Fix the full-repository review findings

.prettierignore

@@ -28,6 +28,9 @@ node_modules
 # Tox
 .tox
 
+# Git worktrees checked out inside the repository
+.worktrees/
+
 # Misc
 .benchmarks
 .cache

docs/docs/tutorials/delta_lorentz.ipynb

@@ -65,7 +65,7 @@
    "id": "0aee03b1",
    "metadata": {},
    "source": [
-    "Both `A_0` and `lorentzian_width` are here allowed to vary with Q. We here change a few of them just to show how this impacts the model. The `# noqa` comment is because we are accessing private members of the model (ones beginning with `_`), which is generally discouraged. Because of these changes, in the figure below, the delta function at Q=1.25 Å^-1 is much larger than the other ones, and the Lorentzian at Q=1.75 Å^-1 is much narrower and taller than the other ones."
+    "Both `A_0` and `lorentzian_width` are here allowed to vary with Q. We here change a few of them just to show how this impacts the model. The `# ruff: ignore[private-member-access]` comment is because we are accessing private members of the model (ones beginning with `_`), which is generally discouraged. Because of these changes, in the figure below, the delta function at Q=1.25 Å^-1 is much larger than the other ones, and the Lorentzian at Q=1.75 Å^-1 is much narrower and taller than the other ones."
    ]
   },
   {

docs/mkdocs.yml

@@ -4,7 +4,7 @@ site_url: https://easyscience.github.io/dynamics-lib
 
 # Repository
 repo_url: https://github.com/easyscience/dynamics-lib
-edit_uri: edit/develop/docs/
+edit_uri: edit/develop/docs/docs/
 
 # Copyright
 copyright: © 2025-2026 EasyDynamics

pixi.toml

@@ -119,7 +119,10 @@ docstring-lint-check = 'pydoclint --quiet src/'
 notebook-lint-check = 'nbqa ruff docs/docs/tutorials/'
 py-lint-check = 'ruff check src/ tests/ docs/docs/tutorials/'
 py-format-check = 'ruff format --check src/ tests/ docs/docs/tutorials/'
-nonpy-format-check = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .'
+# Refreshes prettier first, so the local version can never drift behind the one CI installs.
+nonpy-format-check = { cmd = 'npx prettier --list-different --config=prettierrc.toml --ignore-unknown .', depends-on = [
+  'prettier-install',
+] }
 nonpy-format-check-modified = 'python tools/nonpy_prettier_modified.py'
 
 check = 'pre-commit run --hook-stage manual --all-files'
@@ -134,7 +137,9 @@ notebook-lint-fix = 'nbqa ruff --fix docs/docs/tutorials/'
 py-lint-fix = 'ruff check --fix src/ tests/ docs/docs/tutorials/'
 py-lint-fix-unsafe = 'ruff check --fix --unsafe-fixes src/ tests/ docs/docs/tutorials/'
 py-format-fix = 'ruff format src/ tests/ docs/docs/tutorials/'
-nonpy-format-fix = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .'
+nonpy-format-fix = { cmd = 'npx prettier --write --list-different --config=prettierrc.toml --ignore-unknown .', depends-on = [
+  'prettier-install',
+] }
 nonpy-format-fix-modified = 'python tools/nonpy_prettier_modified.py --write'
 success-message = 'echo "✅ All auto-formatting steps completed successfully!"'
 
@@ -178,9 +183,11 @@ cov = { depends-on = [
 ########################
 
 notebook-convert = 'jupytext docs/docs/tutorials/*.py --from py:percent --to ipynb'
-notebook-strip = 'nbstripout docs/docs/tutorials/*.ipynb'
+notebook-strip = 'nbstripout docs/docs/tutorials/**/*.ipynb'
 notebook-tweak = 'python tools/tweak_notebooks.py docs/docs/tutorials/'
-notebook-exec = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v'
+notebook-exec = { cmd = 'python -m pytest --nbmake docs/docs/tutorials/ --nbmake-timeout=1200 --overwrite --color=yes -n auto -v', depends-on = [
+  'prefetch-tutorial-data',
+] }
 
 notebook-prepare = { depends-on = [
   #'notebook-convert',
@@ -270,7 +277,10 @@ default-build = 'python -m build'
 dist-build = 'python -m build --wheel --outdir dist'
 
 npm-config = 'npm config set registry https://registry.npmjs.org/'
-prettier-install = 'npm install --no-save --no-audit --no-fund prettier prettier-plugin-toml'
+# --prefix . keeps the install inside this repository: without it, npm walks up the directory
+# tree and a stray package.json in a parent directory can silently pin an old prettier.
+# @latest keeps local runs on the same version CI installs.
+prettier-install = 'npm install --prefix . --no-save --no-audit --no-fund prettier@latest prettier-plugin-toml@latest'
 
 clean-pycache = "find . -type d -name '__pycache__' -prune -exec rm -rf '{}' +"
 

pyproject.toml

@@ -24,6 +24,10 @@ classifiers = [
 requires-python = '>=3.12'
 dependencies = [
   'easyscience>=2.5.1', # The base library of the EasyScience framework. 2.5.1 adds fitting.Sampler
+  'numpy',              # Numerical arrays (used directly throughout the library)
+  'scipy',              # Numerical routines (convolution, interpolation, special functions)
+  'scipp',              # Labelled multi-dimensional arrays; backs Experiment data handling
+  'h5py',               # HDF5 backend for scipp's HDF5 I/O (Experiment.load_hdf5)
   'matplotlib',         # Plotting (posterior trace, corner, and predictive plots)
   'pooch',              # Data downloader
   'darkdetect',         # Detecting dark mode (system-level)
@@ -167,7 +171,10 @@ fail_under = 0       # Minimum coverage percentage to pass
 
 [tool.pytest.ini_options]
 addopts = '--import-mode=importlib'
-markers = ['fast: mark test as fast (should be run on every push)']
+markers = [
+  'fast: mark test as fast (should be run on every push)',
+  'network: mark test as downloading data files (deselect with -m "not network" when offline)',
+]
 testpaths = ['tests']
 
 ########################

src/easydynamics/__init__.py

@@ -9,16 +9,16 @@
 """
 
 from easydynamics.analysis import Analysis
+from easydynamics.analysis import Analysis1d
 from easydynamics.analysis import BoundsSuggestion
 from easydynamics.analysis import BoundsSuggestions
+from easydynamics.analysis import FitBinding
 from easydynamics.analysis import MultiQPosteriorSampler
 from easydynamics.analysis import ParameterAnalysis
 from easydynamics.analysis import ParameterLabels
 from easydynamics.analysis import ParameterPosterior
 from easydynamics.analysis import PosteriorSampler
 from easydynamics.analysis import PosteriorSummary
-from easydynamics.analysis.analysis1d import Analysis1d
-from easydynamics.analysis.fit_binding import FitBinding
 from easydynamics.base_classes import EasyDynamicsBase
 from easydynamics.base_classes import EasyDynamicsModelBase
 from easydynamics.convolution import Convolution
@@ -42,11 +42,11 @@
 from easydynamics.settings import ConvolutionSettings
 from easydynamics.settings import DetailedBalanceSettings
 from easydynamics.utils import detailed_balance_factor
+from easydynamics.utils import hbar
 from easydynamics.utils import plot_corner
 from easydynamics.utils import plot_posterior_predictive
 from easydynamics.utils import plot_trace
 from easydynamics.utils import slicerplot_with_residuals
-from easydynamics.utils.utils import hbar
 
 __all__ = [
     'Analysis',

src/easydynamics/analysis/__init__.py

@@ -2,6 +2,8 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 from easydynamics.analysis.analysis import Analysis
+from easydynamics.analysis.analysis1d import Analysis1d
+from easydynamics.analysis.fit_binding import FitBinding
 from easydynamics.analysis.parameter_analysis import ParameterAnalysis
 from easydynamics.analysis.posterior import BoundsSuggestion
 from easydynamics.analysis.posterior import BoundsSuggestions
@@ -13,8 +15,10 @@
 
 __all__ = [
     'Analysis',
+    'Analysis1d',
     'BoundsSuggestion',
     'BoundsSuggestions',
+    'FitBinding',
     'MultiQPosteriorSampler',
     'ParameterAnalysis',
     'ParameterLabels',

src/easydynamics/analysis/analysis.py

@@ -1,10 +1,12 @@
 # SPDX-FileCopyrightText: 2026 EasyScience contributors <https://github.com/easyscience>
 # SPDX-License-Identifier: BSD-3-Clause
 
+import warnings
 from copy import copy
 from typing import Any
 
 import numpy as np
+import plopp as pp
 import scipp as sc
 from easyscience.fitting.minimizers.utils import FitResults
 from easyscience.fitting.multi_fitter import MultiFitter
@@ -298,6 +300,10 @@ def rebin(
             self.instrument_model.clear_Q(confirm=True)
 
         self._analysis_list_is_dirty = True
+        self._owner_index = None
+        # The cached MultiFitter holds the old Analysis1d objects, and the Sampler binds its data
+        # at construction, so both are stale after a rebin.
+        self._invalidate_fitter()
 
     def calculate(
         self,
@@ -448,11 +454,6 @@ def plot_data_and_model(
         self._verify_bool(add_background, 'add_background')
         self._verify_bool(plot_residuals, 'plot_residuals')
 
-        if energy is None:
-            energy = self.energy
-
-        import plopp as pp
-
         data_and_model = self.data_and_model_to_datagroup(
             energy=energy,
             add_background=add_background,
@@ -464,7 +465,8 @@ def plot_data_and_model(
         plot_kwargs_defaults['keep'] = 'energy'
         plot_kwargs_defaults.update(kwargs)
 
-        if plot_residuals:
+        # Residuals may have been omitted (with a warning) for a custom energy grid.
+        if plot_residuals and 'Residuals' in data_and_model:
             fig = slicerplot_with_residuals(
                 data_and_model,
                 residuals_key='Residuals',
@@ -531,8 +533,20 @@ def data_and_model_to_datagroup(
         self._verify_bool(include_components, 'include_components')
         self._verify_bool(include_residuals, 'include_residuals')
 
+        custom_energy = energy is not None
         energy = self._verify_energy(energy) if energy is not None else self.energy
 
+        if include_residuals and custom_energy:
+            # Residuals are data - model on the experiment grid; mixing them with a model on a
+            # custom grid would make the DataGroup internally inconsistent.
+            warnings.warn(
+                'Residuals are computed on the experiment energy grid and are omitted '
+                'when a custom energy grid is given.',
+                UserWarning,
+                stacklevel=2,
+            )
+            include_residuals = False
+
         data_and_model = {
             'Data': self.experiment.binned_data,
             'Model': self._create_model_array(energy=energy),
@@ -683,8 +697,6 @@ def plot_parameters(
 
         plot_kwargs_defaults.update(kwargs)
 
-        import plopp as pp
-
         return pp.plot(
             data_to_plot,
             **plot_kwargs_defaults,
@@ -766,6 +778,18 @@ def _on_convolution_settings_changed(self) -> None:
         self._owner_index = None
         self._invalidate_fitter()
 
+    def _on_detailed_balance_settings_changed(self) -> None:
+        """
+        Update the detailed balance settings when they change.
+
+        The per-Q analyses hold the settings object they were built with, so replacing it on this
+        Analysis requires rebuilding the list for the new object to reach every Q index.
+        """
+        super()._on_detailed_balance_settings_changed()
+        self._analysis_list_is_dirty = True
+        self._owner_index = None
+        self._invalidate_fitter()
+
     def _ensure_analysis_list_current(self) -> None:
         """Rebuild the analysis list if any dependency has changed since it was last built."""
         if self._analysis_list_is_dirty and self.Q is not None:
@@ -953,17 +977,36 @@ def _fit_all_Q_simultaneously(self) -> FitResults:
                 energy=self.experiment.get_masked_energy(Q_index=analysis1d.Q_index, mask=mask_var)
             )
 
-        mf = MultiFitter(
-            fit_objects=self.analysis_list,
-            fit_functions=self.get_fit_functions(),
-        )
-
-        return mf.fit(
+        # Use the configured fitter rather than a throwaway MultiFitter, so minimizer and
+        # tolerance settings applied through the ``fitter`` property take effect.
+        return self.fitter.fit(
             x=xs,
             y=ys,
             weights=ws,
         )
 
+    def get_all_variables(self) -> list[Parameter]:
+        """
+        Get all variables used in the analysis, across every Q index.
+
+        Overrides the easyscience fallback, which scans every attribute of the object and would
+        therefore build the MultiFitter and the Sampler as side effects of merely listing variables
+        (and fail outright on an empty analysis).
+
+        Returns
+        -------
+        list[Parameter]
+            A list of all variables, including any extra parameters.
+        """
+        variables = self.sample_model.get_all_variables()
+
+        variables.extend(self.instrument_model.get_all_variables())
+
+        if self._extra_parameters:
+            variables.extend(self._extra_parameters)
+
+        return variables
+
     def get_fit_functions(self) -> list[callable]:
         """
         Get fit functions for all Q indices, which can be used for simultaneous fitting.
@@ -1057,9 +1100,10 @@ def _create_components_dataset(
     #############
 
     def __repr__(self) -> str:
+        # The property ensures the list is current, so n_analyses is not reported stale.
         return (
             f'{self.__class__.__name__}('
             f'display_name={self.display_name!r}, '
             f'unique_name={self.unique_name!r}, '
-            f'n_analyses={len(self._analysis_list)})'
+            f'n_analyses={len(self.analysis_list)})'
         )