From 90aefd9af954672932f4b43dbda2e153d40bf105 Mon Sep 17 00:00:00 2001 From: Alex Wolf Date: Thu, 28 Nov 2024 11:04:03 +0100 Subject: [PATCH] Simplify README (#116) * Simplify README * Update README.md * Update CHANGELOG * Roxygenise --------- Co-authored-by: Robrecht Cannoodt Co-authored-by: Luke Zappia --- CHANGELOG.md | 12 ++++++++---- README.md | 41 ++++++++++------------------------------- man/laminr-package.Rd | 2 +- 3 files changed, 19 insertions(+), 36 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f046e0c..271d1c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,13 +2,17 @@ ## BUG FIXES -* Allow connecting to private LaminDB instances (PR #118). +- Allow connecting to private LaminDB instances (PR #118) -## DOCUMENTATION +## TESTING -* Update the laminr Getting Started vignette with feedback from demo (PR #113). +- Use the host system user for tests (PR #119) + +## DOCUMENTATION -* Update roadmap (PR #112). +- 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 diff --git a/README.md b/README.md index 33c66c7..fa0a36b 100644 --- a/README.md +++ b/README.md @@ -6,29 +6,15 @@ [![R-CMD-check](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/laminlabs/laminr/actions/workflows/R-CMD-check.yaml) -**{laminr}** is an R client for [LaminDB](https://lamin.ai). - -## What is LaminDB - -If you are new to LaminDB, it's helpful to start with [Lamin's problem statement](https://lamin.ai/blog/problems). -LaminDB is an open-source data framework for biology, built as a Python API that structures data and metadata, tracks analysis lineage, and enables reproducible, scalable research. -With tools for curating data against public ontologies and flexible dataset querying, LaminDB is designed to address core data challenges in the field. -Please refer to [LaminDB's introduction](https://docs.lamin.ai/introduction) for a more detailed introduction. -LaminDB is accompanied by LaminHub which is a data collaboration hub built on LaminDB similar to how Github is built on git. - -## Features of **{laminr}** - -- Connect to a LaminDB instance and list all records in a registry. -- Fetch records by ID or UID. -- Cache artifacts locally. - - Currently supported storage backends: `s3`. - - Planned: `gcs`. -- Load artifacts into memory. - - Currently supported file formats: `.csv`, `.h5ad`, `.html`, `.jpg`, `.json`, `.parquet`, `.png`, `.rds`, `.svg`, `.tsv`, `.yaml`. - - Planned: `.fcs`, `.h5mu`, `.zarr`. -- Create records from data frames, paths and `AnnData` objects. -- Delete records. -- Track code in R scripts and notebooks. +**{laminr}** is an R client for [LaminDB](https://lamin.ai). If you are new to LaminDB, please read this [introduction](https://docs.lamin.ai/introduction). + +- Connect to a LaminDB instance: `db <- connect()` +- Track scripts and notebooks as transforms: `db$track()` +- Get records by UID: `artifact <- db$Artifact$get()` +- Cache artifacts locally: `artifact$cache()` +- Load artifacts into memory for a broad range of storage formats: `artifact$load()` +- Create artifacts from data frames, paths, and `AnnData` objects: `db$Artifact$from_path()` +- Delete records: `artifact$delete()` See the development roadmap for more details (`vignette("development", package = "laminr")`). @@ -69,17 +55,10 @@ If you choose not to install all packages now you will be prompted to do so when The best way to get started with **{laminr}** is to explore the package vignettes (available at [laminr.lamin.ai](https://laminr.lamin.ai)): -- **Getting Started**: Learn the basics and explore practical examples (`vignette("laminr", package = "laminr")`). +- **Get started**: Learn the basics and explore practical examples (`vignette("laminr", package = "laminr")`). - **Package Architecture**: Get a better understanding of how **{laminr}** works (`vignette("architecture", package = "laminr")`). For information on specific modules and functionalities, check out the following vignettes: - **Core Module**: Learn about the core registries available in a LaminDB instance (`vignette("module_core", package = "laminr")`). - **Bionty Module**: Explore the bionty module for biology-related entities (`vignette("module_bionty", package = "laminr")`). - -## Learn more - -For more information about LaminDB and its features, check out the following resources: - -- [LaminDB website](https://lamin.ai/) -- [LaminDB documentation](https://docs.lamin.ai/) diff --git a/man/laminr-package.Rd b/man/laminr-package.Rd index a0b03c5..a15f682 100644 --- a/man/laminr-package.Rd +++ b/man/laminr-package.Rd @@ -4,7 +4,7 @@ \name{laminr-package} \alias{laminr} \alias{laminr-package} -\title{laminr: Interface for 'LaminDB'} +\title{laminr: Client for 'LaminDB'} \description{ Interact with 'LaminDB'. 'LaminDB' is an open-source data framework for biology. This package allows you to query and download data from 'LaminDB' instances. }