fix ruff errors and remove isort and black

.github/workflows/code-style.yml

@@ -25,13 +25,6 @@ jobs:
           python -m pip install --progress-bar off .[style]
       - name: Run Ruff
         run: ruff check .
-      - name: Run isort
-        uses: isort/isort-action@master
-      - name: Run black
-        uses: psf/black@stable
-        with:
-          options: "--check --verbose"
-          version: "23.10.1"
       - name: Run codespell
         uses: codespell-project/actions-codespell@master
         with:

.github/workflows/pytest.yml

@@ -23,7 +23,7 @@ jobs:
         # some tests fail (numerical issues) in older python on mac, so we ...
         exclude:
           - os: macos
-            python-version: 3.9
+            python-version: '3.9'
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
@@ -36,7 +36,6 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          #architecture: 'x64'
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools wheel

examples/Test_Plot.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# Visualization"
+    "# Visualization"
    ]
   },
   {
@@ -20,8 +20,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy import TriaMesh, TetMesh, Solver, plot, io\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy import Solver, TetMesh, TriaMesh, io, plot\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },

examples/Test_ShapeDNA.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# ShapeDNA"
+    "# ShapeDNA"
    ]
   },
   {
@@ -21,8 +21,7 @@
    "outputs": [],
    "source": [
     "# imports\n",
-    "from lapy import TriaMesh, TetMesh\n",
-    "from lapy import shapedna"
+    "from lapy import TetMesh, TriaMesh, shapedna"
    ]
   },
   {

examples/Test_TetMesh_Geodesics.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# TetMesh Geodesics"
+    "# TetMesh Geodesics"
    ]
   },
   {
@@ -39,11 +39,14 @@
    ],
    "source": [
     "import numpy as np\n",
-    "from lapy import TetMesh\n",
-    "from lapy.plot import plot_tet_mesh\n",
+    "\n",
     "# import plotly\n",
     "# plotly.offline.init_notebook_mode(connected=True)\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy import TetMesh\n",
+    "from lapy.plot import plot_tet_mesh\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },
@@ -116,6 +119,7 @@
    ],
    "source": [
     "from lapy import Solver\n",
+    "\n",
     "fem = Solver(T,lump=True)\n",
     "\n",
     "evals, evec = fem.eigs(10)\n"
@@ -168,8 +172,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy.diffgeo import compute_gradient\n",
-    "from lapy.diffgeo import compute_divergence\n",
+    "from lapy.diffgeo import compute_divergence, compute_gradient\n",
+    "\n",
     "grad = compute_gradient(T,evec[:,evnum])\n",
     "divx = -compute_divergence(T,grad)\n",
     "vfunc = Bi*divx\n"
@@ -299,6 +303,7 @@
    "source": [
     "# compute distance\n",
     "from scipy.sparse.linalg import splu\n",
+    "\n",
     "useCholmod = True\n",
     "try:\n",
     "    from sksparse.cholmod import cholesky\n",
@@ -373,8 +378,8 @@
     }
    ],
    "source": [
-    "from lapy.diffgeo import compute_geodesic_f\n",
     "from lapy import heat\n",
+    "from lapy.diffgeo import compute_geodesic_f\n",
     "\n",
     "tria = T.boundary_tria()\n",
     "bvert=np.unique(tria.t)\n",
@@ -473,7 +478,7 @@
    "version": "3"
   },
   "nbsphinx": {
-    "execute": "always"
+   "execute": "always"
   }
  },
  "nbformat": 4,

examples/Test_TriaMesh.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-     "# Triangle Mesh"
+    "# Triangle Mesh"
    ]
   },
   {
@@ -14,6 +14,7 @@
    "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "from lapy import TriaMesh"
    ]
   },

examples/Test_TriaMesh_Geodesics.ipynb

@@ -86,8 +86,10 @@
     "# import plotting functions\n",
     "# import plotly\n",
     "# plotly.offline.init_notebook_mode(connected=True)\n",
-    "from lapy.plot import plot_tria_mesh\n",
     "import plotly.io as pio\n",
+    "\n",
+    "from lapy.plot import plot_tria_mesh\n",
+    "\n",
     "pio.renderers.default = \"sphinx_gallery\""
    ]
   },
@@ -139,6 +141,7 @@
    "source": [
     "# compute first eigenfunction\n",
     "from lapy import Solver\n",
+    "\n",
     "fem = Solver(T,lump=True)\n",
     "eval, evec = fem.eigs()\n",
     "vfunc = evec[:,1]\n",
@@ -221,8 +224,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from lapy.diffgeo import compute_gradient\n",
-    "from lapy.diffgeo import compute_divergence\n",
+    "from lapy.diffgeo import compute_divergence, compute_gradient\n",
+    "\n",
     "grad = compute_gradient(T,vfunc)\n",
     "divx = -compute_divergence(T,grad)\n",
     "plot_tria_mesh(T,Bi*divx,plot_edges=True)"
@@ -254,6 +257,7 @@
    ],
    "source": [
     "from lapy import heat\n",
+    "\n",
     "bvert = T.boundary_loops()\n",
     "u = heat.diffusion(T,bvert,m=1)"
    ]
@@ -338,6 +342,7 @@
    "source": [
     "# compute distance\n",
     "from scipy.sparse.linalg import splu\n",
+    "\n",
     "useCholmod = True\n",
     "try:\n",
     "    from sksparse.cholmod import cholesky\n",
@@ -488,6 +493,7 @@
    ],
    "source": [
     "from lapy.diffgeo import compute_geodesic_f\n",
+    "\n",
     "gf = compute_geodesic_f(T,u)\n",
     "plot_tria_mesh(T,gf,plot_edges=True,plot_levels=True)"
    ]
@@ -545,6 +551,7 @@
    "source": [
     "# testing if we can rotate the function\n",
     "from lapy.diffgeo import compute_rotated_f\n",
+    "\n",
     "gf = compute_rotated_f(T,vf)\n",
     "plot_tria_mesh(T,gf,plot_edges=True,plot_levels=True)"
    ]

lapy/_read_geometry.py

@@ -81,7 +81,7 @@ def _read_volume_info(fobj):
         if not np.array_equal(head, [2, 0, 20]) and not np.array_equal(
             head, [2, 1, 20]
         ):
-            warnings.warn("Unknown extension code.")
+            warnings.warn("Unknown extension code.", stacklevel=2)
             return volume_info
         head = [2, 0, 20]
 
@@ -98,7 +98,7 @@ def _read_volume_info(fobj):
     ]:
         pair = fobj.readline().decode("utf-8").split("=")
         if pair[0].strip() != key or len(pair) != 2:
-            raise IOError("Error parsing volume info.")
+            raise OSError("Error parsing volume info.")
         if key in ("valid", "filename"):
             volume_info[key] = pair[1].strip()
         elif key == "volume":
@@ -176,7 +176,7 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
     ret = (coords, faces)
     if read_metadata:
         if len(volume_info) == 0:
-            warnings.warn("No volume information contained in the file")
+            warnings.warn("No volume information contained in the file", stacklevel=2)
         ret += (volume_info,)
     if read_stamp:
         ret += (create_stamp,)

lapy/_tet_io.py

@@ -29,8 +29,8 @@ def read_gmsh(filename):
         print("[no .msh file] --> FAILED\n")
         return
     try:
-        f = open(filename, "r")
-    except IOError:
+        f = open(filename)
+    except OSError:
         print("[file not found or not readable]\n")
         return
     line = f.readline()
@@ -126,8 +126,8 @@ def read_vtk(filename):
     if verbose > 0:
         print("--> VTK format         ... ")
     try:
-        f = open(filename, "r")
-    except IOError:
+        f = open(filename)
+    except OSError:
         print("[file not found or not readable]\n")
         return
     # skip comments
@@ -209,7 +209,7 @@ def write_vtk(tet, filename):
     # open file
     try:
         f = open(filename, "w")
-    except IOError:
+    except OSError:
         print("[File " + filename + " not writable]")
         return
     # check data structure