Refactor(mfusg), Feat(mfusgcln, mfusggnc) (#1261)

* modflowusg

* refactor(modflowusg)

* Refactor(mfusg), Feat(mfusgcln, mfusggnc)

* refactor(t420_test.py) for mfusg restructure

* rename(modflowusg-->mfusg) rename all modules, classes etc for simplicity

* rename(t420_test.py-->t080_test.py)

Co-authored-by: swfwmd <hua.zhang@swfwmd.state.fl.us>

.gitignore

@@ -88,3 +88,4 @@ autotest/.noseids
 .docs/_temp
 .docs/_notebooks
 
+*.bak

.pylintrc

@@ -346,6 +346,9 @@ single-line-class-stmt=no
 # else.
 single-line-if-stmt=no
 
+# Good variable names which should always be accepted, separated by a comma
+good-names=kv,nr,nc,sy,ss,iu,hy,hk
+
 
 [SIMILARITIES]
 

autotest/t005_test.py

@@ -9,23 +9,26 @@
 
 def test_modflow_unstructured():
     import flopy
+    import numpy as np
 
-    mf = flopy.modflow.Modflow(
-        version="mfusg", structured=False, model_ws=cpth
-    )
-    assert isinstance(mf, flopy.modflow.Modflow)
+    mf = flopy.mfusg.MfUsg(structured=False, model_ws=cpth)
+    assert isinstance(mf, flopy.mfusg.MfUsg)
 
-    dis = flopy.modflow.ModflowDis(mf)
-    assert isinstance(dis, flopy.modflow.ModflowDis)
+    disu = flopy.mfusg.MfUsgDisU(
+        mf, nodes=1, iac=[1], njag=1, ja=np.array([0]), cl12=[1.0], fahl=[1.0]
+    )
+    assert isinstance(disu, flopy.mfusg.MfUsgDisU)
 
     bas = flopy.modflow.ModflowBas(mf)
     assert isinstance(bas, flopy.modflow.ModflowBas)
 
-    lpf = flopy.modflow.ModflowLpf(mf)
-    assert isinstance(lpf, flopy.modflow.ModflowLpf)
+    lpf = flopy.mfusg.MfUsgLpf(mf)
+    assert isinstance(lpf, flopy.mfusg.MfUsgLpf)
 
-    wel = flopy.modflow.ModflowWel(mf, stress_period_data={0: [[0, -100]]})
-    assert isinstance(wel, flopy.modflow.ModflowWel)
+    wel = flopy.mfusg.MfUsgWel(
+        mf, stress_period_data={0: [[0, -100]]}
+    )
+    assert isinstance(wel, flopy.mfusg.MfUsgWel)
 
     ghb = flopy.modflow.ModflowGhb(
         mf, stress_period_data={0: [[1, 5.9, 1000.0]]}
@@ -35,13 +38,13 @@ def test_modflow_unstructured():
     oc = flopy.modflow.ModflowOc(mf)
     assert isinstance(oc, flopy.modflow.ModflowOc)
 
-    sms = flopy.modflow.ModflowSms(mf)
-    assert isinstance(sms, flopy.modflow.ModflowSms)
+    sms = flopy.mfusg.MfUsgSms(mf)
+    assert isinstance(sms, flopy.mfusg.MfUsgSms)
 
     # write well file
     wel.write_file()
     assert os.path.isfile(os.path.join(cpth, f"{mf.name}.wel")) is True
-    wel2 = flopy.modflow.ModflowWel.load(
+    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]

autotest/t016_test.py

@@ -25,11 +25,11 @@ def test_usg_disu_load():
     assert os.path.isfile(fname), f"disu file not found {fname}"
 
     # Create the model
-    m = flopy.modflow.Modflow(modelname="usgload", verbose=True)
+    m = flopy.mfusg.MfUsg(modelname="usgload", verbose=True)
 
     # Load the disu file
-    disu = flopy.modflow.ModflowDisU.load(fname, m)
-    assert isinstance(disu, flopy.modflow.ModflowDisU)
+    disu = flopy.mfusg.MfUsgDisU.load(fname, m)
+    assert isinstance(disu, flopy.mfusg.MfUsgDisU)
 
     # Change where model files are written
     model_ws = tpth
@@ -42,7 +42,7 @@ def test_usg_disu_load():
     )
 
     # Load disu file
-    disu2 = flopy.modflow.ModflowDisU.load(fname, m)
+    disu2 = flopy.mfusg.MfUsgDisU.load(fname, m)
     for (key1, value1), (key2, value2) in zip(
         disu2.__dict__.items(), disu.__dict__.items()
     ):
@@ -67,11 +67,11 @@ def test_usg_sms_load():
     assert os.path.isfile(fname), f"sms file not found {fname}"
 
     # Create the model
-    m = flopy.modflow.Modflow(modelname="usgload", verbose=True)
+    m = flopy.mfusg.MfUsg(modelname="usgload", verbose=True)
 
     # Load the sms file
-    sms = flopy.modflow.ModflowSms.load(fname, m)
-    assert isinstance(sms, flopy.modflow.ModflowSms)
+    sms = flopy.mfusg.MfUsgSms.load(fname, m)
+    assert isinstance(sms, flopy.mfusg.MfUsgSms)
 
     # Change where model files are written
     model_ws = tpth
@@ -84,7 +84,7 @@ def test_usg_sms_load():
     )
 
     # Load sms file
-    sms2 = flopy.modflow.ModflowSms.load(fname, m)
+    sms2 = flopy.mfusg.MfUsgSms.load(fname, m)
     for (key1, value1), (key2, value2) in zip(
         sms2.__dict__.items(), sms.__dict__.items()
     ):
@@ -96,7 +96,7 @@ def test_usg_sms_load():
 
 
 def test_usg_model():
-    mf = flopy.modflow.Modflow(
+    mf = flopy.mfusg.MfUsg(
         version="mfusg",
         structured=True,
         model_ws=tpth,
@@ -105,8 +105,8 @@ def test_usg_model():
     )
     dis = flopy.modflow.ModflowDis(mf, nlay=1, nrow=11, ncol=11)
     bas = flopy.modflow.ModflowBas(mf)
-    lpf = flopy.modflow.ModflowLpf(mf)
-    wel = flopy.modflow.ModflowWel(
+    lpf = flopy.mfusg.MfUsgLpf(mf)
+    wel = flopy.mfusg.MfUsgWel(
         mf, stress_period_data={0: [[0, 5, 5, -1.0]]}
     )
     ghb = flopy.modflow.ModflowGhb(
@@ -119,7 +119,7 @@ def test_usg_model():
         },
     )
     oc = flopy.modflow.ModflowOc(mf)
-    sms = flopy.modflow.ModflowSms(mf, options="complex")
+    sms = flopy.mfusg.MfUsgSms(mf, options="complex")
 
     # run with defaults
     mf.write_input()
@@ -130,7 +130,7 @@ def test_usg_model():
     # try different complexity options; all should run successfully
     for complexity in ["simple", "moderate", "complex"]:
         print(f"testing MFUSG with sms complexity: {complexity}")
-        sms = flopy.modflow.ModflowSms(mf, options=complexity)
+        sms = flopy.mfusg.MfUsgSms(mf, options=complexity)
         sms.write_file()
         if run:
             success, buff = mf.run_model()
@@ -148,22 +148,22 @@ def test_usg_load_01B():
     assert os.path.isfile(fname), f"nam file not found {fname}"
 
     # Create the model
-    m = flopy.modflow.Modflow(modelname="usgload_1b", verbose=True)
+    m = flopy.mfusg.MfUsg(modelname="usgload_1b", verbose=True)
 
     # Load the model, with checking
     m = m.load(fname, check=True)
 
     # assert disu, lpf, bas packages have been loaded
     msg = "flopy failed on loading mfusg disu package"
-    assert isinstance(m.disu, flopy.modflow.mfdisu.ModflowDisU), msg
+    assert isinstance(m.disu, flopy.mfusg.MfUsgDisU), msg
     msg = "flopy failed on loading mfusg lpf package"
-    assert isinstance(m.lpf, flopy.modflow.mflpf.ModflowLpf), msg
+    assert isinstance(m.lpf, flopy.mfusg.MfUsgLpf), msg
     msg = "flopy failed on loading mfusg bas package"
     assert isinstance(m.bas6, flopy.modflow.mfbas.ModflowBas), msg
     msg = "flopy failed on loading mfusg oc package"
     assert isinstance(m.oc, flopy.modflow.mfoc.ModflowOc), msg
     msg = "flopy failed on loading mfusg sms package"
-    assert isinstance(m.sms, flopy.modflow.mfsms.ModflowSms), msg
+    assert isinstance(m.sms, flopy.mfusg.MfUsgSms), msg
 
 
 def test_usg_load_45usg():
@@ -173,26 +173,26 @@ def test_usg_load_45usg():
     assert os.path.isfile(fname), f"nam file not found {fname}"
 
     # Create the model
-    m = flopy.modflow.Modflow(modelname="45usg", verbose=True)
+    m = flopy.mfusg.MfUsg(modelname="45usg", verbose=True)
 
     # Load the model, with checking.
     m = m.load(fname, check=True)
 
     # assert disu, lpf, bas packages have been loaded
     msg = "flopy failed on loading mfusg disu package"
-    assert isinstance(m.disu, flopy.modflow.mfdisu.ModflowDisU), msg
+    assert isinstance(m.disu, flopy.mfusg.MfUsgDisU), msg
     msg = "flopy failed on loading mfusg lpf package"
-    assert isinstance(m.lpf, flopy.modflow.mflpf.ModflowLpf), msg
+    assert isinstance(m.lpf, flopy.mfusg.MfUsgLpf), msg
     msg = "flopy failed on loading mfusg bas package"
     assert isinstance(m.bas6, flopy.modflow.mfbas.ModflowBas), msg
     msg = "flopy failed on loading mfusg oc package"
     assert isinstance(m.oc, flopy.modflow.mfoc.ModflowOc), msg
     msg = "flopy failed on loading mfusg sms package"
-    assert isinstance(m.sms, flopy.modflow.mfsms.ModflowSms), msg
+    assert isinstance(m.sms, flopy.mfusg.MfUsgSms), msg
     msg = "flopy failed on loading mfusg drn package"
     assert isinstance(m.drn, flopy.modflow.mfdrn.ModflowDrn), msg
     msg = "flopy failed on loading mfusg wel package"
-    assert isinstance(m.wel, flopy.modflow.mfwel.ModflowWel), msg
+    assert isinstance(m.wel, flopy.mfusg.MfUsgWel), msg
 
 
 def test_usg_rch_evt_models01():
@@ -205,9 +205,7 @@ def test_usg_rch_evt_models01():
         "..", "examples", "data", "mfusg_test", "rch_evt_tests"
     )
     nam = "usg_rch_evt.nam"
-    m = flopy.modflow.Modflow.load(
-        nam, model_ws=model_ws, version="mfusg", exe_name=v
-    )
+    m = flopy.mfusg.MfUsg.load(nam, model_ws=model_ws, exe_name=v)
     m.riv.check()
     m.model_ws = tpth
     m.write_input()
@@ -226,9 +224,7 @@ def test_usg_rch_evt_models02():
         "..", "examples", "data", "mfusg_test", "rch_evt_tests"
     )
     nam = "usg_rch_evt_nrchop2.nam"
-    m = flopy.modflow.Modflow.load(
-        nam, model_ws=model_ws, version="mfusg", exe_name=v
-    )
+    m = flopy.mfusg.MfUsg.load(nam, model_ws=model_ws, exe_name=v)
     m.model_ws = tpth
     m.write_input()
     if run:
@@ -246,9 +242,7 @@ def test_usg_rch_evt_models02a():
         "..", "examples", "data", "mfusg_test", "rch_evt_tests"
     )
     nam = "usg_rch_evt_nrchop2a.nam"
-    m = flopy.modflow.Modflow.load(
-        nam, model_ws=model_ws, version="mfusg", exe_name=v
-    )
+    m = flopy.mfusg.MfUsg.load(nam, model_ws=model_ws, exe_name=v)
     m.model_ws = tpth
     m.write_input()
     if run:
@@ -263,19 +257,15 @@ def test_usg_ss_to_tr():
         "..", "examples", "data", "mfusg_test", "01A_nestedgrid_nognc"
     )
     nam = "flow.nam"
-    m = flopy.modflow.Modflow.load(
-        nam, model_ws=model_ws, version="mfusg", exe_name=v
-    )
+    m = flopy.mfusg.MfUsg.load(nam, model_ws=model_ws, exe_name=v)
     m.model_ws = tpth
     m.disu.steady = [False]
     m.write_input()
     if run:
         success, buff = m.run_model()
         assert success
 
-    m = flopy.modflow.Modflow.load(
-        nam, model_ws=tpth, version="mfusg", exe_name=v
-    )
+    m = flopy.mfusg.MfUsg.load(nam, model_ws=tpth, exe_name=v)
     if run:
         success, buff = m.run_model()
         assert success

autotest/t038_test.py

@@ -28,8 +28,8 @@ def test_load_usg():
 
 # function to load a MODFLOW-USG model and then write it back out
 def load_model(namfile, model_ws):
-    m = flopy.modflow.Modflow.load(
-        namfile, model_ws=model_ws, version="mfusg", verbose=True, check=False
+    m = flopy.mfusg.MfUsg.load(
+        namfile, model_ws=model_ws, verbose=True, check=False
     )
     assert m, f"Could not load namefile {namfile}"
     assert m.load_fail is False

autotest/t061_test_gridgen.py

@@ -67,9 +67,7 @@ def test_gridgen():
         botm=botm,
     )
 
-    ms_u = flopy.modflow.Modflow(
-        modelname="mymfusgmodel", model_ws=cpth, version="mfusg"
-    )
+    ms_u = flopy.mfusg.MfUsg(modelname="mymfusgmodel", model_ws=cpth)
     dis_usg = flopy.modflow.ModflowDis(
         ms_u,
         nlay=nlay,
@@ -228,7 +226,7 @@ def test_gridgen():
         assert nlist == nlist2, msg
 
         # test getting a modflow-usg disu package
-        mu = flopy.modflow.Modflow(version="mfusg", structured=False)
+        mu = flopy.mfusg.MfUsg(structured=False)
         disu = g.get_disu(mu)
 
         # test mfusg with vertical pass-through (True above at instantiation)

autotest/t420_test.py → autotest/t080_test.py

@@ -18,15 +18,6 @@
 import flopy
 from flopy.utils.gridgen import Gridgen
 
-try:
-    import matplotlib
-    import matplotlib.pyplot as plt
-    from matplotlib.collections import QuadMesh, PathCollection, LineCollection
-except:
-    print("Matplotlib not installed, tests cannot be run.")
-    matplotlib = None
-    plt = None
-
 # Set gridgen executable
 gridgen_exe = "gridgen"
 if platform.system() in "Windows":
@@ -92,18 +83,17 @@ def test_mfusg():
     # create the mfusg modoel
     ws = os.path.join(tpth, "gridgen_mfusg")
     name = "mymodel"
-    m = flopy.modflow.Modflow(
+    m = flopy.mfusg.MfUsg(
         modelname=name,
         model_ws=ws,
-        version="mfusg",
         exe_name=mfusg_exe,
         structured=False,
     )
-    disu = flopy.modflow.ModflowDisU(m, **gridprops)
+    disu = flopy.mfusg.MfUsgDisU(m, **gridprops)
     bas = flopy.modflow.ModflowBas(m)
-    lpf = flopy.modflow.ModflowLpf(m)
+    lpf = flopy.mfusg.MfUsgLpf(m)
     chd = flopy.modflow.ModflowChd(m, stress_period_data=chdspd)
-    sms = flopy.modflow.ModflowSms(m)
+    sms = flopy.mfusg.MfUsgSms(m)
     oc = flopy.modflow.ModflowOc(m, stress_period_data={(0, 0): ["save head"]})
     m.write_input()
 
@@ -137,4 +127,4 @@ def test_mfusg():
     return
 
 if __name__ == '__main__':
-    test_mfusg()
+    test_mfusg()

autotest/t506_test.py

@@ -376,18 +376,17 @@ def test_mfusg():
     # create the mfusg modoel
     ws = os.path.join(tpth, "gridgen_mfusg")
     name = "mymodel"
-    m = flopy.modflow.Modflow(
+    m = flopy.mfusg.MfUsg(
         modelname=name,
         model_ws=ws,
-        version="mfusg",
         exe_name=mfusg_exe,
         structured=False,
     )
-    disu = flopy.modflow.ModflowDisU(m, **gridprops)
+    disu = flopy.mfusg.MfUsgDisU(m, **gridprops)
     bas = flopy.modflow.ModflowBas(m)
-    lpf = flopy.modflow.ModflowLpf(m)
+    lpf = flopy.mfusg.MfUsgLpf(m)
     chd = flopy.modflow.ModflowChd(m, stress_period_data=chdspd)
-    sms = flopy.modflow.ModflowSms(m)
+    sms = flopy.mfusg.MfUsgSms(m)
     oc = flopy.modflow.ModflowOc(m, stress_period_data={(0, 0): ["save head"]})
     m.write_input()
 
@@ -457,12 +456,14 @@ 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.modflow.ModflowLpf(m, novfc=True, nocvcorrection=True)
+        lpf = flopy.mfusg.MfUsgLpf(
+            m, novfc=True, nocvcorrection=True
+        )
         m.write_input()
         m.run_model()
 
         # also test load of unstructured LPF with keywords
-        lpf2 = flopy.modflow.ModflowLpf.load(
+        lpf2 = flopy.mfusg.MfUsgLpf.load(
             os.path.join(ws, f"{name}.lpf"), m, check=False
         )
         msg = "NOCVCORRECTION and NOVFC should be in lpf options but at least one is not."