set namespace as experimental feature

actions.md

@@ -26,17 +26,17 @@ When applying `insert` the class should be stated directly.
 
 ```heta
 // first insert
-#insert  one::c1 @Compartment {title: first} := 1;
+#insert  c1 @Compartment {title: first} := 1;
 
 // second insert with the same index
-#insert  one::c1 @Compartment {title: second};
+#insert  c1 @Compartment {title: second};
 ```
-The compartment with the index `one::c1` will be replaced by the another compartment.
+The compartment with the index `c1` will be replaced by the another compartment.
 The result of two statements will be
 
 ```json
 {
-    "one::c1" : {
+    "c1" : {
         "title": "second",
         "assignment": {} 
     } 
@@ -46,7 +46,7 @@ The result of two statements will be
 ### Example 2
 
 ```heta
-#insert one::S { compartment: comp1 };
+#insert S { compartment: comp1 };
 ```
 
 This statement should throw the error because class is not indicated.
@@ -60,16 +60,16 @@ If an updated property exists it will be rewritten by a new value. The current v
 ### Example 1
 ```heta
 // first insert
-#insert  one::c1 @Compartment {title: first} := 1;
+#insert  c1 @Compartment {title: first} := 1;
 
 // second insert with the same index
-#update  one::c1 { title: second };
+#update  c1 { title: second };
 ```
 
 The result of two statements
 ```json
 [{
-    "one::c1" : {
+    "c1" : {
         "title": "second",
         "assignment": { "ode_": 1 } 
     } 
@@ -79,10 +79,10 @@ The result of two statements
 ### Example 2
 
 ```heta
-#update one::S @Species { compartment: c1 };
+#update S @Species { compartment: c1 };
 ```
 
-The statement throws error because the component with index one::S has not been created before.
+The statement throws error because the component with index `S` has not been created before.
 
 ### Example 3
 

cases/all-classes.heta

@@ -0,0 +1,150 @@
+
+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}
+]};
+
+avogadro @Const {
+  num: 6e23,
+  free: false
+};
+
+x @Record {
+  title: "This is x title",
+  units: items/mole,
+  boundary: true,
+  assignments: {
+    start_: 1
+  }
+};
+
+s @Species {
+  units: mM,
+  isAmount: false,
+  boundary: false,
+  assignments: {
+    start_: 0
+  },
+  compartment: comp1
+};
+comp1 @Compartment {
+  units: L,
+  assignments: {
+    start_: 5.3
+  }
+};
+r1 @Reaction {
+  units: mmole/min
+  assignments: {
+    ode_: k1*comp1*s
+  }
+  actors: 'a=>',
+  modifiers: ['b']
+};
+
+// simulations
+
+simple_task1 @SimpleTask {
+  model: sp1, // reference to space
+  subtasks: [
+    {saveat: [1,2,3], output_ids: [A, B, C]}
+    {saveat: [4,5,6], output_ids: [C]}
+  ],
+  type: simulation,
+  reassign: { // update constant values
+    const1: 3,
+    const2: 4.4
+  },
+  tspan: [0, 120], // time range
+  solver: {
+    alg: Rosenbrock23,
+    reltol: 1e-6,
+    abstol: 1e-12,
+    maxiters: 1e7,
+    dtmax: 0.1,
+    tstops: [] // force calculation in time points
+  },
+  data: {},
+  reduce: {}
+};
+
+simple_task2 @SimpleTask {
+  model: sp1,
+  subtasks: [
+    {saveat: [4,5,6]}
+  ]
+};
+
+multi_task1 @MultiTask { // unscoped
+  task_vec: [simple_task1, simple_task2],
+  sizes: {k1: 1, k2: 2}
+};
+
+// === fitting ===
+dts1 @SimpleData {
+  output_ids: [A, B, C], // depDataMarkers
+  indepData: ['t'], // indepDataMarker
+  t: [1, 2, 3], // indepData
+  val: [ // depData
+    [1, 1, 1],
+    [1, 1, 1],
+    [1, 1, 1]
+  ],
+  evid: [0, 0, 0]
+}
+
+l1 @SimpleTask {
+  model: sp1,
+  sizes: {}
+  subtasks: [{
+    data: dts1
+    reduce: ln_loss2
+  }],
+  reduce: sum
+};
+l2 @SimpleTask {
+  model: sp1,
+  sizes: {dose: 1}
+  subtasks: [{
+    data: dts2
+    reduce: ln_loss2
+  }],
+  reduce: sum
+};
+
+likelihood_sum @MultiTask {
+  tasks: [l1, l2],
+  reduce: sum
+};
+
+fitting_task1 @FittingTask {
+  inter_task: likelihood_sum,
+  fit_sizes: [k1, k2, k3],
+  fitter_opt: {
+    alg: LN_NELDERMEAD
+  }
+};
+
+dts1 @Observation {
+  kind: KineticsObservation,
+  indepDataMarker: t,
+  indepData: [0.1, 0.2, 0.3, 0.4, 0.5],
+  depDataMarkers: [x, y, z, s],
+  depData: [
+    [0, 0, 0, 0],
+    [0, 0, 0, 0],
+    [0, 0, 0, 0],
+    [0, 0, 0, 0],
+    [0, 0, 0, 0]
+  ]
+};

cases/one-compartment.md

@@ -10,25 +10,23 @@ dose @Const = 10;
 kabs @Const = 1e-2;
 kel @Const = 1.2e-3;
 
-namespace one begin
-  gut @Compartment .= 1;
-  Vd @Compartment .= 5;
-  a0 @Species {
-      compartment: gut,
-      isAmount: true
-  };
-  c1 @Species {
-      compartment: central
-  };
-  r_abs @Reaction { actors: a0 => c1 };
-  r_el @Reaction { actors: c1 => };
+gut @Compartment .= 1;
+Vd @Compartment .= 5;
+a0 @Species {
+    compartment: gut,
+    isAmount: true
+};
+c1 @Species {
+    compartment: central
+};
+r_abs @Reaction { actors: a0 => c1 };
+r_el @Reaction { actors: c1 => };
 
-  a0 .= F * dose;
-  c1 .= 0;
-  r_abs := kabs * a0;
-  r_el := kel * c1 * Vd;
-end
+a0 .= F * dose;
+c1 .= 0;
+r_abs := kabs * a0;
+r_el := kel * c1 * Vd;
 
-// this creates SBML formatted file based on namespace "one".
-one::sbml @SBMLExport;
+// this creates SBML formatted file
+sbml @SBMLExport;
 ```

cases/syntax.heta

@@ -0,0 +1,40 @@
+
+// base syntax
+
+ns1::var1 @Type1 'some title' { key1: string value, key2: 1.2, key3: true };
+
+// Component updates
+
+// created component
+mod1::A @Species { compartment: comp1 };
+// can be updated with the following code
+mod1::A { compartment: comp2, isAmount: true }; 
+
+// Namespaces
+
+mod1::A @Species { compartment: comp1 };
+mod2::A @Record .= 1.1;
+
+// Syntax sugar
+
+one::c1 @Compartment;
+one::c1 .= 10; // set initial value to 10
+one::c1 := x*y; // calculates its value at each time point
+one::c1 [sw1]= 4; // change its value to 4 after sw1 event
+
+// blocks
+
+namespace mod1 begin 
+    A @Species { compartment: comp1 };
+ 	B @Species { compartment: comp1 };
+end;
+
+// comments
+
+// Line comments
+/* Multiline
+    comment */
+
+// import
+
+#import { source: module1.heta, type: heta };