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Update release notes (#1597) (#1598)
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* Update release notes (#1597)

* Update with more details.

I will update the schema Release notes too.

* add comment on search by name field

* fix typos

* add links, proper back ticks

* clean up travis error
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kozbo authored and ejacox committed Mar 13, 2017
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Expand Up @@ -19,6 +19,88 @@ For more detail on individual development issues, please see the project's
Release Notes
+++++++++++++

*****
0.3.6
*****

This an alpha pre-release that contains some major updates. The most important
changes are highlighted in **bold** below. We have also made some updates to
the documentation.

Features:

- **Rename package from “ga4gh” to “ga4gh-server”** `#1582 <https://github.com/ga4gh/ga4gh-server/issues/1582>`__, `#1583 <https://github.com/ga4gh/ga4gh-server/issues/1583>`__

- Added **support for BigWig files** in a new Continuous Data object `#1573 <https://github.com/ga4gh/ga4gh-server/issues/1573>`__ New endpoints and message types include:

- ``POST /continuoussets/search``
- ``GET /continuoussets/{id}``
- ``POST /continuous/search``
- Continuous (new)
- ContinuousSet (new)

- Add **ability to list and join peer server networks** `#1507 <https://github.com/ga4gh/ga4gh-server/issues/1507>`__ New endpoints and message types include:

- ``POST /peers/list``
- ``POST /peers/announce``
- ``GET /info``
- ListPeersResponse (new)
- Peer (new)
- AnnouncePeerResponse (new)
- GetInfoResponse (new)

- Remove feature_id from ExpressionLevel and add ability to search by the Name field `#1580 <https://github.com/ga4gh/ga4gh-server/issues/1580>`__ Impacts

- ``POST /expressionlevels/search``
- ``GET /expressionlevels/{id}``

- Replaced info fields with rich type Attributes fields `#1521 <https://github.com/ga4gh/ga4gh-server/issues/1521>`__ Impacts the following message types:

- TranscriptEffect
- VariantAnnotation
- Individual
- Biosample
- Experiment (new)
- Analysis (new)
- Dataset
- ReadGroup
- ReadGroupSet
- ReadAlignment
- Reference
- ReferenceSet
- RnaQuantificationSet
- RnaQuantification
- ExpressionLevel
- Feature
- VariantSetMetadata
- CallSet
- Call
- Variant

- Replace NCBI taxon ID integer with ontology term `#1551 <https://github.com/ga4gh/ga4gh-server/issues/1551>`__ Impacts the following message types:

- Reference
- ReferenceSet

- Changed ontology term “id” to “term_id” `#1513 <https://github.com/ga4gh/ga4gh-server/issues/1513>`__ Impacts the following message types:

- OntologyTerm

Documentation:

- Document auto-releases, constraint instructions `#1578 <https://github.com/ga4gh/ga4gh-server/issues/1578>`__

- Improved development document for virtualenv command `#1550 <https://github.com/ga4gh/ga4gh-server/issues/1550>`__

Infrastructure:

- Automatically deploy tagged releases to Pypi from Travis `#1576 <https://github.com/ga4gh/ga4gh-server/issues/1576>`__

- Refactor transcript annotation `#1334 <https://github.com/ga4gh/ga4gh-server/issues/1334>`__

- Speedups to rna quantification ingest `#1564 <https://github.com/ga4gh/ga4gh-server/issues/1564>`__


*****
0.3.5
*****
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