helmkit 0.3.2__tar.gz → 0.4.0__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 (36) hide show
  1. {helmkit-0.3.2 → helmkit-0.4.0}/.github/workflows/main.yml +2 -0
  2. {helmkit-0.3.2 → helmkit-0.4.0}/.pre-commit-config.yaml +6 -2
  3. {helmkit-0.3.2 → helmkit-0.4.0}/PKG-INFO +1 -1
  4. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/README.md +5 -5
  5. helmkit-0.4.0/benchmarks/profile.prof +246 -0
  6. helmkit-0.4.0/benchmarks/profile2.prof +243 -0
  7. helmkit-0.4.0/benchmarks/profile3.prof +243 -0
  8. helmkit-0.4.0/benchmarks/profile4.prof +243 -0
  9. helmkit-0.4.0/benchmarks/profile5.prof +243 -0
  10. helmkit-0.4.0/benchmarks/profile6.prof +243 -0
  11. {helmkit-0.3.2 → helmkit-0.4.0}/pyproject.toml +2 -1
  12. {helmkit-0.3.2 → helmkit-0.4.0}/src/helmkit/molecule.py +68 -112
  13. {helmkit-0.3.2 → helmkit-0.4.0}/tests/test_random_peptides.py +1 -1
  14. {helmkit-0.3.2 → helmkit-0.4.0}/uv.lock +51 -32
  15. {helmkit-0.3.2 → helmkit-0.4.0}/.github/dependabot.yml +0 -0
  16. {helmkit-0.3.2 → helmkit-0.4.0}/.gitignore +0 -0
  17. {helmkit-0.3.2 → helmkit-0.4.0}/.python-version +0 -0
  18. {helmkit-0.3.2 → helmkit-0.4.0}/LICENSE +0 -0
  19. {helmkit-0.3.2 → helmkit-0.4.0}/README.md +0 -0
  20. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/benchmark-import.py +0 -0
  21. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/data/monomers.sdf +0 -0
  22. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/data/peptides.csv +0 -0
  23. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/helmkit-benchmark.py +0 -0
  24. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/helmkit-parallel-benchmark.py +0 -0
  25. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/helmkit-profile.py +0 -0
  26. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/helmkit-with-reload-benchmark.py +0 -0
  27. {helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/pypept-benchmark.py +0 -0
  28. {helmkit-0.3.2 → helmkit-0.4.0}/src/helmkit/__init__.py +0 -0
  29. {helmkit-0.3.2 → helmkit-0.4.0}/src/helmkit/data/monomers.sdf +0 -0
  30. {helmkit-0.3.2 → helmkit-0.4.0}/src/helmkit/py.typed +0 -0
  31. {helmkit-0.3.2 → helmkit-0.4.0}/tests/data/generate_sdf.py +0 -0
  32. {helmkit-0.3.2 → helmkit-0.4.0}/tests/data/monomers.csv +0 -0
  33. {helmkit-0.3.2 → helmkit-0.4.0}/tests/data/monomers.sdf +0 -0
  34. {helmkit-0.3.2 → helmkit-0.4.0}/tests/data/peptides.csv +0 -0
  35. {helmkit-0.3.2 → helmkit-0.4.0}/tests/test_cycpeptmpdb.py +0 -0
  36. {helmkit-0.3.2 → helmkit-0.4.0}/tests/test_parallel_load.py +0 -0
{helmkit-0.3.2 → helmkit-0.4.0}/.github/workflows/main.yml RENAMED
@@ -4,9 +4,11 @@ on:
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  push:
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  paths:
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  - '**/*.py'
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+ - 'uv.lock'
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  pull_request:
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  paths:
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  - '**/*.py'
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+ - 'uv.lock'
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  workflow_dispatch:
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  jobs:
{helmkit-0.3.2 → helmkit-0.4.0}/.pre-commit-config.yaml RENAMED
@@ -1,4 +1,8 @@
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  repos:
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+ - repo: https://github.com/asottile/dead
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+ rev: v2.1.0
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+ hooks:
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+ - id: dead
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  - repo: https://github.com/pre-commit/pre-commit-hooks
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  rev: v5.0.0
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  hooks:
@@ -16,12 +20,12 @@ repos:
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  hooks:
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  - id: reorder-python-imports
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  - repo: https://github.com/astral-sh/ruff-pre-commit
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- rev: v0.12.5
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+ rev: v0.12.8
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  hooks:
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  - id: ruff-check
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  args: [ --fix ]
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  - id: ruff-format
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  - repo: https://github.com/astral-sh/uv-pre-commit
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- rev: 0.8.3
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+ rev: 0.8.6
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  hooks:
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  - id: uv-lock
{helmkit-0.3.2 → helmkit-0.4.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: helmkit
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- Version: 0.3.2
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+ Version: 0.4.0
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  Summary: Parse HELM strings into RDKit molecules
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  License-File: LICENSE
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  Requires-Python: >=3.11
{helmkit-0.3.2 → helmkit-0.4.0}/benchmarks/README.md RENAMED
@@ -37,13 +37,13 @@ and average parsing time:
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  |-------------------------------------|---------------:|-------------------------:|--------------------:|
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  | `pyPept` | 676.65 | 0.14400 | 6.94 |
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  | `helmkit` (DB reload every peptide) | 252.67 | 0.05383 | 18.58 |
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- | `helmkit` | 2.83 | 0.00060 | 1658.68 |
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- | `helmkit` (parallel loading) | 1.42 | 0.00030 | 3305.63 |
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+ | `helmkit` | 2.07 | 0.00044 | 2267.63 |
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+ | `helmkit` (parallel loading) | 0.95 | 0.00020 | 4926.11 |
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- `helmkit` outperforms `pyPept` by approximately 239× when loading the monomer library
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+ `helmkit` outperforms `pyPept` by approximately 327x when loading the monomer library
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  once per session. When forced to reload the library for every peptide, `helmkit` is
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  still about 3× faster. If we use parallelized loading in `helmkit`, we achieve an
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- additional 2.5× speedup, resulting in a total speedup of approximately 477× over
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+ additional 2× speedup, resulting in a total speedup of approximately 712× over
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  `pyPept`.
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  ## Environment
@@ -55,4 +55,4 @@ versions:
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  - `polars 1.31.0` (CSV parsing and dataframe processing)
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  - `rdkit 2025.3.3` (target output format and structure processing)
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  - `pypept 1.0.0` (commit `ade9f5840691ad1f8fa22d13939a665c25175d5a`)
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- - `helmkit 0.3.0` (local development version)
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+ - `helmkit 0.3.4` (local development version)
helmkit-0.4.0/benchmarks/profile.prof ADDED
@@ -0,0 +1,246 @@
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+ 701302 function calls (701205 primitive calls) in 2.444 seconds
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+
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+ Ordered by: cumulative time
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+
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+ ncalls tottime percall cumtime percall filename:lineno(function)
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