working on microbiorust-py benchmarking

Author: LCrossman

microbiorust-py/asv.conf.json

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+{
+    "version": 1,
+    "project": "microbiorust-py",
+    "project_url": "https://github.com/LCrossman/microBioRust/microbiorust-py",
+    
+    // MONOREPO SETTINGS
+    // 1. The git history is one level up
+    "repo": "..",
+    // 2. The python project is inside this folder
+    "repo_subdir": "microbiorust-py",
+
+    // BUILD SETTINGS
+    // This creates a virtualenv for every test
+    "environment_type": "virtualenv",
+    "pythons": ["3.11"], 
+    "matrix": {
+        "req": {}
+    },
+
+    // Install using pip + pyproject.toml + maturin
+    "install_command": [
+        "pip install ."
+    ],
+    "uninstall_command": [
+        "pip uninstall -y {project}"
+    ],
+
+    // CONFIGURATION
+    "benchmark_dir": "benchmarks",
+    "results_dir": ".asv/results",
+    "html_dir": ".asv/html",
+    "show_commit_url": "https://github.com/LCrossman/microBioRust/microbiorust-py/commit/"
+}

microbiorust-py/benchmarks/bench_pipeline.py

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+import os
+import microbiorust
+
+class PipelineSuite:
+    """
+    Benchmarks for microbiorust-py
+    """
+    # Setup runs before the timer starts
+    def setup(self):
+        bench_dir = os.path.dirname(__file__)
+        
+        # 2. Join it with your filename
+        self.filepath = os.path.join(bench_dir, "Rhiz3841.gbk.gb")
+
+        # Check if it exists just to be safe (helps debugging)
+        if not os.path.exists(self.filepath):
+            raise FileNotFoundError(f"Could not find benchmark file at: {self.filepath}")
+    # 1. Benchmark TIME
+    def time_process_all(self):
+        # This calls your function that returns Vec<String>
+       result = gbk_to_faa(self.filepath)
+       for r in result:
+         print(r)
+
+    # 2. Benchmark MEMORY (The known spike)
+    def peakmem_process_all(self):
+        result = gbk_to_faa(self.filepath)
+        for r in result:
+          print(r)

microbiorust-py/pyproject.toml

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+[build-system]
+# This tells pip: "Use Maturin to build this, not setuptools"
+requires = ["maturin>=1.0,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "microbiorust-py"
+# Valid python versions
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Rust",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+# If you have runtime python dependencies (e.g. Biopython), list them here.
+# For benchmarking pure Rust speed, usually keep this empty.
+dependencies = []
+ 
+# This tells Python to look at Cargo.toml for the version number.
+[tool.maturin]
+bindings = "pyo3"
+module-name = "microbiorust_py"
+features = ["pyo3/extension-module"]