Merge c6723f4 into 7b97622

modflowpy · Oct 13, 2021 · 7ac0139 · 7ac0139
2 parents 7b97622 + c6723f4
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diff --git a/README.md b/README.md
@@ -26,7 +26,7 @@ For general modeling issues, please consult a modeling forum, such as the [MODFL
 Installation
 -----------------------------------------------
 
-FloPy requires **Python** 3.7 (or higher) and **NumPy** 1.15 (or higher).  Dependencies for optional FloPy methods are summarized [here](docs/flopy_method_dependencies.md).
+FloPy requires **Python** 3.7 (or higher), **NumPy** 1.15.0 (or higher), and **matplotlib** 1.4.0 (or higher).  Dependencies for optional FloPy methods are summarized [here](docs/flopy_method_dependencies.md).
 
 To install FloPy type:
 

diff --git a/autotest/t005_test.py b/autotest/t005_test.py
@@ -25,9 +25,7 @@ def test_modflow_unstructured():
     lpf = flopy.mfusg.MfUsgLpf(mf)
     assert isinstance(lpf, flopy.mfusg.MfUsgLpf)
 
-    wel = flopy.mfusg.MfUsgWel(
-        mf, stress_period_data={0: [[0, -100]]}
-    )
+    wel = flopy.mfusg.MfUsgWel(mf, stress_period_data={0: [[0, -100]]})
     assert isinstance(wel, flopy.mfusg.MfUsgWel)
 
     ghb = flopy.modflow.ModflowGhb(
@@ -44,9 +42,7 @@ def test_modflow_unstructured():
     # write well file
     wel.write_file()
     assert os.path.isfile(os.path.join(cpth, f"{mf.name}.wel")) is True
-    wel2 = flopy.mfusg.MfUsgWel.load(
-        os.path.join(cpth, f"{mf.name}.wel"), mf
-    )
+    wel2 = flopy.mfusg.MfUsgWel.load(os.path.join(cpth, f"{mf.name}.wel"), mf)
     assert wel2.stress_period_data[0] == wel.stress_period_data[0]
 
     # write ghb file

diff --git a/autotest/t016_test.py b/autotest/t016_test.py
@@ -106,9 +106,7 @@ def test_usg_model():
     dis = flopy.modflow.ModflowDis(mf, nlay=1, nrow=11, ncol=11)
     bas = flopy.modflow.ModflowBas(mf)
     lpf = flopy.mfusg.MfUsgLpf(mf)
-    wel = flopy.mfusg.MfUsgWel(
-        mf, stress_period_data={0: [[0, 5, 5, -1.0]]}
-    )
+    wel = flopy.mfusg.MfUsgWel(mf, stress_period_data={0: [[0, 5, 5, -1.0]]})
     ghb = flopy.modflow.ModflowGhb(
         mf,
         stress_period_data={

diff --git a/autotest/t069_test_vtkexportmodel.py b/autotest/t069_test_vtkexportmodel.py
@@ -1,5 +1,5 @@
 """
-Test vtk export_model function without packages_names definition 
+Test vtk export_model function without packages_names definition
 """
 
 import os

diff --git a/autotest/t075_test_ugrid.py b/autotest/t075_test_ugrid.py
@@ -225,7 +225,11 @@ def test_triangle_unstructured_grid():
     xc, yc = tri.get_xcyc().T
     ncpl = np.array([len(iverts)])
     g = UnstructuredGrid(
-        vertices=verts, iverts=iverts, ncpl=ncpl, xcenters=xc, ycenters=yc,
+        vertices=verts,
+        iverts=iverts,
+        ncpl=ncpl,
+        xcenters=xc,
+        ycenters=yc,
     )
     assert len(g.grid_lines) == 8190
     assert g.nnodes == g.ncpl == 2730
@@ -293,7 +297,7 @@ def test_voronoi_grid0(plot=False):
     gridprops = vor.get_gridprops_vertexgrid()
     ncpl = gridprops["ncpl"]
     assert (
-            ncpl == answer_ncpl
+        ncpl == answer_ncpl
     ), f"Number of cells should be {answer_ncpl}. Found {ncpl}"
 
     voronoi_grid = VertexGrid(**gridprops, nlay=1)
@@ -329,7 +333,7 @@ def test_voronoi_grid1(plot=False):
     voronoi_grid = VertexGrid(**gridprops, nlay=1)
     ncpl = gridprops["ncpl"]
     assert (
-            ncpl == answer_ncpl
+        ncpl == answer_ncpl
     ), f"Number of cells should be {answer_ncpl}. Found {ncpl}"
 
     if plot:
@@ -362,7 +366,7 @@ def test_voronoi_grid2(plot=False):
     voronoi_grid = VertexGrid(**gridprops, nlay=1)
     ncpl = gridprops["ncpl"]
     assert (
-            ncpl == answer_ncpl
+        ncpl == answer_ncpl
     ), f"Number of cells should be {answer_ncpl}. Found {ncpl}"
 
     if plot:
@@ -405,7 +409,7 @@ def test_voronoi_grid3(plot=False):
     voronoi_grid = VertexGrid(**gridprops, nlay=1)
     ncpl = gridprops["ncpl"]
     assert (
-            ncpl == answer_ncpl
+        ncpl == answer_ncpl
     ), f"Number of cells should be {answer_ncpl}. Found {ncpl}"
 
     if plot:
@@ -441,7 +445,7 @@ def test_voronoi_grid4(plot=False):
     voronoi_grid = VertexGrid(**gridprops, nlay=1)
     ncpl = gridprops["ncpl"]
     assert (
-            ncpl == answer_ncpl
+        ncpl == answer_ncpl
     ), f"Number of cells should be {answer_ncpl}. Found {ncpl}"
 
     if plot:

diff --git a/autotest/t080_test.py b/autotest/t080_test.py
@@ -40,6 +40,7 @@
 if not os.path.exists(gridgen_ws):
     os.makedirs(gridgen_ws)
 
+
 def test_mfusg():
 
     name = "dummy"
@@ -113,18 +114,23 @@ def test_mfusg():
 
         # test if single node idx works
         one_hds = flopy.utils.HeadUFile(head_file).get_ts(idx=300)
-        if one_hds[0,1] != head[0][300]:
-            raise AssertionError("Error head from 'get_ts' != head from 'get_data'")
+        if one_hds[0, 1] != head[0][300]:
+            raise AssertionError(
+                "Error head from 'get_ts' != head from 'get_data'"
+            )
 
         # test if list of nodes for idx works
-        nodes = [300,182,65]
+        nodes = [300, 182, 65]
 
         multi_hds = flopy.utils.HeadUFile(head_file).get_ts(idx=nodes)
         for i, node in enumerate(nodes):
-            if multi_hds[0, i+1] != head[0][node]:
-                raise AssertionError("Error head from 'get_ts' != head from 'get_data'")
+            if multi_hds[0, i + 1] != head[0][node]:
+                raise AssertionError(
+                    "Error head from 'get_ts' != head from 'get_data'"
+                )
 
     return
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     test_mfusg()
diff --git a/autotest/t506_test.py b/autotest/t506_test.py
@@ -456,9 +456,7 @@ def test_mfusg():
 
         # re-run with an LPF keyword specified. This would have thrown an error
         # before the addition of ikcflag to mflpf.py (flopy 3.3.3 and earlier).
-        lpf = flopy.mfusg.MfUsgLpf(
-            m, novfc=True, nocvcorrection=True
-        )
+        lpf = flopy.mfusg.MfUsgLpf(m, novfc=True, nocvcorrection=True)
         m.write_input()
         m.run_model()
 

diff --git a/docs/flopy_method_dependencies.md b/docs/flopy_method_dependencies.md
@@ -2,34 +2,34 @@ Additional dependencies to use optional FloPy helper methods are listed below.
 
 | Method                                                                               | Python Package                                                     |
 | ------------------------------------------------------------------------------------ | ------------------------------------------------------------------ |
-| `.PlotMapView()` in `flopy.plot`                                                     | **matplotlib** >= 1.4                                              |
-| `.PlotCrossSection()` in `flopy.plot`                                                | **matplotlib** >= 1.4                                              |
-| `.plot()`                                                                            | **matplotlib** >= 1.4                                              |
-| `.plot_shapefile()`                                                                  | **matplotlib** >= 1.4 and **Pyshp** >= 1.2                         |
-| `.to_shapefile()`                                                                    | **Pyshp** >= 1.2                                                   |
-| `.export(*.shp)`                                                                     | **Pyshp** >= 1.2                                                   |
-| `.export(*.nc)`                                                                      | **netcdf4** >= 1.1, and **python-dateutil** >= 2.4                 |
+| `.plot_shapefile()`                                                                  | **Pyshp** >= 2.0.0                                                 |
+| `.to_shapefile()`                                                                    | **Pyshp** >= 2.0.0                                                 |
+| `.export(*.shp)`                                                                     | **Pyshp** >= 2.0.0                                                 |
+| `.export(*.nc)`                                                                      | **netcdf4** >= 1.1, and **python-dateutil** >= 2.4.0               |
 | `.export(*.tif)`                                                                     | **rasterio**                                                       |
 | `.export(*.asc)` in `flopy.utils.reference` `SpatialReference` class                 | **scipy.ndimage**                                                  |
 | `.interpolate()` in `flopy.utils.reference` `SpatialReference` class                 | **scipy.interpolate**                                              |
 | `.interpolate()` in `flopy.mf6.utils.reference` `StructuredSpatialReference` class   | **scipy.interpolate**                                              |
 | `._parse_units_from_proj4()` in `flopy.utils.reference` `SpatialReference` class     | **pyproj**                                                         |
-| `.get_dataframes()` in `flopy.utils.mflistfile` `ListBudget` class                   | **pandas** >= 0.15                                                 |
-| `.get_dataframes()` in `flopy.utils.observationfile` `ObsFiles` class                | **pandas** >= 0.15                                                 |
-| `.get_dataframes()` in `flopy.utils.sfroutputfile` `ModflowSfr2` class               | **pandas** >= 0.15                                                 |
-| `.get_dataframes()` in `flopy.utils.util_list` `MfList` class                        | **pandas** >= 0.15                                                 |
-| `.get_dataframes()` in `flopy.utils.zonebud` `ZoneBudget` class                      | **pandas** >= 0.15                                                 |
-| `.pivot_keyarray()` in `flopy.mf6.utils.arrayutils` `AdvancedPackageUtil` class      | **pandas** >= 0.15                                                 |
-| `._get_vertices()` in `flopy.mf6.utils.binaryfile_utils` `MFOutputRequester` class   | **pandas** >= 0.15                                                 |
-| `.get_dataframe()` in `flopy.mf6.utils.mfobservation` `Observations` class           | **pandas** >= 0.15                                                 |
-| `.df()` in `flopy.modflow.mfsfr2` `SfrFile` class                                    | **pandas** >= 0.15                                                 |
-| `.time_coverage()` in `flopy.export.metadata` `acc` class - ***used if available***  | **pandas** >= 0.15                                                 |
-| `.loadtxt()` in `flopy.utils.flopyio` - ***used if available***                      | **pandas** >= 0.15                                                 |
+| `.get_dataframes()` in `flopy.utils.mflistfile` `ListBudget` class                   | **pandas** >= 0.15.0                                               |
+| `.get_dataframes()` in `flopy.utils.observationfile` `ObsFiles` class                | **pandas** >= 0.15.0                                               |
+| `.get_dataframes()` in `flopy.utils.sfroutputfile` `ModflowSfr2` class               | **pandas** >= 0.15.0                                               |
+| `.get_dataframes()` in `flopy.utils.util_list` `MfList` class                        | **pandas** >= 0.15.0                                               |
+| `.get_dataframes()` in `flopy.utils.zonebud` `ZoneBudget` class                      | **pandas** >= 0.15.0                                               |
+| `.pivot_keyarray()` in `flopy.mf6.utils.arrayutils` `AdvancedPackageUtil` class      | **pandas** >= 0.15.0                                               |
+| `._get_vertices()` in `flopy.mf6.utils.binaryfile_utils` `MFOutputRequester` class   | **pandas** >= 0.15.0                                               |
+| `.get_dataframe()` in `flopy.mf6.utils.mfobservation` `Observations` class           | **pandas** >= 0.15.0                                               |
+| `.df()` in `flopy.modflow.mfsfr2` `SfrFile` class                                    | **pandas** >= 0.15.0                                               |
+| `.time_coverage()` in `flopy.export.metadata` `acc` class - ***used if available***  | **pandas** >= 0.15.0                                               |
+| `.loadtxt()` in `flopy.utils.flopyio` - ***used if available***                      | **pandas** >= 0.15.0                                               |
 | `.generate_classes()` in `flopy.mf6.utils`                                           | [**pymake**](https://github.com/modflowpy/pymake)                  |
-| `.intersect()` in `flopy.discretization.VertexGrid`                                  | **matplotlib** >= 1.4                                              |
 | `GridIntersect()` in `flopy.utils.gridintersect`                                     | **shapely**                                                        |
 | `GridIntersect().plot_polygon()` in `flopy.utils.gridintersect`                      | **shapely** and **descartes**                                      |
 | `Raster()` in `flopy.utils.Raster`                                                   | **rasterio**, **affine**, and **scipy**                            |
 | `Raster().sample_polygon()` in `flopy.utils.Raster`                                  | **shapely**                                                        |
 | `Raster().crop()` in `flopy.utils.Raster`                                            | **shapely**                                                        |
 | `.array_at_verts()` in `flopy.discretization.structuredgrid` `StructuredGrid` class  | **scipy.interpolate**                                              |
+| `get_sciencebase_xml_metadata()` in `flopy.export.metadata` `acdd` class             | **defusedxml**                                                     |
+| `flopy.utils.geospatial_utils` `GeoSpatialUtil` class                                | **geojson**                                                        |
+| `flopy.utils.geospatial_utils` `GeoSpatialCollection` class                          | **geojson**                                                        |
+| `flopy.export.vtk` `Vtk` class                                                       | **vtk**                                                            |
diff --git a/etc/environment.yml b/etc/environment.yml
@@ -2,28 +2,38 @@ name: flopy
 channels:
   - conda-forge
 dependencies:
+  # required
   - python>=3.7
+  - numpy>=1.15.0
+  - matplotlib>=1.4.0
+
+  # testing
   - pylint
   - flake8
   - black
   - nose
   - nose-timer
   - coverage
+
+  # optional
   - appdirs
-  - requests
-  - numpy>=1.15
-  - matplotlib
-  - bmipy
+  - python-dateutil>=2.4.0
   - affine
   - scipy
   - pandas
   - netcdf4
-  - pyshp
+  - pyshp>=2.0.0
   - rasterio
   - fiona
   - descartes
   - pyproj
   - shapely
   - geos
   - geojson
-  - vtk
+  - vtk
+
+  # external dependencies
+  - requests
+
+  # MODFLOW API dependencies
+  - bmipy
diff --git a/flopy/discretization/structuredgrid.py b/flopy/discretization/structuredgrid.py
@@ -725,10 +725,6 @@ def map_polygons(self):
         -------
             list of Polygon objects
         """
-        try:
-            import matplotlib.path as mpath
-        except ImportError:
-            raise ImportError("matplotlib required to use this method")
         cache_index = "xyzgrid"
         if (
             cache_index not in self._cache_dict

diff --git a/flopy/discretization/unstructuredgrid.py b/flopy/discretization/unstructuredgrid.py
@@ -471,10 +471,7 @@ def map_polygons(self):
         -------
             list or dict of matplotlib.collections.Polygon
         """
-        try:
-            from matplotlib.path import Path
-        except ImportError:
-            raise ImportError("matplotlib required to use this method")
+        from matplotlib.path import Path
 
         cache_index = "xyzgrid"
         if (

diff --git a/flopy/discretization/vertexgrid.py b/flopy/discretization/vertexgrid.py
@@ -2,10 +2,7 @@
 import copy
 import numpy as np
 
-try:
-    from matplotlib.path import Path
-except (ImportError, RuntimeError):
-    Path = None
+from matplotlib.path import Path
 
 from .grid import Grid, CachedData
 from ..utils.geometry import is_clockwise
@@ -226,10 +223,6 @@ def map_polygons(self):
         -------
             list of Polygon objects
         """
-        try:
-            import matplotlib.path as mpath
-        except ImportError:
-            raise ImportError("matplotlib required to use this method")
         cache_index = "xyzgrid"
         if (
             cache_index not in self._cache_dict
@@ -239,8 +232,7 @@ def map_polygons(self):
             self._polygons = None
         if self._polygons is None:
             self._polygons = [
-                mpath.Path(self.get_cell_vertices(nn))
-                for nn in range(self.ncpl)
+                Path(self.get_cell_vertices(nn)) for nn in range(self.ncpl)
             ]
 
         return copy.copy(self._polygons)
@@ -270,12 +262,6 @@ def intersect(self, x, y, local=False, forgive=False):
             The CELL2D number
 
         """
-        if Path is None:
-            s = (
-                "Could not import matplotlib.  Must install matplotlib "
-                "in order to use VertexGrid.intersect() method"
-            )
-            raise ImportError(s)
 
         if local:
             # transform x and y to real-world coordinates

diff --git a/flopy/export/metadata.py b/flopy/export/metadata.py
@@ -1,10 +1,7 @@
-from flopy.utils.flopy_io import get_url_text
 import numpy as np
 
-try:
-    import pandas as pd
-except:
-    pd = False
+from ..utils.flopy_io import get_url_text
+from ..utils import import_optional_dependency
 
 
 class acdd:
@@ -194,13 +191,15 @@ def time_coverage(self):
         -------
 
         """
+        pd = import_optional_dependency("pandas", errors="ignore")
+
         l = self.sb["dates"]
         tc = {}
         for t in ["start", "end"]:
             tc[t] = [d.get("dateString") for d in l if t in d["type"].lower()][
                 0
             ]
-        if not np.all(self.model_time.steady_state) and pd:
+        if not np.all(self.model_time.steady_state) and pd is not None:
             # replace with times from model reference
             tc["start"] = self.model_time.start_datetime
             strt = pd.Timestamp(self.model_time.start_datetime)
@@ -260,7 +259,6 @@ def get_sciencebase_metadata(self, id):
         url = urlbase.format(id)
 
         import json
-        from flopy.utils.flopy_io import get_url_text
 
         msg = "Need an internet connection to get metadata from ScienceBase."
         text = get_url_text(url, error_msg=msg)
@@ -283,11 +281,8 @@ def get_sciencebase_xml_metadata(self):
         metadata : dict
             Dictionary of metadata
         """
-        try:
-            # use defusedxml to removed XML security vulnerabilities
-            import defusedxml.ElementTree as ET
-        except ImportError:
-            raise ImportError("DefusedXML must be installed to query metadata")
+        # use defusedxml to removed XML security vulnerabilities
+        ET = import_optional_dependency("defusedxml.ElementTree")
 
         url = self.xmlfile
         msg = "Need an internet connection to get metadata from ScienceBase."