## Changes in version 2.20.0

### New features

* Add `copyNumberData` helper function to `cBioPortalData`
* Add `studyId` argument to the `fetchData` function
* Use `molecularProfiles` to determine mutation or copy number molecular profile
type; previously this was deduced from the data name
* Add example for filtering discrete copy number data

### Bug fixes and minor improvements

* Caching calls removed from `cBioPortalData`. API requests will always
be performed. `cBioDataPack` will continue to cache data files.
* Filter out `NULL` parameters in internal `.invoke_fun()` API calls
* Fix edge case in clinical data parsing when only a single file is present
* Update long unit tests expectations to reflect current study coverage (80%)
* Various documentation and example improvements

## Changes in version 2.16.0

### Bug fixes and minor improvements

* Improvements to links in documentation and citation section in the vignette

## Changes in version 2.14.0

### Bug fixes and minor improvements

* Remove error when `studyId` build success is unknown (@vlaufer, #69)
* Parse tokens with different formats, e.g. genie token (@ZWael, #70)
* Clean up duplicate rows created in the `sampleMap` generated from the data
* Fixed warning trigger when empty `molecularProfileId` datasets are found

## Changes in version 2.12.0

### Bug fixes and minor improvements

* Update `successrate` thresholds and fix long tests

## Changes in version 2.10.0

### New features

* Add `cgdsr` to `cBioPortalData` migration vignette (@kmezhoud, #54)
* Unmapped experiments are now added to the metadata in `cBioDataPack`
* Set default `api. = api/v2/api-docs` in `cBioPortal` to access the API
protocol's new location 
* The `fetchData` developer function added to handle both `molecularData` and
`mutationData` requests as deduced from the `molecularProfileIds` vector

### Bug fixes and minor improvements

* Check for valid `studyId`s with `getStudies` in `cBioDataPack`
* `ask` argument correctly passed down to caching mechanism in `cBioDataPack`
* `check_build` option available in `cBioDataPack` particularly for new studies
that have not been checked against.

## Changes in version 2.8.0

### New features

* Auth `token` string or file can now be included in the `cBioPortal` function.
* The `check_build` argument can be set to `FALSE` for alternative APIs, e.g.,
KidsFirst, when using `cBioPortalData` 
* `queryGeneTable` translates gene IDs ('hugoGeneSymbols' <>
'entrezGeneIds') via the API service
* `getDataByGenes` supersedes `getDataByGenePanel`
* `getStudies()` replaces `data('studiesTable')` to discover study IDs

### Bug fixes and minor improvements

* Fixed issue where the `by` argument was not passed to `getDataByGenes` in
internal calls
* Add names to metadata elements that originate from GISTIC datasets.

## Changes in version 2.6.0

### New features

* A study's build status can be obtained from `getStudies()`, which has
replaced `data('studiesTable')`.
* Partial loading of data files supported. A warning is emitted when a
data file is not able to be loaded in `cBioDataPack`.
* `cBioPortalData` checks the `data(studiesTable)` to verify that study
datasets are building, otherwise provide a message in interactive sessions.

## Changes in version 2.4.0

### New features

* Vignettes include additional information (#38, @lwaldron)
* `getDataByGenePanel` deprecated for `getDataByGenes` which handles input
of both gene panels and genes
* `cBioPortalData` now allows for gene inputs as either Entrez IDs or Hugo
symbols (#24, @jucor) and `sampleIds` input
* When `gene` inputs are provided, the `by` argument has to agree with the type
of genes provided (either be `entrezGeneId` or `hugoGeneSymbol`).

### Bug fixes and minor improvements

* Fixed an issue where the labels in the `metadata` from  `cBioDataPack` were
missing ('LICENSE' and 'Fusion'; #37)
* `loadStudy` allows `cleanup=TRUE` for removing files after `untar`-ing
* Published article now available with `citation("cBioPortalData")`

## Changes in version 2.2.0

### New features

* `studiesTable` includes additional columns `pack_build` and `api_build` to
indicate to the user which datasets have been successfully built as
`MultiAssayExperiment` objects. Users will be notified when a dataset, reported
as not building, is requested from the `cBioDataPack` function.
* Add `sampleIds` argument to `getDataByGenePanel` as part of cache re-work
* Allow more flexibility in the hostname when accessing the API with
`cBioPortal` (@inodb, #16)
* `cBioDataPack` downloads from a more robust repository (AWS S3; @inodb, #22)
* `removePackCache` and `removeDataCache` now remove data from the user's
cache based on inputs to respective functions (`cBioDataPack` and
`cBioPortalData`)

### Bug fixes and minor improvements

* Attempt to merge additional clinical data files from tarballs in
`cBioDataPack`.
* Switch to using `read.delim` instead of `read_tsv` internally to avoid
assigning `NA` to chromosome column
* Use 'PATIENT_ID' when available to determine if experiment data is provided
in the tarball files.
* Add tests using `testthat`
* Update and include percentages of studies successfully imported using
`cBioDataPack` and `cBioPortalData` in the documentation
* Fix read-in when identifiers are numeric instead of character (@jucor, #27)
* Include pagination parameters in `geneTable` function (@xinwei-sher, #29)

## Changes in version 2.0.0

### New features

* Bioconductor release!
* Updated the `README.md` file from R Markdown file.
* Uses the latest version of `rapiclient` on CRAN
* Prepare package for Bioconductor submission
* Include protein metadata as a `RaggedExperiment` from mutation molecular
profiles (TCGA only)

### Bug fixes and minor improvements

* API authentication option removed and not needed

## Changes in version 1.0.1

### New features

* Package supports nearly all study identifiers based on recent tests
* Only a handful of study identifiers are unsuccessful (create an issue to
prioritize).

### Bug fixes and minor improvements

* Make better use of the API return values to craft the sample map for
`MultiAssayExperiment` creation
* Additional data included in the metadata slot of the `MultiAssayExperiment`
object. Future revisions will include this data as `rowData`.
* Change vignette titles for build

## Changes in version 0.1.0

### New features

* `cBioDataPack` allows users to download packaged data objects from
download.cbioportal.org/
* Data packs are cached using `BiocFileCache` to avoid re-downloading
* `cBioPortalData` lets users query the cbioportal.org API and retrieve slices
of data according to gene, molecular profile identifiers, etc.
* Queries through `cBioPortalData` use a caching mechanism to avoid repeat
downloads of data and improve load times
* Both functions return a `MultiAssayExperiment` as the primary data
representation
* Only a number of study datasets are currently possible to load. Issues
can arise with mismatched or munged identifiers
* The cBioPortal API representation is handled by the `AnVIL` package
which makes use of `rapiclient` to provide an automatic R interface to the API

### Bug fixes and minor improvements

* Data pack downloads use an alternative method for download when a download
fails
