Jeremy Muhlich
Jeremy Muhlich
Path.copy_stat always copies both mtime/atime and mode, regardless of the `times` and `perms` args it is passed. Given the implementation of Path.copy, this means only times=True,perms=True and times=False,perms=False work properly....
Phospho.ELM is full of detailed information like "EGFR phospho-Y1092 binds the SH2 domain of GRB2". This could help us build a better picture of when certain binding events should be...
This adds support for BNG's energy modeling formalism. Models can now contain EnergyPatterns as well as energy-based Rules with the Arrhenius rate law parameterized by activation energy (E₀) and rate...
This lets us track codegen and simulation performance separately. Also: * Switch from setup to setup_cache to reduce setup overhead. * Remove Earm10 test with empty cython_directives since it's broken...
Some exporter classess provide extra kwargs for `export`, e.g. `SbmlExporter.export` has a `level` arg to control which SBML level/version is used. However the top-level `pysb.export.export` function doesn't accept or pass...
`Annotation.__repr__` should emit just the name of Components and not their entire repr. For example we currently emit this: ```python Annotation(Monomer('RAFi', ['raf']), 'http://identifiers.org/chebi/63637', 'is') ``` When we really want this:...
We will define a new `SpecialSymbol` subclass of `sympy.Symbol` that just serves to manage special/implicit variables like "time". In pysb.core we will define an instance of `SpecialSymbol` named "time" and...
In ScipyOdeSimulator, numpy and scipy's integration with openblas and mkl causes counterproductive parallelization of linear algebra operations that doesn't speed anything up for the matrix sizes we generally deal with,...
I think #395 broke use_analytic_jacobian through a minor typo. In _integrator_process, the block ```python jac_fn = None if jac_eqs: jac_eqs = _get_rhs(... ``` Should be assigning to `jac_fn` inside the...