docs: update install instruction and history

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.

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)
 

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.