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Development #118

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Development #118

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stellaprins and others added 10 commits December 9, 2024 15:48
* Draft add remote outcomes Copasi and Tellurium to  BioModels README table
* adjustments to remote test handling in parse_biomodels.py
* fix error handling in run_biosimulators_remotely
* use utf-8 encoding when writing files in parse_biomodels and update README table  with remote tellurium and copasi results
* update d1 plots for biomodels tables

* update results using original SED-ML files
…olumns, batch remote submissions, enable pickling, skip native tellurium float errors, etc) (#114)
* add omex_file_name to remote simulation dictionary instead of generic 'test'

* set use_original_files to False to use ammended sedml files and remove unnecessary comment

* adjust sedml files to replicate curated  BioModels figures

* add created omex files

* update detailed biomodels tables and d1 plots

* make results table names  more descriptive
* add egg info to gitignore

* remove commented out code

* draft readme

* bugfix level_version tag process_test_suite

* remove BIOMD files that should not be there

* update READMEs

* bugfix command line options overrule main script

* pre-commit comment for developers

* add back BIOMD models, they are needed in validate all sh

* add forward slashes in filepaths,  fix typos
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