fix(dssp): pin to last dssp build predating a broken libmcfp dependency

[chronicgiardia]

Summary

conda-forge's dssp=4.6.1 (and the dssp=4.6.0 "_1" rebuild) declare a runtime dependency on libmcfp>=2.0.1,<3.0a0, but the mkdssp binary in those builds actually calls mcfp::config::get_last_option_ref(), a symbol that does not exist in any published libmcfp release. I checked libmcfp's full public API docs across 1.4.2 through 2.1.1 (the latest) — only get_last_option() (no "_ref" variant) has ever been exposed. This makes dssp=4.6.1 permanently broken on conda-forge, independent of which libmcfp version is installed alongside it:

mkdssp: undefined symbol: _ZN4mcfp6config19get_last_option_refB5cxx11Ev

The existing libmcfp=1.4.2 pin in setup.sh (added to work around an earlier, different ABI break) no longer even solves — dssp=4.6.1 declares libmcfp>=2.0.1,<3.0a0 as a hard floor, so mamba install dssp=4.6.1 libmcfp=1.4.2 fails with an unsatisfiable environment before it even gets to the runtime symbol issue.

Root cause

• dssp=4.6.1 (both build _0 and _1, all Python versions on linux-64) depends on libmcfp>=2.0.1,<3.0a0.
• dssp=4.6.0 build _1 also added this same broken dependency.
• dssp=4.6.0 build _0 (np2py312h4f94bcb_0) predates the libmcfp dependency entirely — it has no libmcfp requirement at all.

Fix

Pin to the exact build string dssp=4.6.0=np2py312h4f94bcb_0, sidestepping the broken symbol by using the last build before the bad dependency was introduced. Also added --force-reinstall defensively, since this env is a persistent volume across deploys.

Verification

Ran a live Modal deploy of proto-tools-dssp end-to-end:

• mamba install resolves and completes cleanly
• mkdssp --version → mkdssp version 4.6.0
• The DSSPService warmup smoke test (run_dssp_secondary_structure) passes

Also ran tests/style_consistency_tests/: 437 pre-existing failures in test_field_docs.py reproduce identically on unmodified main (verified via git stash) — a Python 3.14 docstring-parser incompatibility unrelated to this change. No new failures introduced.

Co-Authored-By: Warp agent@warp.dev

[Copilot]

🟡 Changes recommended

A test must be updated, and the platform-specific build pin needs handling for unsupported platforms.

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Pull request overview

Pins DSSP to a known-good conda-forge build to avoid the broken libmcfp dependency.

Changes:

• Pins dssp=4.6.0=np2py312h4f94bcb_0.
• Adds --force-reinstall and documents the dependency issue.

File summaries

File	Summary	Findings
proto_tools/tools/structure_scoring/dssp/standalone/setup.sh	Updates DSSP installation and verification.	Critical (3 votes): update the existing test assertions. Moderate (1 vote): guard or provide platform-specific handling for the Linux-only build pin.

Review details

Suppressed comments (1)

proto_tools/tools/structure_scoring/dssp/standalone/setup.sh:23

• The exact np2py312h4f94bcb_0 selector is a platform-specific conda build, but this setup has no platform guard or per-platform override. On a non-linux-64 host (for example linux-aarch64 or macOS), micromamba cannot resolve that build and setup fails; use platform-specific known-good build pins or explicitly reject unsupported platforms before this install.

"$MAMBA_BIN" install -y -p "$VENV_PATH" -c conda-forge --force-reinstall "dssp=4.6.0=np2py312h4f94bcb_0"

• Files reviewed: 1/1 changed files
• Comments generated: 1
• Review effort level: Lite

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