gh-231: add ruff linting to pre-commit

.pre-commit-config.yaml

@@ -2,6 +2,7 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.3
     hooks:
+      - id: ruff
       - id: ruff-format
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.23.1

docs/conf.py

@@ -12,7 +12,7 @@
 
 project = "GLASS"
 author = "GLASS developers"
-copyright = f"2022-{datetime.date.today().year} {author}"
+copyright = f"2022-{datetime.date.today().year} {author}"  # noqa: A001, DTZ011
 version = metadata.version("glass")
 release = version
 

examples/1-basic/density.ipynb

@@ -34,20 +34,19 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "from matplotlib.colors import LogNorm\n",
     "\n",
     "# use the CAMB cosmology that generated the matter power spectra\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
     "# GLASS imports: matter, random fields, random points, galaxies\n",
-    "import glass.shells\n",
     "import glass.fields\n",
-    "import glass.points\n",
     "import glass.galaxies\n",
-    "\n",
+    "import glass.points\n",
+    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -59,7 +58,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
@@ -165,7 +167,8 @@
     "for i, delta_i in enumerate(matter):\n",
     "    # simulate positions from matter density\n",
     "    for gal_lon, gal_lat, gal_count in glass.points.positions_from_delta(\n",
-    "        ngal[i], delta_i\n",
+    "        ngal[i],\n",
+    "        delta_i,\n",
     "    ):\n",
     "        # sample redshifts uniformly in shell\n",
     "        gal_z = glass.galaxies.redshifts(gal_count, ws[i])\n",
@@ -174,8 +177,10 @@
     "        z1 = gal_z * np.cos(np.deg2rad(gal_lon)) * np.cos(np.deg2rad(gal_lat))\n",
     "        z2 = gal_z * np.sin(np.deg2rad(gal_lon)) * np.cos(np.deg2rad(gal_lat))\n",
     "        z3 = gal_z * np.sin(np.deg2rad(gal_lat))\n",
-    "        (i, j, k), c = np.unique(\n",
-    "            np.searchsorted(zcub[1:], [z1, z2, z3]), axis=1, return_counts=True\n",
+    "        (i, j, k), c = np.unique(  # noqa: PLW2901\n",
+    "            np.searchsorted(zcub[1:], [z1, z2, z3]),\n",
+    "            axis=1,\n",
+    "            return_counts=True,\n",
     "        )\n",
     "        cube[i, j, k] += c"
    ]

examples/1-basic/lensing.ipynb

@@ -38,20 +38,19 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import healpy as hp\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# use the CAMB cosmology that generated the matter power spectra\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
     "# GLASS imports\n",
-    "import glass.shells\n",
     "import glass.fields\n",
-    "import glass.lensing\n",
     "import glass.galaxies\n",
-    "\n",
+    "import glass.lensing\n",
+    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -63,7 +62,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
@@ -256,22 +258,25 @@
    "source": [
     "# get the angular power spectra of the lensing maps\n",
     "sim_cls = hp.anafast(\n",
-    "    [kappa_bar, gamm1_bar, gamm2_bar], pol=True, lmax=lmax, use_pixel_weights=True\n",
+    "    [kappa_bar, gamm1_bar, gamm2_bar],\n",
+    "    pol=True,\n",
+    "    lmax=lmax,\n",
+    "    use_pixel_weights=True,\n",
     ")\n",
     "\n",
     "# get the expected cls from CAMB\n",
     "pars.min_l = 1\n",
     "pars.set_for_lmax(lmax)\n",
     "pars.SourceWindows = [\n",
-    "    camb.sources.SplinedSourceWindow(z=z, W=dndz, source_type=\"lensing\")\n",
+    "    camb.sources.SplinedSourceWindow(z=z, W=dndz, source_type=\"lensing\"),\n",
     "]\n",
     "theory_cls = camb.get_results(pars).get_source_cls_dict(lmax=lmax, raw_cl=True)\n",
     "\n",
     "# get the HEALPix pixel window function, since the lensing fields have it\n",
     "pw = hp.pixwin(nside, lmax=lmax)\n",
     "\n",
     "# plot the realised and expected cls\n",
-    "l = np.arange(lmax + 1)\n",
+    "l = np.arange(lmax + 1)  # noqa: E741\n",
     "plt.plot(l, sim_cls[0], \"-k\", lw=2, label=\"simulation\")\n",
     "plt.plot(l, theory_cls[\"W1xW1\"] * pw**2, \"-r\", lw=2, label=\"expectation\")\n",
     "plt.xscale(\"symlog\", linthresh=10, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",

examples/1-basic/matter.ipynb

@@ -34,18 +34,17 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import healpy as hp\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# uses the CAMB cosmology which produced the cls\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
     "# these are the GLASS imports: matter and random fields\n",
-    "import glass.shells\n",
     "import glass.fields\n",
-    "\n",
+    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -58,7 +57,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
@@ -136,7 +138,7 @@
     "    theta, phi = hp.vec2ang(np.transpose([x[g] / zmax, y[g] / zmax, zg]))\n",
     "    grid[g] = hp.get_interp_val(delta_i, theta, phi)\n",
     "    ax.add_patch(\n",
-    "        plt.Circle((0, 0), zmax / zend, fc=\"none\", ec=\"k\", lw=0.5, alpha=0.5, zorder=1)\n",
+    "        plt.Circle((0, 0), zmax / zend, fc=\"none\", ec=\"k\", lw=0.5, alpha=0.5, zorder=1),\n",
     "    )\n",
     "\n",
     "# show the grid of shells\n",

examples/1-basic/photoz.ipynb

@@ -35,8 +35,8 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# GLASS imports: matter shells, galaxies, random points, and observational\n",
     "import glass.galaxies\n",
@@ -45,7 +45,6 @@
     "# how many arcmin2 over the entire sphere\n",
     "from glass.core.constants import ARCMIN2_SPHERE\n",
     "\n",
-    "\n",
     "# galaxy density\n",
     "n_arcmin2 = 1e-4\n",
     "\n",

examples/1-basic/shells.ipynb

@@ -38,14 +38,14 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
-    "import glass.shells\n",
     "import glass.ext.camb\n",
-    "\n",
+    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -57,7 +57,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",

examples/2-advanced/cosmic_shear.ipynb

@@ -33,24 +33,23 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import healpy as hp\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# use the CAMB cosmology that generated the matter power spectra\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
     "# GLASS modules: cosmology and everything in the glass namespace\n",
-    "import glass.shells\n",
     "import glass.fields\n",
+    "import glass.galaxies\n",
+    "import glass.lensing\n",
     "import glass.points\n",
     "import glass.shapes\n",
-    "import glass.lensing\n",
-    "import glass.galaxies\n",
+    "import glass.shells\n",
     "from glass.core.constants import ARCMIN2_SPHERE\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -61,7 +60,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
@@ -220,7 +222,12 @@
     "\n",
     "        # apply the shear fields to the ellipticities\n",
     "        gal_she = glass.galaxies.galaxy_shear(\n",
-    "            gal_lon, gal_lat, gal_eps, kappa_i, gamm1_i, gamm2_i\n",
+    "            gal_lon,\n",
+    "            gal_lat,\n",
+    "            gal_eps,\n",
+    "            kappa_i,\n",
+    "            gamm1_i,\n",
+    "            gamm2_i,\n",
     "        )\n",
     "\n",
     "        # map the galaxy shears to a HEALPix map; this is opaque but works\n",
@@ -287,12 +294,12 @@
     "pars.min_l = 1\n",
     "pars.set_for_lmax(lmax)\n",
     "pars.SourceWindows = [\n",
-    "    camb.sources.SplinedSourceWindow(z=z, W=dndz, source_type=\"lensing\")\n",
+    "    camb.sources.SplinedSourceWindow(z=z, W=dndz, source_type=\"lensing\"),\n",
     "]\n",
     "theory_cls = camb.get_results(pars).get_source_cls_dict(lmax=lmax, raw_cl=True)\n",
     "\n",
     "# factor transforming convergence to shear\n",
-    "l = np.arange(lmax + 1)\n",
+    "l = np.arange(lmax + 1)  # noqa: E741\n",
     "fl = (l + 2) * (l + 1) * l * (l - 1) / np.clip(l**2 * (l + 1) ** 2, 1, None)\n",
     "\n",
     "# the noise level from discrete observations with shape noise\n",

examples/2-advanced/stage_4_galaxies.ipynb

@@ -36,24 +36,23 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import healpy as hp\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# use the CAMB cosmology that generated the matter power spectra\n",
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
     "# GLASS modules: cosmology and everything in the glass namespace\n",
-    "import glass.shells\n",
+    "import glass.ext.camb\n",
     "import glass.fields\n",
-    "import glass.points\n",
-    "import glass.shapes\n",
-    "import glass.lensing\n",
     "import glass.galaxies\n",
+    "import glass.lensing\n",
     "import glass.observations\n",
-    "import glass.ext.camb\n",
-    "\n",
+    "import glass.points\n",
+    "import glass.shapes\n",
+    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -65,7 +64,10 @@
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
     "pars = camb.set_params(\n",
-    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    "    H0=100 * h,\n",
+    "    omch2=Oc * h**2,\n",
+    "    ombh2=Ob * h**2,\n",
+    "    NonLinear=camb.model.NonLinear_both,\n",
     ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
@@ -280,7 +282,10 @@
     "\n",
     "    # generate galaxy positions from the matter density contrast\n",
     "    for gal_lon, gal_lat, gal_count in glass.points.positions_from_delta(\n",
-    "        ngal[i], delta_i, bias, vis\n",
+    "        ngal[i],\n",
+    "        delta_i,\n",
+    "        bias,\n",
+    "        vis,\n",
     "    ):\n",
     "        # generate random redshifts over the given shell\n",
     "        gal_z = glass.galaxies.redshifts(gal_count, ws[i])\n",
@@ -296,7 +301,12 @@
     "\n",
     "        # apply the shear fields to the ellipticities\n",
     "        gal_she = glass.galaxies.galaxy_shear(\n",
-    "            gal_lon, gal_lat, gal_eps, kappa_i, gamm1_i, gamm2_i\n",
+    "            gal_lon,\n",
+    "            gal_lat,\n",
+    "            gal_eps,\n",
+    "            kappa_i,\n",
+    "            gamm1_i,\n",
+    "            gamm2_i,\n",
     "        )\n",
     "\n",
     "        # make a mini-catalogue for the new rows\n",

glass/__init__.py

@@ -1,4 +1,6 @@
-try:
+"""GLASS package."""
+
+import contextlib
+
+with contextlib.suppress(ModuleNotFoundError):
     from ._version import __version__, __version_tuple__  # noqa: F401
-except ModuleNotFoundError:
-    pass

glass/core/__init__.py

@@ -1,12 +1,12 @@
 # author: Nicolas Tessore <n.tessore@ucl.ac.uk>
 # license: MIT
 """
-Core functions (:mod:`glass.core`)
+Core functions (:mod:`glass.core`).
 ==================================
 
 .. currentmodule:: glass.core
 
 The :mod:`glass.core` module contains core functionality for developing
 GLASS modules.
 
-"""
+"""  # noqa: D205