From 95250c322bf27ea7ee9ad7146c3981e31233f04e Mon Sep 17 00:00:00 2001 From: Richard Liang Date: Tue, 28 Apr 2026 16:28:38 -0700 Subject: [PATCH 1/3] Closes #22. Added a test that the memory usage doesn't balloon. Also added some other supporting code, like a CI workflow to run the test on a schedule, and also the one-off script that I used to help measure resource consumption of the code. --- .devcontainer/devcontainer.json | 3 +- .../acceptable_memory_usage_test.yml | 41 +++ pyproject.toml | 2 + src/hla_algorithm/hla_algorithm.py | 12 +- src/scripts/measure_resources.py | 96 +++++++ tests/acceptable_memory_usage_test.py | 27 ++ uv.lock | 245 ++++++++---------- 7 files changed, 284 insertions(+), 142 deletions(-) create mode 100644 .github/workflows/acceptable_memory_usage_test.yml create mode 100644 src/scripts/measure_resources.py create mode 100644 tests/acceptable_memory_usage_test.py diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index afcdb87..6a8e404 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -41,7 +41,8 @@ "openssh-client", "libaio-dev", "unzip", - "yamllint" + "yamllint", + "time" ], "install Ruby": [ "/usr/bin/apt", diff --git a/.github/workflows/acceptable_memory_usage_test.yml b/.github/workflows/acceptable_memory_usage_test.yml new file mode 100644 index 0000000..7f5e62e --- /dev/null +++ b/.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 diff --git a/pyproject.toml b/pyproject.toml index 5c4fe3c..efa68a1 100644 --- a/pyproject.toml +++ b/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", diff --git a/src/hla_algorithm/hla_algorithm.py b/src/hla_algorithm/hla_algorithm.py index 3612b16..07240f8 100644 --- a/src/hla_algorithm/hla_algorithm.py +++ b/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 diff --git a/src/scripts/measure_resources.py b/src/scripts/measure_resources.py new file mode 100644 index 0000000..fc1682e --- /dev/null +++ b/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 + + +def get_wall_clock_time(time_output: str) -> str: + time_regex = re.compile( + r"^\s*Elapsed \(wall clock\) time \(h:mm:ss or m:ss\): (.*)$", + flags=re.MULTILINE, + ) + return time_regex.search(time_output).group(1) + + +def get_max_memory_usage(time_output: str) -> str: + memory_regex = re.compile( + r"^\s*Maximum resident set size \(kbytes\): (.*)$", + flags=re.MULTILINE, + ) + return memory_regex.search(time_output).group(1) + + +class ResourceSummary(TypedDict): + sample_name: str + wall_clock_time: str + max_memory_usage_kb: str + + +def main(): + parser = argparse.ArgumentParser( + "Process HLA sequences and report the resource usage." + ) + parser.add_argument("input_dir", help="Directory to scan for HLA sequences") + parser.add_argument("--output_csv", help="CSV file summary", default="out.csv") + args = parser.parse_args() + + resource_summaries: list[ResourceSummary] = [] + sample_regex = re.compile(r"^.*/(.*)\.BA\.txt$") + 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() diff --git a/tests/acceptable_memory_usage_test.py b/tests/acceptable_memory_usage_test.py new file mode 100644 index 0000000..0f4a693 --- /dev/null +++ b/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) diff --git a/uv.lock b/uv.lock index e2e9ef1..6c6a1cd 100644 --- a/uv.lock +++ b/uv.lock @@ -1,10 +1,9 @@ version = 1 revision = 3 -requires-python = ">=3.10" +requires-python = ">=3.11, <=3.13" resolution-markers = [ - "python_full_version < '3.11'", - "python_full_version == '3.11.*'", "python_full_version >= '3.12'", + "python_full_version < '3.12'", ] [[package]] @@ -25,12 +24,6 @@ dependencies = [ ] sdist = { url = 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file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/acceptable_memory_usage_test.yml b/.github/workflows/acceptable_memory_usage_test.yml index 7f5e62e..f33f84e 100644 --- a/.github/workflows/acceptable_memory_usage_test.yml +++ b/.github/workflows/acceptable_memory_usage_test.yml @@ -3,8 +3,8 @@ name: performance_test on: schedule: - cron: "0 0 * * *" - - timezone: "America/Vancouver" - workflow-dispatch: + timezone: "America/Vancouver" + workflow_dispatch: concurrency: group: test-${{ github.head_ref }} From 97b17d6dff107962e4e13cd8bc6c03af9f7c46bc Mon Sep 17 00:00:00 2001 From: rhliang Date: Tue, 5 May 2026 15:49:17 -0700 Subject: [PATCH 3/3] Update src/scripts/measure_resources.py Using David's suggestion from review. Co-authored-by: David Rickett <25559687+va7eex@users.noreply.github.com> --- src/scripts/measure_resources.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/src/scripts/measure_resources.py b/src/scripts/measure_resources.py index fc1682e..a05f4b1 100644 --- a/src/scripts/measure_resources.py +++ b/src/scripts/measure_resources.py @@ -10,20 +10,20 @@ from typing import TypedDict -def get_wall_clock_time(time_output: str) -> str: - time_regex = re.compile( - r"^\s*Elapsed \(wall clock\) time \(h:mm:ss or m:ss\): (.*)$", - flags=re.MULTILINE, - ) - return time_regex.search(time_output).group(1) +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: - memory_regex = re.compile( - r"^\s*Maximum resident set size \(kbytes\): (.*)$", - flags=re.MULTILINE, - ) - return memory_regex.search(time_output).group(1) + return MEMORY_REGEX.search(time_output).group(1) class ResourceSummary(TypedDict):