helmkit 0.3.0__tar.gz → 0.3.2__tar.gz

helmkit-0.3.2/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"

helmkit-0.3.2/.github/workflows/main.yml

@@ -0,0 +1,22 @@
+name: Run tests
+
+on:
+  push:
+    paths:
+      - '**/*.py'
+  pull_request:
+    paths:
+      - '**/*.py'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install dependencies
+        run: uv sync -U
+      - name: Test with pytest
+        run: uv run pytest

helmkit-0.3.2/.pre-commit-config.yaml

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.20.0
+    hooks:
+      - id: pyupgrade
+  - repo: https://github.com/asottile/reorder-python-imports
+    rev: v3.15.0
+    hooks:
+      - id: reorder-python-imports
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.5
+    hooks:
+      - id: ruff-check
+        args: [ --fix ]
+      - id: ruff-format
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.8.3
+    hooks:
+      - id: uv-lock

{helmkit-0.3.0 → helmkit-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helmkit
-Version: 0.3.0
+Version: 0.3.2
 Summary: Parse HELM strings into RDKit molecules
 License-File: LICENSE
 Requires-Python: >=3.11
@@ -11,6 +11,18 @@ Description-Content-Type: text/markdown
 
 A Python library for converting HELM (Hierarchical Editing Language for Macromolecules) notation to RDKit molecules.
 
+## Table of Contents
+
+- [Basic Usage](#basic-usage)
+- [Installation](#installation)
+- [Quick Example](#quick-example)
+- [Understanding HELM Notation](#understanding-helm-notation)
+- [Using Custom Monomer Data](#using-custom-monomer-data)
+- [SDF File Structure Requirements](#sdf-file-structure-requirements)
+- [Parallel Processing of Peptides](#parallel-processing-of-peptides)
+- [Development Setup](#development-setup)
+- [Running Tests](#running-tests)
+
 ## Basic Usage
 
 ```python
@@ -24,6 +36,28 @@ molecule = Molecule(helm_string)
 rdkit_mol = molecule.mol
 ```
 
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
 ## Quick Example
 
 ```python
@@ -129,3 +163,20 @@ helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
 # Process peptides in parallel
 molecules = load_peptides_in_parallel(helm_strings, monomer_db)
 ```
+
+## Development Setup
+
+To set up a development environment, first clone the repository.
+Then, from the root of the repository, use `uv` to sync the environment:
+
+```bash
+uv sync -U
+```
+
+## Running Tests
+
+To run the test suite, execute `pytest` from the root of the repository:
+
+```bash
+pytest
+```

{helmkit-0.3.0 → helmkit-0.3.2}/README.md

@@ -2,6 +2,18 @@
 
 A Python library for converting HELM (Hierarchical Editing Language for Macromolecules) notation to RDKit molecules.
 
+## Table of Contents
+
+- [Basic Usage](#basic-usage)
+- [Installation](#installation)
+- [Quick Example](#quick-example)
+- [Understanding HELM Notation](#understanding-helm-notation)
+- [Using Custom Monomer Data](#using-custom-monomer-data)
+- [SDF File Structure Requirements](#sdf-file-structure-requirements)
+- [Parallel Processing of Peptides](#parallel-processing-of-peptides)
+- [Development Setup](#development-setup)
+- [Running Tests](#running-tests)
+
 ## Basic Usage
 
 ```python
@@ -15,6 +27,28 @@ molecule = Molecule(helm_string)
 rdkit_mol = molecule.mol
 ```
 
+## Installation
+
+To install `helmkit`, you can use either [`uv`](https://github.com/astral-sh/uv) or `pip`.
+
+### With [`uv`](https://github.com/astral-sh/uv)
+
+```bash
+uv pip install helmkit
+```
+
+or if you have added it as a dependency to your `pyproject.toml`:
+
+```bash
+uv add helmkit
+```
+
+### Without `uv`
+
+```bash
+pip install helmkit
+```
+
 ## Quick Example
 
 ```python
@@ -120,3 +154,20 @@ helm_strings = ["PEPTIDE1{A.R.G}$$$$", "PEPTIDE1{S.G.T}$$$$"]
 # Process peptides in parallel
 molecules = load_peptides_in_parallel(helm_strings, monomer_db)
 ```
+
+## Development Setup
+
+To set up a development environment, first clone the repository.
+Then, from the root of the repository, use `uv` to sync the environment:
+
+```bash
+uv sync -U
+```
+
+## Running Tests
+
+To run the test suite, execute `pytest` from the root of the repository:
+
+```bash
+pytest
+```

{helmkit-0.3.0 → helmkit-0.3.2}/benchmarks/README.md

@@ -33,15 +33,18 @@ that `pyPept` cannot handle were excluded (monomers with names containing whites
 hyphens or parenthesis), resulting in a total of 4694 peptides. We measured the total
 and average parsing time:
 
-| Tool                                | Total Time (s) | Avg Time per Peptide (s) |
-|-------------------------------------|----------------|--------------------------|
-| `pyPept`                            | 676.65         | 0.144                    |
-| `helmkit`                           | 3.60           | 0.00077                  |
-| `helmkit` (DB reload every peptide) | 261.81         | 0.056                    |
-
-`helmkit` outperforms `pyPept` by approximately 188× when loading the monomer library
-once per session. When forced to reload the library for every peptide (needs disabling
-memoization in the source code), `helmkit` is still about 3× faster.
+| Tool                                | Total Time (s) | Avg Time per Peptide (s) | Peptides per Second |
+|-------------------------------------|---------------:|-------------------------:|--------------------:|
+| `pyPept`                            |         676.65 |                  0.14400 |                6.94 |
+| `helmkit` (DB reload every peptide) |         252.67 |                  0.05383 |               18.58 |
+| `helmkit`                           |           2.83 |                  0.00060 |             1658.68 |
+| `helmkit` (parallel loading)        |           1.42 |                  0.00030 |             3305.63 |
+
+`helmkit` outperforms `pyPept` by approximately 239× when loading the monomer library
+once per session. When forced to reload the library for every peptide, `helmkit` is
+still about 3× faster. If we use parallelized loading in `helmkit`, we achieve an
+additional 2.5× speedup, resulting in a total speedup of approximately 477× over
+`pyPept`.
 
 ## Environment
 
@@ -52,4 +55,4 @@ versions:
 - `polars 1.31.0` (CSV parsing and dataframe processing)
 - `rdkit 2025.3.3` (target output format and structure processing)
 - `pypept 1.0.0` (commit `ade9f5840691ad1f8fa22d13939a665c25175d5a`)
-- `helmkit 0.1.0` (local development version)
+- `helmkit 0.3.0` (local development version)

helmkit-0.3.2/benchmarks/benchmark-import.py

@@ -0,0 +1,36 @@
+import sys
+import time
+
+
+def benchmark_imports(import_code: str, repeats: int = 100):
+    times = []
+    for _ in range(repeats):
+        start = time.perf_counter()
+        exec(import_code)
+        end = time.perf_counter()
+        times.append(end - start)
+        # Remove imported modules to force fresh import next run
+        for mod in list(sys.modules):
+            if mod.startswith("pyPept") or mod.startswith("helmkit"):
+                del sys.modules[mod]
+    avg_time = sum(times) / repeats
+    print(f"Average import time for:\n{import_code}\n= {avg_time:.6f} seconds\n")
+
+
+pyPept_imports = """from pyPept.converter import Converter
+from pyPept.molecule import Molecule
+from pyPept.sequence import Sequence
+"""
+
+helmkit_imports = """from helmkit import load_monomer_library
+from helmkit import Molecule
+"""
+
+
+def main():
+    benchmark_imports(pyPept_imports)
+    benchmark_imports(helmkit_imports)
+
+
+if __name__ == "__main__":
+    main()