Merge pull request #1191 from akaviaLab/refactor/tests

Refactor/tests
opencobra · Apr 29, 2022 · 91dfcfc · 91dfcfc
2 parents b628572 + e13e8df
commit 91dfcfc
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Showing 138 changed files with 19,186 additions and 2,270 deletions.
diff --git a/benchmarks/cobra-cameo-merge-benchmarks-before-merge.ipynb b/benchmarks/cobra-cameo-merge-benchmarks-before-merge.ipynb
diff --git a/benchmarks/cobra-cameo-merge-benchmarks.ipynb b/benchmarks/cobra-cameo-merge-benchmarks.ipynb
diff --git a/benchmarks/geometric_fba.ipynb b/benchmarks/geometric_fba.ipynb
@@ -22,26 +22,9 @@
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "DEBUG:optlang.util:Gurobi python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/gurobipy\n",
-      "DEBUG:optlang.util:GLPK python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/swiglpk\n",
-      "DEBUG:optlang.util:Mosek python bindings not available.\n",
-      "DEBUG:optlang.util:CPLEX python bindings found at /home/moritz/.virtualenvs/cobra/lib/python3.5/site-packages/cplex\n",
-      "DEBUG:optlang.util:Scipy solver not available\n",
-      "DEBUG:pip._internal.utils.misc:lzma module is not available\n",
-      "DEBUG:pip._internal.vcs:Registered VCS backend: git\n",
-      "DEBUG:pip._internal.vcs:Registered VCS backend: hg\n",
-      "DEBUG:pip._internal.vcs:Registered VCS backend: svn\n",
-      "DEBUG:pip._internal.vcs:Registered VCS backend: bzr\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "from cobra.test import create_test_model"
+    "from cobra.io import load_model"
    ]
   },
   {
@@ -57,9 +40,26 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Scaling...\n",
+      " A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00\n",
+      "Problem data seem to be well scaled\n"
+     ]
+    }
+   ],
    "source": [
-    "model = create_test_model(\"textbook\")"
+    "model = load_model(\"textbook\")"
    ]
   },
   {
@@ -459,7 +459,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -473,7 +473,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.5"
+   "version": "3.7.1"
   }
  },
  "nbformat": 4,