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 .
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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
    1bd9216f · bump version 0.7.0 ·
    [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)
  • 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)