fix(numpy): aliases of builtin types is deprecated as of numpy 1.20 (#…

…1052)

* fix(numpy): aliases of builtin types is deprecated as of numpy 1.20
* black

autotest/t018_test.py

@@ -26,7 +26,7 @@ def test_tpl_constant():
     mfpackage = 'lpf'
     partype = 'hk'
     parname = 'HK_LAYER_1'
-    idx = np.empty((nlay, nrow, ncol), dtype=np.bool)
+    idx = np.empty((nlay, nrow, ncol), dtype=bool)
     idx[0] = True
     idx[1:] = False
 

autotest/t020_test.py

@@ -9,7 +9,7 @@
 
 
 def analyticalWaterTableSolution(h1, h2, z, R, K, L, x):
-    h = np.zeros((x.shape[0]), np.float)
+    h = np.zeros((x.shape[0]), float)
     b1 = h1 - z
     b2 = h2 - z
     h = np.sqrt(b1 ** 2 - (x / L) * (b1 ** 2 - b2 ** 2) + (R * x / K) * (L - x)) + z
@@ -46,10 +46,10 @@ def test_mfnwt_run():
     h2 = 11.
 
     # ibound
-    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)
+    ibound = np.ones((nlay, nrow, ncol), dtype=int)
 
     # starting heads
-    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)
+    strt = np.zeros((nlay, nrow, ncol), dtype=float)
     strt[0, 0, 0] = h1
     strt[0, 0, -1] = h2
 

autotest/t031_test.py

@@ -55,17 +55,17 @@ def test_mpsim():
     node_data = np.array(
         [(3, 12, 12, 'well1', 'skin', -1, 0, 0, 0, 1., 2., 5., 6.2),
          (4, 12, 12, 'well1', 'skin', -1, 0, 0, 0, 0.5, 2., 5., 6.2)],
-        dtype=[('k', np.int), ('i', np.int), ('j', np.int),
-               ('wellid', np.object), ('losstype', np.object),
-               ('pumploc', np.int), ('qlimit', np.int),
-               ('ppflag', np.int), ('pumpcap', np.int),
-               ('rw', np.float), ('rskin', np.float),
-               ('kskin', np.float), ('zpump', np.float)]).view(np.recarray)
+        dtype=[('k', int), ('i', int), ('j', int),
+               ('wellid', object), ('losstype', object),
+               ('pumploc', int), ('qlimit', int),
+               ('ppflag', int), ('pumpcap', int),
+               ('rw', float), ('rskin', float),
+               ('kskin', float), ('zpump', float)]).view(np.recarray)
 
     stress_period_data = {0: np.array([(0, 'well1', -150000.0)],
-                                      dtype=[('per', np.int),
-                                             ('wellid', np.object),
-                                             ('qdes', np.float)])}
+                                      dtype=[('per', int),
+                                             ('wellid', object),
+                                             ('qdes', float)])}
     m.remove_package('WEL')
     mnw2 = flopy.modflow.ModflowMnw2(model=m, mnwmax=1,
                                      node_data=node_data,

autotest/t032_test.py

@@ -48,7 +48,7 @@ def test_polygon_from_ij():
                          (0, 7, 8, .3, True, 's2')],
                         dtype=[('k', '<i8'), ('i', '<i8'), ('j', '<i8'),
                                ('stuff', '<f4'), ('stuf', '|b1'),
-                               ('stf', np.object)]).view(np.recarray)
+                               ('stf', object)]).view(np.recarray)
 
     # vertices for a model cell
     geoms = [Polygon(m.modelgrid.get_cell_vertices(i, j)) for i, j in

autotest/t039_test.py

@@ -61,9 +61,9 @@ def read_zonebudget_file(fname):
         vals = [float(i) for i in items[1:-1]]
         row = (totim, kstp, kper, record,) + tuple(v for v in vals)
         rows.append(row)
-    dtype_list = [('totim', np.float),
-                  ('time_step', np.int),
-                  ('stress_period', np.int),
+    dtype_list = [('totim', float),
+                  ('time_step', int),
+                  ('stress_period', int),
                   ('name', '<U50')] + [(z, '<f8') for z in zonenames]
     dtype = np.dtype(dtype_list)
     return np.array(rows, dtype=dtype)
@@ -120,7 +120,7 @@ def test_compare2zonebudget(rtol=1e-2):
 #     mflistrecs = mflistbud.get_data(idx=-1, incremental=True)
 #     print(repr(mflistrecs))
 #
-#     zon = np.ones((3, 40, 20), dtype=np.int)
+#     zon = np.ones((3, 40, 20), dtype=int)
 #     cbc_fname = os.path.join(loadpth, 'freyberg.cbc')
 #     kstp, kper = CellBudgetFile(cbc_fname).get_kstpkper()[-1]
 #     zb = ZoneBudget(cbc_fname, zon, kstpkper=(kstp, kper))

autotest/t040_test.py

@@ -97,7 +97,7 @@ def test_subwt():
                              vka=[0.4, 0.4, 0.01, 0.4],
                              sy=0.3, ss=1.0e-6)
 
-    # temp_ib = np.ones((ml.nrow,ml.ncol),dtype=np.int)
+    # temp_ib = np.ones((ml.nrow,ml.ncol),dtype=int)
     # np.savetxt('temp_ib.dat',temp_ib,fmt='%1d')
     ibound = np.loadtxt(ibound_path)
     ibound[ibound == 5] = -1

autotest/t041_test.py

@@ -34,7 +34,7 @@ def test_hob_simple():
     nlay, nrow, ncol = 1, 11, 11
     shape3d = (nlay, nrow, ncol)
     shape2d = (nrow, ncol)
-    ib = np.ones(shape3d, dtype=np.int)
+    ib = np.ones(shape3d, dtype=int)
     ib[0, 0, 0] = -1
     m = flopy.modflow.Modflow(modelname=modelname, model_ws=pth,
                               verbose=False, exe_name=exe_name, )

autotest/t047_test.py

@@ -20,7 +20,7 @@ def get_namefile_entries(fpth):
     except:
         print('could not open...{}'.format(fpth))
         return None
-    dtype = [('ftype', '|S12'), ('unit', np.int),
+    dtype = [('ftype', '|S12'), ('unit', int),
              ('filename', '|S128'), ('status', '|S10')]
     lines = f.readlines()
     data = []

autotest/t051_test.py

@@ -50,7 +50,7 @@ def test_mfcbc():
     ml = flopy.modflow.Modflow(modelname='t1', model_ws=cpth, verbose=True)
     dis = flopy.modflow.ModflowDis(ml, nlay=nlay, nrow=nrow, ncol=ncol, top=0,
                                    botm=[-1., -2., -3.])
-    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)
+    ibound = np.ones((nlay, nrow, ncol), dtype=int)
     ibound[0, 1, 1] = 0
     ibound[0, 0, -1] = -1
     bas = flopy.modflow.ModflowBas(ml, ibound=ibound)

autotest/t052_test.py

@@ -33,7 +33,7 @@ def test_binary_well():
                                exe_name=exe_name)
     dis = flopy.modflow.ModflowDis(ml, nlay=nlay, nrow=nrow, ncol=ncol, top=0,
                                    botm=[-1., -2., -3.])
-    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)
+    ibound = np.ones((nlay, nrow, ncol), dtype=int)
     ibound[0, 1, 1] = 0
     ibound[0, 0, -1] = -1
     bas = flopy.modflow.ModflowBas(ml, ibound=ibound)

autotest/t063_test_lgrutil.py

@@ -18,7 +18,7 @@ def test_lgrutil():
     delcp = 100.
     topp = 100.
     botmp = [-100, -200, -300, -400, -500]
-    idomainp = np.ones((nlayp, nrowp, ncolp), dtype=np.int)
+    idomainp = np.ones((nlayp, nrowp, ncolp), dtype=int)
     idomainp[0:2, 1:4, 1:4] = 0
     ncpp = 3
     ncppl = [1, 1, 0, 0, 0]

autotest/t065_test_gridintersect.py

@@ -51,8 +51,8 @@ def get_tri_grid(angrot=0., xyoffset=0., triangle_exe=None):
 
 
 def get_rect_grid(angrot=0., xyoffset=0., top=None, botm=None):
-    delc = 10 * np.ones(2, dtype=np.float)
-    delr = 10 * np.ones(2, dtype=np.float)
+    delc = 10 * np.ones(2, dtype=float)
+    delr = 10 * np.ones(2, dtype=float)
     sgr = fgrid.StructuredGrid(
         delc, delr, top=top, botm=botm, xoff=xyoffset, yoff=xyoffset,
         angrot=angrot)

autotest/t068_test_ssm.py

@@ -18,10 +18,10 @@
 def test_mt3d_ssm_with_nodata_in_1st_sp():
 
     nlay, nrow, ncol = 3, 5, 5
-    perlen = np.zeros((10), dtype=np.float) + 10
+    perlen = np.zeros((10), dtype=float) + 10
     nper = len(perlen)
 
-    ibound = np.ones((nlay,nrow,ncol), dtype=np.int)
+    ibound = np.ones((nlay,nrow,ncol), dtype=int)
 
     botm = np.arange(-1,-4,-1)
     top = 0.

autotest/t075_ugridtests.py

@@ -56,7 +56,7 @@ def test_unstructured_minimal_grid():
     g = UnstructuredGrid(
         vertices=vertices, iverts=iverts, xcenters=xcenters, ycenters=ycenters
     )
-    assert np.allclose(g.ncpl, np.array([2], dtype=np.int))
+    assert np.allclose(g.ncpl, np.array([2], dtype=int))
     assert g.nlay == 1
     assert g.nnodes == 2
     assert g.is_valid
@@ -117,7 +117,7 @@ def test_unstructured_complete_grid():
         top=top,
         botm=botm,
     )
-    assert np.allclose(g.ncpl, np.array([1, 1], dtype=np.int))
+    assert np.allclose(g.ncpl, np.array([1, 1], dtype=int))
     assert g.nlay == 2
     assert g.nnodes == 2
     assert g.is_valid

autotest/t505_test.py

@@ -870,7 +870,7 @@ def test021_twri():
     )
 
     # build stress_period_data for drn package
-    conc = np.ones((15, 15), dtype=np.float) * 35.0
+    conc = np.ones((15, 15), dtype=float) * 35.0
     auxdata = {0: [6, conc]}
 
     stress_period_data = []

examples/Notebooks/flopy3_MT3DMS_examples.ipynb

@@ -111,10 +111,10 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[0, 0, 0] = -1\n",
     "    ibound[0, 0, -1] = -1\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    h1 = q * Lx\n",
     "    strt[0, 0, 0] = h1\n",
     "    bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)\n",
@@ -128,9 +128,9 @@
     "    mt = flopy.mt3d.Mt3dms(modelname=modelname_mt, model_ws=model_ws, \n",
     "                           exe_name=exe_name_mt, modflowmodel=mf)\n",
     "    c0 = 1.\n",
-    "    icbund = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    icbund = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    icbund[0, 0, 0] = -1\n",
-    "    sconc = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    sconc = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    sconc[0, 0, 0] = c0\n",
     "    btn = flopy.mt3d.Mt3dBtn(mt, icbund=icbund, prsity=prsity, sconc=sconc)\n",
     "    dceps = 1.e-5\n",
@@ -358,10 +358,10 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[0, 0, 0] = -1\n",
     "    ibound[0, 0, -1] = -1\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    h1 = q * Lx\n",
     "    strt[0, 0, 0] = h1\n",
     "    bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)\n",
@@ -580,10 +580,10 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[0, :, 0] = -1\n",
     "    ibound[0, :, -1] = -1\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    h1 = q * Lx\n",
     "    strt[0, :, 0] = h1\n",
     "    bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)\n",
@@ -761,7 +761,7 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int) * -1\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int) * -1\n",
     "    ibound[:, 1:nrow - 1, 1:ncol-1] = 1\n",
     "\n",
     "    # set strt as a linear gradient at a 45 degree angle\n",
@@ -995,7 +995,7 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int) * -1\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int) * -1\n",
     "    ibound[:, 1:nrow - 1, 1:ncol-1] = 1\n",
     "    strt = 0.\n",
     "\n",
@@ -1183,7 +1183,7 @@
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   nper=2, perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int) * -1\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int) * -1\n",
     "    ibound[:, 1:nrow - 1, 1:ncol-1] = 1\n",
     "    strt = 0.\n",
     "\n",
@@ -1337,10 +1337,10 @@
     "                                   delr=delr, delc=delc, top=0., \n",
     "                                   botm=[-delv * k for k in range(1, nlay + 1)],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[:, :, 0] = -1\n",
     "    ibound[:, :, -1] = -1\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    h1 = q * Lx\n",
     "    strt[:, :, 0] = h1\n",
     "    bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)\n",
@@ -1487,7 +1487,7 @@
     "\n",
     "    k1 = 5e-4 / 100. * 86400 # m/d\n",
     "    k2 = 1e-2 / 100. * 86400 # m/d\n",
-    "    hk = k1 * np.ones((nlay, nrow, ncol), dtype=np.float)\n",
+    "    hk = k1 * np.ones((nlay, nrow, ncol), dtype=float)\n",
     "    hk[11:19, :, 0:24] = k2\n",
     "    hk[11:19, :, 36:] = k2\n",
     "    laytyp = 6 * [1] + 21 * [0]\n",
@@ -1500,10 +1500,10 @@
     "                                   botm=[6.75 - delv * k for k in range(1, nlay + 1)],\n",
     "                                   perlen=perlen_mf)\n",
     "    f = open(os.path.join(datadir, 'p08shead.dat'))\n",
-    "    strt = np.empty((nlay * ncol), dtype=np.float)\n",
+    "    strt = np.empty((nlay * ncol), dtype=float)\n",
     "    strt = read1d(f, strt).reshape((nlay, nrow, ncol))\n",
     "    f.close()\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[5:, :, -1] = -1\n",
     "    ibound[strt < 0] = 0\n",
     "\n",
@@ -1537,7 +1537,7 @@
     "                             nlsink=nlsink, npsink=npsink, percel=percel, \n",
     "                             itrack=itrack, wd=wd)\n",
     "    dsp = flopy.mt3d.Mt3dDsp(mt, al=al, trpt=trpt, trpv=trpv, dmcoef=dmcoef)\n",
-    "    crch1 = np.zeros((nrow, ncol), dtype=np.float)\n",
+    "    crch1 = np.zeros((nrow, ncol), dtype=float)\n",
     "    crch1[0, 9:18] = 1.\n",
     "    cnc0 = [(0, 0, j, 1, -1) for j in range(8, 16)]\n",
     "    cnc1 = [(0, 0, j, 0., -1) for j in range(8, 16)]\n",
@@ -1662,18 +1662,18 @@
     "    laytyp = 0\n",
     "    k1 = 1.474e-4\n",
     "    k2 = 1.474e-7\n",
-    "    hk = k1 * np.ones((nlay, nrow, ncol), dtype=np.float)\n",
+    "    hk = k1 * np.ones((nlay, nrow, ncol), dtype=float)\n",
     "    hk[:, 5:8, 1:8] = k2\n",
     "\n",
     "    modelname_mf = dirname + '_mf'\n",
     "    mf = flopy.modflow.Modflow(modelname=modelname_mf, model_ws=model_ws, exe_name=exe_name_mf)\n",
     "    dis = flopy.modflow.ModflowDis(mf, nlay=nlay, nrow=nrow, ncol=ncol,\n",
     "                                   delr=delr, delc=delc, top=0., botm=[0 - delv],\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "    ibound[0, 0, :] = -1\n",
     "    ibound[0, -1, :] = -1\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    strt[0, 0, :] = 250.\n",
     "    xc = dis.sr.xcenter\n",
     "    for j in range(ncol):\n",
@@ -1898,7 +1898,7 @@
     "                                   delr=delr, delc=delc, top=top, \n",
     "                                   botm=botm,\n",
     "                                   perlen=perlen_mf)\n",
-    "    ibound = np.ones((nlay, nrow, ncol), dtype=np.int)\n",
+    "    ibound = np.ones((nlay, nrow, ncol), dtype=int)\n",
     "\n",
     "    # left side\n",
     "    ibound[:, :, 0] = -1\n",
@@ -1910,10 +1910,10 @@
     "    ibound[:, -1, :] = -1\n",
     "\n",
     "    f = open(os.path.join(datadir, 'p10shead.dat'))\n",
-    "    s0 = np.empty((nrow * ncol), dtype=np.float)\n",
+    "    s0 = np.empty((nrow * ncol), dtype=float)\n",
     "    s0 = read1d(f, s0).reshape((nrow, ncol))\n",
     "    f.close()\n",
-    "    strt = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    strt = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    for k in range(nlay):\n",
     "        strt[k] = s0\n",
     "    bas = flopy.modflow.ModflowBas(mf, ibound=ibound, strt=strt)\n",
@@ -1940,10 +1940,10 @@
     "    mt = flopy.mt3d.Mt3dms(modelname=modelname_mt, model_ws=model_ws, \n",
     "                           exe_name=exe_name_mt, modflowmodel=mf)\n",
     "    f = open(os.path.join(datadir, 'p10cinit.dat'))\n",
-    "    c0 = np.empty((nrow * ncol), dtype=np.float)\n",
+    "    c0 = np.empty((nrow * ncol), dtype=float)\n",
     "    c0 = read1d(f, c0).reshape((nrow, ncol))\n",
     "    f.close()\n",
-    "    sconc = np.zeros((nlay, nrow, ncol), dtype=np.float)\n",
+    "    sconc = np.zeros((nlay, nrow, ncol), dtype=float)\n",
     "    sconc[1] = 0.2 * c0\n",
     "    sconc[2] = c0\n",
     "    obs = [[3 - 1, 11 - 1, 29 - 1],\n",

examples/Notebooks/flopy3_PEST.ipynb

@@ -84,7 +84,7 @@
     "mfpackage = 'lpf'\n",
     "partype = 'hk'\n",
     "parname = 'HK_LAYER_1'\n",
-    "idx = np.empty((nlay, nrow, ncol), dtype=np.bool)\n",
+    "idx = np.empty((nlay, nrow, ncol), dtype=bool)\n",
     "idx[0] = True\n",
     "idx[1:] = False\n",
     "\n",
@@ -674,7 +674,7 @@
     "transform = None\n",
     "\n",
     "# For a recharge index parameter, span['idx'] must be a boolean array or tuple of array indices\n",
-    "idx = np.empty((nrow, ncol), dtype=np.bool)\n",
+    "idx = np.empty((nrow, ncol), dtype=bool)\n",
     "idx[0:3, 0:3] = True\n",
     "span = {'kpers': [1], 'idx': idx}\n",
     "p = flopy.pest.Params(mfpackage, partype, parname, startvalue,\n",