UC-Davis-molecular-computing ppsim issues

UC-Davis-molecular-computing / ppsim

Python package for simulating population protocols

MIT License

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issues

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ppsim no longer works on Google Colab

#41 EricESeverson opened 1 year ago
1
Fixes #35; Declare build dependency on Cython using pyproject.toml

#40 UnHumbleBen closed 2 years ago
7
add configurable timeout when enumerating states

#39 dave-doty opened 2 years ago
0
allow timescale to be configurable to match between different methods of specifying transition rules

#38 dave-doty closed 2 years ago
1
detect if user specifies parameters in Simulation constructor and do not override if so

#37 dave-doty opened 2 years ago
0
give more useful error message when initial configuration contains invalid states

#36 dave-doty opened 2 years ago
0
Declare build dependency on Cython using pyproject.toml

#35 mkoeppe opened 2 years ago
7
add pandas and numpy lower bound to requirements.txt

#34 dave-doty opened 2 years ago
1
add example to README with transition probabilities

#33 dave-doty opened 2 years ago
2
Import a CRN encoded in SBML format

#32 EricESeverson opened 2 years ago
0
add link to API in README

#31 dave-doty opened 3 years ago
0
add link to paper at top of README

#30 dave-doty opened 3 years ago
0
Use Strings internally instead of Specie objects

#29 EricESeverson opened 3 years ago
0
Bugfix in Simulation.run

#28 EricESeverson closed 3 years ago
0
Dev

#27 EricESeverson closed 3 years ago
0
update README

#26 EricESeverson closed 3 years ago
0
Add CRN section to README

#25 EricESeverson closed 3 years ago
0
clean up type references in docstrings

#24 dave-doty opened 3 years ago
1
Version 0.1.3

#23 EricESeverson closed 3 years ago
0
Version 0.1.2, bugfix in Simulator reactions

#22 EricESeverson closed 3 years ago
0
Dev

#21 EricESeverson closed 3 years ago
0
update readme

#20 EricESeverson closed 3 years ago
0
Update version and README images

#19 EricESeverson closed 3 years ago
0
Dev

#18 EricESeverson closed 3 years ago
0
Instantiation of Simulation with a function is needlessly slow

#17 EricESeverson opened 3 years ago
0
add controllable random number seed for reproducible results

#16 dave-doty opened 3 years ago
1
Update README.md

#15 EricESeverson closed 3 years ago
0
support importing common CRN specification formats

#14 dave-doty opened 3 years ago
0
SimulatorMultiBatch.get_enabled_reactions should check count of reactants with stoichiometric coefficient > 1

#13 dave-doty closed 3 years ago
0
Dev

#12 dave-doty closed 3 years ago
0
work on crn example, fix crn unit tests

#11 EricESeverson closed 3 years ago
0
added Sphinx documentation folder

#10 dave-doty closed 3 years ago
0
Stochkit xml output

#9 dave-doty closed 3 years ago
0
updated example CRN notebook

#8 dave-doty closed 3 years ago
0
GitHub action continuous integration unit tests

#7 dave-doty closed 3 years ago
0
added ability to specify rate constants in stochastic or mass-action units with conversion between them

#6 dave-doty closed 3 years ago
0
added ability to specify protocol using CRN notation, along with a simple example notebook, script, and unit tests

#5 dave-doty closed 3 years ago
0
feature request: simulate large-state-count protocols

#4 dave-doty opened 3 years ago
1
Update ppsim.py

#3 EricESeverson closed 3 years ago
0
make GitHub action for testing compiling API documentation

#2 dave-doty opened 3 years ago
0
make GitHub action for publishing Python package automatically to PyPI

#1 dave-doty opened 3 years ago
1