Full rewrite for speed and logical simplicity

.github/workflows/ci.yml

@@ -35,6 +35,18 @@ jobs:
     - name: Lint with ruff
       run: |
         ruff check .
+    - name: Run codespell on source code
+      uses: codespell-project/actions-codespell@v2
+      with:
+        skip: '*.fits'
+        ignore_words_file: .codespellignore
+        path: punchbowl
+    - name: Run codespell on documentation
+      uses: codespell-project/actions-codespell@v2
+      with:
+        skip: '*.fits'
+        ignore_words_file: .codespellignore
+        path: docs/source
     - name: Test with pytest
       run: |
         coverage run -m pytest

.github/workflows/docs.yml

@@ -21,9 +21,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r ./docs/requirements.txt
-        pip install ".[test]"
-        python setup.py build_ext --inplace
+        pip install ".[docs]"
 
     # Build the book
     - name: Sphinx build

.pre-commit-config.yaml

@@ -11,6 +11,12 @@ repos:
     hooks:
       - id: isort
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunpy/extern)$"
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.1.0
+    hooks:
+      - id: codespell
+        files: ^.*\.(py|c|h|md|rst|yml)$
+        args: [ "--ignore-words", ".codespellignore" ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:

.readthedocs.yaml

@@ -0,0 +1,29 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: docs/requirements.txt

CITATION.cff

@@ -19,7 +19,7 @@ authors:
   given-names: "Daniel"
   orcid: "https://orcid.org/0000-0002-0494-2025"
 title: "regularizepsf"
-version: 0.4.0
+version: 1.0.0
 doi: 10.5281/zenodo.7392170
-date-released: 2024-08-18
+date-released: 2024-09-09
 url: "https://github.com/punch-mission/regularizepsf"

docs/requirements.txt

@@ -1,3 +1,17 @@
+numpy
+h5py
+sep-pjw
+astropy
+scipy
+scikit-image
+matplotlib
+pytest
+pytest-cov
+hypothesis
+coverage
+ruff
+pytest-mpl
+pre-commit
 sphinx
 pydata-sphinx-theme
-sphinx-autoapi
+sphinx-autoapi

docs/source/conf.py

@@ -8,13 +8,15 @@
 import os
 import sys
 
+import regularizepsf
+
 sys.path.insert(0, os.path.abspath("../.."))
 
 
 project = "regularizepsf"
-copyright = "2023, J. Marcus Hughes and the PUNCH Science Operations Center"
-author = "J. Marcus Hughes and the PUNCH Science Operations Center"
-release = "0.4.0"
+copyright = "2024, J. Marcus Hughes and the PUNCH Science Operations Center"
+author = "J. Marcus Hughes, PUNCH Science Operations Center, and collaborators"
+release = regularizepsf.__version__
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -27,7 +29,6 @@
 exclude_patterns = []
 
 
-
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
@@ -48,7 +49,6 @@
     "show_toc_level": 3,
 }
 html_context = {
-    # "github_url": "https://github.com", # or your GitHub Enterprise site
     "github_user": "punch-mission",
     "github_repo": "regularizepsf",
     "github_version": "main",

docs/source/development.rst

@@ -13,7 +13,7 @@ Setting up pre-commit
 
 The first time you develop code, you'll need to install the pre-commit. This checks that our style is consistent.
 It gets installed when you do ``pip install ".[test]"`` but then requires you to activate them by
-running ``pre-commit install``. Now everytime you commit, our checks will run first.
+running ``pre-commit install``. Now every time you commit, our checks will run first.
 
 Building the docs
 ------------------

pyproject.toml

@@ -1,22 +1,12 @@
-[build-system]
-requires = ["setuptools", "wheel", "numpy", "Cython>=0.29.21"]
-build-backend = "setuptools.build_meta"
-
-[tool.setuptools]
-packages = ["regularizepsf"]
-
 [project]
 name = "regularizepsf"
-version = "0.4.0"
+version = "1.0.0"
 requires-python = ">3.10"
 description = "Point spread function modeling and regularization"
 dependencies = [
       "numpy",
-      "dill",
       "h5py",
-      "lmfit",
       "sep-pjw",
-      "cython",
       "astropy",
       "scipy",
       "scikit-image",
@@ -43,15 +33,11 @@ docs = [
 
 dev = ["regularizepsf[test, docs]", "pre-commit"]
 
-
 [tool.ruff]
-exclude = ['tests/*']
+exclude = ['tests/*', 'docs/*']
 line-length = 120
-# lint.select = ["ALL"]
-lint.ignore = [ "FBT001", "FBT002", "ANN401"]
-
-#[tool.ruff.lint]
-#select = ["NPY201"]
+lint.select = ["ALL"]
+lint.ignore = [ "FBT001", "FBT002", "ANN101", "ANN102", "ANN401", "FIX002", "TD", "PD011", "I001"]
 
 [tool.isort]
 balanced_wrapping = true

regularizepsf/__init__.py

@@ -1,9 +1,5 @@
-from regularizepsf.corrector import ArrayCorrector  # noqa: F401
-from regularizepsf.corrector import FunctionalCorrector  # noqa: F401
-from regularizepsf.corrector import calculate_covering  # noqa: F401
-from regularizepsf.fitter import CoordinatePatchCollection  # noqa: F401
-from regularizepsf.psf import simple_psf  # noqa: F401
-from regularizepsf.psf import varied_psf  # noqa: F401
-from regularizepsf.visualize import visualize_patch_counts  # noqa: F401
-from regularizepsf.visualize import visualize_PSFs  # noqa: F401
-from regularizepsf.visualize import visualize_transfer_kernels  # noqa: F401
+"""Global init."""
+
+import importlib.metadata
+
+__version__ = importlib.metadata.version("regularizepsf")

regularizepsf/builder.py

@@ -0,0 +1,27 @@
+"""Functions for building PSF models from images."""
+
+import pathlib
+
+from regularizepsf.psf import ArrayPSF
+
+
+class ArrayPSFBuilder:
+    """A builder that will take a series of images and construct an ArrayPSF to represent their implicit PSF."""
+
+    def __init__(self) -> None:
+        """Initialize an ArrayPSFBuilder."""
+
+    def build(self, image_paths: list[pathlib.Path]) -> ArrayPSF:
+        """Build the PSF model.
+
+        Parameters
+        ----------
+        image_paths : list[pathlib.Path]
+            paths of images to use
+
+        Returns
+        -------
+        ArrayPSF
+            an array PSF
+
+        """