Enabling enhanced Ruff linting (#246)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "2f0f5dd538a1def8d3eacd8bebb16d3bded773c7",
+  "commit": "75f84c4adf1753af67967930c3335bc73bca9bf5",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -16,7 +16,7 @@
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
       "include_cruft_update_github_workflow": "y",
-      "use_extended_ruff_linting": "n",
+      "use_extended_ruff_linting": "y",
       "_sphinx_theme": "sunpy",
       "_parent_project": "",
       "_install_requires": "",

.github/workflows/label_sync.yml

@@ -0,0 +1,23 @@
+name: Label Sync
+on:
+  workflow_dispatch:
+  schedule:
+    #        ┌───────── minute (0 - 59)
+    #        │ ┌───────── hour (0 - 23)
+    #        │ │ ┌───────── day of the month (1 - 31)
+    #        │ │ │ ┌───────── month (1 - 12 or JAN-DEC)
+    #        │ │ │ │ ┌───────── day of the week (0 - 6 or SUN-SAT)
+    - cron: '0 0 * * *' # run every day at midnight UTC
+
+# Give permissions to write issue labels
+permissions:
+  issues: write
+
+jobs:
+  label_sync:
+    runs-on: ubuntu-latest
+    name: Label Sync
+    steps:
+      - uses: srealmoreno/label-sync-action@850ba5cef2b25e56c6c420c4feed0319294682fd
+        with:
+          config-file: https://raw.githubusercontent.com/sunpy/.github/main/labels.yml

.github/workflows/sub_package_update.yml

@@ -21,14 +21,6 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       fail-fast: true
-      matrix:
-        include:
-          - add-paths: .
-            body: apply the changes to this repo.
-            branch: cruft/update
-            commit-message: "Automatic package template update"
-            title: Updates from the package template
-
     steps:
       - uses: actions/checkout@v4
 
@@ -55,25 +47,47 @@ jobs:
           echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
 
       - name: Run update if available
+        id: cruft_update
         if: steps.check.outputs.has_changes == '1'
         run: |
           git config --global user.email "${{ github.actor }}@users.noreply.github.com"
           git config --global user.name "${{ github.actor }}"
 
-          cruft update --skip-apply-ask --refresh-private-variables
+          cruft_output=$(cruft update --skip-apply-ask --refresh-private-variables)
+          echo $cruft_output
           git restore --staged .
 
-      - name: Create pull request
+          if [[ "$cruft_output" == *"Failed to cleanly apply the update, there may be merge conflicts."* ]]; then
+            echo merge_conflicts=1 >> $GITHUB_OUTPUT
+          else
+            echo merge_conflicts=0 >> $GITHUB_OUTPUT
+          fi
+
+      - name: Check if only .cruft.json is modified
+        id: cruft_json
         if: steps.check.outputs.has_changes == '1'
+        run: |
+          git status --porcelain=1
+          if [[ "$(git status --porcelain=1)" == " M .cruft.json" ]]; then
+            echo "Only .cruft.json is modified. Exiting workflow early."
+            echo "has_changes=0" >> "$GITHUB_OUTPUT"
+          else
+            echo "has_changes=1" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Create pull request
+        if: steps.cruft_json.outputs.has_changes == '1'
         uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          add-paths: ${{ matrix.add-paths }}
-          commit-message: ${{ matrix.commit-message }}
-          branch: ${{ matrix.branch }}
+          add-paths: "."
+          commit-message: "Automatic package template update"
+          branch: "cruft/update"
           delete-branch: true
-          branch-suffix: timestamp
-          title: ${{ matrix.title }}
+          draft: ${{ steps.cruft_update.outputs.merge_conflicts == '1' }}
+          title: "Updates from the package template"
           body: |
-            This is an autogenerated PR, which will ${{ matrix.body }}.
-            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Package Template
+            This is an autogenerated PR, which will applies the latest changes from the [SunPy Package Template](https://github.com/sunpy/package-template).
+            If this pull request has been opened as a draft there are conflicts which need fixing.
+
+            **To run the CI on this pull request you will need to close it and reopen it.**

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.7.1"
+    rev: "v0.7.2"
     hooks:
       - id: ruff
         args: ["--fix"]

.ruff.toml

@@ -14,45 +14,69 @@ select = [
   "W",
   "UP",
   "PT",
+  "BLE",
+  "A",
+  "C4",
+  "INP",
+  "PIE",
+  "T20",
+  "RET",
+  "TID",
+  "PTH",
+  "PD",
+  "PLC",
+  "PLE",
+  "FLY",
+  "NPY",
+  "PERF",
+  "RUF",
 ]
 extend-ignore = [
-  # pycodestyle
+  # pycodestyle (E, W)
   "E501", # ignore line length will use a formatter instead
-  "E712", # Avoid equality comparisons to True; use if {cond}: for truth checks
-  "E721", # type comparison Use is and is not for type comparisons, or isinstance() for isinstance checks
-  # upgrades
+  # pyupgrade (UP)
   "UP038", # Use | in isinstance - not compatible with models and is slower
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT004", # Fixtures which don't return anything should have leading _
-  "PT011",  # except(ValueRaises) is too broad
   "PT023", # Always use () on pytest decorators
-  # flake8-pie
+  # flake8-pie (PIE)
   "PIE808", # Disallow passing 0 as the first argument to range
-  # flake8-use-pathlib
+  # flake8-use-pathlib (PTH)
   "PTH123", # open() should be replaced by Path.open()
-  # Ruff
+  # Ruff (RUF)
   "RUF003", # Ignore ambiguous quote marks, doesn't allow ' in comments
-  "RUF012",  # Mutable class attributes should be annotated with `typing.ClassVar`
-  "RUF013",  # PEP 484 prohibits implicit `Optional`
-  "RUF015",  # Prefer `next(iter(...))` over single element slice
+  "RUF012", # Mutable class attributes should be annotated with `typing.ClassVar`
+  "RUF013", # PEP 484 prohibits implicit `Optional`
+  "RUF015", # Prefer `next(iter(...))` over single element slice
 ]
 
 [lint.per-file-ignores]
-# Part of configuration, not a package.
-"setup.py" = ["INP001"]
-"conftest.py" = ["INP001"]
+"setup.py" = [
+  "INP001", # File is part of an implicit namespace package.
+]
+"conftest.py" = [
+  "INP001", # File is part of an implicit namespace package.
+]
 "docs/conf.py" = [
-  "E402"  # Module imports not at top of file
+  "E402" # Module imports not at top of file
 ]
 "docs/*.py" = [
-  "INP001",  # Implicit-namespace-package. The examples are not a package.
+  "INP001", # File is part of an implicit namespace package.
 ]
-"sunkit-image/*.py" = [
+"examples/**.py" = [
   "T201", # allow use of print in examples
+  "INP001", # File is part of an implicit namespace package.
+]
+"__init__.py" = [
+  "E402", # Module level import not at top of cell
+  "F401", # Unused import
+  "F403", # from {name} import * used; unable to detect undefined names
+  "F405", # {name} may be undefined, or defined from star imports
+]
+"test_*.py" = [
+  "E402", # Module level import not at top of cell
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"

examples/calculating_time_lags.py

@@ -14,7 +14,7 @@
 The specific implementation in this package is described in detail
 in Appendix C of `Barnes et al. (2019) <https://doi.org/10.3847/1538-4357/ab290c>`__.
 """
-# sphinx_gallery_thumbnail_number = 4  # NOQA: ERA001
+# sphinx_gallery_thumbnail_number = 4
 
 import dask.array
 import matplotlib.pyplot as plt

examples/detecting_swirls.py

@@ -9,7 +9,7 @@
 
 Unfortunately, currently ASDA within sunkit-image only works on arrays.
 """
-# sphinx_gallery_thumbnail_number = 3 # NOQA: ERA001
+# sphinx_gallery_thumbnail_number = 3
 
 import matplotlib.pyplot as plt
 import numpy as np

examples/finding_sunspots_using_stara.py

@@ -12,7 +12,7 @@
 `this <https://gitlab.com/wtbarnes/aia-on-pleiades/-/blob/master/notebooks/tidy/finding_sunspots.ipynb>`__
 notebook implementation of the same algorithm using dask arrays.
 """
-# sphinx_gallery_thumbnail_number = 2 # NOQA: ERA001
+# sphinx_gallery_thumbnail_number = 2
 
 import matplotlib.pyplot as plt
 from skimage.measure import label, regionprops_table

examples/tracing_loops.py

@@ -12,7 +12,7 @@
 `here <http://www.lmsal.com/~aschwand/software/tracing/tracing_tutorial1.html>`__.
 
 """
-# sphinx_gallery_thumbnail_number = 1  # NOQA: ERA001
+# sphinx_gallery_thumbnail_number = 1
 
 import matplotlib.pyplot as plt
 import numpy as np

sunkit_image/conftest.py

@@ -41,22 +41,22 @@
 
 
 @pytest.fixture(scope="session", autouse=True)
-def _tmp_config_dir(request):  # NOQA: ARG001
+def _tmp_config_dir(request):
     """
     Globally set the default config for all tests.
     """
     tmpdir = tempfile.TemporaryDirectory()
 
     os.environ["SUNPY_CONFIGDIR"] = str(tmpdir.name)
-    astropy.config.paths.set_temp_config._temp_path = str(tmpdir.name)  # NOQA: SLF001
-    astropy.config.paths.set_temp_cache._temp_path = str(tmpdir.name)  # NOQA: SLF001
+    astropy.config.paths.set_temp_config._temp_path = str(tmpdir.name)
+    astropy.config.paths.set_temp_cache._temp_path = str(tmpdir.name)
 
     yield
 
     del os.environ["SUNPY_CONFIGDIR"]
     tmpdir.cleanup()
-    astropy.config.paths.set_temp_config._temp_path = None  # NOQA: SLF001
-    astropy.config.paths.set_temp_cache._temp_path = None  # NOQA: SLF001
+    astropy.config.paths.set_temp_config._temp_path = None
+    astropy.config.paths.set_temp_cache._temp_path = None
 
 
 @pytest.fixture()
@@ -71,7 +71,7 @@ def _undo_config_dir_patch():
 
 
 @pytest.fixture(scope="session", autouse=True)
-def tmp_dl_dir(request):  # NOQA: ARG001
+def tmp_dl_dir(request):
     """
     Globally set the default download directory for the test run to a tmp dir.
     """
@@ -93,7 +93,7 @@ def _undo_download_dir_patch():
 
 
 @pytest.fixture(scope="session", autouse=True)
-def _hide_parfive_progress(request):  # NOQA: ARG001
+def _hide_parfive_progress(request):
     """
     Set the PARFIVE_HIDE_PROGRESS to hide the parfive progress bar in tests.
     """

sunkit_image/granule.py

@@ -76,7 +76,7 @@ def segment(smap, *, skimage_method="li", mark_dim_centers=False, bp_min_flux=No
         resolution,
         bp_min_flux,
     )
-    logging.info(f"Segmentation has identified {granule_count} granules and {brightpoint_count} brightpoint")  # NOQA: G004
+    logging.info(f"Segmentation has identified {granule_count} granules and {brightpoint_count} brightpoint")
     # Create output map using input wcs and adding colormap such that 0 (intergranules) = black, 1 (granule) = white, 2 (brightpoints) = yellow, 3 (dim_centers) = blue.
     segmented_map = sunpy.map.Map(seg_im_markbp, smap.wcs)
     cmap = mpl.colors.ListedColormap(["black", "white", "#ffc406", "blue"])

sunkit_image/tests/test_radial.py

@@ -268,27 +268,27 @@ def test_fit_polynomial_to_log_radial_intensity():
     degree = 1
     expected = np.polyfit(radii.to(u.R_sun).value, np.log(intensity), degree)
 
-    assert np.allclose(rad._fit_polynomial_to_log_radial_intensity(radii, intensity, degree), expected)  # NOQA: SLF001
+    assert np.allclose(rad._fit_polynomial_to_log_radial_intensity(radii, intensity, degree), expected)
 
 
 def test_calculate_fit_radial_intensity():
     polynomial = np.asarray([1, 2, 3])
     radii = (0.001, 0.002) * u.R_sun
     expected = np.exp(np.poly1d(polynomial)(radii.to(u.R_sun).value))
 
-    assert np.allclose(rad._calculate_fit_radial_intensity(radii, polynomial), expected)  # NOQA: SLF001
+    assert np.allclose(rad._calculate_fit_radial_intensity(radii, polynomial), expected)
 
 
 def test_normalize_fit_radial_intensity():
     polynomial = np.asarray([1, 2, 3])
     radii = (0.001, 0.002) * u.R_sun
     normalization_radii = (0.003, 0.004) * u.R_sun
-    expected = rad._calculate_fit_radial_intensity(radii, polynomial) / rad._calculate_fit_radial_intensity(  # NOQA: SLF001
+    expected = rad._calculate_fit_radial_intensity(radii, polynomial) / rad._calculate_fit_radial_intensity(
         normalization_radii,
         polynomial,
     )
 
-    assert np.allclose(rad._normalize_fit_radial_intensity(radii, polynomial, normalization_radii), expected)  # NOQA: SLF001
+    assert np.allclose(rad._normalize_fit_radial_intensity(radii, polynomial, normalization_radii), expected)
 
 
 @skip_windows
@@ -311,13 +311,13 @@ def test_intensity_enhance(map_test1):
         radial_bin_summary.to(u.R_sun).value <= fit_range[1].to(u.R_sun).value,
     )
 
-    polynomial = rad._fit_polynomial_to_log_radial_intensity(  # NOQA: SLF001
+    polynomial = rad._fit_polynomial_to_log_radial_intensity(
         radial_bin_summary[fit_here],
         radial_intensity[fit_here],
         degree,
     )
 
-    enhancement = 1 / rad._normalize_fit_radial_intensity(map_r, polynomial, normalization_radius)  # NOQA: SLF001
+    enhancement = 1 / rad._normalize_fit_radial_intensity(map_r, polynomial, normalization_radius)
     enhancement[map_r < normalization_radius] = 1
 
     assert np.allclose(

sunkit_image/utils/__init__.py

@@ -1,3 +1,3 @@
-from .decorators import *  # NOQA: F403
-from .noise import *  # NOQA: F403
-from .utils import *  # NOQA: F403
+from .decorators import *
+from .noise import *
+from .utils import *

sunkit_image/utils/tests/test_utils.py

@@ -128,7 +128,7 @@ def test_calculate_gamma():
     )
     N = (2 * r + 1) ** 2
     pnorm = np.linalg.norm(pm, axis=1)
-    cross = utils.utils._cross2d(pm, vel[..., 0])  # NOQA: SLF001
+    cross = utils.utils._cross2d(pm, vel[..., 0])
     vel_norm = np.linalg.norm(vel[..., 0], axis=2)
     sint = cross / (pnorm * vel_norm + 1e-10)
     expected = np.nansum(sint, axis=1) / N