updated changelogs and added how to install geniml

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

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

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Feburary 2024, this package and its documentation are undergoing rapid development, leading to some tutorials getting outdated. Please raise [github issues](https://github.com/databio/geniml) if you find outdated or unclear directions, so we know where to focus effort that will benefit users.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
 

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)