Merge branch 'master' of https://github.com/hetalang/heta-compiler

cases/0-hello-world/master/mm_julia/model.jl

@@ -49,24 +49,24 @@ function mm_init_func_(__constants__)
             P * default_comp,
         ],
         Float64[
-            __constants__...,
             default_comp,
+            __constants__...
         ]
     )
 end
 
 ### calculate RHS of ODE
 function mm_ode_func_(__du__, __u__, __p__, t)
-    __constants__ = __p__[1:2]
-    (default_comp,) = __p__[3:3]
+    (default_comp,) = __p__[1:1]
+    __constants__ = __p__[2:3]
     (S_,P_,) = __u__ 
 
     # Heta rules
     P = P_ / default_comp
     S = S_ / default_comp
     r1 = __constants__[1] * S / (__constants__[2] + S) * default_comp
 
-    #__p__[3:3] .= [default_comp,]
+    #__p__[1:1] .= [default_comp,]
     __du__ .= [
       -r1,  # dS_/dt
       r1,  # dP_/dt
@@ -85,8 +85,8 @@ function mm_saving_generator_(__outputIds__::Vector{Symbol})
     end
 
     function saving_(__u__, t, __integrator__)
-        __constants__ = __integrator__.p[1:2]
-        (default_comp,) = __integrator__.p[3:3]
+        (default_comp,) = __integrator__.p[1:1]
+        __constants__ = __integrator__.p[2:3]
         (S_,P_,) = __u__
 
         # Heta rules

cases/24-define-function/src/index.heta

@@ -64,7 +64,7 @@
 
 c1 @Compartment .= 2;
 s1 @Species {compartment: c1} .= 100;
-r1 @Reaction {actors: s1=} := k1 * pow7() * c1;
+r1 @Reaction {actors: s1=} := k1 * pow7(1.1) * c1;
 
 k1 @Const = 0.1;
 

export-formats.md

@@ -413,3 +413,104 @@ Each namespace in separate file.
 |Const: `Infinity`, `NaN`                                |- |- |+ |+ |+ |+ |+ |+ |+ |na 
 |`@Scenario` support                                     |- |- |- |- |- |- |- |+ |+ |na
 |`@Record {ss: true, ...}`                               |- |- |+ |- |- |- |- |+ |+ |na
+|`#defineFunction` support                               |- |- |- |- |+ |- |+ |+ |+ |na
+
+## Math expressions conversions
+
+_Skipped cell means no conversion_
+
+| | SLV/DBSolve | Julia | Mrgsolve/R | Simbio/Matlab |
+|--|--|--|--|--|
+|`abs(x)`| | |`fabs(x)`| |
+|`add(x, y)`|`x + y`|`+(x, y)`| | |
+|`ceil(x)`| | | | |
+|`cube(x)`|`pow(x, 3) or x ^ 3`|`NaNMath.pow(x, 3)`| | |
+|`divide(x, y)`|`x / y`|`/(x, y)`| | |
+|`exp(x)`| | | | |
+|`floor(x)`| | | | |
+|`ln(x)`| |`NaNMath.log(x)`| | |
+|`log(x)`| |`NaNMath.log(x)`| |`log(x)`|
+|`log(x, base)`|`log(x) / log(base)`|`NaNMath.log(base, x)`| |`(log(x)/log(base))`|
+|`log10(x)`| |`NaNMath.log10(x)`| | |
+|`log2(x)`|`log(x) / log(2)`|`NaNMath.log2(x)`| |`(log(x)/log(2))`|
+|`multiply(x, y)`|`x * y`|`*(x, y)`| | |
+|`pow(x, y)`| `pow(x, y)` or `x ^ y`|`NaNMath.pow(x, y)`| |`power(x, y)`|
+|`sign(x)`| | | | |
+|`sqrt(x)`| |`NaNMath.sqrt(x)`| | |
+|`nthRoot(x)`|`pow(x, 1/2)` or `x ^ (1/2)`|`NaNMath.sqrt(x)`| | |
+|`nthRoot(x, n)`|`pow(x, 1/n)` or `x ^ (1/n)`|`NaNMath.pow(x, (1/n))`| | |
+|`square(x)`|`pow(x, 2)` or `x ^ 2`|`NaNMath.pow(x, 2)`| | |
+|`subtract(x, y)`|`x - y`|`-(x, y)`| | |
+|`max(x, y)`|`max2(x, y)`| |`std::max(x, y)`|`max(x, y)`|
+|`max(x, y, z)`|`max3(x, y, z)`| |`std::max(x, y, z)`|`max([x, y, z])`|
+|`min(x, y)`|`min2(x, y)`| |`std::min(x, y)`|`min(x, y)`|
+|`min(x, y, z)`|`min3(x, y, z)`| |`std::min(x, y, z)`|`min([x, y, z])`|
+|`factorial(n)`| |`fact(n)`| | |
+|`ifgt(x, y, z1, z2)`| |`x > y ? z1 : z2`| |`tern__(x>y, z1, z2)`|
+|`ifge(x, y, z1, z2)`| |`x >= y ? z1 : z2`| |`tern__(x>=y, z1, z2)`|
+|`iflt(x, y, z1, z2)`| |`x < y ? z1 : z2`| |`tern__(x<y, z1, z2)`|
+|`ifle(x, y, z1, z2)`| |`x <= y ? z1 : z2`| |`tern__(x<=y, z1, z2)`|
+|`ifeq(x, y, z1, z2)`| |`x == y ? z1 : z2`| |`tern__(x==y, z1, z2)`|
+|`x ^ y`|`x ^ y` or `pow(x, y)`|`NaNMath.pow(x, y)`|`pow(x, y)`| |
+|`e`|`exp(1)`|`exp(1.0)`| | |
+|`pi`|`acos(-1)` | | | |
+|`Infinity`| |`Inf`| | |
+|`NaN`| |`NaN`| | |
+|`t`| | |`SOLVERTIME`|`time`|
+|`a and b`| |`a && b`| |`&`|
+|`a or b`| |`a \|\| b`| |`\|`|
+|`a xor b`| |`xor(a, b)`| |`xor(a, b)`|
+|`not a`| |`!a`| |`~a`|
+|`b1 < b2 ? x : y`| `ifgt(b1, b2, x, y)`| | |`tern__(b1 < b2, x, y)`|
+|`piecewise(value1, cond1, value2, cond2, ..., otherwise)`|not supported| |not supported| |
+|`acos(x)`, `acot(x)`, `acsc(x)`,`asec(x)`, `asin(x)`, `atan(x)`, `cos(x)`, `cot(x)`, `csc(x)`, `sec(x)`, `sin(x)`, `tan(x)`| | | | |
+|`acosh(x)`, `acoth(x)`, `acsch(x)`, `asech(x)`, `asinh(x)`, `atanh(x)`, `cosh(x)`, `coth(x)`, `csch(x)`, `sech(x)`, `sinh(x)`, `tanh(x)`| | | | |
+
+_Conversion to SBML's MathML_
+
+| | SBML |
+|--|--|
+|`abs(x)`|`<apply><abs/>(x)</apply>`|
+|`add(x, y)`|`<apply><plus/>(x) (y)</apply>`|
+|`ceil(x)`|`<apply><ceiling/>(x)</apply>`|
+|`cube(x)`|`<apply><power/>(x)<cn>3</cn></apply>`|
+|`divide(x, y)`|`<apply><divide/>(x) (y)</apply>`|
+|`exp(x)`|`<apply><exp/>(x)</apply>`|
+|`floor(x)`|`<apply><floor/>(x)</apply>`|
+|`ln(x)`|`<apply><ln/>(x)</apply>`|
+|`log(x)`|`<apply><log/>(x)</apply>`|
+|`log(x, base)`|`<apply><log/><logbase>(base)</logbase>(x)</apply>`|
+|`log10(x)`|`<apply><log/>(x)</apply>`|
+|`log2(x)`|`<apply><log/><logbase><cn>2</cn></logbase>(x)</apply>`|
+|`multiply(x, y)`|`<apply><times/>(x) (y)</apply>`|
+|`pow(x, y)`|`<apply><power/>(x) (y)</apply>`|
+|`sign(x)`|`<apply><sign/>(x)</apply>`|
+|`sqrt(x)`|`<apply><root/>(x)</apply>`|
+|`nthRoot(x)`|not supported|
+|`nthRoot(x, n)`|not supported|
+|`square(x)`|`<apply><power/>(x)<cn>2</cn></apply>`|
+|`subtract(x, y)`|`<apply><minus/>(x) (y)</apply>`|
+|`max(x, y)`|`<apply><max/>(x) (y)</apply>`|
+|`max(x, y, z)`|`<apply><max/>(x) (y) (z)</apply>`|
+|`min(x, y)`|`<apply><min/>(x) (y)</apply>`|
+|`min(x, y, z)`|`<apply><min/>(x) (y) (z)</apply>`|
+|`factorial(n)`|`<apply><factorial/>(x)</apply>`|
+|`ifgt(x, y, z1, z2)`|not supported|
+|`ifge(x, y, z1, z2)`|not supported|
+|`iflt(x, y, z1, z2)`|not supported|
+|`ifle(x, y, z1, z2)`|not supported|
+|`ifeq(x, y, z1, z2)`|not supported|
+|`x ^ y`|`<apply><pow/>(x) (y)</apply>`|
+|`e`|not supported|
+|`pi`|not supported|
+|`Infinity`|not supported|
+|`NaN`|not supported|
+|`t`|`<csymbol definitionURL="http://www.sbml.org/sbml/symbols/time">t</csymbol>`|
+|`a and b`|`<apply><and/>(x) (y)</apply>`|
+|`a or b`|`<apply><or/>(x) (y)</apply>`|
+|`a xor b`|`<apply><xor>(x) (y)</apply>`|
+|`not a`|`<apply><not>(x)</apply>`|
+|`b1 < b2 ? x : y`|`<piecewise><piece>(x)<apply><smaller/>(b1) (b2)</apply></piece><otherwise>(y)</otherwise></piecewise>`|
+|`piecewise(value1, cond1, value2, cond2, ..., otherwise)`|`<piecewise><piece>(value1) (cond1)</piece><piece>(value2) (cond2)</piece><otherwise>(otherwise)</otherwise></piecewise>`|
+|`acos(x)`, `acot(x)`, `acsc(x)`,`asec(x)`, `asin(x)`, `atan(x)`, `cos(x)`, `cot(x)`, `csc(x)`, `sec(x)`, `sin(x)`, `tan(x)`|`<apply><arccos/>(x)</apply>`...|
+|`acosh(x)`, `acoth(x)`, `acsch(x)`, `asech(x)`, `asinh(x)`, `atanh(x)`, `cosh(x)`, `coth(x)`, `csch(x)`, `sech(x)`, `sinh(x)`, `tanh(x)`|not supported|

src/julia-export/expression.js

@@ -5,7 +5,7 @@ Expression.prototype.toJuliaString = function(){
     if(node.type==='ConstantNode' && Number.isInteger(node.value)){
       return node.value.toExponential(); // to display 6 => 6e0; 6e23 => 6e+23
     }
-    if(node.type==='FunctionNode' && node.fn.name==='plus'){
+    if(node.type==='FunctionNode' && node.fn.name==='add'){
       let args = node.args
         .map((arg) => arg.toString(options))
         .join(', ');

src/matlab-export/expression.js

@@ -19,7 +19,11 @@ Expression.prototype.toMatlabString = function(){
       let args = node.args
         .map((arg) => arg.toString(options))
         .join(', ');
-      return `min([${args}])`;
+      if (node.args.length <= 2) {
+        return `min(${args})`;
+      } else {
+        return `min([${args}])`;
+      }
     }
     if (node.type==='FunctionNode' && node.fn.name==='log') {
       if(node.args.length===1){

src/templates/julia-model.jl.njk

@@ -101,21 +101,21 @@ function {{ id }}_init_func_(__constants__)
         [ 0.0 ], # init for fake variable
         {%- endif %}
         Float64[
-            __constants__...,
         {%- for record in img.staticRecords %}
             {{ record.id }}{{ '*' + record.compartment if record.instanceOf('Species') and not record.isAmount }},
         {%- endfor %}
+            __constants__...
         ]
     )
 end
 {% set constantMaxIndex = img.constants | length %}
 {%- set staticMaxIndex = img.staticRecords | length %}
 ### calculate RHS of ODE
 function {{ id }}_ode_func_(__du__, __u__, __p__, t)
-    __constants__ = __p__[1:{{ constantMaxIndex }}]
     ({% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-    {%- endfor %}) = __p__[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+    {%- endfor %}) = __p__[1:{{ staticMaxIndex }}]
+    __constants__ = __p__[{{ staticMaxIndex + 1 }}:{{ staticMaxIndex + constantMaxIndex }}]
     ({% for record in img.dynamicRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}) = __u__ {# TODO: replace by __u__[index] #}
@@ -131,7 +131,7 @@ function {{ id }}_ode_func_(__du__, __u__, __p__, t)
     {{ record.id }} = {{ record.id }}_ / {{ record.compartment }}
     {% endif -%}
     {% endfor %}
-    #__p__[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}] .= [{% for record in img.staticRecords -%}
+    #__p__[1:{{ staticMaxIndex }}] .= [{% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}]
     {%- if img.dynamicRecords | length > 0 %}
@@ -163,10 +163,10 @@ function {{ id }}_saving_generator_(__outputIds__::Vector{Symbol})
     end
 
     function saving_(__u__, t, __integrator__)
-        __constants__ = __integrator__.p[1:{{ img.constants | length }}]
         ({% for record in img.staticRecords -%}
         {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-        {%- endfor %}) = __integrator__.p[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+        {%- endfor %}) = __integrator__.p[1:{{ staticMaxIndex }}]
+        __constants__ = __integrator__.p[{{ staticMaxIndex + 1 }}:{{ staticMaxIndex + constantMaxIndex }}]
         ({% for record in img.dynamicRecords -%}
         {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
         {%- endfor %}) = __u__{# TODO: replace by __u__[index] #}
@@ -219,10 +219,10 @@ end
 
 {%- for event in img.events | filter2('switcher.className', 'DSwitcher') %}
 function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator__)
-    __constants__ = __integrator__.p[1:{{ img.constants | length }}]
     ({% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-    {%- endfor %}) = __integrator__.p[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+    {%- endfor %}) = __integrator__.p[1:{{ staticMaxIndex }}]
+    __constants__ = __integrator__.p[{{ staticMaxIndex + 1 }}:{{ staticMaxIndex + constantMaxIndex }}]
     ({% for record in img.dynamicRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}) = __u__
@@ -245,10 +245,10 @@ end
 
 {%- for event in img.events | filter2('switcher.className', 'CSwitcher') %}
 function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator__)
-    __constants__ = __integrator__.p[1:{{ img.constants | length }}]
     ({% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-    {%- endfor %}) = __integrator__.p[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+    {%- endfor %}) = __integrator__.p[1:{{ staticMaxIndex }}]
+    __constants__ = __integrator__.p[{{ staticMaxIndex + 1}}:{{ staticMaxIndex + constantMaxIndex }}]
     ({% for record in img.dynamicRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}) = __u__
@@ -273,10 +273,10 @@ end
 
 {%- for event in img.events | filter2('switcher.className', 'StopSwitcher') %}
 function {{ id }}_{{ event.switcher.id }}_condition_func_(__u__, t, __integrator__)
-    __constants__ = __integrator__.p[1:{{ img.constants | length }}]
     ({% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-    {%- endfor %}) = __integrator__.p[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+    {%- endfor %}) = __integrator__.p[1:{{ staticMaxIndex }}]
+    __constants__ = __integrator__.p[{{ staticMaxIndex + 1 }}:{{ staticMaxIndex + constantMaxIndex }}]
     ({% for record in img.dynamicRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}) = __u__
@@ -301,10 +301,10 @@ end
 {% for event in img.events | exclude2('switcher.className', 'StopSwitcher') -%}
 function {{ id }}_{{ event.switcher.id }}_affect_func_(__integrator__)
     t = __integrator__.t
-    __constants__ = __integrator__.p[1:{{ img.constants | length }}]
     ({% for record in img.staticRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
-    {%- endfor %}) = __integrator__.p[{{ constantMaxIndex + 1 }}:{{ constantMaxIndex + staticMaxIndex }}]
+    {%- endfor %}) = __integrator__.p[1:{{ staticMaxIndex }}]
+    __constants__ = __integrator__.p[{{ staticMaxIndex + 1 }}:{{ staticMaxIndex + constantMaxIndex }}]
     ({% for record in img.dynamicRecords -%}
     {{ record.id }}{{ '_' if record.instanceOf('Species') and not record.isAmount }}, 
     {%- endfor %}) = __integrator__.u
@@ -349,7 +349,7 @@ function {{ id }}_{{ event.switcher.id }}_affect_func_(__integrator__)
     {%- endif %}
     __integrator__.p[[
         {%- for record in img.staticRecords -%}
-        {{ loop.index + constantMaxIndex + ',' if record.getAssignment(event.switcher.id) is defined }}
+        {{ loop.index + ',' if record.getAssignment(event.switcher.id) is defined }}
         {%- endfor -%}
     ]] = [
         {%- for record in img.staticRecords | exclude2('assignments.' + event.switcher.id, undefined) %}

test/julia-export/to-julia-string.js

@@ -24,8 +24,8 @@ describe('Expression exports to Julia', () => {
     let expr = Expression.fromString('divide(x,y)');
     expect(expr.toJuliaString()).to.be.equal('/(x, y)');
   });
-  it('toJuliaString() for "plus(x,y)"', () => {
-    let expr = Expression.fromString('plus(x,y)');
+  it('toJuliaString() for "add(x,y)"', () => {
+    let expr = Expression.fromString('add(x,y)');
     expect(expr.toJuliaString()).to.be.equal('+(x, y)');
   });
   it('toJuliaString() for "square(x)"', () => {