Merge branch 'main' of github.com:sunpy/sunkit-image into pr/207

nabobalis · nabobalis · commit b91015368a99 · 2025-10-07T14:48:26.000-07:00
diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "88a0a31eadf2be84895e32ffd792768c2863f7ca",
+  "commit": "bea8060eef60df35f7df61d9db1d56b838bda01a",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -17,7 +17,7 @@
       "changelog_url": "https://docs.sunpy.org/projects/sunkit-image/en/stable/whatsnew/changelog.html",
       "issue_tracker_url": "https://github.com/sunpy/sunkit-image/issues",
       "license": "BSD 2-Clause",
-      "minimum_python_version": "3.10",
+      "minimum_python_version": "3.12",
       "use_compiled_extensions": "n",
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
@@ -32,7 +32,7 @@
         ".github/workflows/sub_package_update.yml"
       ],
       "_template": "https://github.com/sunpy/package-template",
-      "_commit": "88a0a31eadf2be84895e32ffd792768c2863f7ca"
+      "_commit": "bea8060eef60df35f7df61d9db1d56b838bda01a"
     }
   },
   "directory": null
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,10 +42,10 @@ jobs:
   sdist_verify:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
         with:
-          python-version: '3.12'
+          python-version: '3.13'
       - run: python -m pip install -U --user build
       - run: python -m build . --sdist
       - run: python -m pip install -U --user twine
@@ -60,18 +60,19 @@ jobs:
       toxdeps: tox-pypi-filter
       posargs: -n auto
       envs: |
-        - windows: py311
+        - linux: py314
+        - windows: py312
         - macos: py312
-        - linux: py310-oldestdeps
-        - linux: py313-devdeps
+        - linux: py312-oldestdeps
+        - linux: py314-devdeps
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   docs:
     needs: [core]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v2
     with:
-      default_python: '3.12'
+      default_python: '3.13'
       submodules: false
       pytest: false
       toxdeps: tox-pypi-filter
@@ -86,48 +87,35 @@ jobs:
     needs: [test]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v2
     with:
-      default_python: '3.12'
+      default_python: '3.13'
       submodules: false
       coverage: codecov
       toxdeps: tox-pypi-filter
       posargs: -n 1
       envs: |
-        - linux: py312-online
-    secrets:
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-
-  devdeps:
-    needs: [test]
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
-    with:
-      submodules: false
-      coverage: codecov
-      toxdeps: tox-pypi-filter
-      posargs: -n auto
-      envs: |
-        - linux: py312-devdeps
+        - linux: py313-online
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   conda:
     needs: [online]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           lfs: true
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          installer-url: https://github.com/conda-forge/miniforge/releases/download/24.3.0-0/Miniforge3-24.3.0-0-Linux-x86_64.sh
-          python-version: "3.12"
+          installer-url: https://github.com/conda-forge/miniforge/releases/download/25.3.1-0/Miniforge3-25.3.1-0-Linux-x86_64.sh
+          python-version: "3.13"
           activate-environment: sunkit_image_test
           environment-file: sunkit-test-env.yaml
       - name: Run tests
         shell: bash -el {0}
         run: |
           conda list
-          tox -e py312
+          tox -e py313
       - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -145,7 +133,7 @@ jobs:
     needs: [test, docs]
     uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v2
     with:
-      python-version: '3.12'
+      python-version: '3.13'
       test_extras: 'tests'
       test_command: 'pytest -p no:warnings --doctest-rst -m "not mpl_image_compare" --pyargs sunkit_image'
       submodules: false
diff --git a/.github/workflows/sub_package_update.yml b/.github/workflows/sub_package_update.yml
@@ -22,9 +22,9 @@ jobs:
     strategy:
       fail-fast: true
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.11"
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,16 +1,16 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.1"
+    rev: "v0.13.3"
     hooks:
       - id: ruff
         args: ["--fix", "--unsafe-fixes"]
   - repo: https://github.com/PyCQA/isort
-    rev: 6.0.1
+    rev: 6.1.0
     hooks:
       - id: isort
         exclude: ".*(.fits|.fts|.fit|.header|.txt|tca.*|extern.*|sunkit_image/extern)$"
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
@@ -35,7 +35,7 @@ repos:
     hooks:
       - id: typos
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.16.1"
+    rev: "v1.18.2"
     hooks:
       - id: mypy
         additional_dependencies: ["types-setuptools"]
diff --git a/.ruff.toml b/.ruff.toml
@@ -35,8 +35,6 @@ extend-ignore = [
   "A005", # Module `trace` shadows a Python standard-library module
   # pycodestyle (E, W)
   "E501", # ignore line length will use a formatter instead
-  # pyupgrade (UP)
-  "UP038", # Use | in isinstance - not compatible with models and is slower
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT023", # Always use () on pytest decorators
diff --git a/changelog/290.breaking.rst b/changelog/290.breaking.rst
@@ -0,0 +1,8 @@
+Increased the minimum required versions:
+
+- Python 3.12 (from 3.10)
+- Matplotlib 3.8.0 (from 3.5.0)
+- sunpy 7.0.0 (from 6.0.0)
+- NumPy 1.26.0 (from 1.23.5)
+- Astropy 6.1.0 (from 5.3.0)
+- SciPy 1.11.0 (from 1.10.1)
diff --git a/docs/conf.py b/docs/conf.py
@@ -80,8 +80,7 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-source_suffix = ".rst"
+source_suffix = {".rst": "restructuredtext"}
 
 # The master toctree document.
 master_doc = "index"
diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ build-backend = "setuptools.build_meta"
 name = "sunkit_image"
 dynamic = ["version"]
 description = "An image processing toolbox for Solar Physics."
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 readme = { file = "README.rst", content-type = "text/x-rst" }
 license = { file = "LICENSE.txt" }
 keywords = ["solar physics", "solar", "science", "image analysis"]
@@ -31,12 +31,12 @@ classifiers = [
   "Topic :: Scientific/Engineering :: Physics",
 ]
 dependencies = [
-  "astropy>=5.3.0",
-  "numpy>=1.23.5",
-  "matplotlib>=3.5.0",
-  "scipy>=1.10.1",
+  "astropy>=6.1.0",
+  "numpy>=1.26.0",
+  "matplotlib>=3.8.0",
+  "scipy>=1.11.0",
   "scikit-image>=0.20.0",
-  "sunpy[map]>=6.0.0",
+  "sunpy[map]>=7.0.0",
 ]
 
 [project.optional-dependencies]
@@ -49,7 +49,7 @@ tests = [
   "pytest-astropy",
   "pytest-mpl",
   "pytest-xdist",
-  "sunpy[data,net]>=6.0.0",
+  "sunpy[data,net]>=7.0.0",
 ]
 docs = [
   "sphinx",
@@ -63,7 +63,7 @@ docs = [
   "matplotlib",
   "sphinx-design",
   "sphinx-gallery",
-  "sunpy[data,net]>=6.0.0",
+  "sunpy[data,net]>=7.0.0",
 ]
 dev = ["sunkit_image[all,tests,docs]"]
 
diff --git a/sunkit_image/coalignment/tests/test_coalignment.py b/sunkit_image/coalignment/tests/test_coalignment.py
@@ -132,7 +132,7 @@ def test_unsupported_affine_parameters(incorrect_pointing_cutout_map, aia171_tes
         rotation_matrix=2*np.eye(2),
         translation=[0,0],
     )
-    with pytest.raises(NotImplementedError, match='Changes to the rotation metadata are currently not supported.'):
+    with pytest.raises(NotImplementedError, match=r"Changes to the rotation metadata are currently not supported."):
         _ = _update_fits_wcs_metadata(incorrect_pointing_cutout_map,
                                       aia171_test_map,
                                       affine_rot)
@@ -141,7 +141,7 @@ def test_unsupported_affine_parameters(incorrect_pointing_cutout_map, aia171_tes
         rotation_matrix=np.eye(2),
         translation=[0,0],
     )
-    with pytest.raises(NotImplementedError, match='Changes to the pixel scale metadata are currently not supported.'):
+    with pytest.raises(NotImplementedError, match=r"Changes to the pixel scale metadata are currently not supported."):
         _ = _update_fits_wcs_metadata(incorrect_pointing_cutout_map,
                                       aia171_test_map,
                                       affine_scale)
diff --git a/sunkit_image/coalignment/tests/test_match_template.py b/sunkit_image/coalignment/tests/test_match_template.py
@@ -39,11 +39,11 @@ def test_get_correlation_shifts():
 
     # Input array is too big in either direction
     test_array = np.zeros((4, 3))
-    with pytest.raises(ValueError, match="Input array dimension should not be greater than 3 in any dimension."):
+    with pytest.raises(ValueError, match=r"Input array dimension should not be greater than 3 in any dimension."):
         _get_correlation_shifts(test_array)
 
     test_array = np.zeros((3, 4))
-    with pytest.raises(ValueError, match="Input array dimension should not be greater than 3 in any dimension."):
+    with pytest.raises(ValueError, match=r"Input array dimension should not be greater than 3 in any dimension."):
         _get_correlation_shifts(test_array)
 
 
diff --git a/sunkit_image/tests/figure_hashes_mpl_3100_ft_261_sunpy_700_astropy_710.json b/sunkit_image/tests/figure_hashes_mpl_3100_ft_261_sunpy_700_astropy_710.json
diff --git a/sunkit_image/tests/test_enhance.py b/sunkit_image/tests/test_enhance.py
@@ -35,7 +35,7 @@ def map_test():
 
 def test_nans_raise_warning(map_test):
     map_test[0, 0] = np.nan
-    with pytest.warns(UserWarning, match="One or more entries in the input data are NaN."):
+    with pytest.warns(UserWarning, match=r"One or more entries in the input data are NaN."):
         enhance.mgn(map_test)
 
 
diff --git a/sunkit_image/tests/test_granule.py b/sunkit_image/tests/test_granule.py
@@ -28,7 +28,7 @@ def test_segment(granule_map):
 
 
 def test_segment_errors(granule_map):
-    with pytest.raises(TypeError, match="Input must be an instance of a sunpy.map.GenericMap"):
+    with pytest.raises(TypeError, match=r"Input must be an instance of a sunpy.map.GenericMap"):
         segment(np.array([[1, 2, 3], [1, 2, 3]]))
     with pytest.raises(ValueError, match="Method must be one of: li, otsu, yen, mean, minimum, triangle, isodata"):
         segment(granule_map, skimage_method="banana")
@@ -51,7 +51,7 @@ def test_get_threshold_range():
 
 
 def test_get_threshold_errors():
-    with pytest.raises(TypeError, match="Input data must be an instance of a np.ndarray"):
+    with pytest.raises(TypeError, match=r"Input data must be an instance of a np.ndarray"):
         _get_threshold([], "li")
     with pytest.raises(ValueError, match="Method must be one of: li, otsu, yen, mean, minimum, triangle, isodata"):
         _get_threshold(np.array([[1, 2], [1, 2]]), "banana")
@@ -82,7 +82,7 @@ def test_trim_intergranules_errors():
     rng = np.random.default_rng()
     # Check that raises error if passed array is not binary.
     data = rng.integers(low=0, high=10, size=(10, 10))
-    with pytest.raises(ValueError, match="segmented_image must only have values of 1 and 0."):
+    with pytest.raises(ValueError, match=r"segmented_image must only have values of 1 and 0."):
         _trim_intergranules(data)
 
 
diff --git a/sunkit_image/tests/test_radial.py b/sunkit_image/tests/test_radial.py
@@ -332,5 +332,5 @@ def test_intensity_enhance(map_test1):
 def test_intensity_enhance_errors(map_test1):
     fit_range = [1, 1.5] * u.R_sun
     scale = 1 * map_test1.rsun_obs
-    with pytest.raises(ValueError, match="The fit range must be strictly increasing."):
+    with pytest.raises(ValueError, match=r"The fit range must be strictly increasing."):
         rad.intensity_enhance(map_test1, scale=scale, fit_range=fit_range[::-1])
diff --git a/sunkit_image/utils/tests/test_utils.py b/sunkit_image/utils/tests/test_utils.py
@@ -41,12 +41,12 @@ def test_equally_spaced_bins():
     assert esb2[0, 999] == 1.999
     assert esb2[1, 999] == 2.000
     # The radii have the correct relative sizes
-    with pytest.raises(ValueError, match="The inner value must be strictly less than the outer value."):
+    with pytest.raises(ValueError, match=r"The inner value must be strictly less than the outer value."):
         utils.equally_spaced_bins(inner_value=1.0, outer_value=1.0)
-    with pytest.raises(ValueError, match="The inner value must be strictly less than the outer value."):
+    with pytest.raises(ValueError, match=r"The inner value must be strictly less than the outer value."):
         utils.equally_spaced_bins(inner_value=1.5, outer_value=1.0)
     # The number of bins is strictly greater than 0
-    with pytest.raises(ValueError, match="The number of bins must be strictly greater than 0."):
+    with pytest.raises(ValueError, match=r"The number of bins must be strictly greater than 0."):
         utils.equally_spaced_bins(nbins=0)
 
 
diff --git a/tox.ini b/tox.ini
@@ -1,9 +1,9 @@
 [tox]
 min_version = 4.0
 envlist =
-    py{310,311,312}{,-figure}
-    py312-devdeps
-    py310-oldestdeps
+    py{312,313,314}{,-figure}
+    py314-devdeps
+    py312-oldestdeps
     codestyle
     build_docs
 requires =
@@ -49,9 +49,9 @@ deps =
     # Handle minimum dependencies via minimum_dependencies
     oldestdeps: minimum_dependencies
     # Figure tests need a tightly controlled environment
-    figure-!devdeps: astropy==6.1.0
-    figure-!devdeps: matplotlib==3.9.0
-    figure-!devdeps: sunpy==6.0.0
+    figure-!devdeps: astropy==7.1.0
+    figure-!devdeps: matplotlib==3.10.0
+    figure-!devdeps: sunpy==7.0.0
 # The following indicates which extras_require will be installed
 extras =
     all
