mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
synced 2026-06-04 14:14:24 +08:00
fff63051b4
* Harden MMseqs species ID resolution fallback * Reorganize tests for CPU coverage CI * New * Fix function coverage checker def-line false positives * Expand unit coverage for helper and backend manager utilities * New. * New. * Expand unit coverage for template and post-processing helpers * Expand unit coverage for objects.py edge cases * Publish HTML coverage reports via GitHub Pages * Add CPU unit coverage for AlphaFold3 backend helpers * Reorganize tests and expand backend coverage * Reset shared test flags between cases * Expand AF3 prepare_input unit coverage * Cover AF3 and truemultimer feature creation * Test AF3 multimer MSA translation paths * Cover AF3 duplicate-residue multimer fallback * Cover AF2 resume and postprocess edge paths * Cover AF3 template mmCIF preparation * Test small script entry points * Expand workflow and ModelCIF test coverage * Add backend extras and install guide * Clarify AF3 backend installation path * Stabilize cluster GPU test runners * Document AF3 CMake SQLite hints * Simplify backend installation guide * Align AF3 install with working cluster env * Backfill typing dataclass_transform for AF2 * Pin TensorFlow for cluster installs * Fallback AF2 relax when CUDA OpenMM is unavailable * Raise AF3 default minimum bucket size * Simplify backend cluster installation guide * Fix AF3 wrapper JSON output isolation * Fix AF3 JSON wrapper outputs and MMseqs ID parsing * Fix CI entrypoint stub and Python 3.8 typing * Document release readiness test gates
105 lines
3.7 KiB
Python
105 lines
3.7 KiB
Python
import importlib.util
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import sys
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from pathlib import Path
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REPO_ROOT = Path(__file__).resolve().parents[2]
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AF2_CHECK_PATH = REPO_ROOT / "test" / "cluster" / "check_alphafold2_predictions.py"
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AF2_WRAPPER_PATH = REPO_ROOT / "test" / "cluster" / "run_alphafold2_predictions.py"
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AF3_WRAPPER_PATH = REPO_ROOT / "test" / "cluster" / "run_alphafold3_predictions.py"
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def _load_module(module_name: str, module_path: Path):
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sys.modules.pop(module_name, None)
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spec = importlib.util.spec_from_file_location(module_name, module_path)
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module = importlib.util.module_from_spec(spec)
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sys.modules[module_name] = module
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assert spec.loader is not None
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spec.loader.exec_module(module)
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return module
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def test_af2_cluster_subprocess_env_sets_safe_gpu_defaults(monkeypatch):
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module = _load_module("test_cluster_af2_check_module", AF2_CHECK_PATH)
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for name in (
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"OMP_NUM_THREADS",
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"MKL_NUM_THREADS",
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"NUMEXPR_NUM_THREADS",
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"TF_NUM_INTEROP_THREADS",
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"TF_NUM_INTRAOP_THREADS",
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"TF_FORCE_GPU_ALLOW_GROWTH",
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"TF_CPP_MIN_LOG_LEVEL",
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"XLA_PYTHON_CLIENT_PREALLOCATE",
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"XLA_PYTHON_CLIENT_MEM_FRACTION",
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"JAX_PLATFORM_NAME",
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"XLA_FLAGS",
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):
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monkeypatch.delenv(name, raising=False)
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env = module._af2_subprocess_env()
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assert env["OMP_NUM_THREADS"] == "4"
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assert env["MKL_NUM_THREADS"] == "4"
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assert env["NUMEXPR_NUM_THREADS"] == "4"
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assert env["TF_NUM_INTEROP_THREADS"] == "4"
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assert env["TF_NUM_INTRAOP_THREADS"] == "4"
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assert env["TF_FORCE_GPU_ALLOW_GROWTH"] == "true"
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assert env["TF_CPP_MIN_LOG_LEVEL"] == "2"
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assert env["XLA_PYTHON_CLIENT_PREALLOCATE"] == "false"
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assert env["XLA_PYTHON_CLIENT_MEM_FRACTION"] == "0.8"
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assert env["JAX_PLATFORM_NAME"] == "gpu"
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assert "--xla_gpu_force_compilation_parallelism=0" in env["XLA_FLAGS"]
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def test_af2_cluster_wrapper_job_script_exports_gpu_defaults(tmp_path):
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module = _load_module("test_cluster_af2_wrapper_module", AF2_WRAPPER_PATH)
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job = module.JobSpec(
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index=1,
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nodeid="test/cluster/check_alphafold2_predictions.py::TestRunModes::test__monomer",
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slug="af2_node",
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stdout_path=tmp_path / "stdout.log",
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stderr_path=tmp_path / "stderr.log",
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script_path=tmp_path / "job.sh",
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rerun_command="python -m pytest",
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)
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module.write_job_script(
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job=job,
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python_executable=sys.executable,
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use_temp_dir=True,
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cpus_per_task=8,
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)
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script_text = job.script_path.read_text(encoding="utf-8")
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assert 'OMP_NUM_THREADS="${OMP_NUM_THREADS:-4}"' in script_text
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assert 'TF_NUM_INTRAOP_THREADS="${TF_NUM_INTRAOP_THREADS:-4}"' in script_text
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assert 'JAX_PLATFORM_NAME="${JAX_PLATFORM_NAME:-gpu}"' in script_text
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assert "addopts=-ra --strict-markers" in script_text
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assert "--use-temp-dir" in script_text
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def test_af3_cluster_wrapper_job_script_sets_perf_flag(tmp_path):
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module = _load_module("test_cluster_af3_wrapper_module", AF3_WRAPPER_PATH)
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job = module.JobSpec(
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index=1,
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nodeid="test/cluster/check_alphafold3_predictions.py::TestRunModes::test__monomer",
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slug="af3_node",
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stdout_path=tmp_path / "stdout.log",
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stderr_path=tmp_path / "stderr.log",
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script_path=tmp_path / "job.sh",
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rerun_command="python -m pytest",
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)
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module.write_job_script(
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job=job,
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python_executable=sys.executable,
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use_temp_dir=True,
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include_perf=True,
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)
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script_text = job.script_path.read_text(encoding="utf-8")
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assert "export AF3_RUN_PERF_TESTS=1" in script_text
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assert "addopts=-ra --strict-markers" in script_text
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assert "--use-temp-dir" in script_text
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