Merge branch 'main' into materialPropertyTransfer

.github/bin/install-deps-ubuntu.sh

@@ -4,9 +4,9 @@ apt-get -y update || exit 1
 apt-get -y install libboost-dev libcgal-dev libgmp-dev libmpfr-dev \
            libvtk9-dev libxi-dev libocct-*-dev occt-misc numdiff || exit 1
 
-root_version="6.28.04"
+root_version="6.28.10"
 ROOTSYS="/opt/root"
 
 mkdir -p "$ROOTSYS" || exit 1
-wget -q -O- "https://root.cern/download/root_v${root_version}.Linux-ubuntu22-x86_64-gcc11.3.tar.gz" \
+wget -q -O- "https://root.cern/download/root_v${root_version}.Linux-ubuntu22-x86_64-gcc11.4.tar.gz" \
     | tar --strip-components 1 -C "$ROOTSYS" --strip=1 -x -z || exit 1

.github/dependabot.yml

@@ -5,5 +5,3 @@ updates:
     directory: "/"
     schedule:
       interval: "monthly"
-    ignore:
-      - dependency-name: "actions/*"

.github/workflows/distribution.yml

@@ -11,14 +11,14 @@ jobs:
     name: Make SDist
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Build SDist
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           path: dist/*.tar.gz
 
@@ -31,7 +31,7 @@ jobs:
         os: [ubuntu-latest, macos-latest]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -44,7 +44,7 @@ jobs:
           MAKEFLAGS: -j${{ steps.cpu-cores.outputs.count }}
 
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           path: wheelhouse/*.whl
 
@@ -53,12 +53,12 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'published'
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/[email protected].10
+      - uses: pypa/[email protected].11
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/main.yml

@@ -22,15 +22,15 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
         os: [ubuntu-latest, macOS-latest]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install non-pip dependencies on Ubuntu
         if: runner.os == 'Linux'
         run: sudo .github/bin/install-deps-ubuntu.sh
       - name: Install non-pip dependencies on MacOS
         if: runner.os == 'macOS'
         run: .github/bin/install-deps-macos.sh
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Get number of CPU cores
@@ -49,7 +49,7 @@ jobs:
     runs-on: ubuntu-latest
     container: docker://g4edge/ubuntu:latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Get number of CPU cores
         uses: SimenB/github-actions-cpu-cores@v2
         id: cpu-cores
@@ -65,14 +65,14 @@ jobs:
     name: Calculate and upload test coverage
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - name: Install non-pip dependencies on Ubuntu
         run: |
           sudo .github/bin/install-deps-ubuntu.sh
           .github/bin/setenv-ubuntu.sh
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
       - name: Get number of CPU cores

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
     rev: "v2.2.6"
     hooks:
       - id: codespell
-        args: ["-L", "commun,precess", "-x", "docs/source/authorship.rst"]
+        args: ["-L", "commun,precess"]
         types_or: [rst]
 
   - repo: https://github.com/pre-commit/pygrep-hooks

CITATION.cff

@@ -1,62 +1,62 @@
 cff-version: 1.2.0
-title: "pyg4ometry"
-doi: UPDATEME
-date-released: 2000-01-01
+title: pyg4ometry
+doi: 10.5281/zenodo.10449301
+date-released: 2024-01-01
 url: https://github.com/github-linguist/linguist
 message: "If you use this software, please cite it as below."
 authors:
   - family-names: Boogert
     given-names: Stewart
-    orcid:
+    orcid: https://orcid.org/0000-0002-7742-4237
   - family-names: Abramov
     given-names: Andrey
-    orcid:
+    orcid: https://orcid.org/0000-0003-4764-771X
   - family-names: Nevay
     given-names: Laurence
-    orcid:
+    orcid: https://orcid.org/0000-0001-7225-9327
   - family-names: Shields
     given-names: William
-    orcid:
+    orcid: https://orcid.org/0000-0002-4825-0303
   - family-names: Walker
     given-names: Stuart
-    orcid:
+    orcid: https://orcid.org/0000-0003-1301-2724
   - family-names: Butcher
     given-names: Alistar
-    orcid:
+    affiliation: "Royal Holloway, University of London"
   - family-names: Hernalsteens
     given-names: Cedric
-    orcid:
+    orcid: https://orcid.org/0000-0003-4038-6246
   - family-names: Shellswell
-    given-names: Ben
-    orcid:
+    given-names: Benjamin
+    affiliation: "Royal Holloway, University of London"
   - family-names: Ramoisiaux
     given-names: Eliott
-    orcid:
+    orcid: https://orcid.org/0000-0001-6523-2337
   - family-names: Pertoldi
     given-names: Luigi
     orcid: https://orcid.org/0000-0002-0467-2571
   - family-names: Huber
     given-names: Manuel
-    email: ich@manuelhu.de
+    email: info@manuelhu.de
 
 preferred-citation:
   type: article
   authors:
-  - family-names: "Boogert"
-    given-names: "Stewart"
-    orcid:
-  - family-names: "Abramov"
-    given-names: "Andrey"
-    orcid:
-  - family-names: "Nevay"
-    given-names: "Laurence"
-    orcid:
-  - family-names: "Shields"
-    given-names: "William"
-    orcid:
-  - family-names: "Walker"
-    given-names: "Stuart"
-    orcid:
+  - family-names: Boogert
+    given-names: Stewart
+    orcid: https://orcid.org/0000-0002-7742-4237
+  - family-names: Abramov
+    given-names: Andrey
+    orcid: https://orcid.org/0000-0003-4764-771X
+  - family-names: Nevay
+    given-names: Laurence
+    orcid: https://orcid.org/0000-0001-7225-9327
+  - family-names: Shields
+    given-names: William
+    orcid: https://orcid.org/0000-0002-4825-0303
+  - family-names: Walker
+    given-names: Stuart
+    orcid: https://orcid.org/0000-0003-1301-2724
   doi: 10.1016/j.cpc.2021.108228
   journal: "Comput. Phys. Commun."
   title: "Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries"

README.md

@@ -12,6 +12,7 @@ Carlo (Geant4 and Fluka) geometries.
 ![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)
 
 ## Installing from PyPI
@@ -20,7 +21,7 @@ Carlo (Geant4 and Fluka) geometries.
 > pip install pyg4ometry
 ```
 
-> **Note**
+> [!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.
@@ -33,7 +34,7 @@ Carlo (Geant4 and Fluka) geometries.
 > pip install . # add --editable for a version which you can edit
 ```
 
-> **Note**
+> [!NOTE]
 > If you update your Git clone and the pybind11 C++ has changes you will need
 > to reinstall and thus trigger a rebuild.
 

docs/source/citation.rst

@@ -2,46 +2,33 @@
 Referencing & Citation
 ======================
 
-Any publications including simulations made using pyg4ometry **must** cite:
-
-  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).
-
-
-Run: ::
-
-  pyg4ometry --citation
-
-to get the citation text in a human-readable and bibtex format.
+.. important::
 
-* `<https://doi.org/10.1016/j.cpc.2021.108228>`_
-* Preprint was: `<https://arxiv.org/abs/2010.01109>`_, but the above should be used.
+   Citation information can be obtained on GitHub by pointing your browser to
+   `github.com/g4edge/pyg4ometry <https://github.com/g4edge/pyg4ometry>`_ and
+   selecting "Cite this repository" in the sidebar on the right. pyg4ometry
+   uses a `CITATION.cff
+   <https://github.com/g4edge/pyg4ometry/blob/main/CITATION.cff>`_ file.
 
-The bibtex citation from `<https://inspirehep.net/literature/1821231>`_:
+Citations allow the authors to demonstrably show the code usage and therefore to
+continue to support the development and maintenance of pyg4ometry.
 
-.. code-block:: bibtex
+Any publications including simulations made using pyg4ometry **must** cite:
 
-   @article{Boogert:2020cmn,
-       author = "Boogert, Stewart and Abramov, Andrey and Nevay, Laurence and Shields, William and Walker, Stuart",
-       title = "{Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries}",
-       eprint = "2010.01109",
-       archivePrefix = "arXiv",
-       primaryClass = "physics.comp-ph",
-       doi = "10.1016/j.cpc.2021.108228",
-       journal = "Comput. Phys. Commun.",
-       volume = "272",
-       pages = "108228",
-       year = "2022"
-   }
+  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>`_
 
-Citations allow the authors to demonstrably show the code usage and therefore to
-continue to support the development and maintenance of pyg4ometry.
+Additionally, we automatically generate a DOI for each pyg4ometry code release
+through Zenodo at `this page
+<https://zenodo.org/doi/10.5281/zenodo.10449301>`_, if you wish to cite a
+specific pyg4ometry version.
 
 Other publications on pyg4ometry:
 
-* `Pyg4ometry : A Tool To Create Geometries For Geant4, Bdsim, G4Beamline and
-Fluka For Particle Loss and Energy Deposit Studies, IPAC2019, Melbourne,
-Australia, 2019 <https://doi.org/10.18429/JACoW-IPAC2019-WEPTS054>`_
-(Google scholar `cites
-<https://scholar.google.com/scholar?cites=7483314837088930734&as_sdt=2005&sciodt=0,5&hl=en>`_)
+* S.T. Boogert, A. Abramov, J. Albrecht, G. D’Alessandro, L.J. Nevay, W. Shields, S.D. Walker,
+  *Pyg4ometry : A Tool To Create Geometries For Geant4, Bdsim, G4Beamline and
+  Fluka For Particle Loss and Energy Deposit Studies*, IPAC2019, Melbourne,
+  Australia, 2019. DOI: `10.18429/JACoW-IPAC2019-WEPTS054
+  <https://doi.org/10.18429/JACoW-IPAC2019-WEPTS054>`_

docs/source/index.rst

@@ -22,7 +22,6 @@ particle tracking simulations.
 
    Source Code <https://github.com/g4edge/pyg4ometry>
    License <https://github.com/g4edge/pyg4ometry/blob/main/LICENSE>
-   authorship
    citation
    Changelog <https://github.com/g4edge/pyg4ometry/releases>
    version_history

src/pyg4ometry/cli.py

@@ -78,24 +78,7 @@ def _parseStrPythonAsDict(strPython):
 
 
 def _printCitation():
-    s = "S.D. Walker, A. Abramov, L.J. Nevay, W. Shields, S.T. Boogert,\n"
-    s += "pyg4ometry: A Python library for the creation of Monte Carlo radiation\n"
-    s += "transport physical geometries, Computer Physics Communications **272** 108228 (2022)."
-    print(s)
-    print("Bibtex entry:")
-    s = "@article{Boogert:2020cmn,\n"
-    s += '    author = "Boogert, Stewart and Abramov, Andrey and Nevay, Laurence and Shields, William and Walker, Stuart",\n'
-    s += '    title = "{Pyg4ometry: A Python library for the creation of Monte Carlo radiation transport physical geometries}",\n'
-    s += '    eprint = "2010.01109",\n'
-    s += '    archivePrefix = "arXiv",\n'
-    s += '    primaryClass = "physics.comp-ph",\n'
-    s += '    doi = "10.1016/j.cpc.2021.108228",\n'
-    s += '    journal = "Comput. Phys. Commun.",\n'
-    s += '    volume = "272",\n'
-    s += '    pages = "108228",\n'
-    s += '    year = "2022"\n'
-    s += "}"
-    print(s)
+    print("https://zenodo.org/doi/10.5281/zenodo.10449301")
 
 
 def cli(