release 0.1.1

Author: alexOarga

.github/workflows/main.yml

@@ -63,4 +63,14 @@ jobs:
         python -m twine upload --skip-existing --non-interactive dist/*
     - name: Test install
       run: |
-        pip install findCPcore
+        pip install findCPcore
+    - name: GitHub release
+      uses: actions/create-release@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.TOKEN_GITHUB }}
+      with:
+        tag_name: ${{ github.ref }}
+        release_name: ${{ github.ref }}
+        body_path: ""
+        draft: false
+        prerelease: false

docs/source/CORE.ipynb

@@ -1250,7 +1250,7 @@
    "source": [
     "## 2. Facade & FacadeUtils\n",
     "\n",
-    "The module ```FacadeUtils``` from ```findCPcore``` provides specific methods for the generation of spreadsheets regarding the computation of chokepoint reactions taking into account Flux Variability Analysis and Dead End Metabolites."
+    "Modules ```FacadeUtils``` and ```Facade``` from ```findCPcore``` provides specific methods for the generation of spreadsheets regarding the computation of critical reactions taking into account Flux Variability Analysis and Dead End Metabolites."
    ]
   },
   {
@@ -1264,7 +1264,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1314,7 +1314,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -1339,17 +1339,23 @@
       "LOG:Searching essential genes...\n",
       "LOG:Searching essential genes reactions...\n",
       "LOG:Searching essential reactions...\n",
-      "LOG:Removing"
+      "LOG:Removing Dead End Metabolites (D.E.M.)...\n",
+      "LOG:Searching essential reactions...\n",
+      "LOG:Searching new chokepoint reactions...\n",
+      "LOG:Searching essential genes...\n",
+      "LOG:Searching essential genes reactions...\n",
+      "LOG:Generating spreadsheet...\n"
      ]
     },
     {
      "data": {
-      "text/html": [
-       "* * *"
+      "text/plain": [
+       "(True, 'output.xls')"
       ]
      },
+     "execution_count": 4,
      "metadata": {},
-     "output_type": "display_data"
+     "output_type": "execute_result"
     }
    ],
    "source": [
@@ -1416,39 +1422,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Reading model...\n",
-      "Running Flux Variability Analysis with fraction: 0.0\n",
-      "Running Flux Variability Analysis with fraction: 0.1\n",
-      "Running Flux Variability Analysis with fraction: 0.2\n",
-      "Running Flux Variability Analysis with fraction: 0.3\n",
-      "Running Flux Variability Analysis with fraction: 0.4\n",
-      "Running Flux Variability Analysis with fraction: 0.5\n",
-      "Running Flux Variability Analysis with fraction: 0.6\n",
-      "Running Flux Variability Analysis with fraction: 0.7\n",
-      "Running Flux Variability Analysis with fraction: 0.8\n",
-      "Running Flux Variability Analysis with fraction: 0.9\n",
-      "Running Flux Variability Analysis with fraction: 1.0\n"
+     "ename": "TypeError",
+     "evalue": "'module' object is not callable",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-6-4bebcdd4e316>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      6\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      7\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 8\u001b[0;31m \u001b[0mconfig\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mGrowthDependentCPConfig\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      9\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprint_f\u001b[0m          \u001b[0;34m=\u001b[0m \u001b[0mcallback_print\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     10\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmodel_path\u001b[0m       \u001b[0;34m=\u001b[0m \u001b[0;34m\"aureus.xml\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mTypeError\u001b[0m: 'module' object is not callable"
      ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "(True, 'output.xls')"
-      ]
-     },
-     "execution_count": 35,
-     "metadata": {},
-     "output_type": "execute_result"
     }
    ],
    "source": [
+    "# import config class\n",
+    "from findCPcore.utils import GrowthDependentCPConfig\n",
+    "\n",
+    "\n",
     "def callback_print(message, arg1, arg2):\n",
     "    print(message)\n",
     "\n",
@@ -1461,6 +1454,13 @@
     "facade = Facade()\n",
     "facade.generate_growth_dependent_report(config)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {