#!/usr/bin/env modbuild # Open-source PyMOL, compiled from the GitHub source tarball into a uv venv # (careless-style uv route; conda unreachable from Ra). Default pbuild::prep # downloads + sha-verifies + unpacks both urls from files/config.yaml. # GLEW/libpng/freetype/GL headers must exist as system RPMs on the build host; # msgpack/MMTF, libxml2 (COLLADA) and VMD plugins (libnetcdf) are disabled # because those libs are not on Ra. pbuild::configure() { # modbuild's shell strips ~/.local/bin from PATH; override with UV=/path/to/uv if needed UV="${UV:-$HOME/.local/bin/uv}" # ~/.cache/uv hits the home disk quota; shared cache reuses wheels across MX builds export UV_CACHE_DIR="/opt/psi/MX/.uv-cache" # keep the standalone CPython inside PREFIX so venv symlinks never point at a home cache export UV_PYTHON_INSTALL_DIR="$PREFIX/python" "$UV" venv --python 3.12 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?" # modbuild -f re-untars over the old src dir without deleting extras; a stale # setuptools build/ tree from a failed run then gets packed into the wheel as-is # (pure-python, no _cmd.so). Wipe it so every build compiles from scratch. rm -rf "$SRC_DIR/build" # stage glm where setup.py's PREFIX_PATH lookup expects it: /include/glm. # strip_dirs applies to the glm tarball too, so headers land at $SRC_DIR/glm directly mkdir -p "$SRC_DIR/deps/include" cp -r "$SRC_DIR/glm" "$SRC_DIR/deps/include/" || \ std::die 42 "glm staging failed - glm tarball missing from SRC_DIR?" } pbuild::compile() { : } pbuild::install() { UV="${UV:-$HOME/.local/bin/uv}" export UV_CACHE_DIR="/opt/psi/MX/.uv-cache" # force the gcc module's compilers; uv's standalone CPython records clang in sysconfig export CC=gcc CXX=g++ export PREFIX_PATH="$SRC_DIR/deps" # -C k=v reaches setup.py as `build_ext --k=v` (_custom_build/backend.py). # str2bool accepts ONLY true/false (yes/no -> "Boolean value expected"). # no-vmd-plugins=false is deliberate: upstream dest is vmd_plugins, false disables them. # upstream's documented install is `pip install --no-build-isolation .`; with # default isolation the wheel builds in an env upstream never tests and comes # out pure-python (no _cmd.so) WITHOUT any error. Build deps must therefore # be present in the venv itself. "$UV" pip install --python "$PREFIX/venv/bin/python" setuptools numpy || \ std::die 42 "build deps (setuptools, numpy) install failed" # --no-cache: never reuse a cached pymol wheel — a poisoned pure-python wheel # (built from a half-failed compile) otherwise gets reinstalled forever "$UV" pip install --no-cache --no-build-isolation --python "$PREFIX/venv/bin/python" \ -C use-msgpackc=no -C no-libxml=true -C no-vmd-plugins=false \ "$SRC_DIR" || \ std::die 42 "pymol build failed - check system devel RPMs (glew, libpng, freetype, mesa-libGL)" # Qt GUI; without it pymol falls back to CLI-only "$UV" pip install --python "$PREFIX/venv/bin/python" PyQt5 || \ std::die 42 "PyQt5 install failed" [[ -x "$PREFIX/venv/bin/pymol" ]] || std::die 42 "pymol launcher missing from venv" # launcher can exist while the compiled ext is missing (pure-python wheel from a # poisoned uv cache); import _cmd directly so a broken build dies here, not at runtime "$PREFIX/venv/bin/python" -c "import pymol._cmd" || \ 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" }