Init commit

.github/workflows/citation_cff.yml

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+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v2
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.github/workflows/doc-deploy.yml

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+# Right now this just publishes the docs, does nothing to PyPI
+name: release
+on:
+  workflow_dispatch:
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          cache: pip
+      - run: python -m pip install ".[dev]"
+      - name: "Deploy Docs"
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          git config user.name doc-bot
+          git config user.email [email protected]
+          current_version=$(git tag | sort --version-sort | tail -n 1)
+
+          # This block will rename previous retitled versions
+          retitled_versions=$(mike list -j | jq ".[] | select(.title != .version) | .version" | tr -d '"')
+          for version in $retitled_versions; do
+            mike retitle "${version}" "${version}"
+          done
+
+          echo "Deploying docs for ${current_version}"
+          mike deploy \
+            --push \
+            --title "${current_version} (latest)" \
+            --update-aliases \
+            "${current_version}" \
+            "latest"

.github/workflows/docs.yml

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+# This workflow is just to test that the docs build successfully.
+name: docs-test
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+permissions:
+  contents: write
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: "Install dependencies"
+        run: python -m pip install -e ".[dev]"
+      - name: "Build Docs"
+        run: mkdocs build --clean --strict

.github/workflows/pre-commit.yml

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+name: Pre-commit
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+      - development
+  pull_request:
+    branches:
+      - main
+      - development
+
+jobs:
+  source-test:
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+        os: ["ubuntu-latest"]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+        cache: pip
+    - name: Run Pre Commit
+      run: |
+        pip install pre-commit
+        pre-commit install
+        pre-commit run --all-files

.github/workflows/pytest.yml

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+name: Tests
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+on:
+  # Allow to manually trigger through github API
+  workflow_dispatch:
+
+  # Triggers with push to main
+  push:
+    branches:
+      - main
+
+  # Triggers with push to a PR aimed at main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  source-test:
+    name: ${{ matrix.python-version }}-${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10"]
+        os: ["ubuntu-latest"]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - run: python -m pip install -e ".[dev]"
+    - run: python -m pytest -v tests

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+.idea
+
+# 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/_build/
+
+# 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/
+
+# Yahpo data
+yahpo_data_r
+
+# Container
+containers
+
+data
+outputs
+runs
+runsold
+*.json
+*.code-workspace
+/.idea/misc.xml
+/.idea/modules.xml
+/.idea/inspectionProfiles/profiles_settings.xml
+/.idea/SMACBenchmarking.iml
+/.idea/vcs.xml
+/.idea/.gitignore
+/.codecarbon.config
+
+/carps/container/credentials.yaml
+carps.db
+*.jsonl
+*.sif
+logs
+/*.db
+*.pdf
+*.pickle
+*.csv
+*.tex
+*run_missing.sh
+*.png
+runsold
+multirun
+runs_subset
+runs*
+*.parquet
+run-data*
+*.txt

.pre-commit-config.yaml

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+default_language_version:
+  python: python3
+files: |
+  (?x)^(
+    carps|
+    tests
+  )/.*\.py$
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-added-large-files
+        files: ".*"
+      - id: check-case-conflict
+        files: ".*"
+      - id: check-merge-conflict
+        files: ".*"
+      - id: check-yaml
+        files: ".*"
+      - id: end-of-file-fixer
+        files: ".*"
+        types: ["yaml"]
+      - id: check-toml
+        files: ".*"
+        types: ["toml"]
+      - id: debug-statements
+        files: '^src/.*\.py$'
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - "types-pyyaml"
+        args:
+          - "--no-warn-return-any" # Disable this because it doesn't know about 3rd party imports
+          - "--ignore-missing-imports"
+          - "--show-traceback"
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.4
+    hooks:
+      - id: check-github-workflows
+        files: '^github/workflows/.*\.ya?ml$'
+        types: ["yaml"]
+      - id: check-dependabot
+        files: '^\.github/dependabot\.ya?ml$'
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.4.5
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --no-cache]
+      - id: ruff-format
+