PyPI - refnd - Versions diffs - 0.0.0__tar.gz - Mend

refnd 0.0.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (124) hide show

refnd-0.0.0/Cargo.lock +2412 -0
refnd-0.0.0/Cargo.toml +7 -0
refnd-0.0.0/PKG-INFO +28 -0
refnd-0.0.0/README.md +18 -0
refnd-0.0.0/py/.github/workflows/CI.yml +186 -0
refnd-0.0.0/py/.gitignore +71 -0
refnd-0.0.0/py/AGENTS.md +189 -0
refnd-0.0.0/py/CLAUDE.md +189 -0
refnd-0.0.0/py/Cargo.toml +19 -0
refnd-0.0.0/py/README.md +18 -0
refnd-0.0.0/py/docs/source/_static/css/copy_markdown.css +20 -0
refnd-0.0.0/py/docs/source/_static/js/copy_markdown.js +151 -0
refnd-0.0.0/py/docs/source/api/core.md +45 -0
refnd-0.0.0/py/docs/source/api/kernels.md +28 -0
refnd-0.0.0/py/docs/source/api/utils.md +6 -0
refnd-0.0.0/py/docs/source/conf.py +169 -0
refnd-0.0.0/py/docs/source/index.md +16 -0
refnd-0.0.0/py/src/bin/stub_gen.rs +82 -0
refnd-0.0.0/py/src/core/_utils.rs +99 -0
refnd-0.0.0/py/src/core/edge_store.rs +158 -0
refnd-0.0.0/py/src/core/exact.rs +165 -0
refnd-0.0.0/py/src/core/functional.rs +91 -0
refnd-0.0.0/py/src/core/hnsw.rs +590 -0
refnd-0.0.0/py/src/core/leiden.rs +138 -0
refnd-0.0.0/py/src/core/mod.rs +6 -0
refnd-0.0.0/py/src/kernels/mod.rs +15 -0
refnd-0.0.0/py/src/kernels/molecules/mod.rs +149 -0
refnd-0.0.0/py/src/kernels/protein/mod.rs +1 -0
refnd-0.0.0/py/src/kernels/protein/sequence.rs +416 -0
refnd-0.0.0/py/src/lib.rs +93 -0
refnd-0.0.0/py/src/utils.rs +337 -0
refnd-0.0.0/py/uv.lock +856 -0
refnd-0.0.0/pyproject.toml +32 -0
refnd-0.0.0/python/refnd/__init__.py +7 -0
refnd-0.0.0/python/refnd/__init__.pyi +20 -0
refnd-0.0.0/python/refnd/core/__init__.pyi +646 -0
refnd-0.0.0/python/refnd/kernels/__init__.pyi +20 -0
refnd-0.0.0/python/refnd/kernels/molecules/__init__.pyi +119 -0
refnd-0.0.0/python/refnd/kernels/protein/__init__.pyi +8 -0
refnd-0.0.0/python/refnd/kernels/protein/sequence/__init__.pyi +253 -0
refnd-0.0.0/python/refnd/utils/__init__.pyi +174 -0
refnd-0.0.0/refnd/.gitignore +2 -0
refnd-0.0.0/refnd/AGENTS.md +60 -0
refnd-0.0.0/refnd/CLAUDE.md +60 -0
refnd-0.0.0/refnd/Cargo.lock +1620 -0
refnd-0.0.0/refnd/Cargo.toml +29 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/00_preamble.md +8 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/00_table_of_contents.md +23 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/01_1_color_system.md +195 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/02_2_style_system.md +146 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/03_3_segment_rendering_atom.md +95 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/04_4_markup_parser.md +103 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/05_5_measurement_protocol.md +87 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/06_6_text_object.md +303 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/07_7_console.md +238 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/08_8_box_characters.md +310 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/09_9_table_layout.md +405 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/10_10_panel_padding.md +260 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/11_11_alignment_system.md +139 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/12_12_unicode_cell_width.md +153 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/13_13_text_wrapping.md +91 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/14_14_ratio_distribution.md +189 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/15_15_exclusions_and_not_yet_implemented_features.md +37 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/16_16_live_display_system.md +519 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/17_17_layout_system.md +543 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/18_18_logging_handler_integration.md +373 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/19_19_htmlsvg_export.md +470 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/20_appendix_a_rust_trait_summary.md +23 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/21_appendix_b_recommended_crate_mappings.md +17 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/INDEX.md +32 -0
refnd-0.0.0/refnd/llm_docs/rich_rust/README.md +926 -0
refnd-0.0.0/refnd/src/cli/CLI.md +11 -0
refnd-0.0.0/refnd/src/cli/autocomplete.rs +96 -0
refnd-0.0.0/refnd/src/cli/custer/mod.rs +143 -0
refnd-0.0.0/refnd/src/cli/display.rs +282 -0
refnd-0.0.0/refnd/src/cli/edge/mod.rs +162 -0
refnd-0.0.0/refnd/src/cli/index/mod.rs +124 -0
refnd-0.0.0/refnd/src/cli/kernel_parameters.rs +224 -0
refnd-0.0.0/refnd/src/cli/knn/mod.rs +173 -0
refnd-0.0.0/refnd/src/cli/mod.rs +50 -0
refnd-0.0.0/refnd/src/cli/parameters.rs +133 -0
refnd-0.0.0/refnd/src/cli/renderer.rs +468 -0
refnd-0.0.0/refnd/src/cli/split/mod.rs +173 -0
refnd-0.0.0/refnd/src/cli/utils.rs +410 -0
refnd-0.0.0/refnd/src/core/connected_components.rs +35 -0
refnd-0.0.0/refnd/src/core/distance.rs +6 -0
refnd-0.0.0/refnd/src/core/edge_store.rs +270 -0
refnd-0.0.0/refnd/src/core/exact/exact_edges.rs +56 -0
refnd-0.0.0/refnd/src/core/exact/exact_nearest_neighbors.rs +54 -0
refnd-0.0.0/refnd/src/core/exact/mod.rs +5 -0
refnd-0.0.0/refnd/src/core/hnsw/HNSW.md +38 -0
refnd-0.0.0/refnd/src/core/hnsw/build.rs +86 -0
refnd-0.0.0/refnd/src/core/hnsw/config.rs +147 -0
refnd-0.0.0/refnd/src/core/hnsw/hnsw_index.rs +84 -0
refnd-0.0.0/refnd/src/core/hnsw/insert.rs +135 -0
refnd-0.0.0/refnd/src/core/hnsw/mod.rs +471 -0
refnd-0.0.0/refnd/src/core/hnsw/search.rs +148 -0
refnd-0.0.0/refnd/src/core/hnsw/search_layer.rs +70 -0
refnd-0.0.0/refnd/src/core/hnsw/select_neighbors.rs +178 -0
refnd-0.0.0/refnd/src/core/leiden/LEIDEN.md +40 -0
refnd-0.0.0/refnd/src/core/leiden/csr_graph.rs +66 -0
refnd-0.0.0/refnd/src/core/leiden/leiden.rs +449 -0
refnd-0.0.0/refnd/src/core/leiden/mod.rs +7 -0
refnd-0.0.0/refnd/src/core/leiden/utils.rs +18 -0
refnd-0.0.0/refnd/src/core/mod.rs +12 -0
refnd-0.0.0/refnd/src/core/partition.rs +41 -0
refnd-0.0.0/refnd/src/kernels/mod.rs +2 -0
refnd-0.0.0/refnd/src/kernels/molecules/MOLECULE_KERNELS.md +53 -0
refnd-0.0.0/refnd/src/kernels/molecules/mod.rs +2 -0
refnd-0.0.0/refnd/src/kernels/molecules/tanimoto/mod.rs +28 -0
refnd-0.0.0/refnd/src/kernels/proteins/PROTEIN_KERNELS.md +10 -0
refnd-0.0.0/refnd/src/kernels/proteins/mod.rs +1 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/aligner_config.rs +115 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/global.rs +99 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/local.rs +162 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/matrix.rs +94 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/meta.rs +23 -0
refnd-0.0.0/refnd/src/kernels/proteins/parasail/mod.rs +11 -0
refnd-0.0.0/refnd/src/lib.rs +4 -0
refnd-0.0.0/refnd/src/main.rs +102 -0
refnd-0.0.0/refnd/src/utils/fingerprints.rs +43 -0
refnd-0.0.0/refnd/src/utils/mod.rs +7 -0
refnd-0.0.0/refnd/src/utils/read_fasta.rs +60 -0
refnd-0.0.0/refnd/src/utils/read_sdf.rs +124 -0

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