Merge pull request #62 from hetalang/hc-090

heta-compiler v0.9.0 support

Artifacts.toml

@@ -1,33 +1,33 @@
 [[heta_app]]
 arch = "x86_64"
-git-tree-sha1 = "a23558d3a8dafc1280df998cda01be5f3df5322b"
+git-tree-sha1 = "3555032f7d9bf3667af7c796e7c5e6ef65ab184d"
 libc = "glibc"
 os = "linux"
 
     [[heta_app.download]]
-    sha256 = "c3de7b6935653e4f0e4b0ff7251b639e76d5fecda1a825784f72ee02cb2381c5"
-    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.8.7/heta-compiler-linux.tar.gz"
+    sha256 = "93b951ccf358cdd06f525a6022d1fae801d9e135f7196d082bc1b1ff44069058"
+    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.9.0/heta-compiler-linux.tar.gz"
 [[heta_app]]
 arch = "x86_64"
-git-tree-sha1 = "b31deea146ed62c2f686888074499a99fb876080"
+git-tree-sha1 = "f9a91d0fab917fbd4567bd9c1330670483f77431"
 os = "windows"
 
     [[heta_app.download]]
-    sha256 = "0b8af8715f6a50240dd475599615c466c4d4bd7979477a512c0b8de20d6cacdf"
-    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.8.7/heta-compiler-windows.tar.gz"
+    sha256 = "950b729cf15a60ab83bd3997b9cc0424f0f8885b311d319690052093c9bc2ef6"
+    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.9.0/heta-compiler-windows.tar.gz"
 [[heta_app]]
 arch = "x86_64"
-git-tree-sha1 = "a741cebf5cd6872b9da78a1713e5b835f9bc919b"
+git-tree-sha1 = "0da38cac8b6fbf9d7d20316a2b1c0e6dc1b4adc3"
 os = "macos"
 
     [[heta_app.download]]
-    sha256 = "9454cd0b5a47f5692a5a5decdf47a0e03ef18892f4be5c55d28777bf499176a3"
-    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.8.7/heta-compiler-macos.tar.gz"
+    sha256 = "8cb8bf7d3fe70926726074debd3692ac641903623669e3d0930552eb2c8ed8be"
+    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.9.0/heta-compiler-macos.tar.gz"
 [[heta_app]]
 arch = "aarch64"
-git-tree-sha1 = "a741cebf5cd6872b9da78a1713e5b835f9bc919b"
+git-tree-sha1 = "0da38cac8b6fbf9d7d20316a2b1c0e6dc1b4adc3"
 os = "macos"
 
     [[heta_app.download]]
-    sha256 = "9454cd0b5a47f5692a5a5decdf47a0e03ef18892f4be5c55d28777bf499176a3"
-    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.8.7/heta-compiler-macos.tar.gz"
+    sha256 = "8cb8bf7d3fe70926726074debd3692ac641903623669e3d0930552eb2c8ed8be"
+    url = "https://github.com/hetalang/heta-compiler/releases/download/v0.9.0/heta-compiler-macos.tar.gz"

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Change Log
 
+## 0.7.0
+
+- heta-compiler updated to 0.9.0
+- changes in `load_platform`: add `spaceFilter`
+
 ## 0.6.2
 
 - added aarch64 macos support

TODO.md

@@ -4,10 +4,10 @@ _The rest of ideas and issues are posted in https://github.com/hetalang/heta-dis
 
 ## bugs
 
-- Big models can result in StackOverFlow because of Savings
+- выдает warning при отсутствие параметра в модели - неудобно при фиттниге
 - `parameters` method in Scenario should get the scenario-level parameters but not the full list of constants
-- wrong get parameters from MCResults, Pair{Symbol, MCResults}, Vector{Pair{Symbol, MCResults}}
-- 
+- не выводит параметры уровня `Scenario` в `DataFrame(::SimResult)`
+- "NaN dt detected" при `sim` если параметр задается на уровне `Scenario`
 
 ## fitting
 

artifacts_scripts/build_artifacts.jl

@@ -1,7 +1,7 @@
 using ArtifactUtils
 using Pkg.Artifacts
 
-const HETA_COMPILER_RELEASE = "v0.8.7"
+const HETA_COMPILER_RELEASE = "v0.9.0"
 
 const artifacts_toml = joinpath(@__DIR__, "..", "Artifacts.toml")
 

cases/story_3/index.heta

@@ -48,4 +48,3 @@ Vol1 = 6.000102e+00;
 kmax = 2.221855e+03;
 Km = 9.997290e+03;
 */
-#export {format: Julia, filepath: julia_platform};

docs/src/basics/overview.md

@@ -16,7 +16,7 @@ Heta is a modeling language for quantitative systems pharmacology (QSP) and syst
 It is a DSL (domain-specific language) describing dynamic model or multiple models in process-description format.
 Heta compiler converts it into variety of formats including Julia code, which can be loaded to Julia/HetaSimulator environment.
 
-HetaSimulator supports all features of the [Heta language](https://hetalang.github.io/#/specifications/). One can organize modeling project with re-used modules (files), include any number of models into a single platform with the namespaces mechanism. The platform can use the declaration file __platform.json__ or can be loaded directly from the heta file. 
+HetaSimulator supports all features of the [Heta language](https://hetalang.github.io/#/specifications/). One can organize modeling project with re-used modules (files), include any number of models into a single platform with the namespaces mechanism. The platform can use the declaration file __platform.yml__ or can be loaded directly from the heta file. 
 All Heta modules: Heta code, tables, SBML and JSON can be loaded as a modeling platform and compiled into ODE-based mathematical representation.
 
 To read more about Heta-based modeling platforms and Heta compiler visit the homepage <https://hetalang.github.io/#/>.
@@ -141,20 +141,18 @@ The list of additional arguments is approximately the same as [CLI options](http
 
 Alternatively you can use files generated with stand-alone [Heta compiler](https://hetalang.github.io/#/heta-compiler/).
 
-To do so the model code should be updated with the `#export` statement.
+To do so the model code should be build with `--export Julia` options.
 
 ```heta
 ...
 sw2 @TimeSwitcher {start: 0, period: 24, active: false};
 A0 [sw2]= dose;
-
-#export {format: Julia, filepath: julia_platform};
 ```
 
-Running the code with the console command `heta build my_project` produces the file __my\_example/dist/julia\_platform/model.jl__ which can be loaded with [`load_jlplatform`](@ref) method.
+Running the code with the console command `heta build --export Julia my_project` produces the file __my\_example/dist/julia/model.jl__ which can be loaded with [`load_jlplatform`](@ref) method.
 
 ```julia
-p = load_jlplatform("./my_example/dist/julia_platform/model.jl")
+p = load_jlplatform("./my_example/dist/julia/model.jl")
 ```
 ```julia
 Loading platform... OK!

docs/src/tutorial/fit-files/index.heta

@@ -33,5 +33,3 @@ A0 [sw2]= dose;
 sigma1 @Const = 0.1;
 sigma2 @Const = 0.1;
 sigma3 @Const = 0.1;
-
-#export {format: Julia, filepath: julia_platform};

src/HetaSimulator.jl

@@ -7,7 +7,7 @@ module HetaSimulator
   import Base: SHA1
 
   # heta-compiler supported version
-  const HETA_COMPILER_VERSION = "0.8.7"
+  const HETA_COMPILER_VERSION = "0.9.0"
   #const SUPPORTED_VERSIONS = ["0.8.4", "0.8.5", "0.8.6"]
 
   function heta_compiler_load()

src/heta_cli/connect.jl

@@ -5,8 +5,7 @@ const MODEL_NAME = "model.jl"
 """
     load_platform(  
       target_dir::AbstractString;
-      rm_out::Bool = true,
-      julia_only::Bool = true, 
+      rm_out::Bool = true, 
       dist_dir::String = ".",
       source::String = "index.heta",
       type::String = "heta",
@@ -30,10 +29,16 @@ function load_platform(
   target_dir::AbstractString;
   rm_out::Bool = true,
   dist_dir::String = ".",
+  spaceFilter::Union{String, Vector{:Symbol}, Nothing} = nothing,
   kwargs...
 )
-  # convert heta model to julia 
-  build_res = heta_build(target_dir; julia_only = true, dist_dir = dist_dir, kwargs...)
+  if spaceFilter isa Vector{String}
+    spaceFilter = "^(" * join(spaceFilter, "|") * ")\$"
+  end
+
+  export_ = isnothing(spaceFilter) ? "{format:Julia,filepath:$MODEL_DIR}" : "{format:Julia,filepath:$MODEL_DIR,spaceFilter:'$spaceFilter'}"
+  # convert heta model to julia
+  build_res = heta_build(target_dir; dist_dir = dist_dir, export_ = export_, kwargs...)
 
   # check the exitcode (0 - success, 1 - failure) 
   build_res == 1 && throw("Compilation errors. Likely there is an error in the code of the model. See logs")
@@ -42,7 +47,7 @@ function load_platform(
   _target_dir = abspath(target_dir)
 
   # load model to Main
-  return load_jlplatform("$_target_dir/$MODEL_DIR/$MODEL_NAME"; rm_out)
+  return load_jlplatform("$_target_dir/$dist_dir/$MODEL_DIR/$MODEL_NAME"; rm_out)
 end
 
 """

src/heta_cli/heta.jl

@@ -71,15 +71,14 @@ end
     heta_build(
       target_dir::AbstractString;
       declaration::String = "platform",
-      skip_export::Bool = false,
       units_check::Bool = false,
       log_mode::String = "error",
-      debug::Bool = false,
-      julia_only::Bool = false,
+      debug::Bool = false
       dist_dir::String = "dist",
       meta_dir::String = "meta",
       source::String = "index.heta",
       type::String = "heta"
+      export::String = nothing
     )
 
 Builds the models from Heta-based platform
@@ -91,53 +90,44 @@ Arguments:
 
 - `target_dir` : path to a Heta platform directory
 - `declaration` : path to declaration file. Default is `"platform"`
-- `skip_export` : if set to `true` no files will be created. Default is `false`
 - `units_check` : if set to `true` units will be checked for the consistancy
 - `log_mode` : log mode. Default is `"error"`
 - `debug` : turn on debug mode. Default is `false`
-- `julia_only` : export only julia-based model. Default is `false`
 - `dist_dir` : directory path, where to write distributives to. Default is `"dist"`
 - `meta_dir` : meta directory path. Default is `"meta"`
 - `source` : path to the main heta module. Default is `"index.heta"`
 - `type` : type of the source file. Default is `"heta"`
+- `export` : export the model to the specified format: `Julia,JSON`, `{format:SBML,version:L3V1},JSON`
 """
 function heta_build(
   target_dir::AbstractString;
   declaration::String = "platform",
-  skip_export::Bool = false,
   units_check::Bool = false,
   log_mode::String = "error",
   debug::Bool = false,
-  julia_only::Bool = false,
   dist_dir::String = "dist",
   meta_dir::String = "meta",
   source::String = "index.heta",
-  type::String = "heta"
+  type::String = "heta",
+  export_::Union{String, Nothing} = nothing,
 )
 
   # convert to absolute path
   _target_dir = abspath(target_dir)
 
-  # check if the dir contains src, index.heta, platform.json
-  #isdir("$_target_dir/src") && throw("src directory not found in $_target_dir")
-  #!isfile("$_target_dir/index.heta") && throw("index.heta file not found in $_target_dir")
-  #!isfile("$_target_dir/platform.json") && throw("platform.json file not found in $_target_dir")
-
   # cmd options supported by heta-compiler
   options_array = String[]
 
   declaration != "platform" && push!(options_array, "--declaration", declaration)
-  skip_export && push!(options_array, "--skip-export")
   units_check && push!(options_array, "--units-check")
   log_mode != "error" && push!(options_array, "--log-mode", log_mode)
   debug && push!(options_array, "--debug")
-  julia_only && push!(options_array, "--julia-only")
   dist_dir != "dist" && push!(options_array, "--dist-dir", dist_dir)
   meta_dir != "meta" && push!(options_array, "--meta-dir", meta_dir)
   source != "index.heta" && push!(options_array, "--source", source)
   type != "heta" && push!(options_array, "--type", type)
   push!(options_array, "--skip-updates")
-
+  !isnothing(export_) && push!(options_array, "--export", export_)
 
   run_build = run(ignorestatus(`$heta_exe_path build $options_array $_target_dir`))
 

test/examples/single_comp_events/index.heta

@@ -4,5 +4,3 @@ include ./qsp-units.heta
 // include model.heta
 
 include one-compartment.heta
-
-// #export  { format: DBSolve, filepath: dbsolve_in_vitro };

test/examples/single_comp_events/one-compartment.heta

@@ -43,5 +43,3 @@ switch [sw]= 1;
 
 sw_end @TimeSwitcher { start: time_end, active: false };
 switch [sw_end]= 0;
-
-// #export { format: SBML, filepath: sbml_output };