Pysb

Bugfixes

* Fix path detection for external tools in new Anaconda releases (394)
* Fix errors in tutorials and example models (392)
* Fix error message in ScipyOdeSimulator referring to renamed kwarg (391)
* Fix package name for libsbml in setup.py (390)
* Tests: Fix Python 3.7 libsbml installation on travis (388)

New Features

* Model component names will now tab-complete when accessed as part of a ComponentSet (380)

General Improvements

* Keyword arguments to `__init__` are now validated by `ScipyOdeSimulator` (381), `StochKitSimulator` (382), and `CupSodaSimulator` (383)
* BioNetGen: Extra functions are now supported, including `And`, `Or`, `Floor`, `Ceiling`, `Min`, `Max`, `Abs`, and the constants `pi` and `e` (373)
* SBML exporter: Observables and Expressions are now set by AssignmentRules (370 and 372)

Bugfixes

* Fix Simulator initials_dict when set by array (377)
* Fix BNGSimulator when tspan doesn't start at 0 (379)
* Set a default module name for components when `__name__` isn't set (374)
* Fix StochKit export on Python 3 when lxml is installed (375)
* Fix serialization of components that do not have a model weakref set (386)
* Respect `BngSimulator` cleanup flag in `__init__` (385)

New Features

* Python 3.7 now officially supported (in addition to 3.6 and 2.7) (368)
* Filtering for ComponentSets ([documentation](https://pysb.readthedocs.io/en/stable/modules/core.html#pysb.core.ComponentSet.filter)) (340)
* SBML export now uses [LibSBML](https://pypi.org/project/python-libsbml/) and supports compartments and expressions (#367)
* On demand observable trajectories without adding them to the model ([documentation](https://pysb.readthedocs.io/en/stable/modules/simulator.html#pysb.simulator.SimulationResult.observable)) (337)

General Improvements

* The `<>` operator for reversible rules in Python 2.7 has been formally deprecated. Use `|` instead (344)
* Products of synthesis rules are enforced to be concrete (354)
* Monomers' site and state names are validated upon definition (352)
* Expressions now must be created from sympy.Expr. Previously, unwrapped integers and floats were accepted (350)
* Capture BNG errors into PySB exception messages (363)
* Show line numbers in the debug log for BioNetGen language files to aid interpreting BNG error messages (365)
* Python model exporter now produces Python 3.x compatible code (366)
* Recover from non-functional Cython/weave compilers on Windows (353)
* Better tests for PySB exporters, and explicit `ExpressionsNotSupported` and `CompartmentsNotSupported` exceptions where applicable (357)

Bugfixes

* Fix export to BNG of expressions containing `log` (361)
* Fix Kappa export when using parameters with overlapping (substring) names (346)

New Features

* New reversible rule operator `|`; the previous `<>` operator is now pending deprecation (309)
* Saving and loading of `SimulationResult` objects with metadata in HDF5 format (292)
* PySB now supports Kappa 4, including custom rate laws with PySB `Expression`s. Kappa 3 support has been dropped (334)
* Rule pattern matching and new model test suite (285)
* Model components can now be accessed as attributes (213)
* Importing models from BioModels can now use either the EBI mirror (default) or the CalTech one (325)
* Cython support for `ScipyOdeSimulator`; this allows efficient simulation on Python 3, where `weave` is no longer an option (320)

General Improvements

* Native Python 3 compatibility for the whole PySB codebase (312)
* Internal species for tracking synthesis/degradation rules `__source` and `__sink` have been removed (317)
* Specifying a pattern with a dangling bond now causes an error (328)
* Simulator `run()` arguments are no longer persistent (314)
* State values in patterns are now verified (322)
* Frequently Asked Questions added to documentation (331)
* Loading `CupSodaSimulator` no longer initializes the GPU on import; instead it wait until instantiation (332).
* `pysb.tools.sensitivity_analysis` code updated for compatibility with matplotlib 2.1 (303)
* Improvements to `ScipyOdeSimulator`'s `weave` interface, including better control of console output (299) and ensuring C code is cacheable when unicode variable names are used (301).
* Graph objects in the Kappa interface (e.g. contact maps) are now returned as `networkx` graphs, not `pygraphviz`. `pygraphviz` support for reading .dot files in the Kappa interface has been replaced with `pydot` (335).

Bugfixes

* Fix component rename when not using Self Exporter (321)
* `ComplexPattern.__call__` now raises a `DuplicateMonomerError` when duplicate monomers are present (323)
* Fixes for `ComplexPattern.is_concrete()` (307)
* Reversible `Rule.is_synth()` and `is_deg()` now work for reversible patterns (326)
* Fix error when running Tyson model with `CupSodaSimulator` (332)

New features
`BngSimulator`, an interface to all simulators provided by BioNetGen: ODE, partitioned-leaping, SSA (stochastic) and NFsim (network-free stochastic). See `pysb.simulator.bng.BngSimulator` (272).

General improvements
* Faster and more memory-efficient construction of ODEs from rules (293).
* `ScipyOdeSimulator` is faster in "pure Python" mode (i.e. without `weave` and a C compiler installed). It now also supports a somewhat broader range of sympy expressions in reaction rates. Also an experimental `use_theano` option has been added which uses [theano](http://deeplearning.net/software/theano/) rather than [weave](https://github.com/scipy/weave) for evaluating differential equation expressions. Note that PySB users who previously depended on `scipy.weave` for fast C translation of ODE expressions must now install the standalone `weave` package, as this module has been removed from scipy (#294).
* `StochKitSimulator` adds support for models with expressions. Also the simulation setup process is now faster.
* Performance benchmarking and regression testing with Airspeed Velocity (275). We will eventually work out a way to automatically execute the test suite and publish the results, but for now anyone who's interested in this would have to run it themselves.
* Continuous Integration for Windows with AppVeyor (263).

Bugfixes
* Accessing `SimulationResult.all` no longer crashes when `unicode` strings are used for observable or expression names under Python 2 (291, issue 290). We thought we fixed the whole unicode-and-numpy issue here back in 245, but apparently we missed a spot.
* `MatlabExporter` now correctly handles empty observables, i.e. observables whose pattern doesn't match any reachable species (289).
* Some code errors in the tutorial (module/class names that didn't get updated during a code refactoring) have been corrected (286). Thanks to Michael Retchin for catching this.

New features
- `StochKitSimulator`, an interface to the stochastic simulator [StochKit](https://github.com/StochSS/StochKit). See `pysb.simulator.stochkit.StochKitSimulator`.
- `InitialsSensitivity`, a tool to perform pairwise sensitivity analysis of initial conditions. See `pysb.tools.sensitivity_analysis.InitialSensitivity`. **EXPERIMENTAL**.
- Import models directly from BioModels from just their ID (BIOMDxxx... or MODELxxx...) with `pysb.importers.sbml.model_from_biomodels()`.

General improvements
- Faster simulation runs for models with many expressions (~60x speedup for a 200-expression model).
- Improved accuracy and better error reporting when parsing SBML expressions in `pysb.importers.sbml`.
- The Kappa interface has been upgraded to support Kappa version 4. This also means Kappa v3 is no longer supported.

Bugfixes
- `CupSodaSimulator` now works on Python 3.
- Simulators now fully respect parameter value overrides for initial condition parameters (252).
- Simulators now allow overriding a non-zero initial condition to zero (251).
- Simulators no longer have problems with parameter names that are unicode objects (still only ASCII characters are allowed, though) (278).
- Model components with the same name as a top-level sympy object (anything you would see in `from sympy import *`) no longer cause errors when simulating (259).
- Applying a compartment condition to a MonomerPattern that already has one now correctly raises an exception (258).
- `PysbFlatExporter` now works with compartments using inline size declarations (210).
- `ComplexPattern.is_equivalent_to` now correctly handles certain combinations of compartments that were previously mishandled (257).