diff --git a/docs/bbconf/changelog.md b/docs/bbconf/changelog.md index e50d2b6..0b449f6 100644 --- a/docs/bbconf/changelog.md +++ b/docs/bbconf/changelog.md @@ -2,6 +2,29 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. +# [0.7.0] - 2024-09-20 +## Added +- Table and methods for reference genome validator +- Table with standard metadata schema +- Bed file opening improvements + +# [0.6.1] - 2024-08-21 +## Added + +- DB tables for GEO uploader status + +# [0.6.0] - 2024-05-01 +## Added + +- Added tokenized files and universes. +- Added bed embedding get endpoint to the API #50 +- Fixed test speed #48 +- Added license for the bed files #51 +- Added payloads to qdrant +- Fixed search, and query results info +- Many other small bug fixes + + # [0.5.1] - 2024-04-09 ## Changed @@ -81,4 +104,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [0.0.1] - 2020-02-05 ### Added -- initial project release +- initial project release \ No newline at end of file diff --git a/docs/bedboss/changelog.md b/docs/bedboss/changelog.md index cdd875e..cecdbec 100644 --- a/docs/bedboss/changelog.md +++ b/docs/bedboss/changelog.md @@ -2,6 +2,30 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. +# [0.4.1] - 2024-09-20 +## Added +- Standardization of peps using bedbase bedms schema +- Reference validator module + +## Fixed +- Pipeline failures (due to pipeline manager) +- Failure in cleaning temp files + + +# [0.4.0] - 2024-08-26 +## Added +- Added bbuploader (GEO uploader) + +# [0.3.0] - 2024-08-21 +## Added +- Added classifier +- Added create universe uploader +- Added tokenization and token uploader + +## Changes +- Updated efficiency of CLI help + + # [0.2.1] - 2024-04-09 ## Changed - small naming tweaks @@ -21,4 +45,4 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [0.1.0] - 2024-01-26 ### Added -- Initial alpha release +- Initial alpha release \ No newline at end of file diff --git a/docs/geniml/README.md b/docs/geniml/README.md index 05b2da3..26ccc7a 100644 --- a/docs/geniml/README.md +++ b/docs/geniml/README.md @@ -16,11 +16,35 @@ Geniml is a *genomic interval machine learning toolkit*, a Python package for bu As of Feburary 2024, this package and its documentation are undergoing rapid development, leading to some tutorials getting outdated. Please raise [github issues](https://github.com/databio/geniml) if you find outdated or unclear directions, so we know where to focus effort that will benefit users. -## Install +## Installation +### To install `geniml` use this commands. +Without specifying dependencies, the default dependencies will be installed, +which DO NOT include machine learning (ML) or heavy processing libraries. + + +From pypi: +``` +pip install geniml +``` +or install the latest version from the GitHub repository: ``` -pip install --user --upgrade geniml +pip install git+https://github.com/databio/geniml.git +``` + +### To install Machine learning dependencies use this command: + +From pypi: ``` +pip install geniml[ml] +``` + + +## Development + +Run tests (from `/tests`) with `pytest`. Please read the [contributor guide](https://docs.bedbase.org/geniml/contributing/) to contribute. + + ## Modules and resources diff --git a/docs/geniml/changelog.md b/docs/geniml/changelog.md index 4c5284b..02f70a8 100644 --- a/docs/geniml/changelog.md +++ b/docs/geniml/changelog.md @@ -2,6 +2,19 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. +## [0.4.2] -- 2024-10-07 + +- Cleaned dependencies and separated into 2 groups: basic and ml. +- Improved efficiency of CLI +- Fixed bbcache incorrectly saving files from url #175 + + +## [0.4.1] -- 2024-09-18 + +- Fixed: bbclient ignores --cache-folder on CLI #164 +- Fixed bug in opening bed files + + ## [0.4.0] -- 2024-06-04 - Added bed tokens caching to bbclient [bbclient] Add tokenized file cache and download [#153](https://github.com/databio/geniml_dev/issues/153)