Update project template and CI/docs tooling

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.11.3-3-ga67ebc3
+_commit: v0.13.1
 _src_path: gh:easyscience/templates
 lib_docs_url: https://easyscience.github.io/core
 lib_doi: 10.5281/zenodo.18163581

.github/workflows/coverage.yml

@@ -63,32 +63,8 @@ jobs:
           files: ./coverage-unit.xml
           token: ${{ secrets.CODECOV_TOKEN }}
 
-  # Job 2: Run integration tests with coverage and upload to Codecov
-  integration-tests-coverage:
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Check-out repository
-        uses: actions/checkout@v6
-
-      - name: Set up pixi
-        uses: ./.github/actions/setup-pixi
-
-      - name: Run integration tests with coverage
-        run:
-          pixi run integration-tests-coverage --cov-report=xml:coverage-integration.xml
-
-      - name: Upload integration tests coverage to Codecov
-        if: ${{ !cancelled() }}
-        uses: ./.github/actions/upload-codecov
-        with:
-          name: integration-tests-job
-          flags: integration
-          files: ./coverage-integration.xml
-          token: ${{ secrets.CODECOV_TOKEN }}
-
   # Job 4: Build and publish dashboard (reusable workflow)
   run-reusable-workflows:
-    needs: [docstring-coverage, unit-tests-coverage, integration-tests-coverage] # depend on the previous jobs
+    needs: [docstring-coverage, unit-tests-coverage] # depend on the previous jobs
     uses: ./.github/workflows/dashboard.yml
     secrets: inherit

.github/workflows/docs.yml

@@ -123,11 +123,14 @@ jobs:
 
       # Build the static files for the documentation site for local inspection
       # Input: docs/ directory containing the Markdown files
-      # Output: site/ directory containing the generated HTML files
+      # Output: docs/site/ directory containing the generated HTML files
+      # Also verifies that mkdocstrings generated docs/site/objects.inv.
       - name: Build site for local check
-        run: pixi run docs-build-local
+        run: |
+          pixi run docs-build-local
+          pixi run docs-inventory-check
 
-      # Upload the static files from the site/ directory to be used for
+      # Upload the static files from the docs/site/ directory to be used for
       # local check
       - name: Upload built site as artifact
         uses: ./.github/actions/upload-artifact

.github/workflows/pypi-test.yml

@@ -43,11 +43,15 @@ jobs:
           frozen: false
 
       - name: Init pixi project
-        run: pixi init easyscience
+        run:
+          pixi init --platform linux-64 --platform osx-arm64 --platform win-64
+          easyscience
 
-      - name: Set the minimum system requirements
+      - name: Configure pixi platforms
         working-directory: easyscience
-        run: pixi project system-requirements add macos 14.0
+        run: |
+          pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+          pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
 
       - name: Add Python 3.14 from Conda
         working-directory: easyscience

.github/workflows/test.yml

@@ -211,15 +211,16 @@ jobs:
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
             echo "Initializing pixi project"
-            pixi init easyscience_py$py_ver
+            pixi init --platform linux-64 --platform osx-arm64 --platform win-64 easyscience_py$py_ver
             cd easyscience_py$py_ver
 
+            echo "Configure pixi platforms"
+            pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+            pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
+
             echo "Adding Python $py_ver"
             pixi add "python=$py_ver"
 
-            echo "Setting macOS 14.0 as minimum required"
-            pixi project system-requirements add macos 14.0
-
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"
 

.prettierignore

@@ -25,6 +25,9 @@ docs/docs/assets/
 # Node
 node_modules
 
+# Tox
+.tox
+
 # Misc
 .benchmarks
 .cache

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/core/discussions)
 

docs/docs/assets/stylesheets/extra.css

@@ -200,7 +200,14 @@ label.md-nav__title[for="__drawer"] {
 
 /* Change the overall width of the page */
 .md-grid {
-  max-width: 1280px;
+  max-width: 116em;
+}
+
+/* Keep prose line length stable when sidebars are hidden at narrower widths */
+.md-main .md-content > .md-content__inner {
+  width: min(100%, 40.5em);
+  margin-left: auto !important;
+  margin-right: auto !important;
 }
 
 /* Needed for mkdocs-jupyter to show download and other buttons on top of the notebook */

docs/mkdocs.yml

@@ -153,7 +153,25 @@ plugins:
             show_root_heading: true
             show_root_full_path: false
             show_submodules: true
-            show_source: true
+            show_source: false
+            show_bases: false
+            # Uncomment when the project depends on `easyscience` and inherited
+            # EasyScience base-class members should be shown in the API docs.
+            # preload_modules:
+            #   - easyscience
+            inherited_members: true
+            show_category_heading: true
+            merge_init_into_class: true
+            docstring_options:
+              ignore_init_summary: true
+            summary: true
+            relative_crossrefs: true
+            scoped_crossrefs: true
+            filters: ['!^_[^_]', '!__repr__', '!__dir__'] # This is the default filter minus __repr__ and __dir__
+          inventories:
+            - url: https://scipp.github.io/objects.inv
+            - url: https://numpy.org/doc/stable/objects.inv
+            - url: https://easyscience.github.io/core/latest/objects.inv
   - search
 
 # Determines additional directories to watch when running mkdocs serve

pixi.toml

@@ -5,7 +5,19 @@
 [workspace]
 
 # Supported platforms for the lock file (pixi.lock)
-platforms = ['win-64', 'linux-64', 'osx-arm64']
+platforms = [
+  'win-64',
+  # Set minimum supported version for glibc to be 2.35 to ensure packages
+  # like `crysfml` that only have wheels for glibc 2.35+
+  # (manylinux_2_35_x86_64) are used.
+  #libc = { family = 'glibc', version = '2.35' }
+  { platform = 'linux-64', glibc = '2.35' },
+  # Set minimum supported version for macOS to be 14.0 to ensure packages
+  # like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)
+  # are used instead of building from source. This is a workaround for
+  # Pixi, see https://github.com/prefix-dev/pixi/issues/5667
+  { platform = 'osx-arm64', macos = '14.0' },
+]
 
 # Channels for fetching packages
 channels = ['nodefaults', 'conda-forge']
@@ -19,13 +31,6 @@ channels = ['nodefaults', 'conda-forge']
 [activation.env]
 PYTHONIOENCODING = 'utf-8'
 
-[system-requirements]
-# Set minimum supported version for macOS to be 14.0 to ensure packages
-# like `scipp` that only have wheels for macOS 14.0+ (macosx_14_0_arm64)
-# are used instead of building from source. This is a workaround for
-# Pixi, see https://github.com/prefix-dev/pixi/issues/5667
-macos = '14.0'
-
 # Non-default features:
 
 # Set specific Python versions to be used in CI testing.
@@ -182,8 +187,9 @@ docs-serve = 'pixi run docs-pre serve -f docs/mkdocs.yml'
 docs-serve-dirty = 'pixi run docs-serve --dirty'
 docs-build = 'pixi run docs-pre build -f docs/mkdocs.yml'
 docs-build-local = 'pixi run docs-build --no-directory-urls'
+docs-inventory-check = 'python -c "from pathlib import Path; p = Path(\"docs/site/objects.inv\"); raise SystemExit(0 if p.is_file() and p.stat().st_size > 0 else \"missing or empty docs/site/objects.inv\")"'
 
-docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type redirect'
+docs-deploy-pre = 'mike deploy -F docs/mkdocs.yml --push --branch gh-pages --update-aliases --alias-type copy'
 docs-set-default-pre = 'mike set-default -F docs/mkdocs.yml --push --branch gh-pages'
 
 docs-update-assets = 'python tools/update_docs_assets.py'

pyproject.toml

@@ -180,9 +180,11 @@ testpaths = ['tests']
 [tool.ruff]
 exclude = ['tests', 'legacy', 'src/easyscience/legacy']
 indent-width = 4
-line-length = 99                                        # See also `max-line-length` in [tool.ruff.lint.pycodestyle]
-preview = true                                          # Enable new rules that are not yet stable, like DOC
-
+line-length = 99 # See also `max-line-length` in [tool.ruff.lint.pycodestyle]
+preview = true # Enable new rules that are not yet stable, like DOC
+builtins = [
+  'display',
+] # Clutch-fix/patch to https://github.com/nbQA-dev/nbQA/issues/882
 # Formatting options for Ruff
 
 [tool.ruff.format]
@@ -233,6 +235,9 @@ ignore = [
   'INP001', # https://docs.astral.sh/ruff/rules/implicit-namespace-package/
   'T201',   # https://docs.astral.sh/ruff/rules/print/
 ]
+'docs/docs/tutorials/**' = [
+  'E402', # https://docs.astral.sh/ruff/rules/module-import-not-at-top-of-file/
+]
 
 # Specific options for certain rules
 

src/easyscience/fitting/fitter.py

@@ -433,20 +433,24 @@ def mcmc_sample(
         progress_callback: Optional[Callable[[dict], Optional[bool]]] = None,
         abort_test: Optional[Callable[[], bool]] = None,
     ) -> dict:
-        """Run Bayesian MCMC sampling using the BUMPS DREAM sampler.
+        """
+        Run Bayesian MCMC sampling using the BUMPS DREAM sampler.
 
         Works with both a plain ``Fitter`` (single dataset) and a
         ``MultiFitter`` (multiple datasets) via polymorphic dispatch:
-        ``_precompute_reshaping`` and ``_fit_function_wrapper`` are resolved
-        on the concrete subclass at call time, so multi-dataset flattening
-        is handled automatically when called on a ``MultiFitter`` instance.
+        ``_precompute_reshaping`` and ``_fit_function_wrapper`` are
+        resolved on the concrete subclass at call time, so multi-dataset
+        flattening is handled automatically when called on a
+        ``MultiFitter`` instance.
 
         Parameters
         ----------
         x : np.ndarray
-            Independent variable array (or list of arrays for ``MultiFitter``).
+            Independent variable array (or list of arrays for
+            ``MultiFitter``).
         y : np.ndarray
-            Dependent variable array (or list of arrays for ``MultiFitter``).
+            Dependent variable array (or list of arrays for
+            ``MultiFitter``).
         weights : np.ndarray
             Weight array (or list of arrays for ``MultiFitter``).
         samples : int, default=10000
@@ -459,16 +463,19 @@ def mcmc_sample(
         population : Optional[int], default=None
             BUMPS DREAM population count (number of parallel chains).
         vectorized : bool, default=False
-            When ``True``, each x array may be multi-dimensional (e.g. an
-            ``(N, M, 2)`` grid for a 2D model) and is left as-is.  When
-            ``False`` (default), each x array is expected to be 1-D.
+            When ``True``, each x array may be multi-dimensional (e.g.
+            an ``(N, M, 2)`` grid for a 2D model) and is left as-is.
+            When ``False`` (default), each x array is expected to be
+            1-D.
         sampler_kwargs : Optional[dict], default=None
-            Additional keyword arguments forwarded to the BUMPS DREAM sampler.
+            Additional keyword arguments forwarded to the BUMPS DREAM
+            sampler.
         progress_callback : Optional[Callable[[dict], Optional[bool]]], default=None
-            Optional callback invoked at each DREAM generation.  The payload
-            dict includes ``iteration`` and ``sampling: True``.
+            Optional callback invoked at each DREAM generation.  The
+            payload dict includes ``iteration`` and ``sampling: True``.
         abort_test : Optional[Callable[[], bool]], default=None
-            Optional callable that returns ``True`` to abort sampling early.
+            Optional callable that returns ``True`` to abort sampling
+            early.
 
         Returns
         -------

src/easyscience/fitting/minimizers/minimizer_bumps.py

@@ -118,9 +118,9 @@ def fit(
             ``iteration`` carries the BUMPS optimizer step index. By
             default, None.
         abort_test : Callable[[], bool] | None, default=None
-            Optional callback that returns ``True`` to signal that the fit
-            should be aborted.  Called periodically during the
-            BUMPS optimizer iteration loop.
+            Optional callback that returns ``True`` to signal that the
+            fit should be aborted.  Called periodically during the BUMPS
+            optimizer iteration loop.
         minimizer_kwargs : dict | None, default=None
             Additional keyword arguments passed to the BUMPS minimizer.
             By default, None.
@@ -393,12 +393,14 @@ def mcmc_sample(
         progress_callback: Callable[[dict], bool | None] | None = None,
         abort_test: Callable[[], bool] | None = None,
     ) -> dict:
-        """Run Bayesian MCMC sampling using the BUMPS DREAM sampler.
+        """
+        Run Bayesian MCMC sampling using the BUMPS DREAM sampler.
 
-        Builds a BUMPS `FitProblem` from the current model and runs the DREAM
-        sampler.  This is the public minimizer-level entry point for Bayesian
-        sampling; the higher-level `MultiFitter.mcmc_sample` delegates to this
-        method after flattening multi-dataset arrays.
+        Builds a BUMPS ``FitProblem`` from the current model and runs
+        the DREAM sampler.  This is the public minimizer-level entry
+        point for Bayesian sampling; the higher-level
+        ``MultiFitter.mcmc_sample`` delegates to this method after
+        flattening multi-dataset arrays.
 
         Parameters
         ----------
@@ -417,15 +419,16 @@ def mcmc_sample(
         population : int | None, default=None
             BUMPS DREAM population count (number of parallel chains).
         sampler_kwargs : dict | None, default=None
-            Additional keyword arguments forwarded to `bumps.fitters.fit`.
+            Additional keyword arguments forwarded to
+            ``bumps.fitters.fit``.
         progress_callback : Callable[[dict], bool | None] | None, default=None
             Optional callback for progress updates during sampling.  The
-            payload dict includes ``iteration`` (DREAM generation number) and
-            ``sampling: True``.
+            payload dict includes ``iteration`` (DREAM generation
+            number) and ``sampling: True``.
         abort_test : Callable[[], bool] | None, default=None
-            Optional callback that returns ``True`` to signal that sampling
-            should be aborted. Called periodically during the DREAM sampling
-            loop.
+            Optional callback that returns ``True`` to signal that
+            sampling should be aborted. Called periodically during the
+            DREAM sampling loop.
 
         Returns
         -------
@@ -439,7 +442,8 @@ def mcmc_sample(
             If the input shapes or weights are invalid, or if
             ``progress_callback`` is not callable.
         FitError
-            If DREAM sampling was aborted by the user (via ``abort_test``).
+            If DREAM sampling was aborted by the user (via
+            ``abort_test``).
         Exception
             Re-raised from DREAM fitting if any unexpected error occurs
             (parameter values are restored beforehand).
@@ -545,11 +549,13 @@ def mcmc_sample(
     def _build_sample_progress_payload(
         self, problem, iteration: int, point: np.ndarray, nllf: float
     ) -> dict:
-        """Build a progress payload for Bayesian DREAM sampling steps.
+        """
+        Build a progress payload for Bayesian DREAM sampling steps.
 
-        Called by :class:`BumpsProgressMonitor` at each DREAM generation.
-        The payload includes ``sampling: True`` so downstream consumers can
-        distinguish sampling progress from classical fitting progress.
+        Called by :class:`BumpsProgressMonitor` at each DREAM
+        generation. The payload includes ``sampling: True`` so
+        downstream consumers can distinguish sampling progress from
+        classical fitting progress.
         """
         payload = self._build_progress_payload(problem, iteration, point, nllf)
         payload['sampling'] = True

src/easyscience/fitting/multi_fitter.py

@@ -98,9 +98,10 @@ def _precompute_reshaping(
         weights : list[np.ndarray] | None
             Optional weights for each dataset.
         vectorized : bool
-            When ``True``, each x array may be multi-dimensional (e.g. an
-            ``(N, M, 2)`` grid for a 2D model) and is left as-is.  When
-            ``False`` (default), each x array is expected to be 1-D.
+            When ``True``, each x array may be multi-dimensional (e.g.
+            an ``(N, M, 2)`` grid for a 2D model) and is left as-is.
+            When ``False`` (default), each x array is expected to be
+            1-D.
 
         Returns
         -------