simind-python-connector 1.0.0__tar.gz → 1.0.1__tar.gz

{simind_python_connector-1.0.0/simind_python_connector.egg-info → simind_python_connector-1.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simind-python-connector
-Version: 1.0.0
+Version: 1.0.1
 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>
@@ -87,12 +87,18 @@ install a licensed SIMIND installation.
 pip install simind-python-connector
 ```
 
-Import path remains:
+Import with:
 
 ```python
 import simind_python_connector
 ```
 
+For example plotting dependencies:
+
+```bash
+pip install "simind-python-connector[examples]"
+```
+
 ### Adaptor Dependencies
 
 `SimindPythonConnector` works without SIRF/STIR/PyTomography.
@@ -168,6 +174,9 @@ and ensure SIMIND data files are available under:
 The Docker helper scripts use this layout and automatically wire SIMIND paths
 when the binary exists at `./simind/simind`.
 
+For direct local runs outside the repository helpers, make sure the SIMIND
+executable is available as `simind` on `PATH`.
+
 ## Quick Start
 ```python
 import numpy as np
@@ -268,7 +277,7 @@ bash scripts/run_container_examples.sh
 ```
 
 ## Contributing
-Please see our [Contributing Guide](CONTRIBUTING.md).
+Please see the [Contributing Guide](docs/contributing.rst).
 
 ## License
 Apache License 2.0

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/README.md

@@ -44,12 +44,18 @@ install a licensed SIMIND installation.
 pip install simind-python-connector
 ```
 
-Import path remains:
+Import with:
 
 ```python
 import simind_python_connector
 ```
 
+For example plotting dependencies:
+
+```bash
+pip install "simind-python-connector[examples]"
+```
+
 ### Adaptor Dependencies
 
 `SimindPythonConnector` works without SIRF/STIR/PyTomography.
@@ -125,6 +131,9 @@ and ensure SIMIND data files are available under:
 The Docker helper scripts use this layout and automatically wire SIMIND paths
 when the binary exists at `./simind/simind`.
 
+For direct local runs outside the repository helpers, make sure the SIMIND
+executable is available as `simind` on `PATH`.
+
 ## Quick Start
 ```python
 import numpy as np
@@ -225,7 +234,7 @@ bash scripts/run_container_examples.sh
 ```
 
 ## Contributing
-Please see our [Contributing Guide](CONTRIBUTING.md).
+Please see the [Contributing Guide](docs/contributing.rst).
 
 ## License
 Apache License 2.0

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/backends.rst

@@ -14,7 +14,7 @@ Dependency Matrix
    * - Component
      - Required dependency
    * - ``SimindPythonConnector``
-     - SIMIND only (no SIRF/STIR/PyTomography requirement)
+     - SIMIND executable on ``PATH`` (no SIRF/STIR/PyTomography requirement)
    * - ``StirSimindAdaptor``
      - STIR Python (``stir``)
    * - ``SirfSimindAdaptor``

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/changelog.rst

@@ -7,17 +7,24 @@ All notable changes to this project are documented in this file.
 
 The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_, and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
 
-Unreleased
-----------
+1.0.1 - 2026-04-16
+------------------
 
-Changed
-~~~~~~~
+Fixed
+~~~~~
 
-- Updated user-facing branding to ``simind-python-connector`` and added explicit non-affiliation
-  and external-SIMIND-install disclaimers in README/docs.
+- Corrected installation documentation to lead with the PyPI package install
+  path instead of editable development installs.
+- Clarified that SIMIND is an external runtime dependency and must be available
+  as ``simind`` on ``PATH`` for local connector runs.
+- Updated contributing and testing documentation to use Ruff for linting,
+  import sorting, and formatting checks.
+- Updated examples documentation to include the DICOM-driven adaptor examples.
+- Fixed the GitHub Actions coverage target after the import package rename.
+- Fixed README links and release metadata for the patch release.
 
-[1.0.0] - 2026-03-05
---------------------
+1.0.0 - 2026-04-16
+------------------
 
 **Breaking Changes**
 ~~~~~~~~~~~~~~~~~~~~
@@ -56,6 +63,10 @@ Added
 Changed
 ~~~~~~~
 
+- Renamed the PyPI distribution to ``simind-python-connector``.
+- Renamed the import package to ``simind_python_connector``.
+- Updated user-facing branding to ``simind-python-connector`` and added explicit non-affiliation
+  and external-SIMIND-install disclaimers in README/docs.
 - ``SimindPythonConnector`` is now the central execution path for adaptor
   workflows.
 - ``StirSimindAdaptor`` and ``SirfSimindAdaptor`` now delegate SIMIND setup/run

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/conf.py

@@ -13,7 +13,7 @@ sys.path.insert(0, os.path.abspath(".."))
 project = "simind-python-connector"
 copyright = f"{datetime.now().year}, Sam Porter, Efstathios Varzakis"
 author = "Sam Porter, Efstathios Varzakis"
-release = "1.0.0"
+release = "1.0.1"
 for dist_name in ("simind-python-connector",):
     try:
         release = importlib_metadata.version(dist_name)

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/contributing.rst

@@ -32,10 +32,9 @@ Before submitting:
     # Run all tests
     python -m pytest tests/ -v
 
-    # Check code formatting
-    black --check .
+    # Check linting and formatting
     ruff check .
-    isort --check-only .
+    ruff format --check .
 
 Documentation Updates
 ---------------------
@@ -44,5 +43,4 @@ If you make changes that affect the documentation:
 
 .. code-block:: bash
 
-    cd docs/
-    make html  # Build documentation locally
+    sphinx-build -b html docs docs/_build/html

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/examples.rst

@@ -56,6 +56,18 @@ See the following examples for comprehensive use:
    Simulate with the PyTomography adaptor and run PyTomography OSEM in one Python workflow.
    Uses ``configs/Example.yaml`` plus Y-90 runtime switches (``FI`` and ``CC``).
 
+8A. **STIR Adaptor from DICOM** - ``examples/08A_stir_adaptor_from_dicom.py``
+
+   Build a STIR adaptor workflow from DICOM-derived scanner/input data.
+
+8B. **SIRF Adaptor from DICOM** - ``examples/08B_sirf_adaptor_from_dicom.py``
+
+   Build a SIRF adaptor workflow from DICOM-derived scanner/input data.
+
+8C. **PyTomography Adaptor from DICOM** - ``examples/08C_pytomography_adaptor_from_dicom.py``
+
+   Build a PyTomography adaptor workflow from DICOM-derived scanner/input data.
+
 Running Examples
 ----------------
 
@@ -72,13 +84,16 @@ Each example can be run individually:
     python examples/07A_stir_adaptor_osem.py
     python examples/07B_sirf_adaptor_osem.py
     python examples/07C_pytomography_adaptor_osem.py
+    python examples/08A_stir_adaptor_from_dicom.py
+    python examples/08B_sirf_adaptor_from_dicom.py
+    python examples/08C_pytomography_adaptor_from_dicom.py
 
-Or run all examples sequentially:
+Or run all core Python connector examples sequentially:
 
 .. code-block:: bash
 
     cd scripts/
-    python run_all_examples.py  # Run all examples sequentially
+    python run_all_examples.py
 
 Or run one backend-specific adaptor example inside each isolated Docker image:
 
@@ -100,6 +115,9 @@ Each example creates output in its own directory under ``output/``:
 - ``output/stir_adaptor_osem/`` - STIR adaptor simulation + STIR OSEM reconstruction
 - ``output/sirf_adaptor_osem/`` - SIRF adaptor simulation + SIRF OSEM reconstruction
 - ``output/pytomography_adaptor_osem/`` - PyTomography adaptor simulation + PyTomography OSEM reconstruction
+- ``output/dicom_projection_objects/stir/`` - STIR adaptor setup from DICOM-derived inputs
+- ``output/dicom_projection_objects/sirf/`` - SIRF adaptor setup from DICOM-derived inputs
+- ``output/dicom_projection_objects/pytomography/`` - PyTomography adaptor setup from DICOM-derived inputs
 
 Each OSEM example also writes a summary plot with:
 - input source slice

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/index.rst

@@ -1,5 +1,5 @@
 simind-python-connector Documentation
-====================
+=====================================
 
 .. toctree::
    :maxdepth: 2

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/installation.rst

@@ -7,6 +7,8 @@ Prerequisites
 -------------
 
 - Python 3.9+
+- A separate SIMIND installation for running simulations. SIMIND is not
+  distributed with this package or installed by pip.
 - Optional backend libraries depending on workflow:
   - STIR Python for STIR-based paths
   - SIRF for SIRF-based paths
@@ -15,18 +17,34 @@ Prerequisites
 Install the Python Package
 --------------------------
 
-1. Clone the repository:
+Install the released package from PyPI:
 
-   .. code-block:: bash
+.. code-block:: bash
+
+    pip install simind-python-connector
+
+Import it with:
+
+.. code-block:: python
+
+    import simind_python_connector
+
+Install the examples extra if you want to run the plotting examples:
+
+.. code-block:: bash
+
+    pip install "simind-python-connector[examples]"
 
-      git clone https://github.com/samdporter/simind-python-connector.git
-      cd simind-python-connector
+Development Install
+-------------------
 
-2. Install in editable/development mode:
+For local development from a checkout:
 
-   .. code-block:: bash
+.. code-block:: bash
 
-      pip install -e ".[dev]"
+    git clone https://github.com/samdporter/simind-python-connector.git
+    cd simind-python-connector
+    pip install -e ".[dev,examples]"
 
 SIMIND Requirement (External Dependency)
 ----------------------------------------
@@ -48,10 +66,10 @@ documentation:
 - SIMIND manual page:
   https://www.msf.lu.se/en/research/simind-monte-carlo-program/manual
 
-Recommended Local Layout
-~~~~~~~~~~~~~~~~~~~~~~~~
+Repo/Docker Layout
+~~~~~~~~~~~~~~~~~~
 
-For the package scripts and Docker setup, place SIMIND under:
+For the repository helper scripts and Docker setup, place SIMIND under:
 
 .. code-block:: text
 
@@ -70,11 +88,19 @@ If needed, make the binary executable:
 
     chmod +x ./simind/simind
 
-Local (Non-Docker) Runtime Environment
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Local Runtime Environment
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For direct local runs, ensure the SIMIND executable is available as ``simind``
+on ``PATH``. If your SIMIND installation needs ``SMC_DIR``, set it to the
+SIMIND data directory:
+
+.. code-block:: bash
+
+    export PATH="/path/to/simind/bin:$PATH"
+    export SMC_DIR="/path/to/simind/smc_dir/"
 
-For direct local runs, ensure SIMIND is on ``PATH`` and ``SMC_DIR`` points to
-the SIMIND data directory:
+When working from this repository with the layout above, those commands become:
 
 .. code-block:: bash
 

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/testing.rst

@@ -137,31 +137,36 @@ The default CI job runs the tests that avoid heavyweight dependencies. These foc
 
 * **Conversion maths** – ``tests/test_schneider_density.py`` exercises the HU-to-density pipelines.
 * **Configuration & builders** – ``tests/test_simulation_config.py`` and ``tests/test_acquisition_builder_unit.py`` validate YAML/SMC handling plus Interfile header generation without a SIRF runtime.
-* **Utility helpers** – ``tests/test_components.py``, ``tests/test_utils.py``, and ``tests/test_utils_small.py`` cover enums, file parsing, and temporary-directory/energy-window helpers.
-* **Backend guards** – ``tests/test_backends.py`` ensures the dynamic backend selection code behaves without importing SIRF.
+* **Connector behavior** – ``tests/test_python_connector.py``, ``tests/test_connectors_base.py``, and ``tests/test_connector_backend_separation.py`` cover the connector-first API without requiring reconstruction packages.
+* **Utility helpers** – ``tests/test_utils.py``, ``tests/test_utils_small.py``, ``tests/test_interfile_parser.py``, and ``tests/test_interfile_numpy.py`` cover file parsing and small helper functions.
+* **Backend guards** – ``tests/test_backends.py``, ``tests/test_marker_policy.py``, and ``tests/test_examples_backend_separation.py`` ensure optional backend imports remain isolated.
 
-SIRF-Dependent Suites
-~~~~~~~~~~~~~~~~~~~~~
+Backend-Dependent Suites
+~~~~~~~~~~~~~~~~~~~~~~~~
 
-Tests that construct real SIRF/STIR objects carry the ``requires_sirf`` marker and are skipped in CI. These include:
+Tests that construct real STIR/SIRF/PyTomography objects carry dependency
+markers and are skipped when those packages are unavailable. These include:
 
-* ``tests/test_simind_simulator.py`` and ``tests/test_simind_projector.py`` for the legacy projector/simulator path.
-* ``tests/test_arithmetic_operations.py`` for wrapped acquisition arithmetic.
-* ``tests/test_coordinator.py`` for the SIMIND coordinator.
-* SIRF-backed helpers in ``tests/test_utils.py`` and ``tests/test_components.py``.
+* ``tests/test_native_adaptors.py`` for STIR/SIRF adaptor behavior.
+* ``tests/test_pytomography_adaptor.py`` for PyTomography tensor and output adaptation.
+* ``tests/test_arithmetic_operations.py`` and ``tests/test_sirf_stir_utils.py`` for backend wrapper/helper behavior.
 
-CIL and Hybrid Dependencies
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
+SIMIND and Container Diagnostics
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Two suites rely on additional packages:
+SIMIND-dependent tests use ``requires_simind`` and are skipped unless the
+``simind`` command is available. Container and geometry diagnostics include:
 
-* ``tests/test_cil_partitioner.py`` (``requires_sirf`` + ``requires_cil``) exercises the CIL partitioner adapter.
-* ``tests/test_step_size_rules.py`` (``requires_cil``) checks Armijo step-size helpers with lightweight stand-ins.
+* ``tests/test_integration.py`` for full workflow checks.
+* ``tests/test_container_library_isolation.py`` for backend container import isolation.
+* ``tests/test_geometry_isolation_forward_projection.py`` and ``tests/test_osem_geometry_diagnostics.py`` for backend geometry diagnostics.
 
 Integration Test
 ~~~~~~~~~~~~~~~~
 
-``tests/test_integration.py`` orchestrates a full example run and needs both SIMIND and SIRF. It is marked with ``integration``, ``requires_simind``, and ``requires_sirf``.
+``tests/test_integration.py`` orchestrates a full example run and needs
+external runtime dependencies. It is marked with dependency markers so it is
+skipped in lightweight CI environments.
 
 Configuration Files
 -------------------
@@ -223,7 +228,7 @@ Continuous Integration
 GitHub Actions is used to run tests automatically. The CI workflow:
 
 1. **Installs only basic Python dependencies** (no SIRF/SIMIND)
-2. **Runs code quality checks** (black, isort, ruff)
+2. **Runs code quality checks** (``ruff check`` and ``ruff format --check``)
 3. **Executes CI-friendly tests** using dependency markers
 4. **Generates coverage reports** for the tested code
 5. **Builds and validates the package**

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/docs/usage.rst

@@ -9,6 +9,10 @@ Quick Start
 Use ``SimindPythonConnector`` when you want direct Python control of SIMIND
 inputs/outputs without any reconstruction-package dependency.
 
+The Python package does not bundle SIMIND. Before calling ``run()``, make sure
+the SIMIND executable is available as ``simind`` on ``PATH``; see
+:doc:`installation`.
+
 .. code-block:: python
 
     import numpy as np

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "simind-python-connector"
-version = "1.0.0"
+version = "1.0.1"
 description = "Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors"
 readme = "README.md"
 requires-python = ">=3.9"

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1}/simind_python_connector/__init__.py

@@ -14,7 +14,7 @@ for _dist_name in ("simind-python-connector", __name__):
     except _meta.PackageNotFoundError:
         continue
 else:  # editable / source checkout
-    __version__ = "1.0.0"
+    __version__ = "1.0.1"
 
 
 def __getattr__(name: str) -> Any:

{simind_python_connector-1.0.0 → simind_python_connector-1.0.1/simind_python_connector.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: simind-python-connector
-Version: 1.0.0
+Version: 1.0.1
 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>
@@ -87,12 +87,18 @@ install a licensed SIMIND installation.
 pip install simind-python-connector
 ```
 
-Import path remains:
+Import with:
 
 ```python
 import simind_python_connector
 ```
 
+For example plotting dependencies:
+
+```bash
+pip install "simind-python-connector[examples]"
+```
+
 ### Adaptor Dependencies
 
 `SimindPythonConnector` works without SIRF/STIR/PyTomography.
@@ -168,6 +174,9 @@ and ensure SIMIND data files are available under:
 The Docker helper scripts use this layout and automatically wire SIMIND paths
 when the binary exists at `./simind/simind`.
 
+For direct local runs outside the repository helpers, make sure the SIMIND
+executable is available as `simind` on `PATH`.
+
 ## Quick Start
 ```python
 import numpy as np
@@ -268,7 +277,7 @@ bash scripts/run_container_examples.sh
 ```
 
 ## Contributing
-Please see our [Contributing Guide](CONTRIBUTING.md).
+Please see the [Contributing Guide](docs/contributing.rst).
 
 ## License
 Apache License 2.0