pyg4ometry 1.2.3__tar.gz → 1.2.4__tar.gz

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/.github/workflows/distribution.yml

@@ -69,6 +69,7 @@ jobs:
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
+        id: setup-python
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -77,7 +78,9 @@ jobs:
         id: cpu-cores
 
       - name: Build MacOS wheel ${{ matrix.python-version }}
-        run: pipx run build --wheel
+        run: |
+          ${{ steps.setup-python.outputs.python-path}} -m pip install build
+          ${{ steps.setup-python.outputs.python-path}} -m build .
 
       - name: Upload macos artifact
         uses: actions/upload-artifact@v4

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyg4ometry
-Version: 1.2.3
+Version: 1.2.4
 Summary: Geometry package for high energy physics (Geant4, Fluka)
 Author-Email: "Stewart T. Boogert" <stewart.boogert@rhul.ac.uk>
 Maintainer-Email: "Stewart T. Boogert" <stewart.boogert@rhul.ac.uk>
@@ -737,52 +737,30 @@ Carlo (Geant4 and Fluka) geometries.
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10449301.svg)](https://doi.org/10.5281/zenodo.10449301)
 [![Read the Docs](https://img.shields.io/readthedocs/pyg4ometry?logo=readthedocs)](https://pyg4ometry.readthedocs.io)
 
-## Installing from PyPI
+## How to Install
 
-```console
-> pip install pyg4ometry
-```
-
-> [!NOTE]
-> Most dependencies are available from pip but you will need to install OpenCASCADE
-> cgal, mpfr, gmp, ROOT. Find [here](https://github.com/g4edge/pyg4ometry/tree/main/.github/bin)
-> installers for Ubuntu and MacOS.
-
-## Building
+Pre-built pyg4ometry wheels can be installed [from PyPI](https://pypi.org/project/pyg4ometry)
+using pip:
 
-```console
-> git clone https://github.com/g4edge/pyg4ometry.git
-> cd pyg4ometry
-> pip install . # add --editable for a version which you can edit
 ```
+pip install pyg4ometry
+```
+
+If you cannot find wheels for your operating system / architecture,
+please [open an issue](https://github.com/g4edge/pyg4ometry/issues).
+Building from source requires some non-Python software dependencies.
+More documentation can be found in the developer's guide.
 
-> [!NOTE]
-> If you update your Git clone and the pybind11 C++ has changes you will need
-> to reinstall and thus trigger a rebuild.
+## Referencing and Citation
 
-## Manual
+To support the development and maintenance of pyg4ometry, please cite it!
+Any publications including simulations made using this software must cite
+the pyg4ometry paper:
 
-Online manual available at https://pyg4ometry.readthedocs.io
+> S.D. Walker, A. Abramov, L.J. Nevay, W. Shields, S.T. Boogert,
+> “pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries”,
+> Computer Physics Communications 272 108228 (2022). DOI: [10.1016/j.cpc.2021.108228](https://doi.org/10.1016/j.cpc.2021.108228)
 
-## Developer commands (for detailed developer notes see readthedocs)
+and the Zenodo release: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10449301.svg)](https://doi.org/10.5281/zenodo.10449301)
 
-- Building the manual
-  - `pip install '.[docs]'` to install docs building dependencies
-  - `cd pyg4ometry/docs`
-  - `make`
-  - `<your browser> build/html/index.html` to view the docs
-- Running tests
-  - `pip install '.[test]'` to install test running dependencies
-  - `pytest`
-- Git commit
-  - pre-commit
-    - `pre-commit install` to setup pre-commit in source dir (only once)
-    - `pre-commit run --all-files` run pre-commit locally
-    - `pre-commit run --all-files black` run only black
-  - messages
-    - Start commit message with `submodule : (type of change) detailed notes`
-    - e.g `pycgal : (extra functionality) more 2d mesh processing`
-- Pull requests
-  - PR messages should just explain the change in a concise way as they will form part of the change log
-    - e.g `FLUKA region viewer`
-  - Update the CHANGELOG.md file for generating the release notes
+Citation information can be also obtained on GitHub by selecting “Cite this repository” in the sidebar on the right.

pyg4ometry-1.2.4/README.md

@@ -0,0 +1,44 @@
+# pyg4ometry
+
+Python code for rapid creation and conversion of radiation transport Monte
+Carlo (Geant4 and Fluka) geometries.
+
+[![PyPI](https://img.shields.io/pypi/v/pyg4ometry?logo=pypi)](https://pypi.org/project/pyg4ometry/)
+![GitHub tag (latest by date)](https://img.shields.io/github/v/tag/g4edge/pyg4ometry?logo=git)
+[![GitHub Workflow Status](https://img.shields.io/github/checks-status/g4edge/pyg4ometry/main?label=main%20branch&logo=github)](https://github.com/pyg4ometry/pyg4ometry/actions)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Codecov](https://img.shields.io/codecov/c/github/g4edge/pyg4ometry?logo=codecov)](https://app.codecov.io/gh/pyg4ometry/pyg4ometry)
+![GitHub issues](https://img.shields.io/github/issues/g4edge/pyg4ometry?logo=github)
+![GitHub pull requests](https://img.shields.io/github/issues-pr/g4edge/pyg4ometry?logo=github)
+![License](https://img.shields.io/github/license/g4edge/pyg4ometry)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10449301.svg)](https://doi.org/10.5281/zenodo.10449301)
+[![Read the Docs](https://img.shields.io/readthedocs/pyg4ometry?logo=readthedocs)](https://pyg4ometry.readthedocs.io)
+
+## How to Install
+
+Pre-built pyg4ometry wheels can be installed [from PyPI](https://pypi.org/project/pyg4ometry)
+using pip:
+
+```
+pip install pyg4ometry
+```
+
+If you cannot find wheels for your operating system / architecture,
+please [open an issue](https://github.com/g4edge/pyg4ometry/issues).
+Building from source requires some non-Python software dependencies.
+More documentation can be found in the developer's guide.
+
+## Referencing and Citation
+
+To support the development and maintenance of pyg4ometry, please cite it!
+Any publications including simulations made using this software must cite
+the pyg4ometry paper:
+
+> S.D. Walker, A. Abramov, L.J. Nevay, W. Shields, S.T. Boogert,
+> “pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries”,
+> Computer Physics Communications 272 108228 (2022). DOI: [10.1016/j.cpc.2021.108228](https://doi.org/10.1016/j.cpc.2021.108228)
+
+and the Zenodo release: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10449301.svg)](https://doi.org/10.5281/zenodo.10449301)
+
+Citation information can be also obtained on GitHub by selecting “Cite this repository” in the sidebar on the right.

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/docs/source/manual/exporting.rst

@@ -38,22 +38,26 @@ must be supplied.
    # make a quick bdsim job for the one component in a beam line
    w.writeGmadTester('file.gmad', 'file.gdml')
 
-
-
-
-Export scene to paraview/vtk
+Export scene to Paraview/Vtk
 ----------------------------
 
+The viewers can export to the VTK/Paraview VTP file format
+
 .. code-block :: python
    :linenos:
 
    import pyg4ometry
+   r = pyg4ometry.gdml.Reader("./Chamber.gdml")
+   l = r.getRegistry().getWorldVolume()
+   v = pyg4ometry.visualisation.VtkViewer()
+   v.addLogicalVolume(l)
+   v.exportVTPScene("Chamber")
 
 
-Export scene to unity/unreal
-----------------------------
+Export scene to unity/unreal/blender
+------------------------------------
 
-The quickest way to get geometry to Unity/Unreal is to use a standard asset
+The quickest way to get geometry to Unity/Unreal/blender etc is to use a standard asset
 format. This takes a vtkRenderer and creates a OBJ file. The vtkRenderer
 managed within pyg4ometry from the VtkViewer class, once a geometry is created
 (either from any source) then an OBJ file can be created. Taking the

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/docs/source/manual/installation.rst

@@ -2,18 +2,37 @@
 Installation
 ============
 
+Installing from PyPi
+--------------------
+
+The easiest way to install pyg4ometry is to install from PyPi. Pyg4ometry
+has many external requirements which need to be provided by a package
+manager on your system. To install using PyPi::
+
+    pip install pyg4ometry
+
+If installing for MacOS you will need to install (opencascade, cgal, gmp, mpfr, boost, vtk)::
+
+    brew install opencascade cgal gmp mpfr boost vtk
+
+If installing for Windows you will need to install (opencascade, cgal)::
+
+    conda install occt cgal-cpp
+
+Building from source
+--------------------
 
 Requirements
-------------
+^^^^^^^^^^^^
 
 pyg4ometry is developed exclusively for Python 3 (Python2 is deprecated). It is developed on Python 3.9 and 3.10.
 
-
  * `VTK (Visualisation toolkit) <https://vtk.org>`_ (including Python bindings)
  * `antlr4 <https://www.antlr.org>`_
  * `cython <https://cython.org>`_
  * `CGAL <https://www.cgal.org>`_
  * pybind11
+ * cmake
 
 Packages that are required but will be found through PIP automatically:
 
@@ -25,11 +44,7 @@ Packages that are required but will be found through PIP automatically:
  * numpy
  * sympy
 
-**Optional**
-
- * `Freecad  <https://www.freecadweb.org>`_ for CAD conversion.
-
-.. note:: A full list can be found in :code:`pyg4ometry/setup.py`.
+.. note:: A full list can be found in :code:`pyg4ometry/pyproject.toml`.
 
 .. note:: if you are choosing a python version, it is worth choosing according to which
 	  version VTK provides a python build of through PIP if you use that. See
@@ -37,36 +52,38 @@ Packages that are required but will be found through PIP automatically:
 	  for M1 Mac (ARM64).
 
 
-Installation
-------------
+Building
+^^^^^^^^
 
 To install pyg4ometry, simply run ``make install`` from the root pyg4ometry
 directory::
 
-  cd /my/path/to/repositories/
-  git clone http://bitbucket.org/jairhul/pyg4ometry
-  git checkout develop
-  cd pyg4ometry
+    cd /my/path/to/repositories/
+    git clone https://github.com/g4edge/pyg4ometry
+    cd pyg4ometry
 
-  make install
+    pip install .
 
-.. note::
-   To build using the git directory and not installing into /usr/local use ``make develop``
-   instead of ``make install``
+If you wish to develop an extension or modify pyg4ometry then run::
 
-To build pycsg with cpython::
+    pip install -e .
 
-  make build_ext
+as this will not install pyg4ometry, but the git repository directory will
+be used for the package. To confirm the install location run::
 
-Or install from pypi::
+    pip list | grep pyg4ometry
 
-  pip install pyg4ometry
+.. note::
+    The building uses skikit-build which required cmake. Build errors
+    or warnings are typically from cmake and can help determining the
+    missing dependency
 
-or alternatively, run ``make develop`` from the same directory to ensure
-that any local changes are picked up.
+.. note::
+    If you are building for windows you are going to need Visual Studio and
+    the appropriate command line tools
 
-Docker image
-------------
+Docker image (needs updating)
+-----------------------------
 
 #. Download and install `Docker desktop <https://www.docker.com/products/docker-desktop>`_
 #. open a terminal (linux) or cmd (windows)
@@ -100,38 +117,6 @@ installation for each of these OSes.
 * `Ubuntu 20.02 <https://bitbucket.org/jairhul/pyg4ometry/raw/82373218033874607f682a77be33e03d5b6706aa/docker/Dockerfile-ubuntu-pyg4ometry>`_
 * `Centos 7 <https://bitbucket.org/jairhul/pyg4ometry/raw/befcd36c1213670830b854d02c671ef14b3f0f5c/docker/Dockerfile-centos-pyg4ometry>`_
 
-
-FreeCAD support for CAD to GDML conversion
-------------------------------------------
-
-For FreeCAD support and you already have it installed you need to add library to PYTHONPATH, for example
-
-.. code-block :: console
-
-   export PYTHONPATH=/opt/local/libexec/freecad/lib/
-
-Building FreeCAD can be a pain for MAC so
-
-.. code-block :: console
-
-   mkdir FreeCAD
-   cd FreeCAD
-   set FCROOT=$pwd
-   wget  https://github.com/FreeCAD/FreeCAD/archive/refs/tags/0.19.4.tar.gz
-   tar zxf 0.19.4.tar.gz
-   mkdir build
-   mkdir install
-   cd build
-   cmake ../FreeCAD-0.19.4 -DCMAKE_INSTALL_PREFIX=../install \
-   -DCOIN3D_LIBRARIES=/opt/local/Library/Frameworks/Inventor.framework/Libraries/libCoin.dylib -DBUILD_FEM=0 \
-   -DBUILD_MATERIAL=0 -DBUILD_SHIP=0 -DBUILD_DRAFT=0 -DBUILD_TUX=0 -DBUILD_ARCH=0 -DBUILD_PLOT=0 \
-   -DBUILD_OPENSCAD=0
-   make -jN
-   make install
-   export PYTHONPATH=$PYTHONPATH:$FCROOT/install
-
-
-
 Python 3.9
 ----------
 
@@ -145,3 +130,47 @@ as you know you can :code:`import vtk` ok in your Python installation.
 	     ANRLR version that the one the parser was generated with. It should work
 	     though. We are trying to include multiple versions of the ANTLR parser
 	     to avoid this in future.
+
+Developer notes
+---------------
+
+Building the manual
+^^^^^^^^^^^^^^^^^^^
+
+To build the documentation ::
+
+    pip install '.[docs]' # to install docs building dependencies
+    cd pyg4ometry/docs
+    make
+    <your browser> build/html/index.html` # to view the docs
+
+Running tests
+^^^^^^^^^^^^^
+
+Running tests ::
+
+    pip install '.[test]' # to install test running dependencies
+    pytest
+
+
+Git
+^^^
+
+pre-commit::
+
+    pre-commit install  # to setup pre-commit in source dir (only once)
+    pre-commit run --all-files # run pre-commit locally
+    pre-commit run --all-files black  #run only black
+
+Start commit message with the submodule or area changes::
+
+    submodule : (type of change) detailed notes
+
+for example::
+
+    pycgal : (extra functionality) more 2d mesh processing
+
+Pull requests. PR messages should just explain the change in a concise way as they will form part of the change log
+e.g::
+
+    FLUKA region viewer

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/src/pyg4ometry/__init__.py

@@ -10,6 +10,7 @@ from . import compare
 from . import convert
 from . import exceptions
 from . import fluka
+from . import mcnp
 from . import gdml
 from . import io
 from . import geant4

{pyg4ometry-1.2.3 → pyg4ometry-1.2.4}/src/pyg4ometry/io/ROOTTGeo.py

@@ -481,22 +481,41 @@ def rootShape2pyg4ometry(shape, reader, warnAboutBadShapes=True):
         for iFacet in range(0, nFacet, 1):
             facet = shape.GetFacet(iFacet)
             if facet.GetNvert() == 3:
-                facets.append(
-                    [
-                        facet.GetVertexIndex(0),
-                        facet.GetVertexIndex(1),
-                        facet.GetVertexIndex(2),
-                    ]
-                )
+                if _ROOT.gROOT.GetVersionInt() >= 63301:
+                    facets.append(
+                        [
+                            facet[0],
+                            facet[1],
+                            facet[2],
+                        ]
+                    )
+                else:
+                    facets.append(
+                        [
+                            facet.GetVertexIndex(0),
+                            facet.GetVertexIndex(1),
+                            facet.GetVertexIndex(2),
+                        ]
+                    )
             elif facet.GetNvert() == 4:
-                facets.append(
-                    [
-                        facet.GetVertexIndex(0),
-                        facet.GetVertexIndex(1),
-                        facet.GetVertexIndex(2),
-                        facet.GetVertexIndex(3),
-                    ]
-                )
+                if _ROOT.gROOT.GetVersionInt() >= 63301:
+                    facets.append(
+                        [
+                            facet[0],
+                            facet[1],
+                            facet[2],
+                            facet[3],
+                        ]
+                    )
+                else:
+                    facets.append(
+                        [
+                            facet.GetVertexIndex(0),
+                            facet.GetVertexIndex(1),
+                            facet.GetVertexIndex(2),
+                            facet.GetVertexIndex(3),
+                        ]
+                    )
         shapePyG4 = _g4.solid.TessellatedSolid(
             shapeName,
             [verts, facets],

pyg4ometry-1.2.4/src/pyg4ometry/mcnp/Cell.py

@@ -0,0 +1,76 @@
+class Cell:
+    def __init__(self, surfaces=[], reg=None, cellNumber=None):
+        self.surfaceList = surfaces
+        self.cellNumber = cellNumber
+        # self.geometry = geometry
+        if reg:
+            reg.addCell(self)
+            self.reg = reg
+
+    def addSurface(self, surface):
+        if type(surface) is str and surface in self.reg.surfaceDict:
+            surface = self.reg.surfaceDict[surface]
+        self.surfaceList.append(surface)
+
+    def addSurfaces(self, surfaces):
+        self.surfaceList.extend(surfaces)
+
+    def addMacrobody(self, macrobody):
+        self.addSurface(macrobody)
+
+    def addMacrobodies(self, macrobody):
+        self.addSurfaces(macrobody)
+
+
+class Intersection:
+    """
+    mcnp : blank space between two surface numbers
+    pyg4 : asterisk
+    """
+
+    def __init__(self, left, right):
+        self.left = left
+        self.right = right
+
+    def toOutputString(self):
+        return self.left.toOutputString() + " " + self.right.toOutputString()
+
+
+class Union:
+    """
+    mcnp : colon
+    pyg4 : plus
+    """
+
+    def __init__(self, left, right):
+        self.left = left
+        self.right = right
+
+    def toOutputString(self):
+        return self.left.toOutputString() + ":" + self.right.toOutputString()
+
+
+class Complement:
+    """
+    mcnp : hash
+    pyg4 : hyphen
+    """
+
+    def __init__(self, item):
+        self.item = item
+
+    def toOutputString(self):
+        return "#" + self.item.toOutputString()
+
+
+class Identity:
+    """
+    mcnp : no operator
+    pyg4 : no operator
+    """
+
+    def __init__(self, item):
+        self.item = item
+
+    def toOutputString(self):
+        return str(self.item.surfaceNumber)

pyg4ometry-1.2.4/src/pyg4ometry/mcnp/Material.py

@@ -0,0 +1,90 @@
+class M:
+    """
+    Material Card
+    """
+
+    def __init__(
+        self,
+        zk,
+        fk,
+        GAS=None,
+        ESTEP=None,
+        HSTEP=None,
+        NLIB=None,
+        PLIB=None,
+        PNLIB=None,
+        ELIB=None,
+        HLIB=None,
+        ALIB=None,
+        SLIB=None,
+        TLIB=None,
+        DLIB=None,
+        COND=None,
+        REFI=None,
+        REFIs=None,
+        REFS=None,
+        reg=None,
+        materialNumber=None,
+    ):
+
+        self.zk = []
+        self.fk = []
+
+        self.materialNumber = materialNumber
+        if reg:
+            reg.addMaterial(self)
+            self.reg = reg
+
+
+class MT:
+    """
+    Thermal Neutron Scattering
+    """
+
+    def __init__(self):
+        pass
+
+
+class MT0:
+    """
+    Thermal Neutron Scattering
+    """
+
+    def __init__(self):
+        pass
+
+
+class MX:
+    """
+    Material Card Nuclide Substitution
+    """
+
+    def __init__(self):
+        pass
+
+
+class MPN:
+    """
+    Photonuclear Nuclide Selector
+    """
+
+    def __init__(self):
+        pass
+
+
+class OTFDB:
+    """
+    On-the-fly-Doppler Broadening
+    """
+
+    def __init__(self):
+        pass
+
+
+class TOTNU:
+    """
+    Total Fission
+    """
+
+    def __init__(self):
+        pass