v0.1.7

Release notes for MASSpy 0.1.7

• Dropped support Python 3.6.

Fixes

• Fixed versioning issues in installation
• Fixed documentation issues
• Other minor fixes and maintenance

Full Changelog: v0.1.6...v0.1.7

v0.1.5

Minor fixes

v0.1.4

MASSpy is now on BiosSimulators!!!!!

matplotlib is now an optional dependency. To install MASSpy with visualization dependencies:

pip install "masspy[visualization]"
Important Notice:
Significant changes are coming in the 0.2.0 version, including some API changes and backwards incompatible changes.

Prepare yourself and contact zhaiman@eng.ucsd.edu if you have any questions before or after the 0.2.0 release!

v0.1.3

Release notes for MASSpy 0.1.3

The MASSpy publication can be cited!

New features

Working toward the next major release, in the meantime...

• Added Python 3.8 and 3.9 support

• Installation and setup updates based on the following PEP guidelines:

  • PEP 440
  • PEP 517
  • PEP 518
  • PEP 566

• MASSpy now contains several new tools for standardized testing and development!

  • New CI-CD testing workflow in main.yml for GitHub actions and
    coverage using CodeCov
  • Configuration for tools is primarily in pyproject.toml. Options without
    .toml compatibility are in setup.cfg

Details for installation and setup updates.

• Apply src/ layout to package
• Applied new PEP guidelines for setup using pyproject.toml
  • New file pyproject.toml for building package based on setup.cfg,
    setuptools,
    and pypa/build.

Standardized testing and development tools

• Implemented tox for testing. Configuration is found in pyproject.toml.

  • Utilize pytest for testing, and coverage via pytest-cov for coverage reports.
  • Added lint, safety, and `py3{6,7} testing environments.

• Implemented pre-commit for maintaining repository. Utilizes pre-commit hooks for

  • isort, black, and flake8 for linting.
  • Several additional pre-commit hooks and pygrep hooks
    for formatting other file types.
  • Configuration found in new .pre-commit-config.yaml

Fixes

• Udated CI-CD workflow to one single file (main)
• Updates to sphinx documentation builder to account for new build.
• Code of conduct
• Added security policy
• .gitignore improvements
• Updated manifest
• Updated README.rst to .md
• Dockerfile bugfixes and more organization
• Sphinx make file cleanup
• Additional repository links
• Added MASSpy publication for citation!
• Badge fixes

Backwards incompatible changes

• test data within the MASSpy package is now example_data. methods change to reflect
• Test methods and model still exist, but outside the package in the tests directory

v0.1.1

Release notes for MASSpy 0.1.1

Updates to MASSpy during software publication process! Check it out at the MASSpy-publication GitHub Repository!

New features

• Significant updates to the documentation at ReadTheDocs
• Additional testing data
• Docker containers are now available for MASSpy!

Fixes

• Collection of compartment variables in rate laws fixed for better grouping when multiple compartments involved.
• Documentation fixes

v0.1.0

Release notes for MASSpy 0.1.0

Release of MASSpy during software publication process! Check it out at the MASSpy-publication GitHub Repository!

Updated Notes for restored 0.1.0 version

Original version yanked due to docker compatibility issues with soft dependency requirements.
However, Docker containers are now compatible for 0.1.0

MASSpy 0.1.0 is now a yanked release (not deleted for dev/archival reasons).