biosimulators/Biosimulators_COPASI issues and pull requests

#77 - Bump jinja2 from 3.1.4 to 3.1.5

Pull Request - State: open - Opened by dependabot[bot] about 1 month ago - 1 comment
Labels: dependencies

#76 - Sys bio model fixes part 2

Pull Request - State: closed - Opened by CodeByDrescher 4 months ago - 2 comments

#75 - Update libkisao so we can read VCell-generated SED-ML.

Pull Request - State: closed - Opened by luciansmith 11 months ago - 1 comment

#74 - All biomodels Copasi currently fails for

Issue - State: open - Opened by luciansmith over 1 year ago - 17 comments

#73 - unit test for BIOMD0000000005.omex

Pull Request - State: closed - Opened by CodeByDrescher over 1 year ago - 2 comments

#72 - fixed dependency error

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

#71 - Biosimulators copasi gives incorrect results that normal copasi doesn't

Issue - State: closed - Opened by luciansmith over 1 year ago - 3 comments

#70 - Refactor logic control anti-pattern

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

#69 - adjusted import order to be PEP-compliant

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

#68 - Closes Issue #66:

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

#67 - Changed log level of Capturer Object

Pull Request - State: closed - Opened by AlexPatrie over 1 year ago - 3 comments

#66 - Incorrectly raised Exception regarding number of time points

Issue - State: closed - Opened by leon9812 over 1 year ago - 1 comment

#65 - Update python-copasi package version

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

#64 - Wip custom stdout capture in exec functions

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 1 comment

#63 - Refactor relative imports

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 1 comment

#62 - Updating version of utils backend.

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 3 comments

#61 - Documentation discrepancies between repo and website.

Issue - State: open - Opened by AlexPatrie almost 2 years ago - 1 comment

#60 - Docker run command returning "is not a file" error on omex path

Issue - State: open - Opened by AlexPatrie almost 2 years ago - 1 comment

#59 - refactored config, log, and preprocessed task instance

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 2 comments
Labels: bug

#58 - Lowering Cognitive complexity as per SonarCloud

Issue - State: open - Opened by AlexPatrie almost 2 years ago
Labels: documentation, discussion

#57 - WIP-refactoring nesting

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 3 comments

#56 - biosimulators no longer working on macOS

Issue - State: open - Opened by fbergmann almost 2 years ago - 6 comments

#55 - Explicit typing for arguments in core sub-module.

Pull Request - State: closed - Opened by AlexPatrie almost 2 years ago - 3 comments
Labels: documentation

#54 - #53: time cn should be returned as string

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

#53 - copasi_model_obj_common_name needs to be a string

Issue - State: closed - Opened by eagmon almost 3 years ago - 4 comments

#52 - Allow the COPASI Biosimulator to simulate files exported by COPASI

Pull Request - State: closed - Opened by fbergmann about 3 years ago - 5 comments

#51 - Substitute hybrid runge kutta and LSODA methods to hybrid RK-45 for models with events

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#50 - Substitute algorithm when Radau5 requested for model with events

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

#49 - Setup cron job to pull COPASI releases from PyPi

Issue - State: closed - Opened by jonrkarr over 3 years ago - 1 comment

#48 - Internalize functionality into COPASI itself (obviating the need for this repository)

Issue - State: closed - Opened by jonrkarr over 3 years ago - 7 comments

#47 - Mark Steady State Simulations / Scan as supported

Issue - State: closed - Opened by fbergmann over 3 years ago - 3 comments

#46 - Get values of non-constant parameters

Issue - State: closed - Opened by jonrkarr over 3 years ago - 8 comments
Labels: enhancement

#45 - Expose static and steady-state analyses through SED-ML

Issue - State: open - Opened by jonrkarr about 4 years ago - 1 comment
Labels: enhancement

#44 - Improve messages for COPASI errors

Issue - State: closed - Opened by jonrkarr about 4 years ago - 2 comments
Labels: enhancement

#43 - Support hybrid RK45 method

Issue - State: closed - Opened by jonrkarr about 4 years ago - 2 comments
Labels: enhancement

#42 - Workflows

Pull Request - State: closed - Opened by bilalshaikh42 about 4 years ago

#41 - applying more specific KISAO terms

Pull Request - State: closed - Opened by jonrkarr about 4 years ago

#40 - What are the user-configurable parameters of the hybrid LSODA algorithm?

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

#39 - Add citation for Stochastic Runge-Kutta Method

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

#38 - Apply new KISAO terms for algorithms and parameters

Issue - State: closed - Opened by jonrkarr over 4 years ago - 2 comments

#37 - COPASI or wrapper should support KISAO terms for algorithms and algorithm parameters

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

#36 - Fix tests

Pull Request - State: closed - Opened by gmarupilla over 4 years ago - 1 comment

#35 - Stop generating CSV for non-report SED-ML

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

#34 - Handling `listOfOutputs` for version >= 4.28.226

Issue - State: closed - Opened by gmarupilla over 4 years ago - 1 comment
Labels: discussion

#33 - Enhancements

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

#32 - Add BioContainers-style metadata to Dockerfile

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

#31 - importSedml method only imports a single task

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

#30 - allow tests to run on other platforms, ensure report is always created, resolve task name issue

Pull Request - State: closed - Opened by fbergmann over 4 years ago - 3 comments

#29 - Update python-copasi package to latest version

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

#28 - Correct minor typos, small additions

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

#27 - Delete earlier tags and releases

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

#26 - CCopasiException on invalid archive

Issue - State: closed - Opened by gmarupilla almost 5 years ago - 5 comments

#25 - Review specifications of COPASI's capabilities (biosimulators.json)

Issue - State: closed - Opened by jonrkarr almost 5 years ago - 18 comments

#24 - Restructure

Pull Request - State: closed - Opened by gmarupilla almost 5 years ago - 10 comments