Merge branch 'modflowpy:develop' into develop

autotest/conftest.py

@@ -12,6 +12,7 @@
 from urllib import request
 from warnings import warn
 
+import matplotlib.pyplot as plt
 import pkg_resources
 import pytest
 
@@ -337,6 +338,22 @@ def session_tmpdir(tmpdir_factory, request) -> Path:
         copytree(temp, Path(keep) / temp.name)
 
 
+# fixture to automatically close any plots (or optionally show them)
+
+
+@pytest.fixture(autouse=True)
+def close_plot(request):
+    yield
+
+    # plots only shown if requested via CLI flag,
+    # figures are available, and we're not in CI
+    show = request.config.getoption("--show-plots")
+    if len(plt.get_fignums()) > 0 and not is_in_ci() and show:
+        plt.show()
+    else:
+        plt.close("all")
+
+
 # pytest configuration hooks
 
 
@@ -392,6 +409,14 @@ def pytest_addoption(parser):
         help="Run only smoke tests (should complete in <1 minute).",
     )
 
+    parser.addoption(
+        "--show-plots",
+        action="store_true",
+        default=False,
+        help="Show any figure windows created by test cases. (Useful to display plots for visual inspection, "
+        "but automated tests should probably also check patch collections or figure & axis properties.)",
+    )
+
 
 def pytest_configure(config):
     config.addinivalue_line(

autotest/pytest.ini

@@ -11,4 +11,5 @@ markers =
     slow: tests that don't complete in a few seconds
     example: exercise scripts, tutorials and notebooks
     regression: tests that compare multiple results
-    meta: run by other tests (e.g. testing fixtures)
+    meta: run by other tests (e.g. testing fixtures)
+    mf6: tests for the mf6 module

autotest/regression/test_mf6.py

@@ -50,6 +50,8 @@
 from flopy.utils import CellBudgetFile
 from flopy.utils.datautil import PyListUtil
 
+pytestmark = pytest.mark.mf6
+
 
 @requires_exe("mf6")
 @requires_pkg("pymake")

autotest/regression/test_mf6_examples.py

@@ -7,21 +7,21 @@
 
 from flopy.mf6 import MFSimulation
 
+pytestmark = pytest.mark.mf6
+
 
 @requires_exe("mf6")
 @requires_pkg("pymake")
 @pytest.mark.slow
 @pytest.mark.regression
 def test_mf6_example_simulations(tmpdir, mf6_example_namfiles):
-    """
-    MF6 examples parametrized by simulation. Arg `mf6_example_namfiles` is a list
-    of models to run in order provided. Coupled models share the same workspace.
-
-    Parameters
-    ----------
-    tmpdir: function-scoped temporary directory fixture
-    mf6_example_namfiles: ordered list of namfiles for 1+ coupled models
-    """
+    # MF6 examples parametrized by simulation. `mf6_example_namfiles` is a list
+    # of models to run in order provided. Coupled models share the same tempdir
+    #
+    # Parameters
+    # ----------
+    # tmpdir: function-scoped temporary directory fixture
+    # mf6_example_namfiles: ordered list of namfiles for 1+ coupled models
 
     import pymake
 

autotest/test_binarygrid_util.py

@@ -7,6 +7,8 @@
 from flopy.discretization import StructuredGrid, UnstructuredGrid, VertexGrid
 from flopy.mf6.utils import MfGrdFile
 
+pytestmark = pytest.mark.mf6
+
 
 @pytest.fixture(scope="module")
 def mfgrd_test_path(example_data_path):

autotest/test_cbc_full3D.py

@@ -41,6 +41,7 @@ def load_mf2005(path, ws_out):
     return ml
 
 
+@pytest.mark.mf6
 def load_mf6(path, ws_out):
     sim = MFSimulation.load(
         sim_name=Path(path).name,
@@ -118,6 +119,7 @@ def cbc_eval(cbcobj, nnodes, shape3d, modelgrid):
     cobj_mg.close()
 
 
+@pytest.mark.mf6
 @pytest.mark.parametrize("path", mf6_paths)
 def test_cbc_full3D_mf6(tmpdir, path):
     sim = load_mf6(path, str(tmpdir))

autotest/test_copy.py

@@ -4,6 +4,7 @@
 import inspect
 
 import numpy as np
+import pytest
 
 from flopy.datbase import DataInterface, DataType
 from flopy.mbase import ModelInterface
@@ -226,6 +227,7 @@ def test_mf2005_copy(example_data_path):
     assert not model_is_copy(m, m_c)
 
 
+@pytest.mark.mf6
 def test_mf6_copy(example_data_path):
     sim = MFSimulation.load(
         "mfsim.nam",

autotest/test_export.py

@@ -7,7 +7,6 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import pytest
-from flaky import flaky
 from autotest.conftest import (
     SHAPEFILE_EXTENSIONS,
     get_example_data_path,
@@ -16,6 +15,7 @@
     requires_pkg,
     requires_spatial_reference,
 )
+from flaky import flaky
 
 import flopy
 from flopy.discretization import StructuredGrid, UnstructuredGrid
@@ -29,6 +29,7 @@
     export_array,
     export_array_contours,
     export_contourf,
+    export_contours,
 )
 from flopy.export.vtk import Vtk
 from flopy.mf6 import (
@@ -615,6 +616,35 @@ def test_export_contourf(tmpdir, example_data_path):
             )
 
 
+@pytest.mark.mf6
+@requires_pkg("shapefile", "shapely")
+def test_export_contours(tmpdir, example_data_path):
+    from shapefile import Reader
+
+    filename = os.path.join(tmpdir, "mycontours.shp")
+    mpath = example_data_path / "freyberg"
+    ml = Modflow.load("freyberg.nam", model_ws=mpath)
+    hds_pth = os.path.join(ml.model_ws, "freyberg.githds")
+    hds = flopy.utils.HeadFile(hds_pth)
+    head = hds.get_data()
+    levels = np.arange(10, 30, 0.5)
+
+    mapview = flopy.plot.PlotMapView(model=ml)
+    contour_set = mapview.contour_array(
+        head, masked_values=[999.0], levels=levels
+    )
+
+    export_contours(filename, contour_set)
+    plt.close()
+    if not os.path.isfile(filename):
+        raise AssertionError("did not create contour shapefile")
+
+    with Reader(filename) as r:
+        shapes = r.shapes()
+        assert len(shapes) == 65
+
+
+@pytest.mark.mf6
 @requires_pkg("shapely")
 def test_mf6_grid_shp_export(tmpdir):
     nlay = 2
@@ -1082,6 +1112,7 @@ def test_vtk_export_packages(tmpdir, example_data_path):
     assert os.path.exists(filetocheck)
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk")
 def test_vtk_mf6(tmpdir, example_data_path):
     # test mf6
@@ -1344,6 +1375,7 @@ def load_iverts(fname):
     assert np.allclose(np.ravel(top), top2), "Field data not properly written"
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk")
 def test_vtk_vertex(tmpdir, example_data_path):
     from vtkmodules.util.numpy_support import vtk_to_numpy
@@ -1502,6 +1534,7 @@ def load_iverts(fname, closed=False):
     return iverts, np.array(xc), np.array(yc)
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk")
 def test_vtk_export_model_without_packages_names(tmpdir):
     from vtkmodules.util.numpy_support import vtk_to_numpy
@@ -1559,6 +1592,7 @@ def test_vtk_export_model_without_packages_names(tmpdir):
     assert np.allclose(cell_types, cell_types_answer), errmsg
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk")
 def test_vtk_export_disv1_model(tmpdir):
     from vtkmodules.util.numpy_support import vtk_to_numpy
@@ -1631,6 +1665,7 @@ def test_vtk_export_disv1_model(tmpdir):
     assert np.allclose(cell_types, cell_types_answer), errmsg
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk")
 def test_vtk_export_disv2_model(tmpdir):
     from vtkmodules.util.numpy_support import vtk_to_numpy
@@ -1868,6 +1903,7 @@ def test_vtk_export_disu2_grid(tmpdir, example_data_path):
     assert np.allclose(cell_types, cell_types_answer), errmsg
 
 
+@pytest.mark.mf6
 @requires_pkg("vtk", "shapefile")
 def test_vtk_export_disu_model(tmpdir):
     from vtkmodules.util.numpy_support import vtk_to_numpy

autotest/test_generate_classes.py

@@ -4,6 +4,7 @@
 from flopy.mf6.utils import generate_classes
 
 
+@pytest.mark.mf6
 @pytest.mark.skip(
     reason="TODO: use external copy of the repo, otherwise files are rewritten"
 )