duan_jandClaude Fable 5
3db277e287
Both tarballs unpack stripped into SRC_DIR; glm unpacked last and its CMakeLists.txt shadowed pymol's. setup.py's cmake-based build_ext then configured glm instead of pymol, built glm's test suite successfully (372 .o, ~1min, exit 0) and produced a pure-python wheel with no error. - config.yaml: glm url now FIRST so pymol's top-level files win - build: guard that SRC_DIR/CMakeLists.txt is pymol's (TARGET_NAME) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
72 lines
4.0 KiB
Python
Executable File
72 lines
4.0 KiB
Python
Executable File
#!/usr/bin/env modbuild
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# Open-source PyMOL, compiled from the GitHub source tarball into a uv venv
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# (careless-style uv route; conda unreachable from Ra). Default pbuild::prep
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# downloads + sha-verifies + unpacks both urls from files/config.yaml.
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# GLEW/libpng/freetype/GL headers must exist as system RPMs on the build host;
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# msgpack/MMTF, libxml2 (COLLADA) and VMD plugins (libnetcdf) are disabled
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# because those libs are not on Ra.
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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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# ~/.cache/uv hits the home disk quota; shared cache reuses wheels across MX builds
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export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
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# keep the standalone CPython inside PREFIX so venv symlinks never point at a home cache
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export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
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"$UV" venv --python 3.12 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
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# modbuild -f re-untars over the old src dir without deleting extras; a stale
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# setuptools build/ tree from a failed run then gets packed into the wheel as-is
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# (pure-python, no _cmd.so). Wipe it so every build compiles from scratch.
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rm -rf "$SRC_DIR/build"
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# stage glm where setup.py's PREFIX_PATH lookup expects it: <prefix>/include/glm.
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# strip_dirs applies to the glm tarball too, so headers land at $SRC_DIR/glm directly
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mkdir -p "$SRC_DIR/deps/include"
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cp -r "$SRC_DIR/glm" "$SRC_DIR/deps/include/" || \
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std::die 42 "glm staging failed - glm tarball missing from SRC_DIR?"
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# both tarballs unpack stripped into SRC_DIR and their top-level files
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# collide; the glm tarball once shadowed pymol's CMakeLists.txt and cmake
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# silently built glm's tests instead of _cmd. Guard: pymol's CMakeLists
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# passes TARGET_NAME from setup.py, glm's does not.
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grep -q TARGET_NAME "$SRC_DIR/CMakeLists.txt" || \
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std::die 42 "SRC_DIR/CMakeLists.txt is not pymol's - glm overwrote it; check url order in files/config.yaml (glm must unpack first)"
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}
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pbuild::compile() {
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:
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}
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pbuild::install() {
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UV="${UV:-$HOME/.local/bin/uv}"
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export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
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# force the gcc module's compilers; uv's standalone CPython records clang in sysconfig
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export CC=gcc CXX=g++
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export PREFIX_PATH="$SRC_DIR/deps"
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# -C k=v reaches setup.py as `build_ext --k=v` (_custom_build/backend.py).
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# str2bool accepts ONLY true/false (yes/no -> "Boolean value expected").
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# no-vmd-plugins=false is deliberate: upstream dest is vmd_plugins, false disables them.
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# upstream's documented install is `pip install --no-build-isolation .`; with
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# default isolation the wheel builds in an env upstream never tests and comes
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# out pure-python (no _cmd.so) WITHOUT any error. Build deps must therefore
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# be present in the venv itself.
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"$UV" pip install --python "$PREFIX/venv/bin/python" setuptools numpy || \
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std::die 42 "build deps (setuptools, numpy) install failed"
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# --no-cache: never reuse a cached pymol wheel — a poisoned pure-python wheel
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# (built from a half-failed compile) otherwise gets reinstalled forever
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"$UV" pip install --no-cache --no-build-isolation --python "$PREFIX/venv/bin/python" \
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-C use-msgpackc=no -C no-libxml=true -C no-vmd-plugins=false \
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"$SRC_DIR" || \
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std::die 42 "pymol build failed - check system devel RPMs (glew, libpng, freetype, mesa-libGL)"
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# Qt GUI; without it pymol falls back to CLI-only
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"$UV" pip install --python "$PREFIX/venv/bin/python" PyQt5 || \
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std::die 42 "PyQt5 install failed"
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[[ -x "$PREFIX/venv/bin/pymol" ]] || std::die 42 "pymol launcher missing from venv"
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# launcher can exist while the compiled ext is missing (pure-python wheel from a
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# poisoned uv cache); import _cmd directly so a broken build dies here, not at runtime
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"$PREFIX/venv/bin/python" -c "import pymol._cmd" || \
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std::die 42 "pymol._cmd import failed - ext .so missing; try 'uv cache clean pymol' (dist name is pymol, not pymol-open-source) and rebuild"
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}
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