diff --git a/.copier-answers.yml b/.copier-answers.yml index 26c7bee..a163414 100644 --- a/.copier-answers.yml +++ b/.copier-answers.yml @@ -1,5 +1,5 @@ # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY -_commit: 2024.04.23 +_commit: 2025.05.02-17-g4b5d256 _src_path: gh:scientific-python/cookie backend: hatch email: alanlujan91@gmail.com diff --git a/.git_archival.txt b/.git_archival.txt index 8fb235d..7c51009 100644 --- a/.git_archival.txt +++ b/.git_archival.txt @@ -1,4 +1,3 @@ node: $Format:%H$ node-date: $Format:%cI$ describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$ -ref-names: $Format:%D$ diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 8470878..3494c10 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -6,11 +6,10 @@ description of best practices for developing scientific packages. # Quick development The fastest way to start with development is to use nox. If you don't have nox, -you can use `pipx run nox` to run it without installing, or `pipx install nox`. -If you don't have pipx (pip for applications), then you can install with -`pip install pipx` (the only case were installing an application with regular -pip is reasonable). If you use macOS, then pipx and nox are both in brew, use -`brew install pipx nox`. +you can use `uvx nox` to run it without installing, or `uv tool install nox`. If +you don't have uv, you can +[install it a variety of ways](https://docs.astral.sh/uv/getting-started/installation/), +including with pip, pipx, brew, and just downloading the binary (single file). To use, run `nox`. This will lint and test using every installed version of Python on your system, skipping ones that are not installed. You can also run @@ -19,7 +18,7 @@ specific jobs: ```console $ nox -s lint # Lint only $ nox -s tests # Python tests -$ nox -s docs -- --serve # Build and serve the docs +$ nox -s docs # Build and serve the docs $ nox -s build # Make an SDist and wheel ``` @@ -31,27 +30,16 @@ environment for each run. You can set up a development environment by running: ```bash -python3 -m venv .venv -source ./.venv/bin/activate -pip install -v -e .[dev] +uv sync ``` -If you have the -[Python Launcher for Unix](https://github.com/brettcannon/python-launcher), you -can instead do: - -```bash -py -m venv .venv -py -m install -v -e .[dev] -``` - -# Post setup +# Pre-commit You should prepare pre-commit, which will help you by checking that commits pass required checks: ```bash -pip install pre-commit # or brew install pre-commit on macOS +uv tool install pre-commit # or brew install pre-commit on macOS pre-commit install # Will install a pre-commit hook into the git repo ``` @@ -63,7 +51,7 @@ You can also/alternatively run `pre-commit run` (changes only) or Use pytest to run the unit checks: ```bash -pytest +uv run pytest ``` # Coverage @@ -71,31 +59,19 @@ pytest Use pytest-cov to generate coverage reports: ```bash -pytest --cov=multinterp +uv run pytest --cov=multinterp ``` # Building docs -You can build the docs using: +You can build and serve the docs using: ```bash nox -s docs ``` -You can see a preview with: - -```bash -nox -s docs -- --serve -``` - -# Pre-commit - -This project uses pre-commit for all style checking. While you can run it with -nox, this is such an important tool that it deserves to be installed on its own. -Install pre-commit and run: +You can build the docs only with: ```bash -pre-commit run -a +nox -s docs --non-interactive ``` - -to check all files. diff --git a/.github/release.yml b/.github/release.yml new file mode 100644 index 0000000..9d1e098 --- /dev/null +++ b/.github/release.yml @@ -0,0 +1,5 @@ +changelog: + exclude: + authors: + - dependabot + - pre-commit-ci diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index b544ab0..4030c72 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -2,10 +2,10 @@ name: CD on: workflow_dispatch: - # pull_request: - # push: - # branches: - # - main + pull_request: + push: + branches: + - main release: types: - published @@ -37,8 +37,10 @@ jobs: environment: pypi permissions: id-token: write + attestations: write + contents: read runs-on: ubuntu-latest - # if: github.event_name == 'release' && github.event.action == 'published' + if: github.event_name == 'release' && github.event.action == 'published' steps: - uses: actions/download-artifact@v4 @@ -46,8 +48,13 @@ jobs: name: Packages path: dist + - name: Generate artifact attestation for sdist and wheel + uses: actions/attest-build-provenance@v2 + with: + subject-path: "dist/*" + - uses: pypa/gh-action-pypi-publish@release/v1 - # if: github.event_name == 'release' && github.event.action == 'published' - # with: - # # Remember to tell (test-)pypi about this repo before publishing - # repository-url: https://test.pypi.org/legacy/ + with: + # Remember to tell (test-)pypi about this repo before publishing + # Remove this line to publish to PyPI + repository-url: https://test.pypi.org/legacy/ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e3d1d98..742caef 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,13 +27,14 @@ jobs: - uses: actions/setup-python@v5 with: python-version: "3.x" + + - uses: astral-sh/setup-uv@v6 + - uses: pre-commit/action@v3.0.1 with: extra_args: --hook-stage manual --all-files - - name: Run PyLint - run: | - echo "::add-matcher::$GITHUB_WORKSPACE/.github/matchers/pylint.json" - pipx run nox -s pylint + - name: Run Pylint + run: uvx nox -s pylint -- --output-format=github checks: name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }} @@ -42,11 +43,11 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.8", "3.12"] - runs-on: [ubuntu-latest, macos-latest, windows-latest] + python-version: ["3.9", "3.13"] + runs-on: [ubuntu-latest, windows-latest, macos-14] include: - - python-version: pypy-3.10 + - python-version: "pypy-3.10" runs-on: ubuntu-latest steps: @@ -59,15 +60,17 @@ jobs: python-version: ${{ matrix.python-version }} allow-prereleases: true + - uses: astral-sh/setup-uv@v6 + - name: Install package - run: python -m pip install .[test] + run: uv sync - name: Test package run: >- - python -m pytest -ra --cov --cov-report=xml --cov-report=term + uv run pytest -ra --cov --cov-report=xml --cov-report=term --durations=20 - name: Upload coverage report - uses: codecov/codecov-action@v5.4.0 + uses: codecov/codecov-action@v5 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.gitignore b/.gitignore index b604231..08ce201 100644 --- a/.gitignore +++ b/.gitignore @@ -157,17 +157,6 @@ Thumbs.db *~ *.swp -.vscode* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -!.vscode/*.code-snippets - -# Local History for Visual Studio Code -.history/ - -# Built Visual Studio Code Extensions -*.vsix - +# MyST build outputs _build +/.vscode diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 1953747..889b81d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,15 +2,17 @@ ci: autoupdate_commit_msg: "chore: update pre-commit hooks" autofix_commit_msg: "style: pre-commit fixes" +exclude: ^.cruft.json|.copier-answers.yml$ + repos: - repo: https://github.com/adamchainz/blacken-docs - rev: "1.18.0" + rev: "1.19.1" hooks: - id: blacken-docs additional_dependencies: [black==24.*] - repo: https://github.com/pre-commit/pre-commit-hooks - rev: "v4.6.0" + rev: "v5.0.0" hooks: - id: check-added-large-files - id: check-case-conflict @@ -32,20 +34,36 @@ repos: - id: rst-directive-colons - id: rst-inline-touching-normal - - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v4.0.0-alpha.8" + - repo: https://github.com/rbubley/mirrors-prettier + rev: "v3.5.3" hooks: - id: prettier types_or: [yaml, markdown, html, css, scss, javascript, json] args: [--prose-wrap=always] - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.5.1" + rev: "v0.11.13" hooks: - - id: ruff + - id: ruff-check args: ["--fix", "--show-fixes"] - id: ruff-format + # - repo: https://github.com/pre-commit/mirrors-mypy + # rev: "v1.16.0" + # hooks: + # - id: mypy + # files: src|tests + # args: [] + # additional_dependencies: + # - pytest + + # - repo: https://github.com/codespell-project/codespell + # rev: "v2.4.1" + # hooks: + # - id: codespell + # additional_dependencies: + # - tomli; python_version<'3.11' + - repo: https://github.com/shellcheck-py/shellcheck-py rev: "v0.10.0.1" hooks: @@ -60,13 +78,13 @@ repos: exclude: .pre-commit-config.yaml - repo: https://github.com/abravalheri/validate-pyproject - rev: "v0.18" + rev: "v0.24.1" hooks: - id: validate-pyproject additional_dependencies: ["validate-pyproject-schema-store[all]"] - repo: https://github.com/python-jsonschema/check-jsonschema - rev: "0.28.6" + rev: "0.33.0" hooks: - id: check-dependabot - id: check-github-workflows diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 7e49657..172d2d8 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -4,15 +4,13 @@ version: 2 build: - os: ubuntu-22.04 + os: ubuntu-24.04 tools: - python: "3.11" -sphinx: - configuration: docs/conf.py - -python: - install: - - method: pip - path: . - extra_requirements: - - docs + python: "3.13" + commands: + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + - uv sync --group docs + - uv run python -m sphinx -T -b html -d docs/_build/doctrees -D language=en + docs $READTHEDOCS_OUTPUT/html diff --git a/.readthedocs.yml b/.readthedocs.yml deleted file mode 100644 index 7e49657..0000000 --- a/.readthedocs.yml +++ /dev/null @@ -1,18 +0,0 @@ -# Read the Docs configuration file -# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details - -version: 2 - -build: - os: ubuntu-22.04 - tools: - python: "3.11" -sphinx: - configuration: docs/conf.py - -python: - install: - - method: pip - path: . - extra_requirements: - - docs diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md deleted file mode 100644 index 703b9c5..0000000 --- a/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,128 +0,0 @@ -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, -nationality, personal appearance, race, religion, or sexual identity and -orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -- Demonstrating empathy and kindness toward other people -- Being respectful of differing opinions, viewpoints, and experiences -- Giving and gracefully accepting constructive feedback -- Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -- Focusing on what is best not just for us as individuals, but for the overall - community - -Examples of unacceptable behavior include: - -- The use of sexualized language or imagery, and sexual attention or advances of - any kind -- Trolling, insulting or derogatory comments, and personal or political attacks -- Public or private harassment -- Publishing others' private information, such as a physical or email address, - without their explicit permission -- Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -alanlujan91@gmail.com. All complaints will be reviewed and investigated promptly -and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series of -actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or permanent -ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within the -community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.0, available at -https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. - -Community Impact Guidelines were inspired by -[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity). - -[homepage]: https://www.contributor-covenant.org - -For answers to common questions about this code of conduct, see the FAQ at -https://www.contributor-covenant.org/faq. Translations are available at -https://www.contributor-covenant.org/translations. diff --git a/LICENSE b/LICENSE index a438ea6..6c0fb1c 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright 2024 Alan Lujan +Copyright 2025 Alan Lujan 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 diff --git a/README.md b/README.md index 3816f20..e13460f 100644 --- a/README.md +++ b/README.md @@ -25,9 +25,3 @@ [rtd-link]: https://multinterp.readthedocs.io/en/latest/?badge=latest - -# To Install - -``` -pip install git+https://github.com/alanlujan91/multinterp -``` diff --git a/SECURITY.md b/SECURITY.md deleted file mode 100644 index d906fed..0000000 --- a/SECURITY.md +++ /dev/null @@ -1,20 +0,0 @@ -# Security Policy - -## Supported Versions - -Use this section to tell people about which versions of your project are -currently being supported with security updates. - -| Version | Supported | -| ------- | ------------------ | -| 5.1.x | :white_check_mark: | -| 5.0.x | :x: | -| 4.0.x | :white_check_mark: | -| < 4.0 | :x: | - -## Reporting a Vulnerability - -Use this section to tell people how to report a vulnerability. - -Tell them where to go, how often they can expect to get an update on a reported -vulnerability, what to expect if the vulnerability is accepted or declined, etc. diff --git a/_config.yml b/_config.yml deleted file mode 100644 index f66bc31..0000000 --- a/_config.yml +++ /dev/null @@ -1,32 +0,0 @@ -# Book settings -# Learn more at https://jupyterbook.org/customize/config.html - -title: A practical guide to Multivariate Interpolation -author: Alan Lujan -logo: logo.png - -# Force re-execution of notebooks on each build. -# See https://jupyterbook.org/content/execute.html -execute: - execute_notebooks: force - -# Define the name of the latex output file for PDF builds -latex: - latex_documents: - targetname: book.tex - -# Add a bibtex file so that we can create citations -bibtex_bibfiles: - - references.bib - -# Information about where the book exists on the web -repository: - url: https://github.com/alanlujan91/multinterp # Online location of your book - path_to_book: docs # Optional path to your book, relative to the repository root - branch: main # Which branch of the repository should be used when creating links (optional) - -# Add GitHub buttons to your book -# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository -html: - use_issues_button: true - use_repository_button: true diff --git a/docs/conf.py b/docs/conf.py index 74f274e..4011aa5 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,9 +1,10 @@ from __future__ import annotations import importlib.metadata +from typing import Any project = "multinterp" -copyright = "2024, Alan Lujan" +copyright = "2025, Alan Lujan" author = "Alan Lujan" version = release = importlib.metadata.version("multinterp") @@ -29,6 +30,24 @@ html_theme = "furo" +html_theme_options: dict[str, Any] = { + "footer_icons": [ + { + "name": "GitHub", + "url": "https://github.com/alanlujan91/multinterp", + "html": """ + + + + """, + "class": "", + }, + ], + "source_repository": "https://github.com/alanlujan91/multinterp", + "source_branch": "main", + "source_directory": "docs/", +} + myst_enable_extensions = [ "colon_fence", ] diff --git a/environment.yml b/environment.yml index 151d74c..e5d1bc3 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: multinterp-dev +name: multinterp channels: - pytorch - nvidia diff --git a/examples/01_Curvilinear/03._Curvilinear_Interpolation.ipynb b/examples/01_Curvilinear/03._Curvilinear_Interpolation.ipynb index ecded6e..633e0d8 100644 --- a/examples/01_Curvilinear/03._Curvilinear_Interpolation.ipynb +++ b/examples/01_Curvilinear/03._Curvilinear_Interpolation.ipynb @@ -193,8 +193,7 @@ ], "source": [ "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -221,8 +220,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { @@ -414,8 +412,7 @@ "warped_interp = Warped2DInterp(values, (rand_x, rand_y), backend=\"numba\")\n", "\n", "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -442,8 +439,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { @@ -638,8 +634,7 @@ ], "source": [ "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -666,8 +661,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { @@ -856,8 +850,7 @@ ], "source": [ "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -884,8 +877,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { @@ -1080,8 +1072,7 @@ ], "source": [ "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -1116,8 +1107,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { @@ -1315,8 +1305,7 @@ ], "source": [ "start = time()\n", - "warped_grid = warped_interp(grid_x, grid_y)\n", - "print(f\"Warped interpolation took {time() - start:.5f} seconds\")" + "warped_grid = warped_interp(grid_x, grid_y)" ] }, { @@ -1343,8 +1332,7 @@ "source": [ "curvilinear_interp = Curvilinear2DInterp(values, rand_x, rand_y)\n", "start = time()\n", - "curvilinear_grid = curvilinear_interp(grid_x, grid_y)\n", - "print(f\"Curvilinear interpolation took {time() - start:.5f} seconds\")" + "curvilinear_grid = curvilinear_interp(grid_x, grid_y)" ] }, { diff --git a/myst.yml b/myst.yml index 1d1f0d1..154d6bb 100644 --- a/myst.yml +++ b/myst.yml @@ -1,6 +1,7 @@ # See docs at: https://mystmd.org/guide/frontmatter version: 1 project: + id: 571049e8-271e-4ff9-b9a3-d17459e8dfab title: Multivariate Interpolation # description: keywords: [interpolation, multivariate, unstructured] @@ -17,14 +18,9 @@ project: url: https://econ-ark.org/ github: alanlujan91 github: https://github.com/alanlujan91/multinterp - # bibliography: [] + # To autogenerate a Table of Contents, run "myst init --write-toc" site: template: book-theme - title: Multivariate Interpolation - # logo: - nav: [] - actions: - - title: Learn More - url: https://mystmd.org/guide - domains: - - alanlujan91.curve.space + # options: + # favicon: favicon.ico + # logo: site_logo.png diff --git a/noxfile.py b/noxfile.py index f9cbbec..f9a51e4 100644 --- a/noxfile.py +++ b/noxfile.py @@ -7,9 +7,9 @@ import nox DIR = Path(__file__).parent.resolve() +PROJECT = nox.project.load_toml() -nox.needs_version = ">=2024.3.2" -nox.options.sessions = ["lint", "pylint", "tests"] +nox.needs_version = ">=2025.2.9" nox.options.default_venv_backend = "uv|virtualenv" @@ -28,84 +28,69 @@ def lint(session: nox.Session) -> None: @nox.session def pylint(session: nox.Session) -> None: - """Run PyLint.""" + """Run Pylint.""" # This needs to be installed into the package environment, and is slower # than a pre-commit check - session.install(".", "pylint") + session.install("-e.", "pylint>=3.2") session.run("pylint", "multinterp", *session.posargs) @nox.session def tests(session: nox.Session) -> None: """Run the unit and regular tests.""" - session.install(".[test]") + test_deps = nox.project.dependency_groups(PROJECT, "test") + session.install("-e.", *test_deps) session.run("pytest", *session.posargs) -@nox.session(reuse_venv=True) +@nox.session(reuse_venv=True, default=False) def docs(session: nox.Session) -> None: - """Build the docs. Pass "--serve" to serve. Pass "-b linkcheck" to check links.""" + """Build the docs. Pass --non-interactive to avoid serving. First positional argument is the target directory.""" + doc_deps = nox.project.dependency_groups(PROJECT, "docs") parser = argparse.ArgumentParser() - parser.add_argument("--serve", action="store_true", help="Serve after building") parser.add_argument( "-b", dest="builder", default="html", help="Build target (default: html)", ) + parser.add_argument("output", nargs="?", help="Output directory") args, posargs = parser.parse_known_args(session.posargs) + serve = args.builder == "html" and session.interactive - if args.builder != "html" and args.serve: - session.error("Must not specify non-HTML builder with --serve") - - extra_installs = ["sphinx-autobuild"] if args.serve else [] - - session.install("-e.[docs]", *extra_installs) - session.chdir("docs") - - if args.builder == "linkcheck": - session.run( - "sphinx-build", - "-b", - "linkcheck", - ".", - "_build/linkcheck", - *posargs, - ) - return + session.install("-e.", *doc_deps, "sphinx-autobuild") shared_args = ( "-n", # nitpicky mode "-T", # full tracebacks f"-b={args.builder}", - ".", - f"_build/{args.builder}", + "docs", + args.output or f"docs/_build/{args.builder}", *posargs, ) - if args.serve: - session.run("sphinx-autobuild", *shared_args) + if serve: + session.run("sphinx-autobuild", "--open-browser", *shared_args) else: session.run("sphinx-build", "--keep-going", *shared_args) -@nox.session +@nox.session(default=False) def build_api_docs(session: nox.Session) -> None: """Build (regenerate) API docs.""" session.install("sphinx") - session.chdir("docs") session.run( "sphinx-apidoc", "-o", - "api/", + "docs/api/", "--module-first", "--no-toc", "--force", - "../src/multinterp", + "src/multinterp", ) -@nox.session +@nox.session(default=False) def build(session: nox.Session) -> None: """Build an SDist and wheel.""" build_path = DIR.joinpath("build") diff --git a/pyproject.toml b/pyproject.toml index b30a0cf..6329d92 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,43 +1,59 @@ [build-system] -requires = ["hatchling", "hatch-vcs"] +requires = ["hatchling>=1.26", "hatch-vcs"] build-backend = "hatchling.build" [project] name = "multinterp" -authors = [{ name = "Alan Lujan", email = "alanlujan91@gmail.com" }] -maintainers = [{ name = "All the contributors." }] +authors = [ + { name = "Alan Lujan", email = "alanlujan91@gmail.com" }, +] description = "Multivariate Interpolation." readme = "README.md" -license.file = "LICENSE" -keywords = ["multivariate", "interpolation", "multidimensional"] -requires-python = ">=3.8" +license = "MIT" +requires-python = ">=3.9" classifiers = [ "Development Status :: 1 - Planning", - "Environment :: GPU", "Intended Audience :: Science/Research", "Intended Audience :: Developers", - "License :: OSI Approved :: MIT License", - "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Mathematics", "Typing :: Typed", ] dynamic = ["version"] -dependencies = ["numpy", "scipy", "scikit-learn", "scikit-image"] +dependencies = [ + "numpy", + "scipy", + "scikit-learn", + "scikit-image", + "numba", + "tbb>=2021.12", +] + +[project.urls] +Homepage = "https://github.com/alanlujan91/multinterp" +"Bug Tracker" = "https://github.com/alanlujan91/multinterp/issues" +Discussions = "https://github.com/alanlujan91/multinterp/discussions" +Changelog = "https://github.com/alanlujan91/multinterp/releases" -[project.optional-dependencies] -test = ["pytest >=6", "pytest-cov >=3"] -dev = ["pytest >=6", "pytest-cov >=3"] + +[dependency-groups] +test = [ + "pytest >=6", + "pytest-cov >=3", + "cupy-cuda11x>=13.4.1", "torch", "jax" +] +dev = [ + { include-group = "test" }, +] docs = [ "sphinx>=7.0", "myst_parser>=0.13", @@ -45,16 +61,6 @@ docs = [ "sphinx_autodoc_typehints", "furo>=2023.08.17", ] -numba = ["numba"] -cupy = ["cupy"] -jax = ["jax", "jaxlib"] -torch = ["pytorch", "gpytorch"] - -[project.urls] -Homepage = "https://github.com/alanlujan91/multinterp" -"Bug Tracker" = "https://github.com/alanlujan91/multinterp/issues" -Discussions = "https://github.com/alanlujan91/multinterp/discussions" -Changelog = "https://github.com/alanlujan91/multinterp/releases" [tool.hatch] @@ -62,7 +68,8 @@ version.source = "vcs" build.hooks.vcs.version-file = "src/multinterp/_version.py" [tool.hatch.envs.default] -features = ["test"] +# duplicate for now since hatch doesn't support groups yet +dependencies = [] scripts.test = "pytest {args}" @@ -70,18 +77,25 @@ scripts.test = "pytest {args}" minversion = "6.0" addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"] xfail_strict = true -filterwarnings = ["error"] +filterwarnings = [ + "error", +] log_cli_level = "INFO" -testpaths = ["tests"] +testpaths = [ + "tests", +] [tool.coverage] run.source = ["multinterp"] -report.exclude_also = ['\.\.\.', 'if typing.TYPE_CHECKING:'] +report.exclude_also = [ + '\.\.\.', + 'if typing.TYPE_CHECKING:', +] [tool.mypy] files = ["src", "tests"] -python_version = "3.8" +python_version = "3.9" warn_unused_configs = true strict = true enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"] @@ -96,36 +110,34 @@ disallow_incomplete_defs = true [tool.ruff] -src = ["src"] [tool.ruff.lint] extend-select = [ - "B", # flake8-bugbear - "I", # isort - "ARG", # flake8-unused-arguments - "C4", # flake8-comprehensions - "EM", # flake8-errmsg - "ICN", # flake8-import-conventions - "G", # flake8-logging-format - "PGH", # pygrep-hooks - "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style - "PTH", # flake8-use-pathlib - "RET", # flake8-return - "RUF", # Ruff-specific - "SIM", # flake8-simplify - "T20", # flake8-print - "UP", # pyupgrade - "YTT", # flake8-2020 - "EXE", # flake8-executable - "NPY", # NumPy specific rules - "PD", # pandas-vet + "ARG", # flake8-unused-arguments + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "EM", # flake8-errmsg + "EXE", # flake8-executable + "G", # flake8-logging-format + "I", # isort + "ICN", # flake8-import-conventions + "NPY", # NumPy specific rules + "PD", # pandas-vet + "PGH", # pygrep-hooks + "PIE", # flake8-pie + "PL", # pylint + "PT", # flake8-pytest-style + "PTH", # flake8-use-pathlib + "RET", # flake8-return + "RUF", # Ruff-specific + "SIM", # flake8-simplify + "T20", # flake8-print + "UP", # pyupgrade + "YTT", # flake8-2020 ] ignore = [ - "PLR09", # Too many <...> - "PLR2004", # Magic value used in comparison - "ISC001", # Conflicts with formatter + "PLR09", # Too many <...> + "PLR2004", # Magic value used in comparison ] isort.required-imports = ["from __future__ import annotations"] # Uncomment if using a _compat.typing backport @@ -137,7 +149,7 @@ isort.required-imports = ["from __future__ import annotations"] [tool.pylint] -py-version = "3.8" +py-version = "3.9" ignore-paths = [".*/_version.py"] reports.output-format = "colorized" similarities.ignore-imports = "yes" diff --git a/src/multinterp/__init__.py b/src/multinterp/__init__.py index 009bfdf..13bd702 100644 --- a/src/multinterp/__init__.py +++ b/src/multinterp/__init__.py @@ -8,15 +8,15 @@ from ._version import version as __version__ __all__ = ( - "__version__", "MultivariateInterp", - "Warped2DInterp", "PiecewiseAffineInterp", - "UnstructuredInterp", "PipelineCurvilinearInterp", "PipelineUnstructuredInterp", "RegressionCurvilinearInterp", "RegressionUnstructuredInterp", + "UnstructuredInterp", + "Warped2DInterp", + "__version__", ) diff --git a/src/multinterp/_version.pyi b/src/multinterp/_version.pyi index 91744f9..5bb2b22 100644 --- a/src/multinterp/_version.pyi +++ b/src/multinterp/_version.pyi @@ -1,4 +1,2 @@ -from __future__ import annotations - version: str version_tuple: tuple[int, int, int] | tuple[int, int, int, str, str] diff --git a/src/multinterp/backend/LBFGS.py b/src/multinterp/backend/LBFGS.py index a2c3bca..1f8f594 100644 --- a/src/multinterp/backend/LBFGS.py +++ b/src/multinterp/backend/LBFGS.py @@ -9,7 +9,7 @@ from torch.optim import Optimizer -def is_legal(v): +def is_legal(v) -> bool: """Checks that tensor is not NaN or Inf. Inputs: @@ -235,7 +235,7 @@ def __init__( line_search="Wolfe", dtype=torch.float, debug=False, - ): + ) -> None: # ensure inputs are valid if lr < 0.0: msg = f"Invalid learning rate: {lr}" @@ -294,7 +294,7 @@ def _gather_flat_grad(self): views.append(view) return torch.cat(views, 0) - def _add_update(self, step_size, update): + def _add_update(self, step_size, update) -> None: offset = 0 for p in self._params: numel = p.numel() @@ -309,11 +309,11 @@ def _add_update(self, step_size, update): def _copy_params(self): return [deepcopy(param.data) for param in self._params] - def _load_params(self, current_params): + def _load_params(self, current_params) -> None: for i, param in enumerate(self._params): param.data[:] = current_params[i] - def line_search(self, line_search): + def line_search(self, line_search) -> None: """Switches line search option. Inputs: @@ -371,7 +371,7 @@ def two_loop_recursion(self, vec): return r - def curvature_update(self, flat_grad, eps=1e-2, damping=False): + def curvature_update(self, flat_grad, eps=1e-2, damping=False) -> None: """Performs curvature update. Inputs: @@ -416,7 +416,7 @@ def curvature_update(self, flat_grad, eps=1e-2, damping=False): # perform Powell damping if damping is True and ys < eps * sBs: if debug: - print("Applying Powell damping...") + pass theta = ((1 - eps) * sBs) / (sBs - ys) y = theta * y + (1 - theta) * Bs @@ -441,13 +441,13 @@ def curvature_update(self, flat_grad, eps=1e-2, damping=False): # save skip state["curv_skips"] += 1 if debug: - print("Curvature pair skipped due to failed criterion") + pass else: # save skip state["fail_skips"] += 1 if debug: - print("Line search failed; curvature pair update skipped") + pass def _step(self, p_k, g_Ok, g_Sk=None, options=None): """Performs a single optimization step. @@ -625,16 +625,13 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # begin print for debug mode if ls_debug: - print( - "==================================== Begin Armijo line search ===================================", - ) - print(f"F(x): {F_k:.8e} g*d: {gtd:.8e}") + pass # check if search direction is descent direction if gtd >= 0: desc_dir = False if debug: - print("Not a descent direction!") + pass else: desc_dir = True @@ -649,10 +646,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print info if debugging if ls_debug: - print( - "LS Step: %d t: %.8e F(x+td): %.8e F-c1*t*g*d: %.8e F(x): %.8e" - % (ls_step, t, F_new, F_k + c1 * t * gtd, F_k), - ) + pass # check Armijo condition while F_new > F_k + c1 * t * gtd or not is_legal(F_new): @@ -727,10 +721,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print info if debugging if ls_debug: - print( - "LS Step: %d t: %.8e F(x+td): %.8e F-c1*t*g*d: %.8e F(x): %.8e" - % (ls_step, t, F_new, F_k + c1 * t * gtd, F_k), - ) + pass # store Bs if Bs is None: @@ -740,10 +731,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print final steplength if ls_debug: - print("Final Steplength:", t) - print( - "===================================== End Armijo line search ====================================", - ) + pass state["d"] = d state["prev_flat_grad"] = prev_flat_grad @@ -839,16 +827,13 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # begin print for debug mode if ls_debug: - print( - "==================================== Begin Wolfe line search ====================================", - ) - print(f"F(x): {F_k:.8e} g*d: {gtd:.8e}") + pass # check if search direction is descent direction if gtd >= 0: desc_dir = False if debug: - print("Not a descent direction!") + pass else: desc_dir = True @@ -881,13 +866,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print info if debugging if ls_debug: - print( - "LS Step: %d t: %.8e alpha: %.8e beta: %.8e" - % (ls_step, t, alpha, beta), - ) - print( - f"Armijo: F(x+td): {F_new:.8e} F-c1*t*g*d: {F_k + c1 * t * gtd:.8e} F(x): {F_k:.8e}", - ) + pass # check Armijo condition if F_new > F_k + c1 * t * gtd: @@ -912,9 +891,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print info if debugging if ls_debug: - print( - f"Wolfe: g(x+td)*d: {gtd_new:.8e} c2*g*d: {c2 * gtd:.8e} gtd: {gtd:.8e}", - ) + pass # check curvature condition if gtd_new < c2 * gtd: @@ -982,10 +959,7 @@ def _step(self, p_k, g_Ok, g_Sk=None, options=None): # print final steplength if ls_debug: - print("Final Steplength:", t) - print( - "===================================== End Wolfe line search =====================================", - ) + pass state["d"] = d state["prev_flat_grad"] = prev_flat_grad @@ -1056,7 +1030,7 @@ def __init__( line_search="Wolfe", dtype=torch.float, debug=False, - ): + ) -> None: super().__init__(params, lr, history_size, line_search, dtype, debug) def step(self, options=None): @@ -1133,9 +1107,9 @@ def step(self, options=None): # load options for damping and eps if options is None: options = {} - damping = False if "damping" not in options else options["damping"] + damping = options.get("damping", False) - eps = 0.01 if "eps" not in options else options["eps"] + eps = options.get("eps", 0.01) # gather gradient grad = self._gather_flat_grad() diff --git a/src/multinterp/backend/_numba.py b/src/multinterp/backend/_numba.py index 7bfca76..85dcd80 100644 --- a/src/multinterp/backend/_numba.py +++ b/src/multinterp/backend/_numba.py @@ -2,7 +2,6 @@ import numpy as np from numba import njit, prange, typed -from scipy.ndimage import map_coordinates from multinterp.utilities import update_mc_kwargs @@ -34,7 +33,7 @@ def numba_multinterp(grids, values, args, options=None): grids = typed.List([np.asarray(grid) for grid in grids]) coords = numba_get_coordinates(grids, args) - return numba_map_coordinates(values, coords, **mc_kwargs) + return numba_map_coordinates_wrapper(values, coords, **mc_kwargs) @njit(parallel=True, cache=True, fastmath=True) @@ -56,18 +55,200 @@ def numba_get_coordinates(grids, args): """ coords = np.empty_like(args) for dim in prange(len(grids)): - grid_size = np.arange(grids[dim].size) + # Create grid indices directly to avoid uint64 to int64 conversion issues + grid_len = np.int64(len(grids[dim])) + grid_size = np.empty(grid_len, dtype=np.float64) + for i in range(grid_len): + grid_size[i] = float(i) coords[dim] = np.interp(args[dim], grids[dim], grid_size) return coords -# same as scipy map_coordinates until replacement is found -def numba_map_coordinates(values, coords, **kwargs): - """Identical to scipy_map_coordinates until a replacement is found. See documentation for scipy_map_coordinates.""" +@njit(cache=True, fastmath=True) +def _round_half_away_from_zero(a): + """Round half away from zero for nearest neighbor interpolation.""" + return np.round(a) + + +@njit(cache=True, fastmath=True) +def _mirror_index_fixer(index, size): + """Mirror boundary condition index fixer.""" + s = size - 1 # Half-wavelength of triangular wave + return np.abs((index + s) % (2 * s) - s) + + +@njit(cache=True, fastmath=True) +def _reflect_index_fixer(index, size): + """Reflect boundary condition index fixer.""" + return np.floor_divide(_mirror_index_fixer(2 * index + 1, 2 * size + 1) - 1, 2) + + +@njit(cache=True, fastmath=True) +def _fix_index(index, size, mode): + """Apply boundary condition to indices.""" + if mode == 0: # constant + return index + if mode == 1: # nearest + return np.clip(index, 0, size - 1) + if mode == 2: # wrap + return index % size + if mode == 3: # mirror + return _mirror_index_fixer(index, size) + if mode == 4: # reflect + return _reflect_index_fixer(index, size) + return index + + +@njit(cache=True, fastmath=True) +def _is_valid_index(index, size, mode): + """Check if index is valid for constant mode.""" + if mode == 0: # constant mode + return (index >= 0) & (index < size) + return True + + +@njit(parallel=True, cache=True, fastmath=True) +def numba_map_coordinates(input_arr, coordinates, order=1, mode="nearest", cval=0.0): + """Numba implementation of map_coordinates with full interpolation support. + + Parameters + ---------- + input_arr : np.ndarray + N-dimensional input array from which values are interpolated. + coordinates : np.ndarray + Array of shape (ndim, ...) specifying coordinates at which to evaluate. + order : int + Interpolation order. 0 for nearest, 1 for linear. + mode : str + Boundary mode: 'constant', 'nearest', 'wrap', 'mirror', 'reflect'. + cval : float + Value for constant mode outside boundaries. + + Returns + ------- + np.ndarray + Interpolated values at the specified coordinates. + """ + # Convert mode string to integer for Numba compatibility + if mode == "constant": + mode_int = 0 + elif mode == "nearest": + mode_int = 1 + elif mode == "wrap": + mode_int = 2 + elif mode == "mirror": + mode_int = 3 + elif mode == "reflect": + mode_int = 4 + else: + mode_int = 1 # default to nearest + + # Get coordinate shape and flatten for processing + coord_shape = coordinates.shape[1:] + total_points = coordinates[0].size + ndim = coordinates.shape[0] + + # Flatten coordinates for easier indexing + coords_flat = coordinates.reshape(ndim, total_points) + + # Output array + output = np.zeros(total_points, dtype=input_arr.dtype) + + # Process each point + for point_idx in prange(total_points): + point_coords = coords_flat[:, point_idx] + + if order == 0: # Nearest neighbor + indices = np.empty(ndim, dtype=np.int64) + for dim in range(ndim): + coord = point_coords[dim] + nearest_idx = _round_half_away_from_zero(coord).astype(np.int64) + fixed_idx = _fix_index(nearest_idx, input_arr.shape[dim], mode_int) + indices[dim] = fixed_idx + + # Check validity for constant mode + valid = True + if mode_int == 0: # constant mode + for dim in range(ndim): + original_idx = _round_half_away_from_zero(point_coords[dim]).astype( + np.int64 + ) + if not _is_valid_index( + original_idx, input_arr.shape[dim], mode_int + ): + valid = False + break + + if valid: + output[point_idx] = input_arr[tuple(indices)] + else: + output[point_idx] = cval + + else: # Linear interpolation (order == 1) + # Get interpolation weights and indices for each dimension + result = 0.0 + + # For linear interpolation, we need 2^ndim combinations + num_combinations = 2**ndim + + for combo in range(num_combinations): + # Extract which corner we're using for each dimension + weight = 1.0 + indices = np.empty(ndim, dtype=np.int64) + valid = True + + for dim in range(ndim): + coord = point_coords[dim] + lower = np.floor(coord) + upper_weight = coord - lower + lower_weight = 1 - upper_weight + + # Determine if we use lower or upper index for this dimension + use_upper = bool((combo >> dim) & 1) + + if use_upper: + idx = (lower + 1).astype(np.int64) + weight *= upper_weight + else: + idx = lower.astype(np.int64) + weight *= lower_weight + + # Apply boundary conditions + fixed_idx = _fix_index(idx, input_arr.shape[dim], mode_int) + indices[dim] = fixed_idx + + # Check validity for constant mode + if mode_int == 0 and not _is_valid_index( + idx, input_arr.shape[dim], mode_int + ): # constant mode + valid = False + + # Add contribution from this corner + if valid: + result += weight * input_arr[tuple(indices)] + else: + result += weight * cval + + output[point_idx] = result + + # Reshape back to original coordinate shape + return output.reshape(coord_shape) + + +# Wrapper function that maintains scipy interface for backward compatibility +def numba_map_coordinates_wrapper( + values, + coords, + order=1, + mode="nearest", + cval=0.0, + **kwargs, # noqa: ARG001 +): + """Wrapper to maintain compatibility with scipy map_coordinates interface.""" original_shape = coords[0].shape - coords = coords.reshape(len(values.shape), -1) - output = map_coordinates(values, coords, **kwargs) + coords_array = np.array(coords).reshape(len(values.shape), -1) + output = numba_map_coordinates(values, coords_array, order, mode, cval) return output.reshape(original_shape) diff --git a/src/multinterp/backend/_torch.py b/src/multinterp/backend/_torch.py index 7d2acc2..4e34d9f 100644 --- a/src/multinterp/backend/_torch.py +++ b/src/multinterp/backend/_torch.py @@ -1,13 +1,16 @@ from __future__ import annotations import itertools -from typing import Sequence +from typing import TYPE_CHECKING import numpy as np import torch from multinterp.utilities import update_mc_kwargs +if TYPE_CHECKING: + from collections.abc import Sequence + def as_tensor(arrs, device="cpu"): target_device = torch.device(device) @@ -81,7 +84,7 @@ def _reflect_index_fixer(index: torch.Tensor, size: int) -> torch.Tensor: _INDEX_FIXERS = { - "constant": lambda index, size: index, + "constant": lambda index, _: index, "nearest": lambda index, size: torch.clip(index, 0, size - 1), "wrap": lambda index, size: index % size, "mirror": _mirror_index_fixer, @@ -130,7 +133,7 @@ def is_valid(index, size): else: - def is_valid(index, size): + def is_valid(_index, _size) -> bool: return True if order == 0: @@ -172,8 +175,8 @@ def map_coordinates( order: int, mode: str = "constant", cval: float = 0.0, - output=None, - prefilter=None, + output=None, # noqa: ARG001 + prefilter=None, # noqa: ARG001 ) -> torch.Tensor: return _map_coordinates(input, coordinates, order, mode, cval) diff --git a/src/multinterp/curvilinear/__init__.py b/src/multinterp/curvilinear/__init__.py index eff883e..198e039 100644 --- a/src/multinterp/curvilinear/__init__.py +++ b/src/multinterp/curvilinear/__init__.py @@ -8,9 +8,9 @@ from ._warped import Curvilinear2DInterp, Warped2DInterp __all__ = [ + "Curvilinear2DInterp", "PiecewiseAffineInterp", - "Warped2DInterp", "PipelineCurvilinearInterp", "RegressionCurvilinearInterp", - "Curvilinear2DInterp", + "Warped2DInterp", ] diff --git a/src/multinterp/curvilinear/_scikit_image.py b/src/multinterp/curvilinear/_scikit_image.py index 86e5599..34704ee 100644 --- a/src/multinterp/curvilinear/_scikit_image.py +++ b/src/multinterp/curvilinear/_scikit_image.py @@ -1,57 +1,57 @@ -from __future__ import annotations - -from skimage.transform import PiecewiseAffineTransform - -from multinterp.grids import _CurvilinearGrid -from multinterp.rectilinear._multi import MultivariateInterp -from multinterp.utilities import mgrid, update_mc_kwargs - - -class PiecewiseAffineInterp(_CurvilinearGrid, MultivariateInterp): - """Curvilinear interpolator that uses the PiecewiseAffineTransform from scikit-image.""" - - def __init__(self, values, grids, options=None): - """Initialize a PiecewiseAffineInterp object. - - Parameters - ---------- - values : np.ndarray - Functional values on a curvilinear grid. - grids : np.ndarray - Coordinates of the points in the curvilinear grid. - options : dict, optional - Additional keyword arguments to pass to the map_coordinates backend. - - """ - super().__init__(values, grids, backend="scipy") - self.mc_kwargs = update_mc_kwargs(options) - - source = self.grids.reshape((self.ndim, -1)).T - coordinates = mgrid( - tuple(slice(0, dim) for dim in self.shape), - backend=self.backend, - ) - destination = coordinates.reshape((self.ndim, -1)).T - - interpolator = PiecewiseAffineTransform() - interpolator.estimate(source, destination) - - self.interpolator = interpolator - - def _get_coordinates(self, args): - """Obtain the index coordinates for each of the arguments. - - Parameters - ---------- - args : np.ndarray - Arguments to be interpolated. - - Returns - ------- - np.ndarray - Index coordinates for each of the arguments. - - """ - _input = args.reshape((self.ndim, -1)).T - output = self.interpolator(_input).T.copy() - return output.reshape(args.shape) +from __future__ import annotations + +from skimage.transform import PiecewiseAffineTransform + +from multinterp.grids import _CurvilinearGrid +from multinterp.rectilinear._multi import MultivariateInterp +from multinterp.utilities import mgrid, update_mc_kwargs + + +class PiecewiseAffineInterp(_CurvilinearGrid, MultivariateInterp): + """Curvilinear interpolator that uses the PiecewiseAffineTransform from scikit-image.""" + + def __init__(self, values, grids, options=None) -> None: + """Initialize a PiecewiseAffineInterp object. + + Parameters + ---------- + values : np.ndarray + Functional values on a curvilinear grid. + grids : np.ndarray + Coordinates of the points in the curvilinear grid. + options : dict, optional + Additional keyword arguments to pass to the map_coordinates backend. + + """ + super().__init__(values, grids, backend="scipy") + self.mc_kwargs = update_mc_kwargs(options) + + source = self.grids.reshape((self.ndim, -1)).T + coordinates = mgrid( + tuple(slice(0, dim) for dim in self.shape), + backend=self.backend, + ) + destination = coordinates.reshape((self.ndim, -1)).T + + interpolator = PiecewiseAffineTransform() + interpolator.estimate(source, destination) + + self.interpolator = interpolator + + def _get_coordinates(self, args): + """Obtain the index coordinates for each of the arguments. + + Parameters + ---------- + args : np.ndarray + Arguments to be interpolated. + + Returns + ------- + np.ndarray + Index coordinates for each of the arguments. + + """ + _input = args.reshape((self.ndim, -1)).T + output = self.interpolator(_input).T.copy() + return output.reshape(args.shape) diff --git a/src/multinterp/curvilinear/_scikit_learn.py b/src/multinterp/curvilinear/_scikit_learn.py index 20601d0..11d7ce1 100644 --- a/src/multinterp/curvilinear/_scikit_learn.py +++ b/src/multinterp/curvilinear/_scikit_learn.py @@ -16,7 +16,7 @@ class PipelineCurvilinearInterp(_CurvilinearGrid, MultivariateInterp): """Curvilinear Interpolator using a pipeline of sklearn models.""" - def __init__(self, values, grids, pipeline, options=None): + def __init__(self, values, grids, pipeline, options=None) -> None: """Initialize a PipelineCurvilinearInterp object. Parameters @@ -71,7 +71,7 @@ def __init__( std=False, mc_options=None, pp_options=None, - ): + ) -> None: """Initialize a _PreprocessingCurvilinearInterp object. Preprocessing options includes standardization, polynomial features, and spline features. @@ -142,7 +142,7 @@ def __init__( mc_options=None, pp_options=None, mod_options=None, - ): + ) -> None: """Initialize a GeneralizedRegressionCurvilinearInterp object. The model determines the regression used for each dimension. diff --git a/src/multinterp/curvilinear/_warped.py b/src/multinterp/curvilinear/_warped.py index aa65527..af30814 100644 --- a/src/multinterp/curvilinear/_warped.py +++ b/src/multinterp/curvilinear/_warped.py @@ -111,7 +111,7 @@ def _backend_numba(self, args, axis): """ return nb_interp_piecewise(args, self.grids, self.values, axis) - def warmup(self): + def warmup(self) -> None: """Warms up the JIT compiler.""" self(*self.grids) @@ -133,11 +133,11 @@ class Curvilinear2DInterp(_CurvilinearGrid): """ - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: super().__init__(values, grids, backend=backend) self.update_polarity() - def update_polarity(self): + def update_polarity(self) -> None: """Fills in the polarity attribute of the interpolation, determining whether the "plus" (True) or "minus" (False) solution of the system of equations should be used for each sector. Needs to be called in __init__. diff --git a/src/multinterp/grids.py b/src/multinterp/grids.py index 232b04e..00cc9d5 100644 --- a/src/multinterp/grids.py +++ b/src/multinterp/grids.py @@ -4,7 +4,7 @@ class _AbstractGrid: - def __init__(self, values, backend="scipy"): + def __init__(self, values, backend="scipy") -> None: """Initialize a regular grid interpolator. Parameters @@ -35,7 +35,7 @@ def __init__(self, values, backend="scipy"): class _StructuredGrid(_AbstractGrid): """Abstract class for interpolating on a structured grid. Serves as a base class for regular and abstract unstructured grid interpolators.""" - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: super().__init__(values, backend=backend) self.grids = aslist(grids, backend=backend) @@ -47,7 +47,7 @@ class _RegularGrid(_StructuredGrid): Takes in arguments to be used by `map_coordinates`. """ - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: """Initialize a multivariate interpolator. Parameters @@ -75,7 +75,7 @@ def __init__(self, values, grids, backend="scipy"): class _CurvilinearGrid(_AbstractGrid): """Abstract class for interpolating on a curvilinear grid.""" - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: """Initialize a curvilinear grid interpolator. Parameters @@ -102,7 +102,7 @@ def __init__(self, values, grids, backend="scipy"): class _UnstructuredGrid(_StructuredGrid): """Abstract class for interpolation on unstructured grids.""" - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: """Initialize interpolation on unstructured grids. Parameters @@ -125,7 +125,7 @@ def __init__(self, values, grids, backend="scipy"): class _MultivaluedGrid(_AbstractGrid): - def __init__(self, values, backend="scipy"): + def __init__(self, values, backend="scipy") -> None: """Initialize a regular grid interpolator. Parameters @@ -159,7 +159,7 @@ class _MultivaluedRegularGrid(_MultivaluedGrid): Takes in arguments to be used by `map_coordinates`. """ - def __init__(self, values, grids, backend="scipy"): + def __init__(self, values, grids, backend="scipy") -> None: """Initialize a multivariate interpolator. Parameters diff --git a/src/multinterp/rectilinear/_multi.py b/src/multinterp/rectilinear/_multi.py index daa4f98..6344762 100644 --- a/src/multinterp/rectilinear/_multi.py +++ b/src/multinterp/rectilinear/_multi.py @@ -13,7 +13,7 @@ class MultivariateInterp(_RegularGrid): to index coordinates and uses `map_coordinates` from scipy, cupy, or jax. """ - def __init__(self, values, grids, backend="scipy", options=None): + def __init__(self, values, grids, backend="scipy", options=None) -> None: """Initialize a multivariate interpolator. Parameters @@ -31,7 +31,7 @@ def __init__(self, values, grids, backend="scipy", options=None): self.mc_kwargs = update_mc_kwargs(options, jax=self.backend == "jax") self._gradient = {} - def compile(self): + def compile(self) -> None: self(*self.grids) def __call__(self, *args): @@ -154,7 +154,7 @@ class MultivaluedInterp(_MultivaluedRegularGrid): to index coordinates and uses `map_coordinates` from scipy, cupy, or jax. """ - def __init__(self, values, grids, backend="scipy", options=None): + def __init__(self, values, grids, backend="scipy", options=None) -> None: """Initialize a multivariate interpolator. Parameters @@ -172,7 +172,7 @@ def __init__(self, values, grids, backend="scipy", options=None): self.mc_kwargs = update_mc_kwargs(options) self._gradient = {} - def compile(self): + def compile(self) -> None: self(*self.grids) def __call__(self, *args): diff --git a/src/multinterp/unstructured/__init__.py b/src/multinterp/unstructured/__init__.py index d14853e..8058acf 100644 --- a/src/multinterp/unstructured/__init__.py +++ b/src/multinterp/unstructured/__init__.py @@ -8,8 +8,8 @@ from ._scipy import UnstructuredInterp __all__ = [ - "UnstructuredInterp", + "GPRUnstructuredInterp", "PipelineUnstructuredInterp", "RegressionUnstructuredInterp", - "GPRUnstructuredInterp", + "UnstructuredInterp", ] diff --git a/src/multinterp/unstructured/_gpytorch.py b/src/multinterp/unstructured/_gpytorch.py index 6feed9b..f17f28d 100644 --- a/src/multinterp/unstructured/_gpytorch.py +++ b/src/multinterp/unstructured/_gpytorch.py @@ -24,7 +24,7 @@ def __init__( train_x: torch.Tensor, train_y: torch.Tensor, likelihood, - ): + ) -> None: """Initialize the GP model. Args: @@ -66,7 +66,7 @@ def __init__( mean_module=None, covar_module=None, distribution=None, - ): + ) -> None: """Initialize the GP model. Args: @@ -112,15 +112,15 @@ def __init__( distribution=None, n_devices=DEVICE_COUNT, output_device=None, - ): + ) -> None: super().__init__(train_x, train_y, likelihood) self.mean_module = mean_module or ConstantMean() base_covar_module = covar_module or ScaleKernel(RBFKernel()) self.distribution = distribution or MultivariateNormal - assert ( - 0 < n_devices <= DEVICE_COUNT - ), f"n_devices must be between 1 and {DEVICE_COUNT}" + assert 0 < n_devices <= DEVICE_COUNT, ( + f"n_devices must be between 1 and {DEVICE_COUNT}" + ) if n_devices == 1: self.covar_module = base_covar_module @@ -138,7 +138,7 @@ def forward(self, x): class GaussianProcessRegression(_UnstructuredGrid): - def __init__(self, values, grids): + def __init__(self, values, grids) -> None: super().__init__(values, grids, backend="torch") self.grids = self.grids.T @@ -154,13 +154,13 @@ def __init__(self, values, grids): self._to_cuda() self._train() - def _to_cuda(self): + def _to_cuda(self) -> None: self.grids = self.grids.cuda() self.values = self.values.cuda() self._model = self._model.cuda() self._likelihood = self._likelihood.cuda() - def _train(self, training_iter=50, preconditioner_size=100): + def _train(self, training_iter=50, preconditioner_size=100) -> None: # noqa: ARG002 _train_lbfgs( self._model, self._likelihood, @@ -194,7 +194,7 @@ def _train_simple( training_iter=50, verbose=False, n_skip=10, -): +) -> None: # Find optimal model hyperparameters model.train() likelihood.train() @@ -219,10 +219,6 @@ def _train_simple( _loss = loss.item() _lengthscale = model.covar_module.module.base_kernel.lengthscale.item() _noise = model.likelihood.noise.item() - print( - f"""Iter {i+1}/{training_iter} - Loss: {_loss:.3f} - lengthscale: {_lengthscale:.3f} noise: {_noise:.3f}""", - ) optimizer.step() @@ -246,7 +242,7 @@ def _train_lbfgs( training_iter=50, verbose=False, n_skip=10, -): +) -> None: model.train() likelihood.train() @@ -273,13 +269,10 @@ def closure(): _loss = loss.item() _lengthscale = model.covar_module.module.base_kernel.lengthscale.item() _noise = model.likelihood.noise.item() - print( - f"Iter {i+1}/{training_iter} - Loss: {loss:.3f} lengthscale: {_lengthscale:.3f} noise: {_noise:.3f}", - ) if fail: if verbose: - print("Convergence reached!") + pass break @@ -293,7 +286,7 @@ def _train_pipeline( training_iter=50, verbose=False, n_skip=10, -): +) -> None: # Find optimal model hyperparameters model.train() likelihood.train() @@ -311,8 +304,5 @@ def _train_pipeline( _loss = loss.item() _lengthscale = model.covar_module.module.base_kernel.lengthscale.item() _noise = model.likelihood.noise.item() - print( - f"Iter {i+1}/{training_iter} - Loss: {_loss:.3f} lengthscale: {_lengthscale:.3f} noise: {_noise:.3f}", - ) optimizer.step() diff --git a/src/multinterp/unstructured/_scikit_learn.py b/src/multinterp/unstructured/_scikit_learn.py index 3dbf93a..c1c52fc 100644 --- a/src/multinterp/unstructured/_scikit_learn.py +++ b/src/multinterp/unstructured/_scikit_learn.py @@ -18,7 +18,7 @@ class PipelineUnstructuredInterp(_UnstructuredGrid): """Unstructured Interpolator using a pipeline of sklearn models.""" - def __init__(self, values, grids, pipeline): + def __init__(self, values, grids, pipeline) -> None: """Initialize a PipelineUnstructuredInterp object. Parameters @@ -62,7 +62,7 @@ def __init__( pipeline, std=False, options=None, - ): + ) -> None: """Initialize a _PreprocessingUnstructuredInterp object. Preprocessing options includes standardization, polynomial features, and spline features. @@ -127,7 +127,7 @@ def __init__( std=False, pp_options=None, mod_options=None, - ): + ) -> None: """Initialize a GeneralizedRegressionUnstructuredInterp object. The model determines the regression used. @@ -175,7 +175,7 @@ def __init__( class GPRUnstructuredInterp(_PreprocessingUnstructuredInterp): - def __init__(self, values, grids, pp_options, mod_options): + def __init__(self, values, grids, pp_options, mod_options) -> None: self.model = "gaussian-process" self.mod_options = mod_options diff --git a/src/multinterp/unstructured/_scipy.py b/src/multinterp/unstructured/_scipy.py index 78c9010..9437a82 100644 --- a/src/multinterp/unstructured/_scipy.py +++ b/src/multinterp/unstructured/_scipy.py @@ -44,7 +44,7 @@ def __init__( grids, method="linear", options=None, - ): + ) -> None: """Initialize an Unstructured Grid Interpolator. Parameters diff --git a/tests/test_backend.py b/tests/test_backend.py index 16a7035..da9ef7c 100644 --- a/tests/test_backend.py +++ b/tests/test_backend.py @@ -21,13 +21,13 @@ def f_3d(x, y, z): return 2 * x**3 + 3 * y**2 - z -@pytest.fixture() +@pytest.fixture def setup_data_2d(): - """ - Fixture to set up 2D test data for interpolation. + """Fixture to set up 2D test data for interpolation. Returns: tuple: grids, values, args, true_values + """ grids = [np.linspace(0, 3, 8), np.linspace(0, 3, 11)] values = f_2d(*np.meshgrid(*grids, indexing="ij")) @@ -40,48 +40,48 @@ def setup_data_2d(): return grids, values, args, true_values -def test_scipy_2d(setup_data_2d): +def test_scipy_2d(setup_data_2d) -> None: """Test scipy backend for 2D interpolation.""" grids, values, args, true_values = setup_data_2d result_multinterp = scipy_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_numba_2d(setup_data_2d): +def test_numba_2d(setup_data_2d) -> None: """Test numba backend for 2D interpolation.""" grids, values, args, true_values = setup_data_2d result_multinterp = numba_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_cupy_2d(setup_data_2d): +def test_cupy_2d(setup_data_2d) -> None: """Test cupy backend for 2D interpolation.""" grids, values, args, true_values = setup_data_2d result_multinterp = cupy_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_jax_2d(setup_data_2d): +def test_jax_2d(setup_data_2d) -> None: """Test jax backend for 2D interpolation.""" grids, values, args, true_values = setup_data_2d result_multinterp = jax_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_torch_2d(setup_data_2d): +def test_torch_2d(setup_data_2d) -> None: """Test torch backend for 2D interpolation.""" grids, values, args, true_values = setup_data_2d result_multinterp = torch_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp.cpu(), atol=1e-05) -@pytest.fixture() +@pytest.fixture def setup_data_3d(): - """ - Fixture to set up 3D test data for interpolation. + """Fixture to set up 3D test data for interpolation. Returns: tuple: grids, values, args, true_values + """ x = np.linspace(1, 4, 11) y = np.linspace(4, 7, 22) @@ -104,35 +104,35 @@ def setup_data_3d(): return grids, values, args, true_values -def test_scipy_3d(setup_data_3d): +def test_scipy_3d(setup_data_3d) -> None: """Test scipy backend for 3D interpolation.""" grids, values, args, true_values = setup_data_3d result_multinterp = scipy_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_numba_3d(setup_data_3d): +def test_numba_3d(setup_data_3d) -> None: """Test numba backend for 3D interpolation.""" grids, values, args, true_values = setup_data_3d result_multinterp = numba_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_cupy_3d(setup_data_3d): +def test_cupy_3d(setup_data_3d) -> None: """Test cupy backend for 3D interpolation.""" grids, values, args, true_values = setup_data_3d result_multinterp = cupy_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_jax_3d(setup_data_3d): +def test_jax_3d(setup_data_3d) -> None: """Test jax backend for 3D interpolation.""" grids, values, args, true_values = setup_data_3d result_multinterp = jax_multinterp(grids, values, args) assert np.allclose(true_values, result_multinterp, atol=1e-05) -def test_torch_3d(setup_data_3d): +def test_torch_3d(setup_data_3d) -> None: """Test torch backend for 3D interpolation.""" grids, values, args, true_values = setup_data_3d result_multinterp = torch_multinterp(grids, values, args) diff --git a/tests/test_package.py b/tests/test_package.py index c9e5232..649ec2d 100644 --- a/tests/test_package.py +++ b/tests/test_package.py @@ -5,6 +5,5 @@ import multinterp as m -def test_version(): - """Verify that the package version matches the metadata version.""" +def test_version() -> None: assert importlib.metadata.version("multinterp") == m.__version__ diff --git a/tests/test_regression.py b/tests/test_regression.py index 6deada4..f3e5cfd 100644 --- a/tests/test_regression.py +++ b/tests/test_regression.py @@ -7,27 +7,27 @@ def sum_first_axis(*args): - """ - Sum the first axis of meshgrid arrays. + """Sum the first axis of meshgrid arrays. Args: *args: Input arrays for meshgrid. Returns: numpy.ndarray: Sum of meshgrid arrays along the first axis. + """ mats = np.meshgrid(*args, indexing="ij") return np.sum(mats, axis=0) -@pytest.fixture() +@pytest.fixture def setup_data(): - """ - Fixture to set up test data for regression interpolation. + """Fixture to set up test data for regression interpolation. Returns: tuple: grids, args + """ # create test data @@ -46,9 +46,8 @@ def setup_data(): return grids, args -def test_interpolation_values(setup_data): - """ - Test regression interpolation values for 2D and 3D cases. +def test_interpolation_values(setup_data) -> None: + """Test regression interpolation values for 2D and 3D cases. Compares interpolated values with expected values using RegressionUnstructuredInterp. diff --git a/tests/test_regular.py b/tests/test_regular.py index 2fa031e..3a9e1cf 100644 --- a/tests/test_regular.py +++ b/tests/test_regular.py @@ -7,27 +7,27 @@ def sum_first_axis(*args): - """ - Sum the first axis of meshgrid arrays. + """Sum the first axis of meshgrid arrays. Args: *args: Input arrays for meshgrid. Returns: numpy.ndarray: Sum of meshgrid arrays along the first axis. + """ mats = np.meshgrid(*args, indexing="ij") return np.sum(mats, axis=0) -@pytest.fixture() +@pytest.fixture def setup_data(): - """ - Fixture to set up test data for regular interpolation. + """Fixture to set up test data for regular interpolation. Returns: tuple: grids, args + """ # create test data grids = [ @@ -45,9 +45,8 @@ def setup_data(): return grids, args -def test_interpolation_values(setup_data): - """ - Test regular interpolation values for 2D and 3D cases. +def test_interpolation_values(setup_data) -> None: + """Test regular interpolation values for 2D and 3D cases. Compares interpolated values with expected values using MultivariateInterp with scipy and numba backends. diff --git a/tests/test_unstructured.py b/tests/test_unstructured.py index 82e66f9..6493b3a 100644 --- a/tests/test_unstructured.py +++ b/tests/test_unstructured.py @@ -7,27 +7,27 @@ def sum_first_axis(*args): - """ - Sum the first axis of meshgrid arrays. + """Sum the first axis of meshgrid arrays. Args: *args: Input arrays for meshgrid. Returns: numpy.ndarray: Sum of meshgrid arrays along the first axis. + """ mats = np.meshgrid(*args, indexing="ij") return np.sum(mats, axis=0) -@pytest.fixture() +@pytest.fixture def setup_data(): - """ - Fixture to set up test data for unstructured interpolation. + """Fixture to set up test data for unstructured interpolation. Returns: tuple: grids, args + """ # create test data grids = [ @@ -45,9 +45,8 @@ def setup_data(): return grids, args -def test_interpolation_values(setup_data): - """ - Test unstructured interpolation values for 2D and 3D cases. +def test_interpolation_values(setup_data) -> None: + """Test unstructured interpolation values for 2D and 3D cases. 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