
* change a file read to use with statement
* Change a file read to use ``with`` statement
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 6388`_
* Client library upgrades.
@@ -185,10 +185,10 @@ Enhancements
* Run workflows from published workflows menu
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6428`_
* fix a few tool_deps test errors
* Fix a few tool_deps test errors
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 6436`_
* replace the administration header in admin menu with version
* Replace the administration header in admin menu with version
`Pull Request 6440`_
* Add zoom support to workflow editor.
`Pull Request 6441`_
@@ -220,7 +220,7 @@ Enhancements
`Pull Request 6480`_
* Use bootstrap vue classes for workflow import form
`Pull Request 6489`_
* small improvement to the too xsd docs regarding discovered_datasets
* Small improvement to the tool xsd docs regarding ``discovered_datasets``
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 6490`_
* Implement ``group:`` tags (toward multi-factor analysis with group tagging)
@@ -229,7 +229,7 @@ Enhancements
`Pull Request 6499`_
* Integrate tagging into the rule builder.
`Pull Request 6500`_
* Cache chrom_info generation when mapping over collections.
* Cache ``chrom_info`` generation when mapping over collections.
`Pull Request 6515`_
* More optimized HID generation - in one commit instead of two.
`Pull Request 6516`_
@@ -239,7 +239,7 @@ Enhancements
`Pull Request 6523`_
* Use cached database identity to avoid many DB requests when creating jobs.
`Pull Request 6524`_
* Removal of unreachable exit()
* Removal of unreachable ``exit()``
`Pull Request 6529`_
* Optimizations for history copying.
`Pull Request 6531`_
@@ -274,7 +274,7 @@ Enhancements
* Add download option to workflow editor menu
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 6596`_
* add trr datatype
* Add trr datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 6597`_
* Refresh an expired OIDC ID token
@@ -282,7 +282,7 @@ Enhancements
* Handle driver shutdown, show all tests in pytest
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6608`_
* add dcd datatype for molecular dynamics
* Add dcd datatype for molecular dynamics
(thanks to `@chrisbarnettster <https://github.com/chrisbarnettster>`__).
`Pull Request 6613`_
* Py3 testing cleanups
@@ -295,7 +295,7 @@ Enhancements
`Pull Request 6628`_
* Update some run_tests.sh docs for recent changes.
`Pull Request 6629`_
* Remove check_python_dependencies job from Travis
* Remove ``check_python_dependencies`` job from Travis
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6630`_
* Testing framework improvements
@@ -303,7 +303,7 @@ Enhancements
`Pull Request 6632`_
* Optimize tool execution permission checking
`Pull Request 6635`_
* document config for sniffing compressed files, enable by default
* Document config for sniffing compressed files, enable by default
`Pull Request 6641`_
* Small Optimizations to Adding Datasets to History
`Pull Request 6644`_
@@ -348,7 +348,7 @@ Enhancements
`Pull Request 6011`_
* This strips the graphite-specific middleware
`Pull Request 6018`_
* Make `interactor._{get,post,put,...}` less repetitive
* Make ``interactor._{get,post,put,...}`` less repetitive
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6070`_
* Workflow and remote-user related refactoring and a bug fix
@@ -378,7 +378,7 @@ Enhancements
unit tests
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6446`_
* py3: fixes test_DatasetManager.py:DatasetManagerTestCase
* py3: fixes ``test_DatasetManager.py:DatasetManagerTestCase``
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6452`_
* Fix test_toolbox for python 3
@@ -441,16 +441,16 @@ Fixes
.. bug
* fix bowtie2 link
* Fix bowtie2 link
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 6009`_
* Fix some imports
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6014`_
* Fix JobWrapper.get_destination_configuration() so that it actually checks
the JobDestination params
* Fix ``JobWrapper.get_destination_configuration()`` so that it actually checks
the ``JobDestination`` params
`Pull Request 6087`_
* fixed small typo
* Fixed small typo
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 6094`_
* History click-to-rename bugfix
@@ -460,14 +460,14 @@ Fixes
* cutWrapper: fix wrong path in error message
(thanks to `@abretaud <https://github.com/abretaud>`__).
`Pull Request 6211`_
* Fix optional="True" inputs
* Fix ``optional="True"`` inputs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6222`_
* Two minor aliases for (exterior) backwards compatibility, minor badge tweaks
`Pull Request 6226`_
* Fix broken collection_type_source tool and test.
`Pull Request 6227`_
* Add io_details and link_details in api tools doc
* Add ``io_details`` and ``link_details`` in api tools doc
(thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
`Pull Request 6228`_
* Fix file type error in RuleCollectionBuilder.
@@ -485,7 +485,7 @@ Fixes
`Pull Request 6244`_
* Check context for textable mode of select fields
`Pull Request 6251`_
* Mapping over from_param fixes
* Mapping over ``from_param`` fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6253`_
* Fix history shared with me 'view' link
@@ -507,10 +507,10 @@ Fixes
* Fixes for phenotype association tools
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6269`_
* fix link to workflow list
* Fix link to workflow list
(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
`Pull Request 6270`_
* Fix help text for renaming operation in workflows
* Fix help text for renaming operation in workflows
`Pull Request 6274`_
* Various fixes for mapping over collections
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -540,25 +540,26 @@ Fixes
* Increase sleep if encountering (DB locking) exception
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6304`_
* Fix undefined success_message
* Fix undefined ``success_message``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6316`_
* Allow #if $datasets #end if pattern for file lists
* Allow ``#if $datasets #end if`` pattern for file lists
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6317`_
* Fix target update for rule collection builder after input selection
(thanks to `@scrathat <https://github.com/scrathat>`__).
`Pull Request 6326`_
* Added missing level fatal_oom to xsd
* Added missing level ``fatal_oom`` to galaxy.xsd
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 6341`_
* Update description for installing pbs-python
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6345`_
* Prevent throwing an exception if a dataset doesn't exist (and never w…
* Prevent throwing an exception if a dataset doesn't exist (and never will) due
to a job error
(thanks to `@dpryan79 <https://github.com/dpryan79>`__).
`Pull Request 6349`_
* Fix the --log-file option in the job handlers
* Fix the ``--log-file`` option in the job handlers
(thanks to `@dpryan79 <https://github.com/dpryan79>`__).
`Pull Request 6351`_
* grt - wrap every write in try-except
@@ -578,23 +579,23 @@ Fixes
`Pull Request 6378`_
* Revert "Remove bam to bai converter"
`Pull Request 6385`_
* fix data_column cast error when multiple is false
* Fix ``data_column`` cast error when multiple is false
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 6389`_
* Optimize setting large numbers of HIDs for collection outputs.
`Pull Request 6394`_
* Fixing <conditional> XML example
* Fixing ``<conditional>`` XML example
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
`Pull Request 6399`_
* Fix positioning for tool search box.
`Pull Request 6416`_
* removing binary as input for python compatibility
* Removing binary as input for python compatibility
(thanks to `@eslerm <https://github.com/eslerm>`__).
`Pull Request 6417`_
* GCC2018 python3 unit-test fixes
(thanks to `@ycgong <https://github.com/ycgong>`__).
`Pull Request 6419`_
* python 3 porting
* Python 3 porting
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6420`_
* Fix panel drag resize.
@@ -610,15 +611,15 @@ Fixes
* Do not encode a rendered Mako template
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6431`_
* decode potential encoded id
* Decode potential encoded id
`Pull Request 6433`_
* fixes test/unit/jobs/test_job_output_checker.py; strange default?
* Fixes test/unit/jobs/test_job_output_checker.py; strange default?
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6438`_
* py3 compat: fixes test_vcf, test_sniff_compressed*
(thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
`Pull Request 6442`_
* fix TS: resolve missing closing div and three extra closing divs
* Fix TS: resolve missing closing div and three extra closing divs
`Pull Request 6445`_
* Fix all remaining unit tests under Python 3
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -642,7 +643,7 @@ Fixes
`Pull Request 6481`_
* Fix for show params server error
`Pull Request 6486`_
* Fix ftp_upload_purge in galaxy.yml
* Fix ``ftp_upload_purge`` in galaxy.yml
(thanks to `@phac-nml <https://github.com/phac-nml>`__).
`Pull Request 6494`_
* Fix resume from history panel
@@ -655,12 +656,12 @@ Fixes
`Pull Request 6503`_
* Return a json blob containing redirect URI in OIDC login controller
`Pull Request 6517`_
* Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
* Fix warning in ``CONVERTER_bam_to_bigwig_0`` and ``CONVERTER_sam_to_bigwig_0``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6528`_
* Fix dataset copy tags
`Pull Request 6532`_
* Fix to_dict with io_details=True for tools with collection outputs.
* Fix ``to_dict`` with ``io_details=True`` for tools with collection outputs.
`Pull Request 6538`_
* Fix "filter empty" rule in Python rule handling framework.
`Pull Request 6542`_
@@ -671,9 +672,9 @@ Fixes
* Remove the sharing of toolbox in GRT
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 6553`_
* Restore log_destination = stdout configuration option.
* Restore ``log_destination = stdout`` configuration option.
`Pull Request 6555`_
* Many selenium tests fixes for recent dev changes.
* Many Selenium tests fixes for recent dev changes.
`Pull Request 6557`_
* More Selenium test fixes.
`Pull Request 6562`_
@@ -700,15 +701,15 @@ Fixes
* Fix Location of Plugin Static Content In Documentation for 18.05
(thanks to `@phac-nml <https://github.com/phac-nml>`__).
`Pull Request 6602`_
* Fix cron/build_chrom_db.py and update UCSC builds
* Fix cron/build_chrom_db.py and update UCSC builds
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6623`_
* Fix for workflow extraction cleanup routine.
`Pull Request 6636`_
* row ids that are all numeric become ints...
* Row ids that are all numeric become ints...
(thanks to `@bwlang <https://github.com/bwlang>`__).
`Pull Request 6639`_
* Allow running scripts/galaxy-main without Galaxy on sys.path
* Allow running ``scripts/galaxy-main`` without Galaxy on ``sys.path``
`Pull Request 6642`_
* Fix color of workflow panel background
`Pull Request 6643`_
@@ -716,7 +717,7 @@ Fixes
`Pull Request 6647`_
* Strip API keys option from admin panel left side
`Pull Request 6651`_
* Fix get_fileobj() call in Eland.set_meta()
* Fix ``get_fileobj()`` call in ``Eland.set_meta()``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 6659`_
* Update bx-python to 0.8.2
@@ -732,13 +733,13 @@ Fixes
`Pull Request 6703`_
* Catch additional permutations of Slurm cgroup creation warnings
`Pull Request 6705`_
* unquote the tool_version in the tools API
* Unquote the ``tool_version`` in the tools API
`Pull Request 6707`_
* Fix active highlight
`Pull Request 6725`_
* Badge default fix
`Pull Request 6726`_
* remove html tags and newlines from the help text
* Remove html tags and newlines from the help text
`Pull Request 6728`_
* Fix missing tests for data source sniffing.
`Pull Request 6733`_
@@ -748,38 +749,39 @@ Fixes
* Fix and test anonymous error reports
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6742`_
* fix favicon.ico for uwsgi deployments
* Fix favicon.ico for uWSGI deployments
`Pull Request 6743`_
* dispose of dataset tooltip when the delete is being called
* Dispose of dataset tooltip when the delete is being called
`Pull Request 6744`_
* Generic tooltip hide for onclick faIconButtons
`Pull Request 6745`_
* Fix page editor height for flex panels.
`Pull Request 6747`_
* Use mapped-over collectionType when inferring collectionType through …
* Use mapped-over ``collectionType`` when inferring ``collectionType`` through
``format_source``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6749`_
* Catch any failures encountered while pausing/stopping jobs whose inputs are
terminal and non-ok
`Pull Request 6755`_
* Don't attempt len(None), ensure stdout/stderr are strings in
Job(Like).set_streams().
* Don't attempt ``len(None)``, ensure stdout/stderr are strings in
``Job(Like).set_streams()``.
`Pull Request 6765`_
* Increase the maximum number of stderr lines that will be scanned for slurm
warnings
`Pull Request 6766`_
* backport of: Resilience of success message handling
* Backport of: Resilience of success message handling
`Pull Request 6768`_
* Use UserRoleAssociation to get private roles
* Use ``UserRoleAssociation`` to get private roles
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6771`_
* Update name of Workflow when updating StoredWorkflow name
* Update name of ``Workflow`` when updating ``StoredWorkflow`` name
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6774`_
* All extracted datasets should be visible
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 6780`_
* Fix __encode_invocation signature
* Fix ``__encode_invocation`` signature
`Pull Request 6782`_
* Strip all control characters from rules
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -789,7 +791,7 @@ Fixes
`Pull Request 6789`_
* Flex-related style fixes
`Pull Request 6791`_
* allow making all datasets within history public, when sharing
* Allow making all datasets within history public, when sharing
`Pull Request 6793`_
* Drop unused peek method
`Pull Request 6796`_
@@ -803,7 +805,7 @@ Fixes
`Pull Request 6802`_
* Don't delete referenced Datasets when purging users
`Pull Request 6809`_
* do not rule out numbers that are accessed with shift modifier
* Do not rule out numbers that are accessed with shift modifier
`Pull Request 6810`_
* Upgrade concurrently for 'null' return fix
`Pull Request 6828`_
scripts/bootstrap_history.py
+2 -2
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@@ -103,7 +103,7 @@ Highlights
Get Galaxy
==========
The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
To get a new Galaxy repository run:
.. code-block:: shell
@@ -199,7 +199,7 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
- [ ] Ensure all [blocking milestone PRs](https://github.com/galaxyproject/galaxy/pulls?q=is%3Aopen+is%3Apr+milestone%3A${version}) have been merged or closed.
make release-check-blocking-prs RELEASE_CURR=${version}
- [ ] Ensure previous release is merged into current. [Github branch comparison](https://github.com/galaxyproject/galaxy/compare/release_${version}...release_${previous_version})
- [ ] Ensure previous release is merged into current. [GitHub branch comparison](https://github.com/galaxyproject/galaxy/compare/release_${version}...release_${previous_version})
- [ ] Create and push release tag:
make release-create RELEASE_CURR=${version}