Merge branch 'main' into paddy/ruff-lint

glass-dev · Sep 18, 2024 · d3241fd · d3241fd
2 parents d4ccd3a + 2c4a712
commit d3241fd
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diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -10,6 +10,7 @@ on:
 
 jobs:
   check-pr-title:
+    if: ${{ github.actor != 'pre-commit-ci[bot]' }}
     runs-on: ubuntu-latest
     steps:
       - uses: thehanimo/[email protected]

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,3 +1,7 @@
+ci:
+  autoupdate_commit_msg: "MNT: update pre-commit hooks"
+  autofix_commit_msg: "STY: pre-commit fixes"
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0

diff --git a/docs/user/how-glass-works.rst b/docs/user/how-glass-works.rst
@@ -20,11 +20,11 @@ Radial discretisation
 The discretisation in the radial (line of sight) direction is done in *GLASS*
 using the concept of a :term:`radial window`, which consists of a window
 function :math:`W` that assigns a weight :math:`W(z)` to each redshift
-:math:`z`.  In the *GLASS* code, the :class:`~glass.shells.RadialWindow` named
+:math:`z`.  In the *GLASS* code, the :class:`~glass.RadialWindow` named
 tuple is used to define radial windows.
 
 A sequence :math:`W_1, W_2, \ldots` of such window functions defines the shells
-of the simulation.  For example, the :func:`~glass.shells.tophat_windows`
+of the simulation.  For example, the :func:`~glass.tophat_windows`
 function takes redshift boundaries and returns a sequence of top hat windows,
 which are flat and non-overlapping.
 
@@ -169,7 +169,7 @@ shells:
 
 In short, the requirements say that each shell has an effective redshift which
 partitions the window functions of all other shells. In *GLASS*, it is stored
-as the ``zeff`` attribute of :class:`~glass.shells.RadialWindow`.  Functions
+as the ``zeff`` attribute of :class:`~glass.RadialWindow`.  Functions
 that construct a list of windows for shells should ensure these requirements
 are met.
 

diff --git a/examples/1-basic/density.ipynb b/examples/1-basic/density.ipynb
@@ -42,11 +42,8 @@
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
-    "# GLASS imports: matter, random fields, random points, galaxies\n",
-    "import glass.fields\n",
-    "import glass.galaxies\n",
-    "import glass.points\n",
-    "import glass.shells\n",
+    "# import GLASS for matter, random fields, random points, galaxies\n",
+    "import glass\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -68,10 +65,10 @@
     "cosmo = Cosmology.from_camb(pars)\n",
     "\n",
     "# shells of 200 Mpc in comoving distance spacing\n",
-    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
+    "zb = glass.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# linear radial window functions\n",
-    "ws = glass.shells.linear_windows(zb)\n",
+    "ws = glass.linear_windows(zb)\n",
     "\n",
     "# load the angular matter power spectra previously computed with CAMB\n",
     "cls = np.load(\"cls.npy\")"
@@ -99,10 +96,10 @@
    "outputs": [],
    "source": [
     "# compute Gaussian cls for lognormal fields for 3 correlated shells\n",
-    "gls = glass.fields.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
+    "gls = glass.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
     "\n",
     "# generator for lognormal matter fields\n",
-    "matter = glass.fields.generate_lognormal(gls, nside, ncorr=3)"
+    "matter = glass.generate_lognormal(gls, nside, ncorr=3)"
    ]
   },
   {
@@ -131,7 +128,7 @@
     "dndz = np.full_like(z, 0.01)\n",
     "\n",
     "# distribute the dN/dz over the linear window functions\n",
-    "ngal = glass.shells.partition(z, dndz, ws)"
+    "ngal = glass.partition(z, dndz, ws)"
    ]
   },
   {
@@ -166,12 +163,9 @@
     "# simulate and add galaxies in each matter shell to cube\n",
     "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],\n",
-    "        delta_i,\n",
-    "    ):\n",
+    "    for gal_lon, gal_lat, gal_count in glass.positions_from_delta(ngal[i], delta_i):\n",
     "        # sample redshifts uniformly in shell\n",
-    "        gal_z = glass.galaxies.redshifts(gal_count, ws[i])\n",
+    "        gal_z = glass.redshifts(gal_count, ws[i])\n",
     "\n",
     "        # add counts to cube\n",
     "        z1 = gal_z * np.cos(np.deg2rad(gal_lon)) * np.cos(np.deg2rad(gal_lat))\n",

diff --git a/examples/1-basic/lensing.ipynb b/examples/1-basic/lensing.ipynb
@@ -46,11 +46,8 @@
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
-    "# GLASS imports\n",
-    "import glass.fields\n",
-    "import glass.galaxies\n",
-    "import glass.lensing\n",
-    "import glass.shells\n",
+    "# import GLASS\n",
+    "import glass\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -72,10 +69,10 @@
     "cosmo = Cosmology.from_camb(pars)\n",
     "\n",
     "# shells of 200 Mpc in comoving distance spacing\n",
-    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
+    "zb = glass.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# linear radial window functions\n",
-    "ws = glass.shells.linear_windows(zb)\n",
+    "ws = glass.linear_windows(zb)\n",
     "\n",
     "# load the angular matter power spectra previously computed with CAMB\n",
     "cls = np.load(\"cls.npy\")"
@@ -104,10 +101,10 @@
    "source": [
     "# compute Gaussian cls for lognormal fields for 3 correlated shells\n",
     "# putting nside here means that the HEALPix pixel window function is applied\n",
-    "gls = glass.fields.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
+    "gls = glass.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
     "\n",
     "# generator for lognormal matter fields\n",
-    "matter = glass.fields.generate_lognormal(gls, nside, ncorr=3)"
+    "matter = glass.generate_lognormal(gls, nside, ncorr=3)"
    ]
   },
   {
@@ -132,7 +129,7 @@
    "outputs": [],
    "source": [
     "# this will compute the convergence field iteratively\n",
-    "convergence = glass.lensing.MultiPlaneConvergence(cosmo)"
+    "convergence = glass.MultiPlaneConvergence(cosmo)"
    ]
   },
   {
@@ -162,7 +159,7 @@
     "dndz = np.exp(-((z - 0.5) ** 2) / (0.1) ** 2)\n",
     "\n",
     "# distribute dN/dz over the radial window functions\n",
-    "ngal = glass.shells.partition(z, dndz, ws)"
+    "ngal = glass.partition(z, dndz, ws)"
    ]
   },
   {
@@ -202,7 +199,7 @@
     "    kappa_i = convergence.kappa\n",
     "\n",
     "    # compute shear field\n",
-    "    gamm1_i, gamm2_i = glass.lensing.shear_from_convergence(kappa_i)\n",
+    "    gamm1_i, gamm2_i = glass.shear_from_convergence(kappa_i)\n",
     "\n",
     "    # add to mean fields using the galaxy number density as weight\n",
     "    kappa_bar += ngal[i] * kappa_i\n",

diff --git a/examples/1-basic/matter.ipynb b/examples/1-basic/matter.ipynb
@@ -42,9 +42,8 @@
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
-    "# these are the GLASS imports: matter and random fields\n",
-    "import glass.fields\n",
-    "import glass.shells\n",
+    "# import GLASS for matter and random fields\n",
+    "import glass\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -67,16 +66,16 @@
     "cosmo = Cosmology.from_camb(pars)\n",
     "\n",
     "# shells of 200 Mpc in comoving distance spacing\n",
-    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
+    "zb = glass.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# load precomputed angular matter power spectra\n",
     "cls = np.load(\"cls.npy\")\n",
     "\n",
     "# compute Gaussian cls for lognormal fields with 3 correlated shells\n",
-    "gls = glass.fields.lognormal_gls(cls, ncorr=3, nside=nside)\n",
+    "gls = glass.lognormal_gls(cls, ncorr=3, nside=nside)\n",
     "\n",
     "# this generator will yield the matter fields in each shell\n",
-    "matter = glass.fields.generate_lognormal(gls, nside, ncorr=3)"
+    "matter = glass.generate_lognormal(gls, nside, ncorr=3)"
    ]
   },
   {

diff --git a/examples/1-basic/photoz.ipynb b/examples/1-basic/photoz.ipynb
@@ -38,9 +38,8 @@
     "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",
-    "import glass.observations\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",
@@ -53,7 +52,7 @@
     "\n",
     "# parametric galaxy redshift distribution\n",
     "z = np.linspace(0, 3, 301)\n",
-    "dndz = n_arcmin2 * glass.observations.smail_nz(z, 1.0, 2.2, 1.5)\n",
+    "dndz = n_arcmin2 * glass.smail_nz(z, 1.0, 2.2, 1.5)\n",
     "\n",
     "# compute the over galaxy number density on the sphere\n",
     "ngal = np.trapz(dndz, z)"
@@ -86,10 +85,10 @@
     "n = np.random.poisson(ngal * ARCMIN2_SPHERE)\n",
     "\n",
     "# sample n true redshifts\n",
-    "ztrue = glass.galaxies.redshifts_from_nz(n, z, dndz)\n",
+    "ztrue = glass.redshifts_from_nz(n, z, dndz)\n",
     "\n",
     "# sample n photometric redshifts\n",
-    "zphot = glass.galaxies.gaussian_phz(ztrue, phz_sigma_0)"
+    "zphot = glass.gaussian_phz(ztrue, phz_sigma_0)"
    ]
   },
   {
@@ -146,7 +145,7 @@
    "metadata": {},
    "source": [
     "Now define a number of photometric redshift bins.  They are chosen by the\n",
-    ":func:`~glass.observations.equal_dens_zbins` function to produce the same\n",
+    ":func:`~glass.equal_dens_zbins` function to produce the same\n",
     "number of galaxies in each bin.\n",
     "\n"
    ]
@@ -166,7 +165,7 @@
    "outputs": [],
    "source": [
     "nbins = 5\n",
-    "zbins = glass.observations.equal_dens_zbins(z, dndz, nbins)"
+    "zbins = glass.equal_dens_zbins(z, dndz, nbins)"
    ]
   },
   {
@@ -175,7 +174,7 @@
    "source": [
     "After the photometric bins are defined, make histograms of the *true* redshift\n",
     "distribution $n(z)$ using the *photometric* redshifts for binning.  Use\n",
-    "the :func:`~glass.observations.tomo_nz_gausserr()` function to also plot the\n",
+    "the :func:`~glass.tomo_nz_gausserr()` function to also plot the\n",
     "expected tomographic redshift distributions with the same model.\n",
     "\n"
    ]
@@ -210,7 +209,7 @@
     }
    ],
    "source": [
-    "tomo_nz = glass.observations.tomo_nz_gausserr(z, dndz, phz_sigma_0, zbins)\n",
+    "tomo_nz = glass.tomo_nz_gausserr(z, dndz, phz_sigma_0, zbins)\n",
     "tomo_nz *= ARCMIN2_SPHERE * (z[-1] - z[0]) / 40\n",
     "\n",
     "for (z1, z2), nz in zip(zbins, tomo_nz):\n",

diff --git a/examples/1-basic/shells.ipynb b/examples/1-basic/shells.ipynb
@@ -44,8 +44,8 @@
     "import camb\n",
     "from cosmology import Cosmology\n",
     "\n",
+    "import glass\n",
     "import glass.ext.camb\n",
-    "import glass.shells\n",
     "\n",
     "# cosmology for the simulation\n",
     "h = 0.7\n",
@@ -67,10 +67,10 @@
     "cosmo = Cosmology.from_camb(pars)\n",
     "\n",
     "# shells of 200 Mpc in comoving distance spacing\n",
-    "zgrid = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
+    "zgrid = glass.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# triangular radial windows, equivalent to linear interpolation of n(z)\n",
-    "shells = glass.shells.linear_windows(zgrid)\n",
+    "shells = glass.linear_windows(zgrid)\n",
     "\n",
     "# compute angular matter power spectra with CAMB\n",
     "cls = glass.ext.camb.matter_cls(pars, lmax, shells)"

diff --git a/examples/2-advanced/cosmic_shear.ipynb b/examples/2-advanced/cosmic_shear.ipynb
@@ -42,12 +42,7 @@
     "from cosmology import Cosmology\n",
     "\n",
     "# GLASS modules: cosmology and everything in the glass namespace\n",
-    "import glass.fields\n",
-    "import glass.galaxies\n",
-    "import glass.lensing\n",
-    "import glass.points\n",
-    "import glass.shapes\n",
-    "import glass.shells\n",
+    "import glass\n",
     "from glass.core.constants import ARCMIN2_SPHERE\n",
     "\n",
     "# cosmology for the simulation\n",
@@ -70,10 +65,10 @@
     "cosmo = Cosmology.from_camb(pars)\n",
     "\n",
     "# shells of 200 Mpc in comoving distance spacing\n",
-    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
+    "zb = glass.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# linear window function for shells\n",
-    "ws = glass.shells.linear_windows(zb)\n",
+    "ws = glass.linear_windows(zb)\n",
     "\n",
     "# load the angular matter power spectra previously computed with CAMB\n",
     "cls = np.load(\"../1-basic/cls.npy\")"
@@ -102,10 +97,10 @@
    "source": [
     "# compute Gaussian cls for lognormal fields for 3 correlated shells\n",
     "# putting nside here means that the HEALPix pixel window function is applied\n",
-    "gls = glass.fields.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
+    "gls = glass.lognormal_gls(cls, nside=nside, lmax=lmax, ncorr=3)\n",
     "\n",
     "# generator for lognormal matter fields\n",
-    "matter = glass.fields.generate_lognormal(gls, nside, ncorr=3)"
+    "matter = glass.generate_lognormal(gls, nside, ncorr=3)"
    ]
   },
   {
@@ -130,7 +125,7 @@
    "outputs": [],
    "source": [
     "# this will compute the convergence field iteratively\n",
-    "convergence = glass.lensing.MultiPlaneConvergence(cosmo)"
+    "convergence = glass.MultiPlaneConvergence(cosmo)"
    ]
   },
   {
@@ -167,7 +162,7 @@
     "dndz *= n_arcmin2 / np.trapz(dndz, z)\n",
     "\n",
     "# distribute dN/dz over the radial window functions\n",
-    "ngal = glass.shells.partition(z, dndz, ws)"
+    "ngal = glass.partition(z, dndz, ws)"
    ]
   },
   {
@@ -213,21 +208,16 @@
     "    # compute the lensing maps for this shell\n",
     "    convergence.add_window(delta_i, ws[i])\n",
     "    kappa_i = convergence.kappa\n",
-    "    gamm1_i, gamm2_i = glass.lensing.shear_from_convergence(kappa_i)\n",
+    "    gamm1_i, gamm2_i = glass.shear_from_convergence(kappa_i)\n",
     "\n",
     "    # generate galaxy positions uniformly over the sphere\n",
-    "    for gal_lon, gal_lat, gal_count in glass.points.uniform_positions(ngal[i]):\n",
+    "    for gal_lon, gal_lat, gal_count in glass.uniform_positions(ngal[i]):\n",
     "        # generate galaxy ellipticities from the chosen distribution\n",
-    "        gal_eps = glass.shapes.ellipticity_intnorm(gal_count, sigma_e)\n",
+    "        gal_eps = glass.ellipticity_intnorm(gal_count, sigma_e)\n",
     "\n",
     "        # apply the shear fields to the ellipticities\n",
-    "        gal_she = glass.galaxies.galaxy_shear(\n",
-    "            gal_lon,\n",
-    "            gal_lat,\n",
-    "            gal_eps,\n",
-    "            kappa_i,\n",
-    "            gamm1_i,\n",
-    "            gamm2_i,\n",
+    "        gal_she = glass.galaxy_shear(\n",
+    "            gal_lon, gal_lat, gal_eps, kappa_i, gamm1_i, gamm2_i\n",
     "        )\n",
     "\n",
     "        # map the galaxy shears to a HEALPix map; this is opaque but works\n",