Updates from package template (#180)

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "aec53b81aed2e7e534045e59303d82712fe82fb1",
+  "commit": "75f84c4adf1753af67967930c3335bc73bca9bf5",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -16,7 +16,8 @@
       "enable_dynamic_dev_versions": "n",
       "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": [

.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

@@ -1,7 +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"]

.ruff.toml

@@ -1,5 +1,5 @@
 target-version = "py310"
-line-length = 110
+line-length = 120
 exclude = [
   ".git,",
   "__pycache__",
@@ -8,30 +8,78 @@ exclude = [
 ]
 
 [lint]
-select = ["E", "F", "W", "UP", "PT"]
+select = [
+  "E",
+  "F",
+  "W",
+  "UP",
+  "PT",
+  "BLE",
+  "A",
+  "C4",
+  "INP",
+  "PIE",
+  "T20",
+  "RET",
+  "TID",
+  "PTH",
+  "PD",
+  "PLC",
+  "PLE",
+  "FLY",
+  "NPY",
+  "PERF",
+  "RUF",
+]
 extend-ignore = [
   # 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
   # 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
   "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
+]
+"benchmarks/*.py" = [
+  "NPY002", # TODO: Generator API
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"

benchmarks/benchmark.py

@@ -30,7 +30,6 @@
         dts.append(time.time() - t)
         assert len(tracer.xs) == nseeds
     times += [np.mean(dts)]
-    print(nseeds, times[-1] / nseeds, times[-1])
 
 
 pd.DataFrame({"nseeds": seedlist, "time": times}).to_csv(

benchmarks/benchmark_plot.py

@@ -11,12 +11,11 @@
     "210dev0": "v2.1 (Rust Parallel)",
 }
 
-files = Path(".").glob("v*.csv")
+files = Path().glob("v*.csv")
 
 for file in files:
     label = version_names.get(file.stem[1:], file.stem)
     data = pd.read_csv(file)
-    print(data)
 
     ax.plot(data["nseeds"], data["time"], label=label, marker="o")
 

docs/conf.py

@@ -44,7 +44,7 @@
 ]
 
 # 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.
@@ -87,7 +87,7 @@
 # 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,

pyproject.toml

@@ -45,9 +45,9 @@ tests = [
 docs = [
   "sphinx",
   "sphinx-automodapi",
+  "sunpy-sphinx-theme",
   "packaging",
   "jupyter-sphinx",
-  "sunpy-sphinx-theme",
   "sphinx-changelog",
 ]
 

python/streamtracer/streamline.py

@@ -172,8 +172,7 @@ def _get_coords(self, i):
                 self.grid_spacing[i] * np.arange(self.vectors.shape[i])
                 + self.origin_coord[i]
             )
-        else:
-            return self.coords[i]
+        return self.coords[i]
 
     @property
     def xcoords(self):

python/streamtracer/tests/test_streamline.py

@@ -22,9 +22,9 @@ def uniform_x_field():
 @pytest.mark.parametrize(
     ("direction", "ROTs"),
     [
-        [1, np.array([2, 2, 2])],
-        [-1, np.array([2, 2, 2])],
-        [0, np.array([[2, 2], [2, 2], [2, 2]])],
+        (1, np.array([2, 2, 2])),
+        (-1, np.array([2, 2, 2])),
+        (0, np.array([[2, 2], [2, 2], [2, 2]])),
     ],
 )
 def test_rot(tracer, uniform_x_field, direction, ROTs):
@@ -217,18 +217,18 @@ def test_invalid_max_steps(val, errstr):
 
 
 # Paramatrize to make sure behaviour is same in x,y,z directions
-@pytest.mark.parametrize("dir", [0, 1, 2])
-def test_bounds(dir):
+@pytest.mark.parametrize("dirs", [0, 1, 2])
+def test_bounds(dirs):
     v = np.zeros((3, 3, 3, 3))
     # Make all vectors point along the specified dimension
-    v[:, :, :, dir] = 1
+    v[:, :, :, dirs] = 1
     spacing = [1, 1, 1]
     grid = VectorGrid(v, spacing)
 
     seed = np.array([[0.5, 0.5, 0.5]])
     tracer = StreamTracer(max_steps=10, step_size=1.0)
     tracer.trace(seed, grid)
-    expected = np.roll(np.array([1.5, 0.5, 0.5]), dir)
+    expected = np.roll(np.array([1.5, 0.5, 0.5]), dirs)
     assert (tracer.xs[0][-1, :] == expected).all()
     expected = np.array([0.5, 0.5, 0.5])
     assert (tracer.xs[0][0, :] == expected).all()