helmkit 0.3.1__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/.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-0.3.1 → helmkit-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: helmkit
-Version: 0.3.1
+Version: 0.3.2
 Summary: Parse HELM strings into RDKit molecules
 License-File: LICENSE
 Requires-Python: >=3.11

{helmkit-0.3.1 → helmkit-0.3.2}/benchmarks/README.md

@@ -36,15 +36,15 @@ and average parsing time:
 | Tool                                | Total Time (s) | Avg Time per Peptide (s) | Peptides per Second |
 |-------------------------------------|---------------:|-------------------------:|--------------------:|
 | `pyPept`                            |         676.65 |                  0.14400 |                6.94 |
-| `helmkit` (DB reload every peptide) |         261.81 |                  0.05600 |               17.93 |
-| `helmkit`                           |           3.60 |                  0.00077 |             1303.89 |
+| `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 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. If we use
-parallelized loading in `helmkit`, we achieve an additional 2.5× speedup, resulting in a
-total speedup of approximately 477× over `pyPept`.
+`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
 

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()