update versions

cases/all-classes.heta

@@ -1,57 +1,105 @@
 
-pmid @ReferenceDefinition {
-  prefix: "https://pubmed.org",
-  suffix: /
+// Component
+// Base element annotation
+{
+  id: <ID>,
+  space: <ID>,
+  class: <String>, // class of component
+  title: <String>, // Human readable name of component
+  notes: <String>, // any notes, supports Markdown
+  tags: <String[]>, // tags for component
+  aux: <Dict>, // Any user defined properties
+  ...
 };
 
-pow @FunctionDefinition {
-  args: [x, y],
-  expr: x^y
+''' Notes '''
+sp1::cmd @Component "Title" {
+  tags: [a, b, c],
+  aux: {},
+  ...
 };
 
-kDa @UnitDefinition {components: [
-  {kind: g, multiplier: 1e3, exponent: 1},
-  {kind: mole, exponent: -1}
-]};
+// Record <= Component
+// describes value which can change its value in time
+p1 @Record {
+  boundary: <Boolean>,    // if true it cannot be changed by @Process or @Reaction
+  units: <UnitExpr>,      // units describing the value
+  assignments: {
+    [<ID>]: <MathExpr>,   // any number of key/value pairs describing value changes
+    ...
+  }
+};
+
+// record assignments
+p1 .= <MathExpr>;         // calculated at start, uses start_ switcher
+p1 := <MathExpr>;         // calculated at each time point, uses ode_ switcher
+p1 [sw1]= <MathExpr>;     // calculated at sw1 switcher
+p1 []= <MathExpr>;        // the same as .=
 
-avogadro @Const {
-  num: 6e23,
-  free: false
+// Process <= Record 
+// change record values using ODEs
+pr1 @Process {
+  actors: <ProcessExpr>/<Actor[]> // describes records to change
 };
 
-x @Record {
-  title: "This is x title",
-  units: items/mole,
-  boundary: true,
-  assignments: {
-    start_: 1
-  }
+// correct ProcessExpr
+1*A = 2*B + 3*C
+A => 2B + 3C      // mark as irreversible
+A <=> B + B + 3C  // mark as reversible
+
+// TimeSwitcher <= Component
+// run reassignment of records at specific time points
+sw1 @TimeSwitcher {
+  start: <Number>, // required, when switcher is called
+  period: <Integer>, // >0, if set, the switcher will be called with period
+  repeatCount: <Integer> // >=0, if set the switche will be called (repeatCount + 1) times
 };
 
-s @Species {
-  units: mM,
-  isAmount: false,
-  boundary: false,
-  assignments: {
-    start_: 0
-  },
-  compartment: comp1
+// Const <= Component
+// numerical value which does not change in time
+k1 @Const {
+  units: <UnitExpr>,      // units describing the value
+  num: <Number>,          // required, constant value
+  free: <Boolean>         // if true the value is marked for fitting
 };
+
+// Compartment <= Record <= Component
+// describes volumes where Species instances are located
 comp1 @Compartment {
-  units: L,
-  assignments: {
-    start_: 5.3
-  }
+  // no specific properties
 };
+
+// Species <= Record <= Component
+// describes particles in some location
+s @Species {
+  isAmount: <Boolean>, // 
+  compartment: <ID> // required, reference to Compartment
+};
+
+// Reaction <= Process <= Record
+// The same as Process, but all target references should be Species
 r1 @Reaction {
-  units: mmole/min
-  assignments: {
-    ode_: k1*comp1*s
-  }
-  actors: 'a=>',
-  modifiers: ['b']
+  actors: <ProcessExpr>/<Reactant[]>,   // 
+  modifiers: <Modifier[]>/<Id[]>        // array of references to Species
+};
+
+// ===
+
+pmid @ReferenceDefinition {
+  prefix: "https://pubmed.org",
+  suffix: /
+};
+
+pow @FunctionDefinition {
+  args: [x, y],
+  expr: x^y
 };
 
+kDa @UnitDefinition {components: [
+  {kind: g, multiplier: 1e3, exponent: 1},
+  {kind: mole, exponent: -1}
+]};
+
 // simulations
 
 simple_task1 @SimpleTask {

classes.md

@@ -313,6 +313,9 @@ r1 := k1*A*comp1;
 
 **Parent:** [_Component](#_component)
 
+Run reassignment of records for some contions.
+Switcher id can be used as key in assignments dictionary.
+
 *no specific properties*
 
 ## TimeSwitcher

versions.md

@@ -15,3 +15,4 @@ Each substantial change in Heta syntax or interpretation will update the MINOR n
 | 0.2.0 | v0.4.2 | ^0.4 |
 | 0.2.1 | v0.4.3 | ^0.4 |
 | 0.2.2 | v0.4.4 | ^0.4 |
+| 0.2.3 | v0.4.5 | ^0.4.5 |