update README, CHANGELOG

CHANGELOG.md

@@ -3,30 +3,55 @@
 
 All notable changes to this project will be documented in this file.
 
-The format is based on [Keep a Changelog](http://keepachangelog.com/)
-and this project adheres to [Semantic Versioning](http://semver.org/).
+The format is based on [Keep a Changelog] and this project adheres to [Semantic Versioning].
 
 ## [Unreleased] - yyyy-mm-dd
 
-Initial release of a PyTorch Dataset for SOMA Experiments. This is a port and
-enhancement of code contributed by the Chan Zuckerberg Initiative Foundation
-[CELLxGENE](https://cellxgene.cziscience.com/) project.
+Initial release of a [PyTorch Dataset] for [SOMA] Experiments. This is a port and enhancement of code contributed by the Chan Zuckerberg Initiative Foundation [CELLxGENE] project.
 
-This is not a one-for-one migration of the contributed code. Substantial changes have
-been made to the package utility (e.g., multi-GPU support), improved API UX, performance
-improvements, and more.
+This is not a one-for-one migration of the contributed code. Substantial changes have been made to the package utility (e.g., multi-GPU support), improved API UX, performance improvements, and more.
 
 ### Added
 
-- Initial project organization and other scaffolding [PR #4](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/4)
-- Simple, non-shuffling Dataset/DataPipe implementation [PR #6](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/6)
-- Add CI workflows [PR #7](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/7)
-- Add a DataLoader creation wrapper function [PR #8](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/8)
-- Add shuffling support [PR #9](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/9)
-- Add first draft of tutorial notebooks [PR #10](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/10)
-- Archive script used to populate the repo commit history [PR #11](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/11)
-- I/O buffer performance optimization [PR #13](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/13)
+#### 2025-02
+- [#26]: rm `IterDataPipe`, consolidate into `ExperimentDataset`, add `docs`/`www` builds
+
+#### 2024-12
+- [#23]: Split `{test_,}pytorch.py` into a few files
+- [#20]: Add `vfs.s3.no_sign_request` config
+- [#19]: Support `somacore>=1.0.24` / `tiledbsoma>=1.15`
+
+#### 2024-10
+- [#13]: I/O buffer performance optimization
+- [#11]: Archive script used to populate the repo commit history
+- [#10]: Add first draft of tutorial notebooks
+- [#9]: Add shuffling support
+- [#8]: Add a DataLoader creation wrapper function
+- [#7]: Add CI workflows
+- [#6]: Simple, non-shuffling Dataset/DataPipe implementation
+- [#4]: Initial project organization and other scaffolding
 
 ### Changed
 
 ### Fixed
+
+
+[Keep a Changelog]: http://keepachangelog.com/
+[Semantic Versioning]: http://semver.org/
+
+[PyTorch Dataset]: https://pytorch.org/tutorials/beginner/basics/data_tutorial.html
+[SOMA]: https://github.com/single-cell-data/SOMA
+[CELLxGENE]: https://cellxgene.cziscience.com/
+
+[#26]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/26
+[#23]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/23
+[#20]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/20
+[#19]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/19
+[#13]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/13
+[#11]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/11
+[#10]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/10
+[#9]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/9
+[#8]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/8
+[#7]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/7
+[#6]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/6
+[#4]: https://github.com/single-cell-data/TileDB-SOMA-ML/pull/4

README.md

@@ -1,21 +1,19 @@
+# TileDB-SOMA-ML
 
-# tiledbsoma_ml
-
-A Python package containing ML tools for use with `tiledbsoma`.
+A Python package containing ML tools for use with [TileDB-SOMA].
 
 **NOTE:** this is a _pre-release_ package, and may be subject to breaking API changes prior to first release.
 
 ## Description
 
-The package contains a prototype PyTorch `IterableDataset` for use with the
-[`torch.utils.data.DataLoader`](https://pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader)
+The package contains a prototype PyTorch [`IterableDataset`] for use with the
+[`torch.utils.data.DataLoader`]
 API. For a general introduction to PyTorch data loading,
-[see this tutorial](https://pytorch.org/tutorials/beginner/data_loading_tutorial.html).
+[see this tutorial][torch data tutorial].
 Additional information on the DataLoader/Dataset pattern
-[can be found here](https://pytorch.org/docs/stable/data.html).
+[can be found here][`torch.data`].
 
-Defects and feature requests should be filed as a GitHub issue in this repo. Please include a reproducible
-test case in all bug reports.
+Defects and feature requests should be filed as a GitHub issue in this repo. Please include a reproducible test case in all bug reports.
 
 ## Getting Started
 
@@ -35,8 +33,8 @@ pip install -e .
 
 ### Documentation
 
-Documentation is pending. Preliminary documentation can be found in API docstrings, and in
-the [notebooks](notebooks) directory.
+Documentation is pending. Preliminary documentation can be found at [single-cell-data.github.io/TileDB-SOMA-ML], and in
+the [notebooks] directory.
 
 ## Builds
 
@@ -48,7 +46,7 @@ python -m build .
 
 ## Version History
 
-See the [CHANGELOG.md](CHANGELOG.md) file.
+See the [CHANGELOG.md] file.
 
 ## License
 
@@ -58,3 +56,12 @@ This project is licensed under the MIT License.
 
 The SOMA team is grateful to the Chan Zuckerberg Initiative Foundation [CELLxGENE Census](https://cellxgene.cziscience.com)
 team for their initial contribution.
+
+[TileDB-SOMA]: https://github.com/single-cell-data/TileDB-SOMA
+[`IterableDataset`]: https://pytorch.org/docs/stable/data.html#torch.utils.data.IterableDataset
+[`torch.utils.data.DataLoader`]: https://pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader
+[torch data tutorial]: https://pytorch.org/tutorials/beginner/data_loading_tutorial.html
+[`torch.data`]: https://pytorch.org/docs/stable/data.html
+[single-cell-data.github.io/TileDB-SOMA-ML]: https://single-cell-data.github.io/TileDB-SOMA-ML/
+[notebooks]: notebooks
+[CHANGELOG.md]: CHANGELOG.md