biosimulators Biosimulators_utils issues

biosimulators / Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages

https://docs.biosimulators.org/Biosimulators_utils

MIT License

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issues

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Sanitize paths (remove leading `./` from paths to HDF groups)

#54 jonrkarr closed 3 years ago
0
Use new Smoldyn features that will be added to 2.67

#53 jonrkarr opened 3 years ago
0
Parse algorithm parameters from Smoldyn files

#52 jonrkarr opened 3 years ago
0
Parse time course from actions in BNGL files

#51 jonrkarr opened 3 years ago
1
Switch LEMS validation to use new pyNeuroML method

#50 jonrkarr opened 3 years ago
0
Add method of executing simulations with Singularity images

#49 jonrkarr opened 3 years ago
0
Add warning for model resolution by MIRIAM ids, that this will be deprecated

#48 jonrkarr closed 3 years ago
1
Make smoldyn requirement >= 2.67 once released

#47 jonrkarr opened 3 years ago
0
Remove `seaborn` requirement for bionetgen once a new version of bionetgen is released to PyPI

#46 jonrkarr closed 3 years ago
1
Enhance validation of LEMS to validate all imported content

#45 jonrkarr closed 3 years ago
1
Add method to get observables for LEMS files

#44 jonrkarr opened 3 years ago
0
Support validation of CellML 2.0 with imports

#43 jonrkarr closed 3 years ago
1
Add validation for CellML 1.1

#42 jonrkarr opened 3 years ago
0
Latest version does not install on Ubuntu 20.04 due to missing `python-libcombine==0.2.9`

#41 matthiaskoenig closed 3 years ago
2
Validate kisao ids for algorithm parameters are unique

#40 jonrkarr closed 3 years ago
1
Add warnings

#39 jonrkarr closed 3 years ago
0
Incorporate validation of PETab files

#38 jonrkarr opened 3 years ago
0
Incorporate validation of NeuroML files

#37 jonrkarr closed 3 years ago
1
Incorporate validation of CellML files

#36 jonrkarr closed 3 years ago
2
Incorporate validation of libOmexMeta files

#35 jonrkarr closed 3 years ago
1
Support lambda, bvar

#34 jonrkarr closed 3 years ago
1
Support aggregate mathematical functions

#33 jonrkarr opened 3 years ago
1
Support random number generator functions new to SED-ML L1V4

#32 jonrkarr closed 3 years ago
1
Allow subtasks of a repeated task to use different models

#31 jonrkarr opened 3 years ago
0
Validate that ids of SED-ML objects are globally unique

#30 jonrkarr closed 3 years ago
1
Improve error messaging

#29 jonrkarr closed 3 years ago
1
Support SED-ML files without namespaces defined for model targets

#28 jonrkarr closed 3 years ago
1
Container exits with success code if no sedml is found

#26 bilalshaikh42 closed 3 years ago
4
Annotate the dimensions and slice of reports

#25 jonrkarr opened 3 years ago
0
Support fully not resetting models during repeated tasks

#24 jonrkarr opened 3 years ago
0
Support data descriptions

#23 jonrkarr opened 3 years ago
0
Support new features introduced in SED-ML L1V4

#22 jonrkarr opened 3 years ago
0
Support plots

#20 jonrkarr closed 3 years ago
1
Switch pandas to xarray to support multidimensional reports

#19 jonrkarr closed 3 years ago
1
When a simulator input file is a plain zip archive (not a COMBINE archive), find all SED-ML files anyway

#18 jonrkarr closed 3 years ago
1
Should reports be disallowed from containing datasets with different time scales?

#17 jonrkarr closed 3 years ago
1
Allow datasets to have different shapes through padding with nan

#16 jonrkarr closed 3 years ago
1
Expand capabilities of execution status logging

#15 jonrkarr closed 3 years ago
3
Initialize reports with their eventual shapes

#14 jonrkarr opened 3 years ago
0
Add option to stream reports as soon as available

#13 jonrkarr closed 3 years ago
1
Deployed runBioSimulations API not returning `resultsSize`

#12 jonrkarr closed 3 years ago
2
Allow model.source to be an id of another model

#11 jonrkarr closed 3 years ago
1
Support additional environment variables for simulator CLIs

#10 jonrkarr closed 3 years ago
1
Allow less strict importing of SED-ML

#9 jonrkarr closed 3 years ago
1
Support semantic versioning

#8 jonrkarr opened 3 years ago
0
Use pipenv / pip.lock to better track dependencies of simulators

#7 jonrkarr closed 3 years ago
1
Change default report output formats to just HDF5

#6 jonrkarr closed 3 years ago
1
Annotate axes of HDF5 outputs

#5 jonrkarr closed 3 years ago
1
Optionally infer null SED-ML references

#4 jonrkarr closed 3 years ago
1
Support data generators that aren't equal to a single variable (target or symbol)

#3 jonrkarr closed 3 years ago
1

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