Update Master branch to TTim version 0.7.1

Some bug fixes and minor improvements:
* Add inhomogeneity name to crosssection plot (1D inhom) (#90)
* Added 'names' in plotting of inhom
* Bugfix for old method of selecting layers (#92)
* Specify step for Jacobian (#95)

---------

Co-authored-by: Davíd Brakenhoff <d.brakenhoff@artesia-water.nl>
Co-authored-by: Mattijs Borst <41747007+MattBrst@users.noreply.github.com>

Author: 3 people

docs/03examples/watex_example.ipynb

@@ -364,7 +364,7 @@ def bessells_gauss(x, y, z1, z2, lab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsuni(x, y, z1, z2, lab):
-    """bessellsuni.
+    """Bessellsuni.
 
     # Uniform strength
     implicit none
@@ -402,7 +402,7 @@ def bessellsuni(x, y, z1, z2, lab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsuniv(x, y, z1, z2, lab, rzero):
-    """bessellsuniv.
+    """Bessellsuniv.
 
     # Uniform strength
     implicit none
@@ -513,7 +513,7 @@ def find_d1d2(z1, z2, zc, R):
 
 @numba.njit(nogil=True, cache=True)
 def bessells(x, y, z1, z2, lab, order, d1in, d2in):
-    """bessells.
+    """Bessells.
 
     implicit none
     integer, intent(in) :: order
@@ -783,7 +783,7 @@ def bessellsqxqyv2(x, y, z1, z2, lab, order, R):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsqxqy(x, y, z1, z2, lab, order, d1in, d2in):
-    """bessellsqxqy.
+    """Bessellsqxqy.
 
     implicit none
     integer, intent(in) :: order
@@ -1240,7 +1240,7 @@ def besselldv2(x, y, z1, z2, lab, order, R):
 
 @numba.njit(nogil=True, cache=True)
 def besselld(x, y, z1, z2, lab, order, d1in, d2in):
-    """besselld.
+    """Besselld.
 
     implicit none
     integer, intent(in) :: order
@@ -1495,7 +1495,7 @@ def besselldqxqyv2(x, y, z1, z2, lab, order, R):
 
 @numba.njit(nogil=True, cache=True)
 def besselldqxqy(x, y, z1, z2, lab, order, d1in, d2in):
-    """besselldqxqy.
+    """Besselldqxqy.
 
     implicit none
     integer, intent(in) :: order
@@ -1816,7 +1816,7 @@ def besselld_gauss_ho_qxqy(x, y, z1, z2, lab, order):
 
 @numba.njit(nogil=True, cache=True)
 def besselldpart(x, y, z1, z2, lab, order, d1, d2):
-    """besselldpart.
+    """Besselldpart.
 
     implicit none
     integer, intent(in) :: order

ttim/besselnumba.py

@@ -533,7 +533,7 @@ def lapls_int_ho(x, y, z1, z2, order):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsreal(x, y, x1, y1, x2, y2, lab):
-    """bessellsreal.
+    """Bessellsreal.
 
     implicit none
     real(kind=8), intent(in) :: x,y,x1,y1,x2,y2,lab
@@ -596,7 +596,7 @@ def bessellsreal(x, y, x1, y1, x2, y2, lab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsrealho(x, y, x1, y1, x2, y2, lab, order):
-    """bessellsrealho.
+    """Bessellsrealho.
 
     implicit none
     real(kind=8), intent(in) :: x,y,x1,y1,x2,y2,lab
@@ -1183,7 +1183,7 @@ def bessells_gauss_ho_qxqy_d1d2(x, y, z1, z2, lab, order, d1, d2):
 
 @numba.njit(nogil=True, cache=True)
 def bessells(x, y, z1, z2, lab, order, d1in, d2in):
-    """bessells.
+    """Bessells.
 
     implicit none
     integer, intent(in) :: order
@@ -1229,7 +1229,7 @@ def bessells(x, y, z1, z2, lab, order, d1in, d2in):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsv(x, y, z1, z2, lab, order, R, nlab):
-    """bessellsv.
+    """Bessellsv.
 
     implicit none
     integer, intent(in) :: order
@@ -1278,7 +1278,7 @@ def bessellsv2(x, y, z1, z2, lab, order, R, nlab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsqxqy(x, y, z1, z2, lab, order, d1in, d2in):
-    """bessellsqxqy.
+    """Bessellsqxqy.
 
     implicit none
     integer, intent(in) :: order
@@ -1328,7 +1328,7 @@ def bessellsqxqy(x, y, z1, z2, lab, order, d1in, d2in):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsqxqyv(x, y, z1, z2, lab, order, R, nlab):
-    """bessellsqxqyv.
+    """Bessellsqxqyv.
 
     implicit none
     integer, intent(in) :: order
@@ -1382,7 +1382,7 @@ def bessellsqxqyv2(x, y, z1, z2, lab, order, R, nlab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsuni(x, y, z1, z2, lab):
-    """bessellsuni.
+    """Bessellsuni.
 
     # Uniform strength
     implicit none
@@ -1420,7 +1420,7 @@ def bessellsuni(x, y, z1, z2, lab):
 
 @numba.njit(nogil=True, cache=True)
 def bessellsuniv(x, y, z1, z2, lab, nlab):
-    """bessellsuniv.
+    """Bessellsuniv.
 
     # Uniform strength
     implicit none
@@ -1777,7 +1777,7 @@ def besselld_gauss_ho_d1d2(x, y, z1, z2, lab, order, d1, d2):
 
 @numba.njit(nogil=True, cache=True)
 def besselld(x, y, z1, z2, lab, order, d1in, d2in):
-    """besselld.
+    """Besselld.
 
     implicit none
     integer, intent(in) :: order
@@ -1824,7 +1824,7 @@ def besselld(x, y, z1, z2, lab, order, d1in, d2in):
 
 @numba.njit(nogil=True, cache=True)
 def besselldv(x, y, z1, z2, lab, order, R, nlab):
-    """besselldv.
+    """Besselldv.
 
     implicit none
     integer, intent(in) :: order
@@ -1875,7 +1875,7 @@ def besselldv2(x, y, z1, z2, lab, order, R, nlab):
 
 # @numba.njit(nogil=True, cache=True)
 def besselldpart(x, y, z1, z2, lab, order, d1, d2):
-    """besselldpart.
+    """Besselldpart.
 
     implicit none
     integer, intent(in) :: order
@@ -2256,7 +2256,7 @@ def besselld_gauss_ho_qxqy_d1d2(x, y, z1, z2, lab, order, d1, d2):
 
 # @numba.njit(nogil=True, cache=True)
 def besselldqxqy(x, y, z1, z2, lab, order, d1in, d2in):
-    """besselldqxqy.
+    """Besselldqxqy.
 
     implicit none
     integer, intent(in) :: order
@@ -2308,7 +2308,7 @@ def besselldqxqy(x, y, z1, z2, lab, order, d1in, d2in):
 
 # @numba.njit(nogil=True, cache=True)
 def besselldqxqyv(x, y, z1, z2, lab, order, R, nlab):
-    """besselldqxqyv.
+    """Besselldqxqyv.
 
     implicit none
     integer, intent(in) :: order

ttim/besselnumba_total.py

@@ -198,9 +198,9 @@ def initialize(self):
         self.aqin = self.model.aq.findAquiferData(
             self.x0 + (1 - 1e-8) * self.R, self.y0
         )
-        assert (
-            self.aqin.R == self.R
-        ), "Radius of CircInhom and CircInhomData must be equal"
+        assert self.aqin.R == self.R, (
+            "Radius of CircInhom and CircInhomData must be equal"
+        )
         self.aqout = self.model.aq.find_aquifer_data(
             self.x0 + (1 + 1e-8) * self.R, self.y0
         )

ttim/circinhom.py

@@ -7,8 +7,6 @@
 import pandas as pd
 from scipy.optimize import least_squares, leastsq
 
-# import lmfit
-
 
 class Calibrate:
     def __init__(self, model):
@@ -96,7 +94,7 @@ def set_parameter(
                 from_lay = int(layers_from_name[0])
                 to_lay = from_lay + 1
             elif len(layers_from_name) == 2:
-                from_lay, to_lay = layers_from_name
+                from_lay, to_lay = map(int, layers_from_name)
 
         # get aquifer information and create list if necessary
         if inhoms is None:
@@ -168,9 +166,9 @@ def set_parameter_by_reference(
         """
         assert isinstance(name, str), "Error: name must be string"
         if parameter is not None:
-            assert isinstance(
-                parameter, np.ndarray
-            ), "Error: parameter needs to be numpy array"
+            assert isinstance(parameter, np.ndarray), (
+                "Error: parameter needs to be numpy array"
+            )
             p = parameter
         self.parameters.loc[name] = {
             "optimal": initial,
@@ -311,13 +309,13 @@ def fit_lmfit(self, report=False, printdot=True, **kwargs):
         for name in self.parameters.index:
             p = self.parameters.loc[name]
             self.lmfitparams.add(name, value=p["initial"], min=p["pmin"], max=p["pmax"])
-        # fit_kws = {"epsfcn": 1e-4}
+        fit_kws = {"epsfcn": 1e-4}  # this is essential to specify step for the Jacobian
         self.fitresult = lmfit.minimize(
             self.residuals_lmfit,
             self.lmfitparams,
             method="leastsq",
             kws={"printdot": printdot},
-            # **fit_kws,
+            **fit_kws,
             **kwargs,
         )
         print("", flush=True)

ttim/fit.py

@@ -196,7 +196,7 @@ def create_elements(self):
             )
             HstarXsection(self.model, self.x1, self.x2, tsandhstar=self.tsandhstar)
 
-    def plot(self, ax=None, labels=False, params=False, **kwargs):
+    def plot(self, ax=None, labels=False, params=False, names=False, **kwargs):
         """Plot the cross-section.
 
         Parameters
@@ -207,6 +207,8 @@ def plot(self, ax=None, labels=False, params=False, **kwargs):
             If True, add layer-name labels.
         params : bool, optional
             If True, add parameter labels.
+        names : bool, optional
+            If True, add inhomogeneity names.
         """
         if ax is None:
             _, ax = plt.subplots(1, 1, figsize=(8, 4))
@@ -230,6 +232,17 @@ def plot(self, ax=None, labels=False, params=False, **kwargs):
             lli = None
             aqi = None
 
+        if names:
+            ax.text(
+                r0 + 0.5 * r,
+                0.95,
+                self.name,
+                ha="center",
+                va="center",
+                fontsize=10,
+                transform=ax.get_xaxis_transform(),
+            )
+
         for i in range(self.nlayers):
             if self.ltype[i] == "l":
                 ax.fill_between(

ttim/inhom1d.py

@@ -153,8 +153,7 @@ def xsection(
             if params and self._ml.aq.ltype[i] == "a":
                 if aqi == 0 and self._ml.aq.phreatictop:
                     paramtxt = (
-                        f"$k_h$ = {self._ml.aq.kaq[aqi]}, "
-                        f"$S$ = {self._ml.aq.Saq[aqi]}"
+                        f"$k_h$ = {self._ml.aq.kaq[aqi]}, $S$ = {self._ml.aq.Saq[aqi]}"
                     )
                 else:
                     paramtxt = (

ttim/plots.py

@@ -1,7 +1,7 @@
 from importlib import import_module, metadata
 from platform import python_version
 
-__version__ = "0.7.0"
+__version__ = "0.7.1"
 
 
 def show_versions(optional=True) -> None: