Pysb

This version of PySB supports Python 3.6-3.9. Python 2.7 is no longer supported.

New features

* Implement reversible synthesis rules (499)

Improvements

* ScipyOdeSimulator speedup through refactoring, use of partial (531, 483)
* Use double precision for BNG and Kappa parameters (490)
* Allow constant expressions for compartment sizes (525)
* Faster SimulationResult loading: use slices (491)
* Implement BNG boolean treatment within expressions, e.g. evaluate `(2 > 1)` as `True` (494)
* Import ABC from collections.abc instead of collections for Python 3.9 compatibility (485)
* Implement the assumption that all symbolic variables in a model only take real values. The user can specify integer and non-negative enforced assumptions about parameter values. Changes are relevant for any simplifications of symbolic expressions in the model (475)
* Update tested Python versions on CI (479)
* Remove weave and theano support from ScipyOdeSimulator (482)
* Remove Python 2 support (486, 487)
* Update docs with Python version support (492)
* Update docs with stubs on calibration and PySB modules to tutorial (509)
* Update deprecated pandas call in CupSodaSimulator (523)
* Remove deprecated sympy.boolalg calls (526)
* Specify Python>=3.6 requirement in setup.py (536)

Bug fixes

* Fix sympy 1.6 compatibility (505)
* Fix observable trajectories on HDF5 load (502)
* Fix reading of error messages from cupSODA (510)
* Fix SBML export with unset compartment size (513)
* Fix eqn_mode='python' for models with local functions (495)
* Fix typehints in core (507, 520)
* Fix BNG code generation for `Eq` and `Ne` (528)
* Fix StochKit export of certain PySB rate Expressions (521)
* Copy annotations when creating model from base (493)
* Fix SimulationResult loads when `include_obs_exprs=True` and model has no observables or expressions (481)
* Fix an error when using ScipyOdeSimulator with the num_processors
option >1 (i.e. use multiprocessing) together with compiler='python' (480)
* Fix usage of super in multiple inheritance of sympy.Symbol (474)
* Fix readthedocs error with updated mock (489)
* Fix slice IndexError in tutorial (529)
* Fix tutorial typos (511)
* Fix DeprecationWarning leading to test failure with new versions of h5py (537)

The only change in this release is that Python version requirements are now specified in setup.py metadata (Python 2.7, or >=3.5). This is anticipated to be the final PySB release to support Python 2.7.

New features

* JSON model import and export (469)

Improvements

* Models stored in HDF5 files using `SimulationResult.save()` now use JSON, rather than pickle
* Raise a `ValueError` if a rule defined with reverse rate, but expression is not reversible (471)

Bug fixes

* Fixes for importing certain BNGL and SBML models which previously failed to import (470)
* Fix `SimulationResult.load()` for HDF5 files saved with PySB <1.10, which gave a pickle error when loading on PySB 1.10. Such HDF5 files should be re-saved in order to use the new JSON model format, which should be more durable across PySB versions.

New features

* Local functions (412, 464)

Local functions allow PySB expressions to accept a tagged `MonomerPattern` or `ComplexPattern` as an argument. For example, in the following snippet, `A` synthesizes `C` with rate dependent on bound `B`:

python
Observable('AB_motif', A(b=1) % B(a=1))
Tag('x')
Expression('f_synth', k_synthC * AB_motif(x) ** 2)
Rule('_R1', A() x >> A() x + C(), f_synth)


See [localfunc.py](https://github.com/pysb/pysb/blob/master/pysb/examples/localfunc.py) for a complete example.

* KappaSimulator (447)

New simulation interface for Kappa which supports multiple initial condition sets and parameter sets. Replaces `pysb.kappa.run_simulation`. See [KappaSimulator documentation](http://docs.pysb.org/en/stable/modules/simulator.html#pysb.simulator.KappaSimulator) for further details.

Improvements

* Show `ReusedBondError` when bond connects >2 sites in a reaction pattern (466)
* Add dashed edge when reaction rate is an expression with observables (458)
* Include macros in `rule._function` (451)
* Improved error messages when external tools not found; make Atomizer use `pysb.pathfinder` (460)

Bug fixes

* Fix reading `MultiState` species from BioNetGen models (462)
* Fix `Expression.get_value()` (457)
* PySBFlatExporter now supports `MultiState` (453)
* Fix `ModelNotDefinedError` when self exporter is used and a model
component is declared before Model() (452)

Miscellaneous

* Switch from coveralls to codecov (454)

Bug fixes

* Fix BngSimulator when specifying parameters to change initial conditions (450)

Miscellaneous

* Use Anaconda package of LibSBML on Python 3.7 for testing on Travis (448)

New Features

* `MultiState` capability, which enables a single `Monomer` site to be specified with multiple states ([documentation](https://pysb.readthedocs.io/en/stable/modules/core.html#pysb.core.MultiState)) (410)
* `ScipyOdeSimulator` multiprocessing capability, using `n_processors` argument ([documentation](http://docs.pysb.org/en/stable/modules/simulator.html#pysb.simulator.ScipyOdeSimulator.run)) (395)
* Multi-GPU simulations and chunking support (split large simulation sets into GPU-sized blocks) for `CupSodaSimulator` (409)
* Sensitivity analysis class can now work for model parameter sweeps, in addition to initial conditions ([documentation](https://pysb.readthedocs.io/en/stable/modules/tools/sensitivity_analysis.html)) (#426)
* Support for fixed concentration species (364)
* Initial condition and parameter sets can now be supplied to Simulator instances as Pandas DataFrames (416)
* Drug binding macro `pysb.macros.drug_binding()` ([documentation](https://pysb.readthedocs.io/en/stable/modules/macros.html#pysb.macros.drug_binding)) (387)
* Support `BngSimulator` early stopping using `stop_if` kwarg (example: `sim.run(stop_if='ObsA>9')`) (407)
* BioNetGen importer improvements, including preserving parameter depdendencies in expressions, the `MoveConnected` keyword, and Observables' species compartments (406)

Improvements

* `ScipyOdeSimulator` is now faster when using Cython due to customized compiler directives (403)
* When model components experience a validation error on creation, they're no longer added to the model by the `SelfExporter` (431)
* Use the system `PATH` variable to help find external tools like BioNetGen or Kappa (389)
* SBML Exporter: preserve parameter dependency in initial conditions (417) and specify initial concentrations for all species (420)
* BioNetGen importer now allows relative paths (432)
* StochKit log file contents are now included in error messages (429)
* Clearer error messages when Cython is non-functional on Windows (402)

Bug fixes

* Corrections to the PySB tutorial (422)
* Fix number of simulations calculation for NFsim (445)
* Fix cupSODA when using models with non-alphanumeric characters (404)
* Fix Exception when calling `expand_obs()` on observables which match no species (418)
* Fix for model name being changed in unit test (399)
* Fix Model.update_initial_condition_pattern (446)
* Minor packaging fixes (396, 411, 433)
* Minor code tidy-ups (405, 436)
* Documentation build fixes (424, 444)

Deprecations

* ScipyOdeSimulator's theano backend (428)