Merge pull request #449 from hjellinek/0.6-release-notes

Draft release notes for version 0.6. - A new PR will immediately be re-opened to address outstanding issues from this one.

doc/release-notes.md

@@ -0,0 +1,97 @@
+# Changes to `ga4gh/schemas` `master` branch since version `v0.5.1` (Oct 2, 2014)
+
+### Pervasive changes
+
+Renamed all protocols and records to remove the "`GA`" prefix from
+their names.  (Hence `GASearchVariantSetsRequest` is now
+`SearchVariantSetsRequest`, etc.)  The exception is `GAException`,
+which is unchanged.
+
+There is no longer one unitary namespace.  Objects now reside in
+"`org.ga4gh.models`", methods in "`org.ga4gh.methods`".
+
+Updated the version number to `0.6.0-SNAPSHOT`.
+
+### Added
+
+Datasets are now used throughout the API.
+
+#### Methods:
+
+* `getDataset`
+* `searchDatasets`
+* `getReadGroupSet`
+* `getReadGroup`
+* `getVariant`
+* `getVariantSet`
+* `getCallSet`
+
+#### Records:
+
+* `ExternalIdentifier`
+* `Experiment`
+* `Dataset`
+* `ReadStats`
+* `Fragment` _(apparently unused)_
+
+#### Enum:
+
+* `Strand`
+
+### Removed
+
+* `src/main/resources/avro/beacon.avdl`
+* Files designated "Work In Progress" ("`wip`"):
+    * `src/main/resources/avro/wip/metadata.avdl`
+    * `src/main/resources/avro/wip/metadatamethods.avdl`
+    * `src/main/resources/avro/wip/variationReference.avdl`
+
+### Changed
+
+Moved `GAException` to `methods.avdl`.
+
+#### Field default values:
+
+* `SearchReadsRequest.start` is optional and no longer defaults to 0.
+* Boolean fields in `ReadAlignment` now default to `null` instead of `false`.
+
+#### Field types:
+
+* `SearchVariantSetsRequest` now takes a single dataset ID, not an array.
+* `SearchCallSetsRequest` now takes a single variant set ID, not an array.
+* `SearchReferenceSetsRequest` changed two parameters from arrays to
+singletons:
+
+    * `md5checksum`
+    * `accession`
+
+#### New fields:
+
+* `SearchReferencesRequest` now accepts a `referenceSetId` parameter.
+* `SearchVariantsRequest` now takes a `variantSetId` parameter.
+* `SearchReadsRequest` now includes `readGroupIds`.
+* `SearchReadGroupSetsRequest` takes a `datasetId`.
+* `ReferenceSet` now includes a name.
+* `VariantSet` adds name and reference set ID fields.
+* `ReadGroup` adds `stats`.
+
+## Documentation
+
+Using Doxygen to generate HTML documentation from schema (`*.avdl`) files.
+
+Clarifications:
+
+* How the `SearchReadGroupSetsRequest.name` field is interpreted.
+* The meaning of `SearchCallSetsRequest.name`.
+* `Reference`, `ReferenceSet` docs.
+
+Updated `CONTRIBUTING.md` to describe the latest contribution rules.
+
+Moved `GeneratingDocumentation.md` to `doc/`.
+
+`README.md` now includes information about the Metadata Task Team.
+
+## Tests
+
+Added tests to ensure Maven processes the schemas into a `jar` file
+successfully, and that we can compile the schemas into Python.