Merge branch 'main' into add-3-12-support

.github/workflows/deploy.yml

@@ -1,11 +1,10 @@
 ---
 name: Deploy
 
-# yamllint disable-line rule:truthy
 on:
   push:
     tags:
-      - "v*"
+      - v*
 
 jobs:
   deploy:
@@ -14,7 +13,7 @@ jobs:
       id-token: write
     steps:
       # yamllint disable-line rule:line-length
-      - uses: paddyroddy/.github/actions/python/deployment@5db0473ebf89b7132850d118505c172be8022f97 # v0
+      - uses: paddyroddy/.github/actions/python/deployment@be31e8f5758700dafb58c5852530e750f1ea69d8 # v0
         with:
           pyproject-toml: ./pyproject.toml
           python-version: "3.12"

.github/workflows/documentation.yml

@@ -1,7 +1,6 @@
 ---
 name: Documentation
 
-# yamllint disable-line rule:truthy
 on:
   push:
     branches:
@@ -12,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # yamllint disable-line rule:line-length
-      - uses: paddyroddy/.github/actions/python/pdoc@5db0473ebf89b7132850d118505c172be8022f97 # v0
+      - uses: paddyroddy/.github/actions/python/pdoc@be31e8f5758700dafb58c5852530e750f1ea69d8 # v0
         with:
           docs-dependency-section: .[docs]
           gh-pages-publish-directory: ./html/sleplet

.github/workflows/examples.yml

@@ -1,12 +1,11 @@
 ---
 name: Examples
 
-# yamllint disable-line rule:truthy
 on:
   push:
     branches:
       - main
-      - "renovate/**"
+      - renovate/**
   pull_request:
 
 concurrency:
@@ -22,14 +21,14 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
 
       - name: Cache pooch
-        uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
         with:
           path: ~/.cache/sleplet
           key: readme-${{ hashFiles('pyproject.toml') }}
@@ -47,14 +46,14 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up python
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
 
       - name: Cache pooch
-        uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4
+        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
         with:
           path: ~/.cache/sleplet
           key: examples-${{ hashFiles('pyproject.toml') }}

.github/workflows/licence.yml

@@ -1,17 +1,16 @@
 ---
 name: Update Copyright
 
-# yamllint disable-line rule:truthy
 on:
   schedule:
-    - cron: "0 3 1 1 *"
+    - cron: 0 3 1 1 *
 
 jobs:
   update-licence-year:
     runs-on: ubuntu-latest
     steps:
       # yamllint disable-line rule:line-length
-      - uses: paddyroddy/.github/actions/licence@5db0473ebf89b7132850d118505c172be8022f97 # v0
+      - uses: paddyroddy/.github/actions/licence@be31e8f5758700dafb58c5852530e750f1ea69d8 # v0
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           licence-file: ./LICENCE.txt

.github/workflows/linting.yml

@@ -1,19 +1,18 @@
 ---
 name: Linting
 
-# yamllint disable-line rule:truthy
 on:
   push:
     branches:
       - main
-      - "renovate/**"
+      - renovate/**
   pull_request:
 
 jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
       # yamllint disable-line rule:line-length
-      - uses: paddyroddy/.github/actions/linting@5db0473ebf89b7132850d118505c172be8022f97 # v0
+      - uses: paddyroddy/.github/actions/linting@be31e8f5758700dafb58c5852530e750f1ea69d8 # v0
         with:
           pre-commit-config: ./.pre-commit-config.yaml

.github/workflows/paper.yml

@@ -1,14 +1,13 @@
 ---
 name: Paper
 
-# yamllint disable-line rule:truthy
 on:
   push:
     branches:
       - main
   pull_request:
     paths:
-      - "paper/**"
+      - paper/**
 
 jobs:
   paper:

.github/workflows/test.yml

@@ -1,12 +1,11 @@
 ---
 name: Test
 
-# yamllint disable-line rule:truthy
 on:
   push:
     branches:
       - main
-      - "renovate/**"
+      - renovate/**
   pull_request:
 
 jobs:
@@ -25,7 +24,7 @@ jobs:
           - "3.12"
     steps:
       # yamllint disable-line rule:line-length
-      - uses: paddyroddy/.github/actions/python/tox@5db0473ebf89b7132850d118505c172be8022f97 # v0
+      - uses: paddyroddy/.github/actions/python/tox@be31e8f5758700dafb58c5852530e750f1ea69d8 # v0
         with:
           cache-path: |-
             .tox
@@ -51,6 +50,7 @@ jobs:
         uses: coverallsapp/github-action@3dfc5567390f6fa9267c0ee9c251e4c8c3f18949 # v2
         with:
           parallel-finished: true
+          # yamllint disable-line rule:quoted-strings
           carryforward: "\
             run-macos-latest-3.10,\
             run-ubuntu-latest-3.10,\

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 ---
 repos:
   - repo: https://github.com/paddyroddy/.github
-    rev: v0.130.0
+    rev: v0.157.0
     hooks:
       - id: general-hooks
       - id: python-hooks

README.md

@@ -10,6 +10,7 @@
 [![Coverage Status](https://coveralls.io/repos/github/astro-informatics/sleplet/badge.svg?branch=main)](https://coveralls.io/github/astro-informatics/sleplet?branch=main)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![Renovate](https://img.shields.io/badge/renovate-enabled-orange?logo=renovatebot)](https://renovatebot.com)
+[![repostatus](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
 
 `SLEPLET` is a Python package for the construction of Slepian wavelets in the
 spherical and manifold (via meshes) settings. The API of `SLEPLET` has been

examples/arbitrary/_denoising_slepian_wavelet.py

@@ -11,7 +11,7 @@ def denoising_slepian_wavelet(
     slepian_wavelets: sleplet.functions.SlepianWavelets,
     snr_in: float,
     n_sigma: int,
-) -> npt.NDArray[np.complex_]:
+) -> npt.NDArray[np.complex128]:
     """Denoising demo using Slepian wavelets."""
     # compute wavelet coefficients
     w = sleplet.wavelet_methods.slepian_wavelet_forward(

examples/arbitrary/_slepian_wavelet_covariance.py

@@ -13,7 +13,7 @@ def compute_slepian_wavelet_covariance(
     slepian_wavelets: sleplet.functions.SlepianWavelets,
     *,
     var_signal: float,
-) -> npt.NDArray[np.float_]:
+) -> npt.NDArray[np.float64]:
     """Compute the theoretical covariance of the wavelet coefficients."""
     s_p = sleplet.slepian_methods.compute_s_p_omega(L, slepian_wavelets.slepian)
     wavelets_reshape = slepian_wavelets.wavelets[

examples/arbitrary/africa/denoising_slepian_africa.py

@@ -6,7 +6,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parents[1]))
 
-from _denoising_slepian_wavelet import denoising_slepian_wavelet  # noqa: E402
+from _denoising_slepian_wavelet import denoising_slepian_wavelet
 
 B = 3
 J_MIN = 2

examples/arbitrary/africa/progressive_wavelet_reconstruction_africa.py

@@ -21,7 +21,7 @@ def main() -> None:
     )
 
     # plot
-    f_p = np.zeros(swc.slepian.N, dtype=np.complex_)
+    f_p = np.zeros(swc.slepian.N, dtype=np.complex128)
     for p, coeff in enumerate(swc.wavelet_coefficients):
         print(f"plot reconstruction: {p}")
         f_p += sleplet.wavelet_methods.slepian_wavelet_inverse(

examples/arbitrary/africa/slepian_wavelet_covariance_africa.py

@@ -7,7 +7,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parents[1]))
 
-from _slepian_wavelet_covariance import compute_slepian_wavelet_covariance  # noqa: E402
+from _slepian_wavelet_covariance import compute_slepian_wavelet_covariance
 
 B = 3
 J_MIN = 2
@@ -32,7 +32,7 @@ def main() -> None:
 
     # initialise matrix
     covar_runs_shape = (RUNS, *covar_theory.shape)
-    covar_data_runs = np.zeros(covar_runs_shape, dtype=np.complex_)
+    covar_data_runs = np.zeros(covar_runs_shape, dtype=np.complex128)
 
     # set seed
     rng = np.random.default_rng(RANDOM_SEED)

examples/arbitrary/south_america/denoising_slepian_functions_south_america.py

@@ -19,7 +19,7 @@ def _denoising_slepian_function(
     noised_signal: sleplet.functions.SlepianSouthAmerica,
     snr_in: float,
     n_sigma: int,
-) -> npt.NDArray[np.complex_]:
+) -> npt.NDArray[np.complex128]:
     """Denoising demo using Slepian function."""
     # compute Slepian noise
     sigma_noise = sleplet.noise.compute_sigma_noise(

examples/arbitrary/south_america/denoising_slepian_south_america.py

@@ -6,7 +6,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parents[1]))
 
-from _denoising_slepian_wavelet import denoising_slepian_wavelet  # noqa: E402
+from _denoising_slepian_wavelet import denoising_slepian_wavelet
 
 B = 3
 J_MIN = 2

examples/arbitrary/south_america/progressive_wavelet_reconstruction_south_america.py

@@ -21,7 +21,7 @@ def main() -> None:
     )
 
     # plot
-    f_p = np.zeros(swc.slepian.N, dtype=np.complex_)
+    f_p = np.zeros(swc.slepian.N, dtype=np.complex128)
     for p, coeff in enumerate(swc.wavelet_coefficients):
         print(f"plot reconstruction: {p}")
         f_p += sleplet.wavelet_methods.slepian_wavelet_inverse(

examples/arbitrary/south_america/slepian_wavelet_covariance_south_america.py

@@ -7,7 +7,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parents[1]))
 
-from _slepian_wavelet_covariance import compute_slepian_wavelet_covariance  # noqa: E402
+from _slepian_wavelet_covariance import compute_slepian_wavelet_covariance
 
 B = 3
 J_MIN = 2
@@ -32,7 +32,7 @@ def main() -> None:
 
     # initialise matrix
     covar_runs_shape = (RUNS, *covar_theory.shape)
-    covar_data_runs = np.zeros(covar_runs_shape, dtype=np.complex_)
+    covar_data_runs = np.zeros(covar_runs_shape, dtype=np.complex128)
 
     # set seed
     rng = np.random.default_rng(RANDOM_SEED)

examples/mesh/denoising_slepian_mesh.py

@@ -26,7 +26,7 @@ def _denoising_mesh_slepian(
     mesh_slepian_wavelets: sleplet.meshes.MeshSlepianWavelets,
     snr_in: float,
     n_sigma: int,
-) -> npt.NDArray[np.complex_ | np.float_]:
+) -> npt.NDArray[np.complex128 | np.float64]:
     """Denoising demo using Slepian wavelets."""
     # compute wavelet coefficients
     w = sleplet.wavelet_methods.slepian_wavelet_forward(

examples/mesh/produce_table.py

@@ -3,7 +3,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parent))
 
-from denoising_slepian_mesh import main  # noqa: E402
+from denoising_slepian_mesh import main
 
 MESH_SNR_DICT = {
     "cheetah": -8.64,

examples/misc/_denoising_axisym.py

@@ -20,7 +20,7 @@ def denoising_axisym(  # noqa: PLR0913
     n_sigma: int,
     *,
     rotate_to_south_america: bool = False,
-) -> tuple[npt.NDArray[np.complex_], float | None, float]:
+) -> tuple[npt.NDArray[np.complex128], float | None, float]:
     """Reproduce the denoising demo from S2LET paper."""
     # compute wavelet coefficients
     w = sleplet.wavelet_methods.axisymmetric_wavelet_forward(

examples/misc/denoising_axisym_africa.py

@@ -5,7 +5,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parent))
 
-from _denoising_axisym import denoising_axisym  # noqa: E402
+from _denoising_axisym import denoising_axisym
 
 B = 2
 J_MIN = 0

examples/misc/denoising_axisym_earth.py

@@ -7,7 +7,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parent))
 
-from _denoising_axisym import denoising_axisym  # noqa: E402
+from _denoising_axisym import denoising_axisym
 
 B = 2
 J_MIN = 0

examples/misc/denoising_axisym_south_america.py

@@ -5,7 +5,7 @@
 
 sys.path.append(str(pathlib.Path(__file__).resolve().parent))
 
-from _denoising_axisym import denoising_axisym  # noqa: E402
+from _denoising_axisym import denoising_axisym
 
 B = 2
 J_MIN = 0

examples/misc/wavelet_transform.py

@@ -26,7 +26,7 @@ def main() -> None:
     plt.close()
 
 
-def _ricker(freq: float) -> npt.NDArray[np.float_]:
+def _ricker(freq: float) -> npt.NDArray[np.float64]:
     """Create a Ricker wavelet."""
     t = np.arange(-LENGTH / 2, (LENGTH - DELTA_T) / 2, DELTA_T)
     return (1.0 - 2.0 * (np.pi**2) * (freq**2) * (t**2)) * np.exp(

examples/polar_cap/eigenfunctions.py

@@ -53,7 +53,7 @@ def main() -> None:
 def _helper(
     ax: mpl.axes.Axes,
     slepian: sleplet.slepian.SlepianPolarCap,
-    x: npt.NDArray[np.float_],
+    x: npt.NDArray[np.float64],
     i: int,
     rank: int,
 ) -> None:

examples/polar_cap/simons_5_1.py

@@ -52,7 +52,7 @@ def _helper(  # noqa: PLR0913
     ax: npt.NDArray[typing.Any],
     slepian: sleplet.slepian.SlepianPolarCap,
     resolution: int,
-    x: npt.NDArray[np.float_],
+    x: npt.NDArray[np.float64],
     i: int,
     order: int,
     rank: int,

examples/polar_cap/slepian_coefficients.py

@@ -14,7 +14,7 @@
 def _earth_region_harmonic_coefficients(
     L: int,
     theta_max: int,
-) -> npt.NDArray[np.float_]:
+) -> npt.NDArray[np.float64]:
     """Harmonic coefficients of the Earth for the polar cap region."""
     region = sleplet.slepian.Region(theta_max=np.deg2rad(theta_max))
     earth = sleplet.functions.Earth(L, region=region)
@@ -26,7 +26,7 @@ def _earth_region_harmonic_coefficients(
 def _earth_region_slepian_coefficients(
     L: int,
     theta_max: int,
-) -> npt.NDArray[np.float_]:
+) -> npt.NDArray[np.float64]:
     """Compute the Slepian coefficients."""
     region = sleplet.slepian.Region(theta_max=np.deg2rad(theta_max))
     earth = sleplet.functions.Earth(L, region=region)