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writeYAMLmodel: nest ec-rxns enzymes; printOrange: print \n as line break - #751
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Each ec-rxns entry writes its enzymes as an !!omap under "- enzymes", but the enzyme lines were written at the same indentation as that key. readYAMLmodel does not look at indentation and reads them back, but a YAML parser sees an empty "enzymes" mapping followed by sibling keys: ruamel.yaml, as used by raven-toolbox and geckopy, fails with "'ScalarNode' object has no attribute 'flow_style'", so no ecModel saved by GECKO 4 could be opened in Python. The lines are now indented two spaces deeper, like the metabolite coefficients under "- metabolites". Tested by re-saving the GECKO full_ecModel tutorial's stage-2 ecModel: RAVEN reads it back with identical rxnEnzMat and kcat, and geckopy now loads it (4834 ec reactions, same maximum growth as in MATLAB).
printOrange prints its text with fprintf('%s',...) so that a "%" in
model text is not read as a format directive. That also stopped "\n"
from being expanded, and every caller that ends a message or breaks a
line with "\n" printed a literal backslash-n instead: 15 calls in RAVEN
and 17 in GECKO, including GECKO 4's backward-compatibility notice.
printOrange now turns "\n" into a line break; no other escape sequence
or format directive is interpreted.
Function test results390 tests 351 ✅ 1m 28s ⏱️ Results for commit 3cbe5c1. |
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Two issues found while running GECKO 4's full_ecModel tutorial against RAVEN 3.0.0b1 (see SysBioChalmers/GECKO#481 and CompMetEng/geckopy#54).
writeYAMLmodel: ec-rxns enzymes are not nested under their keyEach
ec-rxnsentry writes its enzyme stoichiometry as an!!omapunder- enzymes, but the enzyme lines were written at the same indentation as that key:readYAMLmodelignores indentation and reads this back correctly. A YAML parser, however, sees an emptyenzymesmapping. ruamel.yaml, as used by raven-toolbox and geckopy, fails with'ScalarNode' object has no attribute 'flow_style', so no ecModel saved from GECKO 4 can be opened in geckopy. The enzyme lines are now two spaces deeper, as the coefficients under- metabolitesalready are.Verification:
rxnEnzMatandkcat.printOrange:\nprinted literallySince
printOrangeprints viafprintf('%s', …)so that a%in model text is not treated as a format directive,\nis no longer expanded either. Callers that end a message with\nprint a literal backslash-n with no line break: 15 calls in RAVEN and 17 in GECKO, including GECKO 4's backward-compatibility notice:printOrangenow turns\ninto a line break; no other escape sequence or format directive is interpreted, so%still prints as-is. All callers in both repositories use only\n.Tests
develop3and passing here:tIO/writeReadYAMLNestsEcRxnEnzymes(indentation plus round trip ofec.enzymes/rxnEnzMat) andtUtils/printOrangeExpandsNewlineWhenPrinting.tIOandtUtilspass locally (MATLAB 2024b); the twoparallelWorkersRAVENtests are filtered by their assumptions on this machine, as before.