simind-python-connector 2.0.1__tar.gz → 2.0.2__tar.gz

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/.github/workflows/docs.yml

@@ -37,15 +37,11 @@ jobs:
             echo "Tag $GITHUB_REF_NAME does not match version v${version}"
             exit 1
           fi
-      - name: Build the documentation without executing examples
-        env:
-          SIMIND_GALLERY_BACKEND: ""
+      - name: Build the documentation
         run: |
           python -m sphinx -b html -W --keep-going docs docs/_build/html
-      - name: Check the generated gallery indexes are committed
-        run: |
-          git status --porcelain -- docs/auto_examples
-          test -z "$(git status --porcelain -- docs/auto_examples)"
+      - name: Check authored documentation inventory and figures
+        run: python scripts/check_docs.py --html-dir docs/_build/html
       - name: Upload the built documentation
         uses: actions/upload-artifact@v4
         with:

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/.github/workflows/tests.yml

@@ -35,11 +35,11 @@ jobs:
         run: |
           ruff check .
           ruff format --check .
-      - name: Check gallery outputs are current
-        run: python scripts/check_gallery_current.py
+      - name: Check authored documentation inventory
+        run: python scripts/check_docs.py
       - name: Run CI-friendly tests
         run: |
-          python -m pytest -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not ci_skip and not validation and not macos_v9" --cov=simind_python_connector --cov-report=xml
+          python -m pytest -m "not integration and not requires_sirf and not requires_stir and not requires_simind and not requires_pytomography and not requires_cil and not ci_skip and not validation" --cov=simind_python_connector --cov-report=xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/.zenodo.json

@@ -31,5 +31,5 @@
   ],
   "access_right": "open",
   "license": "apache-2.0",
-  "version": "2.0.1"
+  "version": "2.0.2"
 }

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/CHANGELOG.md

@@ -7,6 +7,40 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [2.0.2] - 2026-11-10
+
+A v8 compatibility, documentation and correctness release on the 2.0.1 code
+base. It states the supported engine, replaces the generated gallery with
+short authored tutorials, and fixes the pixel-wise Dewaraja scatter estimator
+and the STIR OSEM image output.
+
+### Compatibility
+- SIMIND v8 is the supported engine. v9 remains experimental and unvalidated:
+  the v9.0 Linux build can abort or return silently corrupted projections, so
+  v9 qualification is planned for 2.1.0.
+- The v9 failure-expectation tests, the v9 validation tables and the support
+  claims that depended on them are removed.
+
+### Documentation
+- Each tutorial is now a short authored page: the explanation, the figures and
+  the result, with the runnable script linked rather than reproduced.
+- The example set is consolidated: 02 into 01, 08A/08B/08C into one DICOM
+  recipe, 10 into 11, and 16A/16B/16C into one CT case study. Example 18 is
+  removed.
+- The generated gallery and its provenance machinery are removed. Figures come
+  from recorded runs and were not regenerated for the rewrite.
+
+### Fixed
+- The Dewaraja pixel-wise scatter fraction pre-smooths the Monte Carlo
+  scatter and the total before dividing, removing the low bias that came from
+  dividing two noisy fields.
+- STIR OSEM no longer writes one Interfile image per subiteration into the
+  working directory; only the returned image is kept.
+
+### Known limitations
+- Example 13's residual arm and example 15's instability remain documented
+  limited results, not validated improvements.
+
 ## [2.0.1] - 2026-10-24
 
 The supported successor to 1.2.0, the current public release, and the

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/CITATION.cff

@@ -11,8 +11,8 @@ authors:
 - family-names: Thielemans
   given-names: Kris
   orcid: "https://orcid.org/0000-0001-6353-9538"
-date-released: 2026-10-24
-version: 2.0.1
+date-released: 2026-11-10
+version: 2.0.2
 url: "https://github.com/samdporter/simind-python-connector"
 doi: 10.5281/zenodo.19605198
 license: Apache-2.0

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/MANIFEST.in

@@ -2,16 +2,15 @@
 # --------------------------
 # The sdist ships the complete source tree needed to install the package, build
 # the documentation, run the examples and run the shipped test suite: package
-# sources and bundled data, Sphinx sources, gallery example sources, release and
+# sources and bundled data, Sphinx sources, example sources, release and
 # container scripts, tests and their fixtures, and the CI/docker support files
 # those tests read.
 #
-# Generated output is deliberately excluded. The rendered gallery under
-# docs/auto_examples (pages, images, notebooks, checksums and execution times),
-# Sphinx build trees and generated execution-time files are not shipped.
-# Rendered documentation is built from the tagged repository; the sdist keeps
-# only the sources from which it is generated. Local-only agent notes, audits,
-# build artefacts and simulation data are never shipped.
+# Generated output is deliberately excluded. Sphinx build trees and generated
+# execution-time files are not shipped. Rendered documentation is built from
+# the tagged repository; the sdist keeps only the sources from which it is
+# generated. Local-only agent notes, audits, build artefacts and simulation
+# data are never shipped.
 
 include README.md
 include LICENSE
@@ -26,19 +25,19 @@ include .readthedocs.yaml
 recursive-include simind_python_connector/data *.atn *.json
 recursive-include simind_python_connector/configs *.smc *.yaml
 
-# Documentation sources, not generated gallery output.
-recursive-include docs *.rst *.md *.py LICENSE
+# Documentation sources and the authored-page inventory.
+recursive-include docs *.rst *.rst.txt *.md *.py LICENSE
+include docs/example_pages.json
+recursive-include docs/_static/examples *
 include docs/_static/.gitkeep
-prune docs/auto_examples
-prune docs/examples
+include docs/examples
 prune docs/_build
 prune docs/_generated
-exclude docs/sg_execution_times.rst
 
 # Example sources and their READMEs/helpers.
 recursive-include examples *.py *.rst
 
-# Release, gallery, validation and container scripts.
+# Release, docs-check, validation and container scripts.
 recursive-include scripts *.py *.sh
 
 # Container definitions and the import guard used by the isolation tests.

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simind-python-connector
-Version: 2.0.1
+Version: 2.0.2
 Summary: Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors
 Author-email: Sam Porter <sam.porter.18@ucl.ac.uk>, Rebecca Gillen <rebecca.gillen.18@ucl.ac.uk>, "Efstathios (Stahis) Varzakis" <efstathios.varzakis.22@ucl.ac.uk>
 Maintainer-email: Sam Porter <sam.porter.18@ucl.ac.uk>
@@ -33,8 +33,8 @@ Requires-Dist: scipy; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: sphinx; extra == "dev"
 Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: Pillow; extra == "dev"
 Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
-Requires-Dist: sphinx-gallery<0.23,>=0.22; extra == "dev"
 Requires-Dist: pooch>=1.8; extra == "dev"
 Requires-Dist: myst-parser; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
@@ -58,15 +58,12 @@ SIMIND project and Lund University.
 
 ## Start here
 
-See the [workflow tutorial](docs/tutorial.rst) for an ordered path through a
-core simulation, known-activity NEMA phantom, reconstruction, scatter
-correction, and measured-data calibration. The [gallery](docs/auto_examples/index.rst)
-has every tutorial with its figures and printed output. Rendered documentation,
-including the gallery, is built from the tagged repository; source distributions
-contain the example sources rather than the generated gallery. The
-[documentation](https://simind-python-connector.readthedocs.io/) explains
-installation, geometry, normalisation, backend options, and the
-[observed SIMIND output-component mapping](docs/simind_validation.md).
+The [workflow tutorial](docs/tutorial.rst) walks through a core simulation,
+known-activity NEMA phantom, reconstruction, scatter correction, and
+measured-data calibration; the [example pages](docs/example_pages/index.rst)
+collect the tutorials and figures. The
+[documentation](https://simind-python-connector.readthedocs.io/) covers
+installation, geometry, normalisation and backends.
 
 Install the package and example plotting dependencies:
 
@@ -79,15 +76,15 @@ Select a SIMIND executable and its matching data directory. The binary and
 `simind` on `PATH`; set `SMC_DIR` when required by your installation.
 
 ```bash
-export SIMIND_BIN=/path/to/simind-v9/simind
-export PATH=/path/to/simind-v9:$PATH
-export SMC_DIR=/path/to/simind-v9/smc_dir/
-export SIMIND_VERSION=9
+export SIMIND_BIN=/path/to/simind-v8/simind
+export PATH=/path/to/simind-v8:$PATH
+export SMC_DIR=/path/to/simind-v8/smc_dir/
+export SIMIND_VERSION=8
 ```
 
-Select version `8` or `9` explicitly. The connector uses this choice to place
-voxel source and density maps in the same physical coordinates; the default
-is version 8. A constructor's `simind_version` overrides `SIMIND_VERSION`.
+SIMIND v8 is the supported engine. A constructor's `simind_version` overrides
+`SIMIND_VERSION`; v9 selection is experimental. See
+[installation](docs/installation.rst).
 
 Use the installed connector directly:
 
@@ -96,7 +93,7 @@ import numpy as np
 from simind_python_connector import SimindPythonConnector, configs
 
 connector = SimindPythonConnector(
-    configs.get("Example.yaml"), "output/basic", "case01", simind_version=9
+    configs.get("Example.yaml"), "output/basic", "case01", simind_version=8
 )
 source = np.zeros((32, 32, 32), dtype=np.float32)
 source[12:20, 12:20, 12:20] = 1
@@ -107,42 +104,26 @@ outputs = connector.run()
 print(outputs["tot_w1"].projection.shape)
 ```
 
-Run a complete core simulation example from a source checkout:
-
-```bash
-python examples/getting_started/plot_01_basic_simulation.py
-```
-
 The core connector does not require STIR, SIRF, or PyTomography. Install only
-the optional backend used by your workflow; see
-[installation](docs/installation.rst). The NEMA examples need the optional
-phantomgen package; the install command is in the tutorial.
+the optional backend your workflow uses; the NEMA examples also need
+phantomgen. See [installation](docs/installation.rst) and the tutorial.
 
 ## Example map
 
-- `examples/getting_started/plot_01`–`plot_06`: core NumPy simulations, windows, configurations, scoring,
-  and density conversion.
-- `examples/backends/plot_07a` / `07b` / `07c`: STIR / SIRF / PyTomography adaptors.
-- `examples/backends/plot_08a` / `08b` / `08c`: DICOM setup for STIR / SIRF / PyTomography.
-- `examples/phantoms/plot_09` / `plot_10`: the SIMIND analytic phantom library,
-  and a known-activity NEMA/IEC simulation reconstructed with SIRF OSEM.
-- `examples/mc_scatter/plot_11`–`plot_13`: Monte Carlo scatter in SIRF OSEM,
-  scatter normalisation, and residual correction.
-- `examples/cil/plot_14` / `plot_15`: CIL scatter correction, and an
-  RDP-regularised SVRG reconstruction.
-- `examples/real_data/plot_16a` / `16b` / `16c`: CT-to-SPECT conversion with
-  STIR / SIRF / PyTomography for the measured Y-90 phantom.
-- `examples/real_data/plot_17`: the Y-90 effective attenuation energy with SIRF.
-
-The real-data pages are rendered case studies on restricted Y-90 input, not
-reproducible tutorials. See [datasets](docs/datasets.rst) for the availability
-statement.
-
-Lower `quantization_scale`, fewer projections, or a mostly-zero source map can
-make smoke runs faster. These settings reduce history statistics; they do not
-set projection counts. For quantitative output, use known activity and
-acquisition time or normalise against a measured or analytic reference. Keep
-`NN >= 1`.
+- `examples/getting_started/` and `examples/phantoms/`: core simulations,
+  windows, configurations, scoring, density conversion and phantoms.
+- `examples/backends/`: STIR, SIRF and PyTomography adaptors, plus the DICOM
+  projection recipe in `docs/example_pages/dicom_recipe.rst`.
+- `examples/mc_scatter/` and `examples/cil/`: Monte Carlo scatter and
+  residual correction, including CIL.
+- `examples/real_data/` and `docs/example_pages/y90_*.rst`: restricted Y-90
+  CT conversion and effective attenuation energy, from data that are not
+  redistributed; see [datasets](docs/datasets.rst).
+
+Lower `quantization_scale`, fewer projections, or a mostly-zero source map make
+smoke runs faster without changing projection counts. For quantitative output,
+use known activity and acquisition time or normalise against a measured or
+analytic reference. Keep `NN >= 1`.
 
 ## License
 

simind_python_connector-2.0.2/README.md

@@ -0,0 +1,79 @@
+# simind-python-connector
+
+Python tools for running SIMIND and using its projections with STIR, SIRF, and
+PyTomography. Python 3.10 or newer is required. SIMIND is licensed separately
+and is not included with this package; this project is independent of the
+SIMIND project and Lund University.
+
+## Start here
+
+The [workflow tutorial](docs/tutorial.rst) walks through a core simulation,
+known-activity NEMA phantom, reconstruction, scatter correction, and
+measured-data calibration; the [example pages](docs/example_pages/index.rst)
+collect the tutorials and figures. The
+[documentation](https://simind-python-connector.readthedocs.io/) covers
+installation, geometry, normalisation and backends.
+
+Install the package and example plotting dependencies:
+
+```bash
+pip install "simind-python-connector[examples]"
+```
+
+Select a SIMIND executable and its matching data directory. The binary and
+`smc_dir` must come from the same release. Set `SIMIND_BIN` explicitly or put
+`simind` on `PATH`; set `SMC_DIR` when required by your installation.
+
+```bash
+export SIMIND_BIN=/path/to/simind-v8/simind
+export PATH=/path/to/simind-v8:$PATH
+export SMC_DIR=/path/to/simind-v8/smc_dir/
+export SIMIND_VERSION=8
+```
+
+SIMIND v8 is the supported engine. A constructor's `simind_version` overrides
+`SIMIND_VERSION`; v9 selection is experimental. See
+[installation](docs/installation.rst).
+
+Use the installed connector directly:
+
+```python
+import numpy as np
+from simind_python_connector import SimindPythonConnector, configs
+
+connector = SimindPythonConnector(
+    configs.get("Example.yaml"), "output/basic", "case01", simind_version=8
+)
+source = np.zeros((32, 32, 32), dtype=np.float32)
+source[12:20, 12:20, 12:20] = 1
+connector.configure_voxel_phantom(source, np.zeros_like(source), voxel_size_mm=4)
+connector.set_energy_windows([126], [154], [0])
+connector.add_runtime_switch("NN", 1)
+outputs = connector.run()
+print(outputs["tot_w1"].projection.shape)
+```
+
+The core connector does not require STIR, SIRF, or PyTomography. Install only
+the optional backend your workflow uses; the NEMA examples also need
+phantomgen. See [installation](docs/installation.rst) and the tutorial.
+
+## Example map
+
+- `examples/getting_started/` and `examples/phantoms/`: core simulations,
+  windows, configurations, scoring, density conversion and phantoms.
+- `examples/backends/`: STIR, SIRF and PyTomography adaptors, plus the DICOM
+  projection recipe in `docs/example_pages/dicom_recipe.rst`.
+- `examples/mc_scatter/` and `examples/cil/`: Monte Carlo scatter and
+  residual correction, including CIL.
+- `examples/real_data/` and `docs/example_pages/y90_*.rst`: restricted Y-90
+  CT conversion and effective attenuation energy, from data that are not
+  redistributed; see [datasets](docs/datasets.rst).
+
+Lower `quantization_scale`, fewer projections, or a mostly-zero source map make
+smoke runs faster without changing projection counts. For quantitative output,
+use known activity and acquisition time or normalise against a measured or
+analytic reference. Keep `NN >= 1`.
+
+## License
+
+Apache 2.0. See [LICENSE](LICENSE).

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/docker/python/Dockerfile

@@ -32,7 +32,7 @@ RUN python -m pip install --upgrade pip \
     && pip install "phantomgen @ git+https://github.com/varzakis/phantomgen@d9196118d5caef3f1bd2c27e5732bc03b48aed2a" \
     && python - <<'PY'
 import importlib
-for module in ("numpy", "matplotlib", "pytest", "phantomgen", "pooch", "sphinx_gallery"):
+for module in ("numpy", "matplotlib", "pytest", "phantomgen", "pooch"):
     importlib.import_module(module)
 print("Core Python modules available")
 PY

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/docker/pytomography/Dockerfile

@@ -39,7 +39,7 @@ RUN python -m pip install --upgrade pip \
     && pip install "phantomgen @ git+https://github.com/varzakis/phantomgen@d9196118d5caef3f1bd2c27e5732bc03b48aed2a" \
     && python - <<'PY'
 import importlib
-for module in ("torch", "pytomography", "pytest", "phantomgen", "pooch", "sphinx_gallery"):
+for module in ("torch", "pytomography", "pytest", "phantomgen", "pooch"):
     importlib.import_module(module)
 print("PyTomography modules available")
 PY

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/docker/sirf/Dockerfile

@@ -36,7 +36,7 @@ RUN python -m pip install --upgrade pip \
     && pip install "phantomgen @ git+https://github.com/varzakis/phantomgen@d9196118d5caef3f1bd2c27e5732bc03b48aed2a" \
     && python - <<'PY'
 import importlib
-for module in ("sirf.STIR", "pytest", "cil", "sirf.contrib.partitioner", "phantomgen", "pooch", "sphinx_gallery"):
+for module in ("sirf.STIR", "pytest", "cil", "sirf.contrib.partitioner", "phantomgen", "pooch"):
     importlib.import_module(module)
 print("SIRF Python modules available")
 PY

{simind_python_connector-2.0.1 → simind_python_connector-2.0.2}/docker/stir/Dockerfile

@@ -39,7 +39,6 @@ import stir  # noqa: F401
 import pytest  # noqa: F401
 import phantomgen  # noqa: F401
 import pooch  # noqa: F401
-import sphinx_gallery  # noqa: F401
 from simind_python_connector.utils import _import_stir_extra
 
 _import_stir_extra()