openlifu 0.1.0__tar.gz

openlifu-0.1.0/.dvc/.gitignore

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+/config.local
+/tmp
+/cache

openlifu-0.1.0/.dvc/config

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+[core]
+    remote = shared_gdrive
+    autostage = true
+['remote "shared_gdrive"']
+    url = gdrive://1rGAzqdikeTUzUQADjdP7-fTPdfF15eaO
+    gdrive_acknowledge_abuse = true
+    gdrive_client_id = 78626142150-1ikhqfnmr5p1aa63ji5opa7gveeksn90.apps.googleusercontent.com

openlifu-0.1.0/.dvcignore

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+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore

openlifu-0.1.0/.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

openlifu-0.1.0/.gitattributes

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+.git_archival.txt  export-subst

openlifu-0.1.0/.github/CONTRIBUTING.md

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+See the [Scientific Python Developer Guide][spc-dev-intro] for a detailed
+description of best practices for developing scientific packages.
+
+[spc-dev-intro]: https://learn.scientific-python.org/development/
+
+# Commit and pull request expectations
+
+- Every commit should reference the issue number with which it is associated.
+- Commits should be reasonably granular and semantically atomic.
+- Pull requests should not be squashed upon merging.
+
+# 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`.
+
+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
+specific jobs:
+
+```console
+$ nox -s lint  # Lint only
+$ nox -s tests  # Python tests
+$ nox -s docs -- --serve  # Build and serve the docs
+$ nox -s build  # Make an SDist and wheel
+```
+
+Nox handles everything for you, including setting up an temporary virtual
+environment for each run.
+
+# Setting up a development environment manually
+
+You can set up a development environment by running:
+
+```bash
+python3 -m venv .venv
+source ./.venv/bin/activate
+pip install -v -e '.[dev]'
+```
+
+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
+
+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
+pre-commit install # Will install a pre-commit hook into the git repo
+```
+
+You can also/alternatively run `pre-commit run` (changes only) or
+`pre-commit run --all-files` to check even without installing the hook.
+
+# Testing
+
+Use pytest to run the unit checks:
+
+```bash
+pytest
+```
+
+# Coverage
+
+Use pytest-cov to generate coverage reports:
+
+```bash
+pytest --cov=openlifu
+```
+
+# Building docs
+
+You can build 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:
+
+```bash
+pre-commit run -a
+```
+
+to check all files.

openlifu-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+
+  # Maintain dependencies for Python
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

openlifu-0.1.0/.github/matchers/pylint.json

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+{
+  "problemMatcher": [
+    {
+      "severity": "warning",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): ([A-DF-Z]\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-warning"
+    },
+    {
+      "severity": "error",
+      "pattern": [
+        {
+          "regexp": "^([^:]+):(\\d+):(\\d+): (E\\d+): \\033\\[[\\d;]+m([^\\033]+).*$",
+          "file": 1,
+          "line": 2,
+          "column": 3,
+          "code": 4,
+          "message": 5
+        }
+      ],
+      "owner": "pylint-error"
+    }
+  ]
+}

openlifu-0.1.0/.github/workflows/cd.yml

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+name: CD
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  dist:
+    name: Distribution build
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: hynek/build-and-inspect-python-package@v2
+
+  publish:
+    needs: [dist]
+    name: Publish to PyPI
+    environment: pypi
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event_name == 'release' && github.event.action == 'published'

openlifu-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - 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
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.12"]
+        runs-on: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install system dependencies
+        if: runner.os == 'macOS'
+        run: brew install hdf5 fftw zlib libomp
+
+      - name: Install package
+        run: python -m pip install .[test]
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20
+
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v5.4.0
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

openlifu-0.1.0/.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/
+docs/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+*.ipynb
+
+# 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
+
+# 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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# setuptools_scm
+src/*/_version.py
+
+
+# ruff
+.ruff_cache/
+
+# OS specific stuff
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Common editor files
+*~
+*.swp
+.vscode
+/db_dvc

openlifu-0.1.0/.pre-commit-config.yaml

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+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+        exclude: ^tests/helpers\.py$
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    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: "v0.4.1"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      # - id: ruff-format # Omitting ruff-format for now
+
+  # Disabling static typechecking for now!
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: "v1.9.0"
+  #   hooks:
+  #     - id: mypy
+  #       files: src|tests
+  #       args: []
+  #       additional_dependencies:
+  #         - pytest
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.2.6"
+    hooks:
+      - id: codespell
+        exclude: .*\.ipynb # exclude notebooks because images are sometimes captured in spell check
+
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+        exclude: .pre-commit-config.yaml
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.16"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.28.2"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs

openlifu-0.1.0/.readthedocs.yaml

@@ -0,0 +1,18 @@
+# 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: "3.9"
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs