action ruff checks

Author: HGWright

index.ipynb

@@ -46,9 +46,9 @@
     "\n",
     "nx, ny = 6, 3\n",
     "\n",
-    "np.random.seed(0)\n",
-    "orography = np.random.normal(1000, 600, size=(ny, nx)) - 400\n",
-    "sea_level_temp = np.random.normal(290, 5, size=(ny, nx))"
+    "rng = np.random.default_rng(0)\n",
+    "orography = rng.normal(1000, 600, size=(ny, nx)) - 400\n",
+    "sea_level_temp = rng.normal(290, 5, size=(ny, nx))"
    ]
   },
   {
@@ -85,20 +85,20 @@
     "\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "plt.set_cmap('viridis')\n",
+    "plt.set_cmap(\"viridis\")\n",
     "fig = plt.figure(figsize=(8, 6))\n",
     "\n",
     "plt.subplot(1, 2, 1)\n",
     "plt.pcolormesh(orography)\n",
-    "cbar = plt.colorbar(orientation='horizontal',\n",
-    "                    label='Orography (m)')\n",
+    "cbar = plt.colorbar(orientation=\"horizontal\",\n",
+    "                    label=\"Orography (m)\")\n",
     "# Reduce the maximum number of ticks to 5.\n",
     "cbar.ax.xaxis.get_major_locator().nbins = 5\n",
     "\n",
     "plt.subplot(1, 2, 2)\n",
     "plt.pcolormesh(sea_level_temp)\n",
-    "cbar = plt.colorbar(orientation='horizontal',\n",
-    "                    label='Sea level temperature (K)')\n",
+    "cbar = plt.colorbar(orientation=\"horizontal\",\n",
+    "                    label=\"Sea level temperature (K)\")\n",
     "# Reduce the maximum number of ticks to 5.\n",
     "cbar.ax.xaxis.get_major_locator().nbins = 5\n",
     "\n",
@@ -179,17 +179,17 @@
    "source": [
     "plt.figure(figsize=(8, 6))\n",
     "plt.fill_between(np.arange(6), np.zeros(6), orography[1, :],\n",
-    "                 color='green', linewidth=2, label='Orography')\n",
+    "                 color=\"green\", linewidth=2, label=\"Orography\")\n",
     "\n",
     "plt.plot(np.zeros(nx),\n",
-    "         color='blue', linewidth=1.2,\n",
-    "         label='Sea level')\n",
+    "         color=\"blue\", linewidth=1.2,\n",
+    "         label=\"Sea level\")\n",
     "\n",
     "for i in range(9):\n",
-    "    plt.plot(altitude[i, 1, :], color='gray', linestyle='--',\n",
-    "             label='Model levels' if i == 0 else None)\n",
+    "    plt.plot(altitude[i, 1, :], color=\"gray\", linestyle=\"--\",\n",
+    "             label=\"Model levels\" if i == 0 else None)\n",
     "\n",
-    "plt.ylabel('altitude / m')\n",
+    "plt.ylabel(\"altitude / m\")\n",
     "plt.margins(0.1)\n",
     "plt.legend()\n",
     "plt.show()"
@@ -250,14 +250,12 @@
     }
    ],
    "source": [
-    "from matplotlib.colors import LogNorm\n",
-    "\n",
     "fig = plt.figure(figsize=(8, 6))\n",
     "norm = plt.Normalize(vmin=temperature.min(), vmax=temperature.max())\n",
     "\n",
     "for i in range(nz):\n",
     "    plt.subplot(3, 3, i + 1)\n",
-    "    qm = plt.pcolormesh(temperature[i], cmap='viridis', norm=norm)\n",
+    "    qm = plt.pcolormesh(temperature[i], cmap=\"viridis\", norm=norm)\n",
     "\n",
     "plt.subplots_adjust(right=0.84, wspace=0.3, hspace=0.3)\n",
     "cax = plt.axes([0.85, 0.1, 0.03, 0.8])\n",
@@ -332,21 +330,21 @@
    "source": [
     "plt.figure(figsize=(8, 6))\n",
     "plt.fill_between(np.arange(6), np.zeros(6), orography[1, :],\n",
-    "                 color='green', linewidth=2, label='Orography')\n",
+    "                 color=\"green\", linewidth=2, label=\"Orography\")\n",
     "\n",
     "for i in range(9):\n",
     "    plt.plot(altitude[i, 1, :],\n",
-    "             color='gray', lw=1.2,\n",
-    "             label=None if i > 0 else 'Source levels \\n(model levels)')\n",
+    "             color=\"gray\", lw=1.2,\n",
+    "             label=None if i > 0 else \"Source levels \\n(model levels)\")\n",
     "for i, target in enumerate(target_altitudes):\n",
     "    plt.plot(np.repeat(target, 6),\n",
-    "             color='gray', linestyle='--', lw=1.4, alpha=0.6,\n",
-    "             label=None if i > 0 else 'Target levels \\n(altitude)')\n",
+    "             color=\"gray\", linestyle=\"--\", lw=1.4, alpha=0.6,\n",
+    "             label=None if i > 0 else \"Target levels \\n(altitude)\")\n",
     "\n",
-    "plt.ylabel('height / m')\n",
+    "plt.ylabel(\"height / m\")\n",
     "plt.margins(top=0.1)\n",
     "plt.legend()\n",
-    "plt.savefig('summary.png')\n",
+    "plt.savefig(\"summary.png\")\n",
     "plt.show()"
    ]
   },
@@ -413,7 +411,7 @@
     "plt.figure(figsize=(8, 6))\n",
     "ax1 = plt.subplot(1, 2, 1)\n",
     "plt.fill_between(np.arange(6), np.zeros(6), orography[1, :],\n",
-    "                 color='green', linewidth=2, label='Orography')\n",
+    "                 color=\"green\", linewidth=2, label=\"Orography\")\n",
     "cs = plt.contourf(np.tile(np.arange(6), nz).reshape(nz, 6),\n",
     "             altitude[:, 1],\n",
     "             temperature[:, 1])\n",
@@ -423,7 +421,7 @@
     "\n",
     "plt.subplot(1, 2, 2, sharey=ax1)\n",
     "plt.fill_between(np.arange(6), np.zeros(6), orography[1, :],\n",
-    "                 color='green', linewidth=2, label='Orography')\n",
+    "                 color=\"green\", linewidth=2, label=\"Orography\")\n",
     "plt.contourf(np.arange(6), target_altitudes,\n",
     "             np.ma.masked_invalid(new_temperature[:, 1]),\n",
     "             cmap=cs.cmap, norm=cs.norm)\n",
@@ -432,9 +430,9 @@
     "            c=new_temperature[:, 1])\n",
     "plt.scatter(np.tile(np.arange(nx), target_nz).reshape(target_nz, nx),\n",
     "            np.repeat(target_altitudes, nx).reshape(target_nz, nx),\n",
-    "            s=np.isnan(new_temperature[:, 1]) * 15, marker='x')\n",
+    "            s=np.isnan(new_temperature[:, 1]) * 15, marker=\"x\")\n",
     "\n",
-    "plt.suptitle('Temperature cross-section before and after restratification')\n",
+    "plt.suptitle(\"Temperature cross-section before and after restratification\")\n",
     "plt.show()"
    ]
   }

pyproject.toml

@@ -145,7 +145,6 @@ preview = false
 
 [tool.ruff.lint]
 ignore = [
-
     # flake8-annotations (ANN)
     # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
     "ANN001", # Missing type annotation for function argument {name}
@@ -156,21 +155,6 @@ ignore = [
     "ANN204", # Missing return type annotation for special method {name}
 
     "ARG002", # Unused method argument: {name}
-    "ARG003", # Unused class method argument: {name}
-
-    # flake8-bugbear (B)
-    # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "B028", # No explicit stacklevel keyword argument found
-
-    # flake8-comprehensions (C4)
-    # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "C405", # Unnecessary {obj_type} literal (rewrite as a set literal)
-    "C419", # Unnecessary list comprehension
-
-    # flake8-commas (COM)
-    # https://docs.astral.sh/ruff/rules/#flake8-commas-com
-    "COM812",  # Trailing comma missing.
-    "COM819",  # Trailing comma prohibited.
 
     # pydocstyle (D)
     # https://docs.astral.sh/ruff/rules/#pydocstyle-d
@@ -185,46 +169,12 @@ ignore = [
     # https://docs.astral.sh/ruff/rules/#eradicate-era
     "ERA001", # Found commented-out code
 
-    # flake8-boolean-trap (FBT)
-    # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
-    "FBT002", # Boolean default positional argument in function definition
-
-    # flake8-implicit-str-concat (ISC)
-    # https://docs.astral.sh/ruff/rules/single-line-implicit-string-concatenation/
-    # NOTE: This rule may cause conflicts when used with "ruff format".
-    "ISC001",  # Implicitly concatenate string literals on one line.
-
-    # pep8-naming (N)
-    # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-    "N801", # Class name {name} should use CapWords convention
+    "PT011",
 
-    # Refactor (R)
-    # https://docs.astral.sh/ruff/rules/#refactor-r
-    "PLR2004", # Magic value used in comparison, consider replacing {value} with a constant variable
-
-    # flake8-pytest-style (PT)
-    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-    "PT009", # Use a regular assert instead of unittest-style {assertion}
-    "PT027", # Use pytest.raises instead of unittest-style {assertion}
-
-    # flake8-return (RET)
-    # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-    "RET504", # Unnecessary assignment to {name} before return statement
-
-    # Ruff-specific rules (RUF)
-    # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
-    "RUF005", # Consider {expression} instead of concatenation
-    "RUF012", # Mutable class attributes should be annotated with typing.ClassVar
-
-    # flake8-self (SLF)
-    # https://docs.astral.sh/ruff/rules/#flake8-self-slf
-    "SLF001", # Private member accessed: {access}
+    "PLR2004",
 
-    # flake8-print (T20)
-    # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-    "T201", # print found
-
-    ]
+    "S101", # Use of assert detected.
+]
     preview = false
     select = [
         "ALL",
@@ -239,13 +189,20 @@ known-first-party = ["iris"]
 
 [tool.ruff.lint.per-file-ignores]
 # All test scripts
-
+"src/stratify/tests/performance.py" = [
+    "T201", # print found
+]
+"setup.py" = [
+    "T201", # print found
+    "RUF012", # Mutable class attributes should be annotated with typing.ClassVar
+]
 # Change to match specific package path:
-"lib/iris/tests/*.py" = [
+"src/stratify/tests/*.py" = [
     # https://docs.astral.sh/ruff/rules/undocumented-public-module/
     "D100",  # Missing docstring in public module
     "D205",  # 1 blank line required between summary line and description
     "D401",  # 1 First line of docstring should be in imperative mood
+    "SLF001", # Private member accessed: {access}
 ]
 
 [tool.ruff.lint.pydocstyle]

setup.py

@@ -11,7 +11,7 @@
     from Cython.Build import cythonize  # isort:skip
 except ImportError:
     wmsg = "Cython unavailable, unable to build stratify extensions!"
-    warnings.warn(wmsg)
+    warnings.warn(wmsg, stacklevel=2)
     cythonize = None
 
 
@@ -53,7 +53,7 @@ def run(self):
         [
             ("CYTHON_TRACE", "1"),
             ("CYTHON_TRACE_NOGIL", "1"),
-        ]
+        ],
     )
     cython_directives.update({"linetrace": True})
     if FLAG_COVERAGE in sys.argv:
@@ -70,9 +70,11 @@ def run(self):
     )
     extensions.append(extension)
 
-if cythonize and not any([arg in CMDS_NOCYTHONIZE for arg in sys.argv]):
+if cythonize and not any(arg in CMDS_NOCYTHONIZE for arg in sys.argv):
     extensions = cythonize(
-        extensions, compiler_directives=cython_directives, language_level=3
+        extensions,
+        compiler_directives=cython_directives,
+        language_level=3,
     )
 
 cmdclass = {"clean_cython": CleanCython}

src/stratify/_bounded_vinterp.py

@@ -91,7 +91,8 @@ def interpolate_conservative(z_target, z_src, fz_src, axis=-1):
         )
         raise ValueError(msg.format(tuple(dat_shape), tuple(src_shape)))
 
-    if z_src.shape[-1] != 2:
+    shape_2 = 2
+    if z_src.shape[-1] != shape_2:
         msg = "Unexpected source and target bounds shape. shape[-1] != 2"
         raise ValueError(msg)
 
@@ -100,8 +101,8 @@ def interpolate_conservative(z_target, z_src, fz_src, axis=-1):
 
     # src_data
     bdims = list(range(fz_src.ndim - (z_src.ndim - 1)))
-    data_vdims = [ind for ind in range(fz_src.ndim) if ind not in (bdims + [axis])]
-    data_transpose = bdims + [axis] + data_vdims
+    data_vdims = [ind for ind in range(fz_src.ndim) if ind not in ([*bdims, axis])]
+    data_transpose = [*bdims, axis, *data_vdims]
     fz_src_reshaped = np.transpose(fz_src, data_transpose)
     fz_src_orig = list(fz_src_reshaped.shape)
     shape = (
@@ -113,21 +114,24 @@ def interpolate_conservative(z_target, z_src, fz_src, axis=-1):
 
     # Define our src and target bounds in a consistent way.
     # [axis_interpolation, z_varying, 2]
-    vdims = list(set(range(z_src.ndim)) - set([axis_relative]))
-    z_src_reshaped = np.transpose(z_src, [axis_relative] + vdims)
-    z_target_reshaped = np.transpose(z_target, [axis_relative] + vdims)
+    # vdims = list(set(range(z_src.ndim)) - set([axis_relative]))
+    vdims = list(set(range(z_src.ndim)) - {axis_relative})
+    z_src_reshaped = np.transpose(z_src, [axis_relative, *vdims])
+    z_target_reshaped = np.transpose(z_target, [axis_relative, *vdims])
 
     shape = int(np.prod(z_src_reshaped.shape[1:-1]))
     z_src_reshaped = z_src_reshaped.reshape(
-        [z_src_reshaped.shape[0], shape, z_src_reshaped.shape[-1]]
+        [z_src_reshaped.shape[0], shape, z_src_reshaped.shape[-1]],
     )
     shape = int(np.prod(z_target_reshaped.shape[1:-1]))
     z_target_reshaped = z_target_reshaped.reshape(
-        [z_target_reshaped.shape[0], shape, z_target_reshaped.shape[-1]]
+        [z_target_reshaped.shape[0], shape, z_target_reshaped.shape[-1]],
     )
 
     result = conservative_interpolation(
-        z_src_reshaped, z_target_reshaped, fz_src_reshaped
+        z_src_reshaped,
+        z_target_reshaped,
+        fz_src_reshaped,
     )
 
     # Turn the result into a shape consistent with the source.
@@ -136,5 +140,5 @@ def interpolate_conservative(z_target, z_src, fz_src, axis=-1):
     shape[len(bdims)] = z_target.shape[axis_relative]
     result = result.reshape(shape)
     invert_transpose = [data_transpose.index(ind) for ind in list(range(result.ndim))]
-    result = result.transpose(invert_transpose)
-    return result
+    # result = result.transpose(invert_transpose)
+    return result.transpose(invert_transpose)

src/stratify/tests/performance.py

@@ -6,7 +6,7 @@
 import stratify
 
 
-def src_data(shape=(400, 500, 100), lazy=False):
+def src_data(shape=(400, 500, 100)):
     z = np.tile(np.linspace(0, 100, shape[-1]), np.prod(shape[:2])).reshape(shape)
     if lazy:
         fz = da.arange(np.prod(shape), dtype=np.float64).reshape(shape)