v0.8.0

SBML v0.8.0

Diff since v0.7.0

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

SBML v0.7.0

Diff since v0.6.0

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 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

SBML v0.6.0

Diff since v0.5.6

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 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

SBML v0.5.6

Diff since v0.5.5

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

SBML v0.5.5

Diff since v0.5.4

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

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

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

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

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

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)