StochSS/GillesPy2 issues and pull requests

#953 - Time scales

Issue - State: closed - Opened by chaoui-mu 3 months ago - 2 comments

#952 - Error on module.add_event([event])

Issue - State: closed - Opened by frascalise 3 months ago

#951 - Error encountered while running simulation C++ file (return code: 3221225785)

Issue - State: closed - Opened by michimiura 11 months ago - 2 comments

#950 - Mdip/docs hotfix 7/13

Pull Request - State: open - Opened by mdip226 12 months ago
Labels: bug, Docs

#949 - Assignment and Rate Rules, and Events need to be able to target Parameters

Issue - State: closed - Opened by briandrawert about 1 year ago - 1 comment
Labels: bug

#948 - Mdip226/gillespy2.remote

Pull Request - State: open - Opened by mdip226 about 1 year ago
Labels: enhancement

#947 - Event Assignment: ADD Compartment to valid variable types once implemented

Issue - State: open - Opened by BryanRumsey about 1 year ago
Labels: enhancement

#946 - Component validations

Pull Request - State: open - Opened by BryanRumsey about 1 year ago - 1 comment
Labels: enhancement

#945 - Assignment rule variable not found when variable is a Parameter

Issue - State: open - Opened by BryanRumsey about 1 year ago - 1 comment
Labels: bug

#944 - Updates to CSV

Pull Request - State: closed - Opened by BryanRumsey about 1 year ago
Labels: enhancement

#943 - Model Run Integrator Error

Pull Request - State: closed - Opened by BryanRumsey about 1 year ago
Labels: enhancement

#942 - HOTFIX: Export StochSS Live! Models

Pull Request - State: closed - Opened by BryanRumsey about 1 year ago

#941 - Fixes issues where "lambda" is used as a species or parameter

Pull Request - State: closed - Opened by briandrawert about 1 year ago
Labels: enhancement

#940 - SBML import fails if MathML includes reserved Python words

Issue - State: closed - Opened by leon9812 about 1 year ago
Labels: enhancement, ✔️

#939 - GillesPy2 C extension

Pull Request - State: open - Opened by jtcooper10 about 1 year ago - 1 comment

#938 - Tau hybrid solvers c++ python need argument tau step

Pull Request - State: closed - Opened by briandrawert about 1 year ago
Labels: enhancement

#937 - HOTFIX: SBML Dependent Parameter Expressions

Pull Request - State: closed - Opened by BryanRumsey about 1 year ago

#936 - Unable to import SBM files with Dependent variables

Issue - State: closed - Opened by TorkelE about 1 year ago - 2 comments
Labels: bug, ✔️

#935 - Problem installing gillespy2

Issue - State: closed - Opened by lilt3ddy over 1 year ago - 2 comments
Labels: answered

#934 - Tau hybrid solvers c++ python need argument tau step

Pull Request - State: closed - Opened by briandrawert over 1 year ago
Labels: enhancement

#933 - Timespans are not correctly converted to StochSS

Issue - State: closed - Opened by BryanRumsey over 1 year ago
Labels: bug, ✔️

#932 - Model.run needs to error if integrator is passed as arg

Issue - State: closed - Opened by BryanRumsey over 1 year ago
Labels: bug, ✔️

#931 - 1.8.2 Release

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago

#930 - check python typing in template_gen.py

Issue - State: open - Opened by seanebum over 1 year ago

#929 - Remove references to StochKit

Pull Request - State: closed - Opened by briandrawert over 1 year ago
Labels: bug, Cleanup

#928 - Fix ssa c dependency graph

Pull Request - State: closed - Opened by seanebum over 1 year ago
Labels: bug

#927 - Unexpectedly slow simulation with zvode

Issue - State: open - Opened by TorkelE over 1 year ago - 3 comments

#926 - Bug

Pull Request - State: closed - Opened by mdip226 over 1 year ago

#925 - SSACSolver does not simulate custom propensities correctly

Issue - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: bug

#924 - Fix C++ dependency warning

Pull Request - State: closed - Opened by jtcooper10 over 1 year ago - 1 comment

#923 - Need to update the C++ dependency check to scheck for SCons instead of Make

Issue - State: closed - Opened by jtcooper10 over 1 year ago
Labels: bug

#922 - Copyright Update

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago
Labels: enhancement

#921 - Release 1.8.1

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago

#920 - Fix tests

Pull Request - State: closed - Opened by briandrawert over 1 year ago

#919 - test modules uncommented

Pull Request - State: closed - Opened by briandrawert over 1 year ago

#918 - SSACSolver simulates the telegraph model incorrectly

Pull Request - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: bug

#917 - SSACSolver simulates the telegraph model incorrectly

Issue - State: closed - Opened by briandrawert over 1 year ago - 2 comments
Labels: bug, ✔️

#916 - HOTFIX: Notebook Plotting

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago

#915 - Notebook plot display using plotly fails

Issue - State: closed - Opened by BryanRumsey over 1 year ago
Labels: bug, ✔️

#914 - Cleanup Compiler Warning Messages

Pull Request - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: Cleanup

#913 - TauHybridSolver: using pop() instead of reallocating array

Pull Request - State: closed - Opened by briandrawert over 1 year ago
Labels: Cleanup

#912 - In TauHybrid Python solver, savetimes vector should pop() not slice

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: ✔️, Cleanup

#911 - Cleanup C++ compiler warnings

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: ✔️, Cleanup

#910 - Use SCons instead of Makefiles for compilation of C++ code

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: enhancement

#909 - Release 1.8.0

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago

#908 - Auto update docs

Pull Request - State: closed - Opened by briandrawert over 1 year ago

#907 - build docs on push to develop

Pull Request - State: closed - Opened by briandrawert over 1 year ago

#906 - Docs update testing

Pull Request - State: closed - Opened by briandrawert over 1 year ago

#905 - TauHybridSolver history_length needs to be configurable

Issue - State: open - Opened by briandrawert over 1 year ago
Labels: Cleanup

#904 - Why does this take so long to run? Number of Reactions?

Issue - State: closed - Opened by mdip226 over 1 year ago - 1 comment
Labels: question

#903 - Tauhybridsolver tau selection bugs break opioid model

Pull Request - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: bug

#902 - TauHybridSolver tau selection bugs break Opioid model

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: bug

#901 - Solver interrupts do not work correctly if run outside of main thread

Issue - State: open - Opened by jtcooper10 over 1 year ago
Labels: enhancement

#900 - Events assignment rounding for discrete/continuous species

Pull Request - State: closed - Opened by briandrawert over 1 year ago
Labels: bug

#899 - Coverage badge should look at 'main' branch

Issue - State: open - Opened by briandrawert over 1 year ago
Labels: Cleanup

#898 - TauHybridSolver gives incorrect value at t=0 (not initial value)

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: bug

#897 - Target species of RateRules must be continuous

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: enhancement

#896 - TauHybridSolver does not simulate rate-rule & continuous species model correctly

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: bug

#895 - TauHybridCSolver does not simulate RateRule-only model correctly

Issue - State: closed - Opened by briandrawert over 1 year ago - 3 comments
Labels: bug

#894 - Remove MinGW downgrade from unit tests workflow

Pull Request - State: closed - Opened by jtcooper10 over 1 year ago

#893 - Pylintrc file

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago - 1 comment
Labels: enhancement

#892 - Incorrect Errors

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago
Labels: enhancement

#891 - Fixes #874 for TauHybridSolver

Pull Request - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: Cleanup

#890 - Fixing packaging for SCons

Pull Request - State: closed - Opened by briandrawert over 1 year ago - 1 comment
Labels: bug

#887 - Github docs aren't updating automatically

Issue - State: closed - Opened by BryanRumsey over 1 year ago
Labels: enhancement, ✔️, Docs

#886 - Update documentation

Issue - State: closed - Opened by BryanRumsey over 1 year ago
Labels: enhancement, Docs

#884 - Bug in EventAssignment for SBML import

Issue - State: closed - Opened by vwiela over 1 year ago - 1 comment
Labels: bug, ✔️

#883 - If bad value is passed to Event, throw error

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

#880 - Contradicting error message

Issue - State: closed - Opened by vwiela over 1 year ago - 3 comments
Labels: bug, ✔️

#879 - Replace Makefile build back end with SConstruct

Pull Request - State: closed - Opened by jtcooper10 over 1 year ago - 6 comments

#877 - Release v1.7.2

Pull Request - State: closed - Opened by BryanRumsey over 1 year ago

#876 - Reaction.reactants should throw error if species is repeated

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: bug, ✔️

#875 - Tau-Hybrid C solver: # of SSA steps after negative value should be configurable constant

Issue - State: open - Opened by briandrawert over 1 year ago
Labels: enhancement

#874 - Tau-hybrid Non-negative check needs to be refactored

Issue - State: closed - Opened by briandrawert over 1 year ago
Labels: Cleanup

#859 - Need to make private, or remove methods

Issue - State: open - Opened by briandrawert almost 2 years ago - 1 comment
Labels: Cleanup

#851 - Create an pylintrc file

Issue - State: closed - Opened by BryanRumsey almost 2 years ago
Labels: enhancement, ✔️

#825 - Tau-Hybrid Solvers (c++ & python) need argument 'tau_step'

Issue - State: closed - Opened by briandrawert about 2 years ago
Labels: enhancement

#822 - C++ build system fails if a folder has a space on Windows

Issue - State: closed - Opened by BryanRumsey about 2 years ago - 1 comment
Labels: enhancement, help wanted

#815 - Make example of how to implement "Time Dependent Parameters / Rate Constants" with rate rules

Issue - State: open - Opened by briandrawert about 2 years ago - 1 comment

#804 - Oregonator model species `P` drops significantly at around `t=3.5`

Issue - State: closed - Opened by BryanRumsey about 2 years ago - 2 comments
Labels: bug

#796 - Pause/Resume test case refactor

Pull Request - State: closed - Opened by jtcooper10 about 2 years ago
Labels: enhancement

#792 - Pause/Resume needs refactor

Issue - State: open - Opened by briandrawert about 2 years ago
Labels: enhancement

#790 - Incorrect errors raised

Issue - State: closed - Opened by BryanRumsey about 2 years ago - 1 comment
Labels: bug, ✔️

#783 - Cleanup Unit/Integration/Systems test

Issue - State: closed - Opened by briandrawert about 2 years ago

#782 - Update codebase to utilize Python 3.7 type hints

Issue - State: closed - Opened by ethangreen-dev about 2 years ago
Labels: enhancement

#781 - Exclude internal API from docs

Issue - State: open - Opened by briandrawert about 2 years ago

#772 - Unit tests fail due to model too stiff - check/change model

Issue - State: closed - Opened by briandrawert about 2 years ago - 1 comment
Labels: bug

#771 - Negative Species causes simulation error

Issue - State: closed - Opened by JoshuaFisherC about 2 years ago - 5 comments
Labels: question

#728 - Need unit test to ensure math.ceil, math.floor work in Event assignments

Issue - State: open - Opened by briandrawert over 2 years ago - 1 comment

#714 - We need a signal interrupt unittest

Issue - State: open - Opened by BryanRumsey over 2 years ago - 1 comment
Labels: bug

#710 - EventAssignment: need flag, "round_discrete_populations"

Issue - State: open - Opened by briandrawert over 2 years ago - 3 comments
Labels: wontfix

#709 - TauHybridSolver: event assignments can make discrete species have floating point values

Issue - State: closed - Opened by briandrawert over 2 years ago - 1 comment

#708 - Need unit test to ensure all math functions available in Python solver to propensity functions/constants, are all available in C++

Issue - State: open - Opened by briandrawert over 2 years ago

#696 - Need tests of hybrid simulation

Issue - State: closed - Opened by briandrawert over 2 years ago
Labels: enhancement

#692 - C++ Hybrid Solver: Allow parameters as Rate Rule variables

Issue - State: open - Opened by jtcooper10 over 2 years ago - 1 comment
Labels: enhancement

#691 - C++ Hybrid Solver: Use reaction root-finder instead of bisection on critical Tau steps

Issue - State: closed - Opened by jtcooper10 over 2 years ago - 1 comment
Labels: question

#670 - Check that Run All Notebook unit test is working correctly

Issue - State: open - Opened by briandrawert over 2 years ago

#662 - Keyboard interrupt doesn’t work correctly for pause resume in C solvers

Issue - State: open - Opened by BryanRumsey over 2 years ago - 2 comments
Labels: bug

#642 - Pause Resume doesn't support multiple trajectories for C solvers

Issue - State: open - Opened by BryanRumsey over 2 years ago - 1 comment
Labels: bug

#635 - Implement variable python solvers

Issue - State: open - Opened by seanebum over 2 years ago - 1 comment
Labels: enhancement

GitHub / StochSS/GillesPy2 issues and pull requests