update docs

.vscode/settings.json

@@ -11,7 +11,6 @@
         "sbml",
         "simbio",
         "simbiology",
-        "simsolver",
         "topo"
     ]
 }

CHANGELOG.md

@@ -2,7 +2,10 @@
 
 ## 0.6.8
 
-- support `#setScenario` and `Scenario`
+- `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
 

README.md

@@ -16,6 +16,7 @@ To read the full documentation, visit the Heta project homepage: <https://hetala
 ## Table of contents
 
 - [Introduction](#introduction)
+- [How to cite](#how-to-cite)
 - [Installation](#installation)
 - [Supported tools](#supported-tools)
 - [Usage of command line interface](#usage-of-command-line-interface)
@@ -39,6 +40,10 @@ Heta compiler can be used as the framework for a QSP modeling project of any siz
 - support of models written in human-readable text and table formats;
 - export models and data to different popular formats on the fly.
 
+## How to cite
+
+Metelkin, E., (2021). Heta compiler: a software tool for the development of large-scale QSP models and compilation into simulation formats. __Journal of Open Source Software, 6(67), 3708__, [DOI: 10.21105/joss.03708](https://doi.org/10.21105/joss.03708)
+
 ## Installation
 
 [NodeJS](https://nodejs.org/en/) must be installed prior to Heta compiler installation. Currently **NodeJS v8/v10** are recommended.

TODO.md

@@ -17,7 +17,6 @@
 [x] SBML L3
 [x] mrgsolve (R)
 [x] simbio (Matlab)
-[x] simsolver (Julia)
 [x] xlsx (Heta)
 [x] another xlsx
 [x] matlab
@@ -42,7 +41,7 @@
 - `#move`, `#moveNS`
 - support `@Switcher {active: false}` in Matlab
 - check unit consistency for Species: amount/area if compartment is area 
-- multi-space export in Matlab, DBSolve, SLV, SBML, Simbio, Mrgsolve, SimSolver
+- multi-space export in Matlab, DBSolve, SLV, SBML, Simbio, Mrgsolve, Julia
 - atStart to exports: Matlab, DBSolve
 
 ## ideas

export-formats.md

@@ -11,7 +11,6 @@ Following [Heta specifications](specifications/) exporting to different formats
 - [Mrgsolve](#mrgsolve)
 - [XLSX](#xlsx)
 - [Julia](#julia)
-- [SimSolver](#simsolver)
 - [Matlab](#matlab)
 
 See also [Features support table](#features-support)
@@ -287,31 +286,6 @@ Creation of Julia files (.jl).
 };
 ```
 
-## SimSolver
-
-Creation of Julia files (.jl) supported by SimSolver.
-
-### Properties
-
-| property | type | required | default | ref | description | 
-| ---------|------|----------|---------|-----|-------------|
-| spaceFilter | ID[]/ID | | | namespace | the namespase to export |
-
-### Output files
-
-**[filepath]/model.jl** : File storing model code.
-**[filepath]/run.jl** : Code to run model.
-
-**Example:**
-
-```heta
-#export {
-    format: SimSolver,
-    filepath: julia_code, // save result in directory "dist/julia_code"
-    spaceFilter: nameless // create model based on nameless namespace
-};
-```
-
 ## Matlab
 
 Creation of Matlab files (.m) which represent ODE and code to run ODE.
@@ -359,7 +333,6 @@ Creation of Matlab files (.m) which represent ODE and code to run ODE.
 |`@CSwitcher` with interpolation                         |- |- |+ |- |+ |+ |na|na|na
 |`@DSwitcher` class                                      |+ (for static only) |+ (for static only) |+ |+ |+ |+ |+ |+ |+
 |`@DSwitcher` with interpolation                         |- |- |+ |- |+ |+ |na|na|na
-|`@Dose` class (experimental)                            |- |- |- |- |- |- |- |- |-
 |multispace `#export`                                    |- |- |+ |- |- |- |- |+ |+
 |MathExpr: arithmetic functions                          |+ |+ |+ |+ |+ |+ |+ |+ |+
 |MathExpr: boolean operators                             |- |- |+ |+ |+ |+ |+ |+ |+