Impress r - #58
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…eviews Pipeline changes (examples/small_molecule_binding/): - Rewrite all tasks from capture_stdio to local_task=True using asyncio.create_subprocess_shell; redirect stdout+stderr to per-task .log files (only surface on failure) - Add _gpu_env() helper to propagate Dragon Policy gpu_affinity via CUDA_VISIBLE_DEVICES - Add CIF.GZ→PDB gemmi conversion before MPNN (LigandMPNN only reads PDB format) - Make scripts_path overridable via kwargs - Add mpnn_run.py: numpy deprecated alias shim for LigandMPNN's bundled openfold af2.sh: - Detect colabfold_batch from active venv or pixi env; error if not found - Use COLABFOLD_CACHE_DIR env var for model weights; fallback to ~/.cache/colabfold - Pass --data flag (not --data-dir) and --num-models 1 for integration runs rfd3.sh: - Add --writable-tmpfs --bind /scratch:/scratch to apptainer exec (required on Delta) - Set PYTHONNOUSERSITE=1 to prevent host .local packages contaminating container impress_manager.py (bug fix): - kill_parent path appended bare pipeline instead of (pipeline, future) tuple → ValueError on unpack in cleanup loop; fixed to append (pipeline, pipeline_future) - Surface pipeline exceptions via future.exception() and log via pipeline_failed() logger.py: - Add pipeline_failed() method for error-level pipeline failure reporting Code reviews: - src/CODE_REVIEW.md: bugs and quality issues in impress src/ - examples/small_molecule_binding/CODE_REVIEW.md: pipeline + scripts review - examples/protien_binding_usecase/CODE_REVIEW.md: protein binding example review Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
File was present in origin/main but absent from the ipdps_pdz_usecase base branch. Added with the same DragonExecutionBackendV3 → DragonExecutionBackend update applied to run_small_molecule_binding.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
Conflict resolutions: - examples/protein_binding/protein_binding.py: took origin/main version (standalone Boltz-capable pipeline; moved out of src/impress/pipelines/) - examples/small_molecule_binding/run_nonadaptive.py: kept HEAD version (DragonExecutionBackend, not V3) - examples/protien_binding_usecase/run_protein_binding.py: accepted deletion (file lives in examples/protein_binding/ in main) - AU files (CODE_REVIEW.md, SKILL.md, delta_env_setup.sh, delta_gpu_run.sh): staged at their new location in examples/protein_binding/ per main's rename src/impress/pipelines/protein_binding.py deleted: concrete pipeline moved to examples/protein_binding/protein_binding.py in main branch. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
- src/: remove all protein_binding.py findings (file moved to examples/protein_binding/ in main merge); add note at header - examples/small_molecule_binding/: add run_nonadaptive.py to scope; extend debug-logging finding to cover both runner files; add findings for commented-out backend and hardcoded pipeline index list - examples/protein_binding/: full rewrite — new header (directory renamed protein_binding/), expanded scope to cover protein_binding.py (Boltz), protein_binding_run.py, run_nonadaptive.py; add findings for hardcoded Anvil MPNN_PATH, hardcoded peptide sequence, concurrent Boltz gather, unguarded os.unlink, DragonExecutionBackendV3 rename in all three runner files, stale delta_gpu_run.sh paths; remove resolved typo-directory finding and fixed log-message typo finding Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
…nding/, protein_binding/ Bugs fixed: - filter_shape.py: undefined sfxn → sfxn_clean in RosettaScripts XML; add argparse - packmin.py: rosetta.* → pyrosetta.rosetta.* imports; remove commented dead code - mpnn_wrapper.py (pb): #!/bin/sh shebang → #!/usr/bin/env python3 - mpnn_wrapper.py (pb): temperature type=int → type=float - impress_manager.py: WorkflowEngine shutdown in try/finally; flow=None in __init__; guard submit_new_pipelines - impress_pipeline.py: remove @AbstractMethod from finalize; add no-op base impl Potential issues: - protein_binding.py, small_molecule_binding.py: Anvil hardcoded paths → None + ValueError - protein_binding.py: os.unlink → Path.unlink(missing_ok=True) - protein_binding.py: Boltz gather gated with Semaphore(2) via _guarded_s4 - protein_binding_run.py, run_protein_binding.py, run_nonadaptive.py (pb): DragonExecutionBackendV3 → DragonExecutionBackend - run_protein_binding.py: adaptive_criteria async→def; CSV path uses pipeline.base_path - delta_gpu_run.sh: path typo protien→protein; LD_LIBRARY_PATH guarded; tasks-per-node=1; eval→source Code quality: - run_small_molecule_binding.py: DEBUG→INFO logging; remove unused ThreadPoolExecutor imports - run_nonadaptive.py (smb): DEBUG→INFO; remove commented-out LocalExecutionBackend import - protein_binding_run.py, run_nonadaptive.py (pb): DEBUG→INFO logging - filter_shape.py: remove redundant .close() in with blocks - filter_energy.py: remove unconditional print to stdout - fastrelax.sh: quote $0 in dirname - af2.sh: remove diagnostic echo lines - af2_multimer_reduced.sh: remove unused /tmp/work /tmp/upper - rfd3.sh: fix comment arg order ($4=diffusion_batch_size $5=scaffold_arg) - small_molecule_binding.py: remove dead fixed_residues_file comment - mpnn_wrapper.py (pb): chains==None → chains is None - impress_manager.py: log buffered count before clear (fix stale-0 bug) - logger.py: add min_level filtering; fix error()/critical() to use output_stream Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
…g integration Combines modern IMPRESS protein_binding (Boltz structure prediction) with ROME-A online ProteinMPNN fine-tuning. ROME hooks live entirely in the adaptive function so the pipeline class stays clean. Includes SLURM scripts, env setup, score analysis plotting script, and run 21736435 report. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
Plot 3 now shows depth-stratified mean trajectories (root/sub1/sub2/sub3) instead of a single global mean, surfacing the ROME signal more clearly. Report updated with final 296-design stats, per-depth table, and revised key observations. plot_rome_scores.py updated to match. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
- delta_env_setup.sh (all examples): source lmod in non-interactive bash, use `module load python` for Python detection, fix version formula (major*100+minor), add matplotlib, export VIRTUAL_ENV before PyRosetta installer, pin dragonhpc==0.14.1 (0.14.2 breaks on Delta runtime), remove hardcoded bblj allocation from MINIFORGE and _scratch fallbacks - delta_gpu_run.sh: point default IMPRESS_VENV to correct per-example venv - impress_r/plot_rome_scores.py: remove hardcoded bblj allocation from SCRATCH fallback; require --csv-dir when SCRATCH is unset - small_molecule_binding/small_molecule_binding.py: prefix scaffold_arg with + for Hydra append semantics (scaffoldguided.target_pdb) - small_molecule_binding/delta_env_setup.sh: wrap COLABFOLD_CACHE_DIR in pathlib.Path() for download_alphafold_params Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01DbNxkFCwkCEEkHnN8xGH7Q
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test branch only. mergeable activities moved to other branches. |
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add impress_r use case