Public release of cfspopcon

.github/workflows/make_radas_data.sh

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+set -ex
+
+git clone https://github.com/cfs-energy/radas.git
+
+pushd radas
+
+git checkout d9e23824f2edc46ef35e2fd54cf26438a3180733
+
+poetry install --only main
+
+poetry run python adas_data/fetch_adas_data.py
+
+poetry run python run_radas.py all
+
+popd

.github/workflows/workflow_actions.yml

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+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: workflow_actions
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the "main" branch
+  pull_request: []
+  push:
+    branches:
+      - 'main'
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+    tag: "Manual run"
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  radas:
+    runs-on: ubuntu-22.04
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - name: Install Poetry
+        run: curl -sSL https://install.python-poetry.org | python - --version 1.6.1
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+          cache: 'poetry'
+
+      - name: Cache radas results
+        id: radas
+        uses: actions/cache@v3
+        with:
+          path: radas
+          key: radas-${{ hashFiles('.github/workflows/make_radas_data.sh')}}
+
+      - name: Make radas data
+        if: steps.radas.outputs.cache-hit != 'true'
+        run: bash .github/workflows/make_radas_data.sh
+
+  build:
+    needs: radas
+    # The type of runner that the job will run on
+    runs-on: ubuntu-22.04
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.9', '3.10', '3.11']  # should test the versions we allow for in pyproject.toml
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - name: Install pandoc
+        run: sudo apt-get update && sudo apt-get install pandoc
+
+      - name: Install Poetry
+        run: curl -sSL https://install.python-poetry.org | python - --version 1.6.1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      - name: Setup
+        run: poetry install
+
+      - uses: actions/cache/restore@v3
+        id: radas
+        with:
+          path: radas
+          key: radas-${{ hashFiles('.github/workflows/make_radas_data.sh')}}
+
+      - name: Check cache hit
+        if: steps.radas.outputs.cache-hit != 'true'
+        run: exit 1
+
+      - name: Copy radas data
+        run: cp ./radas/cases/*/output/*.nc cfspopcon/atomic_data/
+
+      - name: Tests
+        run: MPLBACKEND=Agg poetry run pytest tests --nbmake example_cases
+
+      - name: Test package
+        run: |
+          poetry build -f wheel
+          python -m venv test_env
+          source ./test_env/bin/activate
+          pip install $(find ./dist -name "*.whl")
+          # enter tempdir so import cfspopcon doesn't find the cfspopcon directory
+          mkdir tmp_dir && cd tmp_dir
+          echo $(python -c 'from cfspopcon import atomic_data;from pathlib import Path; print(Path(atomic_data.__file__).parent)')
+          cp ../radas/cases/*/output/*.nc $(python -c 'from cfspopcon import atomic_data;from pathlib import Path; print(Path(atomic_data.__file__).parent)')
+          MPLBACKEND=Agg popcon ../example_cases/SPARC_PRD/input.yaml -p ../example_cases/SPARC_PRD/plot_popcon.yaml --show
+
+      - name: Run pre-commit checks
+        run: poetry run pre-commit run --show-diff-on-failure --color=always --all-files
+
+      - name: Test docs
+        # instead of make html we use sphinx-build directly to add more options
+        run: |
+          cd docs
+          poetry run sphinx-build --keep-going -Wnb html . _build/
+          poetry run make doctest
+          poetry run make linkcheck
+

.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/
+pip-wheel-metadata/
+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/
+
+# 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/_*
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# vscode
+*.vscode
+
+#macOS metadata
+.DS_Store
+
+# Mess
+example_cases/SPARC_PRD/output/*
+# avoid committing nc files
+*.nc

.pre-commit-config.yaml

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+# per default we only run over the files in the python package
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: check-added-large-files
+        # but no large files anywhere ;)
+        files: ''
+        exclude: ".*getting_started.ipynb"
+-   repo: local
+    hooks:
+      - id: black
+        name: Black
+        entry: poetry run black
+        language: system
+        types: [python]
+-   repo: local
+    hooks:
+      - id: ruff
+        name: ruff
+        entry: poetry run ruff
+        language: system
+        types: [python]
+        files: '^cfspopcon/'
+-   repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: poetry run mypy
+        language: system
+        types: [python]
+        files: '^cfspopcon/'
+        exclude: ^cfspopcon/plotting

.readthedocs.yaml

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+version: 2
+
+build:
+  os: "ubuntu-20.04"
+  tools:
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+      # Tell poetry to not use a virtual environment
+      - poetry config virtualenvs.create false
+    post_install:
+      - poetry install
+
+sphinx:
+  configuration: docs/conf.py

CONTRIBUTING.md

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+Please make sure to check out our [Developer's Guide](docs/doc_sources/dev_guide.rst).
+It will show you how to setup a development environment for this project and covers our contributing guidelines.

LICENSE

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+Copyright (c) 2023 Commonwealth Fusion Systems
+
+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

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+cfspopcon: 0D Plasma Calculations & Plasma OPerating CONtours
+--------------------------------------------------------------
+
+[![Build Status](https://github.com/cfs-energy/cfspopcon/actions/workflows/workflow_actions.yml/badge.svg)](https://github.com/cfs-energy/cfspopcon/actions)
+[![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
+[![Documentation Status](https://readthedocs.org/projects/cfspopcon/badge/?version=latest)](https://cfspopcon.readthedocs.io/en/latest/?badge=latest)
+
+For more information please have a look at our [documentation](https://cfspopcon.readthedocs.io/en/latest/).