Merge pull request #2323 from modflowpy/v3.8.2

Release 3.8.2

.docs/md/version_changes.md

@@ -1,4 +1,13 @@
 # Changelog
+### Version 3.8.2
+
+#### Bug fixes
+
+* [fix(mp7particledata)](https://github.com/modflowpy/flopy/commit/a0e9219407b7be208d38f4f902cd2b5b96da1351): Fix get_extent() vertical extent calculation (#2307). Committed by wpbonelli on 2024-09-12.
+* [fix(array3d_export)](https://github.com/modflowpy/flopy/commit/693f01a0ce41f08d05395832b540fcc4f7dcff43): Fix exporting of array3d to shp (#2310). Committed by martclanor on 2024-09-16.
+* [fix(binaryfile)](https://github.com/modflowpy/flopy/commit/181e101a605bdb9b628c6781abff7b3276aca635): Accommodate windows drives for in-place reversal  (#2312). Committed by wpbonelli on 2024-09-16.
+* [fix(get_modflow)](https://github.com/modflowpy/flopy/commit/38180335445fa09f5463cf8b9239e6ed0c10bf5b): Accommodate missing ratelimit info on api response (#2320). Committed by wpbonelli on 2024-10-01.
+
 ### Version 3.8.1
 
 #### New features

CITATION.cff

@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   references, and the software itself.
 type: software
 title: FloPy
-version: 3.8.1
-date-released: '2024-09-05'
+version: 3.8.2
+date-released: '2024-10-03'
 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 3.8.1
+### Version 3.8.2
 [![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)
 
@@ -150,7 +150,7 @@ 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., 2024, FloPy v3.8.1: U.S. Geological Survey Software Release, 05 September 2024, 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., 2024, FloPy v3.8.2: U.S. Geological Survey Software Release, 03 October 2024, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)
 
 
 Additional FloPy Related Publications

autotest/test_export.py

@@ -409,7 +409,6 @@ def test_export_shapefile_polygon_closed(function_tmpdir):
     shp.close()
 
 
-@excludes_platform("Windows")
 @requires_pkg("rasterio", "pyshp", "scipy", name_map={"pyshp": "shapefile"})
 def test_export_array(function_tmpdir, example_data_path):
     import rasterio
@@ -467,10 +466,10 @@ def test_export_array(function_tmpdir, example_data_path):
     with rasterio.open(function_tmpdir / "fb.tif") as src:
         arr = src.read(1)
         assert src.shape == (m.nrow, m.ncol)
-        # TODO: these tests currently fail -- fix is in progress
-        # assert np.abs(src.bounds[0] - m.modelgrid.extent[0]) < 1e-6
-        # assert np.abs(src.bounds[1] - m.modelgrid.extent[1]) < 1e-6
-        pass
+        assert np.abs(src.bounds[0] - m.modelgrid.extent[0]) < 1e-6
+        assert np.abs(src.bounds[2] - m.modelgrid.extent[1]) < 1e-6
+        assert np.abs(src.bounds[1] - m.modelgrid.extent[2]) < 1e-6
+        assert np.abs(src.bounds[3] - m.modelgrid.extent[3]) < 1e-6
 
 
 @requires_pkg("netCDF4", "pyproj")
@@ -646,6 +645,65 @@ def test_export_array2(function_tmpdir):
     assert os.path.isfile(filename), "did not create array shapefile"
 
 
+@pytest.mark.mf6
+@requires_pkg("pyshp", name_map={"pyshp": "shapefile"})
+def test_array3d_export_structured(function_tmpdir):
+    from shapefile import Reader
+
+    xll, yll = 468970, 3478635
+    xur, yur = 681010, 3716462
+    spacing = 20000
+    ncol = int((xur - xll) / spacing)
+    nrow = int((yur - yll) / spacing)
+    sim = flopy.mf6.MFSimulation("sim", sim_ws=function_tmpdir)
+    gwf = flopy.mf6.ModflowGwf(
+        sim,
+        modelname="array3d_export_unstructured",
+    )
+    flopy.mf6.ModflowGwfdis(
+        gwf,
+        nlay=3,
+        top=5,
+        botm=[4, 3, 2],
+        delr=spacing,
+        delc=spacing,
+        nrow=nrow,
+        ncol=ncol,
+    )
+
+    shp_file = os.path.join(function_tmpdir, "dis_botm.shp")
+    gwf.dis.botm.export(shp_file)
+
+    with Reader(shp_file) as shp:
+        assert list(shp.shapeRecord(-1).record) == [
+            110,  # node
+            11,  # row
+            10,  # column
+            4.0,  # botm_1
+            3.0,  # botm_2
+            2.0,  # botm_3
+        ]
+
+
+@requires_pkg("pyshp", name_map={"pyshp": "shapefile"})
+def test_array3d_export_unstructured(function_tmpdir):
+    from shapefile import Reader
+
+    name = "array3d_export_unstructured"
+    sim = disu_sim(name, function_tmpdir)
+    gwf = sim.get_model(name)
+
+    shp_file = function_tmpdir / "disu_bot.shp"
+    gwf.disu.bot.export(shp_file)
+
+    with Reader(shp_file) as shp:
+        assert list(shp.shapeRecord(-1).record) == [
+            1770,  # node
+            3,  # layer
+            0.0,  # bot
+        ]
+
+
 @requires_pkg("pyshp", "shapely", name_map={"pyshp": "shapefile"})
 def test_export_array_contours_structured(function_tmpdir):
     nrow = 7

autotest/test_particledata.py

@@ -26,6 +26,7 @@
     ParticleGroupLRCTemplate,
     ParticleGroupNodeTemplate,
 )
+from flopy.modpath.mp7particledata import get_extent
 from flopy.modpath.mp7particlegroup import ParticleGroup
 from flopy.utils.modpathfile import EndpointFile, PathlineFile
 
@@ -47,6 +48,20 @@ def flatten(a):
     ]
 
 
+# test get_extent()
+
+
+def test_get_extent_structured_multilayer():
+    grid = GridCases().structured_small()
+    i, j = 1, 2
+    for k in range(grid.nlay):
+        extent = get_extent(grid, k=k, i=i, j=j)
+        assert extent.minz == grid.botm[k, i, j]
+        assert extent.maxz == (
+            grid.top[i, j] if k == 0 else grid.botm[k - 1, i, j]
+        )
+
+
 # test initializers
 
 

docs/PyPI_release.md

@@ -30,4 +30,4 @@ 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., 2024, FloPy v3.8.1: U.S. Geological Survey Software Release, 05 September 2024, 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., 2024, FloPy v3.8.2: U.S. Geological Survey Software Release, 03 October 2024, https://doi.org/10.5066/F7BK19FH](https://doi.org/10.5066/F7BK19FH)

flopy/export/utils.py

@@ -1207,16 +1207,22 @@ def array3d_export(f: Union[str, os.PathLike], u3d, fmt=None, **kwargs):
         f
     ).suffix.lower() == ".shp":
         array_dict = {}
-        for ilay in range(modelgrid.nlay):
-            u2d = u3d[ilay]
-            if isinstance(u2d, np.ndarray):
-                dname = u3d.name
-                array = u2d
-            else:
-                dname = u2d.name
-                array = u2d.array
-            name = f"{shapefile_utils.shape_attr_name(dname)}_{ilay + 1}"
-            array_dict[name] = array
+        array_shape = u3d.array.shape
+
+        if len(array_shape) == 1:
+            name = shapefile_utils.shape_attr_name(u3d.name)
+            array_dict[name] = u3d.array
+        else:
+            for ilay in range(array_shape[0]):
+                u2d = u3d[ilay]
+                if isinstance(u2d, np.ndarray):
+                    dname = u3d.name
+                    array = u2d
+                else:
+                    dname = u2d.name
+                    array = u2d.array
+                name = f"{shapefile_utils.shape_attr_name(dname)}_{ilay + 1}"
+                array_dict[name] = array
         shapefile_utils.write_grid_shapefile(f, modelgrid, array_dict)
 
     elif isinstance(f, NetCdf) or isinstance(f, dict):

flopy/modpath/mp7particledata.py

@@ -809,7 +809,14 @@ def get_extent(grid, k=None, i=None, j=None, nn=None, localz=False) -> Extent:
     # get cell coords and span in each dimension
     if not (k is None or i is None or j is None):
         verts = grid.get_cell_vertices(i, j)
-        minz, maxz = (0, 1) if localz else (grid.botm[k, i, j], grid.top[i, j])
+        minz, maxz = (
+            (0, 1)
+            if localz
+            else (
+                grid.botm[k, i, j],
+                grid.top[i, j] if k == 0 else grid.botm[k - 1, i, j],
+            )
+        )
     elif nn is not None:
         verts = grid.get_cell_vertices(nn)
         if grid.grid_type == "structured":

flopy/utils/binaryfile.py

@@ -13,6 +13,7 @@
 import tempfile
 import warnings
 from pathlib import Path
+from shutil import move
 from typing import List, Optional, Union
 
 import numpy as np
@@ -460,9 +461,9 @@ class BinaryLayerFile(LayerFile):
     """
 
     def __init__(
-        self, filename: Union[str, os.PathLike], precision, verbose, kwargs
+        self, filename: Union[str, os.PathLike], precision, verbose, **kwargs
     ):
-        super().__init__(filename, precision, verbose, kwargs)
+        super().__init__(filename, precision, verbose, **kwargs)
 
     def _build_index(self):
         """
@@ -661,7 +662,7 @@ def __init__(
         self.header_dtype = BinaryHeader.set_dtype(
             bintype="Head", precision=precision
         )
-        super().__init__(filename, precision, verbose, kwargs)
+        super().__init__(filename, precision, verbose, **kwargs)
 
     def reverse(self, filename: Optional[os.PathLike] = None):
         """
@@ -733,10 +734,18 @@ def reverse_header(header):
             header["pertim"] = perlen - header["pertim"]
             return header
 
-        # reverse record order and write to temporary file
-        temp_dir_path = Path(tempfile.gettempdir())
-        temp_file_path = temp_dir_path / filename.name
-        with open(temp_file_path, "wb") as f:
+        target = filename
+
+        # if rewriting the same file, write
+        # temp file then copy it into place
+        inplace = filename == self.filename
+        if inplace:
+            temp_dir_path = Path(tempfile.gettempdir())
+            temp_file_path = temp_dir_path / filename.name
+            target = temp_file_path
+
+        # reverse record order
+        with open(target, "wb") as f:
             for i in range(len(self) - 1, -1, -1):
                 header = self.recordarray[i].copy()
                 header = reverse_header(header)
@@ -752,16 +761,10 @@ def reverse_header(header):
                     ilay=ilay,
                 )
 
-        # if we're rewriting the original file, close it first
-        if filename == self.filename:
-            self.close()
-
-        # move temp file to destination
-        temp_file_path.replace(filename)
-
         # if we rewrote the original file, reinitialize
-        if filename == self.filename:
-            super().__init__(self.filename, self.precision, self.verbose, {})
+        if inplace:
+            move(target, filename)
+            super().__init__(filename, self.precision, self.verbose)
 
 
 class UcnFile(BinaryLayerFile):
@@ -828,7 +831,7 @@ def __init__(
         self.header_dtype = BinaryHeader.set_dtype(
             bintype="Ucn", precision=precision
         )
-        super().__init__(filename, precision, verbose, kwargs)
+        super().__init__(filename, precision, verbose, **kwargs)
         return
 
 
@@ -898,7 +901,7 @@ def __init__(
         self.header_dtype = BinaryHeader.set_dtype(
             bintype="Head", precision=precision
         )
-        super().__init__(filename, precision, verbose, kwargs)
+        super().__init__(filename, precision, verbose, **kwargs)
 
     def _get_data_array(self, totim=0.0):
         """
@@ -2325,10 +2328,17 @@ def reverse(self, filename: Optional[os.PathLike] = None):
         # get number of records
         nrecords = len(self)
 
-        # open backward budget file
-        temp_dir_path = Path(tempfile.gettempdir())
-        temp_file_path = temp_dir_path / filename.name
-        with open(temp_file_path, "wb") as f:
+        target = filename
+
+        # if rewriting the same file, write
+        # temp file then copy it into place
+        inplace = filename == self.filename
+        if inplace:
+            temp_dir_path = Path(tempfile.gettempdir())
+            temp_file_path = temp_dir_path / filename.name
+            target = temp_file_path
+
+        with open(target, "wb") as f:
             # loop over budget file records in reverse order
             for idx in range(nrecords - 1, -1, -1):
                 # load header array
@@ -2415,13 +2425,7 @@ def reverse(self, filename: Optional[os.PathLike] = None):
                 # Write data
                 data.tofile(f)
 
-        # if we're rewriting the original file, close it first
-        if filename == self.filename:
-            self.close()
-
-        # move temp file to destination
-        temp_file_path.replace(filename)
-
         # if we rewrote the original file, reinitialize
-        if filename == self.filename:
-            self.__init__(self.filename, self.precision, self.verbose)
+        if inplace:
+            move(target, filename)
+            self.__init__(filename, self.precision, self.verbose)

flopy/utils/datafile.py

@@ -157,7 +157,7 @@ class LayerFile:
     """
 
     def __init__(
-        self, filename: Union[str, os.PathLike], precision, verbose, kwargs
+        self, filename: Union[str, os.PathLike], precision, verbose, **kwargs
     ):
         from ..discretization.structuredgrid import StructuredGrid
 

flopy/utils/datautil.py

@@ -606,7 +606,9 @@ def build_list(self, callback):
                             (entry_point[0][-1], new_location)
                         )
                     else:
-                        entry_point[0].append(callback(entry_point[1]))
+                        entry_point[0].append(
+                            callback(tuple(i + val for i in entry_point[1]))
+                        )
             entry_points = new_entry_points
 
     def first_item(self):

flopy/utils/formattedfile.py

@@ -110,8 +110,8 @@ class FormattedLayerFile(LayerFile):
 
     """
 
-    def __init__(self, filename, precision, verbose, kwargs):
-        super().__init__(filename, precision, verbose, kwargs)
+    def __init__(self, filename, precision, verbose, **kwargs):
+        super().__init__(filename, precision, verbose, **kwargs)
 
     def _build_index(self):
         """
@@ -376,7 +376,7 @@ def __init__(
         **kwargs,
     ):
         self.text = text
-        super().__init__(filename, precision, verbose, kwargs)
+        super().__init__(filename, precision, verbose, **kwargs)
 
     def _get_text_header(self):
         """

flopy/utils/get_modflow.py

@@ -160,8 +160,8 @@ def get_release(owner=None, repo=None, tag="latest", quiet=False) -> dict:
         try:
             with urllib.request.urlopen(request, timeout=10) as resp:
                 result = resp.read()
-                remaining = int(resp.headers["x-ratelimit-remaining"])
-                if remaining <= 10:
+                remaining = resp.headers.get("x-ratelimit-remaining", None)
+                if remaining and int(remaining) <= 10:
                     warnings.warn(
                         f"Only {remaining} GitHub API requests remaining "
                         "before rate-limiting"