Merge pull request #26 from larrybradley/min-deps

Update minimum versions of dependencies

.github/dependabot.yml

@@ -0,0 +1,14 @@
+# Keep dependencies updated with Dependabot version updates
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/ci_tests.yml

@@ -31,69 +31,75 @@ jobs:
       matrix:
         include:
           - os: ubuntu-latest
-            python: '3.9'
-            tox_env: 'py39-test-alldeps'
+            python: '3.10'
+            tox_env: 'py310-test-alldeps'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.10'
-            tox_env: 'py310-test-alldeps'
+            python: '3.11'
+            tox_env: 'py311-test-alldeps'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
-            tox_env: 'py311-test-alldeps-cov'
+            python: '3.12'
+            tox_env: 'py312-test-alldeps-cov'
             toxposargs: --remote-data=any
             allow_failure: false
             prefix: ''
 
           - os: macos-latest
-            python: '3.11'
-            tox_env: 'py311-test-alldeps'
+            python: '3.12'
+            tox_env: 'py312-test-alldeps'
             allow_failure: false
             prefix: ''
 
+          - os: macos-14
+            python: '3.12'
+            tox_env: 'py312-test-alldeps'
+            allow_failure: false
+            prefix: 'M1'
+
           - os: windows-latest
-            python: '3.11'
-            tox_env: 'py311-test-alldeps'
+            python: '3.12'
+            tox_env: 'py312-test-alldeps'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
-            tox_env: 'py311-test'
+            python: '3.12'
+            tox_env: 'py312-test'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
+            python: '3.12'
             tox_env: 'linkcheck'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
+            python: '3.12'
             tox_env: 'codestyle'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
+            python: '3.12'
             tox_env: 'pep517'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.11'
+            python: '3.12'
             tox_env: 'bandit'
             allow_failure: false
             prefix: ''
 
           - os: ubuntu-latest
-            python: '3.9'
-            tox_env: 'py39-test-oldestdeps'
+            python: '3.10'
+            tox_env: 'py310-test-oldestdeps'
             allow_failure: false
             prefix: ''
 

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
         # Prevent giant files from being committed.
@@ -29,6 +29,8 @@ repos:
         # source.
       - id: detect-private-key
         # Checks for the existence of private keys.
+      - id: double-quote-string-fixer
+        # Replace double-quoted strings with single-quoted strings.
       - id: end-of-file-fixer
         # Makes sure files end in a newline and only a newline.
         exclude: ".*(svg.*|extern.*|_templates.*)$"
@@ -52,21 +54,26 @@ repos:
         # Enforce that all noqa annotations always occur with specific codes.
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.17.0
     hooks:
       - id: pyupgrade
         args: ["--py39-plus"]
         exclude: ".*(extern.*)$"
 
+  - repo: https://github.com/scientific-python/cookie
+    rev: 2024.04.23
+    hooks:
+      - id: sp-repo-review
+
   - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         name: isort (python)
         additional_dependencies: [toml]
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args: ["--ignore", "E501,W503"]
@@ -77,13 +84,25 @@ repos:
       - id: yesqa
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: ["--write-changes"]
         additional_dependencies:
           - tomli
 
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0rc2
+    hooks:
+      - id: numpydoc-validation
+
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.5
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
+
   # - repo: https://github.com/MarcoGorelli/absolufy-imports
   #   rev: v0.3.1
   #   hooks:

CHANGES.rst

@@ -7,6 +7,16 @@ General
 - The ``lacosmic.test`` function has been removed. Instead use the
   ``pytest --pyarg lacosmic`` command. [#25]
 
+- The minimum required Python version is 3.10. [#26]
+
+- The minimum required Numpy version is 1.24. [#26]
+
+- The minimum required Scipy version is 1.10. [#26]
+
+- The minimum required Matplotlib version is 3.6. [#26]
+
+- The minimum required Astropy version is 5.1. [#26]
+
 
 1.1.0 (2023-11-16)
 ------------------

LICENSE.rst

@@ -1,4 +1,4 @@
-Copyright (c) 2014-2023, Larry Bradley
+Copyright (c) 2014-2024, Larry Bradley
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

docs/conf.py

@@ -1,20 +1,22 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-#
-# Documentation build configuration file.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# file.
-#
-# All configuration values have a default. Some values are defined in
-# the global Astropy configuration which is loaded here before anything
-# else. See astropy.sphinx.conf for which values are set there.
+"""
+Documentation build configuration file.
+
+This file is execfile()d with the current directory set to its
+containing dir.
+
+Note that not all possible configuration values are present in this
+file.
+
+All configuration values have a default. Some values are defined in the
+global Astropy configuration which is loaded here before anything else.
+See astropy.sphinx.conf for which values are set there.
+"""
 
 import os
 import sys
 from datetime import datetime, timezone
+from importlib import metadata
 from pathlib import Path
 
 if sys.version_info < (3, 11):
@@ -51,8 +53,6 @@
 # directories to ignore when looking for source files.
 # exclude_patterns.append('_templates')
 
-plot_formats = ['png', 'hires.png', 'pdf', 'svg']
-
 # This is added to the end of RST files - a good place to put
 # substitutions to be used globally.
 rst_epilog = """
@@ -65,18 +65,18 @@
 # -- Project information ------------------------------------------------------
 project = project_meta['name']
 author = project_meta['authors'][0]['name']
-copyright = f'2014-{datetime.now(tz=timezone.utc).year}, {author}'
+project_copyright = f'2014-{datetime.now(tz=timezone.utc).year}, {author}'
+github_project = 'larrybradley/lacosmic'
 
 # The version info for the project you're documenting, acts as
 # replacement for |version| and |release|, also used in various other
 # places throughout the built documents.
-__import__(project)
-package = sys.modules[project]
 
-# The short X.Y version.
-version = package.__version__.split('-', 1)[0]
 # The full version, including alpha/beta/rc tags.
-release = package.__version__
+release = metadata.version(project)
+# The short X.Y version.
+version = '.'.join(release.split('.')[:2])
+dev = 'dev' in release
 
 # -- Options for HTML output --------------------------------------------------
 # The global astropy configuration uses a custom theme,
@@ -138,7 +138,6 @@
               [author], 1)]
 
 # -- Resolving issue number to links in changelog -----------------------------
-github_project = conf['tool']['build-sphinx']['github_project']
 github_issues_url = f'https://github.com/{github_project}/issues/'
 
 # -- Turn on nitpicky mode for sphinx (to warn about references not found) ----
@@ -161,7 +160,7 @@
 nitpick_filename = 'nitpick-exceptions.txt'
 if os.path.isfile(nitpick_filename):
     for line in open(nitpick_filename):
-        if line.strip() == "" or line.startswith("#"):
+        if line.strip() == '' or line.startswith('#'):
             continue
         dtype, target = line.split(None, 1)
         target = target.strip()

docs/index.rst

@@ -15,13 +15,13 @@ Requirements
 
 ``lacosmic`` has the following requirements:
 
-* `Python <https://www.python.org/>`_ 3.9 or later
+* `Python <https://www.python.org/>`_ 3.10 or later
 
-* `NumPy <https://numpy.org/>`_ 1.22 or later
+* `NumPy <https://numpy.org/>`_ 1.24 or later
 
-* `Scipy <https://scipy.org/>`_ 1.7.2 or later
+* `Scipy <https://scipy.org/>`_ 1.10 or later
 
-* `Astropy`_ 5.0 or later
+* `Astropy`_ 5.1 or later
 
 
 Installation

lacosmic/conftest.py

@@ -14,7 +14,7 @@
     ASTROPY_HEADER = False
 
 # do not remove until we drop support for NumPy < 2.0
-if minversion(np, "2.0.0.dev0+git20230726"):
+if minversion(np, '2.0.0.dev0+git20230726'):
     np.set_printoptions(legacy='1.25')
 
 
@@ -26,7 +26,7 @@ def pytest_configure(config):
         # list of packages for which version numbers are displayed when
         # running the tests.
         PYTEST_HEADER_MODULES.clear()
-        deps = ['NumPy', 'SciPy', 'Matplotlib']
+        deps = ['NumPy', 'SciPy', 'Matplotlib', 'Astropy']
         for dep in deps:
             PYTEST_HEADER_MODULES[dep] = dep.lower()
 

lacosmic/tests/test_core.py

@@ -28,35 +28,45 @@ class TestLACosmic:
     """
 
     def test_lacosmic(self):
-        """Test basic lacosmic."""
+        """
+        Test basic lacosmic.
+        """
         crclean_img, crmask_img = lacosmic(CR_IMG, 1, 40, 50, error=ERROR)
         assert_allclose(crclean_img, IMG, atol=2.)
         assert_array_equal(crmask_img, MASK_REF)
 
     def test_background_scalar(self):
-        """Test lacosmic with a background scalar."""
+        """
+        Test lacosmic with a background scalar.
+        """
         crclean_img, crmask_img = lacosmic(CR_IMG, 1, 40, 50, error=ERROR,
                                            background=10)
         assert_allclose(crclean_img, IMG, atol=2.)
         assert_array_equal(crmask_img, MASK_REF)
 
     def test_background_maxiter(self):
-        """Test lacosmic with a background scalar."""
+        """
+        Test lacosmic with a background scalar.
+        """
         crclean_img, crmask_img = lacosmic(CR_IMG, 1, 40, 50, error=ERROR,
                                            background=10, maxiter=1)
         assert_allclose(crclean_img, IMG, atol=2.)
         assert_array_equal(crmask_img, MASK_REF)
 
     def test_background_image(self):
-        """Test lacosmic with a 2D background image."""
+        """
+        Test lacosmic with a 2D background image.
+        """
         bkgrd_img = np.ones(IMG.shape) * 10.
         crclean_img, crmask_img = lacosmic(CR_IMG, 1, 40, 50, error=ERROR,
                                            background=bkgrd_img)
         assert_allclose(crclean_img, IMG, atol=2.)
         assert_array_equal(crmask_img, MASK_REF)
 
     def test_mask_image(self):
-        """Test lacosmic with an input mask image."""
+        """
+        Test lacosmic with an input mask image.
+        """
         mask = MASK_REF.copy()
         mask[0:10, 0:10] = False
         mask_ref2 = np.logical_and(MASK_REF, ~mask)
@@ -66,7 +76,9 @@ def test_mask_image(self):
         assert_array_equal(crmask_img, mask_ref2)
 
     def test_large_cosmics(self):
-        """Test lacosmic cleaning with large cosmic rays."""
+        """
+        Test lacosmic cleaning with large cosmic rays.
+        """
         test_img = np.ones((7, 7))
         test_img[1:6, 1:6] = 100.
         mask_ref2 = np.zeros((7, 7), dtype=bool)