CHANGELOG.md

Change Log

0.9.3

• build debinan package
• build cholatatey package
• build homebrew package
• update .MSI build
• display error if absolute paths in include and export
• remove logFormat, logPath, logLevel, logMode from platform.yaml
• display heta version in logs
• write full logs into build.log
• add --log-mode option to CLI
• rewrite build process to exclude absolute paths

0.9.2

• remove logLevel option from platform.yaml, use --log-level info instead in CLI

• fix bug with SBML import when use <initialAssignment>

• fix bug with Simbio export with zero outputs

• add Avogadro as base unit

• documentation updates

0.9.1

• more information in error messages
• bug fix: return undefined for empty string in table-module, clean only strings
• velnurability fix: update xlsx module

0.9.0

• Added support for Heta standard v0.5.0.
• Fixed minor parser bugs.
• SimbioExport: Introduced the ausAsNotes option and added aux as UserData.
• Component: Added xmlAnnotation property for SBML Annotation.
• Fixed issues with HetaCodeExport related to the aux property.
• API: Made Component a subclass of Top.
• Enhanced error messages for JSON schema validation.
• Builder API: Now supports both backend and frontend.
• All file paths are now relative.
• Moved export statements to platform.yml.
• Replaced platform.json with platform.yml.
• CLI: Removed --skip-export and --julia-only, added the new --export option.

0.8.7

• check and warn context without Switchers
• build win and linux,macos distributives separately

0.8.6

• fix bug in qsp-units.heta: wrong #defineUnits for mm
• fix strings for Simbio export
• replace ln to log for Matlab/Simbio

0.8.5

• fix bug with class names for easy renaming of class by webpack
• support #forceInsert action
• support null as values of Component properties

0.8.4

• support defineFunction in all exports
• fix SBML import: local parameters for L2, avogadro, bugs
• update uproach for checking next heta version
• remove heta update command

0.8.3

• Update syntax of units (m)^2
• Fix multiple issues with critical build error
• remove exitWithoutError option in Builder settings
• fig issues in SBML module: zero dimentions, delay, defineFunction, csymbol
• add time units import from SBML L3
• add qsp-functions.heta file in init
• prettify HetaCode export
• defineFunction rules: do not allow empty math and arguments

0.8.2

• fix error with comments in base syntax
• fix error in webpack entry

0.8.1

• fix bug with checking units for isAmount: true and ODE
• julia format changes saving_generator
• add windows MSI generation
• documention for standalone installation
• fix path regexp in export to allow C:\xxx

0.8.0

• update Julia format: p vector structure
• additional check of expresions parsed: use only allowed Nodes
• replace log(x, base) by logbase(x, base)
• remove nthRoot(x) support
• remove hyperbolic functions support
• fix bug with SBML import without products
• extend units check for generated ODE and defineFunction
• check number of arguments in defineFunction
• export of format Summary: lost and orphan components, units
• set defineFunction for core elements
• build standalone heta

0.7.4

• use @Reaction {compartment: comp1, ...} in DOT format if set
• Add ss property in @Record to describe algebraic equations
• check unit consistency for Species - amount/area if compartment is area
• Julia format update to include ss

0.7.3

• extend heta update to select version
• fix logPath in init
• Node version in default heta cli
• use ; at the end of include statements

0.7.2

• #export {format: dot} for abstract namespace
• calculate units for pow(x, 2/3), x ^ (2/3)
• heta update for CLI
• #deleteNS
• update heta-parser to use comments in dictionary
• update deps to the latest possible versions

0.7.1

• use 1/0 as boolean
• fix errors if platform.json is incorrect
• splitByClass for table export
• update deps

0.7.0 - export interface updates

• supports heta standard of v0.4.4
• Support of SLV26, fix issues with lost events
• set default filepath for export formats
• store export files in personal folders
• remove support of deprecated @Export class
• spaceFilter as regular expression
• check and display empty export
• minor code refactoring
• remove unnecessary lodash dependences
• node support starting from 14
• update and fix deps

0.6.20

• support webpack: do not use constructor.name
• fix heta init -s
• more info when id is skipped
• fix meta files in heta build

0.6.19

• update syntax of RCT A > B together with A => B
• adaptation for webpack
• remove 'fs' lib from core

0.6.18

• support for Node 12 and newer

0.6.17

• fix fatal error for wrong unit syntax
• functionDef warning for unsupported languages
• minor Matlab code fixes: max(), min()

0.6.16

• add option heta build --skip-updates

0.6.15

• fix bug in Julia export: use __constants__ in tstops

0.6.14

• update Julia export format

0.6.13 - draft defineFunction

• #defineFunction support for imports: SBML, Heta,
• #defineFunction supports for exports: HetaCode, SBML
• minor fixes for Julia export for big numbers like 6e+23
• minor updates to mrgsolve export

0.6.12

• fix NaNMath problem in julia export
• display error if id is not set

0.6.11

• optimize saving_generator in julia export
• Implement include ... type table
• Implement export to CSV and other tabular formats
• Julia export: log10, log2, log, pow, sqrt => NaNMath.log10, etc.

0.6.10

• add format: Dot support
• do not support units syntax like this {units: mL2}
• fix bug: Simbio event without period
• Simbio storage name: nameless => nameless_ns
• use NaNMath in Julia export

0.6.9 - multispace

• remove support of DSwitcher, CSwitcher in {format: SLV}
• support of CSwitcher, DSwitcher in {format: DBSolve}
• support active/inactive events for format: Matlab
• multispace export for format: Matlab
• multispace export for format: Mrgsolve, format: DBSolve, format: SLV
• multispace export for format: SBML, format: Simbio
• spaceFilter prop for format: HetaCode
• remove unnecessary rules from format: Julia

0.6.8

• TimeSwitcher, DSwitcher, CSwitcher support in mrgsolve
• support #setScenario and Scenario (no export)
• sbml export: proper sequence of listOf, remove garbage
• remove SimSolver export

0.6.7 - ready for JOSS

• error messages for unsupported switchers in SLV, DBSolve, mrgsolve
• update reserved words list with "default" (to support mrgsolve)
• extend api documentation
• export only concrete namespaces in Simbio

0.6.6

• remove @SimpleTask Class
• export to SBML L3 + timeUnits from @TimeScale
• replace "markdown" package by "markdown-it"
• support HetaCode export
• fix error with SLV events export
• fix log file creation
• fix error message in case of circular assignments
• support piecewise function in SBML, Matlab, Simbio, Julia
• support piecewise function in SBML module
• remove unsupported period in Simbio message

0.6.5

• Added JuliaExport format
• Add @StopSwitcher class as experimental
• Remove mathjs-translate deps
• Fix bug in comments inside dictionary
• ban <- syntax in Process expression
• remove npm dependance
• prettify internal errors
• skip units check if errors on previous stages

0.6.4

• @TimeScale component and time terms checking
• support periodic @TimeEvent in SBML and Simbio
• bug fix: temporally remove support of {active: false} events in Matlab
• bug fix: powTransform in SLV
• atStart and {active: true} in SimSolver
• fix renaming of function names

0.6.3

• check expressions for (=) sign
• bug fix: JS error in case of circular refs

0.6.2

• update to support SimSolver v0.3

0.6.1

• fix bug with units checking and dimensionless

0.6.0 - supports Heta standard of v0.4

• add #defineUnit instead of @UnitDef class
• checking terms for @Compartment, @Species, @Reaction
• checking units consistency for all @Record's assignments
• options.unitsCheck in declaration file
• supporting of dimensionless units in format [], 1, (1e-3)
• excel sheets numeration from 0 not from 1
• optional "id" property for #export
• advanced units checking for #export {format: Simbio, ...}
• support @_Switcher {active: false}
• fix support of logical operators: and, or, not, xor
• add reversible property (default true) to @Process

0.5.18

• Message for user to install the latest version
• Stop export if compilation errors exist
• support of ternary operator in Simbio

0.5.17

• replace SimSolverPlatform by Platform function in SimSolver export
• output property in @Record
• support output prop for SimSolver
• support output prop for DBSolve, SLV
• support output prop for Mrgsolve
• support output prop for Matlab
• bug fix in XLSX module

0.5.16

• fix bugs in sbml-module: unary minus in

0.5.15

• add scope prop in julia's events
• use > instead of >= in SBML and Simbio events to support run at start
• add atStart prop to _Switcher
• extend julia format
• rename #export Julia to SimSolver
• add properties to @Const: scale, lower, upper
• sbml-module: use dimensionless for simplified units
• sbml-module: support base units
• minor bug fixes

0.5.14

• update matlab run
• ternary operators support in Matlab
• remove ifg0 support

0.5.13 - SimSolver support

• add default tasks to Julia export
• notify in limitation in SBML module: StoichiometryMath, EventWithDelay, FastReaction
• fix Julia export for static and dynamic when switches compartment
• add --distDir, --metaDir, --juliaOnly to CLI options
• add "options.juliaOnly" to declaration
• week unit support in Matlab

0.5.12

• fix transformation in Julia: nthRoot, exponentiale, zero dynamic, ode_ priority, factorial
• add bind() method to DSwitcher
• export DSwitcher to formats: SLV, DBSolve, Matlab, Simbiology, SBML
• multispace Julia export
• use trigger instead of condition in CSwitcher
• export CSwitcher to formats: SLV, DBSolve, Matlab, Simbiology, SBML

0.5.11

• fix bug when trigger is empty
• add messages about unsupported SBML features
• add logFormat builder option for saving logs in JSON
• fix slv/dbsolve multiple stop

0.5.10 - skipped

0.5.9

• remove repeatCount prop from @TimeSwitcher
• support of multiple @TimeSwitcher in Matlab
• prettify code in SLV/DBSolve with groupConstBy prop
• fix error in DBSolve event target

0.5.8

• add spaceFilter for Mrgsolve, Julia
• version selection in #export {format: SBML}: support for L2V3, L2V4, L2V5
• add support @TimeSwitcher as event in SimBiology (instead of doses)
• fix bug with "not a deep clone in Expression"
• fix bug with empty period in Matlab
• include correct description of TimeSwitcher in Julia
• update structure of Julia format

0.5.7

• add spaceFilter for SLV, DBSolve, Simbio, Matlab, SBML
• fix UnitsExpr: empty units prop, dot in string
• output all dynamic in SLV, DBSolve

0.5.6 - multispace export

• default export of units as UnitExpr in @UnitDef
• multispace for JSON, YAML, XLSX: spaceFilter property
• catch error when XLSX file is busy

0.5.5 - sbml export

• fixes in unit conversion for SBML export
• support time symbol in SBML export
• remove name from SBML assignments

0.5.4

• add AnotherXLSX export
• fix rounding problems in units with prefixes
• fix name of container in Simbio export

0.5.3

• Add Export of format DBSolve
• Fix errors in unit rebase
• Add DSwitcher class
• Rename CondSwitcher to CSwitcher
• draft DSwitcher in Julia export

0.5.2

• rewrites Heta logs: all logs are stored in container
• fix Matlab export without event
• SBML module: support speciesType
• pretty Unit.toHTML
• faster clone() method for components
• support multiplier in Unit's hash
• minute as qsp unit

0.5.1 - IRT ready

• support {free: true} in #export DBSolve
• update _Component.clone() method to exclude cloning of namespace
• fixes to sbmlParse() function for clear math expressions
• "src/browser.js" is an entry point for browser apps and webpack
• method references() to _Component
• add "omit" property to #export formats: JSON, YAML, XLSX
• exclude "fs" and "path" libs from core code for browser support
• updates to nunjucks templates for easy usage in browser apps
• remove specific JS errors from Container and components
• multiple dependencies updates

0.5.0 - first public

• corresponds to Heta standard v0.2.4, see https://hetalang.github.io/