UC-Davis-molecular-computing/ppsim issues and pull requests

#41 - ppsim no longer works on Google Colab

Issue - State: open - Opened by EricESeverson over 1 year ago - 1 comment
Labels: bug

#40 - Fixes #35; Declare build dependency on Cython using pyproject.toml

Pull Request - State: closed - Opened by UnHumbleBen over 2 years ago - 7 comments

#39 - add configurable timeout when enumerating states

Issue - State: open - Opened by dave-doty almost 3 years ago
Labels: enhancement

#38 - allow timescale to be configurable to match between different methods of specifying transition rules

Issue - State: closed - Opened by dave-doty almost 3 years ago - 1 comment
Labels: invalid

#37 - detect if user specifies parameters in Simulation constructor and do not override if so

Issue - State: open - Opened by dave-doty almost 3 years ago
Labels: enhancement

#36 - give more useful error message when initial configuration contains invalid states

Issue - State: open - Opened by dave-doty almost 3 years ago
Labels: enhancement

#35 - Declare build dependency on Cython using pyproject.toml

Issue - State: open - Opened by mkoeppe almost 3 years ago - 7 comments
Labels: bug

#34 - add pandas and numpy lower bound to requirements.txt

Issue - State: open - Opened by dave-doty almost 3 years ago - 1 comment
Labels: bug

#33 - add example to README with transition probabilities

Issue - State: open - Opened by dave-doty almost 3 years ago - 2 comments
Labels: documentation

#32 - Import a CRN encoded in SBML format

Issue - State: open - Opened by EricESeverson about 3 years ago
Labels: enhancement

#31 - add link to API in README

Issue - State: open - Opened by dave-doty about 3 years ago
Labels: documentation

#30 - add link to paper at top of README

Issue - State: open - Opened by dave-doty about 3 years ago
Labels: documentation

#29 - Use Strings internally instead of Specie objects

Issue - State: open - Opened by EricESeverson about 3 years ago
Labels: enhancement

#28 - Bugfix in Simulation.run

Pull Request - State: closed - Opened by EricESeverson about 3 years ago

#27 - Dev

Pull Request - State: closed - Opened by EricESeverson about 3 years ago

#26 - update README

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#25 - Add CRN section to README

Issue - State: closed - Opened by EricESeverson over 3 years ago

#24 - clean up type references in docstrings

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: documentation

#23 - Version 0.1.3

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#22 - Version 0.1.2, bugfix in Simulator reactions

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#21 - Dev

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#20 - update readme

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#20 - update readme

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#19 - Update version and README images

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#19 - Update version and README images

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#18 - Dev

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#18 - Dev

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#17 - Instantiation of Simulation with a function is needlessly slow

Issue - State: open - Opened by EricESeverson over 3 years ago

#17 - Instantiation of Simulation with a function is needlessly slow

Issue - State: open - Opened by EricESeverson over 3 years ago

#16 - add controllable random number seed for reproducible results

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: enhancement

#16 - add controllable random number seed for reproducible results

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: enhancement

#15 - Update README.md

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#15 - Update README.md

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#14 - support importing common CRN specification formats

Issue - State: open - Opened by dave-doty over 3 years ago
Labels: enhancement

#14 - support importing common CRN specification formats

Issue - State: open - Opened by dave-doty over 3 years ago
Labels: enhancement

#13 - SimulatorMultiBatch.get_enabled_reactions should check count of reactants with stoichiometric coefficient > 1

Issue - State: closed - Opened by dave-doty over 3 years ago
Labels: bug

#13 - SimulatorMultiBatch.get_enabled_reactions should check count of reactants with stoichiometric coefficient > 1

Issue - State: closed - Opened by dave-doty over 3 years ago
Labels: bug

#12 - Dev

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#12 - Dev

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#11 - work on crn example, fix crn unit tests

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#11 - work on crn example, fix crn unit tests

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#10 - added Sphinx documentation folder

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#9 - Stochkit xml output

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#9 - Stochkit xml output

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#8 - updated example CRN notebook

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#8 - updated example CRN notebook

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#7 - GitHub action continuous integration unit tests

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#7 - GitHub action continuous integration unit tests

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#6 - added ability to specify rate constants in stochastic or mass-action units with conversion between them

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#6 - added ability to specify rate constants in stochastic or mass-action units with conversion between them

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#5 - added ability to specify protocol using CRN notation, along with a simple example notebook, script, and unit tests

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#5 - added ability to specify protocol using CRN notation, along with a simple example notebook, script, and unit tests

Pull Request - State: closed - Opened by dave-doty over 3 years ago

#4 - feature request: simulate large-state-count protocols

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: enhancement

#3 - Update ppsim.py

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#3 - Update ppsim.py

Pull Request - State: closed - Opened by EricESeverson over 3 years ago

#2 - make GitHub action for testing compiling API documentation

Issue - State: open - Opened by dave-doty over 3 years ago
Labels: enhancement

#2 - make GitHub action for testing compiling API documentation

Issue - State: open - Opened by dave-doty over 3 years ago
Labels: enhancement

#1 - make GitHub action for publishing Python package automatically to PyPI

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: enhancement

#1 - make GitHub action for publishing Python package automatically to PyPI

Issue - State: open - Opened by dave-doty over 3 years ago - 1 comment
Labels: enhancement

GitHub / UC-Davis-molecular-computing/ppsim issues and pull requests