Merge pull request #1972 from modflowpy/v3.4.3

Release 3.4.3

CITATION.cff

@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   and the software itself.
 type: software
 title: FloPy
-version: 3.4.2
-date-released: '2023-08-25'
+version: 3.4.3
+date-released: '2023-09-30'
 doi: 10.5066/F7BK19FH
 abstract: A Python package to create, run, and post-process MODFLOW-based models.
 repository-artifact: https://pypi.org/project/flopy

README.md

@@ -1,7 +1,7 @@
 
 <img src="https://raw.githubusercontent.com/modflowpy/flopy/master/examples/images/flopy3.png" alt="flopy3" style="width:50;height:20">
 
-### Version 3.4.2
+### Version 3.4.3
 [![flopy continuous integration](https://github.com/modflowpy/flopy/actions/workflows/commit.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/commit.yml)
 [![Read the Docs](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml/badge.svg?branch=develop)](https://github.com/modflowpy/flopy/actions/workflows/rtd.yml)
 
@@ -142,7 +142,7 @@ How to Cite
 
 ##### ***Software/Code citation for FloPy:***
 
-[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., Brakenhoff, D. A., and Bonelli, W. P., 2023, FloPy v3.4.2: U.S. Geological Survey Software Release, 25 August 2023, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
+[Bakker, Mark, Post, Vincent, Hughes, J. D., Langevin, C. D., White, J. T., Leaf, A. T., Paulinski, S. R., Bellino, J. C., Morway, E. D., Toews, M. W., Larsen, J. D., Fienen, M. N., Starn, J. J., Brakenhoff, D. A., and Bonelli, W. P., 2023, FloPy v3.4.3: U.S. Geological Survey Software Release, 30 September 2023, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
 
 
 Additional FloPy Related Publications

autotest/test_binaryfile.py

@@ -1,11 +1,14 @@
 import os
+from itertools import repeat
 
 import numpy as np
 import pytest
 from autotest.conftest import get_example_data_path
 from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
+from modflow_devtools.markers import requires_exe
 
+import flopy
 from flopy.modflow import Modflow
 from flopy.utils import (
     BinaryHeader,
@@ -545,3 +548,170 @@ def test_cellbudgetfile_readrecord_waux(example_data_path):
                 record
             )
     v.close()
+
+
+@pytest.fixture
+@pytest.mark.mf6
+@requires_exe("mf6")
+def mf6_gwf_2sp_st_tr(function_tmpdir):
+    """
+    A basic flow model with 2 stress periods,
+    first steady-state, the second transient.
+    """
+
+    name = "mf6_gwf_2sp"
+    sim = flopy.mf6.MFSimulation(
+        sim_name=name,
+        version="mf6",
+        exe_name="mf6",
+        sim_ws=function_tmpdir,
+    )
+
+    tdis = flopy.mf6.ModflowTdis(
+        simulation=sim,
+        nper=2,
+        perioddata=[(0, 1, 1), (10, 10, 1)],
+    )
+
+    ims = flopy.mf6.ModflowIms(
+        simulation=sim,
+        complexity="SIMPLE",
+    )
+
+    gwf = flopy.mf6.ModflowGwf(
+        simulation=sim,
+        modelname=name,
+        save_flows=True,
+    )
+
+    dis = flopy.mf6.ModflowGwfdis(
+        model=gwf, nlay=1, nrow=1, ncol=10, delr=1, delc=10, top=10, botm=0
+    )
+
+    npf = flopy.mf6.ModflowGwfnpf(
+        model=gwf,
+        icelltype=[0],
+        k=10,
+    )
+
+    ic = flopy.mf6.ModflowGwfic(
+        model=gwf,
+        strt=0,
+    )
+
+    wel = flopy.mf6.ModflowGwfwel(
+        model=gwf,
+        stress_period_data={0: 0, 1: [[(0, 0, 0), -1]]},
+    )
+
+    sto = flopy.mf6.ModflowGwfsto(
+        model=gwf,
+        ss=1e-4,
+        steady_state={0: True},
+        transient={1: True},
+    )
+
+    chd = flopy.mf6.ModflowGwfchd(
+        model=gwf,
+        stress_period_data={0: [[(0, 0, 9), 0]]},
+    )
+
+    oc = flopy.mf6.ModflowGwfoc(
+        model=gwf,
+        budget_filerecord=f"{name}.cbc",
+        head_filerecord=f"{name}.hds",
+        saverecord=[("HEAD", "ALL"), ("BUDGET", "ALL")],
+    )
+
+    return sim
+
+
+def test_read_mf6_2sp(mf6_gwf_2sp_st_tr):
+    sim = mf6_gwf_2sp_st_tr
+    gwf = sim.get_model()
+    sim.write_simulation(silent=False)
+    success, _ = sim.run_simulation(silent=False)
+    assert success
+
+    # load heads and flows
+    hds = gwf.output.head()
+    cbb = gwf.output.budget()
+
+    # check times
+    exp_times = [float(t) for t in range(11)]
+    assert hds.get_times() == exp_times
+    assert cbb.get_times() == exp_times
+
+    # check stress periods and time steps
+    exp_kstpkper = [(0, 0)] + [(i, 1) for i in range(10)]
+    assert hds.get_kstpkper() == exp_kstpkper
+    assert cbb.get_kstpkper() == exp_kstpkper
+
+    # check head data access by time
+    exp_hds_data = np.array([[list(repeat(0.0, 10))]])
+    hds_data = hds.get_data(totim=0)
+    assert np.array_equal(hds_data, exp_hds_data)
+
+    # check budget file data by time
+    cbb_data = cbb.get_data(totim=0)
+    assert len(cbb_data) > 0
+
+    # check head data access by kstp and kper
+    hds_data = hds.get_data(kstpkper=(0, 0))
+    assert np.array_equal(hds_data, exp_hds_data)
+
+    # check budget file data by kstp and kper
+    cbb_data_kstpkper = cbb.get_data(kstpkper=(0, 0))
+    assert len(cbb_data) == len(cbb_data_kstpkper)
+    for i in range(len(cbb_data)):
+        assert np.array_equal(cbb_data[i], cbb_data_kstpkper[i])
+
+
+@pytest.mark.parametrize("compact", [True, False])
+def test_read_mf2005_freyberg(example_data_path, function_tmpdir, compact):
+    m = flopy.modflow.Modflow.load(
+        example_data_path / "freyberg" / "freyberg.nam",
+    )
+    m.change_model_ws(function_tmpdir)
+    oc = m.get_package("OC")
+    oc.compact = compact
+
+    m.write_input()
+    success, buff = m.run_model(silent=False)
+    assert success
+
+    # load heads and flows
+    hds_file = function_tmpdir / "freyberg.hds"
+    cbb_file = function_tmpdir / "freyberg.cbc"
+    assert hds_file.is_file()
+    assert cbb_file.is_file()
+    hds = HeadFile(hds_file)
+    cbb = CellBudgetFile(cbb_file, model=m)  # failing to specify a model...
+
+    # check times
+    exp_times = [10.0]
+    assert hds.get_times() == exp_times
+    assert cbb.get_times() == exp_times  # ...causes get_times() to be empty
+
+    # check stress periods and time steps
+    exp_kstpkper = [(0, 0)]
+    assert hds.get_kstpkper() == exp_kstpkper
+    assert cbb.get_kstpkper() == exp_kstpkper
+
+    # check head data access by time
+    hds_data_totim = hds.get_data(totim=exp_times[0])
+    assert hds_data_totim.shape == (1, 40, 20)
+
+    # check budget file data by time
+    cbb_data = cbb.get_data(totim=exp_times[0])
+    assert len(cbb_data) > 0
+
+    # check head data access by kstp and kper
+    hds_data_kstpkper = hds.get_data(kstpkper=(0, 0))
+    assert np.array_equal(hds_data_kstpkper, hds_data_totim)
+
+    # check budget file data by kstp and kper
+    cbb_data_kstpkper = cbb.get_data(kstpkper=(0, 0))
+    assert len(cbb_data) == len(cbb_data_kstpkper)
+    for i in range(len(cbb_data)):
+        assert np.array_equal(cbb_data[i], cbb_data_kstpkper[i])

autotest/test_export.py

@@ -51,6 +51,10 @@
 from flopy.utils.crs import get_authority_crs
 from flopy.utils.geometry import Polygon
 
+HAS_PYPROJ = has_pkg("pyproj", strict=True)
+if HAS_PYPROJ:
+    import pyproj
+
 
 def namfiles() -> List[Path]:
     mf2005_path = get_example_data_path() / "mf2005_test"
@@ -677,6 +681,13 @@ def test_export_contourf(function_tmpdir, example_data_path):
             len(shapes) >= 65
         ), "multipolygons were skipped in contourf routine"
 
+        # debugging
+        # for s in shapes:
+        #     x = [i[0] for i in s.points[:]]
+        #     y = [i[1] for i in s.points[:]]
+        #     plt.plot(x, y)
+        # plt.show()
+
 
 @pytest.mark.mf6
 @requires_pkg("shapefile", "shapely")
@@ -706,6 +717,13 @@ def test_export_contours(function_tmpdir, example_data_path):
         # expect 65 with standard mpl contours (structured grids), 86 with tricontours
         assert len(shapes) >= 65
 
+        # debugging
+        # for s in shapes:
+        #     x = [i[0] for i in s.points[:]]
+        #     y = [i[1] for i in s.points[:]]
+        #     plt.plot(x, y)
+        # plt.show()
+
 
 @pytest.mark.mf6
 @requires_pkg("shapely")

autotest/test_generate_classes.py

@@ -3,10 +3,29 @@
 from pprint import pprint
 
 import pytest
+from modflow_devtools.misc import get_current_branch
+
+branch = get_current_branch()
 
 
 @pytest.mark.mf6
-def test_generate_classes_from_dfn(virtualenv, project_root_path):
+@pytest.mark.slow
+@pytest.mark.regression
+@pytest.mark.skipif(
+    branch == "master" or branch.startswith("v"),
+    reason="skip on master and release branches",
+)
+def test_generate_classes_from_github_refs(
+    request, virtualenv, project_root_path, ref, worker_id
+):
+    argv = (
+        request.config.workerinput["mainargv"]
+        if hasattr(request.config, "workerinput")
+        else []
+    )
+    if worker_id != "master" and "loadfile" not in argv:
+        pytest.skip("can't run in parallel")
+
     python = virtualenv.python
     venv = Path(python).parent
     print(f"Using temp venv at {venv} with python {python}")

autotest/test_mbase.py

@@ -10,6 +10,8 @@
 from flopy.mbase import resolve_exe
 from flopy.utils.flopy_io import relpath_safe
 
+_system = system()
+
 
 @pytest.fixture
 def mf6_model_path(example_data_path):
@@ -18,10 +20,7 @@ def mf6_model_path(example_data_path):
 
 @requires_exe("mf6")
 @pytest.mark.parametrize("use_ext", [True, False])
-def test_resolve_exe_by_name(function_tmpdir, use_ext):
-    if use_ext and system() != "Windows":
-        pytest.skip(".exe extensions are Windows-only")
-
+def test_resolve_exe_by_name(use_ext):
     ext = ".exe" if use_ext else ""
     expected = which("mf6").lower()
     actual = resolve_exe(f"mf6{ext}")
@@ -31,13 +30,14 @@ def test_resolve_exe_by_name(function_tmpdir, use_ext):
 
 @requires_exe("mf6")
 @pytest.mark.parametrize("use_ext", [True, False])
-def test_resolve_exe_by_abs_path(function_tmpdir, use_ext):
-    if use_ext and system() != "Windows":
-        pytest.skip(".exe extensions are Windows-only")
-
-    ext = ".exe" if use_ext else ""
+def test_resolve_exe_by_abs_path(use_ext):
+    abs_path = which("mf6")
+    if _system == "Windows" and not use_ext:
+        abs_path = abs_path[:-4]
+    elif _system != "Windows" and use_ext:
+        abs_path = f"{abs_path}.exe"
     expected = which("mf6").lower()
-    actual = resolve_exe(which(f"mf6{ext}"))
+    actual = resolve_exe(abs_path)
     assert actual.lower() == expected
     assert which(actual)
 
@@ -46,9 +46,6 @@ def test_resolve_exe_by_abs_path(function_tmpdir, use_ext):
 @pytest.mark.parametrize("use_ext", [True, False])
 @pytest.mark.parametrize("forgive", [True, False])
 def test_resolve_exe_by_rel_path(function_tmpdir, use_ext, forgive):
-    if use_ext and system() != "Windows":
-        pytest.skip(".exe extensions are Windows-only")
-
     ext = ".exe" if use_ext else ""
     expected = which("mf6").lower()
 
@@ -59,10 +56,11 @@ def test_resolve_exe_by_rel_path(function_tmpdir, use_ext, forgive):
 
     with set_dir(inner_dir):
         # copy exe to relative dir
-        copy(expected, bin_dir / "mf6")
-        assert (bin_dir / "mf6").is_file()
+        new_exe_path = bin_dir / Path(expected).name
+        copy(expected, new_exe_path)
+        assert new_exe_path.is_file()
 
-        expected = which(str(Path(bin_dir / "mf6").absolute())).lower()
+        expected = which(str(new_exe_path.absolute())).lower()
         actual = resolve_exe(f"../bin/mf6{ext}")
         assert actual.lower() == expected
         assert which(actual)
@@ -77,7 +75,7 @@ def test_resolve_exe_by_rel_path(function_tmpdir, use_ext, forgive):
 
 
 def test_run_model_when_namefile_not_in_model_ws(
-    mf6_model_path, example_data_path, function_tmpdir
+    mf6_model_path, function_tmpdir
 ):
     # copy input files to temp workspace
     ws = function_tmpdir / "ws"

autotest/test_modflow.py

@@ -207,31 +207,31 @@ def test_exe_selection(example_data_path, function_tmpdir):
 
     # no selection defaults to mf2005
     exe_name = "mf2005"
-    assert Path(Modflow().exe_name).name == exe_name
-    assert Path(Modflow(exe_name=None).exe_name).name == exe_name
+    assert Path(Modflow().exe_name).stem == exe_name
+    assert Path(Modflow(exe_name=None).exe_name).stem == exe_name
     assert (
-        Path(Modflow.load(namfile_path, model_ws=model_path).exe_name).name
+        Path(Modflow.load(namfile_path, model_ws=model_path).exe_name).stem
         == exe_name
     )
     assert (
         Path(
             Modflow.load(
                 namfile_path, exe_name=None, model_ws=model_path
             ).exe_name
-        ).name
+        ).stem
         == exe_name
     )
 
     # user-specified (just for testing - there is no legitimate reason
     # to use mp7 with Modflow but Modpath7 derives from BaseModel too)
     exe_name = "mp7"
-    assert Path(Modflow(exe_name=exe_name).exe_name).name == exe_name
+    assert Path(Modflow(exe_name=exe_name).exe_name).stem == exe_name
     assert (
         Path(
             Modflow.load(
                 namfile_path, exe_name=exe_name, model_ws=model_path
             ).exe_name
-        ).name
+        ).stem
         == exe_name
     )