Changes in version 2026-02-27                      

Added

  - pullProject() to fetch PEPs from PEPhub API via registry paths
    (e.g., databio/example:default)
  - saveProject() to write a Project object to local files (config YAML
    + sample CSVs)
  - saveJWT() to store an authentication token for private PEPs
  - PEPhub integration vignette examples in Getting Started guide

Changed

  - Replaced httr with httr2 for PEPhub API calls
  - Replaced tidyr dependency with base R for subsample unnesting
  - Added mocked tests for PEPhub API (CRAN-compatible)
  - Graceful error handling when PEPhub API is unreachable

Changed

  - Removed dependency on archived pryr package; replaced
    pryr::partial() with base R anonymous functions
  - Fixed BugReports URL in DESCRIPTION
  - Updated all pep.databio.org URLs to current paths
  - Removed codecov badge from README

                     Changes in version 2023-11-16                      

Fixed

  - result class of appended attributes; it's no longer wrapped in a
    list
  - various other fixes and improvements

Changed

  - error message when nonexistent attribute is derived

Added

  - possibility to configure the sample and subsample table index
    attributes in the Project object constructor
  - possibility to initialize Project with no configuration file
  - ability to initialize a project from URL
  - auto initialization file detection: CSV (sample table) or YAML
    (project config)
  - duplicated sample auto-merging

                     Changes in version 2020-10-14                      

Changed

  - added multiple subsample_table support

Fixed

  - issues with config file determination

                     Changes in version 2020-06-03                      

Changed

  - package description

                     Changes in version 2020-05-27                      

Fixed

  - issues with auto path expansion in objects of Config class on
    Windows
  - issues with path absoluteness determination on Windows

                     Changes in version 2020-05-26                      

This version introduced backwards-incompatible changes.

Added

  - auto path expansion in Config class
  - attribute duplication functionality
  - config importing functionality
  - attribute removal functionality
  - possibility to define multi-attribute rules in attribute implication

Changed

  - project configuration file to follow PEP2.0.0 specification. Browse
    the specification for changes related to config format

                     Changes in version 2020-01-09                      

Changed

  - downgrade exception from error to warining when missing envieonment
    variable is found

Fixed

  - issues related to subsample table functionality; #33

                     Changes in version 2019-06-21                      

Changed

  - checkSection method can be used with a mixture of section names and
    indices.
  - improved interaction between pepr and BiocProject

                     Changes in version 2019-04-17                      

Changed

  - keys in the config file: sample_annotation to sample_table,
    sample_subannotation to subsample_table. Backwards compatibility is
    preserved.

                     Changes in version 2019-02-01                      

Added

  - add activateSubproject method
  - add fetchSamples function
  - add checkSection method on Config object

Changed

  - if the subproject argument of the Project() function is not present
    in the config, the original project is returned
  - paths in the bioconductor section of the config are made absolute
    and environment variables are read
  - no sample annotation is allowed if any subprojects are defined in
    the config
  - fixed the problem with paths expansions in sample subannotations
    case

                     Changes in version 2018-11-14                      

Changed

  - change the Project object construction, the subproject can be
    activated at construction time
  - change implied/derived_columns to implied/derived_attributes.
    Backwards compatible
  - change constants to constantAttributes. Backwards compatible
  - fix expandPath() function, add error when environment variable not
    found

                     Changes in version 2018-09-12                      

Added

  - add derived_columns functionality
  - add implied_columns functionality
  - add subannotation functionality

                     Changes in version 2018-09-06                      

Added

  - first release, includes basic PEP reading functions