Updates from package template

.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": [

.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: "v0.7.1"
     hooks:
       - id: ruff
         args: ["--fix"]

.ruff.toml

@@ -10,31 +10,84 @@ exclude = [
 ]
 
 [lint]
-select = ["E", "F", "W", "UP", "PT"]
+select = [
+  "E",
+  "F",
+  "W",
+  "UP",
+  "PT",
+  "N",
+  "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
+  # PEP8 Naming
+  "N802", # Function name should be lowercase
+  "N803", # Argument name should be lowercase
+  "N806", # Variable in function should be lowercase
 ]
 
 [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
-  "F403"
+  "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
+]
+# Be a bit more lax on legacy
+"sunkit_spex/legacy/tests/*.py" = [
+  "PT011", # `pytest.raises(ValueError)` is too broad
 ]
-"__init__.py" = ["E402", "F401", "F403"]
-"test_*.py" = ["B011", "D", "E402", "PGH001", "S101"]
 
 [lint.pydocstyle]
 convention = "numpy"

docs/conf.py

@@ -51,7 +51,7 @@
 ]
 
 # 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.
@@ -101,7 +101,7 @@
 # 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,

examples/fitting_RHESSI_spectra.py

@@ -19,6 +19,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+from numpy.exceptions import VisibleDeprecationWarning
 from parfive import Downloader
 
 from astropy.time import Time
@@ -28,7 +29,7 @@
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 try:
-    warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
+    warnings.filterwarnings("ignore", category=VisibleDeprecationWarning)
 except AttributeError:
     warnings.filterwarnings("ignore", category=np.exceptions.VisibleDeprecationWarning)
 

examples/fitting_custom_spectra.py

@@ -18,12 +18,13 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+from numpy.exceptions import VisibleDeprecationWarning
 
 from sunkit_spex.legacy.fitting.fitter import Fitter
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 try:
-    warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
+    warnings.filterwarnings("ignore", category=VisibleDeprecationWarning)
 except AttributeError:
     warnings.filterwarnings("ignore", category=np.exceptions.VisibleDeprecationWarning)
 
@@ -74,7 +75,7 @@ def gauss(a, b, c, energies=None):
 chan_bins = np.stack((np.arange(0, maxi, step), np.arange(step, maxi + step, step)), axis=-1)
 gauss_mod1 = gauss(1.3e4, 350, 60, energies=chan_bins)
 gauss_mod2 = gauss(3e3, 600, 60, energies=chan_bins)
-noise = np.random.randint(low=10, high=100, size=(len(chan_bins))) / 100 * 5
+noise = np.random.default_rng().integers(low=10, high=100, size=(len(chan_bins))) / 100 * 5
 
 fake_data = gauss_mod1 + gauss_mod2 + noise
 

examples/skip_fitting_NuSTAR_spectra.py

@@ -10,13 +10,14 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+from numpy.exceptions import VisibleDeprecationWarning
 from parfive import Downloader
 
 from sunkit_spex.legacy.fitting.fitter import Fitter, load
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 try:
-    warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
+    warnings.filterwarnings("ignore", category=VisibleDeprecationWarning)
 except AttributeError:
     warnings.filterwarnings("ignore", category=np.exceptions.VisibleDeprecationWarning)
 

pyproject.toml

@@ -45,10 +45,10 @@ tests = [
 docs = [
   "sphinx",
   "sphinx-automodapi",
+  "sunpy-sphinx-theme",
   "packaging",
   "sphinx-changelog",
   "sphinx-gallery",
-  "sunpy-sphinx-theme",
 ]
 
 [project.urls]

sunkit_spex/_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:

sunkit_spex/legacy/emission.py

@@ -102,7 +102,7 @@ def __init__(self, *, p, q, eelow, eebrk, eehigh, norm=True):
 
     def __eq__(self, other):
         return all(
-            [getattr(self, name) == getattr(other, name) for name in ["p", "q", "eelow", "eebrk", "eehigh"]]
+            getattr(self, name) == getattr(other, name) for name in ["p", "q", "eelow", "eebrk", "eehigh"]
         ) and isinstance(other, self.__class__)
 
     def flux(self, electron_energy):
@@ -211,9 +211,7 @@ def collisional_loss(electron_energy):
     beta = np.sqrt(1.0 - (1.0 / gamma**2))
 
     # TODO figure out what number is?
-    energy_loss_rate = np.log(6.9447e9 * electron_energy) / beta
-
-    return energy_loss_rate
+    return np.log(6.9447e9 * electron_energy) / beta
 
 
 def bremsstrahlung_cross_section(electron_energy, photon_energy, z=1.2):
@@ -301,9 +299,7 @@ def bremsstrahlung_cross_section(electron_energy, photon_energy, z=1.2):
     fe = (a2 / a1) * (1.0 - np.exp(-2.0 * np.pi * a1)) / (1.0 - np.exp(-2.0 * np.pi * a2))
 
     # Compute the differential cross section (units cm^2).
-    cross_section = twoar02 * fe * crtmp
-
-    return cross_section
+    return twoar02 * fe * crtmp
 
 
 def _get_integrand(x_log, *, model, electron_dist, photon_energy, z, efd=True):
@@ -354,18 +350,18 @@ def _get_integrand(x_log, *, model, electron_dist, photon_energy, z, efd=True):
         return (
             electron_energy * np.log(10) * density * brem_cross * pc / collision_loss / ((electron_energy / mc2) + 1.0)
         )
-    elif model == "thin-target":
+    if model == "thin-target":
         if efd:
             return electron_energy * np.log(10) * electron_dist.flux(electron_energy) * brem_cross * (mc2 / clight)
-        else:
-            return (
-                electron_energy
-                * np.log(10)
-                * electron_dist.flux(electron_energy)
-                * brem_cross
-                * pc
-                / ((electron_energy / mc2) + 1.0)
-            )
+        return (
+            electron_energy
+            * np.log(10)
+            * electron_dist.flux(electron_energy)
+            * brem_cross
+            * pc
+            / ((electron_energy / mc2) + 1.0)
+        )
+    return None
 
 
 def _integrate_part(
@@ -469,6 +465,7 @@ def _integrate_part(
         # If all point have reached criterion return value and flags
         if i.size == 0:
             return intsum, ier
+    return None
 
 
 def _split_and_integrate(*, model, photon_energies, maxfcn, rerr, eelow, eebrk, eehigh, p, q, z, efd, integrator=None):
@@ -641,10 +638,11 @@ def _split_and_integrate(*, model, photon_energies, maxfcn, rerr, eelow, eebrk,
         DmlinO = (intsum1 + intsum2 + intsum3) * (mc2 / clight)
         ier = ier1 + ier2 + ier3
         return DmlinO, ier
-    elif model == "thin-target":
+    if model == "thin-target":
         Dmlin = intsum2 + intsum3
         ier = ier2 + ier3
         return Dmlin, ier
+    return None
 
 
 def bremsstrahlung_thin_target(photon_energies, p, eebrk, q, eelow, eehigh, efd=True, integrator=None):
@@ -742,8 +740,7 @@ def bremsstrahlung_thin_target(photon_energies, p, eebrk, q, eelow, eehigh, efd=
         flux *= fcoeff
 
         return flux
-    else:
-        raise Warning("The photon energies are higher than the highest electron energy or not " "greater than zero")
+    raise Warning("The photon energies are higher than the highest electron energy or not " "greater than zero")
 
 
 def bremsstrahlung_thick_target(photon_energies, p, eebrk, q, eelow, eehigh, integrator=None):
@@ -836,8 +833,6 @@ def bremsstrahlung_thick_target(photon_energies, p, eebrk, q, eelow, eehigh, int
             integrator=integrator,
         )
 
-        flux = (fcoeff / decoeff) * flux
+        return (fcoeff / decoeff) * flux
 
-        return flux
-    else:
-        raise Warning("The photon energies are higher than the highest electron energy or not " "greater than zero")
+    raise Warning("The photon energies are higher than the highest electron energy or not " "greater than zero")