refactor (python): apply ruff check rules ISC, UP and RUF (#235)

This refactor applies pyupgrade (UP) and Ruff-specific rules (RUF) to the Python code base. A few manual edits are done on top of automated fixes to apply flake8-implicit-str-concat (ISC).

.doc/conf.py

@@ -39,7 +39,7 @@
     lines += (len(lines) - 1) * "-" + "\n\n"
     lines += (
         "The Jupyter Notebooks used to create the input files and figures for \n"
-        + "each of the MODFLOW 6 `examples <examples.html>`_.\n\n"
+        "each of the MODFLOW 6 `examples <examples.html>`_.\n\n"
     )
     f.write(lines)
 

etc/ci_create_examples_rst.py

@@ -112,7 +112,8 @@
     if stdout:
         print(stdout.decode("utf-8"))
     if stderr:
-        print("Errors:\n{}".format(stderr.decode("utf-8")))
+        print("Errors:")
+        print(stderr.decode("utf-8"))
 
     # read restructured text file as a string
     print(f"reading...'{dst}'")
@@ -125,10 +126,10 @@
     eq_labels = []
     for v in ex_regex.findall(lines):
         tag = f"\\label{{{v}}}"
-        label = "   :label: {}".format(v.replace(":", "-"))
+        label = f"   :label: {v.replace(':', '-')}"
         eq_labels.append(label)
-        tag = "`[{0}] <#{0}>`__".format(v)
-        replace_eq_labels[tag] = ":eq:`{}`".format(v.replace(":", "-"))
+        tag = f"`[{v}] <#{v}>`__"
+        replace_eq_labels[tag] = f":eq:`{v.replace(':', '-')}`"
 
     # find figure references in lines
     ex_regex = re.compile("\\`(.*?)\\`__")
@@ -168,7 +169,7 @@
                 if key in line:
                     line = line.replace(key, value)
 
-            tag = " "
+            tag = "\xa0"  # non-breaking space
             if tag in line:
                 line = line.replace(tag, " ")
 
@@ -273,9 +274,9 @@
         line += "----------------\n\n"
         line += (
             "The Jupyter notebook used to create the MODFLOW 6 input files\n"
-            + "for this example and post-process the results is:\n\n"
+            "for this example and post-process the results is:\n\n"
         )
-        line += "* `{0} <../_notebooks/{0}.html>`_\n".format(ex_root)
+        line += f"* `{ex_root} <../_notebooks/{ex_root}.html>`_\n"
         line += "\n"
 
         # Check to see if there is a gif with the same name as the example name

ruff.toml

@@ -7,10 +7,15 @@ select = [
     "E",    # pycodestyle error
     "F",    # Pyflakes
     "I001", # isort - unsorted-imports
+    # "ISC",  # implicitly concatenated strings
+    "RUF",  # Ruff-specific rules
+    "UP",   # Pyupgrade
 ]
 ignore = [
     "E501", # line too long TODO FIXME
     "E722", # do not use bare `except`
     "E741", # ambiguous variable name
     "F841", # local variable assigned but never used
+    "RUF005", # collection literal concatenation
+    "UP015", # redundant open modes
 ]

scripts/ex-gwe-ates.py

@@ -564,7 +564,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         vertices=verts,
         cell2d=cell2d,
         pname="DISV",
-        filename="{}.disv".format(gwfname),
+        filename=f"{gwfname}.disv",
     )
 
     # Instantiating MODFLOW 6 node property flow package
@@ -582,7 +582,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         save_specific_discharge=True,
         save_saturation=True,
         pname="NPF",
-        filename="{}.npf".format(gwfname),
+        filename=f"{gwfname}.npf",
     )
 
     # Instantiating MODFLOW 6 initial conditions package
@@ -596,7 +596,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         sy=sy,
         transient={0: True},
         pname="STO",
-        filename="{}.sto".format(gwfname),
+        filename=f"{gwfname}.sto",
     )
 
     # Instantiate WEL package
@@ -622,12 +622,12 @@ def build_model(sim_name, verts, cell2d, top, botm):
         save_flows=True,
         stress_period_data=wel_spd,
         pname="WEL",
-        filename="{}.wel".format(gwfname),
+        filename=f"{gwfname}.wel",
     )
 
     # Instantiating MODFLOW 6 output control package (flow model)
-    head_filerecord = "{}.hds".format(gwfname)
-    budget_filerecord = "{}.cbc".format(gwfname)
+    head_filerecord = f"{gwfname}.hds"
+    budget_filerecord = f"{gwfname}.cbc"
     flopy.mf6.ModflowGwfoc(
         gwf,
         head_filerecord=head_filerecord,
@@ -645,7 +645,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         sim,
         model_type="gwe6",
         modelname=gwename,
-        model_nam_file="{}.nam".format(gwename),
+        model_nam_file=f"{gwename}.nam",
     )
 
     # Create iterative model solution and register the gwe model with it
@@ -674,8 +674,8 @@ def build_model(sim_name, verts, cell2d, top, botm):
         number_orthogonalizations=2,
         preconditioner_levels=8,
         preconditioner_drop_tolerance=0.001,
-        rcloserecord="{} strict".format(rclose),
-        filename="{}.ims".format(gwename),
+        rcloserecord=f"{rclose} strict",
+        filename=f"{gwename}.ims",
     )
     sim.register_ims_package(imsgwe, [gwe.name])
 
@@ -692,18 +692,14 @@ def build_model(sim_name, verts, cell2d, top, botm):
         vertices=verts,
         cell2d=cell2d,
         pname="DISV-GWE",
-        filename="{}.disv".format(gwename),
+        filename=f"{gwename}.disv",
     )
 
     # Instantiating MODFLOW 6 heat transport initial temperature
-    flopy.mf6.ModflowGweic(
-        gwe, strt=strt_temp, pname="IC", filename="{}.ic".format(gwename)
-    )
+    flopy.mf6.ModflowGweic(gwe, strt=strt_temp, pname="IC", filename=f"{gwename}.ic")
 
     # Instantiating MODFLOW 6 heat transport advection package
-    flopy.mf6.ModflowGweadv(
-        gwe, scheme=scheme, pname="ADV", filename="{}.adv".format(gwename)
-    )
+    flopy.mf6.ModflowGweadv(gwe, scheme=scheme, pname="ADV", filename=f"{gwename}.adv")
 
     # Instantiating MODFLOW 6 heat transport energy storage package (consider renaming to est)
     prsity = determine_param(low_k_id, high_k_id, "prsity")
@@ -717,7 +713,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         heat_capacity_solid=cps,
         density_solid=rhos,
         pname="EST",
-        filename="{}.est".format(gwename),
+        filename=f"{gwename}.est",
     )
 
     # Instantiating MODFLOW 6 heat transport dispersion package
@@ -730,7 +726,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         ktw=ktw,
         kts=kts,
         pname="CND",
-        filename="{}.cnd".format(gwename),
+        filename=f"{gwename}.cnd",
     )
 
     # Instantiating MODFLOW 6 source/sink mixing package for dealing with
@@ -739,14 +735,14 @@ def build_model(sim_name, verts, cell2d, top, botm):
         ("WEL", "AUX", "TEMPERATURE"),
     ]
     flopy.mf6.ModflowGwessm(
-        gwe, sources=sourcerecarray, pname="SSM", filename="{}.ssm".format(gwename)
+        gwe, sources=sourcerecarray, pname="SSM", filename=f"{gwename}.ssm"
     )
 
     # Instantiating MODFLOW 6 heat transport output control package
     flopy.mf6.ModflowGweoc(
         gwe,
-        budget_filerecord="{}.cbc".format(gwename),
-        temperature_filerecord="{}.ucn".format(gwename),
+        budget_filerecord=f"{gwename}.cbc",
+        temperature_filerecord=f"{gwename}.ucn",
         temperatureprintrecord=[("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")],
         saverecord=[("TEMPERATURE", "ALL"), ("BUDGET", "ALL")],
         printrecord=[("TEMPERATURE", "ALL"), ("BUDGET", "ALL")],
@@ -759,7 +755,7 @@ def build_model(sim_name, verts, cell2d, top, botm):
         exgtype="GWF6-GWE6",
         exgmnamea=gwfname,
         exgmnameb=gwename,
-        filename="{}.gwfgwe".format(gwename),
+        filename=f"{gwename}.gwfgwe",
     )
 
     return sim
@@ -950,7 +946,7 @@ def update(i):
     ani = FuncAnimation(fig, update, range(1, len(times)), init_func=init)
     # interval=25,
     writer = PillowWriter(fps=10)
-    fpth = figs_path / "{}{}".format(sim_name, ".gif")
+    fpth = figs_path / f"{sim_name}.gif"
     ani.save(fpth, writer=writer)
 
 

scripts/ex-gwe-barends.py

@@ -4,7 +4,7 @@
 #  Barends, F.B.J., 2010. Complete Solution for Transient Heat Transport in
 #    Porous Media, Following Lauwerier's Concept. Society of Petroleum '
 #    Engineers, Annual Technical Conference and Exhibition, Florence, Italy,
-#    19–22 September 2010.
+#    19-22 September 2010.
 #    https://doi.org/10.2118/134670-MS
 #
 # Below is a diagram of the model cell numbering (assuming delr = 4.0; values
@@ -275,7 +275,7 @@ def build_mf6_flow_model():
         top=top_overburden,
         botm=botm,
         pname="DIS",
-        filename="{}.dis".format(gwf_name),
+        filename=f"{gwf_name}.dis",
     )
 
     # Instantiate node-property flow (NPF) package
@@ -289,12 +289,12 @@ def build_mf6_flow_model():
         k=k11,
         k33=k33,
         pname="NPF-1",
-        filename="{}.npf".format(gwf_name),
+        filename=f"{gwf_name}.npf",
     )
 
     # Instantiate initial conditions package for the GWF model
     flopy.mf6.ModflowGwfic(
-        gwf, strt=top_overburden, pname="IC-1", filename="{}.ic".format(gwf_name)
+        gwf, strt=top_overburden, pname="IC-1", filename=f"{gwf_name}.ic"
     )
 
     # Instantiating MODFLOW 6 storage package
@@ -306,7 +306,7 @@ def build_mf6_flow_model():
         sy=0,
         steady_state={0: True},
         pname="STO",
-        filename="{}.sto".format(gwf_name),
+        filename=f"{gwf_name}.sto",
     )
 
     # Instantiate WEL package for adding water on the left and removing
@@ -316,19 +316,19 @@ def build_mf6_flow_model():
         auxiliary="TEMPERATURE",
         stress_period_data=wel_spd_left,
         pname="WEL-left",
-        filename="{}.wel-left".format(gwf_name),
+        filename=f"{gwf_name}.wel-left",
     )
     # Instantiate WEL package for extracting water on the right
     flopy.mf6.ModflowGwfwel(
         gwf,
         stress_period_data=wel_spd_right,
         pname="WEL-right",
-        filename="{}.wel-right".format(gwf_name),
+        filename=f"{gwf_name}.wel-right",
     )
 
     # Instantiating MODFLOW 6 output control package (flow model)
-    head_filerecord = "{}.hds".format(sim_name)
-    budget_filerecord = "{}.cbc".format(sim_name)
+    head_filerecord = f"{sim_name}.hds"
+    budget_filerecord = f"{sim_name}.cbc"
     flopy.mf6.ModflowGwfoc(
         gwf,
         head_filerecord=head_filerecord,
@@ -344,7 +344,7 @@ def build_mf6_flow_model():
 
 # +
 def build_mf6_heat_model():
-    print("Building mf6gwe model...{}".format(sim_name))
+    print(f"Building mf6gwe model...{sim_name}")
     gwename = sim_name
     sim_ws = os.path.join(workspace, sim_name, "mf6gwe")
 
@@ -355,7 +355,7 @@ def build_mf6_heat_model():
         sim,
         model_type="gwe6",
         modelname=gwename,
-        model_nam_file="{}.nam".format(gwename),
+        model_nam_file=f"{gwename}.nam",
     )
 
     # Instantiate Iterative model solution package
@@ -390,18 +390,14 @@ def build_mf6_heat_model():
         top=top_overburden,
         botm=botm,
         pname="DIS",
-        filename="{}.dis".format(gwename),
+        filename=f"{gwename}.dis",
     )
 
     # Instantiating MODFLOW 6 heat transport initial temperature
-    flopy.mf6.ModflowGweic(
-        gwe, strt=T0, pname="IC-gwe", filename="{}.ic".format(gwename)
-    )
+    flopy.mf6.ModflowGweic(gwe, strt=T0, pname="IC-gwe", filename=f"{gwename}.ic")
 
     # Instantiating MODFLOW 6 heat transport advection package
-    flopy.mf6.ModflowGweadv(
-        gwe, scheme=scheme, pname="ADV", filename="{}.adv".format(gwename)
-    )
+    flopy.mf6.ModflowGweadv(gwe, scheme=scheme, pname="ADV", filename=f"{gwename}.adv")
 
     # Instantiating MODFLOW 6 heat transport dispersion package
     if ktw != 0:
@@ -413,7 +409,7 @@ def build_mf6_heat_model():
             ktw=ktw,
             kts=kts,
             pname="CND",
-            filename="{}.cnd".format(gwename),
+            filename=f"{gwename}.cnd",
         )
 
     # Instantiating MODFLOW 6 heat transport mass storage package (consider renaming to est)
@@ -425,7 +421,7 @@ def build_mf6_heat_model():
         density_solid=rhos,
         density_water=rhow,
         pname="EST",
-        filename="{}.est".format(gwename),
+        filename=f"{gwename}.est",
     )
 
     flopy.mf6.ModflowGwectp(
@@ -435,7 +431,7 @@ def build_mf6_heat_model():
         maxbound=1,
         stress_period_data=ctp_spd,
         pname="CTP",
-        filename="{}.ctp".format(gwename),
+        filename=f"{gwename}.ctp",
     )
 
     # Instantiating MODFLOW 6 source/sink mixing package for dealing with
@@ -446,15 +442,15 @@ def build_mf6_heat_model():
         print_flows=True,
         sources=sourcerecarray,
         pname="SSM",
-        filename="{}.ssm".format(gwename),
+        filename=f"{gwename}.ssm",
     )
 
     # Instantiating MODFLOW 6 heat transport output control package
     # e.g., day 100 = 100 * 86400 = 8,640,000 = 8.64e6
     flopy.mf6.ModflowGweoc(
         gwe,
-        budget_filerecord="{}.cbc".format(gwename),
-        temperature_filerecord="{}.ucn".format(gwename),
+        budget_filerecord=f"{gwename}.cbc",
+        temperature_filerecord=f"{gwename}.ucn",
         temperatureprintrecord=[("COLUMNS", 10, "WIDTH", 15, "DIGITS", 6, "GENERAL")],
         saverecord={
             0: [
@@ -520,7 +516,7 @@ def plot_thermal_bleeding(sim_gwe):
     if plot_show:
         plt.show()
     if plot_save:
-        fpth = os.path.join(figs_path / "{}-gridView{}".format(sim_name, ".png"))
+        fpth = os.path.join(figs_path / f"{sim_name}-gridView.png")
         fig.savefig(fpth, dpi=600)
 
     # Next, plot model output
@@ -594,7 +590,7 @@ def plot_thermal_bleeding(sim_gwe):
     if plot_show:
         plt.show()
     if plot_save:
-        fpth = os.path.join(figs_path / "{}-200yrs{}".format(sim_name, ".png"))
+        fpth = os.path.join(figs_path / f"{sim_name}-200yrs.png")
         fig2.savefig(fpth, dpi=600)
 
     return