chore: reformat codebase with longer line length (#2362)

The codebase currently has a line length limit of 79 (via #954) as suggested in PEP 8 (which is related to a 80 char limit of decades old IBM punch cards and terminals). However, longer line lengths are generally encouraged for modern Python development, which is a language that commonly has four-space indents needed to define logic structures, thus requiring more horizontal space than other programming languages. Black has a default of 88, which is the same default for Ruff. Is this the ideal length for the flopy codebase? Not sure, but a quick scan of the suggested changes look much better. Despite the size of this PR, it was quickly automated using these ruff commands (including quick fixes to ISC001): ruff format ruff check --select ISC001 --fix ruff format There are no functional changes in this PR, thus the code "runs the same". As such, .git-blame-ignore-revs can be amended to ignore these changes with (e.g.) GitHub's blame view (this would be a follow-up PR).
modflowpy · Nov 13, 2024 · 12a3bcd · 12a3bcd
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diff --git a/.docs/Notebooks/dis_triangle_example.py b/.docs/Notebooks/dis_triangle_example.py
@@ -198,9 +198,7 @@
 sim = flopy.mf6.MFSimulation(
     sim_name=name, version="mf6", exe_name="mf6", sim_ws=workspace
 )
-tdis = flopy.mf6.ModflowTdis(
-    sim, time_units="DAYS", perioddata=[[1.0, 1, 1.0]]
-)
+tdis = flopy.mf6.ModflowTdis(sim, time_units="DAYS", perioddata=[[1.0, 1, 1.0]])
 gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
 ims = flopy.mf6.ModflowIms(
     sim,
@@ -227,9 +225,7 @@
     vertices=vertices,
     cell2d=cell2d,
 )
-npf = flopy.mf6.ModflowGwfnpf(
-    gwf, xt3doptions=[(True)], save_specific_discharge=None
-)
+npf = flopy.mf6.ModflowGwfnpf(gwf, xt3doptions=[(True)], save_specific_discharge=None)
 ic = flopy.mf6.ModflowGwfic(gwf)
 
 

diff --git a/.docs/Notebooks/dis_voronoi_example.py b/.docs/Notebooks/dis_voronoi_example.py
@@ -130,9 +130,7 @@
 sim = flopy.mf6.MFSimulation(
     sim_name=name, version="mf6", exe_name="mf6", sim_ws=sim_ws
 )
-tdis = flopy.mf6.ModflowTdis(
-    sim, time_units="DAYS", perioddata=[[1.0, 1, 1.0]]
-)
+tdis = flopy.mf6.ModflowTdis(sim, time_units="DAYS", perioddata=[[1.0, 1, 1.0]])
 gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
 ims = flopy.mf6.ModflowIms(
     sim,
@@ -145,9 +143,7 @@
 nlay = 1
 top = 1.0
 botm = [0.0]
-disv = flopy.mf6.ModflowGwfdisv(
-    gwf, nlay=nlay, **disv_gridprops, top=top, botm=botm
-)
+disv = flopy.mf6.ModflowGwfdisv(gwf, nlay=nlay, **disv_gridprops, top=top, botm=botm)
 npf = flopy.mf6.ModflowGwfnpf(
     gwf,
     xt3doptions=[(True)],
@@ -209,9 +205,7 @@
 nlay = 1
 top = 1.0
 botm = [0.0]
-disv = flopy.mf6.ModflowGwtdisv(
-    gwt, nlay=nlay, **disv_gridprops, top=top, botm=botm
-)
+disv = flopy.mf6.ModflowGwtdisv(gwt, nlay=nlay, **disv_gridprops, top=top, botm=botm)
 ic = flopy.mf6.ModflowGwtic(gwt, strt=0.0)
 sto = flopy.mf6.ModflowGwtmst(gwt, porosity=0.2)
 adv = flopy.mf6.ModflowGwtadv(gwt, scheme="TVD")

diff --git a/.docs/Notebooks/export_tutorial.py b/.docs/Notebooks/export_tutorial.py
@@ -31,9 +31,7 @@
 # Load our old friend...the Freyberg model
 
 nam_file = "freyberg.nam"
-model_ws = os.path.join(
-    "..", "..", "examples", "data", "freyberg_multilayer_transient"
-)
+model_ws = os.path.join("..", "..", "examples", "data", "freyberg_multilayer_transient")
 ml = flopy.modflow.Modflow.load(nam_file, model_ws=model_ws, check=False)
 
 # We can see the ``Modelgrid`` instance has generic entries, as does ``start_datetime``
@@ -44,9 +42,7 @@
 
 # Setting the attributes of the ``ml.modelgrid`` is easy:
 
-ml.modelgrid.set_coord_info(
-    xoff=123456.7, yoff=765432.1, angrot=15.0, crs=3070
-)
+ml.modelgrid.set_coord_info(xoff=123456.7, yoff=765432.1, angrot=15.0, crs=3070)
 ml.dis.start_datetime = "7/4/1776"
 
 ml.modeltime.start_datetime
@@ -125,9 +121,7 @@
 export_dict = {"hds": hds, "cbc": cbc}
 
 # export head and cell budget outputs to netcdf
-fnc = flopy.export.utils.output_helper(
-    os.path.join(pth, "output.nc"), ml, export_dict
-)
+fnc = flopy.export.utils.output_helper(os.path.join(pth, "output.nc"), ml, export_dict)
 # -
 
 try:

diff --git a/.docs/Notebooks/export_vtk_tutorial.py b/.docs/Notebooks/export_vtk_tutorial.py
@@ -45,9 +45,7 @@
 # load model for examples
 nam_file = "freyberg.nam"
 model_ws = Path(
-    os.path.join(
-        "..", "..", "examples", "data", "freyberg_multilayer_transient"
-    )
+    os.path.join("..", "..", "examples", "data", "freyberg_multilayer_transient")
 )
 ml = flopy.modflow.Modflow.load(nam_file, model_ws=model_ws, check=False)
 
@@ -107,9 +105,7 @@
 # 3D Array export
 # hk export, with points
 model_hk_dir = output_dir / "HK"
-ml.upw.hk.export(
-    model_hk_dir, smooth=True, fmt="vtk", name="HK", point_scalars=True
-)
+ml.upw.hk.export(model_hk_dir, smooth=True, fmt="vtk", name="HK", point_scalars=True)
 
 # ### Package export to .vtu files
 #
@@ -312,9 +308,7 @@
 
 # +
 # export heads as point scalars
-vtkobj = vtk.Vtk(
-    ml, xml=True, pvd=True, point_scalars=True, vertical_exageration=10
-)
+vtkobj = vtk.Vtk(ml, xml=True, pvd=True, point_scalars=True, vertical_exageration=10)
 
 # export heads for time step 1, stress periods 1, 50, 100, 1000
 vtkobj.add_heads(hds, kstpkper=[(0, 0), (0, 49), (0, 99), (0, 999)])
@@ -559,9 +553,7 @@ def run_vertex_grid_example(ws):
     # riv
     riverline = [[(Lx - 1.0, Ly), (Lx - 1.0, 0.0)]]
     rivcells = g.intersect(riverline, "line", 0)
-    rivspd = [
-        [(0, icpl), 320.0, 100000.0, 318] for icpl in rivcells["nodenumber"]
-    ]
+    rivspd = [[(0, icpl), 320.0, 100000.0, 318] for icpl in rivcells["nodenumber"]]
     riv = flopy.mf6.ModflowGwfriv(gwf, stress_period_data=rivspd)
 
     # output control

diff --git a/.docs/Notebooks/external_file_handling_tutorial.py b/.docs/Notebooks/external_file_handling_tutorial.py
@@ -100,11 +100,7 @@
 # list the files in model_ws that have 'hk' in the name
 print(
     "\n".join(
-        [
-            name
-            for name in os.listdir(ml.model_ws)
-            if "hk" in name or "impor" in name
-        ]
+        [name for name in os.listdir(ml.model_ws) if "hk" in name or "impor" in name]
     )
 )
 

diff --git a/.docs/Notebooks/get_transmissivities_example.py b/.docs/Notebooks/get_transmissivities_example.py
@@ -76,9 +76,7 @@
 model_ws = temp_dir.name
 
 m = flopy.modflow.Modflow("junk", version="mfnwt", model_ws=model_ws)
-dis = flopy.modflow.ModflowDis(
-    m, nlay=nl, nrow=nr, ncol=nc, botm=botm, top=top
-)
+dis = flopy.modflow.ModflowDis(m, nlay=nl, nrow=nr, ncol=nc, botm=botm, top=top)
 upw = flopy.modflow.ModflowUpw(m, hk=hk)
 # -
 
@@ -88,9 +86,7 @@
 #   (cells that are partially within the open interval have reduced thickness, cells outside of the open interval have transmissivities of 0). If no `sctop` or `scbot` arguments are supplied, trasmissivites reflect the full saturated thickness in each column of cells (see plot below, which shows different open intervals relative to the model layering)
 
 r, c = np.arange(nr), np.arange(nc)
-T = flopy.utils.get_transmissivities(
-    heads, m, r=r, c=c, sctop=sctop, scbot=scbot
-)
+T = flopy.utils.get_transmissivities(heads, m, r=r, c=c, sctop=sctop, scbot=scbot)
 np.round(T, 2)
 
 m.dis.botm.array[:, r, c]

diff --git a/.docs/Notebooks/gridgen_example.py b/.docs/Notebooks/gridgen_example.py
@@ -55,9 +55,7 @@
     )
     print(msg)
 else:
-    print(
-        f"gridgen executable was found at: {flopy_io.relpath_safe(gridgen_exe)}"
-    )
+    print(f"gridgen executable was found at: {flopy_io.relpath_safe(gridgen_exe)}")
 
 # +
 # temporary directory
@@ -264,9 +262,7 @@
 gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
 disv = flopy.mf6.ModflowGwfdisv(gwf, **disv_gridprops)
 ic = flopy.mf6.ModflowGwfic(gwf)
-npf = flopy.mf6.ModflowGwfnpf(
-    gwf, xt3doptions=True, save_specific_discharge=True
-)
+npf = flopy.mf6.ModflowGwfnpf(gwf, xt3doptions=True, save_specific_discharge=True)
 chd = flopy.mf6.ModflowGwfchd(gwf, stress_period_data=chdspd)
 budget_file = f"{name}.bud"
 head_file = f"{name}.hds"
@@ -367,9 +363,7 @@
 gwf = flopy.mf6.ModflowGwf(sim, modelname=name, save_flows=True)
 disu = flopy.mf6.ModflowGwfdisu(gwf, **disu_gridprops)
 ic = flopy.mf6.ModflowGwfic(gwf)
-npf = flopy.mf6.ModflowGwfnpf(
-    gwf, xt3doptions=True, save_specific_discharge=True
-)
+npf = flopy.mf6.ModflowGwfnpf(gwf, xt3doptions=True, save_specific_discharge=True)
 chd = flopy.mf6.ModflowGwfchd(gwf, stress_period_data=chdspd)
 budget_file = f"{name}.bud"
 head_file = f"{name}.hds"

diff --git a/.docs/Notebooks/groundwater2023_watershed_example.py b/.docs/Notebooks/groundwater2023_watershed_example.py
@@ -70,9 +70,7 @@ def densify_geometry(line, step, keep_internal_nodes=True):
     lines_strings = []
     if keep_internal_nodes:
         for idx in range(1, len(line)):
-            lines_strings.append(
-                shapely.geometry.LineString(line[idx - 1 : idx + 1])
-            )
+            lines_strings.append(shapely.geometry.LineString(line[idx - 1 : idx + 1]))
     else:
         lines_strings = [shapely.geometry.LineString(line)]
 
@@ -262,9 +260,7 @@ def set_idomain(grid, boundary):
 multiplier = 1.175
 transition = 20000.0
 ncells = 7
-smoothr = [
-    transition * (multiplier - 1.0) / (multiplier ** float(ncells) - 1.0)
-]
+smoothr = [transition * (multiplier - 1.0) / (multiplier ** float(ncells) - 1.0)]
 for i in range(ncells - 1):
     smoothr.append(smoothr[i] * multiplier)
 smooth = smoothr.copy()
@@ -326,9 +322,7 @@ def set_idomain(grid, boundary):
     alpha=0.2,
     cmap="Reds_r",
 )
-cg = pmv.contour_array(
-    top_sg_vrc, levels=levels, linewidths=0.3, colors="0.75"
-)
+cg = pmv.contour_array(top_sg_vrc, levels=levels, linewidths=0.3, colors="0.75")
 pmv.plot_inactive()
 
 ax.plot(bp[:, 0], bp[:, 1], "k-")
@@ -503,9 +497,7 @@ def set_idomain(grid, boundary):
     delc=dx,
 )
 g = Gridgen(gwf.modelgrid, model_ws=temp_path)
-adpoly = [
-    [[(1000, 1000), (3000, 1000), (3000, 2000), (1000, 2000), (1000, 1000)]]
-]
+adpoly = [[[(1000, 1000), (3000, 1000), (3000, 2000), (1000, 2000), (1000, 1000)]]]
 adpoly = boundary_polygon + [boundary_polygon[0]]
 adpoly = [[adpoly]]
 g.add_refinement_features([lgr_poly], "polygon", 2, range(1))
@@ -570,9 +562,7 @@ def set_idomain(grid, boundary):
 nodes = np.array(nodes)
 
 # +
-tri = Triangle(
-    maximum_area=5000 * 5000, angle=30, nodes=nodes, model_ws=temp_path
-)
+tri = Triangle(maximum_area=5000 * 5000, angle=30, nodes=nodes, model_ws=temp_path)
 poly = bp
 tri.add_polygon(poly)
 tri.build(verbose=False)
@@ -753,9 +743,7 @@ def set_idomain(grid, boundary):
                 gg = grids[idx]
                 tt = topo_grids[idx]
                 for g, t in zip(gg[1:], tt[1:]):
-                    pmvc = flopy.plot.PlotMapView(
-                        modelgrid=g, ax=ax, extent=extent
-                    )
+                    pmvc = flopy.plot.PlotMapView(modelgrid=g, ax=ax, extent=extent)
                     pmvc.plot_array(top_ngc, vmin=vmin, vmax=vmax)
                     pmvc.plot_grid(**grid_dict)
                     cgc = pmvc.contour_array(top_ngc, **contour_dict)
@@ -873,9 +861,7 @@ def set_idomain(grid, boundary):
         length=9,
         pad=2,
     )
-    cbar.ax.set_title(
-        "Elevation (m)", pad=2.5, loc="center", fontdict=font_dict
-    )
+    cbar.ax.set_title("Elevation (m)", pad=2.5, loc="center", fontdict=font_dict)
 # -
 
 # ### Plot the river intersection for the six grids
@@ -939,12 +925,8 @@ def set_idomain(grid, boundary):
                 gg = grids[idx]
                 tt = intersections[idx]
                 for g, t in zip(gg[1:], tt[1:]):
-                    pmvc = flopy.plot.PlotMapView(
-                        modelgrid=g, ax=ax, extent=extent
-                    )
-                    pmvc.plot_array(
-                        t, masked_values=(0,), cmap=intersection_cmap
-                    )
+                    pmvc = flopy.plot.PlotMapView(modelgrid=g, ax=ax, extent=extent)
+                    pmvc.plot_array(t, masked_values=(0,), cmap=intersection_cmap)
                     pmvc.plot_grid(**grid_dict)
 
             # plot lgr polyline

diff --git a/.docs/Notebooks/groundwater_paper_example_1.py b/.docs/Notebooks/groundwater_paper_example_1.py
@@ -48,9 +48,7 @@
 
 # The discretization of the model is specified with the discretization file (DIS) of MODFLOW. The aquifer is divided into 201 cells of length 10 m and width 1 m.  The first input of the discretization package is the name of the model object. All other input arguments are self explanatory.
 
-fpm.ModflowDis(
-    model, nlay=1, nrow=1, ncol=201, delr=10, delc=1, top=50, botm=0
-)
+fpm.ModflowDis(model, nlay=1, nrow=1, ncol=201, delr=10, delc=1, top=50, botm=0)
 
 # Active cells and the like are defined with the Basic package (BAS), which is required for every MODFLOW model. It contains the {\tt ibound} array, which is used to specify which cells are active (value is positive), inactive (value is 0), or fixed head (value is negative). The {\tt numpy} package (aliased as {\tt np}) can be used to quickly initialize the {\tt ibound} array with values of 1, and then set the {\tt ibound} value for the first and last columns to -1. The {\tt numpy} package (and Python, in general) uses zero-based indexing and supports negative indexing so that row 1 and column 1, and row 1 and column 201, can be referenced as [0, 0], and [0, -1], respectively.  Although this simulation is for steady flow, starting heads still need to be specified. They are used as the head for fixed-head cells (where {\tt ibound} is negative), and as a starting point to compute the saturated thickness for cases of unconfined flow.
 

diff --git a/.docs/Notebooks/groundwater_paper_uspb_example.py b/.docs/Notebooks/groundwater_paper_uspb_example.py
@@ -109,21 +109,15 @@
 # +
 hedObj = flopy.utils.HeadFile(os.path.join(ws, "DG.hds"), precision="double")
 h = hedObj.get_data(kstpkper=(0, 0))
-cbcObj = flopy.utils.CellBudgetFile(
-    os.path.join(ws, "DG.cbc"), precision="double"
-)
+cbcObj = flopy.utils.CellBudgetFile(os.path.join(ws, "DG.cbc"), precision="double")
 
 frf = cbcObj.get_data(kstpkper=(0, 0), text="FLOW RIGHT FACE")[0]
 fff = cbcObj.get_data(kstpkper=(0, 0), text="FLOW FRONT FACE")[0]
-qx, qy, qz = flopy.utils.postprocessing.get_specific_discharge(
-    (frf, fff, None), ml
-)
+qx, qy, qz = flopy.utils.postprocessing.get_specific_discharge((frf, fff, None), ml)
 
 # +
 cnt = np.arange(1200, 1700, 100)
-f, (ax1, ax2) = plt.subplots(
-    1, 2, figsize=(6.75, 4.47), constrained_layout=True
-)
+f, (ax1, ax2) = plt.subplots(1, 2, figsize=(6.75, 4.47), constrained_layout=True)
 ax1.set_xlim(0, xmax)
 ax1.set_ylim(0, ymax)
 ax2.set_xlim(0, xmax)
@@ -177,9 +171,7 @@
 cb = plt.colorbar(h2, cax=ax3)
 cb.ax.set_ylabel("Simulated head, m")
 
-ax1.plot(
-    [-10000, 0], [-10000, 0], color="purple", lw=0.75, label="STR reaches"
-)
+ax1.plot([-10000, 0], [-10000, 0], color="purple", lw=0.75, label="STR reaches")
 ax1.plot(
     [-10000],
     [-10000],
@@ -193,9 +185,7 @@
 leg = ax1.legend(loc="upper left", numpoints=1, prop={"size": 6})
 leg.draw_frame(False)
 
-ax1.text(
-    0.0, 1.01, "Model layer 4", ha="left", va="bottom", transform=ax1.transAxes
-)
+ax1.text(0.0, 1.01, "Model layer 4", ha="left", va="bottom", transform=ax1.transAxes)
 ax2.text(
     0.98,
     0.02,
@@ -204,9 +194,7 @@
     va="bottom",
     transform=ax2.transAxes,
 )
-ax2.text(
-    0.0, 1.01, "Model layer 5", ha="left", va="bottom", transform=ax2.transAxes
-)
+ax2.text(0.0, 1.01, "Model layer 5", ha="left", va="bottom", transform=ax2.transAxes)
 
 plt.savefig(os.path.join(ws, "uspb_heads.png"), dpi=300)
 # -

diff --git a/.docs/Notebooks/mf6_complex_model_example.py b/.docs/Notebooks/mf6_complex_model_example.py
@@ -112,9 +112,7 @@
 )
 
 # initial conditions
-ic = flopy.mf6.ModflowGwfic(
-    gwf, pname="ic", strt=50.0, filename=f"{model_name}.ic"
-)
+ic = flopy.mf6.ModflowGwfic(gwf, pname="ic", strt=50.0, filename=f"{model_name}.ic")
 
 # node property flow
 npf = flopy.mf6.ModflowGwfnpf(
@@ -143,9 +141,7 @@
 for layer in range(0, 3):
     sy[layer]["data"] = 0.2
 
-ss = flopy.mf6.ModflowGwfsto.ss.empty(
-    gwf, layered=True, default_value=0.000001
-)
+ss = flopy.mf6.ModflowGwfsto.ss.empty(gwf, layered=True, default_value=0.000001)
 
 sto = flopy.mf6.ModflowGwfsto(
     gwf,
@@ -296,9 +292,7 @@
 
 obs_recarray = {
     "head_obs.csv": [("h1_13_8", "HEAD", (2, 12, 7))],
-    "intercell_flow_obs1.csv": [
-        ("ICF1_1.0", "FLOW-JA-FACE", (0, 4, 5), (0, 5, 5))
-    ],
+    "intercell_flow_obs1.csv": [("ICF1_1.0", "FLOW-JA-FACE", (0, 4, 5), (0, 5, 5))],
     "head-hydrographs.csv": [
         ("h3-13-9", "HEAD", (2, 12, 8)),
         ("h3-12-8", "HEAD", (2, 11, 7)),