move to autoapi for docs

ruff format/check

docs/03examples/line-sink-ditch.ipynb

@@ -37,7 +37,7 @@
     "ml = ttim.ModelMaq(kaq=10, z=[10, 0], Saq=1e-4, tmin=0.01, tmax=10)\n",
     "x = np.linspace(-100, 100, 21)\n",
     "y = np.zeros(len(x))\n",
-    "lsd = ttim.LineSinkDitchString(ml, xy=list(zip(x, y)), tsandQ=[(0, 100)])\n",
+    "lsd = ttim.LineSinkDitchString(ml, xy=list(zip(x, y, strict=False)), tsandQ=[(0, 100)])\n",
     "ml.solve()"
    ]
   },
@@ -114,7 +114,9 @@
     "ml = ttim.ModelMaq(kaq=10, z=[10, 0], Saq=1e-4, tmin=0.01, tmax=10)\n",
     "x = np.linspace(-100, 100, 21)\n",
     "y = np.zeros(len(x))\n",
-    "lsd = ttim.LineSinkDitchString(ml, xy=list(zip(x, y)), tsandQ=[(0, 100)], Astorage=100)\n",
+    "lsd = ttim.LineSinkDitchString(\n",
+    "    ml, xy=list(zip(x, y, strict=False)), tsandQ=[(0, 100)], Astorage=100\n",
+    ")\n",
     "ml.solve()"
    ]
   },

docs/03examples/line_sink_well_sol.ipynb

@@ -77,7 +77,7 @@
     "yls = [-500, -300, -200, -100, -50, 0, 50, 100, 200, 300, 500]\n",
     "xls = 50 * np.ones(len(yls))\n",
     "ls1 = ttim.HeadLineSinkString(\n",
-    "    ml, list(zip(xls, yls)), tsandh=\"fixed\", layers=0, label=\"river\"\n",
+    "    ml, list(zip(xls, yls, strict=False)), tsandh=\"fixed\", layers=0, label=\"river\"\n",
     ")\n",
     "ml.solve()\n",
     "ml.xsection(x1=-200, x2=200, npoints=100, t=100, layers=[0, 1, 2], sstart=-200)"
@@ -227,7 +227,7 @@
     "yls = [-500, -300, -200, -100, -50, 0, 50, 100, 200, 300, 500]\n",
     "xls = 50 * np.ones(len(yls))\n",
     "ls1 = ttim.HeadLineSinkString(\n",
-    "    ml, list(zip(xls, yls)), tsandh=\"fixed\", layers=0, label=\"river\"\n",
+    "    ml, list(zip(xls, yls, strict=False)), tsandh=\"fixed\", layers=0, label=\"river\"\n",
     ")\n",
     "ml.solve()\n",
     "\n",

docs/03examples/well_near_river_or_wall.ipynb

@@ -103,7 +103,9 @@
     "    w = ttim.Well(ml2, 0, 0, rw=0.3, tsandQ=[(0, 1000)])\n",
     "    yls = np.arange(ystart, -ystart + 1, 20)\n",
     "    xls = 50 * np.ones(len(yls))\n",
-    "    lss = ttim.HeadLineSinkString(ml2, xy=list(zip(xls, yls)), tsandh=\"fixed\")\n",
+    "    lss = ttim.HeadLineSinkString(\n",
+    "        ml2, xy=list(zip(xls, yls, strict=False)), tsandh=\"fixed\"\n",
+    "    )\n",
     "    ml2.solve()\n",
     "    h2 = ml2.head(20, 0, t)\n",
     "    plt.plot(t, h2[0], \"--\", label=f\"line-sink string from {ystart} to {-ystart}\")\n",
@@ -199,7 +201,9 @@
     "    w = ttim.Well(ml2, 0, 0, rw=0.3, tsandQ=[(0, 1000)])\n",
     "    yls = np.arange(ystart, -ystart + 1, 20)\n",
     "    xls = 50 * np.ones(len(yls))\n",
-    "    lss = ttim.LeakyLineDoubletString(ml2, xy=list(zip(xls, yls)), res=\"imp\")\n",
+    "    lss = ttim.LeakyLineDoubletString(\n",
+    "        ml2, xy=list(zip(xls, yls, strict=False)), res=\"imp\"\n",
+    "    )\n",
     "    ml2.solve()\n",
     "    h2 = ml2.head(20, 0, t)\n",
     "    plt.plot(t, h2[0], \"--\", label=f\"line-doublet string from {ystart} to {-ystart}\")\n",

docs/04pumpingtests/confined1_oude_korendijk.ipynb

@@ -1614,7 +1614,9 @@
     "]\n",
     "\n",
     "# Looping through all calibration objects and fetching the desired values\n",
-    "for calib, w_sto, obs_dts in zip([ca1, ca2, ca, ca3, ca4, ca0], w_storage, obs_dataset):\n",
+    "for calib, w_sto, obs_dts in zip(\n",
+    "    [ca1, ca2, ca, ca3, ca4, ca0], w_storage, obs_dataset, strict=False\n",
+    "):\n",
     "    p = (\n",
     "        calib.parameters\n",
     "    )  # Accessing the parameters Dataframe inside the Calibrate object\n",

docs/conf.py

@@ -15,7 +15,8 @@
 
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.autosummary",
+    "autoapi.extension",
+    # "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
     "sphinx.ext.doctest",
     # "sphinx.ext.intersphinx",
@@ -77,18 +78,22 @@
 
 autodoc_typehints = "description"
 autodoc_typehints_format = "short"
+# autosummary_generate = True
+# autoclass_content = "class"
+autosectionlabel_prefix_document = True
 
-autosummary_generate = True
-
-autoclass_content = "class"
+# -- AutoAPI settings -----------------------------------------------------------------
 
-autosectionlabel_prefix_document = True
+autoapi_dirs = ["../ttim"]
+autoapi_root = "05api"
 
 # -- Numpydoc settings ----------------------------------------------------------------
 
 numpydoc_class_members_toctree = True
 numpydoc_show_class_members = False
 
+# -- Intersphinx settings -------------------------------------------------------------
+
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
     "numpy": ("https://numpy.org/devdocs", None),

examples/linesinkex.py

@@ -18,7 +18,7 @@
     f2py=False,
 )
 ls1 = ttim.HeadLineSinkString(
-    ml1, list(zip(xls, yls)), tsandh=[(0, 2)], layers=0, label="river"
+    ml1, list(zip(xls, yls, strict=False)), tsandh=[(0, 2)], layers=0, label="river"
 )
 ml1.solve()
 
@@ -35,7 +35,7 @@
     f2py=True,
 )
 ls2 = ttim.HeadLineSinkString(
-    ml2, list(zip(xls, yls)), tsandh=[(0, 2)], layers=0, label="river"
+    ml2, list(zip(xls, yls, strict=False)), tsandh=[(0, 2)], layers=0, label="river"
 )
 ml2.solve()
 

pyproject.toml

@@ -14,15 +14,8 @@ maintainers = [
     { name = "Mark Bakker", email = "[email protected]" },
     { name = "Davíd Brakenhoff", email = "[email protected]" },
 ]
-requires-python = ">= 3.8"
-dependencies = [
-    "numpy>=1.17",
-    "scipy>=1.5",
-    "numba>=0.5",
-    "matplotlib>=3.1",
-    "lmfit>=1.0",
-    "pandas>=1.1",
-]
+requires-python = ">= 3.10"
+dependencies = ["numpy", "scipy", "numba", "matplotlib", "lmfit", "pandas"]
 
 keywords = ["hydrology", "groundwater", "model", "analytic element method"]
 classifiers = [
@@ -54,12 +47,13 @@ documentation = "http://mbakker7.github.io/ttim/docs/builddocs/html/index.html"
 ci = ["pytest>=4.6", "pytest-cov", "jupyter>=1.0.0", "shapely", "flake8", "coveralls"]
 docs = [
     "ttim[ci]",
-    "sphinx>=3.1, <6.0",
+    "sphinx",
     "sphinx-design",
     "pydata-sphinx-theme",
     "numpydoc",
     "myst_nb",
     "sphinxcontrib-bibtex",
+    "sphinx-autoapi",
 ]
 
 [tool.setuptools]

ttim/linedoublet.py

@@ -320,7 +320,7 @@ def __init__(
         self.model.addelement(self)
 
     def __repr__(self):
-        return self.name + " with nodes " + str(zip(self.x, self.y))
+        return self.name + " with nodes " + str(zip(self.x, self.y, strict=False))
 
     def initialize(self):
         for ld in self.ldlist:

ttim/linesink.py

@@ -351,7 +351,7 @@ def __init__(
         self.lslist = []
 
     def __repr__(self):
-        return self.name + " with nodes " + str(zip(self.x, self.y))
+        return self.name + " with nodes " + str(zip(self.x, self.y, strict=False))
 
     def initialize(self):
         self.ncp = self.nls