Merge pull request #227 from dynamicslab/external-examples

External examples functionality

README.rst

@@ -167,9 +167,14 @@ At a minimum, we need to be able to run the example notebooks in the normal mode
    |-example_data.py # has functions to create/load data
    |-mock_data.py # has functions with same name as in example_data.py which create/load smaller datasets
    |-example.ipynb # run python examples/publish_notebook/<name_of_example> to generate this.  Needs packages in requirements-dev.txt
-   |-other files, if required (helper module, data, etc)
+   |-utils.py (Any other names example.py needs to import.  Any additional local modules imported by example.py need to be submodules of utils.py, e.g. utils.plotting)
+
+You can optimize your notebook for testing by checking ``__name__``.  When our tests run ``example.py`` they set the ``__name__`` global to ``"testing"``.  For instance, your notebook should determine whether to import from ``mock_data`` or ``example_data`` using this method (another example: you could also use this method to set ``max_iter``).  It's a bit arbitrary, but try to make your examples run in under ten seconds using the mock data.  You can use our test to verify your example in testing mode: 
+
+.. code-block::
+
+   pytest -k test_external --external-notebook="path/to/<name_of_example>"
 
-You can optimize your notebook for testing by checking ``__name__``.  When our tests run ``example.py`` they set the ``__name__`` global to ``"testing"``.  For instance, your notebook should determine whether to import from ``mock_data`` or ``example_data`` using this method.
 
 Contributing code
 ^^^^^^^^^^^^^^^^^

test/conftest.py

@@ -1,6 +1,8 @@
 """
 Shared pytest fixtures for unit tests.
 """
+from pathlib import Path
+
 import numpy as np
 import pytest
 from scipy.integrate import solve_ivp
@@ -19,6 +21,29 @@
 from pysindy.utils.odes import lorenz_control
 
 
+def pytest_addoption(parser):
+    parser.addoption(
+        "--external-notebook",
+        action="append",
+        default=[],
+        help=(
+            "name of notebook to test.  Only valid if running"
+            " test_notebooks.test_external"
+        ),
+    )
+
+
+def pytest_generate_tests(metafunc):
+    if "external_notebook" in metafunc.fixturenames:
+        metafunc.parametrize(
+            "external_notebook",
+            [
+                Path(f.lstrip('"').rstrip('"'))
+                for f in metafunc.config.getoption("external_notebook")
+            ],
+        )
+
+
 @pytest.fixture
 def data_1d():
     t = np.linspace(0, 5, 100)

test/test_notebooks.py

@@ -55,12 +55,13 @@ def purge_notebook_modules():
     This might be better served by fixing imports in notebooks using
     importlib.
     """
-    SENTINEL = object()
-    sys.modules.pop("utils", SENTINEL)
-    sys.modules.pop("mock_data", SENTINEL)
+    local_modules = [
+        key for key in sys.modules if key[:5] == "utils" or key[:9] == "mock_data"
+    ]
+    [sys.modules.pop(mod) for mod in local_modules]
     yield
-    sys.modules.pop("utils", SENTINEL)
-    sys.modules.pop("mock_data", SENTINEL)
+    SENTINEL = object()
+    [sys.modules.pop(mod, SENTINEL) for mod in local_modules]
 
 
 @pytest.mark.parametrize("directory", notebook_scripts)
@@ -70,6 +71,11 @@ def test_notebook_script(directory: Path, purge_notebook_modules):
         runpy.run_path(str(notebook_dir / directory / "example.py"), run_name="testing")
 
 
+def test_external(external_notebook: Path, purge_notebook_modules):
+    with _cwd(external_notebook.resolve()):
+        runpy.run_path(str("example.py"), run_name="testing")
+
+
 @pytest.mark.parametrize("filename", notebooks)
 @pytest.mark.slow
 def test_notebook(filename):