Core fixes

.github/workflows/pypi-test.yml

@@ -71,7 +71,9 @@ jobs:
 
       - name: Run integration tests to verify the installation
         working-directory: easyreflectometry
-        run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto
+        # No -n auto: concurrent xdist workers race on arviz's daily-warning
+        # stamp file when they import easyreflectometry. See pixi.toml.
+        run: pixi run python -m pytest ../tests/integration/ --color=yes
 
   # Job 2: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:

.github/workflows/test.yml

@@ -293,7 +293,9 @@ jobs:
             cd easyreflectometry_py$py_ver
 
             echo "Running tests"
-            pixi run python -m pytest ../tests/integration/ --color=yes -n auto -v ${{ needs.env-prepare.outputs.pytest-marks }}
+            # No -n auto: concurrent xdist workers race on arviz's daily-warning
+            # stamp file when they import easyreflectometry. See pixi.toml.
+            pixi run python -m pytest ../tests/integration/ --color=yes -v ${{ needs.env-prepare.outputs.pytest-marks }}
 
             echo "Exiting pixi project directory"
             cd ..

CHANGELOG.md

@@ -1,5 +1,36 @@
 # Unreleased
 
+Fixed inconsistent interpretation of vector resolution functions between
+the refnx and refl1d engines (issue #367).
+
+- **Reflectivity results change for two engine / resolution
+  combinations.** `LinearSpline` on refl1d previously **over-smeared by
+  a factor of 2.355** (its FWHM widths were passed to refl1d's
+  `probe.dQ`, which expects sigma). `Pointwise` on refnx previously
+  **under-smeared by the same factor** (its sigma widths were passed to
+  refnx's `x_err`, which expects FWHM). Both are now correct. Fits and
+  simulations that used either combination will produce different —
+  previously wrong — results and should be re-run. `PercentageFwhm` on
+  either engine, `LinearSpline` on refnx, and `Pointwise` on refl1d are
+  numerically unchanged.
+- `ResolutionFunction.smearing()` now returns **sigma** (the Gaussian
+  standard deviation) for every subclass; each engine wrapper converts
+  to its backend's convention. This is a behavioural change to a public
+  method. Most visibly, `PercentageFwhm.smearing(q)` used to return the
+  _percentage_ itself (e.g. `5.0`) and now returns an absolute sigma
+  (e.g. `0.00212` at `q=0.1`); `LinearSpline.smearing(q)` returns its
+  `fwhm_values` divided by `2*sqrt(2*ln2)`. Callers relying on the old
+  values need to convert. The new `SIGMA_TO_FWHM` constant is exported
+  from `easyreflectometry.model.resolution_functions`.
+- Constructors are **unchanged**: `PercentageFwhm(5)` still means 5%
+  FWHM and `LinearSpline(q, fwhm_values)` still takes FWHM. Only the
+  `smearing()` output convention moved, so existing model-building code
+  needs no edits.
+- `PercentageFwhm.smearing(q)` given a scalar `q` now returns a 0-d
+  numpy scalar rather than a shape-`(1,)` array, matching
+  `LinearSpline`. `smearing(0.1)[0]` therefore raises `IndexError` where
+  it previously returned a value.
+
 Migrated sample / model classes off the deprecated `easyscience.ObjBase`
 and `easyscience.CollectionBase` pipeline.
 

CONTRIBUTING.md

@@ -42,8 +42,7 @@ Please make sure you follow the EasyScience organization-wide
 If you are not planning to contribute code, you may want to:
 
 - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues)
-- 🛡 Report a security issue — see
-  [Security Issues](#12-security-issues)
+- 🛡 Report a security issue — see [Security Issues](#12-security-issues)
 - 💬 Ask a question or start a discussion at
   [Project Discussions](https://github.com/easyscience/reflectometry-lib/discussions)
 

docs/mkdocs.yml

@@ -208,7 +208,8 @@ nav:
       - Elements:
           - Layers:
               - Layer: api-reference/elements/layer.md
-              - Layer Area Per Molecule: api-reference/elements/layer_area_per_molecule.md
+              - Layer Area Per Molecule:
+                  api-reference/elements/layer_area_per_molecule.md
           - Materials:
               - Material: api-reference/elements/material.md
               - Material Density: api-reference/elements/material_density.md

pixi.toml

@@ -94,7 +94,15 @@ user = { features = ['py-max', 'user'] }
 
 unit-tests = 'python -m pytest tests/unit/ --color=yes -v'
 functional-tests = 'python -m pytest tests/functional/ --color=yes -v'
-integration-tests = 'python -m pytest tests/integration/ --color=yes -n auto -v'
+# No -n auto: importing easyreflectometry pulls in arviz, and arviz 0.23.4
+# (py-311-env) writes a "warn once per day" stamp file on import via a
+# _atomic_write_text() that is not atomic -- every process writes the same
+# fixed `daily_warning.tmp` and renames it onto `daily_warning`. Concurrent
+# xdist workers therefore race on that rename: FileNotFoundError on Linux,
+# PermissionError (WinError 32) on Windows. The real fix is
+# to stop importing arviz in easyreflectometry/__init__.py, after which
+# xdist can come back.
+integration-tests = 'python -m pytest tests/integration/ --color=yes -v'
 notebook-tests = 'python -m pytest --nbmake docs/docs/tutorials/**/ --nbmake-timeout=1200 --color=yes -n auto -v'
 
 test = { depends-on = ['unit-tests'] }

pyproject.toml

@@ -23,7 +23,8 @@ classifiers = [
 ]
 requires-python = '>=3.11'
 dependencies = [
-  'easyscience @ git+https://github.com/easyscience/corelib.git@develop',
+  # 'easyscience @ git+https://github.com/easyscience/corelib.git@develop',
+  'easyscience @ git+https://github.com/easyscience/corelib.git@bayesian_extend',
   # 'easyscience',
   'scipp',
   'refnx',

src/easyreflectometry/analysis/bayesian.py

@@ -1332,8 +1332,9 @@ def load_posterior(path: str, skip: int = 0) -> 'PosteriorResults':
     """Reload a trace saved by :func:`save_posterior` into a
     :class:`PosteriorResults`.
 
-    The returned object's ``sampler_state`` can be fed back into
-    ``MultiFitter.mcmc_sample(..., resume_state=...)`` to extend the chain.
+    The returned object's ``sampler_state`` can be fed back into the core
+    ``Sampler`` (via ``Sampler.load_state(...)`` / ``Sampler.extend(...)``)
+    to extend the chain.
 
     :param path: File path prefix used in :func:`save_posterior`.
     :type path: str

src/easyreflectometry/calculators/refl1d/wrapper.py

@@ -8,8 +8,6 @@
 from refl1d import names
 from refl1d.sample.layers import Repeat
 
-from easyreflectometry.model import PercentageFwhm
-
 from ..wrapper_base import WrapperBase
 
 RESOLUTION_PADDING = 3.5
@@ -205,12 +203,9 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
             Reflectivity calculated at q.
         """
         sample = _build_sample(self.storage, model_name)
+        # smearing() returns sigma, which is exactly what refl1d's probe.dQ expects.
         dq_array = self._resolution_function.smearing(q_array)
 
-        if isinstance(self._resolution_function, PercentageFwhm):
-            # Get percentage of Q and change from sigma to FWHM
-            dq_array = dq_array * q_array / 100 / (2 * np.sqrt(2 * np.log(2)))
-
         if not self._magnetism:
             probe = _get_probe(
                 q_array=q_array,

src/easyreflectometry/calculators/refnx/wrapper.py

@@ -8,6 +8,7 @@
 from refnx import reflect
 
 from easyreflectometry.model import PercentageFwhm
+from easyreflectometry.model.resolution_functions import SIGMA_TO_FWHM
 
 from ..wrapper_base import WrapperBase
 
@@ -191,9 +192,12 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
 
         dq_vector = self._resolution_function.smearing(q_array)
         if isinstance(self._resolution_function, PercentageFwhm):
-            # FWHM Percentage resolution is constant given as
-            # For a constant resolution percentage refnx supports to pass a scalar value rather than a vector
-            dq_vector = dq_vector[0]
+            # refnx interprets a scalar x_err as a constant dq/q (FWHM percentage),
+            # so pass the percentage directly rather than a per-point vector.
+            dq_vector = self._resolution_function.constant
+        else:
+            # smearing() returns sigma; refnx expects the FWHM at each point.
+            dq_vector = dq_vector * SIGMA_TO_FWHM
 
         return model(x=q_array, x_err=dq_vector)