Merge branch 'main' into saransh/test_fields

.github/workflows/examples.yml

@@ -52,3 +52,14 @@ jobs:
         run: nox -s examples
         env:
           FORCE_COLOR: 1
+
+      - name: Generate HTML
+        run: nox -s examples -- html
+        env:
+          FORCE_COLOR: 1
+
+      - name: Upload artefact
+        uses: actions/upload-artifact@v4
+        with:
+          name: Examples
+          path: examples/**/*.html

.gitignore

@@ -9,4 +9,5 @@ dist
 .env
 .coverage*
 coverage*
+*.html
 .ipynb_checkpoints

.pre-commit-config.yaml

@@ -72,3 +72,9 @@ repos:
         files: ^glass/
         additional_dependencies:
           - numpy
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+        args:
+          - --keep-output

glass/lensing.py

@@ -168,13 +168,13 @@ def from_convergence(  # noqa: PLR0913
     alm = hp.map2alm(kappa, lmax=lmax, pol=False, use_pixel_weights=True)
 
     # mode number; all conversions are factors of this
-    l = np.arange(lmax + 1)  # noqa: E741
+    ell = np.arange(lmax + 1)
 
     # this tuple will be returned
     results: tuple[npt.NDArray[np.float64], ...] = ()
 
     # convert convergence to potential
-    fl = np.divide(-2, l * (l + 1), where=(l > 0), out=np.zeros(lmax + 1))
+    fl = np.divide(-2, ell * (ell + 1), where=(ell > 0), out=np.zeros(lmax + 1))
     hp.almxfl(alm, fl, inplace=True)
 
     # if potential is requested, compute map and add to output
@@ -190,9 +190,8 @@ def from_convergence(  # noqa: PLR0913
     blm = np.zeros_like(alm)
 
     # compute deflection alms in place
-    fl = np.sqrt(l * (l + 1))
-    # TODO(ntessore): missing spin-1 pixel window function here # noqa: FIX002
-    # https://github.com/glass-dev/glass/issues/243
+    fl = np.sqrt(ell * (ell + 1))
+    # missing spin-1 pixel window function here
     hp.almxfl(alm, fl, inplace=True)
 
     # if deflection is requested, compute spin-1 maps and add to output
@@ -207,7 +206,7 @@ def from_convergence(  # noqa: PLR0913
 
     # compute shear alms in place
     # if discretised, factor out spin-0 kernel and apply spin-2 kernel
-    fl = np.sqrt((l - 1) * (l + 2), where=(l > 0), out=np.zeros(lmax + 1))
+    fl = np.sqrt((ell - 1) * (ell + 2), where=(ell > 0), out=np.zeros(lmax + 1))
     fl /= 2
     if discretized:
         pw0, pw2 = hp.pixwin(nside, lmax=lmax, pol=True)
@@ -250,9 +249,9 @@ def shear_from_convergence(
     blm = np.zeros_like(alm)
 
     # factor to convert convergence alm to shear alm
-    l = np.arange(lmax + 1)  # noqa: E741
-    fl = np.sqrt((l + 2) * (l + 1) * l * (l - 1))
-    fl /= np.clip(l * (l + 1), 1, None)
+    ell = np.arange(lmax + 1)
+    fl = np.sqrt((ell + 2) * (ell + 1) * ell * (ell - 1))
+    fl /= np.clip(ell * (ell + 1), 1, None)
     fl *= -1
 
     # if discretised, factor out spin-0 kernel and apply spin-2 kernel

glass/observations.py

@@ -23,7 +23,6 @@
 
 .. autofunction:: vmap_galactic_ecliptic
 
-
 """  # noqa: D205, D400
 
 from __future__ import annotations

glass/shapes.py

@@ -86,13 +86,13 @@ def triaxial_axis_ratio(
     x2 = np.square(xi)
 
     # eq. (11) multiplied by xi^2 zeta^2
-    A = (1 + z2m1 * sin2_phi) * cos2_theta + x2 * sin2_theta  # noqa: N806
-    B2 = 4 * z2m1**2 * cos2_theta * sin2_phi * cos2_phi  # noqa: N806
-    C = 1 + z2m1 * cos2_phi  # noqa: N806
+    a = (1 + z2m1 * sin2_phi) * cos2_theta + x2 * sin2_theta
+    b2 = 4 * z2m1**2 * cos2_theta * sin2_phi * cos2_phi
+    c = 1 + z2m1 * cos2_phi
 
     # eq. (12)
     return np.sqrt(  # type: ignore[no-any-return]
-        (A + C - np.sqrt((A - C) ** 2 + B2)) / (A + C + np.sqrt((A - C) ** 2 + B2)),
+        (a + c - np.sqrt((a - c) ** 2 + b2)) / (a + c + np.sqrt((a - c) ** 2 + b2)),
     )
 
 

glass/shells.py

@@ -40,6 +40,7 @@
 .. autofunction:: distance_weight
 .. autofunction:: volume_weight
 .. autofunction:: density_weight
+
 """  # noqa: D205, D400
 
 from __future__ import annotations

noxfile.py

@@ -47,14 +47,29 @@ def doctests(session: nox.Session) -> None:
 
 @nox.session
 def examples(session: nox.Session) -> None:
-    """Run the example notebooks."""
+    """Run the example notebooks. Pass "html" to build html."""
     session.install("-e", ".[examples]")
-    session.run(
-        "jupyter",
-        "execute",
-        *Path().glob("examples/**/*.ipynb"),
-        *session.posargs,
-    )
+
+    if session.posargs:
+        if "html" in session.posargs:
+            print("Generating HTML for the example notebooks")
+            session.run(
+                "jupyter",
+                "nbconvert",
+                "--to",
+                "html",
+                "--embed-images",
+                "examples/**/*.ipynb",
+            )
+        else:
+            print("Unsupported argument to examples")
+    else:
+        session.run(
+            "jupyter",
+            "execute",
+            *Path().glob("examples/**/*.ipynb"),
+            *session.posargs,
+        )
 
 
 @nox.session

pyproject.toml

@@ -131,6 +131,10 @@ show-fixes = true
 src = [
     "glass",
 ]
+lint.allowed-confusables = [
+    "α",
+    "γ",
+]
 lint.ignore = [
     "COM812", # missing-trailing-comma (ruff-format recommended)
     "D203", # one-blank-line-before-class

tests/test_fits.py

@@ -60,32 +60,51 @@ def _test_append(
 
 @pytest.mark.skipif(not HAVE_FITSIO, reason="test requires fitsio")
 def test_write_exception(tmp_path: pathlib.Path) -> None:
+    class TestWriteError(Exception):
+        """Custom exception for controlled testing."""
+
+    def raise_error(msg: str) -> None:
+        """Raise a custom exception for controlled testing.
+
+        Parameters
+        ----------
+        msg
+            A message to be passed to the exception.
+
+        Raises
+        ------
+        TestWriteError
+            A custom exception for controlled testing.
+
+        """
+        raise TestWriteError(msg)
+
     try:
         with user.write_catalog(tmp_path / filename, ext="CATALOG") as out:
             for i in range(my_max):
                 if i == except_int:
                     msg = "Unhandled exception"
-                    raise Exception(msg)  # noqa: TRY002, TRY301
+                    raise_error(msg)
                 array = np.arange(i, i + 1, delta)  # array of size 1/delta
                 array2 = np.arange(i + 1, i + 2, delta)  # array of size 1/delta
                 out.write(RA=array, RB=array2)
 
-    except Exception:  # noqa: BLE001
+    except TestWriteError:
         import fitsio
 
         with fitsio.FITS(tmp_path / filename) as hdul:
             data = hdul[1].read()
             assert data["RA"].size == except_int / delta
             assert data["RB"].size == except_int / delta
 
-            fitsMat = data["RA"].reshape(except_int, int(1 / delta))  # noqa: N806
-            fitsMat2 = data["RB"].reshape(except_int, int(1 / delta))  # noqa: N806
+            fits_mat = data["RA"].reshape(except_int, int(1 / delta))
+            fits_mat2 = data["RB"].reshape(except_int, int(1 / delta))
             for i in range(except_int):
                 array = np.arange(
                     i,
                     i + 1,
                     delta,
                 )  # re-create array to compare to read data
                 array2 = np.arange(i + 1, i + 2, delta)
-                assert array.tolist() == fitsMat[i].tolist()
-                assert array2.tolist() == fitsMat2[i].tolist()
+                assert array.tolist() == fits_mat[i].tolist()
+                assert array2.tolist() == fits_mat2[i].tolist()