Defer BioNetGen app setup in library imports#108
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…on (#108) * Optimize getSpeciesFromFileName in NamingDatabase by batching queries. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #108 remove forbidden artifacts and run black * chore: remove generated artifact files from PR #108 --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Summary
BioNetGen().setup()from modelapi, network, and C simulator importsBNGFileis constructed without an explicitBNGPATHBNGPATH/suppressoptions throughbngmodel -> BNGParser -> BNGFileApp.setup()Tests
uvx black --check bionetgen/modelapi/bngfile.py bionetgen/modelapi/bngparser.py bionetgen/modelapi/model.py bionetgen/network/network.py bionetgen/network/networkparser.py bionetgen/simulator/csimulator.py tests/test_deferred_app_setup.py tests/test_csimulator_errors.py tests/test_modelapi_export_errors.py.venv/bin/python -m pytest tests/test_deferred_app_setup.py tests/test_csimulator_errors.py tests/test_modelapi_export_errors.py tests/test_main_accessors.py -qLocal full-suite note
.venv/bin/python -m pytest -qcurrently reaches unrelated local environment failures for missinglibsbml, missing/undiscoveredBNG2.pl, and visualization output checks.