duan_jandClaude Fable 5
4ffc1b152d
Separate module from PanDDA (different library): self-contained python 3.9 venv (torch==1.13.1 caps at py3.10), torch from the pytorch CPU wheel index, ~1 GB of CNN scoring models pre-fetched at build time because the package dir is read-only for users under /opt/psi. ccp4/9.0 runtime dep only, for pandda.inspect / pandda.export. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_0152MuuYUaapP7CtxrDAfvBh
52 lines
2.5 KiB
Python
52 lines
2.5 KiB
Python
#!/usr/bin/env modbuild
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pbuild::prep() {
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:
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}
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pbuild::configure() {
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# modbuild's shell strips ~/.local/bin from PATH; override with UV=/path/to/uv if needed
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UV="${UV:-$HOME/.local/bin/uv}"
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export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
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export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
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# python 3.9: PanDDA2's torch==1.13.1 pin has no wheels past 3.10, README targets 3.9
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"$UV" venv --python 3.9 "$PREFIX/venv" || \
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std::die 42 "PanDDA2: uv venv failed — is uv at \$UV?"
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}
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pbuild::compile() {
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:
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}
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pbuild::install() {
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UV="${UV:-$HOME/.local/bin/uv}"
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export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
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# xchem/PanDDA2 master @ 2026-08-18, pinned for reproducibility — the repo
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# has no usable release tags (only 'alpha'). Bump sha to update.
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local -r sha=d513af6d8c49b602d4fd91c084fe62b7fb19da8e
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# cpu extra-index: plain torch==1.13.1 from PyPI drags the ~2 GB CUDA build;
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# the project's own [tool.uv.pip] cpu index only applies inside its repo dir
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"$UV" pip install --python "$PREFIX/venv/bin/python" \
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--extra-index-url https://download.pytorch.org/whl/cpu \
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"pandda_2_gemmi @ git+https://github.com/xchem/PanDDA2.git@${sha}" || \
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std::die 42 "PanDDA2: uv pip install from GitHub failed"
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# First run gdown-fetches ~1 GB of CNN scoring models NEXT TO THE INSTALLED
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# CODE (pandda_gemmi/pandda/get_scoring_models.py) — read-only for users
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# under /opt/psi, so fetch them now into the exact dir the code checks.
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local cnn_dir
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cnn_dir=$("$PREFIX/venv/bin/python" -c 'import os, inspect; from pandda_gemmi.cnn import LitEventScoring; print(os.path.dirname(inspect.getfile(LitEventScoring)))') || \
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std::die 42 "PanDDA2: import pandda_gemmi.cnn failed — install is broken"
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local -r GD="$PREFIX/venv/bin/gdown"
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"$GD" 1b58MUIJdIYyYHr-UhASVCvIWtIgrLYtV -O "$cnn_dir/model_event.ckpt" && \
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"$GD" 1qyPqPylOguzXmt6XSFaXCKrnvb8gZ8E2 -O "$cnn_dir/model_event_config.yaml" && \
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"$GD" 15RnkrGtEmFvtBvIlwfaUE1QfQrD2npnu -O "$cnn_dir/event_score_quantiles.csv" && \
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"$GD" 17ow_rxuEvi0LitMP_jTWGMSDt-FfJCkR -O "$cnn_dir/model_build.ckpt" && \
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"$GD" 1HEXHZ6kfh92lQoWBHalGbUJ-iCsOIkFo -O "$cnn_dir/model_build_config.yaml" || \
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std::die 42 "PanDDA2: model fetch from Google Drive failed (blocked or quota) — download the 5 files by hand and copy them into ${cnn_dir}"
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[[ -x "$PREFIX/venv/bin/pandda2.analyse" ]] || \
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std::die 42 "PanDDA2: venv/bin/pandda2.analyse missing — install incomplete"
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}
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