Merge pull request #58 from RangamaniLabUCSD/finsberg/add-first-tests

Add first unit tests

.github/workflows/run_examples.yml

@@ -0,0 +1,37 @@
+name: Run examples
+
+on:
+  push:
+    # The CI is executed on every push on every branch
+    branches:
+      - development
+  pull_request:
+    # The CI is executed on every pull request to the main branch
+    branches:
+      - development
+
+  schedule:
+    # The CI is executed every day at 8am
+    - cron: "0 8 * * *"
+jobs:
+  check-code:
+    runs-on: ubuntu-22.04
+    # Runs against FEniCS main branch built the 16-01-2023
+    container: ghcr.io/scientificcomputing/fenics-gmsh:2023-02-17a
+    steps:
+      # This action sets the current path to the root of your github repo
+      - uses: actions/checkout@v3
+
+      - name: "Install code"
+        run: python3 -m pip install --no-binary=h5py .[dev] jupytext
+
+      - name: Run example 1
+        run: |
+          cd examples/example1/
+          jupytext example1.ipynb --to py
+          python3 example1.py
+
+      # - name: Run tests
+      #   run: |
+      #     cd tests/
+      #     python3 -m pytest .

.github/workflows/test_fenics_stubs.yml

@@ -23,15 +23,8 @@ jobs:
       - uses: actions/checkout@v3
 
       - name: "Install code"
-        run: python3 -m pip install --no-binary=h5py .[dev] jupytext
+        run: python3 -m pip install .[test]
 
-      - name: Run example 1
+      - name: Run tests
         run: |
-          cd examples/example1/
-          jupytext example1.ipynb --to py
-          python3 example1.py
-
-      # - name: Run tests
-      #   run: |
-      #     cd tests/
-      #     python3 -m pytest .
+         python3 -m pytest

pytest.ini

@@ -0,0 +1,10 @@
+[pytest]
+addopts = --cov=stubs --cov-report html --cov-report term-missing -v
+testpaths =
+    tests
+    integration
+markers =
+    stubs_model_init:  tests for model initialiation (deselect with '-m "not slow"')
+filterwarnings =
+    ignore::UserWarning
+    ignore::DeprecationWarning

setup.py

@@ -44,11 +44,13 @@
         "termplotlib",
         "meshio",
         "gmsh",
-        "h5py"
+        "h5py",
     ],  # Required packages, pulls from pip if needed; do not use for Conda deployment
     # python_requires=">=3.5",          # Python version restrictions
-    extras_require={"docs": [
-        "jupyter-book@git+https://github.com/executablebooks/jupyter-book.git@master"]},
+    extras_require={
+        "docs": ["jupyter-book"],
+        "test": ["pytest", "pytest-cov"],
+    },
     # Manual control if final package is compressible or not, set False to prevent the .egg from being made
     # zip_safe=False,
 )

stubs/config.py

@@ -200,13 +200,6 @@ class Config():
     directory: OutputConfig = field(default_factory=OutputConfig)
     probe_plot: Dict[str, npt.NDArray[np.float64]] = field(default_factory=dict)
 
-    def __init__(self):
-        self.solver = SolverConfig()
-        self.flags = FlagsConfig()
-        self.directory = OutputConfig()
-        self.loglevel = LogLevelConfig()
-        self.plot_settings = PlottingConfig()
-
     @property
     def reaction_database(self) -> Dict[str, str]:
         """

stubs/model_assembly.py

@@ -23,8 +23,7 @@
 from sympy.parsing.sympy_parser import parse_expr
 from tabulate import tabulate
 
-import stubs.common as common
-
+from . import common
 from .common import _fancy_print as fancy_print
 from .common import (np_smart_hstack, pint_quantity_to_unit,
                      pint_unit_to_quantity, sub)

tests/test_compartment.py

@@ -0,0 +1,66 @@
+import pytest
+
+import stubs
+
+
+@pytest.fixture(name="Cyto_kwargs")
+def example_compartment():
+    kwargs = dict(
+        dimensionality=3,
+        name="Cyto",
+        compartment_units=stubs.unit.um,
+        cell_marker=1,
+    )
+
+    Cyto = stubs.model_assembly.Compartment(**kwargs)
+    return (Cyto, kwargs)
+
+
+def test_Compartment_initialization(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+
+    assert Cyto.V is None
+    assert Cyto.cell_marker == kwargs["cell_marker"]
+    assert Cyto.dimensionality == kwargs["dimensionality"]
+    assert Cyto.name == kwargs["name"]
+    assert Cyto.num_dofs == 0
+    assert Cyto.num_dofs_local == 0
+    assert Cyto.species == {}
+    assert Cyto.u == {}
+    assert Cyto.v is None
+
+
+@pytest.mark.xfail
+def test_Compartment_access_dolfin_mesh(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.dolfin_mesh
+
+
+@pytest.mark.xfail
+def test_Compartment_access_mesh_id(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.mesh_id
+
+
+@pytest.mark.xfail
+def test_Compartment_access_num_cells(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.num_cells
+
+
+@pytest.mark.xfail
+def test_Compartment_access_num_facets(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.num_facets
+
+
+@pytest.mark.xfail
+def test_Compartment_access_num_vertices(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.num_vertices
+
+
+@pytest.mark.xfail
+def test_Compartment_access_nvolume(Cyto_kwargs):
+    Cyto, kwargs = Cyto_kwargs
+    Cyto.nvolume

tests/test_species.py

@@ -0,0 +1,65 @@
+import math
+
+import pytest
+
+import stubs
+
+
+@pytest.fixture(name="A_kwargs")
+def example_species():
+    kwargs = dict(
+        concentration_units=stubs.unit.uM,
+        diffusion_units=stubs.unit.um**2 / stubs.unit.sec,
+        initial_condition=0.01,
+        D=2.0,
+        name="A",
+        compartment_name="Cyto",
+        group="Some group",
+    )
+
+    A = stubs.model_assembly.Species(**kwargs)
+    return (A, kwargs)
+
+
+def test_Species_initialization(A_kwargs):
+    A, kwargs = A_kwargs
+    assert A.name == kwargs["name"]
+    assert A.latex_name == kwargs["name"]
+    assert str(A.sym) == kwargs["name"]
+
+    assert math.isclose(A.initial_condition, kwargs["initial_condition"])
+    assert (
+        A.initial_condition_quantity
+        == kwargs["initial_condition"] * kwargs["concentration_units"]
+    )
+    assert A.concentration_units == stubs.common.pint_unit_to_quantity(
+        kwargs["concentration_units"]
+    )
+    assert math.isclose(A.D, kwargs["D"])
+    assert A.diffusion_units == stubs.common.pint_unit_to_quantity(
+        kwargs["diffusion_units"]
+    )
+    assert A.D_quantity == kwargs["D"] * kwargs["diffusion_units"]
+
+    assert A.compartment_name == kwargs["compartment_name"]
+    assert A.group == kwargs["group"]
+    assert A.dof_map is None
+    assert A.ut is None
+    assert A.v is None
+    assert A.u == {}
+    assert A.is_an_added_species is False
+    assert A.is_in_a_reaction is False
+
+
+@pytest.mark.xfail
+def test_access_vscalar(A_kwargs):
+    A, kwargs = A_kwargs
+    # We should have proper error handling here
+    A.vscalar
+
+
+@pytest.mark.xfail
+def test_access_dolfin_quatity(A_kwargs):
+    A, kwargs = A_kwargs
+    # We should have proper error handling here
+    A.dolfin_quantity