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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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
Encode additional features of XPP ODE files into SED-ML

#101 jonrkarr opened 2 years ago
0
Skip SED-ML L1V4 curves/surfaces that aren't of supported types

#100 jonrkarr closed 2 years ago
1
Fixes the temp-biomodels github actions failure.

#99 luciansmith closed 2 years ago
4
Fix for #96: consolidate warnings

#98 luciansmith closed 2 years ago
3
Clarify warning about limited support for plotting results of repeated tasks

#97 luciansmith closed 2 years ago
1
Consolidate descriptions of similar errors and warnings

#96 luciansmith closed 2 years ago
13
Update io.py

#95 luciansmith closed 2 years ago
3
fix: fix local parameter check

#94 luciansmith closed 2 years ago
3
Generate SED-ML repeated task from XPP ranges

#93 jonrkarr closed 2 years ago
1
Handle XPP array variables

#92 jonrkarr closed 2 years ago
1
Use appropriate foaf predicates for email and telephone rather than `accountName`

#91 jonrkarr closed 2 years ago
1
Support new regex patterns in identifiers.org for GitLab

#90 jonrkarr closed 2 years ago
1
Additional potential formats

#89 bilalshaikh42 closed 2 years ago
7
Add method to get `CombineArchiveContentFormat` from file endings

#88 bilalshaikh42 closed 2 years ago
1
Add format types to `CombineArchiveContentFormat`

#87 bilalshaikh42 closed 2 years ago
6
fix: handle case when getting pmc_id raises error

#86 bilalshaikh42 closed 2 years ago
2
Getting pmc_records may raise error even for valid pubmed_id

#85 bilalshaikh42 closed 2 years ago
1
fix: handle case when author key is not present

#84 bilalshaikh42 closed 2 years ago
2
fix: handle case when enterez throws

#83 bilalshaikh42 closed 2 years ago
2
Invalid pubmed ids can cause error thrown in Enterez

#82 bilalshaikh42 closed 2 years ago
0
fix: handle case when doi is of type `<class 'str'>` with value 'None'

#81 bilalshaikh42 closed 2 years ago
2
`TripleOmexMetaWriter` receives a `Tuple` instead of `Triple` if `license` is provided

#80 bilalshaikh42 closed 2 years ago
3
Convert data models to subclasses of `dataclass`

#79 jonrkarr opened 2 years ago
0
Add to_json and from_json method to JournalArticle class

#78 bilalshaikh42 closed 2 years ago
3
Recognize metadata for auto-generated SED-ML

#77 jonrkarr closed 2 years ago
1
Raise warning for manifests which don't have entries for their parent archives

#76 jonrkarr closed 2 years ago
1
Allow entries for OMEX manifests in OMEX manifests

#75 jonrkarr closed 2 years ago
1
docs: add bilalshaikh42 as a contributor for code, ideas

#74 allcontributors[bot] closed 2 years ago
0
fix: change exception "type" to "category"

#73 bilalshaikh42 closed 2 years ago
5
docs: add jonrkarr as a contributor for code

#72 allcontributors[bot] closed 3 years ago
0
docs: add bilalshaikh42 as a contributor for bug

#71 allcontributors[bot] closed 3 years ago
2
Validate that metadata is about URIs that begin with `http://omex-library.org/` prefix

#70 jonrkarr closed 3 years ago
3
Where possible return unit information with `get_parameters_variables_outputs_for_simulation`

#69 jonrkarr opened 3 years ago
3
Add option to get reaction flux observables for SBML kinetic models

#68 jonrkarr closed 3 years ago
1
Add option to get model changes for `exec_sed_task` for SBML-FBC which support different changes than `exec_sed_doc`

#67 jonrkarr closed 3 years ago
1
Debug simulation submission to runBioSimulations via files with Python

#66 jonrkarr closed 3 years ago
4
Support additional BNGL simulation arguments

#65 jonrkarr closed 3 years ago
1
Support additional actions of BNGL format

#64 jonrkarr opened 3 years ago
0
Support plotting multidimensional results of repeated tasks

#63 jonrkarr closed 3 years ago
2
Organize arguments to SED-ML/COMBINE execution methods to `Config`

#61 jonrkarr closed 3 years ago
1
Correct HDF5 path handling for Windows

#60 jonrkarr closed 3 years ago
0
Add validation rules for SED-ML L1V4

#59 jonrkarr opened 3 years ago
0
Not all SED-ML containers need children

#58 luciansmith closed 3 years ago
5
Add warning to SED-ML validation that repeated tasks may not be portable across simulation tools

#57 jonrkarr closed 3 years ago
1
Improve support for ZGINML format

#56 jonrkarr opened 3 years ago
0
Update BioNetGen requirement when installation fixed

#55 jonrkarr opened 3 years ago
0

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