Merge branch 'main' into all-collaborators3

.github/workflows/ci.yml

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+name: CI testing
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: Install system packages
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+
+      - name: checkout actions
+        uses: actions/checkout@v4
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+          environment-file: environment_dev.yml
+          init-shell: bash
+          cache-environment: true
+          post-cleanup: 'all'
+
+      - name: install dependencies run tests
+        shell: bash -el {0}
+        run: |
+          python -m pip install .[tests]
+        
+      - name: Test with pytest
+        shell: bash -el {0}
+        run: |
+          pytest -v
+          python examples/plasma.py
+          python examples/spherical_tokamak_from_plasma_minimal.py
+          python examples/spherical_tokamak_from_plasma_with_divertor.py
+          python examples/spherical_tokamak_from_plasma_with_pf_magnets_and_divertors.py
+          python examples/spherical_tokamak_from_plasma_with_pf_magnets.py
+          python examples/spherical_tokamak_from_plasma_with_tf_magnets.py
+          python examples/spherical_tokamak_minimal.py
+          python examples/tokamak_from_plasma_with_divertor.py
+          python examples/tokamak_minimal.py
+          python examples/tokamak_from_plasma_minimal.py
+

.github/workflows/documentation_update.yml

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+name: documentation release
+
+on:
+    pull_request:
+        branches:
+            - main
+    push:
+        branches:
+            - main
+        tags:
+            - '*'
+
+
+permissions:
+  contents: write
+
+jobs:
+  testing:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - name: checkout actions
+        uses: actions/checkout@v4
+
+      - name: Install system packages
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libgl1 libglx-mesa0 libgl1-mesa-dev libglu1-mesa-dev freeglut3-dev libosmesa6 libosmesa6-dev libgles2-mesa-dev libarchive-dev libpangocairo-1.0-0
+
+
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          micromamba-version: '1.5.8-0' # any version from https://github.com/mamba-org/micromamba-releases
+          environment-file: environment_dev.yml
+          init-shell: bash
+          cache-environment: true
+          post-cleanup: 'all'
+
+      - name: install package
+        run: |
+          pip install --upgrade pip
+          pip install .[docs]
+      - name: Sphinx build tagged version
+        if: startsWith(github.ref, 'refs/tags/')
+        run: |
+          sphinx-build docs _build/${{ github.ref_name }}
+          rm -rf _build/stable
+          mkdir -p _build/stable
+          sphinx-build docs _build/stable
+      - name: Sphinx build dev version
+        if: (github.event_name == 'push' || github.event_name == 'pull_request') && !startsWith(github.ref, 'refs/tags/')
+        run: |
+          rm -rf _build/dev
+          mkdir -p _build/dev
+          sphinx-build docs _build/dev
+      - name: Deploy docs to GitHub Pages
+        if: github.event_name == 'push' || startsWith(github.ref, 'refs/tags/')
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _build
+          # with next rlease of actions-gh-pages
+          # issue to allow force_orphan will be fixed
+          # https://github.com/peaceiris/actions-gh-pages/issues/455
+          # force_orphan: true
+          keep_files: true

.github/workflows/python-publish.yml

@@ -0,0 +1,25 @@
+name: PyPI Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build package
+        run: python -m build
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+src/_version.py
+
+# openmc files
+*.h5
+*.out
+*.xml
+*.h5m
+*.h5
+
+# cad files
+*.step
+*.stp
+*.sql
+*.html

LICENSE

@@ -0,0 +1,17 @@
+MIT License
+Copyright (c) 2024 Fusion Energy and Paramak contributors
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,20 @@
+
+[![N|Python](https://www.python.org/static/community_logos/python-powered-w-100x40.png)](https://www.python.org)
+
+[![CI testing](https://github.com/fusion-energy/paramak/actions/workflows/ci.yml/badge.svg)](https://github.com/fusion-energy/paramak/actions/workflows/ci.yml)
+
+[![documentation release](https://github.com/fusion-energy/paramak/actions/workflows/documentation_update.yml/badge.svg)](https://github.com/fusion-energy/paramak/actions/workflows/documentation_update.yml)
+
+[![PyPI release](https://github.com/fusion-energy/paramak/actions/workflows/python-publish.yml/badge.svg)](https://github.com/fusion-energy/paramak/actions/workflows/python-publish.yml)
+
+
+# Paramak
+
+Paramak python package allows rapid production of 3D CAD models and neutronics
+models of fusion reactors.
+
+The purpose of Paramak is to provide geometry for parameter studies and therefore the models are created from parameters.
+
+Paramak produces [CadQuery](https://github.com/CadQuery/CadQuery) objects which can easily be saved to CAD files in several formats (STEP, STL, BRep) and also readily convertable to DAGMC h5m neutronics geometry using tools such as [Cad-to_DAGMC](https://github.com/fusion-energy/cad_to_dagmc).
+
+:point_right: Please see the [online documentation](https://fusion-energy.github.io/paramak) for installation, usage and API documentation.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)