rewrite heta compilation

.github/workflows/convert-to-heta.yml

@@ -0,0 +1,42 @@
+name: convert to Heta
+
+on:
+  workflow_dispatch: {}
+  push:
+    branches: [ master, '*-result' ]
+
+jobs:
+  convert-to-heta:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+
+      - name: Install Node.js 16
+        uses: actions/setup-node@v3
+        with:
+          node-version: 16
+
+      - name: Installations
+        run: |
+          npm i -g heta-compiler
+          heta -v
+
+      - name: Create file structure
+        run: |
+          bash ./bash/make-description.sh
+
+      - name: copy static
+        run: |
+          cp -r static/* result/
+
+      - name: Commit changes to result branch
+        uses: JamesIves/github-pages-deploy-action@releases/v3
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: result # The branch the action should deploy to.
+          FOLDER: result # The folder the action should deploy.
+          CLEAN: false

.gitignore

@@ -9,3 +9,6 @@
 
 /cases/semantic/julia
 /cases/semantic/json.json
+
+/results
+/result

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Ivan Borisov
+Copyright (c) 2024 Heta project
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,23 +1,22 @@
 # SBML Heta Cases
 
-The package is designed to test Simulation Software against [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite) cases in Julia.
-
-See results here <https://insysbio.github.io/sbml-heta-cases/>
+The package is designed to test different aspects of Heta formats on [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite).
 
 [![Heta project](https://img.shields.io/badge/%CD%B1-Heta_project-blue)](https://hetalang.github.io/)
 [![Copy visualization](https://github.com/insysbio/sbml-heta-cases/workflows/Copy%20visualization/badge.svg)](https://insysbio.github.io/sbml-heta-cases/)
-![Build and simulate](https://github.com/insysbio/sbml-heta-cases/workflows/Build%20and%20simulate/badge.svg)
+[![Build and simulate](https://github.com/insysbio/sbml-heta-cases/actions/workflows/convert-to-heta.yml/badge.svg)](https://github.com/insysbio/sbml-heta-cases/actions/workflows/convert-to-heta.yml)
 [![GitHub issues](https://img.shields.io/github/issues/insysbio/sbml-heta-cases.svg)](https://GitHub.com/insysbio/sbml-heta-cases/issues/)
 [![GitHub license](https://img.shields.io/github/license/insysbio/sbml-heta-cases.svg)](https://github.com/insysbio/sbml-heta-cases/blob/master/LICENSE)
 
-## Overview
 
-SBML Heta Cases contains:
+1. Conversion of cases into Heta code and JSON format
+2. Load models in SBML format and make simulations in 
+
+## File content
+
 - [SBML Test Suite](https://github.com/sbmlteam/sbml-test-suite) cases in `cases_path = "./cases/semantic"`. The original Matlab models were converted to Julia with Heta compiler. Julia code for each model is stored in `./cases/semantic/<case_num>/julia`, while models' settings and tags are stored in `cases_db = "./cases.json"`.
 - API (documented in the *Usage* section) to upload `cases_db`, run simulations, save results to `output_path = "./cases/output"` and update status in `results_db = "./results.json"`. A simulation can end with one of the three status: `success` indicates the output file has passed [tolerance test](https://github.com/sbmlteam/sbml-test-suite/blob/master/cases/semantic/README.md#tolerances-and-errors-for-timecourse-tests), `failure` signifies that tolerance test for a given simulation was not passed and `error` stands for any error during the simulation (error message is printed to the `message` field in `results_db`).
 
-Currently SBML Heta Cases suport only one `SimSolver` Simulation Backend.
-
 ## Usage
 
 SBML Heta Cases exports the following functions:

bash/index.heta

@@ -0,0 +1,9 @@
+#defineUnit volume { units: metre^3 };
+#defineUnit area { units: metre^2 };
+#defineUnit length { units: metre };
+#defineUnit substance { units: (1e-6 mole) };
+
+#include { source: ./model-sbml-l2v5.xml, type: sbml };
+
+#export { format: HetaCode };
+#export { format: JSON };

bash/make-description.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+echo Create of file structure
+mkdir -p result
+rm -rf result/*
+
+echo Collect compiler information
+echo "{" > result/summary.json
+hetaCompilerVersion=$(heta --version)
+echo "  \"hetaCompilerVersion\": \"$hetaCompilerVersion\"," >> result/summary.json
+started=$(date)
+echo "  \"started\": \"$started\"," >> result/summary.json
+dirs=$(find ./cases/semantic/ -type d -regex '.*/[0-9]+' -print0 | xargs -0 -n1 basename ) # find all directories with numbers
+#dirs=$(find ./cases/semantic/ -type f -name "*-sbml-l2v5.xml" -exec dirname {} \; | xargs -n1 basename )
+totalCasesCount=$(echo "$dirs" | wc -l)
+echo "  \"totalCasesCount\": \"$totalCasesCount\"," >> result/summary.json
+
+echo Copy files from cases and build models
+echo "  \"cases\": [" >> result/summary.json
+
+counter=0
+for dir in $dirs; do
+    counter=$((counter+1))
+    [ $counter==$totalCasesCount ] && delimiter="" || delimiter=","
+
+    mkdir -p result/$dir
+    cp bash/index.heta result/$dir/index.heta
+
+    # Extract line starting from "synopsis" until the end of line
+    synopsis=$(sed -n '/(\*/,/*)/p' cases/semantic/$dir/$dir-model.m | sed '1d;$d')
+    echo "$synopsis" > result/$dir/synopsis.txt
+
+    cp cases/semantic/$dir/$dir-sbml-l2v5.xml result/$dir/model-sbml-l2v5.xml > /dev/null 2>&1
+    if [ $? -ne 0 ]; then
+        echo "    {\"id\": \"$dir\", \"retCode\": 9}$delimiter" >> result/summary.json
+        echo "$dir has no SBML file"
+        continue
+    fi
+
+    # supress logs
+    heta build --skip-updates --dist-dir . --log-mode error result/$dir > /dev/null 2>&1 
+    retCode=$(echo $?)
+    echo "    {\"id\": \"$dir\", \"retCode\": $retCode}$delimiter" >> result/summary.json
+    echo "$dir finished with $retCode"
+done
+
+echo "  ]," >> result/summary.json
+finished=$(date)
+echo "  \"finished\": \"$finished\"" >> result/summary.json
+echo "}" >> result/summary.json
+
+# Save list of directories in JSON file
+# sudo apt-get install jq
+# echo "$dirs" | jq -R . | jq -s . > result/dirs.json

static/config.js

@@ -1,4 +1,5 @@
 window.config = {
     results: './results.json',
-    figPath: './cases/output'
+    figPath: './cases/output',
+    summaryPath: '/result/summary.json',
 };