test notebooks: ensure all can be run under pycov

Author: willfurnass

TestNotebooks/MiscTests/MuMoTtest_1dstream.ipynb

@@ -75,7 +75,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MiscTests/MuMoTtest_3dstream.ipynb

@@ -131,7 +131,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MiscTests/MuMoTtest_GreekLetters.ipynb

@@ -197,7 +197,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.4"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MiscTests/MuMoTtest_MasterEq.ipynb

@@ -9,9 +9,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Created `%%model` as an alias for `%%latex`.\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "'1.0.0'"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "import mumot\n",
     "\n",
@@ -20,15 +38,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%model\n",
-    "$\n",
+    "model1_str = (r\"\"\"\n",
     "A -> B : k_1\n",
     "B -> A : k_2\n",
-    "$"
+    "\"\"\")"
    ]
   },
   {
@@ -37,7 +54,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "model1 = mumot.parseModel(In[2])"
+    "model1 = mumot.parseModel(model1_str)"
    ]
   },
   {
@@ -118,8 +135,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%model\n",
-    "$\n",
+    "model2 = mumot.parseModel(r\"\"\"\n",
     "U -> A : g_1\n",
     "U -> B : g_2\n",
     "A -> U : a_1\n",
@@ -128,16 +144,7 @@
     "B + U -> B + B : r_2\n",
     "A + B -> A + U : s_1\n",
     "A + B -> B + U : s_2\n",
-    "$"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "model2 = mumot.parseModel(In[12])"
+    "\"\"\")"
    ]
   },
   {
@@ -308,8 +315,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%model\n",
-    "$\n",
+    "model4 = mumot.parseModel(r\"\"\"\n",
     "U -> A : g_1\n",
     "U -> B : g_2\n",
     "U -> C : g_3\n",
@@ -325,16 +331,7 @@
     "A + C -> C + U : s_4\n",
     "B + C -> B + U : s_5\n",
     "B + C -> C + U : s_6\n",
-    "$"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "model4 = mumot.parseModel(In[44])"
+    "\"\"\")"
    ]
   },
   {
@@ -516,7 +513,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.4"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MiscTests/MuMoTtest_MultiController.ipynb

@@ -262,7 +262,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MiscTests/MuMoTtest_bifurcation.ipynb

@@ -24,8 +24,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%model\n",
-    "$\n",
+    "model1 = mumot.parseModel(r\"\"\"\n",
     "U -> A : g_A\n",
     "U -> B : g_B\n",
     "A -> U : a_A\n",
@@ -34,7 +33,7 @@
     "B + U -> B + B : r_B\n",
     "A + B -> A + U : s\n",
     "A + B -> B + U : s\n",
-    "$"
+    "\"\"\")"
    ]
   },
   {
@@ -151,7 +150,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.5.4"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

TestNotebooks/MuMoTtest.ipynb

@@ -1044,7 +1044,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,

tox.ini

@@ -12,24 +12,27 @@ whitelist_externals =
     test
     wc
     make
-    xargs
-    find
 commands = 
     ; Ensure ipywidgets Jupyter extension is installed
     jupyter nbextension enable --py --sys-prefix widgetsnbextension
 
     ; Run unit tests and generate code coverage report
     pytest --verbose --cov-config=tox.ini --cov="{envsitepackagesdir}/mumot" tests
 
-    ; Ensure user manual, test and demo Notebooks run *without errors* (do not check for regressions yet)
+    ; Ensure the user manual Notebook runs *without errors* (do not check for regressions yet)
     ; (add --nbdime if running tox locally and want to visualise/explore diffs in web browser)
-    pytest --verbose --maxfail=1 --nbval-lax --nbval-cell-timeout=120 --cov-config=tox.ini --cov="{envsitepackagesdir}/mumot" --cov-append \
-        docs/*.ipynb \
-        TestNotebooks/*.ipynb \
-        TestNotebooks/MiscTests/*.ipynb \
-        DemoNotebooks/*
+    pytest --verbose --maxfail=1 --nbval-lax --nbval-cell-timeout=120 docs/MuMoTuserManual.ipynb
 
-    ; Ensure the user manual and regression test Notebooks do not show regressions (TODO; leave commented)
+    ; Ensure test Notebooks run *without errors* (do not check for regressions yet)
+    ; (add --nbdime if running tox locally and want to visualise/explore diffs in web browser)
+    pytest --verbose --maxfail=1 --nbval-lax --nbval-cell-timeout=120 \
+        --cov-config=tox.ini --cov="{envsitepackagesdir}/mumot" TestNotebooks 
+
+    ; Ensure demo Notebooks run *without errors* (do not check for regressions yet)
+    ; (add --nbdime if running tox locally and want to visualise/explore diffs in web browser)
+    pytest --verbose --maxfail=1 --nbval-lax --nbval-cell-timeout=120 DemoNotebooks
+
+    ; Ensure the main regression test Notebook does not show regressions (TODO; leave commented)
     ; (add --nbdime if running tox locally and want to visualise/explore diffs in web browser)
     ; pytest --verbose --maxfail=1 --nbval --nbval-cell-timeout=120 --cov-config=tox.ini --cov="{envsitepackagesdir}/mumot" --cov-append TestNotebooks/MuMoTtest.ipynb