Merge branch 'main' into saransh/remove-file-headers

glass-dev · Sep 19, 2024 · 1adf2aa · 1adf2aa
2 parents a726dd8 + 09bef8a
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -2,3 +2,5 @@
 b42067f6776dcd763827000d585a88e071b78af3
 # applied prettier - https://github.com/glass-dev/glass/pull/227
 f9bac62f497a7288aa71fd4dbd948945c37f854e
+# applied ruff-linting - https://github.com/glass-dev/glass/pull/232
+e58d8616c03b8447aba90996905a98b42f18ba0a
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -27,6 +27,8 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.6.3
     hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
       - id: ruff-format
   - repo: https://github.com/pappasam/toml-sort
     rev: v0.23.1

diff --git a/docs/conf.py b/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
 

diff --git a/examples/1-basic/density.ipynb b/examples/1-basic/density.ipynb
@@ -34,8 +34,8 @@
    },
    "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",
@@ -45,7 +45,6 @@
     "# import GLASS for matter, random fields, random points, galaxies\n",
     "import glass\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -56,7 +55,10 @@
     "\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",
@@ -169,8 +171,10 @@
     "        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"
    ]

diff --git a/examples/1-basic/lensing.ipynb b/examples/1-basic/lensing.ipynb
@@ -38,9 +38,9 @@
    },
    "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",
@@ -49,7 +49,6 @@
     "# import GLASS\n",
     "import glass\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -60,7 +59,10 @@
     "\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",
@@ -253,22 +255,25 @@
    "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",

diff --git a/examples/1-basic/matter.ipynb b/examples/1-basic/matter.ipynb
@@ -34,9 +34,9 @@
    },
    "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",
@@ -45,7 +45,6 @@
     "# import GLASS for matter and random fields\n",
     "import glass\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -57,7 +56,10 @@
     "\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",
@@ -135,7 +137,7 @@
     "    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",

diff --git a/examples/1-basic/photoz.ipynb b/examples/1-basic/photoz.ipynb
@@ -35,16 +35,15 @@
    },
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "# import GLASS for matter shells, galaxies, random points, and observational\n",
     "import glass\n",
     "\n",
     "# 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",

diff --git a/examples/1-basic/shells.ipynb b/examples/1-basic/shells.ipynb
@@ -38,15 +38,15 @@
    },
    "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\n",
     "import glass.ext.camb\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\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",

diff --git a/examples/2-advanced/cosmic_shear.ipynb b/examples/2-advanced/cosmic_shear.ipynb
@@ -33,18 +33,18 @@
    },
    "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\n",
     "from glass.core.constants import ARCMIN2_SPHERE\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -55,7 +55,10 @@
     "\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",
@@ -281,12 +284,12 @@
     "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",

diff --git a/examples/2-advanced/stage_4_galaxies.ipynb b/examples/2-advanced/stage_4_galaxies.ipynb
@@ -36,18 +36,18 @@
    },
    "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\n",
     "import glass.ext.camb\n",
     "\n",
-    "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
     "Oc = 0.25\n",
@@ -58,7 +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",

diff --git a/glass/__init__.py b/glass/__init__.py
@@ -1,70 +1,71 @@
+"""GLASS package."""
+
+import contextlib
 from importlib.metadata import PackageNotFoundError
 
-try:
+with contextlib.suppress(PackageNotFoundError):
     from ._version import __version__, __version_tuple__
-except PackageNotFoundError:
-    pass
 
 from glass.fields import (
-    iternorm,
     cls2cov,
-    multalm,
-    transform_cls,
+    effective_cls,
     gaussian_gls,
-    lognormal_gls,
     generate_gaussian,
     generate_lognormal,
     getcl,
-    effective_cls,
+    iternorm,
+    lognormal_gls,
+    multalm,
+    transform_cls,
 )
 from glass.galaxies import (
-    redshifts,
-    redshifts_from_nz,
     galaxy_shear,
     gaussian_phz,
+    redshifts,
+    redshifts_from_nz,
 )
 from glass.lensing import (
-    from_convergence,
-    shear_from_convergence,
     MultiPlaneConvergence,
+    deflect,
+    from_convergence,
     multi_plane_matrix,
     multi_plane_weights,
-    deflect,
+    shear_from_convergence,
 )
 from glass.observations import (
-    vmap_galactic_ecliptic,
+    equal_dens_zbins,
+    fixed_zbins,
     gaussian_nz,
     smail_nz,
-    fixed_zbins,
-    equal_dens_zbins,
     tomo_nz_gausserr,
+    vmap_galactic_ecliptic,
 )
 from glass.points import (
     effective_bias,
     linear_bias,
     loglinear_bias,
+    position_weights,
     positions_from_delta,
     uniform_positions,
-    position_weights,
 )
 from glass.shapes import (
-    triaxial_axis_ratio,
-    ellipticity_ryden04,
     ellipticity_gaussian,
     ellipticity_intnorm,
+    ellipticity_ryden04,
+    triaxial_axis_ratio,
 )
 from glass.shells import (
-    distance_weight,
-    volume_weight,
+    RadialWindow,
+    combine,
+    cubic_windows,
     density_weight,
-    tophat_windows,
+    distance_grid,
+    distance_weight,
     linear_windows,
-    cubic_windows,
-    restrict,
     partition,
     redshift_grid,
-    distance_grid,
-    combine,
-    RadialWindow,
+    restrict,
+    tophat_windows,
+    volume_weight,
 )
-from glass.user import save_cls, load_cls, write_catalog
+from glass.user import load_cls, save_cls, write_catalog