Updates from package template

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/sunpy/package-template",
-  "commit": "cd21e0d710513a891ed03f29e8afd6e0b9217f04",
+  "commit": "c60ccf2ddc71d3cf126cea15132a15da307864f7",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -10,6 +10,12 @@
       "author_name": "The SunPy Community",
       "author_email": "[email protected]",
       "project_url": "https://sunkit-spex.readthedocs.io",
+      "github_repo": "",
+      "sourcecode_url": "",
+      "download_url": "https://pypi.org/project/sunkit-spex",
+      "documentation_url": "",
+      "changelog_url": "",
+      "issue_tracker_url": "",
       "license": "BSD 3-Clause",
       "minimum_python_version": "3.10",
       "use_compiled_extensions": "n",

.github/workflows/ci.yml

@@ -1,3 +1,4 @@
+# Main CI Workflow
 name: CI
 
 on:
@@ -21,7 +22,7 @@ concurrency:
 
 jobs:
   core:
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       submodules: false
       coverage: codecov
@@ -45,7 +46,7 @@ jobs:
 
   test:
     needs: [core, sdist_verify]
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       submodules: false
       coverage: codecov
@@ -60,7 +61,7 @@ jobs:
 
   docs:
     needs: [core]
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       default_python: '3.12'
       submodules: false
@@ -78,7 +79,7 @@ jobs:
         github.event_name == 'pull_request' &&
         contains(github.event.pull_request.labels.*.name, 'Run cron CI')
       )
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@main
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
     with:
       default_python: '3.12'
       submodules: false
@@ -99,7 +100,7 @@ jobs:
         contains(github.event.pull_request.labels.*.name, 'Run publish')
       )
     needs: [test, docs]
-    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@v1
     with:
       python-version: '3.12'
       test_extras: 'tests'

.github/workflows/sub_package_update.yml

@@ -86,6 +86,8 @@ jobs:
           delete-branch: true
           draft: ${{ steps.cruft_update.outputs.merge_conflicts == '1' }}
           title: "Updates from the package template"
+          labels: |
+            No Changelog Entry Needed
           body: |
             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.

.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: "v0.7.4"
+    rev: "v0.8.3"
     hooks:
       - id: ruff
         args: ["--fix"]

.ruff.toml

@@ -40,7 +40,6 @@ extend-ignore = [
   "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 _
   "PT023", # Always use () on pytest decorators
   # flake8-pie (PIE)
   "PIE808", # Disallow passing 0 as the first argument to range

docs/index.rst

@@ -33,3 +33,10 @@ will help you know where to look for certain things:
    discussion/index
    reference/index
    whatsnew/index
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

pyproject.toml

@@ -45,14 +45,16 @@ tests = [
 docs = [
   "sphinx",
   "sphinx-automodapi",
+  "sphinx-changelog",
   "sunpy-sphinx-theme",
   "packaging",
   "sphinx-changelog",
   "sphinx-gallery",
 ]
 
 [project.urls]
-repository = "https://sunkit-spex.readthedocs.io"
+Homepage = "https://sunkit-spex.readthedocs.io"
+Download = "https://pypi.org/project/sunkit-spex"
 
 [tool.setuptools]
 zip-safe = false
@@ -65,61 +67,62 @@ exclude = ["sunkit_spex._dev*"]
 [tool.setuptools_scm]
 write_to = "sunkit_spex/_version.py"
 
-[ tool.gilesbot ]
-
-  [ tool.gilesbot.pull_requests ]
-    enabled = true
+[tool.gilesbot]
+  [tool.gilesbot.pull_requests]
+  enabled = true
 
-  [ tool.gilesbot.towncrier_changelog ]
-    enabled = true
-    verify_pr_number = true
-    changelog_skip_label = "No Changelog Entry Needed"
-    help_url = "https://github.com/sunpy/sunkit-spex/blob/master/changelog/README.rst"
+  [tool.gilesbot.towncrier_changelog]
+  enabled = true
+  verify_pr_number = true
+  changelog_skip_label = "No Changelog Entry Needed"
+  help_url = "https://github.com/sunpy/sunkit-spex/blob/main/changelog/README.rst"
 
-    changelog_missing_long = "There isn't a changelog file in this pull request. Please add a changelog file to the `changelog/` directory following the instructions in the changelog [README](https://github.com/sunpy/sunkit-spex/blob/master/changelog/README.rst."
+  changelog_missing_long = "There isn't a changelog file in this pull request. Please add a changelog file to the `changelog/` directory following the instructions in the changelog [README](https://github.com/sunpy/sunkit-spex/blob/main/changelog/README.rst)."
 
-    type_incorrect_long = "The changelog file you added is not one of the allowed types. Please use one of the types described in the changelog [README](https://github.com/sunpy/sunkit-spex/blob/master/changelog/README.rst)"
+  type_incorrect_long = "The changelog file you added is not one of the allowed types. Please use one of the types described in the changelog [README](https://github.com/sunpy/sunkit-spex/blob/main/changelog/README.rst)"
 
-    number_incorrect_long = "The number in the changelog file you added does not match the number of this pull request. Please rename the file."
+  number_incorrect_long = "The number in the changelog file you added does not match the number of this pull request. Please rename the file."
 
+# TODO: This should be in towncrier.toml but Giles currently only works looks in
+# pyproject.toml we should move this back when it's fixed.
 [tool.towncrier]
-    package = "sunkit_spex"
-    filename = "CHANGELOG.rst"
-    directory = "changelog/"
-    issue_format = "`#{issue} <https://github.com/sunpy/sunkit-spex/pull/{issue}>`__"
-    title_format = "{version} ({project_date})"
-
-    [[tool.towncrier.type]]
-        directory = "breaking"
-        name = "Breaking Changes"
-        showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "deprecation"
-      name = "Deprecations"
-      showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "removal"
-      name = "Removals"
-      showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "feature"
-      name = "New Features"
-      showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "bugfix"
-      name = "Bug Fixes"
-      showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "doc"
-      name = "Documentation"
-      showcontent = true
-
-    [[tool.towncrier.type]]
-      directory = "trivial"
-      name = "Internal Changes"
-      showcontent = true
+  package = "sunkit_spex"
+  filename = "CHANGELOG.rst"
+  directory = "changelog/"
+  issue_format = "`#{issue} <https://github.com/sunpy/sunkit-spex/pull/{issue}>`__"
+  title_format = "{version} ({project_date})"
+
+  [[tool.towncrier.type]]
+  directory = "breaking"
+  name = "Breaking Changes"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "deprecation"
+  name = "Deprecations"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "removal"
+  name = "Removals"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "feature"
+  name = "New Features"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "bugfix"
+  name = "Bug Fixes"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "doc"
+  name = "Documentation"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "trivial"
+  name = "Internal Changes"
+  showcontent = true

sunkit_spex/legacy/emission.py

@@ -24,12 +24,12 @@
 
 __all__ = [
     "BrokenPowerLawElectronDistribution",
-    "collisional_loss",
     "_get_integrand",
     "_integrate_part",
     "_split_and_integrate",
-    "bremsstrahlung_thin_target",
     "bremsstrahlung_thick_target",
+    "bremsstrahlung_thin_target",
+    "collisional_loss",
 ]
 
 

sunkit_spex/legacy/fitting/fitter.py

@@ -2441,7 +2441,7 @@ def _calc_hessian(self, mod_without_x, fparams, step=0.01, _abs_step=None):
                 replacement_steps = np.mean(self._minimize_solution.final_simplex[0][:, zero_steps], axis=0) * step
             except AttributeError:
                 replacement_steps = 0
-            steps[zero_steps] = replacement_steps if replacement_steps > 0 else step
+            steps[zero_steps] = replacement_steps if replacement_steps.size > 0 else step
         else:
             steps = _abs_step
 

sunkit_spex/legacy/integrate.py

@@ -1,7 +1,7 @@
 import numpy as np
 from scipy.integrate._quadrature import _cached_roots_legendre
 
-__all__ = ["gauss_legendre", "fixed_quad"]
+__all__ = ["fixed_quad", "gauss_legendre"]
 
 
 def _legendre_roots(a, b, n=5):

sunkit_spex/legacy/io.py

@@ -10,7 +10,7 @@
 from sunpy.data import manager
 from sunpy.io.special.genx import read_genx
 
-__all__ = ["load_chianti_lines_lite", "load_chianti_continuum", "read_abundance_genx", "load_xray_abundances"]
+__all__ = ["load_chianti_continuum", "load_chianti_lines_lite", "load_xray_abundances", "read_abundance_genx"]
 
 
 @manager.require(

sunkit_spex/legacy/thermal.py

@@ -11,12 +11,12 @@
 from .io import load_chianti_continuum, load_chianti_lines_lite, load_xray_abundances
 
 __all__ = [
-    "thermal_emission",
     "continuum_emission",
     "line_emission",
     "setup_continuum_parameters",
-    "setup_line_parameters",
     "setup_default_abundances",
+    "setup_line_parameters",
+    "thermal_emission",
 ]
 
 doc_string_params = """

sunkit_spex/models/models.py

@@ -4,7 +4,7 @@
 
 from astropy.modeling import Fittable1DModel, Parameter
 
-__all__ = ["StraightLineModel", "GaussianModel"]
+__all__ = ["GaussianModel", "StraightLineModel"]
 
 
 class StraightLineModel(Fittable1DModel):

sunkit_spex/models/physical/io.py

@@ -10,7 +10,7 @@
 from sunpy.data import manager
 from sunpy.io.special.genx import read_genx
 
-__all__ = ["load_chianti_lines_lite", "load_chianti_continuum", "read_abundance_genx", "load_xray_abundances"]
+__all__ = ["load_chianti_continuum", "load_chianti_lines_lite", "load_xray_abundances", "read_abundance_genx"]
 
 
 @manager.require(

sunkit_spex/models/physical/thermal.py

@@ -15,12 +15,12 @@
 )
 
 __all__ = [
-    "thermal_emission",
     "continuum_emission",
     "line_emission",
     "setup_continuum_parameters",
-    "setup_line_parameters",
     "setup_default_abundances",
+    "setup_line_parameters",
+    "thermal_emission",
 ]
 
 doc_string_params = """

sunkit_spex/spectrum/spectrum.py

@@ -8,7 +8,7 @@
 from astropy.modeling.tabular import Tabular1D
 from astropy.utils import lazyproperty
 
-__all__ = ["gwcs_from_array", "SpectralAxis", "Spectrum"]
+__all__ = ["SpectralAxis", "Spectrum", "gwcs_from_array"]
 
 
 def gwcs_from_array(array):