This project is mirrored from https://*****@github.com/LCSB-BioCore/SBML.jl.git.
Pull mirroring updated .
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v1.4.3
[Diff since v1.4.2](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.4.2...v1.4.3) **Closed issues:** - Bad annotation crashes the cvterm extraction (#248) **Merged pull requests:** - do not crash on misclassified bqbiol/bqmodel cvterms (#249) (@exaexa)
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v1.4.2
[Diff since v1.4.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.4.1...v1.4.2) **Merged pull requests:** - fixup throw_severities, allow converters to change error reporting (#246) (@exaexa) - support more CVTerms and annotations (#247) (@exaexa)
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v1.4.1
[Diff since v1.4.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.4.0...v1.4.1) **Closed issues:** - writing/exporting SBML (#239) **Merged pull requests:** - add functions that make it easy to get models from a url and sbml-test-suite (#241) (@anandijain) - [CI] Use `julia-actions/cache` for caching (#242) (@giordano) - make throwing SBML load errors configurable (#243) (@exaexa) - clean up the SBML test suite URL machinery (#245) (@exaexa)
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v1.4.0
[Diff since v1.3.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.3.0...v1.4.0) **Merged pull requests:** - `use_value_from_trigger_time` is semantically a Bool (#236) (@exaexa) - include ccov badge (#237) (@exaexa) - add convert_promote_expand (#238) (@paulflang)
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v1.3.0
[Diff since v1.2.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.2.0...v1.3.0) **Closed issues:** - support reading of the CV terms (#27) - SBML model does not load with reaction or metabolite annotations (#208) - Use XML.jl to represent annotations (#209) **Merged pull requests:** - implement the special handling for avogadro constant (#233) (@exaexa) - Fix backwards compatibility of `interpret_math` with Avogadroes (#234) (@exaexa) - support CV terms (#235) (@exaexa)
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v1.2.0
[Diff since v1.1.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.1.0...v1.2.0) **Closed issues:** - Check possible silent errors while building SBML structure (#217) **Merged pull requests:** - allow github collaborators to `/format` stuff (#227) (@exaexa) - update compathelper scriptage (#228) (@exaexa) - support SBO terms (+ bonuses) (#229) (@exaexa) - fix sbmlRelational error with `Num` arguments (#230) (@paulflang) - cleanup&fix the sbmlRelational patch (#231) (@exaexa) - bump version to 1.2.0 (#232) (@exaexa)
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v1.1.0
[Diff since v1.0.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v1.0.0...v1.1.0) **Closed issues:** - Add `exponentiale` to `default_constants` (#213) - Power fails with negative exponents (#214) - Import species reference metadata (#218) **Merged pull requests:** - Pl/interpret fixes (#215) (@paulflang) - finish #215 (#219) (@exaexa) - remove the debugging leftover (#220) (@exaexa) - enable multiple arguments for comparisons (#221) (@paulflang) - use rule.variable instead of rule.id in seemsdefined (#222) (@paulflang) - implement full species references (#224) (@exaexa) - use the safer Object_createChild SBML methods. (#225) (@exaexa) - Formatting for #221 (#226) (@exaexa)
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v1.0.0
[Diff since v0.10.2](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.10.2...v1.0.0) **Closed issues:** - writeSBML (#11) - Events: Trigger may need to be a struct (#202) **Merged pull requests:** - Add `writeSBML` (#143) (@giordano) - Test starting from Julia v1.6 in CI (#205) (@giordano) - simplify format check reporting (#206) (@exaexa) - do not store kinetic law parameters as global parameters (#210) (@exaexa) - Add `Objective` struct (#211) (@giordano) - 2 tiny fixes (#212) (@exaexa) - [dramatic voice:] Time has come. (#216) (@exaexa)
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v0.10.2
[Diff since v0.10.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.10.1...v0.10.2) **Closed issues:** - Remove direct dependency on Symbolics (#195) **Merged pull requests:** - Add precompilation statement for `readSBML` (#193) (@giordano) - Read also name of unit definitions (#196) (@giordano) - add format checker & format cmd to github actions (#197) (@exaexa) - externalize the support for converting to Symbolics (#198) (@exaexa) - extensive math correctly exposes compartment identifications (#199) (@exaexa) - DocStringExtensions + some extra fixes (#200) (@exaexa) - further formatter improvements (#203) (@exaexa) - fix isfreein() (#204) (@paulflang)
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v0.10.1
[Diff since v0.10.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.10.0...v0.10.1) **Merged pull requests:** - avoid eval by directly using functions (#189) (@exaexa) - bump version 0.10.1 (#190) (@exaexa)
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v0.10.0
[Diff since v0.9.2](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.9.2...v0.10.0) **Merged pull requests:** - Clean up the parameter handling (#182) (@exaexa) - separate substance units from initial amounts and concentrations (#183) (@exaexa) - extract reaction names (#184) (@exaexa) - species constantness (#185) (@exaexa) - bump version 0.10 (#186) (@exaexa)
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v0.9.2
[Diff since v0.9.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.9.1...v0.9.2) **Closed issues:** - Model attributes (#175) **Merged pull requests:** - load units annotations from Model_t (#174) (@exaexa) - add Genie shield to README (#176) (@exaexa) - Add CompatHelper (#177) (@ChrisRackauckas) - Read `name`, `id` and `conversionFactor` model attributes (#178) (@giordano) - bemp release 0.9.2 (#179) (@exaexa)
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v0.9.1
[Diff since v0.9.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.9.0...v0.9.1) **Closed issues:** - new jll with experimental builds (m1) (#152) **Merged pull requests:** - isfile(fn) in readsbml (#132) (@anandijain) - add downstream SBMLToolkit testing (#146) (@anandijain) - Mention UCL contribution to the package (#172) (@giordano) - supply sane defaults to most SBML structures (#173) (@exaexa)
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v0.9.0
[Diff since v0.8.2](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.8.2...v0.9.0) **Closed issues:** - Rate rules (#53) - Find and add good tests for loading converters (#56) - Handling of lb, ub and oc in `Reaction`s (#85) - Support for math in initial assignments (orig: case 00489 fails) (#134) - functions with more than ~3 parameters should be converted to keyword parameters (#167) **Merged pull requests:** - fix function name in README (#161) (@exaexa) - Follow the SBML structure of bounds and objectives (#162) (@exaexa) - Support initial assignments (#163) (@giordano) - Add test cases for loading dynamic models and convert.jl (#164) (@giordano) - Events support (#165) (@anandijain) - Support list of rules (#166) (@giordano) - Define keywords-based constructors for `Model` and `Reaction` (#168) (@giordano) - Support list of constraints (#170) (@giordano) - Improve the documentation (#171) (@exaexa)
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v0.8.2
[Diff since v0.8.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.8.1...v0.8.2) **Merged pull requests:** - Rollback (temporarily) the unitful units (#160) (@exaexa)
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v0.8.1
[Diff since v0.8.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.8.0...v0.8.1) **Closed issues:** - Parameters should not just be `Dict{String,Float64}` (#130) - case 01296 fails (#139) **Merged pull requests:** - custom show for SBML.Model (#153) (@anandijain) - support default compartment sizes (#154) (@exaexa) - Read units of parameters [potentially breaking] (#155) (@giordano) - Add mapping of `rateOf` for Symbolics (#156) (@giordano) - symbolics 4 (#157) (@anandijain) - Fix typo in name of `sbmlRateOf` function (#158) (@giordano) - fix rateOf attempt 3 (#159) (@exaexa)
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v0.8.0
[Diff since v0.7.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.7.0...v0.8.0) **Closed issues:** - Tag? (#149) **Merged pull requests:** - simplify stoichiometry_matrix API & make it more efficient (#147) (@exaexa) - Update to Symbolics 3 (#148) (@ChrisRackauckas) - release 0.8 (#150) (@exaexa)
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v0.7.0
[Diff since v0.6.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.6.0...v0.7.0) **Closed issues:** - Adding `substoich` and `prodstoich` fields to `Reaction` (#119) - test suite case 00198 fails (#133) - DocStringExtensions usage (particularly on structs) (#136) - SBML doesn't respect math <cn> rationals (#140) **Merged pull requests:** - support for logical operators (#135) (@exaexa) - docstringextensions (#137) (@anandijain) - rational mathval (#141) (@anandijain) - separate reactants and product stoichiometries (#142) (@anandijain) - Make `sbml` slightly more type-stable (#144) (@giordano) - Fix definition of units (#145) (@giordano)
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v0.6.0
[Diff since v0.5.6](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.6...v0.6.0) **Closed issues:** - `parseSBML` function to directly pass in an XML string (#111) - piecewise handling fails (#112) - Rename helper functions like `getS` to nicer names (#121) - Extracting math with <geq/> returns a zero character (#124) - expandInitialAssignments converter fails on case 01234 (#125) **Merged pull requests:** - Use `Unitful` for units, instead of a custom struct (#109) (@giordano) - Rename `SBMLVersion` -> `Version` and unexport it (#120) (@giordano) - Rename some functions to something easier understand (#122) (@giordano) - Add function to read SBML model from a string (#123) (@giordano) - Fix checking of errors in `libsbml_convert` (#126) (@giordano) - Always pass `report_severities` argument to `check_errors` (#127) (@giordano) - fix parsing of relational operators (#128) (@exaexa) - version bump to 0.6.0 (#129) (@exaexa)
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v0.5.6
[Diff since v0.5.5](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.5...v0.5.6) **Closed issues:** - Reversible Reaction handling through direct lowering to ODESystem (#51) - Throw warning instead of error when not hOSU and compartment unsized (#101) - piecewise handling fails (#112) - Stoichiometry extraction fails when species appears on both sides of chemical reaction equation (#115) **Merged pull requests:** - Turn some anonymous functions into proper named functions (#110) (@giordano) - add issue templates to promote decent format of bug reports (#113) (@exaexa) - fix argument order and count for piecewise function (#114) (@exaexa) - quickfix: do not break stoichiometry if 2 species references are present (#116) (@exaexa) - handle SBML error severities (and don't throw on warnings) (#117) (@exaexa) - Allow rescue in very deep failure with hOSU and extensive math (#118) (@exaexa)