Some initial work on release highlights, still completely broken.

doc/source/releases/18.01.rst

@@ -15,32 +15,21 @@ Enhancements
 .. feature
 
 
-* Run Galaxy fully under uWSGI, including job handlers
-  `Pull Request 4475`_
 * Clone tools in workflows
   (thanks to `@anatskiy <https://github.com/anatskiy>`__).
   `Pull Request 5087`_
-* Libraries to collections
-  `Pull Request 5080`_
 * Cloud ObjectStore
   (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 4487`_
 * Reload tools immediatelly if a macro changes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4635`_
-* Galaxy client tooling overhaul and ES6 support
-  `Pull Request 4435`_
-* Vue integration, bibtex replacement
-  `Pull Request 4978`_
 * Skip job execution if equivalent job exists
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 4690`_
 * Add AskOmics Interactive Environment
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 4737`_
-* Allow downloading collections (through UI) at arbitrary levels of nesting
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 4942`_
 * Implement github error report backend
   (thanks to `@erasche <https://github.com/erasche>`__).
   `Pull Request 4765`_
@@ -49,8 +38,6 @@ Enhancements
   `Pull Request 4916`_
 * Create the $GALAXY_MEMORY_MB tool job environment variable
   `Pull Request 4958`_
-* Enhance hdca creation API endpoint to accept lddas
-  `Pull Request 4998`_
 * Add API that allows admins to decode galaxy objects' ids
   `Pull Request 5018`_
 * Add sorting options for data library folders
@@ -81,18 +68,12 @@ Enhancements
 * Add Classical linkage and haplotype datatypes
   (thanks to `@mtekman <https://github.com/mtekman>`__).
   `Pull Request 4894`_
-* Add BamNative datatype
-  (thanks to `@bgruening <https://github.com/bgruening>`__).
-  `Pull Request 5180`_
 * Add support for the ideaspre datatype
   (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
   `Pull Request 5445`_
 * add fasta.gz support
   `Pull Request 5561`_
-* Add queryname sorted and input sorted datatypes
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 5589`_
-* add cool datatype
+* add ``cool`` datatype
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 5023`_
 * Neostore Zip datatype support
@@ -342,13 +323,9 @@ Enhancements
 * i18n improvements French localization the sequel
   (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
   `Pull Request 5089`_
-* Render arbitrarily large collections in the UI.
-  `Pull Request 5091`_
 * Update Jupyter IE default image
   (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
   `Pull Request 5095`_
-* Convert options file to YAML and use uWSGI by default
-  `Pull Request 5105`_
 * Determine dynamically if an extension corresponds to an unsniffable binary
   datatype
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -365,8 +342,6 @@ Enhancements
   `Pull Request 5125`_
 * Client build check
   `Pull Request 5128`_
-* Migrate documentation for setting up a production instance to Galaxy.
-  `Pull Request 5135`_
 * Postpone depends_list generation
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 5137`_
@@ -419,11 +394,8 @@ Enhancements
   (thanks to `@istevenshen <https://github.com/istevenshen>`__).
   `Pull Request 5232`_
 * Added support for recursively discovering output datasets
-  (thanks to `@gvlproject <https://github.com/gvlproject>`__).
+  (thanks to `@gvlproject <https://github.com/gvlproject>`__). TODO: fix author
   `Pull Request 5240`_
-* Fix and enhance job resume functionality
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 5247`_
 * Make pam a conditional dependency
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 5251`_
@@ -434,9 +406,6 @@ Enhancements
   `Pull Request 5262`_
 * Clarify some FTP purging behaviors with tests.
   `Pull Request 5266`_
-* Copy element_identifier to resumed job
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 5270`_
 * Allow sorting collection elements based on file
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5273`_
@@ -452,22 +421,15 @@ Enhancements
   `Pull Request 5299`_
 * allow message to be modified on ldda
   `Pull Request 5312`_
-* Add option to replace failed elements on job rerun
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 5321`_
 * Tag editor size constraint
   `Pull Request 5337`_
 * Webhooks improvements
   `Pull Request 5342`_
 * Environment variable to skip client build.
-  `Pull Request 5371`_
-* improve config options docs
-  `Pull Request 5373`_
+  `Pull Request 5371`_  
 * Make TabularToolDataTable._deduplicate_data() faster
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 5383`_
-* Update framework dependencies documentation
-  `Pull Request 5390`_
 * Allow map-over when discovering dataset collections
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5413`_

doc/source/releases/18.01_announce.rst

@@ -9,23 +9,58 @@ Highlights
 ===========================================================
 
 **Performance and User Experience Improvements**
-We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time.
-We achieved this by optimising queries, implementing cache, rethinking presentation, and adding progress bars and loading indicators where needed.
-
-**Collection Overhaul**
-  Feature description.
-
-**uWSGI**
-  Feature description.
+  We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time.
+  We achieved this by optimising queries, implementing cache, rethinking presentation, and adding progress bars and loading indicators where needed.
+
+**Web Server and Configuration**
+  The default web server used by Galaxy has changed from Paste to uWSGI and the default configuration file for Galaxy is now ``config/galaxy.yml`` instead of ``config/galaxy.ini``. 
+  uWSGI is more production ready and should allow Galaxy to scale better in its default
+  configuration. In the future uWSGI will allow Galaxy to setup GIE proxies without additional
+  configuration and use modern web technology such as web sockets.
+
+  To minimize the impact of this on existing Galaxy instances, if a Galaxy has an existing ``galaxy.ini``
+  file configured it will continue to use Paste by default unless additional steps are
+  taken by the administrator (one can force Galaxy to start in uWSGI even with an older configuration file 
+  by setting ``APP_WEBSERVER=uwsgi`` in the environment). As part of the transition to YAML-based 
+  configuration files we have implemented a schema to validate Galaxy configuration files. Run
+  ``make config-validate`` from Galaxy's root directory to validate a schema and ``make config-lint`` to
+  check for best practices. While there is no need to convert your configuration file (``galaxy.ini`` hasn't
+  been deprecated), we have included make targets ``make config-convert-dry-run`` and ``make config-convert``
+  to assist converting an ``ini`` configuration file to a YAML one.
+
+  These are big changes that affect many parts of Galaxy's administration documentation and makes
+  this documentation very dependent on which Galaxy version they are targetting. To address this, we have
+  moved a signifcant amount of administration documentation into Galaxy's code
+  base and made it available on a per release basis. The latest administration documentation for
+  the previous release of Galaxy (17.09) which reference galaxy.ini files and Paste servers can
+  be found `here <https://docs.galaxyproject.org/en/release_17.09/admin/index.html>`__, while documentation for this release can be found `here <https://docs.galaxyproject.org/en/release_18.01/admin/index.html>`__.
+
+  `Pull Request 4475`_, `Pull Request 5135`_, `Pull Request 5390`_, `Pull Request 5373`_, `Pull Request 5105`_
 
 **ES6 + Vue**
   Feature description.
 
+  `Pull Request 4435`_, `Pull Request 4978`_
+
 **New BAM datatypes**
-  Feature description.
+  TODO: Feature description.
+  `Pull Request 5180`_, `Pull Request 5589`_
 
 **Job Replacement**
-  Feature description.
+  TODO: Feature description.  
+  `Pull Request 4690`_
+
+**Dataset Collection Usability**
+  This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements
+  to collections have been made, some the key highlights include:
+
+    - Data library folders can now be sent to histories as a dataset collection. `Pull Request 4998`_, `Pull Request 5080`_
+    - Failed dataset collection elements can now be fixed using job re-running (thanks to `@mvdbeek <https://github.com/mvdbeek>`__). `Pull Request 5321`_, `Pull Request 5247`_, `Pull Request 5270`_
+    - The Galaxy web interface works with collections with arbitrary nesting and size (with help
+      from `@mvdbeek <https://github.com/mvdbeek>`__). `Pull Request 4942`_, `Pull Request 5091`_
+    - TODO: more of these...
+    - TODO: a couple small screenshots - libraries, resume, and collection progress bar.
+
 
 Get Galaxy
 ==========