Some minor updates (#109)

* ruff formatting * format notebooks * update nbs * attempt adding level in toc for tutorials * display inline math in notebooks * ruff formatting * format notebooks * update nbs * attempt adding level in toc for tutorials * display inline math in notebooks * up version * update citation
mbakker7 · Feb 13, 2024 · 975a074 · 975a074
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diff --git a/docs/00tutorials/index.rst b/docs/00tutorials/index.rst
@@ -4,7 +4,7 @@ Tutorials
 TimML tutorials.
 
 .. toctree::
-    :maxdepth: 3
+    :maxdepth: 2
     :hidden:
     :glob:
 

diff --git a/docs/00tutorials/tutorial0_well_single_layer_aquifer.ipynb b/docs/00tutorials/tutorial0_well_single_layer_aquifer.ipynb
@@ -4,7 +4,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# TimML Tutorial 0\n",
+    "# TimML Tutorial 0"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Uniform flow to a well in a single layer"
    ]
   },
@@ -225,7 +231,7 @@
     "    decimals=1,  # print labels with 1 decimal place\n",
     "    legend=True,  # add a legend\n",
     "    figsize=(5, 5),  # specify a figure size of 5 by 5 inches\n",
-    ");"
+    ")"
    ]
   },
   {

diff --git a/docs/00tutorials/tutorial1_well_multi_layer_aquifer.ipynb b/docs/00tutorials/tutorial1_well_multi_layer_aquifer.ipynb
@@ -4,7 +4,13 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# TimML Tutorial 1\n",
+    "# TimML Tutorial 1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
     "## Uniform flow to a well in a multi-aquifer system"
    ]
   },
@@ -60,7 +66,7 @@
    "outputs": [],
    "source": [
     "ml = tml.ModelMaq(\n",
-    "    kaq=[10, 20, 5],  # hydraulic conductivity, m/d \n",
+    "    kaq=[10, 20, 5],  # hydraulic conductivity, m/d\n",
     "    z=[0, -20, -40, -80, -90, -140],  # tops and bottoms of aquifers, m\n",
     "    c=[4000, 10000],  # resistance of leaky layers, d\n",
     "    npor=0.3,  # porosity of the aquifers, one value so the same for all aquifers, -\n",
@@ -72,7 +78,7 @@
     "    Qw=10_000,  # discharge of well, positive for extraction, m^3/d\n",
     "    rw=0.2,  # well radius, m\n",
     "    layers=1,  # layer numbere where well is screened (may also be a list)\n",
-    "    label='well 1',\n",
+    "    label=\"well 1\",\n",
     ")\n",
     "tml.Constant(\n",
     "    model=ml,  # model to which element is added\n",
@@ -125,7 +131,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print('leakage factors of model (m)')\n",
+    "print(\"leakage factors of model (m)\")\n",
     "print(ml.aq.lab)"
    ]
   },
@@ -153,7 +159,7 @@
     "ml.contour(\n",
     "    win=[-3000, 3000, -3000, 3000],  # window to contour [xmin, xmax, ymin, ymax]\n",
     "    ngr=50,  # number of points where to compute the head\n",
-    "    layers=[0, 1, 2], # layers to contour\n",
+    "    layers=[0, 1, 2],  # layers to contour\n",
     "    levels=10,  # draw 10 contours in each layer\n",
     "    labels=True,  # add labels along the contours\n",
     "    decimals=1,  # print labels with 1 decimal place\n",
@@ -175,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f'The head at the well is: {w.headinside()} m')"
+    "print(f\"The head at the well is: {w.headinside()} m\")"
    ]
   },
   {
@@ -210,7 +216,7 @@
    "source": [
     "win = [-3000, 3000, -3000, 3000]  # window that is plotted [xmin, xmax, ymin, ymax]\n",
     "ml.plot(\n",
-    "    win=win,  \n",
+    "    win=win,\n",
     "    orientation=\"both\",  # plot both a plan view and a vertical cross-section\n",
     "    figsize=(5, 5),  # specify a figure size of 5 by 5 inches\n",
     ")\n",

diff --git a/docs/03examples/normal_flux.ipynb b/docs/03examples/normal_flux.ipynb
diff --git a/docs/03examples/timml_notebook3_3D_sol.ipynb b/docs/03examples/timml_notebook3_3D_sol.ipynb
@@ -120,7 +120,7 @@
    "source": [
     "ml.contour(\n",
     "    win=[-200, 800, 0, 800], ngr=50, layers=[0, 1], levels=20, labels=1, decimals=2\n",
-    ");"
+    ")"
    ]
   },
   {
@@ -136,7 +136,7 @@
     "    levels=50,\n",
     "    labels=1,\n",
     "    decimals=2,\n",
-    ");"
+    ")"
    ]
   },
   {
@@ -273,7 +273,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ml.contour(win=[-200, 1000, 0, 1200], ngr=50, layers=[0, 1], levels=20);"
+    "ml.contour(win=[-200, 1000, 0, 1200], ngr=50, layers=[0, 1], levels=20)"
    ]
   }
  ],

diff --git a/docs/03examples/timml_notebook4_sol.ipynb b/docs/03examples/timml_notebook4_sol.ipynb
diff --git a/docs/06about/publications.bib b/docs/06about/publications.bib
@@ -20,7 +20,7 @@ @article{bakker_analytic_2006
 	volume = {29},
 	doi = {10.1016/j.advwatres.2005.11.005},
 	abstract = {An analytic element approach is presented for the modeling of steady groundwater flow through multi-aquifer systems with piecewise constant aquifer and leaky layer properties. Different properties may be specified for domains bounded by closed polygons, referred to as polygonal inhomogeneities. The boundary of these inhomogeneities is modeled with two types of high-order line elements. First, a string of single-aquifer line-doublets is used; these elements cut through all aquifers and are valid both inside and outside the inhomogeneity. Second, two strings of multi-aquifer line-sinks are used, one string that is valid inside the inhomogeneity and one string that is valid outside; the comprehensive extraction of these line-sinks is zero at any point along the string. The proposed approach results in a comprehensive flow field of which the component normal to the boundary of the inhomogeneity is continuous across the boundary at any point. Within each individual aquifer, continuity of head and the component of flow normal to the boundary are met approximately across the boundary; the accuracy increases when the order of the line elements is increased and/or when shorter line elements are used. The proposed analytic element approach produces results that are virtually identical to the exact solution for a cylindrical inhomogeneity, and a high-resolution MODFLOW2000 model of two rectangular inhomogeneities with a shared boundary. The practical application of the approach is demonstrated through the solution of a problem with an irregularly shaped inhomogeneity with rivers crossing the inhomogeneity boundary.},
-	journal = {Advances in Water Resources - ADV WATER RESOUR},
+	journal = {Advances in Water Resources},
 	author = {Bakker, Mark},
 	month = oct,
 	year = {2006},

diff --git a/docs/conf.py b/docs/conf.py
@@ -102,6 +102,8 @@
 nb_execution_allow_errors = True  # Allow errors in notebooks, to see the error online
 nb_execution_mode = "auto"
 nb_merge_streams = True
+myst_enable_extensions = ["dollarmath", "amsmath"]
+myst_dmath_double_inline = True
 
 # -- bibtex options ------------------------------------------------------------------
 

diff --git a/timml/aquifer.py b/timml/aquifer.py
@@ -62,8 +62,8 @@ def initialize(self):
         dm1 = -1.0 / (self.c[1:] * self.T[:-1])
         A = np.diag(dm1, -1) + np.diag(d0, 0) + np.diag(dp1, 1)
         w, v = np.linalg.eig(A)
-        # take the real part for the rare occasion that the eig 
-        # function returns a complex answer with very small 
+        # take the real part for the rare occasion that the eig
+        # function returns a complex answer with very small
         # imaginary part
         w = w.real
         v = v.real

diff --git a/timml/stripareasink.py b/timml/stripareasink.py
@@ -8,11 +8,11 @@
 
 
 class StripAreaSinkInhom(Element):
-    """Create a strip area-sink in combination with an inhomogeneity. 
-    
+    """Create a strip area-sink in combination with an inhomogeneity.
+
     Notes
     -----
-    Created automatically using StripInhomMaq or StripInhom3D. 
+    Created automatically using StripInhomMaq or StripInhom3D.
     Can only be created if top boundary is confined.
 
     Parameters

diff --git a/timml/uflow.py b/timml/uflow.py
@@ -8,9 +8,9 @@
 
 
 class Uflow(Element):
-    """Add uniform flow to the model. 
-    
-    Uniform flow may only be added to a model of which the background aquifer system 
+    """Add uniform flow to the model.
+
+    Uniform flow may only be added to a model of which the background aquifer system
     is confined.
 
     Parameters
@@ -28,9 +28,7 @@ class Uflow(Element):
     """
 
     def __init__(self, model, slope, angle, label=None):
-        assert (
-            model.aq.ilap
-        ), "TimML Error: Uflow can only be added to model with background confined aquifer"
+        assert model.aq.ilap, "TimML Error: Uflow can only be added to model with background confined aquifer"
         self.storeinput(inspect.currentframe())
         Element.__init__(
             self, model, nparam=2, nunknowns=0, layers=0, name="Uflow", label=label

diff --git a/timml/version.py b/timml/version.py
@@ -1 +1 @@
-__version__ = "6.4.0"
+__version__ = "6.4.1"