Docs updated for version 1.0.10.

.github/workflows/deploy-book.yml

@@ -24,6 +24,15 @@ jobs:
       run: |
         pip install -r docs/requirements.txt
 
+    # Defensive cleanup: strip any orphaned ipywidgets state (metadata.widgets
+    # entries no longer referenced by a cell's widget-view output) before
+    # building, so stale widget content (e.g. old progress-bar text) can't
+    # leak into the published HTML even if it was hand-edited back in after
+    # the lint-notebooks check last ran.
+    - name: Strip orphaned ipywidgets state
+      run: |
+        python scripts/check_notebook_widgets.py --fix
+
     # Build the book
     - name: Build the book
       run: |

.github/workflows/lint-notebooks.yml

@@ -0,0 +1,31 @@
+name: lint-notebooks
+
+# Reject notebooks with stale/orphaned ipywidgets state (metadata.widgets
+# entries no longer referenced by any cell's widget-view output). Left in
+# place, MyST-NB/nbconvert renders that leftover state into the built docs,
+# so old widget content (e.g. stale progress-bar text) can silently reappear
+# in published pages even after the code that produced it is gone.
+on:
+  pull_request:
+    paths:
+      - "**/*.ipynb"
+      - "scripts/check_notebook_widgets.py"
+  push:
+    branches: [main]
+    paths:
+      - "**/*.ipynb"
+      - "scripts/check_notebook_widgets.py"
+
+jobs:
+  check-notebook-widgets:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Check for orphaned ipywidgets state
+        run: python scripts/check_notebook_widgets.py

.gitignore

@@ -134,7 +134,11 @@ dmypy.json
 
 # data
 *.zarr
+*.zarr.zip
 mydask.html
 
 # IDE
-.idea/
+.idea/
+
+# Claude
+.claude/

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: local
+    hooks:
+      - id: check-notebook-widgets
+        name: Check for orphaned ipywidgets state in notebooks
+        description: >-
+          Fails if a notebook's metadata.widgets state is not referenced by
+          any cell's widget-view output. Stale state like this is invisible
+          in the notebook diff but gets rendered into the built docs by
+          MyST-NB/nbconvert (e.g. old tqdm progress-bar text reappearing).
+        entry: python scripts/check_notebook_widgets.py
+        language: system
+        files: \.ipynb$

docs/_config.yml

@@ -2,9 +2,10 @@
 # Learn more at https://jupyterbook.org/customize/config.html
 
 title: ""
-author: abTEM developers
+author: ""
+copyright: ""
 logo: images/logo.png
-exclude_patterns: ["_templates", "_build", "reference/benchmarks"]
+exclude_patterns: ["_templates", "_ext", "_build", "reference/benchmarks"]
 only_build_toc_files: false
 
 # Force re-execution of notebooks on each build.
@@ -42,6 +43,8 @@ sphinx:
   - 'sphinx.ext.autosummary'
   - 'sphinx_autodoc_typehints'
   - 'matplotlib.sphinxext.roles'
+  local_extensions:
+    abtem_version_footer: _ext
   config:
     autosummary_generate: true
     templates_path: [ "_templates" ]

docs/_ext/abtem_version_footer.py

@@ -0,0 +1,25 @@
+"""Show the installed abTEM version (the one the docs were built/tested against)
+in the page footer, replacing the theme's static copyright notice.
+"""
+
+
+def _set_abtem_version_footer(app, config):
+    try:
+        import abtem
+
+        version = abtem.__version__
+    except Exception:
+        version = "unknown"
+
+    theme_options = dict(config.html_theme_options or {})
+    theme_options["extra_footer"] = (
+        "<p>Tested against "
+        '<a href="https://github.com/abTEM/abTEM">abTEM</a>'
+        f" v{version}.</p>"
+    )
+    config.html_theme_options = theme_options
+
+
+def setup(app):
+    app.connect("config-inited", _set_abtem_version_footer)
+    return {"parallel_read_safe": True, "parallel_write_safe": True}

docs/abtem/changelog.md

@@ -1,33 +1,93 @@
 # Changelog
 
-Starting the changelog with version 1.0.8.
+## Upcoming: major features
+
+Features:
+- Energy ensemble support across the codebase (PlaneWave, Probe, SMatrix, Bloch) ([PR #257](https://github.com/abTEM/abTEM/pull/257))
+- Significant improvements on simulating large potentials on GPU, alongside minor performance improvements ([PR #269](https://github.com/abTEM/abTEM/pull/269))
+- In addition to the Gaussian (G) distribution, now also implemented Lorentzian (L), Voigtian (convolution L * G) and 
+pseudo-Voigtian (L + G) source-size distributions and filters ([PR #270](https://github.com/abTEM/abTEM/pull/270))
+- Support for skewed pixels (non-orthogonal x,y,z cell axes) ([PR #282](https://github.com/abTEM/abTEM/pull/282))
+- Linear-scaling PRISM-EELS for core-loss simulations ([PR #289](https://github.com/abTEM/abTEM/pull/289))
+- Radially variable detector sensitivity ([PR #283](https://github.com/abTEM/abTEM/pull/283))
+- Plasmons: fast `PhaseScramblePlasmons` for multislice and PRISM, and `MonteCarloPlasmons` for Bloch wave
+- CBED patterns for Bloch waves ([PR #254](https://github.com/abTEM/abTEM/pull/254))
+
+## 1.0.10
 
-## 1.0.10 (upcoming)
 Features:
-- Greatly expanded real-space multislice with propagator- and fully-corrected algorithms, as well as backscattered waves
-- Updated `BullseyeAperture` to use smoothed aperture edges
+
+- Expanded real-space multislice with propagator- and fully-corrected algorithms, and backscattered waves ([PR #236](https://github.com/abTEM/abTEM/pull/236))
+    - Related internal function name change: standard multislice is now properly called `FourierMultislice`
+- Updated `BullseyeAperture` to use smoothed aperture edges/corners ([PR #266](https://github.com/abTEM/abTEM/pull/266))
+- Logarithmic scale display for `DiffractionPatterns` and images ([PR #303](https://github.com/abTEM/abTEM/pull/303))
+- Finite-projection integrals 7x faster on CPU ([PR #309](https://github.com/abTEM/abTEM/pull/309))
+
+Documentation:
+
+- Expanded tutorial on real-space multislice
+- Depth-profile visualization of potentials in the walkthrough
+- Single-file Zarr zip storage, logarithmic display scaling, soft Bullseye apertures, anisotropic
+  Debye-Waller factors and B-factor conversion helpers
+- All published notebooks verified to run with this release
 
 Dependencies:
-- Support for Zarr 3 `ZipStore` (requiring `rich` as an additional dependency)
-- Deprecated `[gpu]` optional dependency (just asking for `cupy` won't install the correct CUDA version)
-- Moved testing, docs, and dev from optional dependencies to groups
+
+- NumPy 2.0 or newer is now required ([PR #245](https://github.com/abTEM/abTEM/pull/245))
+- GitHub actions based on `uv` and now cover more versions (including Python 3.14) ([PR #308](https://github.com/abTEM/abTEM/pull/308))
+- New branching structure: `dev` for development, `main` for releases (only via PRs from `dev`)
+- Support for Zarr 3 `ZipStore` (requiring `zarr>=3.1`)
+    - Added Zstandard compression of the arrays in the ZipStore at default level 4 (hat tip: quantEM) ([PR #252](https://github.com/abTEM/abTEM/pull/252))
+- Deprecated `[gpu]` optional dependency (as just specifying `cupy` will not install the correct CUDA version)
+- Moved `testing`, `docs`, and `dev` from optional dependencies to groups
+- Narrow Dask version exclusion to !=2025.12.*,!=2026.1.0,!=2026.1.1 ([PR #285](https://github.com/abTEM/abTEM/pull/285))
+- Declared `sympy` as an optional dependency (`core-loss` extra), required for core-loss EELS form
+  factors ([PR #320](https://github.com/abTEM/abTEM/pull/320))
+
+
+Bugfixes:
+
+- Frozen-phonon ensemble handling ([PR #267](https://github.com/abTEM/abTEM/pull/267) & [PR #292](https://github.com/abTEM/abTEM/pull/292))
+  - May also have resulted in incorrect behavior with `ensemble_mean = False` for e.g. defocus distributions
+- `CrystalPotential` with frozen phonons bugs (especially bad on – luckily rare – eager compute) ([PR #306](https://github.com/abTEM/abTEM/pull/306))
+- Minor bugs, unsafe patterns, and dead code ([PR #265](https://github.com/abTEM/abTEM/pull/265))
+- Anistropic Debye-Waller factors for Bloch wave ([PR #271](https://github.com/abTEM/abTEM/pull/271))
+  - Added helper functions to convert between crystallographic B-factors and thermal sigmas
+- Added missing `.calculate_exit_waves` for `BlochwaveEnsamble` ([PR #294](https://github.com/abTEM/abTEM/pull/294))
+- Silent atom drop when `z`-position lands in SliceIndexedAtoms blind spot  ([PR #273](https://github.com/abTEM/abTEM/pull/273))
+- Early-exit bug in orthogonalize_cell ([PR #291](https://github.com/abTEM/abTEM/pull/291))
+- Fixed broken tutorial workflow for core-loss filtered imaging ([PR #284](https://github.com/abTEM/abTEM/pull/284))
+  - Minor performance improvements for `transition_potential_scan` ([PR #286](https://github.com/abTEM/abTEM/pull/286))
+- `Bullseye` aperture: `ring_width` and `spoke_width` are now validated, rejecting values that previously
+  produced a silently wrong (solid disk) aperture; docstring corrected to describe the actual fractional
+  units introduced by the soft-edge redesign ([PR #319](https://github.com/abTEM/abTEM/pull/319))
+- Unified the task-level progress bar config key on `diagnostics.task_progress` (Bloch-wave code paths
+  previously read a different, non-functional key) ([PR #321](https://github.com/abTEM/abTEM/pull/321))
 
 ## 1.0.9
+
 Dependencies:
+
 - Support for `scipy>=1.7` and `cupy>=12`.
-- Restricted Dask versions (>=2022.12.1,!=2025.12.*,!=2026.1.*") to avoid an issue with Numba in the latest ones 
+- Restricted Dask versions (`>=2022.12.1,!=2025.12.*,!=2026.1.*"`) to avoid an issue with Numba in the latest ones
 
 ## 1.0.8
+
+Starting the changelog with version 1.0.8.
+
 Features:
+
 - Fully featured Bloch-wave simulations
 - Simple real-space multislice algorithm
-- Fully tested core-loss filtered imaging
+- Core-loss filtered imaging
 - Structured illumination (custom apertures and phase plates)
 
 Documentation:
+
 - Updated and fixed example gallery
 - Appendix on convergence
 - Expanded tutorial on orthogonal periodic supercells
 
 Bugfixes:
+
 - Numerous small bugfixes and improvements

docs/abtem/contribute.md

@@ -74,13 +74,21 @@ git clone https://github.com/abtem/abtem
 cd abtem
 ```
 
-Next, install:
+Next, install. The development dependencies are declared as [PEP 735 dependency groups](https://peps.python.org/pep-0735/)
+(`dev`, `test`, and `docs`), so use a tool that understands them. We recommend [uv](https://docs.astral.sh/uv/),
+which is also what our continuous integration uses:
 
 ```{code-block}
-python -m pip install -e ".[testing,docs]"
+uv sync --group test --group docs
 ```
 
-This will install *ab*TEM locally in your Python environment (we recommend using Conda), along with the packages needed
+Alternatively, with a recent pip (25.1 or newer):
+
+```{code-block}
+python -m pip install -e . --group test --group docs
+```
+
+This will install *ab*TEM locally in your Python environment, along with the packages needed
 to test it and the packages for producing documentation.
 
 ### Optional: Install the pre-commit hooks

docs/getting_started/basics.md

@@ -1,11 +1,6 @@
 (getting_started:basic_examples)=
 # Basic examples
 
-:::{admonition} {material-regular}`engineering;1.5rem;sd-mr-1` Under construction
-:class: no-icon
-The examples are currently a work in progress. 
-:::
-
 This is a selection of basic code examples for the most common types of simulations of electron microscopy experiments.
 
 If you have previous experience with multislice simulations, you should be able to jump right in and modify the most 
@@ -88,17 +83,4 @@ the [gallery](user_guide:example_gallery).
 ```{image} ../user_guide/examples/thumbnails/4d-stem_quickstart.png
 :align: center
 ```
-:::
-
-:::{grid-item-card}
-:link: examples:prism_quickstart
-:link-type: ref
-:class-body: text-center
-:class-header: bg-light text-center
-
-**PRISM**
-^^^
-```{image} ../user_guide/examples/thumbnails/prism_quickstart.png
-:align: center
-```
 ::::

docs/reference/default_config.yaml

@@ -8,7 +8,7 @@ fft: fftw
 precision: float32
 diagnostics:
   # Show the progress bar. Options are 'true', 'false' or 'tqdm'
-  progress_bar: true
+  progress_bar: tqdm
   # Show the progress of each task. Options are 'true' or 'false'
   task_progress: false
 dask: