Compatibility fixes for modern NumPy / sklearn / HMMER / CheckM #49
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…+, PyTorch 2.2+) Python code fixes: - Replace sklearn.cluster._kmeans private imports with public APIs - KMeans: algorithm="full" → "lloyd", drop removed n_jobs param - stable_cumsum → np.cumsum(dtype=float64) - np.int → np.int64 (removed alias in NumPy 1.24+) - .item(0) → .item() (deprecated positional arg) - torch.cuda.amp → torch.amp with explicit device_type (PyTorch 2.4+) - ruamel.yaml: Path() → file handle loading - hmmsearch: add -E 1e-10 fallback when --cut_tc fails (HMMER 3.3+) Runtime hardening: - Auto-resolve CHECKM_DATA_PATH from conda prefix - Auto-set MPLCONFIGDIR to avoid writes to restricted home dirs - Lazy imports to avoid loading ML libs for lightweight subcommands - Suppress pkg_resources deprecation warning from CheckM Environment (comebin_env.yaml): - Modernize all deps: Python 3.10-3.11, NumPy <2.0, scikit-learn 1.4+ - Move pip packages to conda-forge where available - Pin pplacer=1.1.alpha19 (>=1.1 doesn't match alpha version strings) - Pin python<3.12 for CheckM1 compatibility - Add missing ruamel.yaml and tqdm dependencies - CPU-only PyTorch (conda-forge default) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
Update COMEBin to run with modern dependencies (Python 3.11, NumPy 1.26, scikit-learn 1.4+, PyTorch 2.2+), replacing removed/deprecated APIs and fixing env solver failures.
What changed
Python code fixes:
sklearn.cluster._kmeansprivate imports → public APIs (KMeans,euclidean_distances,check_random_state,row_norms)KMeans(algorithm="full", n_jobs=-1)→KMeans(algorithm="lloyd", n_init=10)stable_cumsum→np.cumsum(dtype=np.float64)np.int→np.int64(5 instances across 3 files).item(0)→.item()(deprecated positional arg in NumPy 2.x)torch.cuda.amp.{GradScaler,autocast}→torch.amp.{GradScaler,autocast}with explicitdevice_type(PyTorch 2.4+)ruamel.yamlPath loading → file handle (avoids deprecation warning)-E 1e-10when--cut_tcfails (HMMER ≥3.3)Runtime hardening:
CHECKM_DATA_PATHfrom$CONDA_PREFIXMPLCONFIGDIRto output dir (avoids writes to restricted$HOME)pkg_resourcesdeprecation warning from CheckMEnvironment (
comebin_env.yaml):<3.12for CheckM1 compatibility)>=1.26,<2.0, scikit-learn>=1.4, PyTorch>=2.2hnswlib,python-igraph,leidenalg,scanpyfrom pip to conda-forgepplacer=1.1.alpha19(>=1.1doesn't match alpha version strings → solver failure)ruamel.yamlandtqdmdependenciesIssue tags
Fixes #44
Refs #29, #38, #11
Validation
mamba env create -f comebin_env.yamlAI Assistance
Portions of this PR were developed with assistance from OpenAI Codex (initial refactoring) and Claude Code (code review, additional fixes, env debugging).