Ruff formatting + checks (#116)

* Ruff formatting + checks - add ruff ruff settings to pyproject.toml - use ruff gh actions - add python 3.12, remove python 3.8 - fix most ruff issues in code base (see pyproject.toml for ignore list). * Use ruff to format and lint (#114) * Use ruff to format and lint, fix all issues that came up. * Git blame: ignore ruff style changes * Looks like ruff trivialized test_import * Do not exclude examples from ruff * Remove unused computation in StripAreaSink.changetrace * Add ruff format --check in linting step * Also format the examples * Add examples ruff format to git-blame-ignore * more ruff after merge * this file shouldnt be in this PR. * speed up building docs using autoapi * formatting * more formatting --------- Co-authored-by: Huite <huitebootsma@gmail.com>
mbakker7 · Sep 26, 2024 · 202b5b6 · 202b5b6
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,2 +1,6 @@
 # Migrate code style to black
-998b86fc128e35f1506e3d4facb169c558679bde
+998b86fc128e35f1506e3d4facb169c558679bde
+
+# Migrate code style to ruff
+a11f92ff2732d7fdc548559f15f009e4a3d5ea7a
+571e4b5af45bd1ca6f025dd883b9ea800acb4aef
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,12 +16,12 @@ 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 }}
 
@@ -30,13 +30,14 @@ 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: |
           py.test ./tests

diff --git a/docs/00tutorials/tutorial0_well_single_layer_aquifer.ipynb b/docs/00tutorials/tutorial0_well_single_layer_aquifer.ipynb
@@ -30,6 +30,7 @@
    "outputs": [],
    "source": [
     "import numpy as np  # import numpy package\n",
+    "\n",
     "import timml as tml  # import timml package"
    ]
   },

diff --git a/docs/00tutorials/tutorial1_well_multi_layer_aquifer.ipynb b/docs/00tutorials/tutorial1_well_multi_layer_aquifer.ipynb
@@ -45,7 +45,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
+    "\n",
     "import timml as tml"
    ]
   },

diff --git a/docs/03examples/BuildingPit.ipynb b/docs/03examples/BuildingPit.ipynb
@@ -14,8 +14,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import timml as tml"
    ]
   },
@@ -59,8 +60,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "l = 40.0  # length building pit in m\n",
-    "b = 30.0  # width building pit in m\n",
+    "length = 40.0  # length building pit in m\n",
+    "width = 30.0  # width building pit in m\n",
     "\n",
     "h_bem = -6.21  # m\n",
     "offset = 5.0  # distance groundwater extraction element from sheetpiles in m"
@@ -73,11 +74,11 @@
    "outputs": [],
    "source": [
     "xy = [\n",
-    "    (-l / 2, -b / 2),\n",
-    "    (l / 2, -b / 2),\n",
-    "    (l / 2, b / 2),\n",
-    "    (-l / 2, b / 2),\n",
-    "    (-l / 2, -b / 2),\n",
+    "    (-length / 2, -width / 2),\n",
+    "    (length / 2, -width / 2),\n",
+    "    (length / 2, width / 2),\n",
+    "    (-length / 2, width / 2),\n",
+    "    (-length / 2, -width / 2),\n",
     "]"
    ]
   },
@@ -211,28 +212,28 @@
     "\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
-    "    y1=b / 2 - offset,\n",
-    "    x2=l / 2 - offset,\n",
-    "    y2=b / 2 - offset,\n",
+    "    x1=-length / 2 + offset,\n",
+    "    y1=width / 2 - offset,\n",
+    "    x2=length / 2 - offset,\n",
+    "    y2=width / 2 - offset,\n",
     "    hls=h_bem,\n",
     "    layers=np.arange(last_lay_dw + 1),\n",
     ")\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
+    "    x1=-length / 2 + offset,\n",
     "    y1=0,\n",
-    "    x2=l / 2 - offset,\n",
+    "    x2=length / 2 - offset,\n",
     "    y2=0,\n",
     "    hls=h_bem,\n",
     "    layers=np.arange(last_lay_dw + 1),\n",
     ")\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
-    "    y1=-b / 2 + offset,\n",
-    "    x2=l / 2 - offset,\n",
-    "    y2=-b / 2 + offset,\n",
+    "    x1=-length / 2 + offset,\n",
+    "    y1=-width / 2 + offset,\n",
+    "    x2=length / 2 - offset,\n",
+    "    y2=-width / 2 + offset,\n",
     "    hls=h_bem,\n",
     "    layers=np.arange(last_lay_dw + 1),\n",
     ")\n",
@@ -248,7 +249,7 @@
     "\n",
     "print(\"\\nDischarge =\", np.round(Qtot.sum(), 2), \"m^3/dag\")\n",
     "\n",
-    "y = np.linspace(-b / 2 - 25, b / 2 + 1100, 201)\n",
+    "y = np.linspace(-width / 2 - 25, width / 2 + 1100, 201)\n",
     "hl = ml.headalongline(np.zeros(201), y, layers=[0])\n",
     "y_5cm = np.interp(\n",
     "    -0.05, ml.headalongline(np.zeros(201), y, layers=0).squeeze(), y, right=np.nan\n",
@@ -298,7 +299,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x = np.linspace(0.0, l / 2 + 1100, 201)\n",
+    "x = np.linspace(0.0, length / 2 + 1100, 201)\n",
     "hl = ml.headalongline(x, np.zeros(201), layers=[last_lay_dw, last_lay_dw + 1])"
    ]
   },
@@ -337,7 +338,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x = np.linspace(-l / 2 - 25, 0.0, 201)\n",
+    "x = np.linspace(-length / 2 - 25, 0.0, 201)\n",
     "hl = ml.headalongline(x, np.zeros(201), layers=[last_lay_dw, last_lay_dw + 1])"
    ]
   },
@@ -378,7 +379,7 @@
    "source": [
     "xoffset = 50\n",
     "zoffset = 15\n",
-    "x1, x2, y1, y2 = [-l / 2 - xoffset, 0.0, 0, 0]\n",
+    "x1, x2, y1, y2 = [-length / 2 - xoffset, 0.0, 0, 0]\n",
     "nudge = 1e-6\n",
     "n = 301"
    ]
@@ -581,29 +582,29 @@
     "\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
-    "    y1=b / 2 - offset,\n",
-    "    x2=l / 2 - offset,\n",
-    "    y2=b / 2 - offset,\n",
+    "    x1=-length / 2 + offset,\n",
+    "    y1=width / 2 - offset,\n",
+    "    x2=length / 2 - offset,\n",
+    "    y2=width / 2 - offset,\n",
     "    hls=h_bem,\n",
     "    layers=wlayers,\n",
     ")\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
+    "    x1=-length / 2 + offset,\n",
     "    y1=0,\n",
-    "    x2=l / 2 - offset,\n",
+    "    x2=length / 2 - offset,\n",
     "    y2=0,\n",
     "    hls=h_bem,\n",
     "    layers=wlayers,\n",
     "    order=5,\n",
     ")\n",
     "tml.HeadLineSink(\n",
     "    ml,\n",
-    "    x1=-l / 2 + offset,\n",
-    "    y1=-b / 2 + offset,\n",
-    "    x2=l / 2 - offset,\n",
-    "    y2=-b / 2 + offset,\n",
+    "    x1=-length / 2 + offset,\n",
+    "    y1=-width / 2 + offset,\n",
+    "    x2=length / 2 - offset,\n",
+    "    y2=-width / 2 + offset,\n",
     "    hls=h_bem,\n",
     "    layers=wlayers,\n",
     ")\n",
@@ -619,7 +620,7 @@
     "\n",
     "print(\"\\nDischarge =\", np.round(Qtot.sum(), 2), \"m^3/dag\")\n",
     "\n",
-    "y = np.linspace(-b / 2 - 25, b / 2 + 1100, 201)\n",
+    "y = np.linspace(-width / 2 - 25, width / 2 + 1100, 201)\n",
     "hl = ml.headalongline(np.zeros(201), y, layers=[0])\n",
     "y_5cm = np.interp(\n",
     "    -0.05, ml.headalongline(np.zeros(201), y, layers=0).squeeze(), y, right=np.nan\n",
@@ -642,7 +643,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x = np.linspace(0.0, l / 2 + 1100, 201)\n",
+    "x = np.linspace(0.0, length / 2 + 1100, 201)\n",
     "hl = ml.headalongline(x, np.zeros(201), layers=[0, last_lay_dw, last_lay_dw + 1])"
    ]
   },
@@ -682,7 +683,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x = np.linspace(-l / 2 - 25, 0.0, 201)\n",
+    "x = np.linspace(-length / 2 - 25, 0.0, 201)\n",
     "hl = ml.headalongline(x, np.zeros(201), layers=[0, last_lay_dw, last_lay_dw + 1])"
    ]
   },
@@ -724,7 +725,7 @@
    "source": [
     "xoffset = 50\n",
     "zoffset = 15\n",
-    "x1, x2, y1, y2 = [-l / 2 - xoffset, 0.0, 0, 0]\n",
+    "x1, x2, y1, y2 = [-length / 2 - xoffset, 0.0, 0, 0]\n",
     "nudge = 1e-6\n",
     "n = 301"
    ]

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

diff --git a/docs/03examples/circular_buildingpit.ipynb b/docs/03examples/circular_buildingpit.ipynb
@@ -124,6 +124,7 @@
     "    zip(\n",
     "        shapely.get_coordinates(circle)[:, 0],\n",
     "        shapely.get_coordinates(circle)[:, 1],\n",
+    "        strict=False,\n",
     "    )\n",
     ")[::-1]"
    ]

diff --git a/docs/03examples/lake_horizontal_well.ipynb b/docs/03examples/lake_horizontal_well.ipynb
@@ -13,9 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import timml as tml\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "import timml as tml"
    ]
   },
   {

diff --git a/docs/03examples/normal_flux.ipynb b/docs/03examples/normal_flux.ipynb
@@ -21,9 +21,10 @@
    "outputs": [],
    "source": [
     "# import packages\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import timml as tml\n",
-    "import matplotlib.pyplot as plt"
+    "\n",
+    "import timml as tml"
    ]
   },
   {

diff --git a/docs/03examples/test_linesink_discharge.ipynb b/docs/03examples/test_linesink_discharge.ipynb
@@ -13,9 +13,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import timml as tml\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "\n",
+    "import timml as tml"
    ]
   },
   {
@@ -969,7 +970,7 @@
     "    topthick=2,\n",
     "    hstar=7,\n",
     ")\n",
-    "xy = list(zip(np.linspace(-10, 10, 21), np.zeros(21)))\n",
+    "xy = list(zip(np.linspace(-10, 10, 21), np.zeros(21), strict=False))\n",
     "ls = tml.LineSinkDitchString(\n",
     "    ml, xy=xy, Qls=100, wh=2, res=5, order=2, layers=np.arange(10, 30, 1)\n",
     ")\n",

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

diff --git a/docs/03examples/test_well_near_lake.ipynb b/docs/03examples/test_well_near_lake.ipynb
@@ -13,9 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import timml as tml\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "import timml as tml"
    ]
   },
   {

diff --git a/docs/03examples/timml_notebook0_sol.ipynb b/docs/03examples/timml_notebook0_sol.ipynb
@@ -28,14 +28,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# install timml if it is not installed already\n",
-    "try:\n",
-    "    import timml as tml\n",
-    "except:\n",
-    "    !pip install timml\n",
-    "    import timml as tml\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "\n",
+    "import timml as tml"
    ]
   },
   {
@@ -393,7 +389,9 @@
     "w = tml.Well(ml, xw=-400, yw=0, Qw=200, rw=0.2)\n",
     "xls = np.zeros(21)\n",
     "yls = np.linspace(-800, 800, 21)\n",
-    "ls = tml.HeadLineSinkString(ml, xy=list(zip(xls, yls)), hls=40, layers=0, label=\"river\")\n",
+    "ls = tml.HeadLineSinkString(\n",
+    "    ml, xy=list(zip(xls, yls, strict=False)), hls=40, layers=0, label=\"river\"\n",
+    ")\n",
     "ml.solve()\n",
     "ml.contour(\n",
     "    win=[-1000, 100, -500, 500], ngr=50, levels=np.arange(39, 42, 0.1), figsize=(6, 6)\n",

diff --git a/docs/03examples/timml_notebook1_sol.ipynb b/docs/03examples/timml_notebook1_sol.ipynb
@@ -46,9 +46,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import timml as tml\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "import timml as tml\n",
     "\n",
     "figsize = (8, 8)"
    ]

diff --git a/docs/03examples/timml_notebook2_sol.ipynb b/docs/03examples/timml_notebook2_sol.ipynb
@@ -36,9 +36,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import timml as tml\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "import timml as tml\n",
     "\n",
     "figsize = (8, 8)"
    ]