rebop - v0.9.2

Dependencies

• drop python 3.10 and upgrade dependencies
• upgrade rand to v0.9.1 and rand_distr to v0.5.1
• upgrade winnow to v0.7.10
• upgrade pyo3 to v0.24.2
• update rand to v0.9 and rand_distr to v0.5
• bump actions/create-github-app-token in the actions group

Fixed

• allow inf or nan in parameter names (thank you @maurosilber!)
• add a few test cases for float parsing

Miscellaneous

• update github CI

- Rust
Published by armavicas-release-app[bot] 10 months ago

rebop - v0.9.1

Added

• Allow parameters to be used in rate expressions.

Changed

• change error message for species not involved in reactions
• allow species not in reactions to be init but with warning
• rename lib::Rate into lib::PRate
• rename PExpr::Concentration into PExpr::Variable

Documentation

• fix parameters in docs index page
• add example with Michaelis-Menten rate
• improve docstrings to explain reaction rates
• fix some docstrings of the rust API

Fixed

• use Mapping and Sequence instead of dict and list in type hints
• raise error on erroneous rate expressions
• make the rates more strict
• ensure that the dataset returned has a time coordinate

Miscellaneous

• update pixi.lock with new version
• add test with crossed rates
• remove useless clone
• remove unused imports

- Rust
Published by armavicas-release-app[bot] about 1 year ago

rebop - v0.9.0

Added

• Reaction rates can now be arbitrary formulas, instead of just LMA (Python API).
• Reaction rates can be internally sparse, leading to drastic speedups for models with many species (thank you @maurosilber!) (Python API).
• One can specify to not export all variables, with the var_names argument (thank you @maurosilber!) (Python API).

Changed

• The seed argument was renamed to rng to conform to SPEC-7 (Python API).

Dependencies

• upgrade pyo3 to 0.23

Documentation

• organize badges on README
• add badges for the PyPI version and RTD docs
• fix name of optional dependencies in rtd config
• add rust tooling to the readthedocs environment
• fix readthedocs install
• add a readthedocs page
• document the Python interface

Fixed

• fix arbitrary rates overwriting previous definitions
• fix benches with a sparsity argument

Miscellaneous

• check all targets in pre-commit
• add tests for exprs
• robustify Gillespie tests
• Add tests for gillespie::Jump
• add tests for gillespie::Rate
• add tests for gillespie::Rate
• fix pixi build task
• update CI
• update pre-commit hooks
• upgrade dependencies
• cancel CI on repeated PRs
• enable dependabot update grouping
• use a markdown formatter
• add custom pre-commit CI message
• enable mypy
• update pre-commit hooks
• make ruff show fixes
• enable docstring format by ruff
• add pytest config options

- Rust
Published by armavicas-release-app[bot] about 1 year ago

rebop - v0.8.3

Miscellaneous

• Use GitHub app to make release-plz trigger workflows

- Rust
Published by armavicas-release-app[bot] over 1 year ago

rebop - v0.8.2

Test release with release-plz.

Documentation

• Update image links in the README

- Rust
Published by github-actions[bot] over 1 year ago