docs: add standardized check commands to README #686
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- Replace direct URL downloads with ScienceBase API client (sciencebasepy) - Remove niquests dependency in favor of native ScienceBase download handling - Enhance logging for better debugging of file downloads and extractions - Add explicit ZIP file cleanup after TIF extraction - Update dependencies to include sciencebasepy and setuptools
Restructures the species habitat analysis script: - Implement modular architecture with ScienceBaseClient, RasterSet, and HabitatDataProcessor classes for better maintainability - Integrate sciencebasepy for ZIP-based habitat map downloads from USGS ScienceBase, with automatic cleanup of temporary files - Add multi-format output support (CSV/Parquet/Arrow) with Arrow as default, using dictionary encoding for optimized storage and performance - Enhance metadata by including species common and scientific names from ScienceBase API - Add comprehensive CLI arguments for configuration and debug logging - Improve robustness with better error handling and type annotations
* Switch to using zipfile.Path for more Pythonic ZIP file handling * Enforce expectation of exactly one TIF file per ZIP * Add error handling for unexpected file counts
Refactors `species.py` to use TOML configuration (`_data/species.toml`) instead of `argparse`, improving flexibility and maintainability. Settings include `item_ids`, `vector_fp`, `output_dir`, `output_format`, and `debug`. Relative paths (e.g., `../data/us-10m.json`) are resolved relative to the TOML file, and basic validation is added. `RasterSet.extract_tifs_from_zips()` now uses `zipfile.Path` and enforces a single `.tif` file per ZIP, raising a `RuntimeError` otherwise. Type hinting fixes are also included.
- Rename species columns for consistency and clarity: - GAP_Species -> gap_species_code - percent_habitat -> habitat_yearround_pct - CommonName -> common_name - ScientificName -> scientific_name - Expand module docstring with detailed information about: - Data sources and resolution - Projection details - Habitat value meanings - Output format options - Improve code comments for future extensibility - reference habitat data source in species.toml - list alternative output format options in toml The changes prepare for potential future addition of seasonal habitat data (and summer/winter habitat data) while maintaining backward compatibility.
Enhance docstrings in the ScienceBaseClient class for clarity and completeness, specifically for the __init__, download_zip_files, and get_species_info methods. Add note about RuntimeWarning to analyze_habitat_rasters. Clarify error handling behavior in download_zip_files.
Document standardized check commands in README for local development. This provides a simple interim solution for running quality checks that match CI, without introducing additional dependencies. Closes #685
dsmedia
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Closing this PR. The branch (feature/add-uv-test-task) includes commits that are part of another open PR. I'll be creating a new PR shortly with a clean history, containing only the README changes. This avoids rewriting shared history. I will update this comment with a link to the new PR once it's created. |
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Documents the standard quality check commands in the README to help contributors run the same checks locally that are performed in CI. This provides a simple, documented way to validate changes before submitting PRs, without introducing additional tooling dependencies.
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Related Issues
Closes #685
Notes
uv runas a task runner astral-sh/uv#5903