diff --git a/HISTORY.md b/HISTORY.md index 691869d..a247818 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,9 +1,67 @@ # History -## 0.1.0 (2022-11-17) +## 0.3.3 (2023-11-20) +- **Fix**: Pin snakemake to v7.31.1 for compatibility with panoptes-ui job monitoring. [PR #35](https://github.com/NBChub/bgcflow_wrapper/pull/35) +- **Chore**: Security updates. [PR #35](https://github.com/NBChub/bgcflow_wrapper/pull/35) +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.3.2...v0.3.3) + +## 0.3.2 (2023-10-12) +- Release package in [PyPi](https://pypi.org/project/bgcflow_wrapper) +- **Change**: Downgrade pandas. [PR #29](https://github.com/NBChub/bgcflow_wrapper/pull/29) +- **Chore**: Dependency updates including urllib3 and cryptography. [PR #31](https://github.com/NBChub/bgcflow_wrapper/pull/31), [PR #30](https://github.com/NBChub/bgcflow_wrapper/pull/30) +- **New Contributor**: @dependabot. [PR #31](https://github.com/NBChub/bgcflow_wrapper/pull/31) +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.3.1...v0.3.2) + +## 0.3.1 (2023-08-27) +- **Update**: Read project metadata for dbt models synchronization. Manual definition of dbt models to exclude also added. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.3.0...v0.3.1) + +## 0.3.0 (2023-08-26) +- **Docs**: Refer to wiki for tutorial. [PR #26](https://github.com/NBChub/bgcflow_wrapper/pull/26) +- **Feature**: Use metabase API and dbt-metabase for uploading and syncing model relationships. [PR #27](https://github.com/NBChub/bgcflow_wrapper/pull/27) +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.8...v0.3.0) + +## 0.2.8 (2023-08-21) +- **Improvement**: Enhanced `mkdocs` report handling, dependency management, and example copying in `bgcflow init`. +- **Update**: Utilize BGCFlow v0.7.2 version dependencies metadata. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.7...v0.2.8) + +## 0.2.7 (2023-08-09) +- **New Feature**: Organize report by subcategory. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.6...v0.2.7) + +## 0.2.6 (2023-08-09) +- **Security Update**: Addressed security concerns. +- **Improvements**: CLI, testing, and new features including panoptes wrapper and subworkflows. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.5...v0.2.6) + +## 0.2.5 (2023-08-01) +- **Fix**: Correct alias parsing to accommodate bgcflow v0.7.0. [PR #20](https://github.com/NBChub/bgcflow_wrapper/pull/20) +- **Chore**: Security update. [PR #21](https://github.com/NBChub/bgcflow_wrapper/pull/21) +- **New Contributor**: @OmkarSaMo. [PR #19](https://github.com/NBChub/bgcflow_wrapper/pull/19) +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.4...v0.2.5) + +## 0.2.4 (2023-06-27) +- **Update**: Dependency update for improved stability and performance. [PR #17](https://github.com/NBChub/bgcflow_wrapper/pull/17), [PR #18](https://github.com/NBChub/bgcflow_wrapper/pull/18) +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.3...v0.2.4) + +## 0.2.3 (2023-06-15) +- **Fix**: Correct UnicodeEncodeError in Windows. [PR #7](https://github.com/NBChub/bgcflow_wrapper/pull/7) +- **Docs**: Add graphical abstract. [PR #16](https://github.com/NBChub/bgcflow_wrapper/pull/16) +- This release is compatible with BGCFlow version 0.6.1 and version 0.6.2. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.2-alpha...v0.2.3) + +## 0.2.2 (2023-01-30) +- **Pre-release**: Compatibility with BGCFlow 0.6.0. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.1-alpha...v0.2.2-alpha) + +## 0.2.1 (2022-11-18) +- **Migration**: Migrate to [NBChub repo](https://github.com/NBChub/bgcflow_wrapper). +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.2.0...v0.2.1-alpha) + ## 0.2.0 (2022-11-18) -## 0.2.1 (2022-11-18) Migrate to [NBChub repo](https://github.com/NBChub/bgcflow_wrapper) -## 0.2.2 (2023-01-30) Pre-release with BGCFlow 0.6.0 -## 0.2.3 (2023-06-15) Update compatibility with BGCFlow version 0.6.1 and version 0.6.2 -## 0.2.4 (2023-06-27) Dependency update -## 0.2.5 (2023-08-01) Security update +- Minor updates and enhancements. +- [Full Changelog](https://github.com/NBChub/bgcflow_wrapper/compare/v0.1.0...v0.2.0) + +## 0.1.0 (2022-11-17) +- Initial release of the package. diff --git a/README.md b/README.md index 00b0215..e294cff 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,10 @@ A snakemake wrapper and utility tools for [BGCFlow](https://github.com/NBChub/bg For more details, see [documentation](https://NBChub.github.io/bgcflow_wrapper/). +Please refer to the `BGCFlow` WIKI for detailed examples and use cases: + +[![wiki](https://img.shields.io/badge/wiki-documentation-forestgreen)](https://github.com/NBChub/bgcflow/wiki) + ## Publication > Matin Nuhamunada, Omkar S. Mohite, Patrick V. Phaneuf, Bernhard O. Palsson, and Tilmann Weber. (2023). BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets. bioRxiv 2023.06.14.545018; doi: [https://doi.org/10.1101/2023.06.14.545018](https://doi.org/10.1101/2023.06.14.545018) diff --git a/docs/installation.md b/docs/installation.md index f8f7f8e..a90971b 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -2,7 +2,7 @@ To install bgcflow_wrapper, run this command in your terminal: ``` console -pip install git+https://github.com/NBChub/bgcflow_wrapper.git +pip install bgcflow_wrapper ``` This is the preferred method to install bgcflow_wrapper, as it will always install the most recent stable release.