Updates from the package template (#260) (#262)

Co-authored-by: DanRyanIrish <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Nabil Freij <[email protected]>
sunpy · Nov 11, 2024 · a28532a · a28532a
1 parent d89c36a
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "aec53b81aed2e7e534045e59303d82712fe82fb1",
+  "commit": "4ca8e60aac805d5f736de80c45ae0aba96b4cb85",
   "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/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
@@ -1,4 +1,10 @@
 repos:
+    # This should be before any formatting hooks like isort
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.7.1"
+    hooks:
+      - id: ruff
+        args: ["--fix"]
   - repo: https://github.com/PyCQA/autoflake
     rev: v2.3.1
     hooks:

diff --git a/.ruff.toml b/.ruff.toml
@@ -1,5 +1,5 @@
 target-version = "py310"
-line-length = 110
+line-length = 120
 exclude = [
   ".git,",
   "__pycache__",
@@ -8,30 +8,75 @@ 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
 ]
-"__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
@@ -53,7 +53,7 @@
 automodapi_toctreedirnm = "generated/api"
 
 # 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.
@@ -103,7 +103,7 @@
 # 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,

diff --git a/pyproject.toml b/pyproject.toml
@@ -36,6 +36,9 @@ tests = [
 ]
 docs = [
   "sphinx",
+  "sphinx-automodapi",
+  "sunpy-sphinx-theme",
+  "packaging",
   "sphinx_automodapi",
   "sphinx-changelog",
   "sphinx-gallery",

diff --git a/pytest.ini b/pytest.ini
@@ -48,3 +48,4 @@ filterwarnings =
     ignore: invalid value encountered in true_divide
     # https://github.com/pytest-dev/pytest-cov/issues/557
     ignore:The --rsyncdir command line argument and rsyncdirs config variable are deprecated.:DeprecationWarning
+    ignore:Please use astropy.wcs.wcsapi.high_level_api.values_to_high_level_objects:DeprecationWarning
diff --git a/sunraster/_dev/scm_version.py b/sunraster/_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/sunraster/extern/meta.py b/sunraster/extern/meta.py
@@ -78,7 +78,7 @@ def __init__(self, header=None, comments=None, axes=None, data_shape=None):
             axes = dict(axes)
             if not set(axes.keys()).issubset(set(header_keys)):
                 raise ValueError("All axes must correspond to a value in header under the same key.")
-            self._axes = dict([(key, self._sanitize_axis_value(axis, header[key], key)) for key, axis in axes.items()])
+            self._axes = {key: self._sanitize_axis_value(axis, header[key], key) for key, axis in axes.items()}
 
     def _sanitize_axis_value(self, axis, value, key):
         if axis is None:
@@ -100,7 +100,7 @@ def _sanitize_axis_value(self, axis, value, key):
         shape_error_msg = f"{key} must have shape {tuple(self.shape[axis])} as it is associated with axes {axis}"
         if len(axis) == 1 and not hasattr(value, "__len__") or len(axis) != 1 and not hasattr(value, "shape"):
             raise TypeError(shape_error_msg)
-        elif len(axis) == 1:
+        if len(axis) == 1:
             meta_shape = (len(value),)
         else:
             meta_shape = value.shape
@@ -189,51 +189,50 @@ def __getitem__(self, item):
         # If item is single string, slicing is simple.
         if isinstance(item, str):
             return super().__getitem__(item)
-        elif self.shape is None:
+        if self.shape is None:
             raise TypeError("Meta object does not have a shape and so cannot be sliced.")
-        else:
-            new_meta = copy.deepcopy(self)
-            # Convert item to array of ints and slices for consistent behaviour.
-            if isinstance(item, (numbers.Integral, slice)):
-                item = [item]
-            item = np.array(list(item) + [slice(None)] * (len(self.shape) - len(item)), dtype=object)
-
-            # Edit data shape and calculate which axis will be dropped.
-            dropped_axes = np.zeros(len(self.shape), dtype=bool)
-            new_shape = new_meta.shape
-            for i, axis_item in enumerate(item):
-                if isinstance(axis_item, numbers.Integral):
-                    dropped_axes[i] = True
-                elif isinstance(axis_item, slice):
-                    start = axis_item.start
-                    if start is None:
-                        start = 0
-                    if start < 0:
-                        start = self.shape[i] - start
-                    stop = axis_item.stop
-                    if stop is None:
-                        stop = self.shape[i]
-                    if stop < 0:
-                        stop = self.shape[i] - stop
-                    new_shape[i] = stop - start
-                else:
-                    raise TypeError("Unrecognized slice type. " "Must be an int, slice and tuple of the same.")
-            new_meta._data_shape = new_shape[np.invert(dropped_axes)]
-
-            # Calculate the cumulative number of dropped axes.
-            cumul_dropped_axes = np.cumsum(dropped_axes)
-
-            # Slice all metadata associated with axes.
-            for key, value in self.items():
-                axis = self.axes.get(key, None)
-                if axis is not None:
-                    new_item = tuple(item[axis])
-                    new_value = value[new_item[0]] if len(new_item) == 1 else value[new_item]
-                    new_axis = np.array([-1 if isinstance(i, numbers.Integral) else a for i, a in zip(new_item, axis)])
-                    new_axis -= cumul_dropped_axes[axis]
-                    new_axis = new_axis[new_axis >= 0]
-                    if len(new_axis) == 0:
-                        new_axis = None
-                    new_meta.add(key, new_value, self.comments.get(key, None), new_axis, overwrite=True)
-
-            return new_meta
+        new_meta = copy.deepcopy(self)
+        # Convert item to array of ints and slices for consistent behaviour.
+        if isinstance(item, (numbers.Integral, slice)):
+            item = [item]
+        item = np.array(list(item) + [slice(None)] * (len(self.shape) - len(item)), dtype=object)
+
+        # Edit data shape and calculate which axis will be dropped.
+        dropped_axes = np.zeros(len(self.shape), dtype=bool)
+        new_shape = new_meta.shape
+        for i, axis_item in enumerate(item):
+            if isinstance(axis_item, numbers.Integral):
+                dropped_axes[i] = True
+            elif isinstance(axis_item, slice):
+                start = axis_item.start
+                if start is None:
+                    start = 0
+                if start < 0:
+                    start = self.shape[i] - start
+                stop = axis_item.stop
+                if stop is None:
+                    stop = self.shape[i]
+                if stop < 0:
+                    stop = self.shape[i] - stop
+                new_shape[i] = stop - start
+            else:
+                raise TypeError("Unrecognized slice type. " "Must be an int, slice and tuple of the same.")
+        new_meta._data_shape = new_shape[np.invert(dropped_axes)]
+
+        # Calculate the cumulative number of dropped axes.
+        cumul_dropped_axes = np.cumsum(dropped_axes)
+
+        # Slice all metadata associated with axes.
+        for key, value in self.items():
+            axis = self.axes.get(key, None)
+            if axis is not None:
+                new_item = tuple(item[axis])
+                new_value = value[new_item[0]] if len(new_item) == 1 else value[new_item]
+                new_axis = np.array([-1 if isinstance(i, numbers.Integral) else a for i, a in zip(new_item, axis)])
+                new_axis -= cumul_dropped_axes[axis]
+                new_axis = new_axis[new_axis >= 0]
+                if len(new_axis) == 0:
+                    new_axis = None
+                new_meta.add(key, new_value, self.comments.get(key, None), new_axis, overwrite=True)
+
+        return new_meta