Pysb

New features
- CupSodaSimulator, a wrapper for the [cupSODA](https://github.com/aresio/cupSODA) GPU-based ODE integrator. No special Python libraries are necessary since cupSODA comes as a standalone binary, but if PyCUDA is installed then PySB can auto-detect the configuration details of your GPU. See the documentation in `pysb.simulator.CupSodaSimulator` for more.
- Simulators can now support multiple parameter sets and/or initial condition sets, especially helpful for internally parallel simulators such as CupSodaSimulator.
- PySB internals now use the `logging` module to emit diagnostics, making debugging (or silencing output) easier. This is exposed externally through the `PYSB_LOG` environment variable -- set it to one of the standard logging levels (DEBUG, INFO, etc.) to control which messages are printed.

Bugfixes
- BNGL and SBML importers now work on Windows.
- Observables and Expressions with unicode objects for names (rather than strings) no longer trigger an internal numpy exception in the PySB Simulator code on Python 2. An exception will still be raised if the unicode names do contain non-ascii-safe characters, but the error message is now more intelligible.

Bugfixes
- The SBML exporter works again (it's been broken ever since v1.0.0 :grimacing:)

Other
- Documentation improvements

Bugfixes
- Python 3 / unicode compatibility fixes.

New features
- Brand new Simulator classes and SimulationResult classes in the `pysb.simulator` package. The old `pysb.integrate` API is unchanged but has been reimplemented using the Simulator class.
- Model import from other types of models in the `pysb.importers` package. Currently supports BNGL and SBML model import.

Bugfixes
- pysb_flat exporter now supports `MatchOnce`.
- Some Python 2 Unicode issues were addressed by eliminating uses of `type(...) == str`.

Release to fix one minor bug with the PyPI upload.

Bugfixes
- The source distribution on PyPI now includes ez_setup.py.

PySB has officially adopted semantic versioning. This means v1.1.0 includes new features as compared to v1.0.x, but is still backwards compatible so you won't have to change any of your models to upgrade to it.

New features
- Full Python 3 compatibility. All tests pass under Python 3.4 and 3.5.
- BioNetGen 2.2.6 support, and a new API for interfacing with BioNetGen which can execute any BioNetGen commands and operate in batch or interactive mode. The old run_ssa function is still available.
- BioNetGen temporary files are now created in system temporary directories by default.
- Kappa 4.0 support, and a new API here as well. The old run_simulation, contact_map, and influence_map functions are still available. The Kappa install location is now configurable via the KAPPAPATH environment variable. Note that Kappa 4.0 hasn't yet been released, so until it is you will need to use the development version from the Kappa GitHub repository at https://github.com/Kappa-Dev/KaSim.
- Support for models without initial conditions, provided there’s at least one zero-order synthesis rule present, e.g. `Rule(‘Rule1’, None >> A(), Parameter(‘ksynth’, 1))`
- Automatic analytical Jacobian generation in the ODE solver. PySB can now optionally calculate a closed-form expression for the Jacobian of a model's ODEs which can help speed up the solver in some cases.
- pysb_flat exporter which serializes a model to Python/PySB code which can be saved to a file and imported again later. We found this useful for writing out dynamically generated models as "native" PySB model code. The code is just a straight list of all the component definitions so macro calls etc. are lost.

Other stuff
- Package installation now uses setuptools instead of distutils.
- We are now publishing coverage testing results at https://coveralls.io/github/pysb/pysb .
- Documentation of the PySB requirements and installation procedure has been improved significantly.
- Numerous bugfixes. We will try to be more explicit about enumerating these in future releases.