🎨 Pair and lint test_ipynb notebook using jupytext and black

Only a few newlines added to the actual code with black linter. This notebook/script pairing almost goes without saying. But I do wonder if I can simplify the _load_ipynb_modules function in environment.py now that we have paired notebooks.

test_ipynb.ipynb

@@ -19,7 +19,9 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "from features.environment import _load_ipynb_modules\n",
@@ -29,6 +31,7 @@
     "import os\n",
     "import sys\n",
     "\n",
+    "\n",
     "def _unit_test_ipynb(path: str):\n",
     "    \"\"\"\n",
     "    Unit tests on loaded modules from a .ipynb file.\n",
@@ -41,6 +44,7 @@
     "    if num_failures > 0:\n",
     "        sys.exit(num_failures)\n",
     "\n",
+    "\n",
     "def _integration_test_ipynb(path: str, summary: bool = False):\n",
     "    \"\"\"\n",
     "    Integration tests on various feature behaviours inside a .feature file.\n",
@@ -64,7 +68,6 @@
    "metadata": {},
    "source": [
     "## Unit tests\n",
-    "\n",
     "Uses [doctest](https://en.wikipedia.org/wiki/Doctest).\n",
     "Small tests for each individual function."
    ]
@@ -450,6 +453,15 @@
   }
  ],
  "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:percent",
+   "text_representation": {
+    "extension": ".py",
+    "format_name": "percent",
+    "format_version": "1.2",
+    "jupytext_version": "0.8.6rc0"
+   }
+  },
   "kernelspec": {
    "display_name": "deepbedmap",
    "language": "python",

test_ipynb.py

@@ -0,0 +1,87 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.2'
+#       jupytext_version: 0.8.6rc0
+#   kernelspec:
+#     display_name: deepbedmap
+#     language: python
+#     name: deepbedmap
+# ---
+
+# %% [markdown]
+# # Behavioural Driven Development Testing for Jupyter Notebooks
+#
+# Handy way to process the run unit tests (via doctest) and integration tests (via behave) in jupyter notebooks (.ipynb) containing Python functions.
+# The script will convert an .ipynb to a string format (basically a .py file), loads them as modules, and runs the tests on them.
+# To run it in the console, do:
+#
+#     python -m pytest --verbose --disable-warnings --nbval test_ipynb.ipynb
+#
+# The script should tell you which ipynb file's doctests has failed (e.g. srgan_train.ipynb).
+# You can then open up this very jupyter notebook to debug and inspect the situation further.
+
+# %%
+from features.environment import _load_ipynb_modules
+import behave.__main__
+
+import doctest
+import os
+import sys
+
+
+def _unit_test_ipynb(path: str):
+    """
+    Unit tests on loaded modules from a .ipynb file.
+    Uses doctest.
+    """
+    assert path.endswith(".ipynb")
+
+    module = _load_ipynb_modules(ipynb_path=path)
+    num_failures, num_attempted = doctest.testmod(m=module, verbose=True)
+    if num_failures > 0:
+        sys.exit(num_failures)
+
+
+def _integration_test_ipynb(path: str, summary: bool = False):
+    """
+    Integration tests on various feature behaviours inside a .feature file.
+    Uses behave.
+    """
+    assert os.path.exists(path=path)
+    assert path.endswith(".feature")
+
+    if summary == False:
+        args = f"--tags ~@skip --no-summary {path}"
+    elif summary == True:
+        args = f"--tags ~@skip {path}"
+
+    num_failures = behave.__main__.main(args=args)
+    if num_failures > 0:
+        sys.exit(num_failures)
+
+
+# %% [markdown]
+# ## Unit tests
+# Uses [doctest](https://en.wikipedia.org/wiki/Doctest).
+# Small tests for each individual function.
+
+# %%
+_unit_test_ipynb(path="data_prep.ipynb")
+
+# %%
+_unit_test_ipynb(path="srgan_train.ipynb")
+
+# %% [markdown]
+# ## Integration tests
+#
+# Uses [behave](https://github.com/behave/behave).
+# Medium sized tests which checks that components work together properly.
+# Ensures that the behaviour of features (made up of units) is sound.
+
+# %%
+_integration_test_ipynb(path="features/data_prep.feature")