"Modernise GrainSizeTools: uv, importable package, and PyPI release"#20
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jwestraadt wants to merge 7 commits intomarcoalopez:masterfrom
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"Modernise GrainSizeTools: uv, importable package, and PyPI release"#20jwestraadt wants to merge 7 commits intomarcoalopez:masterfrom
jwestraadt wants to merge 7 commits intomarcoalopez:masterfrom
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- Add pyproject.toml with project metadata and dependencies (including pyyaml which was missing from requirements.txt) - Add uv.lock for reproducible installs - Pin Python 3.11 via .python-version - Update README.md with uv installation instructions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add grain_size_tools/__init__.py exposing summarize, get_filepath, function_list and all submodules (averages, plot, stereology, piezometers, template) - Fix GrainSizeTools_script.py: move averages import to module level so summarize() works when imported (not just when %run) - Fix piezometers.py: resolve piezometric_database.yaml via Path(__file__).parent so it loads correctly from any working directory - Fix plot.py: remove emoji characters causing UnicodeEncodeError on Windows - Update DOCS notebooks to use new import style (import grain_size_tools as gst) replacing all %run usage and hardcoded local paths - Update README.md with Usage section and import examples Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Replace Anaconda/pip install instructions with uv workflow in _first_steps.md and getting started_src.md - Replace '%run GrainSizeTools_script.py' with 'import grain_size_tools as gst' throughout all docs - Update all module calls: plot.* -> gst.plot.*, stereology.* -> gst.stereology.*, averages.* -> gst.averages.*, summarize() -> gst.summarize() - Update piezometers API: old piezometers.quartz() -> load_piezometers_from_yaml() + list_piezometers(db) + calc_diffstress(db.phase.__dict__['name'], grain_size=x) - Replace hardcoded local filepaths with URL in stereology_module.md, _describe.md, _Paleopizometry.md - Replace calc_shape() with two_step() in stereology_module.md - Remove emoji from _Plot_module.md console output - Update Step 4 package structure description in getting started_src.md - Add deprecation notice to brief_tutorial.md (legacy v2.0 docs) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Rename package to grainsizetools-jwestraadt - Update author/maintainer to Johan Westraadt - Update repository URL to jwestraadt fork, keep original project link - Add optional jupyter extra for jupyterlab - Bump version to 3.2.1 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add Option A: pip install from PyPI (with jupyter extra) - Rename Option B: install from source using uv - Update clone URL to jwestraadt fork Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This PR modernises the GrainSizeTools project with the following changes:
Package management
pyproject.tomlwith all dependencies (includingpyyamlwhich was previously missing).python-versiongrainsizetools-jwestraadtwith an optional[jupyter]extraImportable package
grain_size_tools/into a proper Python package with__init__.pyimport grain_size_tools as gstpiezometers.py(Path(__file__).parent)averagesmodule-level import inGrainSizeTools_script.pyplot.pycausingUnicodeEncodeErroron WindowsDocumentation
quatifying_grain_size_pops.ipynb,paleopiezometry_module.ipynb,stereology_module.ipynb) to use newgst.*import styleplot.*→gst.plot.*,stereology.*→gst.stereology.*, etc.calc_shape()withtwo_step()in stereology docsbrief_tutorial.md)README.mdwith PyPI and uv install instructionsTest plan
pip install "grainsizetools-jwestraadt[jupyter]"installs correctlyimport grain_size_tools as gstworks after installgst.summarize(),gst.plot.distribution(),gst.stereology.Saltykov(),gst.piezometers.calc_diffstress()all function correctly🤖 Generated with Claude Code"