Closes #22. Added a test that the memory usage doesn't balloon.

.devcontainer/devcontainer.json

@@ -41,7 +41,8 @@
 			"openssh-client",
 			"libaio-dev",
 			"unzip",
-			"yamllint"
+			"yamllint",
+			"time"
 		],
 		"install Ruby": [
 			"/usr/bin/apt",

.github/workflows/acceptable_memory_usage_test.yml

@@ -0,0 +1,41 @@
+name: performance_test
+
+on:
+  schedule:
+    - cron: "0 0 * * *"
+      timezone: "America/Vancouver"
+  workflow_dispatch:
+
+concurrency:
+  group: test-${{ github.head_ref }}
+  cancel-in-progress: true
+
+env:
+  PYTHONUNBUFFERED: "1"
+  FORCE_COLOR: "1"
+
+jobs:
+  run:
+    name: Python ${{ matrix.python-version }} Performance Tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          apt update && apt install yamllint
+          pip install uv
+
+      - name: Run slow tests
+        run: uv run pytest --memray -m slow --no-cov

pyproject.toml

@@ -39,6 +39,7 @@ dependencies = [
 
 [dependency-groups]
 dev = [
+  "gprof2dot>=2025.4.14",
   "mypy>=1.15.0",
   "mypy-extensions>=1.0.0",
   "pandas>=2.2.3",
@@ -47,6 +48,7 @@ dev = [
   "pytest>=8.3.5",
   "pytest-cov>=6.0.0",
   "pytest-html>=4.1.1",
+  "pytest-memray>=1.8.0",
   "pytest-mock>=3.14.0",
   "pytest-xdist>=3.6.1",
   "ruff>=0.9.9",

src/hla_algorithm/hla_algorithm.py

@@ -259,9 +259,6 @@ def combine_standards_stepper(
         - this is below our mismatch threshold.
         If the mismatch threshold is 0, then we will only ever get the former.
         """
-        # Keep track of matches we've already found:
-        combos: dict[tuple[int, ...], int] = {}
-
         current_rejection_threshold: int | float = float("inf")
         for std_ai, std_a in enumerate(matching_stds):
             if std_a.mismatch > current_rejection_threshold:
@@ -278,14 +275,7 @@ def combine_standards_stepper(
                 # same sequence, so check if this one's already been found.
                 combined_std_bin: tuple[int, ...] = tuple(int(s) for s in std_bin)
 
-                mismatches: int = -1
-                if combined_std_bin in combos:
-                    mismatches = combos[combined_std_bin]
-
-                else:
-                    # Note that seq is implicitly cast to a NumPy array:
-                    mismatches = np.count_nonzero(std_bin ^ seq != 0)
-                    combos[combined_std_bin] = mismatches  # cache this value
+                mismatches: int = np.count_nonzero(std_bin ^ seq != 0)
 
                 if mismatches > current_rejection_threshold:
                     continue

src/scripts/measure_resources.py

@@ -0,0 +1,96 @@
+#! /usr/bin/env python
+
+import argparse
+import csv
+import glob
+import json
+import os.path
+import re
+import subprocess
+from typing import TypedDict
+
+
+TIME_REGEX = re.compile(
+    r"^\s*Elapsed \(wall clock\) time \(h:mm:ss or m:ss\): (.*)$",
+    flags=re.MULTILINE,
+)
+MEMORY_REGEX = re.compile(
+    r"^\s*Maximum resident set size \(kbytes\): (.*)$",
+    flags=re.MULTILINE,
+)
+
+def get_wall_clock_time(time_output: str) -> str:
+    return TIME_REGEX.search(time_output).group(1)
+
+def get_max_memory_usage(time_output: str) -> str:
+    return MEMORY_REGEX.search(time_output).group(1)
+
+
+class ResourceSummary(TypedDict):
+    sample_name: str
+    wall_clock_time: str
+    max_memory_usage_kb: str
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        "Process HLA sequences and report the resource usage."
+    )
+    parser.add_argument("input_dir", help="Directory to scan for HLA sequences")
+    parser.add_argument("--output_csv", help="CSV file summary", default="out.csv")
+    args = parser.parse_args()
+
+    resource_summaries: list[ResourceSummary] = []
+    sample_regex = re.compile(r"^.*/(.*)\.BA\.txt$")
+    for exon1_filename in glob.glob(f"{args.input_dir}/*.BA.txt"):
+        sample_name: str = sample_regex.match(exon1_filename).group(1)
+        exon2_filename: str = os.path.join(args.input_dir, f"{sample_name}.BB.txt")
+        with open(exon1_filename) as f:
+            exon1: str = f.read().strip()
+        with open(exon2_filename) as f:
+            exon2: str = f.read().strip()
+
+        json_input = {
+            "seq1": exon1,
+            "seq2": exon2,
+            "locus": "B",
+        }
+        json_filename: str = os.path.join(args.input_dir, f"{sample_name}.json")
+        with open(json_filename, "w") as f:
+            json.dump(json_input, f)
+
+        print(f"----\nSample {sample_name}:")
+        result = subprocess.run(
+            [
+                "/usr/bin/time",
+                "-v",
+                "interpret_from_json",
+                json_filename,
+            ],
+            capture_output=True,
+            text=True,
+        )
+        print("stdout:")
+        print(result.stdout)
+        print("stderr:")
+        print(result.stderr)
+
+        resource_summaries.append(
+            {
+                "sample_name": sample_name,
+                "wall_clock_time": get_wall_clock_time(result.stderr),
+                "max_memory_usage_kb": get_max_memory_usage(result.stderr),
+            }
+        )
+
+    with open(args.output_csv, "w") as f:
+        resource_summary_writer = csv.DictWriter(
+            f,
+            fieldnames=("sample_name", "wall_clock_time", "max_memory_usage_kb"),
+        )
+        resource_summary_writer.writeheader()
+        resource_summary_writer.writerows(resource_summaries)
+
+
+if __name__ == "__main__":
+    main()

tests/acceptable_memory_usage_test.py

@@ -0,0 +1,27 @@
+import numpy as np
+import pytest
+
+from hla_algorithm.hla_algorithm import HLAAlgorithm
+from hla_algorithm.models import HLASequence, HLAStandard
+
+
+@pytest.mark.slow
+@pytest.mark.limit_memory("500 MB")
+def test_acceptable_memory_usage():
+    # We process a sequence produced by "mushing together" B*07:02:01G
+    # and B*45:01:01G, which as of the v2.63.0-alpha HLA alleles produces
+    # an expensive calculation.
+    hla_alg = HLAAlgorithm()
+
+    allele_1: HLAStandard = hla_alg.hla_standards["B"]["B*07:02:01G"]
+    allele_2: HLAStandard = hla_alg.hla_standards["B"]["B*45:01:01G"]
+
+    expensive_sequence = HLASequence(
+        two=(int(s) for s in np.array(allele_1.two) | np.array(allele_2.two)),
+        intron=(),
+        three=(int(s) for s in np.array(allele_1.three) | np.array(allele_2.three)),
+        name="expensive_sequence",
+        locus="B",
+    )
+
+    hla_alg.interpret(expensive_sequence)