Fix Jupyter Notebook pytest

.appveyor.yml

@@ -19,4 +19,4 @@ install:
   - pip install tables pytest nbval django
   - python setup.py install
 test_script:
-  - pytest --nbval
+  - pytest --nbval doc/tutorial.ipynb --sanitize-with doc/pytest-sanitize.ini

.travis.yml

@@ -6,7 +6,7 @@ before_install:
 install:
 - python setup.py install
 script:
-- pytest --nbval --cov=thunor
+- pytest --nbval doc/tutorial.ipynb --sanitize-with doc/pytest-sanitize.ini --cov=thunor
 after_success:
 - codecov
 deploy:

doc/pytest-sanitize.ini

@@ -0,0 +1,3 @@
+[Section1]
+regex: [0-9a-f]{8}-[0-9a-f]{4}-4[0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}
+replace: __plotly_uuid__

doc/requirements.txt

@@ -4,6 +4,7 @@ https://github.com/Juanlu001/sphinx_rtd_theme/archive/js-head.zip
 nbsphinx
 jupyter_client
 notebook
+nbformat>4,<5  # https://github.com/plotly/plotly.py/issues/692
 numpy
 scipy
 plotly==4.5.0

doc/tutorial.ipynb

@@ -61,8 +61,8 @@
    "outputs": [],
    "source": [
     "# If the import doesn't work, uncomment the following two lines, or \"pip install thunor\"\n",
-    "# import os, sys\n",
-    "# sys.path.insert(0, os.path.abspath('../'))\n",
+    "import os, sys\n",
+    "sys.path.insert(0, os.path.abspath('../'))\n",
     "\n",
     "import thunor"
    ]
@@ -178,9 +178,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from thunor.plots import plot_drc, plot_drc_params, plot_time_course, plot_ctrl_dip_by_plate, plot_plate_map\n",
-    "from plotly.offline import plot, iplot, init_notebook_mode\n",
-    "init_notebook_mode()"
+    "from thunor.plots import plot_drc, plot_drc_params, plot_time_course, plot_ctrl_dip_by_plate, plot_plate_map"
    ]
   },
   {
@@ -198,7 +196,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iplot(plot_drc(fp))"
+    "plot_drc(fp)"
    ]
   },
   {
@@ -216,7 +214,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iplot(plot_drc_params(fp, 'auc'))"
+    "plot_drc_params(fp, 'auc')"
    ]
   },
   {
@@ -237,7 +235,7 @@
     "fit_params_bt20_pac = fp[fp.index.isin(['BT20'], level='cell_line') & \\\n",
     "                         fp.index.isin(['paclitaxel'], level='drug')]\n",
     "\n",
-    "iplot(plot_drc(fit_params_bt20_pac))"
+    "plot_drc(fit_params_bt20_pac)"
    ]
   },
   {
@@ -255,9 +253,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iplot(plot_time_course(\n",
+    "plot_time_course(\n",
     "    hts007.filter(drugs=['paclitaxel'], cell_lines=['BT20'])\n",
-    "))"
+    ")"
    ]
   },
   {
@@ -275,7 +273,7 @@
    },
    "outputs": [],
    "source": [
-    "iplot(plot_ctrl_dip_by_plate(ctrl_dip_data))"
+    "plot_ctrl_dip_by_plate(ctrl_dip_data)"
    ]
   },
   {
@@ -300,7 +298,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iplot(plot_plate_map(plate_data, color_by='dip_rates'))"
+    "plot_plate_map(plate_data, color_by='dip_rates')"
    ]
   }
  ],
@@ -320,7 +318,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.8.1"
   }
  },
  "nbformat": 4,

setup.py

@@ -20,7 +20,7 @@ def main():
         url='https://www.thunor.net',
         packages=['thunor'],
         install_requires=['numpy', 'scipy', 'pandas', 'plotly==4.5.0', 'seaborn', 'tables'],
-        tests_require=['pytest', 'nbval', 'django'],
+        tests_require=['pytest', 'nbval', 'django', 'nbformat>4,<5'],
         cmdclass=versioneer.get_cmdclass(),
         zip_safe=True,
         classifiers=[