Merge branch 'main' of github.com:sunpy/ndcube into meta

sunpy · Nov 13, 2024 · 5c0e2cb · 5c0e2cb
2 parents 39d675d + 60a0c79
commit 5c0e2cb
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "7b0225e0a206b7b6249752991334dea7e9ffcfd4",
+  "commit": "51fb616094a4d7577c8898445aa50effb89afa31",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -16,7 +16,8 @@
       "enable_dynamic_dev_versions": "y",
       "include_example_code": "n",
       "include_cruft_update_github_workflow": "y",
-      "_sphinx_theme": "alabaster",
+      "use_extended_ruff_linting": "y",
+      "_sphinx_theme": "sunpy",
       "_parent_project": "",
       "_install_requires": "",
       "_copy_without_render": [

diff --git a/.github/workflows/label_sync.yml b/.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
diff --git a/.github/workflows/sub_package_update.yml b/.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.**
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 repos:
     # This should be before any formatting hooks like isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.7.2"
     hooks:
       - id: ruff
         args: ["--fix"]

diff --git a/.ruff.toml b/.ruff.toml
@@ -1,5 +1,5 @@
 target-version = "py310"
-line-length = 110
+line-length = 120
 exclude = [
   ".git,",
   "__pycache__",
@@ -12,34 +12,75 @@ select = [
   "E",
   "F",
   "W",
-  #"UP",
-  #"PT"
+  "UP",
+  "PT",
+  "BLE",
+  "A",
+  "C4",
+  "INP",
+  "PIE",
+  "T20",
+  "RET",
+  "TID",
+  "PTH",
+  "PD",
+  "PLC",
+  "PLE",
+  "FLY",
+  "NPY",
+  "PERF",
+  "RUF",
 ]
 extend-ignore = [
-  "E712",
-  "E721",
   # pycodestyle (E, W)
-  "E501", # LineTooLong                             # TODO! fix
+  "E501", # ignore line length will use a formatter instead
+  # pyupgrade (UP)
+  "UP038", # Use | in isinstance - not compatible with models and is slower
+  # numpy
+  "NPY002", # TODO: migrate from np.random.rand to np.random.Generator
   # pytest (PT)
   "PT001", # Always use pytest.fixture()
   "PT004", # Fixtures which don't return anything should have leading _
-  "PT007", # Parametrize should be lists of tuples  # TODO! fix
-  "PT011", # Too broad exception assert             # TODO! fix
+  "PT011", # TODO: except(ValueRaises) is too broad
+  "PT012", # TODO: except statement is too lengthy
   "PT023", # Always use () on pytest decorators
+  # flake8-pie (PIE)
+  "PIE808", # Disallow passing 0 as the first argument to range
+  # flake8-use-pathlib (PTH)
+  "PTH123", # open() should be replaced by Path.open()
+  # 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
 ]
 
 [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.
+]
+"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"
diff --git a/docs/conf.py b/docs/conf.py
@@ -3,6 +3,7 @@
 import os
 import warnings
 import datetime
+from pathlib import Path
 
 from astropy.utils.exceptions import AstropyDeprecationWarning
 from matplotlib import MatplotlibDeprecationWarning
@@ -58,7 +59,7 @@
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-# templates_path = ["_templates"]  # NOQA: ERA001
+# templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -116,7 +117,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ["_static"]  # NOQA: ERA001
+# html_static_path = ["_static"]
 
 # By default, when rendering docstrings for classes, sphinx.ext.autodoc will
 # make docs with the class-level docstring and the class-method docstrings,
@@ -146,11 +147,11 @@
 # -- Sphinx Gallery ---------------------------------------------------------
 
 sphinx_gallery_conf = {
-    'backreferences_dir': os.path.join('generated', 'modules'),
+    'backreferences_dir': Path('generated/modules'),
     'filename_pattern': '^((?!skip_).)*$',
-    'examples_dirs': os.path.join('..', 'examples'),
+    'examples_dirs': Path('../examples'),
     'within_subsection_order': "ExampleTitleSortKey",
-    'gallery_dirs': os.path.join('generated', 'gallery'),
+    'gallery_dirs': Path('generated/gallery'),
     'matplotlib_animations': True,
     "default_thumb_file": png_icon,
     'abort_on_example_error': False,

diff --git a/examples/creating_even_spaced_wavelength_visualisation.py b/examples/creating_even_spaced_wavelength_visualisation.py
@@ -34,7 +34,7 @@
 # `sequence=True` causes a sequence of maps to be returned, one for each image file.
 sequence_of_maps = sunpy.map.Map(aia_files, sequence=True)
 # Sort the maps in the sequence in order of wavelength.
-sequence_of_maps.maps = list(sorted(sequence_of_maps.maps, key=lambda m: m.wavelength))
+sequence_of_maps.maps = sorted(sequence_of_maps.maps, key=lambda m: m.wavelength)
 
 #############################################################################
 # Using an `astropy.units.Quantity` of the wavelengths of the images, we can construct

diff --git a/ndcube/__init__.py b/ndcube/__init__.py
@@ -1,8 +1,9 @@
 """
+======
 ndcube
 ======
 
-A base package for multi-dimensional contiguous and non-contiguous coordinate-aware arrays.
+A package for multi-dimensional contiguous and non-contiguous coordinate-aware arrays.
 
 * Homepage: https://github.com/sunpy/ndcube
 * Documentation: https://docs.sunpy.org/projects/ndcube/
@@ -15,4 +16,17 @@
 from .ndcube_sequence import NDCubeSequence, NDCubeSequenceBase
 from .version import version as __version__
 
-__all__ = ['NDCube', 'NDCubeSequence', "NDCollection", "NDMeta", "ExtraCoords", "GlobalCoords", "ExtraCoordsABC", "GlobalCoordsABC", "NDCubeBase", "NDCubeSequenceBase", "__version__"]
+
+__all__ = [
+    "NDCube",
+    "NDCubeSequence",
+    "NDCollection",
+    "NDMeta",
+    "ExtraCoords",
+    "GlobalCoords",
+    "ExtraCoordsABC",
+    "GlobalCoordsABC",
+    "NDCubeBase",
+    "NDCubeSequenceBase",
+    "__version__",
+]
diff --git a/ndcube/_dev/scm_version.py b/ndcube/_dev/scm_version.py
@@ -1,11 +1,11 @@
 # Try to use setuptools_scm to get the current version; this is only used
 # in development installations from the git repository.
-import os.path
+from pathlib import Path
 
 try:
     from setuptools_scm import get_version
 
-    version = get_version(root=os.path.join('..', '..'), relative_to=__file__)
+    version = get_version(root=Path('../..'), relative_to=__file__)
 except ImportError:
     raise
 except Exception as e:

diff --git a/ndcube/conftest.py b/ndcube/conftest.py
@@ -496,8 +496,7 @@ def ndcube_2d_ln_lt_uncert(wcs_2d_lt_ln):
     shape = (10, 12)
     data_cube = data_nd(shape)
     uncertainty = astropy.nddata.StdDevUncertainty(data_cube * 0.1)
-    cube = NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty)
-    return cube
+    return NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty)
 
 
 @pytest.fixture
@@ -510,8 +509,7 @@ def ndcube_2d_ln_lt_mask_uncert(wcs_2d_lt_ln):
     mask[2, 0] = True
     mask[3, 3] = True
     mask[4:6, :4] = True
-    cube = NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty, mask=mask)
-    return cube
+    return NDCube(data_cube, wcs=wcs_2d_lt_ln, uncertainty=uncertainty, mask=mask)
 
 
 @pytest.fixture