Biobb PMX changelog

What’s new in version 5.0.0?

Changes

  • FIX: Accept lists in different formats on input properties.

  • FIX: Removing compatibility with python 3.11

  • DEPENDENCIES: Force scipy to <1.14 because of simps deprecation

  • CI/CD: Update set-up micromamba.

  • CI/CD: Adding global properties to test yaml configuration

  • CI/CD: Update GA test workflow to Python >3.9

  • DOCS: Updating to Python 3.9

  • CI/CD: Update .gitignore to include the new file extensions to ignore

  • CI/CD: Change test conf.yml to adapt to new settings configuration

  • [FEATURE] New sandbox_path property

What’s new in version 4.2.1?

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?

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?

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?

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?

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?

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?

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?

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?

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

  • Replace wrong arguments in pmxgentop.py commandline (commandline)

Other changes

  • New documentation styles (documentation) #8