laminr v0.2.0

This release adds support for creating new artifacts in a LaminDB instance.

NEW FUNCTIONALITY

• Add support for more loaders (PR #81).
  Currently supported: .csv, .h5ad, .html, .jpg, .json, .parquet, .png, .rds, .svg, .tsv, .yaml.
• Add a from_df() method to the Registry class to create new artifacts from data frames (PR #78)
• Create TemporaryRecord classes for new artifacts before they have been saved to the database (PR #78)
• Add a delete() method to the Record class (PR #78)
• Add track() and finish() methods to the Instance class (PR #83)
• Add a from_path() method to the Registry class to create new artifacts from paths (PR #85)
• Add a from_anndata() method to the Registry class to create new artifacts from AnnData objects (PR #85)
• Add RStudio add-in for saving a notebook (PR #90).

MAJOR CHANGES

• Running connect(slug = NULL) now connects to the default instance that is allowed to create records.
  The default instance must be changed using the Lamin CLI. (PR #78)
• User setting are stored in a global option the first time connect() is run (PR #78)

MINOR CHANGES

• Adjusted argument order in Instance$track() and improved Python error handling (PR #89)

TESTING

• Add a test for creating artifacts from data frames (PR #78).
• Add tests for creating artifacts from paths and AnnData objects (PR #85)

DOCUMENTATION

• Updated installation instructions after {laminr} was released on CRAN (PR #74).
• Updated the architecture vignette to include new methods and the new TemporaryRecord class (PR #78, PR #83, PR #85)
• Updated the development vignette with new functionality (PR #78, PR #83, PR #85)

laminr v0.1.0

First CRAN release of the LaminDB API client for R. This release focuses on connecting to a LaminDB instance, fetching an individual record from the instance, and fetching related data for that record.

Features:

• Connect to a LaminDB instance
• Auto-generate modules and classes from the instance schema
• Fetch a record
• Fetch a record's related data
• Fetch record summary table
• Cache S3 artifact
• Load AnnData artifact

For more information, please visit the package website.

NEW FUNCTIONALITY

• Query instance settings from Lamin Hub (PR #8).
• Read user settings from env file created by lamin Python package (PR #2, PR #8).
• Add to_string() and print() methods to the Record class and (incomplete) describe() method to the Artifact() class (PR #22).
• Add to_string() and print() methods to remaining classes (PR #31)
• Add InstanceAPI$get_records() and Registry$df() methods (PR #54)
• Add a RelatedRecords class and RelatedRecords$df() method (PR #59)

MAJOR CHANGES

• Refactored the internal class data structures for better modularity and extensibility (PR #8).

• Added GitHub actions to the project (PR #11):

  • Standard R-CMD-check workflow.
  • Linting action.
  • Commands for roxygenizing (/document) and restyling the source code (/style).

• Allow unauthenticated users to connect to an instance if they ran lamin connect <instance> beforehand (PR #19).

MINOR CHANGES

• Do not complain when foreign keys are not found in a record, but also do not complain when they are (PR #13).
• Define a current user and current instance with lamin-cli prior to testing and generating documentation in the CI (PR #23).
• Add progress bars to Artifact$cache() (PR #58)
• Remove link tables from object print output (PR #55)
• Improve checking for suggested packages and provide installation instructions if missing (PR #56)
• Add the status code to API error messages (PR #70)
• Adjust colours in print output (PR #69)
• Modify Registry print output to separate relational fields by module (PR #71)

TESTING

• Add a simple unit test which queries laminlabs/lamindata (PR #27).
• Added unit test for the InstanceAPI class (PR #30).
• Add a regular expression to the API test for missing records (PR #70)

DOCUMENTATION

• Update README with new set up instructions and simplify (PR #14).
• Add a pkgdown website to the project (PR #13).
• Further simplify the README, and move the detailed usage description to a separate vignette (PR #13).
• Generate vignettes using Quarto (PR #13).
• Add vignette to showcase laminr usage (PR #18).
• Replace all mentions of lamin load with lamin connect (PR #29).
• Improve the README (PR #29).
• Set Python requirements to lamindb[aws] for now (PR #33). Will be changed to lamin_cli once
  laminlabs/lamin-cli#90 is solved.
• Improve documentation for installing suggested dependencies and what they are required for (PR #56).
• Update the README to give a better overview of the package (PR #67).
• Rename the usage vignette to laminr and added an overview of the core concepts of LaminDB (PR #67).
• Update the architecture vignette to relate the class structure of the package to the core concepts (PR #67).
• Add a development vignette to document the list of current, planned and unplanned functionality (PR #67).
• Add vignettes to document registries in the core, bionty, and wetlab modules (PR #67).

BUG FIXES

• Fixed the parsing of the env files in ~/.lamin due to changes in the lamindb-setup Python package (PR #12).
• Return NULL when a record's related field is empty (PR #28).
• Add alternative error message when no message is returned from the API (PR #30).
• Handle when error detail returned by the API is a list (PR #59)
• Manually install OpenBLAS on macOS (PR #62).
• Switch to Python 3.12 for being able to install scipy on macOS (PR #66).

laminr v0.0.1

Initial POC implementation of the LaminDB API client for R.

Functionality:

• Connect to a LaminDB instance
• Fetch instance schema
• Auto-generate classes from schema
• See available modules and classes
• Get a record
• Get a record's related data
• Cache S3 artifact
• Load AnnData artifact