refactor: run pyupgrade and adjust a few f-strings (#1710)

.docs/conf.py

@@ -23,7 +23,7 @@
 on_rtd = os.environ.get("READTHEDOCS") == "True"
 
 # -- determine if this version is a release candidate
-with open("../README.md", "r") as f:
+with open("../README.md") as f:
     lines = f.readlines()
 rc_text = ""
 for line in lines:
@@ -38,7 +38,7 @@
 
 # -- update version number in main.rst
 rst_name = "main.rst"
-with open(rst_name, "r") as f:
+with open(rst_name) as f:
     lines = f.readlines()
 with open(rst_name, "w") as f:
     for line in lines:
@@ -51,7 +51,7 @@
 
 # -- update authors in introduction.rst
 rst_name = "introduction.rst"
-with open(rst_name, "r") as f:
+with open(rst_name) as f:
     lines = f.readlines()
 tag_start = "FloPy Development Team"
 tag_end = "How to Cite"

autotest/regression/test_mf6.py

@@ -533,7 +533,7 @@ def test_np001(function_tmpdir, example_data_path):
     mpath = sim.simulation_data.mfpath.get_model_path(model.name)
     spath = sim.simulation_data.mfpath.get_sim_path()
     found_cellid = False
-    with open(os.path.join(mpath, "np001_mod.wel"), "r") as fd:
+    with open(os.path.join(mpath, "np001_mod.wel")) as fd:
         for line in fd:
             line_lst = line.strip().split()
             if (
@@ -561,7 +561,7 @@ def test_np001(function_tmpdir, example_data_path):
     found_begin = False
     found_end = False
     text_between_begin_and_end = False
-    with open(os.path.join(mpath, "file_rename.wel"), "r") as fd:
+    with open(os.path.join(mpath, "file_rename.wel")) as fd:
         for line in fd:
             if line.strip().lower() == "begin period  2":
                 found_begin = True
@@ -587,7 +587,7 @@ def test_np001(function_tmpdir, example_data_path):
     found_begin = False
     found_end = False
     text_between_begin_and_end = False
-    with open(os.path.join(mpath, "np001_spd_test.wel"), "r") as fd:
+    with open(os.path.join(mpath, "np001_spd_test.wel")) as fd:
         for line in fd:
             if line.strip().lower() == "begin period  2":
                 found_begin = True

autotest/test_binarygrid_util.py

@@ -116,7 +116,7 @@ def test_mfgrddisv_modelgrid(mfgrd_test_path):
         f"does not equal {nvert}"
     )
 
-    cellxy = np.column_stack((mg.xyzcellcenters[:2]))
+    cellxy = np.column_stack(mg.xyzcellcenters[:2])
     errmsg = (
         f"shape of flow.disv centroids {cellxy.shape} not equal to (218, 2)."
     )

autotest/test_get_modflow.py

@@ -123,9 +123,9 @@ def test_get_release(repo):
 
     if repo == "modflow6":
         # can remove if modflow6 releases follow asset name conventions followed in executables and nightly build repos
-        assert set([a.rpartition("_")[2] for a in actual_assets]) >= set(
-            [a for a in expected_assets if not a.startswith("win")]
-        )
+        assert {a.rpartition("_")[2] for a in actual_assets} >= {
+            a for a in expected_assets if not a.startswith("win")
+        }
     else:
         assert set(actual_assets) >= set(expected_assets)
 

autotest/test_grid.py

@@ -501,7 +501,7 @@ def test_unstructured_from_gridspec(example_data_path):
     spec_path = str(model_path / "freyberg.usg.gsf")
     grid = UnstructuredGrid.from_gridspec(spec_path)
 
-    with open(spec_path, "r") as file:
+    with open(spec_path) as file:
         lines = file.readlines()
         split = [line.strip().split() for line in lines]
 
@@ -1019,11 +1019,9 @@ def test_get_lni_unstructured(grid):
         layer, i = grid.get_lni([nn])[0]
         csum = [0] + list(
             np.cumsum(
-                (
-                    list(grid.ncpl)
-                    if not isinstance(grid.ncpl, int)
-                    else [grid.ncpl for _ in range(grid.nlay)]
-                )
+                list(grid.ncpl)
+                if not isinstance(grid.ncpl, int)
+                else [grid.ncpl for _ in range(grid.nlay)]
             )
         )
         assert csum[layer] + i == nn

autotest/test_gridintersect.py

@@ -1220,7 +1220,7 @@ def test_polygon_offset_rot_structured_grid_shapely(rtree):
 # %% test rasters
 
 
-@requires_pkg("rasterstats")
+@requires_pkg("rasterstats", "scipy")
 def test_rasters(example_data_path):
     ws = str(example_data_path / "options")
     raster_name = "dem.img"

autotest/test_lake_connections.py

@@ -255,11 +255,7 @@ def test_lake(function_tmpdir, example_data_path):
     # mm = flopy.plot.PlotMapView(modelgrid=gwf.modelgrid)
     # mm.plot_array(k11_tm)
 
-    (
-        idomain,
-        pakdata_dict,
-        connectiondata,
-    ) = get_lak_connections(
+    idomain, pakdata_dict, connectiondata = get_lak_connections(
         gwf.modelgrid,
         lakes,
         bedleak=5e-9,
@@ -459,11 +455,7 @@ def test_embedded_lak_ex01(function_tmpdir, example_data_path):
         printrecord=[("HEAD", "ALL"), ("BUDGET", "ALL")],
     )
 
-    (
-        idomain,
-        pakdata_dict,
-        connectiondata,
-    ) = get_lak_connections(
+    idomain, pakdata_dict, connectiondata = get_lak_connections(
         gwf.modelgrid,
         lake_map,
         bedleak=0.1,
@@ -559,11 +551,7 @@ def test_embedded_lak_prudic(example_data_path):
     )
 
     # flopy test
-    (
-        idomain_rev,
-        pakdata_dict,
-        connectiondata,
-    ) = get_lak_connections(
+    idomain_rev, pakdata_dict, connectiondata = get_lak_connections(
         model_grid,
         lake_map,
         idomain=idomain,
@@ -668,11 +656,7 @@ def test_embedded_lak_prudic_mixed(example_data_path):
     )
 
     # test mixed lakebed leakance list
-    (
-        _,
-        _,
-        connectiondata,
-    ) = get_lak_connections(
+    _, _, connectiondata = get_lak_connections(
         model_grid,
         lake_map,
         idomain=idomain,

autotest/test_mf6.py

@@ -173,8 +173,8 @@ def get_gwf_model(sim, gwfname, gwfpath, modelshape, chdspd=None, welspd=None):
     # output control
     oc = ModflowGwfoc(
         gwf,
-        budget_filerecord="{}.cbc".format(gwfname),
-        head_filerecord="{}.hds".format(gwfname),
+        budget_filerecord=f"{gwfname}.cbc",
+        head_filerecord=f"{gwfname}.hds",
         headprintrecord=[("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")],
         saverecord=[("HEAD", "LAST"), ("BUDGET", "LAST")],
         printrecord=[("HEAD", "LAST"), ("BUDGET", "LAST")],
@@ -226,8 +226,8 @@ def get_gwt_model(sim, gwtname, gwtpath, modelshape, sourcerecarray=None):
     # output control
     oc = ModflowGwtoc(
         gwt,
-        budget_filerecord="{}.cbc".format(gwtname),
-        concentration_filerecord="{}.ucn".format(gwtname),
+        budget_filerecord=f"{gwtname}.cbc",
+        concentration_filerecord=f"{gwtname}.ucn",
         concentrationprintrecord=[
             ("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")
         ],
@@ -1031,6 +1031,7 @@ def test_output_add_observation(function_tmpdir, example_data_path):
         sfr_obs, Mf6Obs
     ), "remove and add observation test (Mf6Output) failed"
 
+@requires_exe("mf6")
 def test_sfr_connections(function_tmpdir, example_data_path):
     '''MODFLOW just warns if any reaches are unconnected
     flopy fails to load model if reach 1 is unconnected, fine with other unconnected'''
@@ -1039,7 +1040,7 @@ def test_sfr_connections(function_tmpdir, example_data_path):
     for test in ['sfr0', 'sfr1']:
         sim_name = "test_sfr"
         model_name = "test_sfr"
-        tdis_name = "{}.tdis".format(sim_name)
+        tdis_name = f"{sim_name}.tdis"
         sim = MFSimulation(
             sim_name=sim_name, version="mf6", exe_name="mf6", sim_ws=sim_ws
         )
@@ -1053,7 +1054,7 @@ def test_sfr_connections(function_tmpdir, example_data_path):
             complexity="SIMPLE",
         )
         model = ModflowGwf(
-            sim, modelname=model_name, model_nam_file="{}.nam".format(model_name)
+            sim, modelname=model_name, model_nam_file=f"{model_name}.nam"
         )
 
         dis = ModflowGwfdis(
@@ -1077,7 +1078,7 @@ def test_sfr_connections(function_tmpdir, example_data_path):
             icelltype=1,
             k=50.0,
         )
-        
+
         cnfile = f'mf6_{test}_connection.txt'
         pkfile = f'mf6_{test}_package.txt'
 
@@ -1115,7 +1116,7 @@ def test_array(function_tmpdir):
     sim_name = "test_array"
     model_name = "test_array"
     out_dir = function_tmpdir
-    tdis_name = "{}.tdis".format(sim_name)
+    tdis_name = f"{sim_name}.tdis"
     sim = MFSimulation(
         sim_name=sim_name, version="mf6", exe_name="mf6", sim_ws=out_dir
     )
@@ -1138,7 +1139,7 @@ def test_array(function_tmpdir):
         number_orthogonalizations=2,
     )
     model = ModflowGwf(
-        sim, modelname=model_name, model_nam_file="{}.nam".format(model_name)
+        sim, modelname=model_name, model_nam_file=f"{model_name}.nam"
     )
 
     dis = ModflowGwfdis(
@@ -1700,7 +1701,7 @@ def test_namefile_creation(tmpdir):
     model = ModflowGwf(
         sim,
         modelname=test_ex_name,
-        model_nam_file="{}.nam".format(test_ex_name),
+        model_nam_file=f"{test_ex_name}.nam",
     )
 
     # try to create simulation name file

autotest/test_mnw.py

@@ -353,7 +353,7 @@ def test_mnw2_create_file(function_tmpdir):
         mnwmax=len(wells),
         mnw=wells,
         itmp=list(
-            (np.ones((len(stress_period_data.index))) * len(wellids)).astype(
+            (np.ones(len(stress_period_data.index)) * len(wellids)).astype(
                 int
             )
         ),

autotest/test_modpathfile.py

@@ -66,7 +66,7 @@ def get_nodes(locs):
     )
 
     # Create the Flopy groundwater flow (gwf) model object
-    model_nam_file = "{}.nam".format(name)
+    model_nam_file = f"{name}.nam"
     gwf = ModflowGwf(
         sim, modelname=name, model_nam_file=model_nam_file, save_flows=True
     )
@@ -113,9 +113,9 @@ def get_nodes(locs):
     ModflowGwfriv(gwf, stress_period_data={0: rd})
 
     # Create the output control package
-    headfile = "{}.hds".format(name)
+    headfile = f"{name}.hds"
     head_record = [headfile]
-    budgetfile = "{}.cbb".format(name)
+    budgetfile = f"{name}.cbb"
     budget_record = [budgetfile]
     saverecord = [("HEAD", "ALL"), ("BUDGET", "ALL")]
     oc = ModflowGwfoc(

autotest/test_mp6.py

@@ -834,8 +834,8 @@ def test_mp_wpandas_wo_pandas(ml):
     assert success
 
     # read the two files and ensure they are identical
-    with open(mp_pandas.get_package("loc").fn_path, "r") as f:
+    with open(mp_pandas.get_package("loc").fn_path) as f:
         particles_pandas = f.readlines()
-    with open(mp_no_pandas.get_package("loc").fn_path, "r") as f:
+    with open(mp_no_pandas.get_package("loc").fn_path) as f:
         particles_no_pandas = f.readlines()
     assert particles_pandas == particles_no_pandas

autotest/test_pcg.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 This simple script tests that the pcg load function works for both free-
 and fixed-format pcg files for mf2005 models.

autotest/test_zonbud_utility.py

@@ -29,7 +29,7 @@ def zbud_f(loadpth):
 
 
 def read_zonebudget_file(fname):
-    with open(fname, "r") as f:
+    with open(fname) as f:
         lines = f.readlines()
 
     rows = []
@@ -112,8 +112,8 @@ def test_compare2zonebudget(cbc_f, zon_f, zbud_f, rtol):
         zb_arr = zba[zba["totim"] == time]
         fp_arr = fpa[fpa["totim"] == time]
         for name in fp_arr["name"]:
-            r1 = np.where((zb_arr["name"] == name))
-            r2 = np.where((fp_arr["name"] == name))
+            r1 = np.where(zb_arr["name"] == name)
+            r2 = np.where(fp_arr["name"] == name)
             if r1[0].shape[0] < 1 or r2[0].shape[0] < 1:
                 continue
             if r1[0].shape[0] != r2[0].shape[0]:
@@ -167,7 +167,7 @@ def test_zonbud_to_csv(function_tmpdir, cbc_f, zon_f):
     zb = ZoneBudget(str(cbc_f), zon, kstpkper=[(0, 1094), (0, 1096)])
     f_out = os.path.join(str(function_tmpdir), "test.csv")
     zb.to_csv(f_out)
-    with open(f_out, "r") as f:
+    with open(f_out) as f:
         lines = f.readlines()
     assert len(lines) > 0, "No data written to csv file."
 

examples/groundwater_paper/scripts/uspb_capture.py

@@ -99,12 +99,10 @@ def cf_model(model, k, i, j, base, Q=-100):
 ncol2 = ncol // nstep
 
 # open summary file
-fs = open(
-    os.path.join("data", "uspb", "uspb_capture_{}.out".format(nstep)), "w", 0
-)
+fs = open(os.path.join("data", "uspb", f"uspb_capture_{nstep}.out"), "w", 0)
 
 # write some summary information
-fs.write("Problem size: {} rows and {} columns.\n".format(nrow, ncol))
+fs.write(f"Problem size: {nrow} rows and {ncol} columns.\n")
 fs.write(
     "Capture fraction analysis performed every {} rows and columns.\n".format(
         nstep
@@ -141,7 +139,7 @@ def cf_model(model, k, i, j, base, Q=-100):
             s0 = time.time()
             cf = cf_model(ml, 3, i, j, baseQ)
             s1 = time.time()
-            line = "  model {} run time: {} seconds\n".format(idx, s1 - s0)
+            line = f"  model {idx} run time: {s1 - s0} seconds\n"
             fs.write(line)
             sys.stdout.write(line)
             idx += 1
@@ -158,9 +156,9 @@ def cf_model(model, k, i, j, base, Q=-100):
 ets = end - start
 line = (
     "\n"
-    + "streamflow capture analysis took {} seconds.\n".format(ets)
-    + "streamflow capture analysis took {} minutes.\n".format(ets / 60.0)
-    + "streamflow capture analysis took {} hours.\n".format(ets / 3600.0)
+    + f"streamflow capture analysis took {ets} seconds.\n"
+    + f"streamflow capture analysis took {ets / 60.0} minutes.\n"
+    + f"streamflow capture analysis took {ets / 3600.0} hours.\n"
 )
 fs.write(line)
 sys.stdout.write(line)
@@ -179,7 +177,7 @@ def cf_model(model, k, i, j, base, Q=-100):
 for idx in range(10):
     fn = os.path.join(
         res_pth,
-        "USPB_capture_fraction_{:02d}_{:02d}.dat".format(nstep, idx + 1),
+        f"USPB_capture_fraction_{nstep:02d}_{idx + 1:02d}.dat",
     )
-    print("saving capture fraction data to...{}".format(os.path.basename(fn)))
+    print(f"saving capture fraction data to...{os.path.basename(fn)}")
     np.savetxt(fn, cf_array[idx, :, :], delimiter=" ")