Merge branch 'release/4.4.13'

.gitlab-ci.yml

@@ -43,7 +43,7 @@ pages:
         - if [ -r content.zip ]; then unzip content.zip; rm -f content.zip public/*.zip ; fi
         - mkdir -p public
         - cp -r doc devdoc web/*.{html,png,zip} public
-        - if [[ -n "$CI_COMMIT_TAG" ]] ; then cp public/biocham.zip public/biocham_$CI_COMMIT_TAG.zip ; mv public/doc public/doc_$CI_COMMIT_TAG ; ln -s doc_$CI_COMMIT_TAG public/doc ; fi
+        - if [[ -n "$CI_COMMIT_TAG" ]] ; then cp public/biocham.zip public/biocham_$CI_COMMIT_TAG.zip ; rm -rf public/doc_$CI_COMMIT_TAG ; mv public/doc public/doc_$CI_COMMIT_TAG ; ln -s doc_$CI_COMMIT_TAG public/doc ; fi
         - cp public/biocham.zip public/biocham_latest.zip
         - zip -r content.zip public
         - mv content.zip public

about.pl

@@ -8,7 +8,7 @@
     about/0
   ]).
 
-version('4.4.12').
+version('4.4.13').
 
 copyright(
   'Copyright (C) 2003-2020 Inria, EPI Lifeware, Saclay-Île de France, France'

binder/Dockerfile

-FROM registry.gitlab.inria.fr/lifeware/biocham:v4.4.12
+FROM registry.gitlab.inria.fr/lifeware/biocham:v4.4.13

biocham_jupyter/guinbextension/package.json

 {
   "name": "gui",
-  "version": "4.4.12",
+  "version": "4.4.13",
   "description": "biocham gui in jupyter notebook",
   "main": "src/index.js",
   "scripts": {

biocham_jupyter/kernel/biocham_kernel/__init__.py

 """Example magic"""
-__version__ = '4.4.12'
+__version__ = '4.4.13'

library/examples/cmsb_2020/rate_independence.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Biocham 4.4.11\n",
+    "Copyright (C) 2003-2020 Inria, EPI Lifeware, Saclay-Île de France, France,\n",
+    "license GNU GPL 2, http://lifeware.inria.fr/biocham4/\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a + b => c."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "The output c is rate independent.\r\n",
+       "Time: 0.025 s\r\n"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "% testing outputs for permanence\n",
+    "test_rate_independence_invariants."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "The model is rate independent.\r\n",
+       "Time: 0.01 s\r\n"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "% testing the whole model for funnel conditions\n",
+    "test_rate_independence."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example 2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "clear_model.\n",
+    "a => x+c.\n",
+    "b => y+c.\n",
+    "x+y => z.\n",
+    "c+z => r."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "The output r is rate independent.\r\n",
+       "Time: 0.135 s\r\n"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_rate_independence_invariants."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "The model is rate independent.\r\n",
+       "Time: 0.029 s\r\n"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "test_rate_independence."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Biocham",
+   "language": "",
+   "name": "biocham"
+  },
+  "language_info": {
+   "codemirror_mode": "biocham",
+   "file_extension": ".bc",
+   "mimetype": "text/plain",
+   "name": "biocham",
+   "pygments_lexer": "prolog"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

web/index.html

@@ -32,7 +32,7 @@
 </head>
 <body>
 <h1>The Biochemical Abstract Machine BIOCHAM 4</h1>
-<h1>version 4.4.12 May 2020</h1>
+<h1>version 4.4.13 May 2020</h1>
 
 <div class="authors">
 <p>