Tags give the ability to mark specific points in history as being important
This project is mirrored from https://*****@github.com/LCSB-BioCore/SBML.jl.git. Pull mirroring updated .
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
    1bd9216f · bump version 0.7.0 ·
  • 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)
  • 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)
  • v0.5.5   [Diff since v0.5.4](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.4...v0.5.5) **Closed issues:** - Stable docs don't seem to be updated (#92) - convert does not always return Num (#100) - Segfault on sbml-test-suite 01289-sbml-l3v2.xml (#102) **Merged pull requests:** - Add SSH key to let TagBot trigger building documentation (#93) (@giordano) - Remove unneeded dependencies from the package (#103) (@giordano) - check output of converters and throw julia errors in case something is wrong (#104) (@exaexa) - Improve reporting of errors in documents (#106) (@giordano) - 0.5.5 release prep (cleaning) (#107) (@exaexa) - link other packages (#108) (@exaexa)
  • v0.5.4   ## SBML v0.5.4 [Diff since v0.5.3](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.3...v0.5.4) **Merged pull requests:** - add ln, exp, to symbolics.jl (#94) (@anandijain) - bump Symbolics (#95) (@paulflang) - comprehensive math (#98) (@exaexa) - bemp version once again (#99) (@exaexa)
  • v0.5.4+doc1   ## SBML v0.5.4 [Diff since v0.5.3](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.3...v0.5.4) **Merged pull requests:** - add ln, exp, to symbolics.jl (#94) (@anandijain) - bump Symbolics (#95) (@paulflang) - comprehensive math (#98) (@exaexa) - bemp version once again (#99) (@exaexa)
  • v0.5.3   ## SBML v0.5.3 [Diff since v0.5.2](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.2...v0.5.3) **Closed issues:** - Support easy collection of initial amounts/concentrations (#71) - Fix getInitialConcentration (#87) **Merged pull requests:** - fix getInitialConcentrations (#88) (@paulflang) - implement extensive math conversion (#89) (@exaexa) - bemp version to 0.5.3 (#91) (@exaexa)
  • v0.5.2   ## SBML v0.5.2 [Diff since v0.5.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.1...v0.5.2) **Closed issues:** - Make `GPAAnd` and `GPAOr` parametric? (#72) - include runs on Julia 1.5 and Julia 1.6 (#80) **Merged pull requests:** - Strip whitespaces when reporting error messages from `readSBML` (#73) (@giordano) - Remove `DocumenterTools` from `docs/` environment (#74) (@giordano) - Run CI with GitHub Actions on pull requests (#75) (@giordano) - Gitignore files downloaded during the tests (#76) (@giordano) - Make `sbml` a proper function, instead of a non-const anononymous one (#77) (@giordano) - Make `convert_simplify_math` constant (#78) (@giordano) - Make `default_symbolics_mapping` constant (#79) (@giordano) - Fix minimum compatible version of Julia and run CI on 1.5 and 1 (#81) (@giordano) - Move test files to `test/data` to keep `test` clean (#82) (@giordano) - symbolics compat (#83) (@anandijain) - fun accessors for initial amounts and concentrations (#84) (@exaexa) - version bump to 0.5.2 (#86) (@exaexa)
  • v0.5.1   ## SBML v0.5.1 [Diff since v0.5.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.5.0...v0.5.1) **Closed issues:** - Representation of independent `time` variable in SBML.Model (#54) **Merged pull requests:** - parse out and test specially marked time math (#63) (@exaexa) - Pl sbml2symbolics (#65) (@paulflang) - Sanitize `libsbml_converter` types (#66) (@exaexa) - Tune up the converter type :] (#67) (@exaexa) - Minor cleaning&merge of #65 (#68) (@exaexa) - Support MathTime conversion to Symbolics, document the whole thing (#69) (@exaexa) - Update Project.toml (#70) (@anandijain)
  • v0.5.0   ## SBML v0.5.0 [Diff since v0.4.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.4.0...v0.5.0) **Closed issues:** - SBML.jl and SciML integration (#31) - bump version 0.4.0 (#45) - Converting SBML.Math types to Symbolics.jl (#47) - WARNING: using ModelingToolkit.Reaction in module SBML conflicts with an existing identifier. (#48) - Conversion of `piecewise` kineticLaws` (#52) **Merged pull requests:** - efficient cronless tagbot trigger (#46) (@exaexa) - merge cleaned-up #49 (#50) (@exaexa) - add support for running SBML converters (#55) (@exaexa) - add reversible flag (#57) (@exaexa) - add initial concentration, fix certainty of units (#58) (@exaexa) - support relational operators in math (#59) (@exaexa) - document the converter usage (#60) (@exaexa) - bump version to 0.5.0 (#61) (@exaexa) - import `download` from Downloads (#62) (@exaexa)
  • v0.5.0+doc1   ## SBML v0.5.0 [Diff since v0.4.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.4.0...v0.5.0) **Closed issues:** - SBML.jl and SciML integration (#31) - bump version 0.4.0 (#45) - Converting SBML.Math types to Symbolics.jl (#47) - WARNING: using ModelingToolkit.Reaction in module SBML conflicts with an existing identifier. (#48) - Conversion of `piecewise` kineticLaws` (#52) **Merged pull requests:** - efficient cronless tagbot trigger (#46) (@exaexa) - merge cleaned-up #49 (#50) (@exaexa) - add support for running SBML converters (#55) (@exaexa) - add reversible flag (#57) (@exaexa) - add initial concentration, fix certainty of units (#58) (@exaexa) - support relational operators in math (#59) (@exaexa) - document the converter usage (#60) (@exaexa) - bump version to 0.5.0 (#61) (@exaexa) - import `download` from Downloads (#62) (@exaexa)
  • v0.4.0   v0.4.0
  • v0.3.2   ## SBML v0.3.2 [Diff since v0.3.1](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.3.1...v0.3.2) **Closed issues:** - Bump version 0.3.1 (#30) **Merged pull requests:** - Avoid global namespace creep by `Maybe` (#33) (@exaexa)
  • v0.3.1   ## SBML v0.3.1 [Diff since v0.3.0](https://github.com/LCSB-BioCore/SBML.jl/compare/v0.3.0...v0.3.1) **Closed issues:** - Bump version (#25) - read gene product associations (#26) **Merged pull requests:** - correctly read gene product associations (#28) (@exaexa) - bump version to 0.3.1 (#29) (@exaexa)