Drop cubic fit for interpolated broadening

.github/workflows/check_changelog.yml

@@ -0,0 +1,23 @@
+name: Changelog updated
+
+on:
+  pull_request:
+    types: [opened, reopened, labeled, synchronize]
+
+jobs:
+  check_log:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Get changes
+        run: |
+          set +e  # Don't immediately fail when bash sees exit 1
+          git diff --exit-code "origin/${GITHUB_BASE_REF}" -- CHANGELOG.rst
+          if [ $? -eq 1 ]; then
+              exit 0
+          fi
+          # git-diff did not return 1; either no changes or another error encountered
+          exit 1

.github/workflows/run_tests.yml

@@ -8,6 +8,12 @@ on:
   pull_request:
     types: [opened, reopened, labeled, synchronize]
   workflow_dispatch:
+    inputs:
+      push_coverage_badge:
+        description: 'Push coverage badge (even if not running on master)'
+        required: true
+        type: boolean
+        default: false
 
 jobs:
   lint:
@@ -97,4 +103,42 @@ jobs:
       - name: Publish test results
         uses: EnricoMi/publish-unit-test-result-action@v2
         with:
-          junit_files: artifacts/**/junit_report*.xml
+          files: artifacts/**/junit_report*.xml
+
+  publish-coverage:
+    needs: test
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: artifacts
+          name: 'Coverage XML (ubuntu-latest)'
+
+      - name: Get Coverage
+        uses: orgoro/coverage@v3.2
+        continue-on-error: true
+        with:
+          coverageFile: 'artifacts/coverage-combined.xml'
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+  publish-coverage-badge:
+    needs: test
+    runs-on: ubuntu-latest
+    if: ${{(github.event_name == 'push' && github.ref == 'refs/heads/master') || (github.event_name == 'workflow_dispatch' && inputs.push_coverage_badge)}}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: badges
+          fetch-depth: 0
+
+      - name: Download Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: .
+          name: 'Coverage Badge (ubuntu-latest)'
+
+      - uses: EndBug/add-and-commit@v9
+        with:
+          add: 'badge_shieldsio_linecoverage_lightgrey.svg'
+          message: 'Update coverage badge'

.github/workflows/test_checkout_one_os.yml

@@ -95,16 +95,39 @@ jobs:
           name: Unit test results ${{ inputs.os }}
           path: tests_and_analysis/test/reports/junit_report*.xml
 
-      - name: Publish Codacy coverage
-        uses: codacy/codacy-coverage-reporter-action@v1
+      - name: Merge coverage reports
         if: inputs.coverage
+        shell: bash -l {0}
+        run: |
+          dotnet tool install -g dotnet-coverage
+          dotnet coverage merge --reports "tests_and_analysis/test/reports/coverage*.xml" -f cobertura -o "tests_and_analysis/test/reports/coverage-combined.xml"
+
+      - name: Create coverage outputs
+        if: inputs.coverage
+        shell: bash -l {0}
+        run: |
+          dotnet tool install --global dotnet-reportgenerator-globaltool --version 5.5.1
+          reportgenerator -reports:tests_and_analysis/test/reports/coverage-combined.xml -targetdir:tests_and_analysis/test/reports/html -reporttypes:Html_Dark
+          reportgenerator -reports:tests_and_analysis/test/reports/coverage-combined.xml -targetdir:tests_and_analysis/test/reports -reporttypes:Badges
+
+      - name: Upload coverage XML
+        if: inputs.coverage
+        uses: actions/upload-artifact@v4
         with:
-          project-token: ${{ secrets.codacy_project_token }}
-          coverage-reports: tests_and_analysis/test/reports/coverage*.xml
+          name: Coverage XML (${{ inputs.os }})
+          path: tests_and_analysis/test/reports/coverage-combined.xml
 
-      - uses: codecov/codecov-action@v4
+      - name: Upload coverage HTML
         if: inputs.coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: Coverage HTML (${{ inputs.os }})
+          path: tests_and_analysis/test/reports/html
+          include-hidden-files: true
+
+      - name: Upload coverage Badge
+        if: inputs.coverage
+        uses: actions/upload-artifact@v4
         with:
-          files: tests_and_analysis/test/reports/coverage*.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          name: Coverage Badge (${{ inputs.os }})
+          path: tests_and_analysis/test/reports/badge_shieldsio_linecoverage_lightgrey.svg

CHANGELOG.rst

@@ -1,8 +1,47 @@
 `Unreleased <https://github.com/pace-neutrons/Euphonic/compare/v1.6.0...HEAD>`_
 -------------------------------------------------------------------------------
 
+- API changes
+
+  - Public functions in ``euphonic.powder`` now use mandatory keyword arguments
+    - This will break code that depends on these arguments being in a specific order
+
+  - The various Spectrum classes have an ``assert_regular_bins``
+    method. It is now forbidden to use positional arguments and in the
+    2D cases ``bin_ax`` has a default value of "y". This makes the API
+    safer and more formally correct.
+
+  - Unused argument ``use_brille`` is removed from
+    ``euphonic.cli.brille_convergence.check_brille_settings``.
+
+  - "Adaptive fit" parameter is removed from spectrum broaden()
+    methods and euphonic-dos; "cubic" parametrisation is removed and
+    superior "cheby-log" fit always used.
+
+- Features
+
+  - Spectrum1DCollection and Spectrum2DCollection can be indexed with
+    slices where the stop value exceeds the collection
+    length. (e.g. if a collection of 5 spectra is indexed with [3:10]
+    it will return a collection with the spectra at indices 3 and 4.)
+    This is consistent with the behaviour of Python lists and numpy
+    arrays.
+
+    Previously this would raise an IndexError. Technically it is a
+    **breaking change** as somebody's code could depend on this
+    IndexError. At this stage it seems an acceptable risk.
+
+- Other changes
+
+  - Error messages have been overhauled and now follow a consistent format::
+
+      summary
+
+      [reason]
+
+      fix
+
 `v1.6.0 <https://github.com/pace-neutrons/Euphonic/compare/v1.5.1...v1.6.0>`_
------------------------------------------------------------------------------
 
 - Requirements
 
@@ -14,7 +53,7 @@
   - Security
 
     - Bumped *wheel* requirement for docs and testing to 0.46.2. (`CVE-2026-24049 <https://www.cve.org/CVERecord?id=CVE-2026-24049>`_)
-  
+
 
 - Bug fixes
 

README.rst

@@ -2,7 +2,7 @@
 Euphonic
 ========
 
-|PyPI Version| |Conda Version| |Documentation Status| |Tests| |License| |DOI|
+|PyPI Version| |Conda Version| |Documentation Status| |Tests| |Coverage| |License| |DOI|
 
 .. |PyPI Version| image:: https://img.shields.io/pypi/v/euphonic
    :target: https://pypi.org/project/euphonic/
@@ -20,6 +20,9 @@ Euphonic
    :target: https://github.com/pace-neutrons/Euphonic/actions/workflows/run_tests.yml
    :alt: Tests
 
+.. |Coverage| image:: https://raw.githubusercontent.com/pace-neutrons/Euphonic/refs/heads/badges/badge_shieldsio_linecoverage_lightgrey.svg
+   :target: https://github.com/pace-neutrons/Euphonic/actions/workflows/run_tests.yml                      :alt: Coverage   
+
 .. |License| image:: https://img.shields.io/pypi/l/euphonic
    :target: https://github.com/pace-neutrons/Euphonic/blob/master/LICENSE
    :alt: License

euphonic/brille.py

@@ -10,9 +10,11 @@
     import brille as br
 except ModuleNotFoundError as err:
     err_msg = textwrap.dedent("""
-        Cannot import Brille for use with BrilleInterpolator
-        (maybe Brille is not installed?). To install Euphonic's
-        optional Brille dependency, try:
+        Cannot import Brille for use with BrilleInterpolator.
+
+        This may be because Brille is not installed.
+
+        To install Euphonic's optional Brille dependency, try:
 
             pip install euphonic[brille]
         """)
@@ -25,6 +27,7 @@
     QpointPhononModes,
     ureg,
 )
+from euphonic.util import comma_join, format_error
 from euphonic.validate import _check_constructor_inputs
 
 
@@ -194,7 +197,11 @@ def from_force_constants(
         """
         grid_type_opts = ('trellis', 'mesh', 'nest')
         if grid_type not in grid_type_opts:
-            msg = f'Grid type "{grid_type}" not recognised'
+            msg = format_error(
+                f'Grid type "{grid_type}" not recognised.',
+                fix=('Acceptable grid types are:'
+                     f' {comma_join(grid_type_opts)}.'),
+            )
             raise ValueError(msg)
 
         crystal = force_constants.crystal

euphonic/broadening.py

@@ -13,9 +13,8 @@
 from scipy.stats import norm
 
 from euphonic.ureg import ureg
-from euphonic.util import dedent_and_fill
+from euphonic.util import format_error
 
-ErrorFit = Literal['cheby-log', 'cubic']
 KernelShape = Literal['gauss', 'lorentz']
 
 
@@ -33,7 +32,6 @@ def variable_width_broadening(
     width_convention: Literal['fwhm', 'std'] = 'fwhm',
     adaptive_error: float = 1e-2,
     shape: KernelShape = 'gauss',
-    fit: ErrorFit = 'cheby-log',
     ) -> Quantity:
     r"""Apply x-dependent Gaussian broadening to 1-D data series
 
@@ -70,25 +68,24 @@ def variable_width_broadening(
         approximate gaussians.
     shape
         Select broadening kernel function.
-    fit
-        Select parametrisation of kernel width spacing to adaptive_error.
-        'cheby-log' is recommended: for shape 'gauss', 'cubic' is also
-        available.
     """
 
     if width_convention.lower() == 'fwhm' and shape == 'gauss':
         def sigma_function(x: Quantity) -> Quantity:
             return width_function(x) * FWHM_TO_SIGMA
     elif width_convention.lower() == 'std' and shape == 'lorentz':
-        msg = (
-            'Standard deviation unavailable for Lorentzian '
-            'function: please use FWHM.'
+        msg = format_error(
+            'Standard deviation unavailable.',
+            fix='For Lorentzian function: please use FWHM.',
         )
         raise ValueError(msg)
     elif width_convention.lower() in ('std', 'fwhm'):
         sigma_function = width_function
     else:
-        msg = 'width_convention must be "std" or "fwhm".'
+        msg = format_error(
+            f'Invalid width convention: {width_convention}.',
+            fix='`width_convention` must be "std" or "fwhm".',
+        )
         raise ValueError(msg)
 
     widths = sigma_function(x)
@@ -107,8 +104,7 @@ def sigma_function(x: Quantity) -> Quantity:
     return width_interpolated_broadening(bins, x, widths,
                                          weights.magnitude,
                                          adaptive_error=adaptive_error,
-                                         shape=shape,
-                                         fit=fit) * weights_unit
+                                         shape=shape) * weights_unit
 
 
 def width_interpolated_broadening(
@@ -118,7 +114,6 @@ def width_interpolated_broadening(
     weights: np.ndarray,
     adaptive_error: float,
     shape: KernelShape = 'gauss',
-    fit: ErrorFit = 'cheby-log',
     ) -> Quantity:
     """
     Uses a fast, approximate method to broaden a spectrum
@@ -147,10 +142,6 @@ def width_interpolated_broadening(
     shape
         Select kernel shape. Widths will correspond to sigma or gamma
         parameters respectively.
-    fit
-        Select parametrisation of kernel width spacing to adaptive_error.
-        'cheby-log' is recommended: for shape 'gauss', 'cubic' is also
-        available.
 
     Returns
     -------
@@ -164,33 +155,20 @@ def width_interpolated_broadening(
                                           widths.to(bins.units).magnitude,
                                           weights,
                                           adaptive_error,
-                                          shape=shape,
-                                          fit=fit) / bins.units
+                                          shape=shape) / bins.units
 
 
 def _lorentzian(x: np.ndarray, gamma: np.ndarray) -> np.ndarray:
     return gamma / (2 * np.pi * (x**2 + (gamma / 2)**2))
 
 
 def _get_spacing(error,
-                 shape: KernelShape = 'gauss',
-                 fit: ErrorFit = 'cheby-log'):
+                 shape: KernelShape = 'gauss'):
     """
     Determine suitable spacing value for mode_width given accepted error level
 
     Coefficients have been fitted to plots of error vs spacing value
     """
-
-    if fit == 'cubic' and shape == 'gauss':
-        return np.polyval([612.7, -122.7, 15.40, 1.0831], error)
-
-    if fit != 'cheby-log':
-        msg = dedent_and_fill(f"""
-            Fit "{fit}" is not available for shape "{shape}". The "cheby-log"
-            fit is recommended for "gauss" and "Lorentz" shapes.'
-            """)
-        raise ValueError(msg)
-
     if shape == 'lorentz':
         cheby = Chebyshev(
             [1.26039672, 0.39900457, 0.20392176, 0.08602507,
@@ -209,9 +187,9 @@ def _get_spacing(error,
 
     log_error = np.log10(error)
     if not safe_domain[0] < log_error < safe_domain[1]:
-        msg = (
-            'Target error is out of fit range; value must lie '
-            f'in range {np.power(10, safe_domain)}.'
+        msg = format_error(
+            f'Target error ({error}) is out of fit range.',
+            fix=f'Value must lie in range {np.power(10, safe_domain)}.',
         )
         raise ValueError(msg)
     return cheby(log_error)
@@ -224,7 +202,7 @@ def _width_interpolated_broadening(
     weights: np.ndarray,
     adaptive_error: float,
     shape: KernelShape = 'gauss',
-    fit: ErrorFit = 'cheby-log') -> np.ndarray:
+) -> np.ndarray:
     """
     Broadens a spectrum using a variable-width kernel, taking the
     same arguments as `variable_width` but expects arrays with
@@ -234,7 +212,7 @@ def _width_interpolated_broadening(
     x = np.ravel(x)
     widths = np.ravel(widths)
     weights = np.ravel(weights)
-    spacing = _get_spacing(adaptive_error, shape=shape, fit=fit)
+    spacing = _get_spacing(adaptive_error, shape=shape)
 
     # bins should be regularly spaced, check that this is the case and
     # raise a warning if not