Bioscrape version 1.0.3 out

[Ayush Pandey]

Hey everyone,

New version of bioscrape is now out, and pip installable. Many new features and some bug fixes (especially in Lineages, thanks @Sam Clamons)! Here is an overview:

Major Changes:
* New inference features: py_inference wrapper, beta, gamma, and custom prior, least squares fitting using lmfit (talk to @Ayush Pandey for details)
* New rule types: for ODEs and new rule frequences: "dt" fires every dt and [numerical] fires when the time is that exact number, used as events.  (Talk to @William Poole for details)
* New Lineages Features: Turbidostat in allows a fixed population of cells to be simulated. SafeLineageCSimInterface provides a safe mode for lineage simulation us via the py_simulate_....(....safe = True) methods. (Talk to @Sam Clamons for details)
* New Analysis New features: Sensitivity analysis (@Ayush Pandey) and fast cython functions to calculate statistics such as means, correlations, and marginal distributions from stochastic trajectories (@William Poole)
* Bioscrape XML is removed. Replaced completely by SBML. (Bioscrape XML reading still supported, for the time being)
* Deterministic Safe Mode: this can be activated via py_simulate_model(...safe = True) or by using a SafeModelCSimInterface

> pip install bioscrape

or (if you already have it installed)

> pip install bioscrape --upgrade