STY: add ruff-format and remove flake8 (#199)

The maintainer of `flake8` can be a bit difficult, so nice to remove. I will add `ruff` the linter in a separate PR, but would be nice to get formatting done first. `ruff-format` is basically faster `black` (but some subtle differences). Reviewed-by: Saransh Chopra <[email protected]>
glass-dev · Sep 17, 2024 · b42067f · b42067f
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diff --git a/.flake8 b/.flake8
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,2 @@
+# applied ruff-format - https://github.com/glass-dev/glass/pull/199
+c894d9c7d349e44ac7fd50ba35859695758bbb95
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -16,12 +16,13 @@ concurrency:
 
 jobs:
 
-  style:
-    name: Style
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - run: pipx run flake8 glass
+# TODO: replace with a more general pre-commit linter
+#   style:
+#     name: Style
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v4
+#     - run: pipx run flake8 glass
 
   tests:
     name: Tests

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,16 +1,14 @@
 repos:
-- repo: https://github.com/pycqa/flake8
-  rev: 7.1.1
-  hooks:
-    - id: flake8
-      additional_dependencies:
-        - flake8-print
-- repo: https://github.com/pappasam/toml-sort
-  rev: v0.23.1
-  hooks:
-    - id: toml-sort-fix
-      args:
-        - --all
-        - --in-place
-        - --spaces-indent-inline-array=4
-        - --trailing-comma-inline-array
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.3
+    hooks:
+      - id: ruff-format
+  - repo: https://github.com/pappasam/toml-sort
+    rev: v0.23.1
+    hooks:
+      - id: toml-sort-fix
+        args:
+          - --all
+          - --in-place
+          - --spaces-indent-inline-array=4
+          - --trailing-comma-inline-array
diff --git a/docs/conf.py b/docs/conf.py
@@ -10,9 +10,9 @@
 import datetime
 from importlib import metadata
 
-project = 'GLASS'
-author = 'GLASS developers'
-copyright = f'2022-{datetime.date.today().year} {author}'
+project = "GLASS"
+author = "GLASS developers"
+copyright = f"2022-{datetime.date.today().year} {author}"
 version = metadata.version("glass")
 release = version
 
@@ -23,37 +23,37 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'numpydoc',
-    'sphinx.ext.intersphinx',
-    'sphinxcontrib.katex',
-    'matplotlib.sphinxext.plot_directive',
-    'nbsphinx',
+    "numpydoc",
+    "sphinx.ext.intersphinx",
+    "sphinxcontrib.katex",
+    "matplotlib.sphinxext.plot_directive",
+    "nbsphinx",
     "sphinx.ext.viewcode",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'furo'
+html_theme = "furo"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
-html_logo = '_static/logo.png'
-html_favicon = '_static/favicon.ico'
+html_logo = "_static/logo.png"
+html_favicon = "_static/favicon.ico"
 html_css_files = []
 
 
@@ -62,14 +62,14 @@
 # This config value contains the locations and names of other projects that
 # should be linked to in this documentation.
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
 }
 
 
 # -- autodoc -----------------------------------------------------------------
 
-autodoc_typehints = 'none'
+autodoc_typehints = "none"
 
 
 # -- numpydoc ----------------------------------------------------------------
@@ -89,12 +89,12 @@
 plot_html_show_formats = False
 
 # File formats to generate (default: ['png', 'hires.png', 'pdf']).
-plot_formats = [('svg', 150), ('png', 150)]
+plot_formats = [("svg", 150), ("png", 150)]
 
 # A dictionary containing any non-standard rcParams that should be applied
 # before each plot (default: {}).
 plot_rcparams = {
-    'axes.facecolor': (1.0, 1.0, 1.0, 1.0),
-    'savefig.facecolor': (1.0, 1.0, 1.0, 0.5),
-    'savefig.transparent': False,
+    "axes.facecolor": (1.0, 1.0, 1.0, 1.0),
+    "savefig.facecolor": (1.0, 1.0, 1.0, 0.5),
+    "savefig.transparent": False,
 }
diff --git a/examples/1-basic/density.ipynb b/examples/1-basic/density.ipynb
@@ -58,20 +58,21 @@
     "nside = lmax = 128\n",
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
-    "pars = camb.set_params(H0=100*h, omch2=Oc*h**2, ombh2=Ob*h**2,\n",
-    "                       NonLinear=camb.model.NonLinear_both)\n",
+    "pars = camb.set_params(\n",
+    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
     "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.)\n",
+    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# linear radial window functions\n",
     "ws = glass.shells.linear_windows(zb)\n",
     "\n",
     "# load the angular matter power spectra previously computed with CAMB\n",
-    "cls = np.load('cls.npy')"
+    "cls = np.load(\"cls.npy\")"
    ]
   },
   {
@@ -124,7 +125,7 @@
    "outputs": [],
    "source": [
     "# constant galaxy density distribution\n",
-    "z = np.linspace(0., 1., 100)\n",
+    "z = np.linspace(0.0, 1.0, 100)\n",
     "dndz = np.full_like(z, 0.01)\n",
     "\n",
     "# distribute the dN/dz over the linear window functions\n",
@@ -158,22 +159,24 @@
    "source": [
     "# make a cube for galaxy number in redshift\n",
     "zcub = np.linspace(-zb[-1], zb[-1], 21)\n",
-    "cube = np.zeros((zcub.size-1,)*3)\n",
+    "cube = np.zeros((zcub.size - 1,) * 3)\n",
     "\n",
     "# simulate and add galaxies in each matter shell to cube\n",
     "for i, delta_i in enumerate(matter):\n",
-    "\n",
     "    # simulate positions from matter density\n",
-    "    for gal_lon, gal_lat, gal_count in glass.points.positions_from_delta(ngal[i], delta_i):\n",
-    "\n",
+    "    for gal_lon, gal_lat, gal_count in glass.points.positions_from_delta(\n",
+    "        ngal[i], delta_i\n",
+    "    ):\n",
     "        # sample redshifts uniformly in shell\n",
     "        gal_z = glass.galaxies.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",
-    "        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(np.searchsorted(zcub[1:], [z1, z2, z3]), axis=1, return_counts=True)\n",
+    "        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",
+    "        )\n",
     "        cube[i, j, k] += c"
    ]
   },
@@ -217,19 +220,28 @@
    ],
    "source": [
     "# positions of grid cells of the cube\n",
-    "z = (zcub[:-1] + zcub[1:])/2\n",
+    "z = (zcub[:-1] + zcub[1:]) / 2\n",
     "z1, z2, z3 = np.meshgrid(z, z, z)\n",
     "\n",
     "# plot the galaxy distribution in pseudo-3D\n",
     "fig = plt.figure()\n",
-    "ax = fig.add_subplot(111, projection='3d', proj_type='ortho')\n",
+    "ax = fig.add_subplot(111, projection=\"3d\", proj_type=\"ortho\")\n",
     "norm = LogNorm(vmin=np.min(cube[cube > 0]), vmax=np.max(cube), clip=True)\n",
-    "for i in range(len(zcub)-1):\n",
+    "for i in range(len(zcub) - 1):\n",
     "    v = norm(cube[..., i])\n",
     "    c = plt.cm.inferno(v)\n",
-    "    c[..., -1] = 0.2*v\n",
-    "    ax.plot_surface(z1[..., i], z2[..., i], z3[..., i], rstride=1, cstride=1,\n",
-    "                    facecolors=c, linewidth=0, shade=False, antialiased=False)\n",
+    "    c[..., -1] = 0.2 * v\n",
+    "    ax.plot_surface(\n",
+    "        z1[..., i],\n",
+    "        z2[..., i],\n",
+    "        z3[..., i],\n",
+    "        rstride=1,\n",
+    "        cstride=1,\n",
+    "        facecolors=c,\n",
+    "        linewidth=0,\n",
+    "        shade=False,\n",
+    "        antialiased=False,\n",
+    "    )\n",
     "fig.tight_layout()\n",
     "plt.show()"
    ]

diff --git a/examples/1-basic/lensing.ipynb b/examples/1-basic/lensing.ipynb
@@ -62,20 +62,21 @@
     "nside = lmax = 256\n",
     "\n",
     "# set up CAMB parameters for matter angular power spectrum\n",
-    "pars = camb.set_params(H0=100*h, omch2=Oc*h**2, ombh2=Ob*h**2,\n",
-    "                       NonLinear=camb.model.NonLinear_both)\n",
+    "pars = camb.set_params(\n",
+    "    H0=100 * h, omch2=Oc * h**2, ombh2=Ob * h**2, NonLinear=camb.model.NonLinear_both\n",
+    ")\n",
     "\n",
     "# get the cosmology from CAMB\n",
     "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.)\n",
+    "zb = glass.shells.distance_grid(cosmo, 0.0, 1.0, dx=200.0)\n",
     "\n",
     "# linear radial window functions\n",
     "ws = glass.shells.linear_windows(zb)\n",
     "\n",
     "# load the angular matter power spectra previously computed with CAMB\n",
-    "cls = np.load('cls.npy')"
+    "cls = np.load(\"cls.npy\")"
    ]
   },
   {
@@ -156,7 +157,7 @@
     "# localised redshift distribution\n",
     "# the actual density per arcmin2 does not matter here, it is never used\n",
     "z = np.linspace(0.0, 1.0, 101)\n",
-    "dndz = np.exp(-(z - 0.5)**2/(0.1)**2)\n",
+    "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)"
@@ -186,13 +187,12 @@
    "outputs": [],
    "source": [
     "# the integrated convergence and shear field over the redshift distribution\n",
-    "kappa_bar = np.zeros(12*nside**2)\n",
-    "gamm1_bar = np.zeros(12*nside**2)\n",
-    "gamm2_bar = np.zeros(12*nside**2)\n",
+    "kappa_bar = np.zeros(12 * nside**2)\n",
+    "gamm1_bar = np.zeros(12 * nside**2)\n",
+    "gamm2_bar = np.zeros(12 * nside**2)\n",
     "\n",
     "# main loop to simulate the matter fields iterative\n",
     "for i, delta_i in enumerate(matter):\n",
-    "\n",
     "    # add lensing plane from the window function of this shell\n",
     "    convergence.add_window(delta_i, ws[i])\n",
     "\n",
@@ -255,26 +255,29 @@
    ],
    "source": [
     "# get the angular power spectra of the lensing maps\n",
-    "sim_cls = hp.anafast([kappa_bar, gamm1_bar, gamm2_bar],\n",
-    "                     pol=True, lmax=lmax, use_pixel_weights=True)\n",
+    "sim_cls = hp.anafast(\n",
+    "    [kappa_bar, gamm1_bar, gamm2_bar], pol=True, lmax=lmax, 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 = [camb.sources.SplinedSourceWindow(z=z, W=dndz, source_type='lensing')]\n",
+    "pars.SourceWindows = [\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",
-    "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",
-    "plt.yscale('symlog', linthresh=1e-9, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
-    "plt.xlabel(r'angular mode number $l$')\n",
-    "plt.ylabel(r'angular power spectrum $C_l^{\\kappa\\kappa}$')\n",
+    "l = np.arange(lmax + 1)\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",
+    "plt.yscale(\"symlog\", linthresh=1e-9, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
+    "plt.xlabel(r\"angular mode number $l$\")\n",
+    "plt.ylabel(r\"angular power spectrum $C_l^{\\kappa\\kappa}$\")\n",
     "plt.legend(frameon=False)\n",
     "plt.show()"
    ]