Changes in version 1.18.0                        

USER VISIBLE CHANGES

  - (v 1.17.18) Added has_avworkspace function to check for the
    existence of an AnVIL workspace environment.

  - (v 1.17.10) Internal functions now use AnVILGCP for gcloud
    utilities.

  - (v 1.17.8) Functions that use gcloud utilities are deprecated and
    will be moved to AnVILGCP. See help(package = "AnVIL") for a
    complete list. Documentation pages have a *-deprecated suffix.

  - (v 1.17.3) Added Terra Data Repository (TDR) service as TDR(). See
    service at https://data.terra.bio.

  - (v 1.17.1) Gen3 services, avworkflow*_configuration() functions,
    install(), repository(), and repositories() have been removed.

  - (v 1.17.1) Defunct repository_stats function in favor of
    BiocPkgTools::repositoryStats (@LiNk-NY)

BUG FIXES AND MINOR IMPROVEMENTS

  - (v 1.17.20) Use lifeCycle from BiocBaseUtils to mark functions as
    deprecated or defunct.

  - (v 1.17.19) Increase robustness of gcloud_exists by testing gcloud
    with the version command.

  - (v 1.17.18) Remove mentions of AnVIL::install from the vignette.

  - (v 1.17.13) Update to changes in rapiclient and use native pipe
    operator.

  - (v 1.17.7) Do not evaluate vignette chunks if gcloud_exists() is
    FALSE

  - (v 1.17.6) Update Dockstore API file, version, and URL

  - (v 1.17.2) Use application/json as default Content-Type.

                       Changes in version 1.16.0                        

USER VISIBLE CHANGES

  - (v 1.15.10) Validate API versions against hardcoded variables;
    produce warning when discordant (@LiNk-NY, #101).

  - (v 1.15.8) Add gcloud_storage() and gcloud_storage_buckets() to
    create and manage Google Cloud Storage buckets (@LiNk-NY, #72).

  - Gen3 services, avworkflow*_configuration() functions, install(),
    repository(), and repositories() are defunct.

  - (v 1.15.5) Catch avtable_import_status() errors in the response
    object.

  - (v 1.15.1) Update vignette with examples for avworkflow_info()
    (@mtmorgan, @yubocheng).

BUG FIXES AND MINOR IMPROVEMENTS

  - (v 1.15.11) Update Dockstore API file, version, and URL

  - (v 1.15.9) Use assertions from BiocBaseUtils

  - (v 1.15.7) Use URLencode for table in avtable and direct request to
    Rawls endpoint (@LiNk-NY, #98)

  - (v 1.15.6) Update the Dockstore API reference URL and use
    api_referenc_url instead of API file (@LiNk-NY).

  - Update namespace in vignette and examples (@kozo2, #54)

                       Changes in version 1.14.0                        

NEW FEATURES

  - (v 1.13.1) Add paged support for large tables in avtable_import()
    and avtable_import_set().

  - (v 1.13.2) Only show avtable_paged() and avtable_import*() progress
    bar in interactive() sessions

  - (v 1.13.4) Report messages when avtable_import_status() contains
    one. https://github.com/Bioconductor/AnVIL/issues/79

  - (v 1.13.3) Use 'op' when .avworkflow_response() calls
    avstop_for_status(). https://github.com/Bioconductor/AnVIL/issues/80

  - (v 1.13.7) Check requester pays for destination URIs when using
    gsutil_cp (@smgogarten, #82)

USER VISIBLE CHANGES

  - (v 1.13.8) Update documentation on updating workflow configurations.
    (@amstilp, #84)

  - (v 1.13.11) Added workflowId to avworkflow_files() and
    avworkflow_localize() to allow for filtering by workflow
    (@yubocheng, #90).

                       Changes in version 1.12.0                        

USER VISIBLE CHANGES

  - (v 1.11.2) update workflow file discovery to use API, rather than
    'scraping' google bucket.
    https://github.com/Bioconductor/AnVIL/issues/69

  - (v 1.11.3) Gen3 services deprecated

  - (v 1.11.5) Add na = to handle NA encoding in avtable() /
    avtable_import(). Changes default behavior.
    https://github.com/Bioconductor/AnVIL/issues/75

BUG FIXES

  - (v 1.11.1) consistently URLencode workspace and workflow name, to
    allow for spaces. https://github.com/Bioconductor/AnVIL/issues/67

                       Changes in version 1.10.0                        

NEW FEATURES

  - (v 1.9.1) add drs_access_url() to returned signed https:// URLs from
    drs:// URIs. Enhance drs_cp().

  - (v 1.9.4) add auto_unbox= argument to Service class, allowing other
    developers flexibility in unboxing values passed to REST APIs.

  - (v 1.9.7) add developer facilities for tracking API changes in
    Rawls, Terra, and Leonardo services

USER VISIBLE CHANGES

  - (v 1.9.2) Deprecate AnVIL::install() & friends in favor of
    BiocManager::install(), which now knows about container binary
    repositories.

  - (v 1.9.8) Update Rawls, Terra, and Leonardo services. Changed
    endpoints include:
    
    ## Rawls
    $removed
    [1] admin_delete_refresh_token admin_statistics_get
    [3] refreshToken               refreshTokenDate
    
    $updated
    [1] listUserBillingAccounts createWorkspace         getTags
    [4] clone                   entity_type_metadata    get_entity
    [7] entityQuery             createSubmission        validateSubmission
    
    ## Terra
    $removed
    [1] userTrial         listImportPFBJobs importPFBStatus
    
    $updated
     [1] deleteBillingProject       billingAccounts
     [3] createWorkspace            cloneWorkspace
     [5] entityQuery                flexibleImportEntities
     [7] importEntities             createSubmission
     [9] validateSubmission         browserDownloadEntitiesTSV
    [11] setProfile
    
    ## Leonardo
    $removed
    [1] batchNodepoolCreate
    
    $updated
     [1] listApp                listAppByProject       deleteApp
     [4] createApp              listDisks              listDisksByProject
     [7] createDisk             updateRuntime          createRuntime
    [10] setCookie              proxyClusterJupyter    proxyClusterJupyterLab
    [13] proxyClusterRStudio

  - (v 1.9.9) add 'gadgets' (simple graphical interfaces) to key
    functions, avworkspace_gadget(), avtable_gadget(),
    avworkflow_gadget(). Also browse_workspace() for opening a terra
    workspace in the browser.

BUG FIXES

  - (v 1.9.3 / 1.8.2) avworkflow_localize() looks for submissionId files
    correctly.

  - (v 1.9.5 / 1.8.3) drs_stat() works when accessUrl is included in
    response.

  - (v 1.9.6 / 1.8.5) gsutil_cp() and gsutil_rsync() use normalizePath()
    on source and destination arguments to avoid creating directories in
    unexpected locations when provided with paths containing ~, . or ...

  - (v 19.10 / v 1.8.6) gcloud_account("<new account>") did not
    invalidate cached access tokens.
    https://github.com/Bioconductor/AnVIL/issues/66

  - (v 1.9.11 / v 1.8.7) avoid changing status of 'Done' workflows to
    'Aborted' https://github.com/Bioconductor/AnVIL/issues/64

  - (v 1.9.11 / v 1.8.7) allow 'NULL' for entity arguments of
    avworkflow_run() https://github.com/Bioconductor/AnVIL/issues/65

                        Changes in version 1.8.0                        

NEW FEATURES

  - (v 1.7.4) add avworkflow_configuration_*() functions for
    manipulating workflow configurations, and a vignette describing use.

  - (v 1.7.5) add avdata_import() to import 'REFERENCE DATA' and 'OTHER
    DATA' tables.

  - (v 1.7.9) export repository_stats() to summarize binary package
    availability.

USER VISIBLE CHANGES

  - (v 1.7.4) Deprecate avworkflow_configuration(),
    avworkflow_import_configuration().

  - (v 1.7.4) Update Dockstore md5sum.

  - (v 1.7.5) avdata() is re-implemented to more faithfully report only
    'REFERENCE DATA' and 'OTHER DATA' workspace attributes; previously,
    other attributes such as the description and tags (from the
    workspace landing page) were also reported.

BUG FIXES

  - (v 1.7.4) avworkflow_files() and avworkflow_localize() do not fail
    when the workflow has produced no files.

  - (v 1.7.6) improve handling of authentication token for gcloud
    utilities.

  - (v 1.8.2) avworkflow_localize() looks for submissionId files
    correctly.

  - (v 1.8.3) drs_stat() works when accessUrl is included in response.

                       Changes in version 1.7.13                        

BUG FIXES

  - Correct gcloud_project() when user environment variable set.
    https://github.com/Bioconductor/AnVIL/pull/52

                        Changes in version 1.6.6                        

BUG FIXES

  - Correct gsutil_pipe() argument mis-match, see
    https://support.bioconductor.org/p/9141780/

                        Changes in version 1.6.0                        

NEW FEATURES

  - (v. 1.5.5) add repository() to return the binary repository
    location, if available.

  - (v. 1.5.7) drs_stat() and drs_cp() support signed URLs

USER VISIBLE CHANGES

  - (v. 1.5.2) drs_stat() uses multiple cores (on non-Windows) to
    enhance performance

  - (v. 1.5.6) install() delegates to BiocManager::install(), providing
    more flexibility (e.g., installing from GitHub) and robustness.

  - (v. 1.5.7) drs_stat() returns fields more selectively.

                        Changes in version 1.4.1                        

BUG FIXES

  - Only install binary packages on Bioconductor docker images

                        Changes in version 1.4.0                        

NEW FEATURES

  - (v 1.3.1) support Rawls() service (more fine-grained implementation
    / extension of the 'Terra()' orchestration API).

  - (v 1.3.2) introduce avworkspace_*() functions for viewing and
    updating workflow configurations.

  - (v 1.3.3) introduce avnotebooks_() functions for managing notebooks
    on workspaces and runtimes.

  - (v 1.3.11) introduce avtable_paged() for page-wise access to tables

  - (v 1.3.14) introduce avworkspace_clone() for cloning existing
    workspaces.

  - (v 1.3.21) avworkspaces() returns a tibble of available workspaces.

  - (v 1.3.24) gsutil_rsync() supports a regular expresion exclude = to
    exclude files from synchronization.

  - (v 1.3.24) avworkflow_localize() copies workflow control and / or
    output files to the local disk.

USER VISIBLE CHANGES

  - (v 1.3.1) service functions have signatures like fun(x, ...,
    .__body__ = list(y)), where x is a argument for the 'URL' of the
    RESTful interface, and y is an argument for the 'BODY' of POST and
    similar requests. The ... provide backward compatibility, and is
    used to populate elements of .__body__; the full interface is
    required when URL and BODY have identically named arguments.

  - (v 1.3.10, 1.3.11) return 'entity' column with name 'table_id',
    rather than 'name'.

  - (v 1.3.22) localize() / delocalize() warn when dry = TRUE, so that
    lack of localization is more apparent.

  - (v 1.3.24) gsutil_stat() returns a tibble summaring bucket status,
    rather than character().

  - (v 1.3.30) Add Referer: header to all Leonardo requests

BUG FIXES

  - (v 1.3.6) when .__body__ consists of 1 argument, it is represented
    as an unnamed set.

  - (v 1.3.7) allow positional matching for .__body__ arguments

  - (v. 1.2.1 / 1.3.31) drs_stat() returns a single record per URL when
    multiple hashes available.

                        Changes in version 1.2.0                        

NEW FEATURES

  - (v 1.1.3) introduce .deprecated flag in operations() / tags(); don't
    include deprecated APIs by default; warn on use of deprecated APIs.

  - (v 1.1.4) add repositories() to return binary (if available),
    Bioconductor, and CRAN repository paths.

  - (v 1.1.6) provide md5sum as check on service version.

  - (v 1.1.9) add avfiles_*() for managing workspace bucket files.

  - (v 1.1.15) add avtable_import_set() to create subsets of tables,
    following the Terra data model.

  - (v 1.1.16) add avruntimes(), avworkspace_jobs() to query for
    runtimes and jobs associated with the active billing account.

  - (v 1.1.17) add avdisks() to query for persistent disks associate
    with the active billing account.

  - (v 1.1.21) add avworkflow_*() for interacting with workflow jobs and
    outputs.

                         Changes in version 1.0                         

BUG FIXES

  - (v 1.0.1) collapse 'produces' vectors to scalars, for httr::accept()

  - (v 1.0.3) access correct binary repository, more robustly

USER VISIBLE CHANGES

  - (v 1.0.2) support updated Leonardo listRuntimes() and friends
    (listClusters() deprecated)

                        Changes in version 1.0.0                        

  - AnVIL is _finally on Bioconductor!
  - Support OpenAPI Specification version 2 (aka Swagger 2.0)
  - av, gcloud, gsutil type functions added to interface with AnVIL and
    the cloud
  - Support leonardo, terra, dockstore and gen3* APIs

                       Changes in version 0.0.20                        

  - Support untagged swagger

                       Changes in version 0.0.17                        

  - leonardo, terra, dockstore and gen3* symbols not defined; users must
    create these themselves, e.g., `leonardo <-

  - Added a NEWS.md file to track changes to the package.