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pepr 0.6.1 - 2026-07-08

Fixed

• Updated pullProject() to match the current PEPhub API response schema (the raw-project keys sample_list/subsample_list were renamed to samples/subsamples), which had caused a fetch error against the live API.
• pullProject() now fails with an informative message when a PEP is missing or the API response is malformed, instead of a cryptic internal error.

Changed

• Moved the live PEPhub API test into an opt-in integration suite (set PEPR_INTEGRATION_TESTS=true) that never runs on CRAN; the pullProject() example is no longer executed during checks.

pepr 0.6.0 - 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

pepr 0.5.1 - 2026-02-27

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

pepr 0.5.0 - 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

pepr 0.4.0 - 2020-10-14

Changed

• added multiple subsample_table support

Fixed

• issues with config file determination

pepr 0.3.2 - 2020-06-03

Changed

• package description

pepr 0.3.1 - 2020-05-27

Fixed

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

pepr 0.3.0 - 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

pepr 0.2.2 - 2020-01-09

Changed

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

Fixed

• issues related to subsample table functionality; #33

pepr 0.2.1 - 2019-06-21

Changed

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

pepr 0.2 - 2019-04-17

Changed

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

pepr 0.1 - 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

pepr 0.0.4 - 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

pepr 0.0.3 - 2018-09-12

Added

• add derived_columns functionality
• add implied_columns functionality
• add subannotation functionality

pepr 0.0.2 - 2018-09-06

Added

• first release, includes basic PEP reading functions

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