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biosimulators
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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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lxml doesn't have xpath.execute() any more.
#151
luciansmith
closed
6 months ago
2
added higher level conversion function to exec method
#150
AlexPatrie
opened
11 months ago
1
imported biosimulators simularium conversion method
#149
AlexPatrie
closed
11 months ago
2
Get values from anywhere
#148
luciansmith
closed
1 year ago
1
Att changes split
#147
luciansmith
closed
1 year ago
2
More sed changes fixes
#146
luciansmith
closed
1 year ago
2
Add callbacks for setting, getting, and resetting.
#145
luciansmith
closed
1 year ago
2
Allow XPath references to model objects, not just attributes
#144
luciansmith
opened
1 year ago
0
Capturer clashes with Pycharm due to rebinding of io.FileIO based sys.stdout and sys.stderr streams
#143
CodeByDrescher
opened
1 year ago
0
New evalidate
#142
luciansmith
closed
1 year ago
1
Warn about duplicate figure names (or fix)
#141
luciansmith
opened
1 year ago
1
Better curve labels
#140
luciansmith
closed
1 year ago
2
feat: allow unary subtraction operator in SEDML validation
#139
jcschaff
closed
1 year ago
3
Generalized `stdout` *clean version*
#138
AlexPatrie
opened
1 year ago
1
Generalized macOS stdout handler in `Config`
#137
AlexPatrie
opened
1 year ago
3
adjusted capturer log level and added arguments.
#136
AlexPatrie
closed
1 year ago
1
dependency on `capturer`
#135
fbergmann
opened
1 year ago
2
Refactor Stdout capturer to handle serialization.
#134
AlexPatrie
closed
1 year ago
2
Typing for config
#133
AlexPatrie
closed
1 year ago
1
Iss129
#132
b-tao
closed
1 year ago
2
Subdirectories in OMEX files not working
#131
luciansmith
opened
1 year ago
0
Use tolerances even when changing simulation algorithm.
#130
luciansmith
opened
1 year ago
0
get_pubmed_central_open_access_graphics leaves tar.gz file in directory.
#129
luciansmith
closed
1 year ago
6
Fixes to allow collection of metadata from biomodels.
#128
luciansmith
closed
1 year ago
2
Fix failing XPP validation tests
#127
luciansmith
opened
1 year ago
0
Update metadata.rdf handling.
#126
luciansmith
closed
1 year ago
3
first pass
#125
CodeByDrescher
closed
1 year ago
2
Incorrect validation error for tasks that reference models.
#124
luciansmith
opened
1 year ago
0
NumPy bug with newest version
#123
eagmon
closed
1 year ago
0
Fix numpy bug
#122
eagmon
closed
1 year ago
5
fix: NumPy slice error
#121
eagmon
closed
1 year ago
1
infix math doesn't follow Python conventions
#120
luciansmith
opened
1 year ago
1
substitute '**' for '^' for python execution of sedml changes
#119
jcschaff
closed
1 year ago
1
infix math from libsedml uses '^' instead of '**' in python, validation fails
#118
jcschaff
closed
1 year ago
4
CVE-2007-4559 Patch
#117
TrellixVulnTeam
closed
1 year ago
2
fix(report): update multidimensional indexing
#116
bilalshaikh42
closed
1 year ago
2
Biosimulators_utils is incompatible with numpy>=1.23.0
#115
CodeByDrescher
opened
1 year ago
0
Round-tripping created OMEX files gives a warning
#114
luciansmith
opened
2 years ago
0
The sed-ml validator doesn't accept empty lists of variables / parameters in SetValue.
#113
danv61
closed
2 years ago
1
The validator rejects a sedml file that uses a model Sid reference in the source attribute of a model.
#112
danv61
closed
2 years ago
6
CellML 1.1 validation
#111
bilalshaikh42
opened
2 years ago
3
Raise Issue with CellML team regarding incorrect schema
#110
bilalshaikh42
opened
2 years ago
3
fix(cellml): skip variables that do not have a valid observable
#109
bilalshaikh42
closed
2 years ago
8
Allow element math to have attribute "id" in CellML files
#108
bilalshaikh42
closed
2 years ago
4
fix (cellml): use integers for the number of steps
#107
bilalshaikh42
closed
2 years ago
2
SED-ML generated by CellML utils raises type error
#106
bilalshaikh42
closed
2 years ago
1
Allow more-specific algorithm substitution.
#105
luciansmith
closed
1 year ago
2
Add the 'ode' type to the list.
#104
luciansmith
closed
2 years ago
7
Check for perl before loading BioNetGen files
#103
luciansmith
closed
2 years ago
5
feat: check all SED-ML XPath targets and warn appropriately
#102
luciansmith
closed
2 years ago
19
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