Merge pull request #67 from mbakker7/dev

Release 0.6.7
mbakker7 · Sep 26, 2024 · 66cbb16 · 66cbb16
2 parents 297343e + 31e3ca2
commit 66cbb16
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,2 +1,5 @@
 # Migrate code style to black
-a8aa6904034da74b91f8046e2440ebb4359d63e2
+a8aa6904034da74b91f8046e2440ebb4359d63e2
+
+# Migrate code style to ruff
+c1e21219503158d714f2bc8a582b098ed97852f4
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -17,12 +17,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9, "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -31,12 +31,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e .[ci]
 
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
+      - name: ruff-lint
+        uses: chartboost/ruff-action@v1
+
+      - name: ruff-format
+        uses: chartboost/ruff-action@v1
+        with:
+          args: "format --check"
 
       - name: Run tests
         run: |

diff --git a/docs/01howto/howto_pumpingtest.ipynb b/docs/01howto/howto_pumpingtest.ipynb
@@ -18,8 +18,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim as ttm\n",
     "\n",
     "#\n",
@@ -71,15 +72,17 @@
     "ho1 = -data[:, 1]\n",
     "ro1 = 30\n",
     "print(\n",
-    "    f\"first measurement time: {np.min(to1):.2e}, last measurement time: {np.max(to1):.2e} d\"\n",
+    "    f\"first measurement time: {np.min(to1):.2e}, \"\n",
+    "    f\"last measurement time: {np.max(to1):.2e} d\"\n",
     ")\n",
     "\n",
     "drawdown = np.loadtxt(\"data/oudekorendijk_h90.dat\")\n",
     "to2 = drawdown[:, 0] / 60 / 24\n",
     "ho2 = -drawdown[:, 1]\n",
     "ro2 = 90\n",
     "print(\n",
-    "    f\"first measurement time: {np.min(to2):.2e}, last measurement time: {np.max(to2):.2e} d\"\n",
+    "    f\"first measurement time: {np.min(to2):.2e}, \"\n",
+    "    f\"last measurement time: {np.max(to2):.2e} d\"\n",
     ")\n",
     "\n",
     "plt.plot(to1, ho1, \"C0.\", label=\"r=30 m\")\n",

diff --git a/docs/03examples/aem_ttim_sol.ipynb b/docs/03examples/aem_ttim_sol.ipynb
@@ -7,8 +7,9 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },
@@ -39,14 +40,14 @@
     "        tmin=0.001,\n",
     "        tmax=100,\n",
     "    )\n",
-    "    w = ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
+    "    ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
     "    ml.solve()\n",
     "    t = np.logspace(-2, 1, 100)\n",
     "    h = ml.head(10, 0, t)\n",
     "    plt.figure()\n",
-    "    r = 0.01 * np.random.randn(100)\n",
+    "    r = 0.01 * rnd.random(100)\n",
     "    n = np.zeros_like(r)\n",
-    "    alpha = 0.8\n",
+    "    # alpha = 0.8\n",
     "    for i in range(1, len(n)):\n",
     "        n[i] = 0.8 * n[i - 1] + r[i]\n",
     "    ho = h[0] + n\n",
@@ -83,7 +84,7 @@
     }
    ],
    "source": [
-    "np.random.seed(11)\n",
+    "rnd = np.random.default_rng(11)\n",
     "data = generate_data()\n",
     "to = data[:, 0]\n",
     "ho = data[:, 1]"
@@ -99,7 +100,7 @@
     "    k = p[0]\n",
     "    S = p[1]\n",
     "    ml = ttim.ModelMaq(kaq=k, z=[0, -20], Saq=S, tmin=0.001, tmax=100)\n",
-    "    w = ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
+    "    ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
     "    ml.solve(silent=True)\n",
     "    if returnmodel:\n",
     "        return ml\n",
@@ -283,7 +284,7 @@
     "    ml = ttim.ModelMaq(\n",
     "        kaq=k, z=[2, 0, -20], Saq=S, c=c, topboundary=\"semi\", tmin=0.001, tmax=100\n",
     "    )\n",
-    "    w = ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
+    "    ttim.Well(ml, 0, 0, rw=0.3, tsandQ=[(0, 800)])\n",
     "    ml.solve(silent=True)\n",
     "    if returnmodel:\n",
     "        return ml\n",

diff --git a/docs/03examples/circareasink_example.ipynb b/docs/03examples/circareasink_example.ipynb
@@ -7,8 +7,9 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },

diff --git a/docs/03examples/compare_wells_linesink.ipynb b/docs/03examples/compare_wells_linesink.ipynb
@@ -13,9 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },

diff --git a/docs/03examples/line-sink-ditch.ipynb b/docs/03examples/line-sink-ditch.ipynb
@@ -14,9 +14,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
+    "\n",
     "import ttim"
    ]
   },
@@ -38,7 +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()"
    ]
   },
@@ -115,7 +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()"
    ]
   },

diff --git a/docs/03examples/line_sink_well_sol.ipynb b/docs/03examples/line_sink_well_sol.ipynb
@@ -13,8 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },
@@ -76,7 +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)"
@@ -226,7 +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",

diff --git a/docs/03examples/meandering_river.ipynb b/docs/03examples/meandering_river.ipynb
@@ -13,8 +13,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
     "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },

diff --git a/docs/03examples/pathline_trace.ipynb b/docs/03examples/pathline_trace.ipynb
@@ -13,8 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim as tt"
    ]
   },

diff --git a/docs/03examples/pumpingtest.ipynb b/docs/03examples/pumpingtest.ipynb
@@ -13,10 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
-    "%matplotlib inline\n",
     "import ttim"
    ]
   },

diff --git a/docs/03examples/pumpingtest_hypothetical.ipynb b/docs/03examples/pumpingtest_hypothetical.ipynb
@@ -13,9 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },
@@ -63,8 +63,8 @@
     "ml = ttim.ModelMaq(kaq=60, z=(-18, -25), Saq=1e-4, tmin=1e-5, tmax=1)\n",
     "w = ttim.Well(ml, xw=0, yw=0, rw=0.1, tsandQ=[(0, 788)], layers=0)\n",
     "ml.solve()\n",
-    "np.random.seed(2)\n",
-    "hobs = ml.head(robs, 0, tobs)[0] + 0.05 * np.random.randn(len(tobs))"
+    "rnd = np.random.default_rng(2)\n",
+    "hobs = ml.head(robs, 0, tobs)[0] + 0.05 * rnd.random(len(tobs))"
    ]
   },
   {
@@ -609,8 +609,8 @@
     "ml = ttim.ModelMaq(kaq=60, z=(-18, -25), Saq=1e-4, tmin=1e-5, tmax=1)\n",
     "w = ttim.Well(ml, xw=0, yw=0, rw=0.3, res=0.02, tsandQ=[(0, 788), (0.6, 0)], layers=0)\n",
     "ml.solve()\n",
-    "np.random.seed(2)\n",
-    "hobs2 = w.headinside(tobs2)[0] + 0.05 * np.random.randn(len(tobs2))"
+    "rnd = np.random.default_rng(2)\n",
+    "hobs2 = w.headinside(tobs2)[0] + 0.05 * rnd.random(len(tobs2))"
    ]
   },
   {

diff --git a/docs/03examples/theis_storage.ipynb b/docs/03examples/theis_storage.ipynb
@@ -14,9 +14,8 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "from scipy.special import exp1\n",
-    "from scipy.integrate import solve_ivp, quad"
+    "from scipy.integrate import quad, solve_ivp\n",
+    "from scipy.special import exp1"
    ]
   },
   {

diff --git a/docs/03examples/ttim_exercise1_sol.ipynb b/docs/03examples/ttim_exercise1_sol.ipynb
@@ -13,9 +13,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%matplotlib inline\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import ttim"
    ]
   },