CHANGES IN VERSION 2.15.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o (2.15.9) The Hubs have been updated to use BiocFileCache as a backend
    utility for managing and downloading resources. This allows for file
    specific caching mechanism. This change is a significant user change as it
    changed the default directories for the Hubs (AnnotationHub/ExperimentHub)
    as well as the base directory no longer being hidden.

NEW FEATURES

    o (2.15.15) Added BamFile Resource method
    o (2.15.9) Add helper function to get additional information on
    resources. getInfoOnIds
    o (2.15.2) Add function to list currently available DispatchClass

USER-VISIBLE MODIFICATIONS

    o (2.15.3)  Bioconductor will no longer accept random, Individual resources
    without an accompanied package.
    o (2.15.4)  We also encourage the use of AnnotationHub rather than very
    large annotation packages. We added sections for users wishing to convert
    existing packages to use AnnotationHub as well.
    o (2.15.7) There were substantial updates to Rsamtools. Rsamtools no longer
    supports razip files. These files have been removed from the hub and
    vignette updated to use the twobit and gff files

BUG FIXES
    o (2.15.5) Fixed bug. If resources are removed from the hub, this should
    only be reflected in the devel branch but still be available in release
    branch. The filter for exposed resources was refined to respect
    datadateremoved


CHANGES IN VERSION 2.12.0
-------------------------

MODIFICATIONS

    o Updated code from BiocInstaller to BiocManager

CHANGES IN VERSION 2.12.0
-------------------------

BUG FIXES

    o Prompt for permission when downloading many (more than
    AnnotationHubOption("MAX_DOWNLOADS")) resources.

MODIFICATIONS

    o Moved readMetadataFromCsv back to AnnotationHubData.

    o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv

CHANGES IN VERSION 2.10.0
------------------------

NEW FEATURES

    o AnnotationHub will now work offline utilizing argument 'localHub'; will
    also use this option automatically if no internet connection is detected.

    o Added new GDSResource class

    o Added documentation for creating an AnnotationHub package

MODIFICATIONS

    o Modified tags vector when passed to display to improve speed of display
    querying

    o Moved readMetadataFromCsv from AnnotationHubData.

    o Removed listResources and loadResource from AnnotationHub; not implemented
    and only valid in ExperimentHub

BUG FIXES

    o Expose snapshot less than or equal to release date

    o Force rebuild of index if index file corrput or out of date

CHANGES IN VERSION 2.8.0
------------------------

NEW FEATURES

    o add .get1,RDSResource-method

    o add RdsResource class

    o add EnsDb dispatch class

    o expose rdatapath in metadata

MODIFICATIONS

    o modify records exposed as metadata
      - expose records added <= snapshot date
      - expose a single OrgDb per organism per BioC version

    o edits to .get1,GenomicScores-method and .get1,GenomicScoresResource-method

    o work on biocVersion and snapshotDate relationship:
      - snapshotDate() must be <= biocVersion() release date
      - possibleDates() are now filtered by snapshotDate()

    o remove GenomicScoresResource; Robert Castelo will handle loading these
    resources in his GenomicScores software package

    o Changed show method for hub object
      - removed sourcelastmodifieddate
      - added rdatadateadded


BUG FIXES

    o fix bug in ordering of output from .uid0()

    o fix bugs in 'snapshotDate<-' method

CHANGES IN VERSION 2.6.0
------------------------

NEW FEATURES

    o add vignette section on sharing resources on clusters

    o add 'preparerclass' to index.rda to allow search by package name for
      ExperimentHub objects

    o add GenomicScoresResource class for Robert Castelo

MODIFICATIONS

    o return 'tags' metadata as list instead of comma-separated character
      vector

    o move AnnotationHubRecipes vignette to AnnotationHubData

    o move listResources() and loadResources() from ExperimentHub

    o expose additional fields in .DB_RESOURCE_FIELDS()

    o modify cache path to avoid creating a '~' directory on Mac

    o use https: NCBI rul in documentation

    o modify .get1,EpiExpressionTextResource-method to use 'gene_id'
      column as row names


CHANGES IN VERSION 2.4.0
------------------------

NEW FEATURES

    o add new status codes '4' and '5' to 'statuses' mysql table;
      change 'status_id' field to '4' for all removed records to date

    o add getRecordStatus() generic

    o add package() generic

    o create 'Hub' VIRTUAL class
      - add new .Hub() base constructor for all hubs
      - add getAnnotationHubOption() and setAnnotationHubOption()
      - promote cache() to generic
      - add getHub() getter for AnnotationHubResource class
      - add getUrl(), getCache(), getDate() getters
      - export as few db helpers as possible

    o add 'EpigenomeRoadmapNarrowAllPeaks' and
      'EpigenomeRoadmapNarrowFDR' classes

MODIFICATIONS

    o distinguish between broad and narrow peak files in
      EpigenomeRoadmapFileResource dispatch class

    o don't use cache for AnnotationHub SQLite connection
      - originally introduced so could be closed if needed, but
	creates complexity
      - instead, open / close connection around individual queries (not a
	performance concern)
      - expose hub, cache, proxy in AnnotationHub constructor
      - document dbconn,Hub-method, dbfile,Hub-method, .db_close

    o snapshotDate now uses timestamp (last date any row was modified) instead
      of rdatadateadded

    o .require fails rather than emits warning
      - unit test on .require()
      - also, cache(hub[FALSE]) does not create spurious error

    o work on removed records and biocVersion
      - .uid0() was reorganized and no longer groups by record_id
      - metadata is returned for records with
	biocversion field <= current biocVersion
	instead of an exact match with the current version
      - metadata is not returned for removed records

BUG FIXES

    o Work around httr() progress() bug by disabling progress bar


CHANGES IN VERSION 2.2.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o seqinfo(GRanges) for all genomes supported by GenomeInfoDb now
      contain seqlengths.


CHANGES IN VERSION 2.1.21
--------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o fileName() returns the cache path on the disk for a file that
      has been cached and NA for files which have not been cached.

    o The error message (when file is not downloaded from the hub)
      displays the AnnotationHub name, title, and reason for failure.


CHANGES IN VERSION 2.1
----------------------

NEW FEATURES

    o as.list() splits AnnotationHub instances into a list of
    instances, each with a single record. c() concatenates hubs.

BUG FIXES

    o cache<- now behaves as documented, e.g., removing the cached
    version of the file.

CHANGES IN VERSION 2.0.0
------------------------

NEW FEATURES

    o AnnotationHub is all new.  We basically rewrote the entire thing.

    o The back end is new (new database, new way of tracking/routing
    data etc.)

    o The front end is new (new AnnotationHub object, new methods, new
    behaviors, new ways of finding and downloading data)

    o The metadata has also been cleaned up and made more
    consistent/searchable

    o The recipes that are used to populate these data have also been
    cleaned up.

    o There is also a new vignette to explain how to use the new
    AnnotationHub in detail

IMPROVEMENTS SINCE LAST TIME

    o The old way of finding data (an enormous tree of paths), was not
    really scalable to the amount of data we have to provide access
    to.  So we junked it.  Now you have a number of better methods to
    allow you to search for terms instead.

    o The new hub interface can be searched using a new display
    method, but it can *also* be searched entirely from the command
    line.  This allows you to use it in examples and scripts in a way
    that is friendlier for reproducible research.

    o For users who want to contribute valuable new annotation
    resources to the AnnotationHub, it is now possible to write a
    recipe and test that it works for yourself.  Then once you are
    happy with it, you can contact us and we can add data to the
    AnnotationHub.
