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Compatibility processing - reformat compatibility message (remove colour coding of text) - In addition to recognizing .sbml and .sedml files as SBML and SED-ML format, .xml files with 'sedml' + 'sbml' or 'sbml' but not 'sedml' in their filename are recognized as SBML and SED-ML files. Other file types are not recognized but this can be extended in the future. - Instead of ❌ FAIL, unrecognized filetypes will marked as ❓UNSURE (this hasn't happened so far). At the moment all engines that do not support SBML/SED-ML are still marked as⚠ XFAIL. Test suite - Updated the results table of case 00001 - Added a table of case 01186 (steady state Flux Balance Analysis) Add back foldout menu in Engines column (went lost with the previous PR when the engine names were reformated)
add test suite results and improved table formatting
* improve file compatibility check * improve handling of engine_list input and make it possible to modify SED-ML files without them being overwritten (use_original_files) * update BIOMD0000000001 SED-ML and plot (x log scale) * update BIOMD0000000001 jsons and add BIOMD0000000138 table and plots with modified x limit * update plots and SED-ML files in attempt to replicate curated figures * increase max_wait_time to 600 seconds and update results tables and plots * Update test_biomodels_compatibility_biosimulators.py * bug fix (copy from temp files if files don't exist) * fix typo compatibe -> compatible
* add fbc attribute if missing * remove temp omex files and add 0001 to test suite cases * first check whether m == None before getting m.span() and improve clarity of add_xmlns_fbc_attribute documentation * remove unnecessary 'else:' in add_xmlns_fbc_attribute
* add fbc attribute if missing * improve compatibility messages and update tables * update results table SBML example
* Remove commented-out get_filetypes function from utils * Remove unused imports * Remove unused variables
* Draft biomodels tables * improve file compatibility check * improve handling of engine_list input and make it possible to modify SED-ML files without them being overwritten (use_original_files) * update BIOMD0000000001 SED-ML and plot (x log scale) * update BIOMD0000000001 jsons and add BIOMD0000000138 table and plots with modified x limit * update plots and SED-ML files in attempt to replicate curated figures * increase max_wait_time to 600 seconds and update results tables and plots * remove spaces from omex filenames before submitting to docker * add BIOMD0000001077 * add BIOMD0000000724 * only remove omex_file if it exists in __init__.py * add ValueError to remove_spaces_from_filename if dir contains spaces. Put unix command between single quotes. * fix temp SED-ML file handling bug in add_xmlns_sbml_attribute and add_xmlns_fbc_attribute * tweak XFAIL message and update plots and tables
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I think this PR can be closed and the experimental branch is out of date and can be removed, all relevant changes were merged into |
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