smoothcon 0.0.3__tar.gz

smoothcon-0.0.3/.gitattributes

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+*.ipynb linguist-vendored

smoothcon-0.0.3/.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Run pre-commit
+        run: uv run pre-commit run -a

smoothcon-0.0.3/.github/workflows/pypi.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  workflow_dispatch: # trigger manually from GitHub UI
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: "Set up Python"
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Build package
+        run: uv build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_UPLOAD }}

smoothcon-0.0.3/.github/workflows/pytest-notebooks.yml

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+name: notebooks
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Add R shared libraries to LD_LIBRARY_PATH
+        run: |
+          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest notebooks --nbval-lax --nbval-current-env

smoothcon-0.0.3/.github/workflows/pytest.yml

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+name: pytest
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+          use-public-rspm: true
+
+      - name: Install Package
+        run: uv sync --locked --group dev
+
+      - name: Add R shared libraries to LD_LIBRARY_PATH
+        run: |
+          echo "LD_LIBRARY_PATH=$(python -m rpy2.situation LD_LIBRARY_PATH):\$LD_LIBRARY_PATH" >> $GITHUB_ENV
+
+      - name: Debug R environment
+        run: |
+          echo "R_HOME=$(R RHOME)"
+          echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+          find $(R RHOME) -name methods.so
+          find $(R RHOME) -name libR.so
+
+
+      - name: Run pytest
+        run: uv run pytest --cov=smoothcon
+
+      - name: Create coverage badge
+        uses: tj-actions/coverage-badge-py@v2
+        with:
+          output: tests/coverage.svg
+          overwrite: true
+
+      - name: Commit coverage.svg
+        run: |
+          git config --local user.name "github-actions[bot]"
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git ls-remote | grep refs/heads/pytest-cov && git remote set-branches --add origin pytest-cov && git fetch
+          git add tests/coverage.svg
+          git diff --staged --quiet || git commit -m "Updated coverage.svg"
+
+      - name: Push coverage.svg
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: ${{ github.ref }}

smoothcon-0.0.3/.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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+.python-version
+/.vscode

smoothcon-0.0.3/.pre-commit-config.yaml

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+# see https://pre-commit.com for more information
+# see https://pre-commit.com/hooks.html for more hooks
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.8
+    hooks:
+      # Run the formatter.
+      - id: ruff-format
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+  - repo: local
+    hooks:
+      - id: mypy
+        name: mypy
+        entry: mypy
+        language: python
+        types_or: [python, pyi]
+        args: [--ignore-missing-imports, --scripts-are-modules]
+        require_serial: true
+        exclude: ^docs/