Fabian Fröhlich

fix aes argument typehint according to PEP0484

4

https://www.python.org/dev/peps/pep-0484/#arbitrary-argument-lists-and-default-argument-values

Support for CSRMatrix

4

I am currently working on code that computes matrix-matrix products of large, sparse matrices (>1k rows/columns, similar number of non-zero entries), which is relatively slow (multiple hours per product). I...

Extend function support in BNGL import and pysb export

2

This adds support of all BNGL supported functions during import of BNGL models. For export of pysb models to file, all supported functions are always imported from sympy such that...

PySB native reaction generation

2

- Adds constructors for ReactionPattern/ComplexPattern/MonomerPattern from graphs - Adds functionality to compute action of Rules on species using graph differences - Adds functionality to compute reaction rates the action of...

Still a bit of work to, but feedback is already welcome at this stage.

Amici Simulator

6

Implements support for https://github.com/ICB-DCM/AMICI as Simulator class

Deprecation for `get_for_key` notice suggests code that will error.

2

Maybe I am misunderstanding what I am supposed to do, but this doesn't seem to work.

Use markers to indicate exit_message in waterfall plot

3

Would be nice to have this as quick visual inspection

Software using pymc

2

As soon as pymc 4.0.0 is released we should probably contact the developers about including pypesto in the list of software tools using pymc.

`ReturnDataReportingMode` not handled correctly for `AggregatedObjective`

9

`AggregatedObjective` calls `call_unprocessed`, not `__call__`, so then handling via `__call__` introduced in #835 doesn't have any effect and rdata will not be fully populated.