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Developement version

Source: CHANGELOG.md

BREAKING CHANGES

NEW FEATURES

  • Add a lamin_settings() function that displays information from running lamin settings (PR #201)
  • Add a laminr_status() function that returns a laminr_status object with information useful for debugging. This has pretty print output. (PRs #201, #215)
  • Add a get_current_lamin_settings() function that returns the current LaminDB settings as an R list (PR #210, fixes #207)
  • Add LAMINR_LAMINDB_VERSION and LAMINR_LAMINDB_OPTIONS environment variables to control the version of Python lamindb that is installed (PR #194)

MAJOR CHANGES

  • Isolate functions that made CLI calls so they do not interfere with the main session/environment (PR #201)
  • Require instance modules before importing lamindb so they should be available (PR #201)
  • Save a simplified R environment file when ln$finish() is called instead of a {pak} lockfile (PR #213, related to #195, #205)

MINOR CHANGES

  • Add an alert if an instance module is not available with importing lamindb (PR #201)
  • Add a status message to require_module(), can be suppressed with silent = TRUE (PR #201)
  • Add wrapping for the lamindb.models.sqlrecord.Registry class (PR #203)
  • Remove {nanoparquet} as a suggested dependency, loading Parquet files now requires {arrow} (PR #203)
  • Increase {reticulate} dependency to >=1.41.0 to make sure the py_require() functionality is available (PR #208)
  • Add a minimal requirement for scipy>=1.7 to avoid an issue where {reticulate} attempted and failed to install scipy==1.6 (PR #209, fixes #206)

BUG FIXES

  • Handle missing setting values in lamin_settings() (PR #202)
  • Handle list columns when creating artifacts from data frames (PR #203)

TESTING

  • Tidy and reorganise test GitHub actions (PR #201)

DOCUMENTATION

  • Port updates to the introduction vignette from the main documentation site (PR #203)
  • Use laminr::import_module("lamindb") in quickstart (PR #204)

laminr v1.1.1

BUG FIXES

  • Surround pak lockfile creation with try-catch to avoid breaking the finish process (PR #198)

laminr v1.1.0

NEW FEATURES

  • Add tracking of the R environment using {pak} lockfiles (PR #179)
  • Allow setting of object slots (PR #188)
  • Enable the view_lineage() functionality to properly display lineage graphs (PR #180)

MINOR CHANGES

  • Update reticulate dependency to >= 1.38.0 (PR #158)
  • Use {rmarkdown} instead of {quarto} for articles (PR #159)
  • Improve inheritance of arguments when wrapping and overwriting Python functions (PR #191)

BUG FIXES

  • Fix an issue that was preventing lamin_connect() from being run multiple times with the same instance (PR #176)
  • Properly clear and delete temporary instances created using lamin_init_temp() (PR #189)

DOCUMENTATION

  • Update the feel and structure of the documentation website (PR #159, PR #160, PR #161, PR #163, PR #172, PR #175)
  • Update the content of the introduction article to match the main documentation site (PR #188)
  • Update the welcome vignette to point to the main LaminDB documentation website (PR #190)

laminr v1.0.1

MINOR CHANGES

  • Update dependencies to fix CRAN issues (PR #156)

laminr v1.0.0

LaminR now has feature parity with LaminDB (PR #146).

Migration guide:

  • Run install_lamindb(), which will ensure lamindb >= 1.2 in the Python environment used by reticulate.
  • Replace db <- connect() with ln <- import_module("lamindb") and see the table below. The ln object is largely similar to the db object in {laminr} < v1 and matches lamindb’s Python API up to replacing . with $.
What Before After
Connect to the default LaminDB instance db <- connect() ln <- import_module("lamindb")
Start tracking db$track() ln$track()
Get an artifact from another instance new_instance <- connect("another/instance"); new_instance$Artifact$get(...) ln$Artifact$using("another/instance")$get(...)
Create an artifact from a path db$Artifact$from_path(path) ln$Artifact(path)
Finish tracking db$finish() ln$finish()

See the updated “Get started” vignette for more information.

User-facing changes:

  • Add an import_module() function to import Python modules with additional functionality, e.g., import_module("lamindb") for lamindb
  • Add functions for accessing more lamin CLI commands
  • Add a new “Introduction” vignette that replicates the code from the Python lamindb introduction guide

Internal changes:

  • Add an internal wrap_python() function to wrap Python objects while replacing Python methods with R methods as needed, leaving most work to {reticulate}
  • Update the internal check_requires() function to handle Python packages
  • Add custom cache()/load() methods to the Artifact class
  • Add custom track()/finish() methods to the lamindb module

MINOR CHANGES

  • Skip tests that require Python on CRAN (PR #153).

laminr v0.4.1

MINOR CHANGES

  • Bump R dependency to >= 4.1.0 to fix note on CRAN (PR #142).

laminr v0.4.0

Minor (breaking) changes to support the Python lamindb v1.0 release.

BREAKING CHANGES

  • Updates for compatibility with the Python lamindb v1.0 release (PR #136)

MINOR CHANGES

  • db$track() can now automatically create a transform UID when not supplied (PR #136)

laminr v0.3.1

This release improves the UX for setting up the Python environment and adds functions to allow access to CLI functionality from R.

NEW FUNCTIONALITY

DOCUMENTATION

  • Add a set up vignette and update other documentation with instructions for how to set up a Python environment (PR #129).

laminr v0.3.0

This release contains mostly UX improvements:

  • Support for interacting with private LaminDB instances
  • Support for interacting with TileDB-SOMA / CELLxGENE Census
  • Improved UX for tracking and finishing runs

NEW FUNCTIONALITY

  • Allow tracking of artifacts loaded for non-default instances (PR #124).
  • Interact with TileDB-SOMA stores (PR #117). Add a open() method to the Artifact class to connect to TileDB-SOMA stores.

MINOR CHANGES

  • Improve UX of db$track() and db$finish() (PR #120).

BUG FIXES

  • Allow connecting to private LaminDB instances (PR #118).
  • Fix error message when fetching the instance details fails (PR #123).

TESTING

  • Use the host system user for tests (PR #119)

DOCUMENTATION

  • Update the laminr Getting Started vignette with feedback from demo (PR #113).
  • Update roadmap (PR #112).
  • Simplify README content (PR #116).

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