Ecosyste.ms: Issues

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GitHub / StochSS/GillesPy2 issues and pull requests

#788 - Look into removing internal APIs from exposed public package

Issue - State: closed - Opened by jtcooper10 over 2 years ago
Labels: enhancement

#784 - Enhancement/type hinting

Pull Request - State: closed - Opened by ethangreen-dev over 2 years ago
Labels: enhancement

#783 - Cleanup Unit/Integration/Systems test

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

#782 - Update codebase to utilize Python 3.7 type hints

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

#781 - Exclude internal API from docs

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

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

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

#771 - Negative Species causes simulation error

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

#766 - Updated `run-full-tests` GH action.

Pull Request - State: closed - Opened by ethangreen-dev over 2 years ago
Labels: enhancement

#755 - FIX: Live graphing in `ODECSolver` using wrong decoder

Pull Request - State: closed - Opened by jtcooper10 over 2 years ago
Labels: bug

#753 - Remove deprecated features

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

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

Issue - State: closed - Opened by briandrawert almost 3 years ago - 1 comment

#727 - added unit test for hybrid solvers based on multifiring event notebook

Pull Request - State: closed - Opened by seanebum almost 3 years ago

#714 - We need a signal interrupt unittest

Issue - State: closed - Opened by BryanRumsey almost 3 years ago - 1 comment
Labels: bug

#710 - EventAssignment: need flag, "round_discrete_populations"

Issue - State: closed - Opened by briandrawert almost 3 years ago - 3 comments
Labels: wontfix

#696 - Need tests of hybrid simulation

Issue - State: closed - Opened by briandrawert almost 3 years ago
Labels: enhancement

#693 - Improve expression error handling

Pull Request - State: closed - Opened by jtcooper10 almost 3 years ago
Labels: bug

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

Issue - State: closed - Opened by jtcooper10 almost 3 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 almost 3 years ago - 1 comment
Labels: question

#681 - Fixes #679

Pull Request - State: closed - Opened by briandrawert almost 3 years ago

#678 - Fixes issues if a propensity is none

Pull Request - State: closed - Opened by briandrawert almost 3 years ago - 1 comment

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

Issue - State: closed - Opened by briandrawert almost 3 years ago

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

Issue - State: closed - Opened by BryanRumsey almost 3 years ago - 2 comments
Labels: bug

#645 - initial commit to logically remove model.run(solver=) argument

Pull Request - State: closed - Opened by mdip226 about 3 years ago
Labels: enhancement

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

Issue - State: closed - Opened by BryanRumsey about 3 years ago - 1 comment
Labels: bug

#635 - Implement variable python solvers

Issue - State: closed - Opened by seanebum about 3 years ago - 1 comment
Labels: enhancement

#632 - Events are not firing correctly in the python TauHybrid solver

Issue - State: closed - Opened by BryanRumsey about 3 years ago - 1 comment
Labels: bug

#624 - Sometimes GillesPy2 produces results that are inconsistent with other tools

Issue - State: closed - Opened by jonrkarr about 3 years ago - 4 comments

#614 - Add compression to Jsonify

Issue - State: closed - Opened by briandrawert about 3 years ago
Labels: enhancement

#613 - Jsonify need better unit tests

Issue - State: closed - Opened by briandrawert about 3 years ago

#612 - Solvers need to implement interrupts correctly

Issue - State: closed - Opened by briandrawert about 3 years ago - 1 comment

#611 - Jsonify should have a version number for JSON format

Issue - State: closed - Opened by briandrawert about 3 years ago

#599 - Return values of predicted reaction fluxes

Issue - State: closed - Opened by jonrkarr over 3 years ago - 2 comments
Labels: enhancement, question

#597 - Improve logging to be customizable by users

Issue - State: closed - Opened by BryanRumsey over 3 years ago
Labels: enhancement

#585 - C++ solvers: Tau operations seg fault on some models

Issue - State: closed - Opened by jtcooper10 over 3 years ago
Labels: bug

#584 - Cleanup compiler warnings from C++ solvers

Pull Request - State: closed - Opened by jtcooper10 over 3 years ago

#574 - Clean up verbose warning logs from C++ solvers

Issue - State: closed - Opened by jtcooper10 over 3 years ago - 1 comment
Labels: enhancement

#563 - Implementation of a per-version performance profiler.

Pull Request - State: closed - Opened by ethangreen-dev over 3 years ago
Labels: enhancement

#529 - Implement profiling tests for releases

Issue - State: closed - Opened by jtcooper10 over 3 years ago
Labels: enhancement

#526 - GillesPy2 Model Converters Organization

Issue - State: closed - Opened by ethangreen-dev over 3 years ago
Labels: enhancement

#494 - Organization of project documentation

Issue - State: closed - Opened by ethangreen-dev over 3 years ago
Labels: enhancement, help wanted, good first issue

#465 - implement phase plotting

Issue - State: closed - Opened by seanebum about 4 years ago
Labels: enhancement, help wanted

#454 - added "Variable" alias for "Species"

Pull Request - State: closed - Opened by seanebum about 4 years ago - 2 comments

#433 - Need a "How to Cite" section in Readme

Issue - State: closed - Opened by briandrawert about 4 years ago - 1 comment
Labels: enhancement, help wanted, good first issue

#430 - make a gitter for GillesPy2

Issue - State: closed - Opened by seanebum over 4 years ago
Labels: enhancement, help wanted, good first issue

#427 - Is there any way to get "exact" times of reaction events?

Issue - State: closed - Opened by jonstrutz11 over 4 years ago - 10 comments
Labels: question

#419 - Improved Error Messages for incorrect strings

Issue - State: closed - Opened by seanebum over 4 years ago - 3 comments
Labels: enhancement, help wanted

#408 - numpy ssa performance fixes

Pull Request - State: closed - Opened by seanebum over 4 years ago

#398 - Need to test: live_output='text' when there are a large number of species

Issue - State: closed - Opened by briandrawert over 4 years ago - 1 comment

#279 - SBML Documentation

Issue - State: closed - Opened by seanebum over 4 years ago

#141 - Need accuracy test for each solver

Issue - State: closed - Opened by seanebum over 5 years ago