# Biobb PMX changelog

## What's new in version [5.2.2](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.2)?

### Changes

* [UPDATE] Update to biobb_common 5.2.2

## What's new in version [5.2.1](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.1)?

### Changes

* [UPDATE] Add compatibility with python 3.11 and 3.12


## What's new in version [5.2.0](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.0)?

### Changes

* [UPDATE] Update to biobb_common 5.2.0

## What's new in version [5.1.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v5.1.0)?

### Changes

* [UPDATE]: Update to biobb_common 5.1.0

## What's new in version [5.0.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v5.0.0)?

### Changes

* [FIX](all): Accept lists in different formats on input properties.
* [FIX](all): Removing compatibility with python 3.11
* [DEPENDENCIES](all): Force scipy to <1.14 because of simps deprecation
* [CI/CD](linting_and_testing.yml): Update set-up micromamba.
* [CI/CD](conf.yml): Adding global properties to test yaml configuration
* [CI/CD](linting_and_testing.yaml): Update GA test workflow to Python >3.9
* [DOCS](.readthedocs.yaml): Updating to Python 3.9
* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
* [FEATURE] New sandbox_path property

## What's new in version [4.2.1](https://github.com/bioexcel/biobb_pmx/releases/tag/v5.0.0)?

### Changes

* [DOCS] Update JSON
* [TEST] Updating GMXLIB of docker test
* [CI/CD] Update actions/checkout to v4
* [FIX] Fix type hints

## What's new in version [4.2.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v5.0.0)?

### Changes

* [UPDATE] Updating json schemas
* [DOCS] Adding description to all modules
* [FIX] Adding additional paths
* [DOCS] Adding fair software badge and GA
* [DOCS] Added references file
* [CI/CD] Adding Castiel Gitlab push sync github Action
* [DOCS] Fixing Read the Docs
* [DOCS] Updating README
* [DOCS] Change json file

## What's new in version [4.1.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.1.0)?
In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
New Python minimum version is 3.8.0.

## What's new in version [4.0.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v4.0.0)?
In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.
Three new modules have been added

### New features

* Update to biobb_common 4.0.0 (general)
* Support for ligands in PMX

## What's new in version [3.8.1](https://github.com/bioexcel/biobb_pmx/releases/tag/v3.8.1)?
In version 3.8.1 the dependency biobb_common has been updated to 3.8.1 version.
Three new modules have been added

### New features

* Update to biobb_common 3.8.1 (general)
* Three new modules have been added

## What's new in version [3.7.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v3.7.0)?
In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.

### New features

* Update to biobb_common 3.7.0 (general)

## What's new in version [3.6.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v3.5.0)?
In version 3.0.3 the dependency biobb_common has been updated to 3.5.1 version. Also, there has been implemented the new version of docstrings, therefore the JSON Schemas have been modified.

### New features

* Update to biobb_common 3.6.0 (general)
* Update to Biopython 1.79 (general)
* New extended and improved JSON schemas (Galaxy and CWL-compliant) (general)

### Other changes

* New docstrings

## What's new in version [3.6.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v3.6.0)?
In version 3.6.0 PMX software has been updated to its python 3 version and thus, biobb_pmx breaks its dependence from docker.

### New features

* First full python 3 compatible version of biobb_pmx

## What's new in version [3.6.0](https://github.com/bioexcel/biobb_pmx/releases/tag/v3.6.0)?
In version 3.6.0 Python has been updated to version 3.7 and Biopython to version 1.79.
Big changes in the documentation style and content. Finally a new conda installation recipe has been introduced.

### New features

* Update to Python 3.7 (general)
* Update to Biopython 1.79 (general)
* New conda installer (installation)
* Adding type hinting for easier usage (API)
* Deprecating os.path in favour of pathlib.path (modules)
* New command line documentation (documentation)

### Bug fixes

* Replace container Quay.io badge (documentation)
* Remove unused system and step arguments from command line causing execution errors (cli) [#9](https://github.com/bioexcel/biobb_model/issues/9)
* Replace wrong arguments in pmxgentop.py commandline (commandline)

### Other changes

* New documentation styles (documentation) [#8](https://github.com/bioexcel/biobb_model/issues/8)