diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..d668511 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,113 @@ +name: CI + +on: + push: + branches: [main] + pull_request: + branches: [main] + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +env: + FORCE_COLOR: "1" + +jobs: + lint: + name: Lint + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + + - name: Set up Python + run: uv python install 3.13 + + - name: Install dependencies + run: make install + + - name: Lint and format check + run: make lint format-check + + type-check: + name: Type Check + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + + - name: Set up Python + run: uv python install 3.13 + + - name: Install dependencies + run: make install + + - name: Run ty type checker + run: make type-check + + test: + name: Test (Python ${{ matrix.python-version }}) + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ["3.10", "3.11", "3.12", "3.13"] + + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + + - name: Set up Python ${{ matrix.python-version }} + run: uv python install ${{ matrix.python-version }} + + - name: Install dependencies + run: make install + + - name: Run tests with coverage + run: make test-cov + + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v4 + with: + token: ${{ secrets.CODECOV_TOKEN }} + files: ./coverage.xml + fail_ci_if_error: false + + dependency_scan: + name: Dependency Scan + runs-on: ubuntu-latest + steps: + - name: Checkout repository + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: astral-sh/setup-uv@v5 + - uses: dtolnay/rust-toolchain@stable + - run: make install + - run: make pysentry + + sast_with_semgrep: + name: semgrep scan + runs-on: ubuntu-latest + container: + image: semgrep/semgrep + + # Skip any PRs created by dependabot or renovate to avoid permission issues: + if: ${{ github.actor != 'dependabot[bot]' && github.actor != 'dependabot-preview[bot]' && github.actor != 'Renovate[bot]' }} + + steps: + - uses: actions/checkout@v4 + - run: semgrep scan diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 0000000..95cd533 --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,57 @@ + +name: Documentation + +on: + push: + branches: [main] + workflow_dispatch: + +permissions: + contents: read + pages: write + id-token: write + +concurrency: + group: "pages" + cancel-in-progress: true + +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + + - name: Set up Python + run: uv python install 3.13 + + - name: Install dependencies + run: make install + + - name: Build documentation + run: make docs + + - name: Setup Pages + uses: actions/configure-pages@v4 + + - name: Upload artifact + uses: actions/upload-pages-artifact@v3 + with: + path: site + + deploy: + environment: + name: github-pages + url: ${{ steps.deployment.outputs.page_url }} + runs-on: ubuntu-latest + needs: build + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..95c1ed1 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,86 @@ + +name: Release + +on: + push: + tags: + - "v*" + +permissions: + contents: write + id-token: write + +jobs: + build: + name: Build distribution + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + + - name: Set up Python + run: uv python install 3.13 + + - name: Build package + run: uv build + + - name: Store distribution packages + uses: actions/upload-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + publish-pypi: + name: Publish to PyPI + needs: [build] + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/pxr_reduce + steps: + - name: Download distributions + uses: actions/download-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + - name: Publish to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + + github-release: + name: Create GitHub Release + needs: [publish-pypi] + runs-on: ubuntu-latest + steps: + - name: Check out repository + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Download distributions + uses: actions/download-artifact@v4 + with: + name: python-package-distributions + path: dist/ + + - name: Generate a changelog + uses: orhun/git-cliff-action@v4 + with: + config: cliff.toml + args: --verbose + env: + OUTPUT: RELEASE_NOTES.md + GITHUB_REPO: ${{ github.repository }} + + - name: Create GitHub Release + uses: softprops/action-gh-release@v2 + with: + body_path: RELEASE_NOTES.md + files: dist/* + generate_release_notes: false diff --git a/.gitignore b/.gitignore index b7faf40..639662e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ # Byte-compiled / optimized / DLL files __pycache__/ -*.py[codz] +*.py[cod] *$py.class # C extensions @@ -27,8 +27,6 @@ share/python-wheels/ 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 @@ -46,10 +44,9 @@ htmlcov/ nosetests.xml coverage.xml *.cover -*.py.cover +*.py,cover .hypothesis/ .pytest_cache/ -cover/ # Translations *.mo @@ -83,48 +80,12 @@ 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 +.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 -#poetry.toml - -# pdm -# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. -# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. -# https://pdm-project.org/en/latest/usage/project/#working-with-version-control -#pdm.lock -#pdm.toml -.pdm-python -.pdm-build/ - -# pixi -# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. -#pixi.lock -# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one -# in the .venv directory. It is recommended not to include this directory in version control. -.pixi - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +Pipfile.lock + +# PEP 582 __pypackages__/ # Celery stuff @@ -136,7 +97,6 @@ celerybeat.pid # Environments .env -.envrc .venv env/ venv/ @@ -162,46 +122,27 @@ 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/ - -# Abstra -# Abstra is an AI-powered process automation framework. -# Ignore directories containing user credentials, local state, and settings. -# Learn more at https://abstra.io/docs -.abstra/ - -# Visual Studio Code -# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore -# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore -# and can be added to the global gitignore or merged into this file. However, if you prefer, -# you could uncomment the following to ignore the entire vscode folder -# .vscode/ - -# Ruff stuff: +# ruff .ruff_cache/ -# PyPI configuration file -.pypirc +# ty +.ty_cache/ + +# IDE +.idea/ +.vscode/ -# Cursor -# Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to -# exclude from AI features like autocomplete and code analysis. Recommended for sensitive data -# refer to https://docs.cursor.com/context/ignore-files -.cursorignore -.cursorindexingignore +# Cursor (local hook state) +.cursor/hooks/state/ +*.swp +*.swo +*~ -# Marimo -marimo/_static/ -marimo/_lsp/ -__marimo__/ +# OS +.DS_Store +Thumbs.db + +# Project specific +*.log +.env.* +!.env.example diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..92937be --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,33 @@ +# Prek hooks configuration +# See https://prek.j178.dev for more information + +repos: + # General hooks + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-toml + - id: check-added-large-files + - id: check-merge-conflict + - id: debug-statements + + # Ruff - Fast Python linter and formatter + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.8.4 + hooks: + - id: ruff + args: [--fix] + - id: ruff-format + + # ty - Astral's type checker (local hook since no prek repo yet) + - repo: local + hooks: + - id: ty + name: ty type checker + entry: uv run ty check + language: system + types: [python] + pass_filenames: false diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..701c964 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,17 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [Unreleased] + +### Added + +- Initial project structure +- Basic package setup with pxr_reduce +- CLI interface with Typer +- Documentation with MkDocs +- GitHub Actions CI/CD pipelines +- Prek hooks for code quality diff --git a/LICENSE b/LICENSE index d58e5a2..00934cb 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,7 @@ + MIT License -Copyright (c) 2025 ALS RSOXS +Copyright (c) 2026 Harlan D Heilman Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..4c0758a --- /dev/null +++ b/Makefile @@ -0,0 +1,55 @@ +.PHONY: verify fix lint format format-check type-check install test test-cov test-matrix test-matrix-cov pysentry docs docs-serve + +# Verify - check everything without making changes +verify: lint format-check type-check + +# Fix - automatically fix what can be fixed +fix: + uv run ruff check --fix . + uv run ruff format . + +# Individual targets +lint: + uv run ruff check . + +format-check: + uv run ruff format --check . + +format: + uv run ruff format . + +type-check: + uv run ty check + +# Install all dependencies +install: + uv sync --all-groups + +# Run tests +test: + uv run pytest tests/ -v + +# Run tests with coverage +test-cov: + uv run pytest --cov --cov-report=xml --cov-report=term-missing + +# Run tests across all Python versions +test-matrix: + uv run hatch test + +# Run tests with coverage across all Python versions +test-matrix-cov: + uv run hatch test --cover + + +# Dependency vulnerability scanning +pysentry: + uv run pysentry-rs + + +# Documentation +docs: + uv run mkdocs build + +docs-serve: + uv run mkdocs serve diff --git a/README.md b/README.md index c4284fe..89e5ce7 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,110 @@ # pxr-reduce -A collection of standalone tools for reducing polarized X-ray reflectivity collected at the RSOXS beamline at the ALS. + +[CI](https://github.com/als-rsoxs/pxr-reduce/actions/workflows/ci.yml) +[PyPI version](https://badge.fury.io/py/pxr_reduce) +[codecov](https://codecov.io/gh/als-rsoxs/pxr-reduce) +[Python 3.13+](https://www.python.org/downloads/) +[uv](https://github.com/astral-sh/uv) +[Ruff](https://github.com/astral-sh/ruff) +[ty](https://github.com/astral-sh/ty) +[License: MIT](https://github.com/als-rsoxs/pxr-reduce/blob/main/LICENSE) +[Renovate](https://renovateapp.com/) + +A collection of standalone tools for reducing pxr data from bl 11.0.1.2 at the ALS. + +## Features + +- Fast and modern Python toolchain using Astral's tools (uv, ruff, ty) +- Type-safe with full type annotations +- Command-line interface built with Typer +- Comprehensive documentation with MkDocs — [View Docs](https://als-rsoxs.github.io/pxr-reduce/) + +## Installation + +```bash +pip install pxr_reduce +``` + +Or using uv (recommended): + +```bash +uv add pxr_reduce +``` + +## Quick Start + +```python +import pxr_reduce + +print(pxr_reduce.__version__) +``` + +### CLI Usage + +```bash +# Show version +pxr_reduce --version + +# Say hello +pxr_reduce hello World +``` + +## Development + +### Prerequisites + +- Python 3.13+ +- [uv](https://docs.astral.sh/uv/) for package management + +### Setup + +```bash +git clone https://github.com/als-rsoxs/pxr-reduce.git +cd pxr-reduce +make install +``` + +### Running Tests + +```bash +make test + +# With coverage +make test-cov + +# Across all Python versions +make test-matrix +``` + +### Code Quality + +```bash +# Run all checks (lint, format, type-check) +make verify + +# Auto-fix lint and format issues +make fix +``` + +### Prek + +```bash +prek install +prek run --all-files +``` + +### Documentation + +```bash +make docs-serve +``` + +## Dependency Updates + +This project uses [Renovate](https://renovateapp.com/) to keep dependencies up to date automatically. Renovate will open pull requests when new versions of dependencies are available. + +To enable it, install the [Renovate GitHub App](https://github.com/apps/renovate) and grant it access to this repository. + +## License + +This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details. diff --git a/cliff.toml b/cliff.toml new file mode 100644 index 0000000..2ee45ce --- /dev/null +++ b/cliff.toml @@ -0,0 +1,49 @@ +# git-cliff configuration +# https://git-cliff.org/docs/configuration + +[changelog] +header = """ +# Changelog + +All notable changes to this project will be documented in this file. + +""" +body = """ +{% if version -%} +## [{{ version | trim_start_matches(pat="v") }}] - {{ timestamp | date(format="%Y-%m-%d") }} +{% else -%} +## [Unreleased] +{% endif -%} +{% for group, commits in commits | group_by(attribute="group") %} +### {{ group | striptags | trim | upper_first }} +{% for commit in commits %} +- {% if commit.scope %}**{{ commit.scope }}:** {% endif %}{{ commit.message | upper_first }}\ +{% endfor %} +{% endfor %} +""" +footer = """ + +""" +trim = true + +[git] +conventional_commits = true +filter_unconventional = true +split_commits = false +commit_parsers = [ + { message = "^feat", group = "Features" }, + { message = "^fix", group = "Bug Fixes" }, + { message = "^doc", group = "Documentation" }, + { message = "^perf", group = "Performance" }, + { message = "^refactor", group = "Refactor" }, + { message = "^style", group = "Styling" }, + { message = "^test", group = "Testing" }, + { message = "^chore\\(release\\)", skip = true }, + { message = "^chore\\(deps\\)", skip = true }, + { message = "^chore|^ci", group = "Miscellaneous Tasks" }, + { body = ".*security", group = "Security" }, +] +protect_breaking_commits = false +filter_commits = false +topo_order = false +sort_commits = "oldest" diff --git a/docs/api.md b/docs/api.md new file mode 100644 index 0000000..ae63fc2 --- /dev/null +++ b/docs/api.md @@ -0,0 +1,14 @@ +# API Reference + +::: pxr_reduce + options: + show_root_heading: true + show_source: true + members_order: source + +## CLI Module + +::: pxr_reduce.cli + options: + show_root_heading: true + show_source: true diff --git a/docs/contributing.md b/docs/contributing.md new file mode 100644 index 0000000..0bf3aeb --- /dev/null +++ b/docs/contributing.md @@ -0,0 +1,88 @@ +# Contributing to pxr-reduce + +Thank you for your interest in contributing to pxr-reduce! + +## Development Setup + +1. Fork and clone the repository: + ```bash + git clone https://github.com/als-rsoxs/pxr-reduce.git + cd pxr-reduce + ``` +2. Install dependencies using uv: + ```bash + uv sync --group dev + ``` +3. Install prek hooks: + ```bash + prek install + ``` + +## Making Changes + +1. Create a new branch for your feature or bugfix: + ```bash + git checkout -b feature/your-feature-name + ``` +2. Make your changes and ensure tests pass: + ```bash + uv run pytest + ``` +3. Ensure code quality: + ```bash + uv run ruff check . + uv run ruff format . + uv run ty check + ``` +4. Commit your changes using [conventional commits](https://www.conventionalcommits.org/): + ```bash + git commit -m "feat: add new feature" + ``` + +## Commit Message Format + +We use [Conventional Commits](https://www.conventionalcommits.org/). Here are some examples: + +- `feat: add new feature` - A new feature +- `fix: resolve bug in X` - A bug fix +- `docs: update README` - Documentation changes +- `refactor: simplify code` - Code refactoring +- `test: add tests for X` - Adding tests +- `chore: update dependencies` - Maintenance tasks + +## Pull Request Process + +1. Update documentation if needed +2. Add tests for new functionality +3. Ensure all tests pass +4. Submit a pull request with a clear description + +## Dependency Updates + +This project uses [Renovate](https://renovateapp.com/) for automated dependency updates. Renovate will automatically open pull requests when new versions are available for: + +- GitHub Actions +- Python dependencies (via `pyproject.toml`) +- `uv.lock` lockfile + +To activate it: + +1. Go to [github.com/apps/renovate](https://github.com/apps/renovate) and click **Install** +2. Choose your GitHub account or organization +3. Under **Repository access**, select this repository (or all repositories) +4. Click **Install & Authorize** +5. Renovate will open an onboarding pull request titled `Configure Renovate` — merge it to activate +6. Renovate will now open PRs automatically when new dependency versions are available + +The `renovate.json` at the root of this project is pre-configured to manage: + +- GitHub Actions workflow dependencies +- Python dependencies (via `pyproject.toml`) + +## Code Style + +- We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting +- We use [ty](https://docs.astral.sh/ty/) for type checking +- All code should be properly typed +- Write docstrings for public functions and classes + diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..eff1bc9 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,85 @@ +# pxr-reduce + +Reducing pxr data from bl 11.0.1.2 + +## Installation + +Install using pip: + +```bash +pip install pxr_reduce +``` + +Or using uv (recommended): + +```bash +uv add pxr_reduce +``` + +## Quick Start + +```python +import pxr_reduce + +print(pxr_reduce.__version__) +``` + +### Command Line Interface + +pxr-reduce provides a command-line interface: + +```bash +# Show version +pxr_reduce --version + +# Say hello +pxr_reduce hello World +``` + +## Development + +### Prerequisites + +- Python 3.13+ +- [uv](https://docs.astral.sh/uv/) for package management + +### Setup + +Clone the repository and install dependencies: + +```bash +git clone https://github.com/als-rsoxs/pxr-reduce.git +cd pxr-reduce +uv sync --group dev +``` + +### Running Tests + +```bash +uv run pytest +``` + +### Code Quality + +```bash +# Lint +uv run ruff check . + +# Format +uv run ruff format . + +# Type check +uv run ty check +``` + +### Prek Hooks + +Install prek hooks: + +```bash +prek install +``` + +## License + +This project is licensed under the MIT License - see the [LICENSE](https://github.com/als-rsoxs/pxr-reduce/blob/main/LICENSE) file for details. diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..a7f1e8b --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,63 @@ +site_name: pxr-reduce +site_description: Reducing pxr data from bl 11.0.1.2 +site_url: https://als-rsoxs.github.io/pxr-reduce +repo_url: https://github.com/als-rsoxs/pxr-reduce +repo_name: als-rsoxs/pxr-reduce +edit_uri: edit/main/docs/ + +extra: + als_group: + full_name: ALS RSOXS Group Project + acronym: REIXS + github_url: https://github.com/als-rsoxs + reixs_url: https://als.lbl.gov/science/photon-science-programs/rixs-program/ + +theme: + name: rsoxs + show_title: true + show_stargazers: true + topbar_sections: false + features: + - content.code.copy + - content.code.annotate + - navigation.instant + - navigation.tracking + - navigation.sections + - navigation.top + - search.suggest + - search.highlight + - toc.follow + +plugins: + - rsoxs + - search + - mkdocstrings: + handlers: + python: + paths: + - src + options: + show_source: true + show_root_heading: true + show_root_toc_entry: true + docstring_style: google + merge_init_into_class: true + +markdown_extensions: + - admonition + - pymdownx.details + - pymdownx.superfences + - pymdownx.highlight: + anchor_linenums: true + css_class: codehilite + - pymdownx.inlinehilite + - pymdownx.snippets + - pymdownx.tabbed: + alternate_style: true + - toc: + permalink: true + +nav: + - Home: index.md + - API Reference: api.md + - Contributing: contributing.md diff --git a/pyproject.toml b/pyproject.toml index 7f59e1a..de41a3f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,19 +1,166 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + [project] -name = "pxr-reduce" +name = "pxr_reduce" version = "0.1.0" -description = "Add your description here" +description = "Reducing pxr data from bl 11.0.1.2" readme = "README.md" +license = "MIT" requires-python = ">=3.13" +authors = [ + { name = "Thomas J Ferron", email = "186758855+tjferron@users.noreply.github.com" }, + { name = "Harlan D Heilman", email = "73567020+HarlanHeilman@users.noreply.github.com" } +] +classifiers = [ + "Development Status :: 3 - Alpha", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Typing :: Typed", +] +keywords = [] dependencies = [ "astropy>=7.2.0", - "matplotlib>=3.10.8", - "numpy>=2.4.3", - "pandas>=3.0.1", + "matplotlib>=3.10.9", + "numpy>=2.4.4", + "pandas>=3.0.2", "scipy>=1.17.1", "tqdm>=4.67.3", ] [dependency-groups] dev = [ - "ruff>=0.15.5", + "pytest>=9.0.0", + "pytest-cov>=7.0.0", + "ruff>=0.14.14", + "ty>=0.0.14", + "hatch>=1.16.3", + "prek>=0.1.0", + "pysentry-rs>=0.1.0", +] +docs = [ + "mkdocs>=1.6.0", + "mkdocs-rsoxs>=0.1.2", + "mkdocstrings-python>=2.0.1", + "pymdown-extensions>=10.0.0", +] + +[project.urls] +Homepage = "https://github.com/als-rsoxs/pxr-reduce" +Documentation = "https://als-rsoxs.github.io/pxr-reduce" +Repository = "https://github.com/als-rsoxs/pxr-reduce" +Issues = "https://github.com/als-rsoxs/pxr-reduce/issues" +Changelog = "https://github.com/als-rsoxs/pxr-reduce/blob/main/CHANGELOG.md" + +[project.scripts] +pxr_reduce = "pxr_reduce.cli:app" + +# ============================================================================= +# Hatch +# ============================================================================= + +[tool.hatch.build.targets.sdist] +include = [ + "/src", +] + +[tool.hatch.build.targets.wheel] +packages = ["src/pxr_reduce"] + +# Matrix testing across Python versions +[tool.hatch.envs.test] + +[[tool.hatch.envs.test.matrix]] +python = ["3.10", "3.11", "3.12", "3.13"] + +# ============================================================================= +# Ruff +# ============================================================================= + +[tool.ruff] +target-version = "py313" +line-length = 88 +src = ["src", "tests"] + +[tool.ruff.lint] +ignore = ["ERA001"] # Ignore "eradicate" errors (e.g., unused imports) +select = [ + "E", # pycodestyle errors + "W", # pycodestyle warnings + "F", # Pyflakes + "I", # isort + "B", # flake8-bugbear + "C4", # flake8-comprehensions + "UP", # pyupgrade + "ARG", # flake8-unused-arguments + "SIM", # flake8-simplify + "TCH", # flake8-type-checking + "PTH", # flake8-use-pathlib + "ERA", # eradicate + "RUF", # Ruff-specific rules +] + +[tool.ruff.lint.isort] +known-first-party = ["pxr_reduce"] + +[tool.ruff.lint.per-file-ignores] +"tests/**/*.py" = ["ARG001"] + +# ============================================================================= +# ty (Astral type checker) +# ============================================================================= + +[tool.ty.src] +include = ["**/*.py"] + +# ============================================================================= +# Pytest +# ============================================================================= + +[tool.pytest.ini_options] +testpaths = ["tests"] +pythonpath = ["src"] +addopts = [ + "-ra", + "-q", + "--strict-markers", + "--strict-config", ] +markers = [ + "slow: marks tests as slow (deselect with '-m \"not slow\"')", +] + +# ============================================================================= +# Coverage +# ============================================================================= + +[tool.coverage.run] +source = ["src/pxr_reduce"] +branch = true +parallel = true + +[tool.coverage.report] +exclude_lines = [ + "pragma: no cover", + "def __repr__", + "raise AssertionError", + "raise NotImplementedError", + "if __name__ == .__main__.:", + "if TYPE_CHECKING:", + "@abstractmethod", +] +show_missing = true + +# ============================================================================= +# git-cliff (Changelog generation) +# ============================================================================= + +[tool.git-cliff] +config = "cliff.toml" diff --git a/renovate.json b/renovate.json new file mode 100644 index 0000000..fe22c84 --- /dev/null +++ b/renovate.json @@ -0,0 +1,8 @@ +{ + "$schema": "https://docs.renovatebot.com/renovate-schema.json", + "extends": [ + "config:recommended" + ], + "enabledManagers": ["github-actions", "pep621" + ] +} diff --git a/src/pxr_reduce/__init__.py b/src/pxr_reduce/__init__.py index 3dffc22..4ff463e 100644 --- a/src/pxr_reduce/__init__.py +++ b/src/pxr_reduce/__init__.py @@ -1,4 +1,12 @@ -""" """ +""" +Reducing pxr data from bl 11.0.1.2 + +This package provides a loader for PRSoXR data from beamline 11.0.1.2 taken with the +area detector camera. +""" + +from pxr_reduce.loader import PrsoxrLoader __author__ = "Thomas Ferron" __email__ = "tjferron@lbl.gov" +__all__ = ["PrsoxrLoader"] diff --git a/src/pxr_reduce/loader.py b/src/pxr_reduce/loader.py index f8a70a4..e9a6a74 100644 --- a/src/pxr_reduce/loader.py +++ b/src/pxr_reduce/loader.py @@ -1,28 +1,33 @@ +"""Loader for PRSoXR data from beamline 11.0.1.2 taken with the CCD camera.""" + # Basic modules -import warnings -import copy -import re import pathlib +import re +import warnings +from collections.abc import Iterable, Mapping +from pathlib import Path +from typing import Any, ClassVar, Final + +import matplotlib.colors as mpl_colors + +# Plotting libraries +import matplotlib.pyplot as plt # Math libraries import numpy as np import pandas as pd -from scipy.odr import ODR, Model, RealData # For finding stitch ratio -from scipy.ndimage import median_filter # Image libraries from astropy.io import fits # To load .fits files - -# Plotting libraries -import matplotlib.pyplot as plt -import matplotlib.colors as mpl_colors +from scipy.ndimage import median_filter +from scipy.odr import ODR, Model, RealData # For finding stitch ratio # Other libraries from tqdm.auto import tqdm -tqdm.pandas() +from pxr_reduce.utils import attributes, image, name, units -from pxr_reduce.utils import attributes, image, units, name, file_sort +tqdm.pandas() default_cmap = "terrain" @@ -60,6 +65,36 @@ stitch_motors = ["sam_th"] +_DEFAULT_PROCESS_VARS: Final[dict[str, Any]] = { + "exposure_offset": 0.00389278, # [s] + "energy_resolution": 20, # 0.05eV step resolution + "sam_th_offset": None, # [deg] + "sam_th_correction": True, + "energy_offset": 0, # [eV] + "det_pixel_size": 0.027, # [mm/pixel] + "roi_height": 10, # [pixels] + "roi_width": 10, # [pixels] + "trim_x": 10, # [pixels] + "trim_y": 10, # [pixels], + "stitch_cutoff": 1.003, # [ratio] + "drop_failed_stitch": True, + "stitch_mark_tol": 1e-5, # [unitless] + "dark_pix_offset": 20, # [pixels] + "new_scan_marker": 15, # [deg] # Way to indicate a new sample by th-motion + "drift_distance": 25, # [pixels] # Distance that the beam can drift from + # the nominal positions + "mask_threshold": 800, # [counts] # Counts that indicate an easy spot for mask + "filter_size": 3, + "darkside": "LHS", + "reprocess_vars": True, + "saturate_threshold": 2, +} + + +def _new_process_vars(**overrides: Any) -> dict[str, Any]: + """Fresh dict for ``instance.process_vars``.""" + return {**_DEFAULT_PROCESS_VARS, **overrides} + @attributes.process_vars_properties class PrsoxrLoader: @@ -91,8 +126,8 @@ class PrsoxrLoader: Attributes ----------- exposure_offset: float [s] - Offset to add to camera exposure time. Time it takes to physically open and close shutter. - This should be measured in advanced and not changed often. + Offset to add to camera exposure time. Time it takes to physically open and + close shutter. This should be measured in advanced and not changed often. energy_resoltion: float Energy will be normalized based on the following equation: np.round(self.data['energy']*energy_resolution)/energy_resolution @@ -100,7 +135,8 @@ class PrsoxrLoader: sam_th_offset: float [th] Offset added to sam_th at the time of measurement default is None sam_th_correction: Bool - Default is True. It will determine the sam_th_offset based on the initial measurement positions + Default is True. It will determine the sam_th_offset based on the initial + measurement positions energy_offset: float [eV] Optional offset to the energy value. Defaults at 0 det_pixel_size: float [mm/pixel] @@ -112,7 +148,8 @@ class PrsoxrLoader: trim_x: int Number of pixels on the edge of the detector to remove fromm consideration trim_y: int - Number of pixels on the edge of the detector (vertical) to remove from considerations + Number of pixels on the edge of the detector (vertical) to remove from + considerations stitch_cutoff: float ['ratio'] Used to identify positions at which a 'stitch' has occured between the data. drop_failed_stitch: bool @@ -121,9 +158,11 @@ class PrsoxrLoader: stitch_mark_tol: float Value used to verify whether or not a tracked motor for stitching has moved dark_pix_offset: int [pixels] - Number of pixels to offset the region used for dark subtraction from the edge of the frame + Number of pixels to offset the region used for dark subtraction from the edge of + the frame new_scan_marker: float [deg] - How far the 'sam_th' motor needs to move in order to indicate a new 'scan' starting from 0 + How far the 'sam_th' motor needs to move in order to indicate a new 'scan' + starting from 0 drift_distance: int [pixels] Distance that the beam can drift from its nominal positions mask_threshold: int [counts] @@ -140,7 +179,8 @@ class PrsoxrLoader: Notes ------ - Print the loader to view variables that will be used in reduction. Update them using the attributes listed in this API. + Print the loader to view variables that will be used in reduction. Update them using + the attributes listed in this API. >>> loader = PrsoxrLoader(files, name='MF114A_spol') >>> print(loader) #Default values @@ -167,7 +207,8 @@ class PrsoxrLoader: mask : np.ndarray (Boolean) - Array with dimensions equal to an image. Elements set to `False` will be excluded when finding beamcenter. + Array with dimensions equal to an image. Elements set to `False` will be + excluded when finding beamcenter. >>> # Recommended usage >>> loader = loader = PrsoxrLoader(files) @@ -176,71 +217,50 @@ class PrsoxrLoader: >>> loader.mask = mask >>> - Once process attributes have been setup by the user, the function can be called to load the data. An ROI will need - to be specified at the time of processing. Use the ``self.check_spot()`` function to find appropriate dimensions. + Once process attributes have been setup by the user, the function can be called to + load the data. An ROI will need + to be specified at the time of processing. Use the ``self.check_spot()`` function + to find appropriate dimensions. >>> refl = loader(h=40, w=30) - Data that has been loaded can be exported using the ``self.save_csv(path)`` and ``self.save_hdf5(path)`` functions. + Data that has been loaded can be exported using the ``self.save_csv(path)`` and + ``self.save_hdf5(path)`` functions. """ - process_vars = { - "exposure_offset": 0.00389278, # [s] - "energy_resolution": 20, # 0.05eV step resolution - "sam_th_offset": None, # [deg] - "sam_th_correction": True, - "energy_offset": 0, # [eV] - "det_pixel_size": 0.027, # [mm/pixel] - "roi_height": 10, # [pixels] - "roi_width": 10, # [pixels] - "trim_x": 10, # [pixels] - "trim_y": 10, # [pixels], - "stitch_cutoff": 1.003, # [ratio] - "drop_failed_stitch": True, - "stitch_mark_tol": 1e-5, # [unitless] - "dark_pix_offset": 20, # [pixels] - "new_scan_marker": 15, # [deg] # Way to indicate a new sample by th-motion - "drift_distance": 25, # [pixels] # Distance that the beam can drift from the nominal positions - "mask_threshold": 800, # [counts] # Counts that indicate an easy spot for masking - "filter_size": 3, - "darkside": "LHS", - "reprocess_vars": True, - "saturate_threshold": 2, - } + process_vars_defaults: ClassVar[Mapping[str, Any]] = _DEFAULT_PROCESS_VARS def __init__( - self, files, AI_file=None, auto_load=False, energy_resolution=20, **kwargs + self, + files: Iterable[str | Path] | Path | str, + AI_file: str | Path | None = None, + *, + auto_load: bool = False, + energy_resolution=20, + **kwargs, ): # Update the process variables with any initial conditions - self.process_vars = self.process_vars.copy() - self.process_vars.update(kwargs) - - # Check type of files of input--- - self.files = [] - # Is files empty? - if len(files) == 0: - print(f"The 'files' input is empty. Nothing can be loaded.") - print(f"Check your directory for FITS files.") - return 0 - msg = f"Found samples: {len(files)}\n" - msg += f"Beginning data loading..." - print(msg) - # Is files a single list? - if isinstance(files, (str, pathlib.Path)): - print( - f"A single file is being loaded. This will not process correctly as a RSoXR experiment." - ) - path_list = [files] - elif isinstance(files, list): - path_list = files - else: - msg = "PrsoxrLoader was not given a correct input. Only paths to FITS files are currently accepted." - raise ValueError(msg) - return 0 - # Convert path_list to paths if needed - path_list = file_sort.ensure_paths(path_list) - # Verify that the files have an order associated with the name + self.process_vars = _new_process_vars(**kwargs) + if energy_resolution not in self.process_vars: + self.process_vars["energy_resolution"] = energy_resolution + + # Assert breaking behaviour on incorrect IO inputs + self.files: list[Path] = [] + match files: + case Path(): + # Check if it is a directory if so glob for .fits files + if files.is_dir(): + path_list = list(files.rglob("**/**.fits")) + else: + from warnings import warn + + warn("A single file will not process correctly", stacklevel=2) + path_list = [files] + case list(): + path_list = [Path(file) for file in files] + case _: + raise TypeError(f"Invalid files input: {files}") try: re_name = name.infer_index_regex( [path.name for path in path_list], prefix_group="re_sample_name" @@ -248,54 +268,56 @@ def __init__( msg = f"\n Naming convention successfully identified: {re_name}\n" print(msg) except ValueError as ve: - msg = f"Filenames do not appear to have a numeric index that can be inferred for ordering.\n" + msg = "Files do not conform to any known naming convention.\n" msg += f"Error details: {ve}" - raise ValueError(msg) + raise ValueError(msg) from ve for fp in path_list: - file = pathlib.Path(fp) + file: Path = Path(fp) if not file.is_file(): - msg = f"{file} is not a valid file." - raise FileNotFoundError(msg) + raise FileNotFoundError(f"{file} is not a valid file.") if file.suffix != ".fits": - msg = f"{file} is not a FITS file." - raise ValueError(msg) + raise ValueError(f"{file} is not a FITS file.") self.files.append(file) # Check AI File if isinstance(AI_file, (str, pathlib.Path)): - print(f"Loading AI-file to supplement FITS meta-data") + print("Loading AI-file to supplement FITS meta-data") AI_file = pathlib.Path(AI_file) if not AI_file.is_file(): msg = f"{AI_file} is not a valid file." raise FileNotFoundError(msg) if AI_file.suffix != ".txt": - msg = f"{AI_file} is not a txt file, it is unlikely the correct AI companion file." + msg = f"{AI_file} is not valid for provided data" raise ValueError(msg) else: - AI_file = None + # Look for a companion AI file in the parent directory of the first file + AI_file = ( + self.files[0].parent / f"{self.files[0].stem.split('-')[0]}-AI.txt" + ) + AI_file = AI_file.resolve() if AI_file.exists() else None # Load the files into the Loader tmp = [] # Get information about the sample / path from the first fits file path0 = self.files[0] self.path = path0.parent - # self.name = re.search(r'^(.*?)[ _-](\d+)\.fits$', path0.name).group('re_sample_name') - self.name = re.search(re_name, path0.name).group("re_sample_name") + m = re.search(re_name, path0.name) + self.name = m.group("re_sample_name") if m else "Unknown Sample" print("") print(f"Sample name identified as: {self.name}") print("") - for i, fits in tqdm( - enumerate(self.files), "Loading .fits", total=len(self.files) - ): + for file in tqdm(self.files, "Loading .fits", total=len(self.files)): # Collect information about the filepath to save -- - fits_name = fits.name # The name of the current file - # fits_index = int(re.search(r'[ _-](\d+)\.fits$', fits_name).group(1)) # Index of the file (if it gets messed up for some reason) + fits_name = file.name # The name of the current file + # fits_index = int(re.search(r'[ _-](\d+)\.fits$', fits_name).group(1)) + # Index of the file (if it gets messed up for some reason) # fits_index = extract_index(fits_name) - fits_index = int(re.search(re_name, fits_name).group("index")) + m = re.search(re_name, fits_name) + fits_index = int(m.group("index")) if m else -1 # Load the data - df_fits = dict_load_fits(fits) # Load .fits files into a dictionary + df_fits = dict_load_fits(file) # Load .fits files into a dictionary if ( AI_file is not None ): # Only run if the meta-data needs to be reuplodaed from the .txt file @@ -305,10 +327,10 @@ def __init__( ) # get the correct line item in the AI file -- df_fits["fits_index"] = fits_index # Save the index tmp.append(df_fits) # save the file - data_dict = {key: [d[key] for d in tmp] for key in tmp[0].keys()} + data_dict = {key: [d[key] for d in tmp] for key in tmp[0]} df = pd.DataFrame(data_dict) # Rename the files and only extract those that matter-- - self.data = ( + self.data: pd.DataFrame = ( df[list(header_names.keys())] .rename(columns=header_names) .round(header_resolutions) @@ -352,9 +374,10 @@ def meta(self): def __call__(self): return self.calc_refl() - def load_AI_meta(self, file=None): + def load_AI_meta(self, file: str | Path): # Load .txt file here to supplement metadata if needed - with open(file, "r") as f: + with Path(file).open("r") as f: + header_line = 0 for i, line in enumerate(f): if "DATA" in line: header_line = i @@ -382,8 +405,8 @@ def update_meta(self, meta_fits, meta_AI): def reprocess_images(self): self.cleanup_metadata() - self.clean_images() # Filter and zing the images for further reduction. Only do this once. - self.generate_series_mask() # Create a mask based on the total drift of teh beam and a radial threshold. + self.clean_images() # Filter and zing the images for further reduction. + self.generate_series_mask() # Create a total drift radial mask # self.locate_beam_byscan() self.process_images() self.reprocess_vars = False @@ -398,7 +421,8 @@ def cleanup_metadata(self): lambda x: x + self.process_vars["exposure_offset"] if x > 0 else 1 ) - # Label each sample in terms of the 'scan'. different scans can have the same energy/pol/steps + # Label each sample in terms of the 'scan'. different scans can have the same + # energy/pol/steps new_scan_markers = ( np.abs(self.data["sam_th"].diff()) > self.process_vars["new_scan_marker"] ) @@ -409,7 +433,7 @@ def cleanup_metadata(self): self.data["energy"] += self.process_vars["energy_offset"] # Theta if ( - self.process_vars["sam_th_offset"] == None + self.process_vars["sam_th_offset"] is None and self.process_vars["sam_th_correction"] ): # Was a sample theta offset given to the loader? # [data['sam_z'][np.abs(data['sam_z'].diff()) > 0].index+1] @@ -429,16 +453,22 @@ def cleanup_metadata(self): ) # Should be in th-2th configuration self.data["sam_th"] += sam_th_offset # Correct for offset self.process_vars["sam_th_offset"] # Save offset - print(f"----") - print(f"sam_th offset not given.") + print("----") + print("sam_th offset not given.") print( - f"Assuming a th-2th geometry -> Offset determed to be sam_th_offset = {sam_th_offset} [deg]" + f""" + Assuming a th-2th geometry -> Offset determed:\n + am_th_offset = {sam_th_offset} [deg] + """ ) - print(f"Applying offset to data") + print("Applying offset to data") print( - f"Reprocess data with 'loader.process_vars['sam_th_correction']=False' to prevent automatic offset" + """ + Reprocess data with 'loader.process_vars['sam_th_correction']=False' + to prevent automatic offset + """ ) - print(f"----") + print("----") # Now that energy and theta are calculated correctly, make the q-col self.data["wavelength"] = self.data["energy"].apply( lambda x: units.energy_to_wavelength(x) @@ -479,12 +509,13 @@ def generate_series_mask(self): r = self.process_vars[ "drift_distance" ] # The distance that you will allow for the beam to move between each photo - # Identify all the locations where the beam will likely be located. Hot spots are eay to grab + # Identify all the locations where the beam will likely be located. Hot spots + # are eay to grab mask_temp = self.data["zinged_image"].copy().sum() / len( self.data["zinged_image"] ) - mask_loc = np.argwhere((mask_temp > threshold)) + mask_loc = np.argwhere(mask_temp > threshold) grid_map = np.indices(mask_temp.shape) # Get a grid mask = np.zeros_like(mask_temp, bool) # Initially mask all points for xy in mask_loc: @@ -528,7 +559,8 @@ def process_images(self): self.data["roi_d"] = self.data.apply( lambda df: self.update_dark_roi(df["beam_spot"]), axis=1 ) - # Find the locations of the collected image to integrate for beam and the dark frame + # Find the locations of the collected image to integrate for beam and the dark + # frame self.data["spot"] = self.data.apply( lambda df: df["reduced_image"][df["roi"]], axis=1 ) @@ -600,7 +632,7 @@ def update_dark_roi(self, beam_spot): return (sly, slx) - def subtract_background(self, image, dark): + def subtract_background(self, image): bkg_sub = self.process_vars["bkg_sub"] left = image[:, :bkg_sub] right = image[:, -bkg_sub:] @@ -612,10 +644,7 @@ def subtract_background(self, image, dark): def check_saturation(self, image, threshold=1): maxcounts = image.max() - if (2**16 - maxcounts) < threshold: - return True - else: - return False + return 2**16 - maxcounts < threshold def locate_beam_byscan(self, save_mask=True): current_scan = 0 @@ -687,14 +716,12 @@ def find_maximum(self, init_image, init=None, w=20, h=20): # Calculate the spot yloc += h // 2 return (yloc, xloc), distance_mask - def check_spot(self, fits_index, d=1): + def check_spot(self, fits_index, d=1, *, extended_output=False): if fits_index not in self.data["fits_index"]: - print(f"FITS file not found in loaded data, please verify index.") + print("FITS file not found in loaded data, please verify index.") return 0 elif not self.data_processed: - print( - f"Data has not yet been processed. Please run 'loader.reprocess_images()'." - ) + print("Data not processed. Please run 'loader.reprocess_images()'") return 0 elif self.process_vars["reprocess_vars"]: self.cleanup_metadata() @@ -745,7 +772,7 @@ def check_spot(self, fits_index, d=1): # Mask if necessary if self.mask is not None: - mask_display = np.ma.masked_where(self.mask == True, self.mask) + mask_display = np.ma.masked_where(self.mask, self.mask) ax[0, 0].imshow(mask_display, cmap="Greys_r") ax[0, 1].imshow(mask_display, cmap="Greys_r") @@ -774,9 +801,10 @@ def check_spot(self, fits_index, d=1): plt.tight_layout() plt.show() + if extended_output: + return fig, ax - def display_fits(self, fits_index, bs=True): - + def display_fits(self, fits_index, bs=True, extended_output=False): df = self.data[self.data["fits_index"] == fits_index] fig, ax = plt.subplots( @@ -793,7 +821,7 @@ def display_fits(self, fits_index, bs=True): # Mask if necessary if self.mask is not None: - mask_display = np.ma.masked_where(self.mask == True, self.mask) + mask_display = np.ma.masked_where(self.mask, self.mask) ax[0, 0].imshow(mask_display, cmap="Greys_r") ax[0, 1].imshow(mask_display, cmap="Greys_r") @@ -823,17 +851,18 @@ def display_fits(self, fits_index, bs=True): plt.tight_layout() plt.show() + if extended_output: + return fig, ax def calc_refl(self, drop_duplicates=True): """ Function that performs a data reduction of PRSOXR data. """ - # Verify that the data has been processed and the metadata does not need to be recalculated + # Verify that the data has been processed and the metadata does not need to be + # recalculated if not self.data_processed: - print( - f"Data has not yet been processed. Please run 'loader.reprocess_images()'." - ) + print("Data has not processed. Please run 'loader.reprocess_images()'.") return 0 elif self.process_vars["reprocess_vars"]: self.cleanup_metadata() @@ -843,10 +872,11 @@ def calc_refl(self, drop_duplicates=True): if self.data["is_saturated"].sum() > 0: warnings.warn( - f"The CCD was likely saturated during data collection. Stitching may be impacted" + "The CCD was likely saturated. Stitching may be impacted", + stacklevel=2, ) - scans = ( + _scans = ( self.data["scan"].iloc[-1] + 1 ) # How many total scans are included in each calculation? (starts at 0) self.data = ( @@ -866,12 +896,14 @@ def calc_refl(self, drop_duplicates=True): ) self.data["R"] = self.data.apply(lambda df: df["R"] / df["scale"], axis=1) # self.data['R_err'] = self.data.apply( - # lambda df: df['R'] * ((df['R_err']/df['R'])**2 + (df['scale_err']/df['scale'])**2)**0.5, + # lambda df: ( + # df['R'] * ((df['R_err']/df['R'])**2 + # + (df['scale_err']/df['scale'])**2)**0.5) , # axis=1 # ) # Generate output mask mask = self.data["i0_mask"] < 1 - mask &= self.data["is_saturated"] == False + mask &= not self.data["is_saturated"] mask &= self.data["R"] > 0 if self.process_vars["drop_failed_stitch"]: mask &= self.data["failed_stitch_mask"] < 1 @@ -896,7 +928,10 @@ def normalize_scan(self, df): i0_err = df["counts_err"].loc[:i0_cutoff].std() except IndexError: print( - f"No direct beam found for scan #{df['fits_index'].iloc[0]}. Not normalizing the beam." + f""" + No direct beam found for scan #{df["fits_index"].iloc[0]}. + Not normalizing the beam. + """ ) print(np.abs(df["sam_z"].diff()) > 0.1) i0 = 1 @@ -937,7 +972,7 @@ def find_stitch_points(self, df): skip = False skip_count = 0 elif abs(val) > self.process_vars["stitch_mark_tol"]: - if df["mark"].iloc[i] == None: + if df["mark"].iloc[i] is None: df.loc[igroup + i + 1, "mark"] = ( 1 # adds to the 'next' position ) @@ -959,14 +994,14 @@ def calc_scale_factors(self, df): linear = Model(stitchratio) prev_mark_index = 0 for i in range(len(df)): # row in df.iterrows(): - if df["mark"].iloc[i] == None: + if df["mark"].iloc[i] is None: continue # If here, we are at a stitch point sam_th_stitch = df["sam_th"].iloc[i] # Calculate the number of datapoints are repeated. repeat = 0 - for j, val in enumerate(df["sam_th"].iloc[i:]): + for val in df["sam_th"].iloc[i:]: if ( val == sam_th_stitch ): # I have entered a region where qstitch matches the value @@ -985,7 +1020,7 @@ def calc_scale_factors(self, df): if val in df["sam_th"].iloc[i + repeat :].values and jj not in ipre: if df["is_saturated"].iloc[jj]: print( - f"Saturation found in pre-change stitch point, dropping index: {jj}" + f"Saturation found in pre-change stitch point, dropping: {jj}" # noqa: E501 ) else: ipre.append(jj) @@ -997,7 +1032,7 @@ def calc_scale_factors(self, df): if val in df["sam_th"].iloc[ipre].values and jj not in ipost: if df["is_saturated"].iloc[jj]: print( - f"Saturation found in post-change stitch point, dropping index: {jj}" + f"Saturation found in post-change stitch point, dropping index: {jj}" # noqa: E501 ) else: ipost.append(jj) @@ -1005,14 +1040,14 @@ def calc_scale_factors(self, df): # drop_points = [] # maxcounts = int(df['zinged_image'].iloc[j].max()) # if np.abs(maxcounts - 65535) < 2: - # print(f"Saturation found in pre-change stitch point, dropping index: {j}") + # print(f"Saturation found in pre-change stitch point, dropping index: {j}") # noqa: E501 # drop_points.append(j) # ipre = [index for index in ipre if index not in drop_points] # for j in ipost: # drop_points = [] # maxcounts = int(df['zinged_image'].iloc[j].max()) # if np.abs(maxcounts - 65535) < 2: - # print(f"Saturation found in post-change stitch point, dropping index: {j}") + # print(f"Saturation found in post-change stitch point, dropping index: {j}") # noqa: E501 # drop_points.append(j) # ipost = [index for index in ipost if index not in drop_points] @@ -1035,19 +1070,22 @@ def calc_scale_factors(self, df): df.loc[igroup + i, "num_stitch_points"] = len(safe_stitch_values) # If no values were determined "SAFE" for stitching, if len(safe_stitch_values) == 0 & self.process_vars["drop_failed_stitch"]: - print(f"----") + print("----") print(f"Failed stitch occured at index {igroup + i}") print(f"Energy: {df['energy'].iloc[i]} eV") print(f"Theta: {df['sam_th'].iloc[i]}") - print(f"Masking all non-stitched points") - print(f"Check processing variables and re-calculate to try again") - print(f"----") + print("Masking all non-stitched points") + print("Check processing variables and re-calculate to try again") + print("----") df.loc[igroup + i :, "failed_stitch_mask"] = 1 break # We successfully found a stitch point and are moving on. if len(safe_stitch_values) == 1: warnings.warn( - f"The scan starting with index {df['fits_index'].iloc[0]} only has one stitch point." + f""" + The scan starting with index {df["fits_index"].iloc[0]} + only has one stitch point.""", + stacklevel=2, ) # Proceed with stitching @@ -1061,13 +1099,12 @@ def calc_scale_factors(self, df): scale_erri = stitch_output.sd_beta[0] df.loc[igroup + i :, "scale"] = ( - df["scale"].iloc[i:].apply(lambda x: x * scalei) + df["scale"].iloc[i:].apply(lambda x, si=scalei: x * si) ) df.loc[igroup + i :, "scale_err"] = df.iloc[i:].apply( - lambda x: ( + lambda x, si=scalei, se=scale_erri: ( x["scale"] - * ((x["scale_err"] / x["scale"]) ** 2 + (scale_erri / scalei) ** 2) - ** 0.5 + * ((x["scale_err"] / x["scale"]) ** 2 + (se / si) ** 2) ** 0.5 ), axis=1, ) diff --git a/src/pxr_reduce/py.typed b/src/pxr_reduce/py.typed new file mode 100644 index 0000000..e69de29 diff --git a/src/pxr_reduce/utils/__init__.py b/src/pxr_reduce/utils/__init__.py index e69de29..d7f566a 100644 --- a/src/pxr_reduce/utils/__init__.py +++ b/src/pxr_reduce/utils/__init__.py @@ -0,0 +1 @@ +"""Utility functions for the pxr_reduce package.""" diff --git a/src/pxr_reduce/utils/attributes.py b/src/pxr_reduce/utils/attributes.py index 418f0f5..c956e5d 100644 --- a/src/pxr_reduce/utils/attributes.py +++ b/src/pxr_reduce/utils/attributes.py @@ -22,7 +22,6 @@ def getter(instance, k=key): def setter(instance, value, k=key): """Sets the value in instance.process_vars[k].""" - # print(f"--- Setting '{k}' to '{value}'. Updating process_vars dictionary. ---") instance.process_vars[k] = value if "reprocess_vars" not in k: instance.process_vars["reprocess_vars"] = True diff --git a/src/pxr_reduce/utils/file_sort.py b/src/pxr_reduce/utils/file_sort.py index 47dd207..23914fd 100644 --- a/src/pxr_reduce/utils/file_sort.py +++ b/src/pxr_reduce/utils/file_sort.py @@ -1,8 +1,9 @@ +from collections.abc import Iterable from pathlib import Path -from typing import Iterable, List, Union +from typing import Any -def ensure_paths(items: Union[Iterable[Union[str, Path]], str, Path]) -> List[Path]: +def ensure_paths(items: Iterable[str | Path | Any] | str | Path) -> list[Path]: """ Ensure `items` is a list of `pathlib.Path` objects. - Accepts a single `str` or `Path`, or an iterable of `str`/`Path`. @@ -15,17 +16,21 @@ def ensure_paths(items: Union[Iterable[Union[str, Path]], str, Path]) -> List[Pa try: iterator = iter(items) - except TypeError: - raise TypeError("Input must be a Path/str or an iterable of Path/str") + except TypeError as e: + raise TypeError("Input must be a Path/str or an iterable of Path/str") from e out = [] for i, it in enumerate(iterator): - if isinstance(it, Path): - out.append(it) - elif isinstance(it, str): - out.append(Path(it)) - else: - raise TypeError( - f"Item at index {i} has unsupported type {type(it)}; expected str or pathlib.Path" - ) + match it: + case Path(): + out.append(it) + case str(): + out.append(Path(it)) + case _: + raise TypeError( + f""" + Item at index {i} has unsupported type {type(it)}; + expected str or pathlib.Path got {type(it)} + """ + ) from None return out diff --git a/src/pxr_reduce/utils/image.py b/src/pxr_reduce/utils/image.py index 7f80998..0f71b12 100644 --- a/src/pxr_reduce/utils/image.py +++ b/src/pxr_reduce/utils/image.py @@ -2,12 +2,14 @@ from scipy.ndimage import median_filter -# Replace pixels above a threshold with the average defined by a box of SIZE x SIZE around the pixel +# Replace pixels above a threshold with the average defined by a box of SIZE x SIZE +# around the pixel # -- From Jan Ilavsky's IGOR implementation. def dezinger_image(image, med_result=None, threshold=10, size=3): """ Function to remove potential hot pixels during data collection. - Replaces pixels that have intensity greater than threshold above its nearest neighbors + Replaces pixels that have intensity greater than threshold above its nearest + neighbors. Parameters ----------- diff --git a/src/pxr_reduce/utils/name.py b/src/pxr_reduce/utils/name.py index 8d0d44a..d3c0ac5 100644 --- a/src/pxr_reduce/utils/name.py +++ b/src/pxr_reduce/utils/name.py @@ -1,21 +1,20 @@ import re -from typing import List, Optional def infer_index_regex( - filenames: List[str], + filenames: list[str], *, index_group: str = "index", - prefix_group: Optional[str] = None, + prefix_group: str | None = None, ) -> str: """ - Infer a regular‑expression that captures the integer which increments by 1 + Infer a regular-expression that captures the integer which increments by 1 across a list of FITS filenames. Parameters ---------- filenames : list[str] - List of filenames (at least two entries). All must end with a similar extension – + List of filenames (at least two entries). All must end with a similar extension the suffix is not enforced, the algorithm works on any common pattern. index_group : str, optional @@ -105,8 +104,8 @@ def infer_index_regex( pattern = f"^{prefix_pat}{index_pat}{suffix_lit}$" return pattern - - + + def _natural_sort_key(s: str): """ Generate a sort key that orders strings with embedded integers numerically. @@ -114,6 +113,5 @@ def _natural_sort_key(s: str): lexicographically as ["file_10", "file_100", "file_9"]. 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pytest, stable ``__all__``, and + that the primary public symbol remains importable without beamline data. + """ + assert "PrsoxrLoader" in pxr_reduce.__all__ + assert pxr_reduce.PrsoxrLoader.__name__ == "PrsoxrLoader" diff --git a/uv.lock b/uv.lock index 4f8833f..9024f32 100644 --- a/uv.lock +++ b/uv.lock @@ -10,6 +10,18 @@ resolution-markers = [ "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] +[[package]] +name = "anyio" +version = "4.13.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "idna" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/19/14/2c5dd9f512b66549ae92767a9c7b330ae88e1932ca57876909410251fe13/anyio-4.13.0.tar.gz", hash = "sha256:334b70e641fd2221c1505b3890c69882fe4a2df910cba14d97019b90b24439dc", size = 231622, upload-time = "2026-03-24T12:59:09.671Z" } +wheels = [ + { url = 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