phenoms 0.2.0__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 (79) hide show
  1. phenoms-0.2.0/.dockerignore +26 -0
  2. phenoms-0.2.0/.github/workflows/docs.yml +59 -0
  3. phenoms-0.2.0/.github/workflows/release.yml +97 -0
  4. phenoms-0.2.0/.github/workflows/tests.yml +47 -0
  5. phenoms-0.2.0/.gitignore +55 -0
  6. phenoms-0.2.0/Cargo.lock +322 -0
  7. phenoms-0.2.0/Cargo.toml +16 -0
  8. phenoms-0.2.0/LICENSE +21 -0
  9. phenoms-0.2.0/PKG-INFO +95 -0
  10. phenoms-0.2.0/README.md +56 -0
  11. phenoms-0.2.0/assets/phenoms.png +0 -0
  12. phenoms-0.2.0/docker/README.md +108 -0
  13. phenoms-0.2.0/docker/benchmark-one-cpu.Dockerfile +36 -0
  14. phenoms-0.2.0/docs/Makefile +19 -0
  15. phenoms-0.2.0/docs/_static/.gitkeep +0 -0
  16. phenoms-0.2.0/docs/api/comparison.rst +10 -0
  17. phenoms-0.2.0/docs/api/core.rst +18 -0
  18. phenoms-0.2.0/docs/api/detection.rst +6 -0
  19. phenoms-0.2.0/docs/api/index.rst +15 -0
  20. phenoms-0.2.0/docs/api/plotting.rst +14 -0
  21. phenoms-0.2.0/docs/api/preprocess.rst +10 -0
  22. phenoms-0.2.0/docs/api/qc_cleanup.rst +14 -0
  23. phenoms-0.2.0/docs/cli.rst +56 -0
  24. phenoms-0.2.0/docs/conf.py +109 -0
  25. phenoms-0.2.0/docs/index.rst +49 -0
  26. phenoms-0.2.0/docs/installation.rst +40 -0
  27. phenoms-0.2.0/docs/outputs.rst +55 -0
  28. phenoms-0.2.0/docs/requirements.txt +4 -0
  29. phenoms-0.2.0/docs/usage.rst +198 -0
  30. phenoms-0.2.0/environment.yml +31 -0
  31. phenoms-0.2.0/phenoms/__init__.py +346 -0
  32. phenoms-0.2.0/phenoms/__main__.py +6 -0
  33. phenoms-0.2.0/phenoms/analysis.py +130 -0
  34. phenoms-0.2.0/phenoms/cleanup.py +540 -0
  35. phenoms-0.2.0/phenoms/cli.py +177 -0
  36. phenoms-0.2.0/phenoms/comparison.py +161 -0
  37. phenoms-0.2.0/phenoms/comparison_set.py +360 -0
  38. phenoms-0.2.0/phenoms/connectivity.py +649 -0
  39. phenoms-0.2.0/phenoms/dimensionality_reduction.py +151 -0
  40. phenoms-0.2.0/phenoms/hbond.py +356 -0
  41. phenoms-0.2.0/phenoms/io.py +91 -0
  42. phenoms-0.2.0/phenoms/outputs.py +26 -0
  43. phenoms-0.2.0/phenoms/plotting.py +367 -0
  44. phenoms-0.2.0/phenoms/preprocess.py +243 -0
  45. phenoms-0.2.0/phenoms/qc.py +144 -0
  46. phenoms-0.2.0/phenoms/simulation.py +530 -0
  47. phenoms-0.2.0/phenoms/structure.py +214 -0
  48. phenoms-0.2.0/phenoms/viewer_bfactor_html.py +169 -0
  49. phenoms-0.2.0/pyproject.toml +57 -0
  50. phenoms-0.2.0/scripts/benchmark_kernel.py +310 -0
  51. phenoms-0.2.0/scripts/benchmark_plcg2_truncations.py +627 -0
  52. phenoms-0.2.0/scripts/compare_rust_mdtraj_difference_plot.py +235 -0
  53. phenoms-0.2.0/scripts/debug_docker_all_methods.py +85 -0
  54. phenoms-0.2.0/scripts/debug_docker_isolate.py +57 -0
  55. phenoms-0.2.0/scripts/fix_plcg2_table_totals.py +119 -0
  56. phenoms-0.2.0/scripts/preprocess_gromacs_to_pdb.py +124 -0
  57. phenoms-0.2.0/scripts/preprocess_plcg2_for_benchmark.py +66 -0
  58. phenoms-0.2.0/scripts/renumber_many_to_reference.py +73 -0
  59. phenoms-0.2.0/scripts/renumber_pdb_to_reference.py +80 -0
  60. phenoms-0.2.0/scripts/run_benchmark_docker_1cpu.sh +30 -0
  61. phenoms-0.2.0/scripts/run_benchmark_plcg2_docker.sh +83 -0
  62. phenoms-0.2.0/scripts/run_test_data_plots.py +417 -0
  63. phenoms-0.2.0/src/lib.rs +327 -0
  64. phenoms-0.2.0/tests/__init__.py +0 -0
  65. phenoms-0.2.0/tests/fixtures/__init__.py +0 -0
  66. phenoms-0.2.0/tests/fixtures/minimal.pdb +5 -0
  67. phenoms-0.2.0/tests/fixtures/tiny_protein.pdb +363 -0
  68. phenoms-0.2.0/tests/test_analysis.py +79 -0
  69. phenoms-0.2.0/tests/test_api_extensions.py +70 -0
  70. phenoms-0.2.0/tests/test_cleanup_renumber.py +92 -0
  71. phenoms-0.2.0/tests/test_comparison.py +35 -0
  72. phenoms-0.2.0/tests/test_comparison_set.py +60 -0
  73. phenoms-0.2.0/tests/test_connectivity.py +144 -0
  74. phenoms-0.2.0/tests/test_hbond.py +58 -0
  75. phenoms-0.2.0/tests/test_plotting.py +74 -0
  76. phenoms-0.2.0/tests/test_preprocess.py +61 -0
  77. phenoms-0.2.0/tests/test_qc.py +66 -0
  78. phenoms-0.2.0/tests/test_rust_hbond_speed.py +168 -0
  79. phenoms-0.2.0/tests/test_simulation_set.py +120 -0
phenoms-0.2.0/.dockerignore ADDED
@@ -0,0 +1,26 @@
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+ # Docker build context (repo root). Keep phenoms/test_data/ for benchmarks.
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+ .git
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+ **/__pycache__
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+ *.pyc
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+ .pytest_cache
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+ .mypy_cache
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+ .ruff_cache
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+ *.egg-info
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+ target/
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+ phenoms/test_outputs/
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+ old_scripts/
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+ H_bond_work/
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+ .vscode/
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+ .cursor/
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+ **/.ipynb_checkpoints
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+ phenom_outputs/
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+ protein_pdb_exports/
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+ plcg2_data/
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+ paper_materials/
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+ H_bond_work/
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+ target/
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+ *.ai
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+ *.tif
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+ *.pdf
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+ *.docx
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+ *.pse
phenoms-0.2.0/.github/workflows/docs.yml ADDED
@@ -0,0 +1,59 @@
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+ name: Docs
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+
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+ on:
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+ push:
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+ branches: [main]
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+ pull_request:
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+ branches: [main]
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+ workflow_dispatch:
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+
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+ permissions:
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+ contents: read
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+ pages: write
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+ id-token: write
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+
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+ concurrency:
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+ group: pages
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+ cancel-in-progress: true
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+
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+ jobs:
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+ build:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - name: Checkout
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+ uses: actions/checkout@v5
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+
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+ - name: Set up Python
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+ uses: actions/setup-python@v6
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+ with:
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+ python-version: "3.12"
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+ cache: pip
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+ cache-dependency-path: |
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+ docs/requirements.txt
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+ pyproject.toml
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+
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+ - name: Install package and docs dependencies
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+ run: |
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+ python -m pip install --upgrade pip
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+ python -m pip install -e .
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+ python -m pip install -r docs/requirements.txt
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+
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+ - name: Build Sphinx HTML
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+ run: sphinx-build -b html -W --keep-going docs docs/_build/html
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+
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+ - name: Upload Pages artifact
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+ uses: actions/upload-pages-artifact@v4
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+ with:
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+ path: docs/_build/html
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+
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+ deploy:
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+ if: github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/API_and_docs')
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+ needs: build
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+ runs-on: ubuntu-latest
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+ environment:
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+ name: github-pages
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+ url: ${{ steps.deployment.outputs.page_url }}
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+ steps:
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+ - name: Deploy to GitHub Pages
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+ id: deployment
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+ uses: actions/deploy-pages@v4
phenoms-0.2.0/.github/workflows/release.yml ADDED
@@ -0,0 +1,97 @@
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+ name: Release
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+
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+ on:
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+ push:
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+ tags: ["v*"]
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+ workflow_dispatch:
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+
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+ jobs:
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+ linux:
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+ runs-on: ubuntu-latest
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+ strategy:
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+ matrix:
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+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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+ steps:
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+ - uses: actions/checkout@v5
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+ - uses: actions/setup-python@v6
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+ with:
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+ python-version: ${{ matrix.python-version }}
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+ - name: Build wheel (manylinux)
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+ uses: PyO3/maturin-action@v1
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+ with:
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+ target: x86_64
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+ manylinux: auto
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+ args: --release --out dist --interpreter python${{ matrix.python-version }}
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: wheels-linux-${{ matrix.python-version }}
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+ path: dist/*.whl
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+
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+ macos:
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+ runs-on: macos-latest
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+ strategy:
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+ matrix:
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+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
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+ steps:
36
+ - uses: actions/checkout@v5
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+ - uses: actions/setup-python@v6
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+ with:
39
+ python-version: ${{ matrix.python-version }}
40
+ - name: Build wheel (universal2, arm64 + x86_64)
41
+ uses: PyO3/maturin-action@v1
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+ with:
43
+ target: universal2-apple-darwin
44
+ args: --release --out dist --interpreter python${{ matrix.python-version }}
45
+ - uses: actions/upload-artifact@v4
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+ with:
47
+ name: wheels-macos-${{ matrix.python-version }}
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+ path: dist/*.whl
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+
50
+ windows:
51
+ runs-on: windows-latest
52
+ strategy:
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+ matrix:
54
+ python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
55
+ steps:
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+ - uses: actions/checkout@v5
57
+ - uses: actions/setup-python@v6
58
+ with:
59
+ python-version: ${{ matrix.python-version }}
60
+ - name: Build wheel
61
+ uses: PyO3/maturin-action@v1
62
+ with:
63
+ target: x64
64
+ args: --release --out dist --interpreter python
65
+ - uses: actions/upload-artifact@v4
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+ with:
67
+ name: wheels-windows-${{ matrix.python-version }}
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+ path: dist/*.whl
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+
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+ sdist:
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+ runs-on: ubuntu-latest
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+ steps:
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+ - uses: actions/checkout@v5
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+ - name: Build sdist
75
+ uses: PyO3/maturin-action@v1
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+ with:
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+ command: sdist
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+ args: --out dist
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+ - uses: actions/upload-artifact@v4
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+ with:
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+ name: sdist
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+ path: dist/*.tar.gz
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+
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+ publish:
85
+ needs: [linux, macos, windows, sdist]
86
+ runs-on: ubuntu-latest
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+ permissions:
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+ id-token: write
89
+ steps:
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+ - uses: actions/download-artifact@v4
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+ with:
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+ path: dist
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+ merge-multiple: true
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+ - name: Publish to PyPI
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+ uses: pypa/gh-action-pypi-publish@release/v1
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+ with:
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+ packages-dir: dist
phenoms-0.2.0/.github/workflows/tests.yml ADDED
@@ -0,0 +1,47 @@
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+ name: Tests
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+
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+ on:
4
+ push:
5
+ branches: [main]
6
+ pull_request:
7
+ branches: [main]
8
+ workflow_dispatch:
9
+
10
+ jobs:
11
+ test:
12
+ strategy:
13
+ fail-fast: false
14
+ matrix:
15
+ os: [ubuntu-latest, macos-latest]
16
+ python-version: ["3.10", "3.12"]
17
+ runs-on: ${{ matrix.os }}
18
+ steps:
19
+ - name: Checkout
20
+ uses: actions/checkout@v5
21
+
22
+ - name: Set up Python
23
+ uses: actions/setup-python@v6
24
+ with:
25
+ python-version: ${{ matrix.python-version }}
26
+ cache: pip
27
+ cache-dependency-path: pyproject.toml
28
+
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+ - name: Set up Rust
30
+ uses: dtolnay/rust-toolchain@stable
31
+
32
+ - name: Cache Cargo registry
33
+ uses: actions/cache@v4
34
+ with:
35
+ path: |
36
+ ~/.cargo/registry
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+ ~/.cargo/git
38
+ target
39
+ key: ${{ runner.os }}-cargo-${{ hashFiles('Cargo.lock') }}
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+
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+ - name: Install phenoms (builds the Rust kernel)
42
+ run: |
43
+ python -m pip install --upgrade pip
44
+ python -m pip install -e ".[dev]"
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+
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+ - name: Run tests
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+ run: pytest -q
phenoms-0.2.0/.gitignore ADDED
@@ -0,0 +1,55 @@
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+ # Python bytecode / caches
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+ __pycache__/
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+ *.py[cod]
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+
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+ # Test and tooling caches
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+ .pytest_cache/
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+ .coverage
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+ .mypy_cache/
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+
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+ # Build / packaging artifacts
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+ build/
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+ dist/
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+ *.egg-info/
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+ pip-wheel-metadata/
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+
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+ # Rust extension build artifacts
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+ target/
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+ # Compiled extension from `maturin develop` (lands inside phenoms/ in editable installs)
19
+ phenoms/*.so
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+ phenoms/*.pyd
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+ phenoms/*.dll
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+
23
+ # Conda build artifacts
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+ condaenv.*.requirements.txt
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+
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+ # Local heavy test artifacts (not source code)
27
+ phenoms/test_data/
28
+ phenoms/test_outputs/
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+ phenom_outputs/
30
+
31
+ # Paper / manuscript materials (local only)
32
+ paper_materials/
33
+
34
+ # Local heavy trajectory / topology data
35
+ plcg2_data/
36
+
37
+ # Non-package project/work-in-progress
38
+ H_bond_work/
39
+ old_scripts/
40
+
41
+ # Local editor/project state
42
+ .vscode/
43
+ .cursor/
44
+
45
+ # Local exported structures
46
+ protein_pdb_exports/
47
+
48
+ *.svg
49
+ *.cdxml
50
+
51
+ # Sphinx
52
+ docs/_build/
53
+
54
+ # Local scratch / publication notes
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+ for_publication_*.txt
phenoms-0.2.0/Cargo.lock ADDED
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+ # It is not intended for manual editing.
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+ "pyo3",
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+ [[package]]
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+ [[package]]
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+ name = "phenoms_hbond_rs"
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+ dependencies = [
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+ "ndarray",
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+ "numpy",
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phenoms-0.2.0/Cargo.toml ADDED
@@ -0,0 +1,16 @@
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+ [package]
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+ name = "phenoms_hbond_rs"
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+ version = "0.1.0"
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+ edition = "2021"
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+ description = "Baker-Hubbard H-bond detection in Rust for PHENOMS"
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+ readme = "README.md"
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+
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+ [lib]
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+ name = "phenoms_hbond_rs"
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+ crate-type = ["cdylib"]
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+ rayon = "1.10"
phenoms-0.2.0/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2024 Brandon Novy
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.