install qfit

qfit/README.md

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+# qfit
+
+qFit 3 — automated multiconformer model building for X-ray
+crystallography and cryo-EM (`qfit_protein`, `qfit_ligand`,
+`qfit_covalent_ligand`, `edia`, ...). Repo is named `qfit-3.0`; module
+follows the name/version rule as `qfit/<version>`.
+
+- Upstream: https://github.com/ExcitedStates/qfit-3.0
+- License: MIT
+
+## How it is built
+
+uv route (careless-style) from the sha-pinned GitHub tag tarball into
+`$PREFIX/venv`, Python **3.10** (upstream pins `numpy<1.22`, which has
+no 3.11+ wheels). The small C extension builds with the gcc/12.3.0
+module (plain C, no gcc runtime dep). Upstream quirks the recipe
+handles:
+
+- `use_scm_version=True` but the tarball has no `.git` →
+  `SETUPTOOLS_SCM_PRETEND_VERSION=<version>` is exported for the build.
+- MIQP solvers are only listed in upstream's conda `environment.yml`,
+  not in `install_requires` → `cvxopt` and `cplex` are pip-installed
+  explicitly.
+
+**CPLEX caveat**: the pip `cplex` wheel is the IBM Community Edition,
+limited to 1000 variables/constraints. Large residues/ligands may hit
+the cap; the fix is a full academic CPLEX install into the venv
+(https://www.ibm.com/academic/) — documented by upstream.
+
+`uv` must be on the build host (default `~/.local/bin/uv`, override
+with `UV=/path/to/uv`).
+
+## Building on Ra
+
+```sh
+module use unstable && module load modbuild/2.1.3
+cd qfit
+modbuild build \
+    --tmpdir=/das/work/p21/p21515/.cache/Pmodules \
+    --distdir=/das/work/p21/p21515/.cache/Pmodules \
+    3.2.2
+module use MX unstable && module load qfit/3.2.2
+```
+
+## Verifying the install
+
+```sh
+which qfit_protein                     # -> .../qfit/3.2.2/venv/bin/qfit_protein
+qfit_protein --help                    # argparse usage, no traceback
+"$QFIT_ENV/bin/python" -c "import qfit, cplex, cvxopt; print(qfit.__version__)"
+```
+
+The post-refinement scripts (`qfit_final_refine_xray.sh`) call phenix:
+`module load phenix` before using them.
+
+## Adding a new version
+
+Add version + tarball sha256 in `files/config.yaml` (`sha256sum` the
+downloaded `v<ver>.tar.gz`), check whether upstream unpinned
+numpy/pandas (a newer pin may allow a newer venv Python), then build as
+above.

qfit/build

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+#!/usr/bin/env modbuild
+
+# qFit (multiconformer model building), uv route from the sha-pinned GitHub
+# tarball. Three upstream traps handled here:
+# - use_scm_version needs git metadata the tarball lacks -> SETUPTOOLS_SCM_PRETEND_VERSION
+# - numpy pinned <1.22 -> newest CPython with wheels is 3.10
+# - MIQP solvers (cvxopt, cplex) are only in environment.yml, not
+#   install_requires -> pip them explicitly or qfit dies at runtime
+
+pbuild::configure() {
+    # modbuild's shell strips ~/.local/bin from PATH; override with UV=/path/to/uv if needed
+    UV="${UV:-$HOME/.local/bin/uv}"
+    export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
+    export UV_PYTHON_INSTALL_DIR="$PREFIX/python"
+    "$UV" venv --python 3.10 "$PREFIX/venv" || std::die 42 "uv venv failed - is uv at \$UV?"
+}
+
+pbuild::compile() {
+    :
+}
+
+pbuild::install() {
+    UV="${UV:-$HOME/.local/bin/uv}"
+    export UV_CACHE_DIR="/opt/psi/MX/.uv-cache"
+    export CC=gcc
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${V_PKG}"
+    # cplex is the IBM Community Edition pip wheel (problem-size limited);
+    # full CPLEX needs an academic license, see README
+    "$UV" pip install --python "$PREFIX/venv/bin/python" \
+        cvxopt cplex "$SRC_DIR" || \
+        std::die 42 "qfit install failed - check build log above"
+    [[ -x "$PREFIX/venv/bin/qfit_protein" ]] || std::die 42 "qfit_protein missing from venv"
+}

qfit/files/config.yaml

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+---
+format: 1
+qfit:
+  defaults:
+    group: MX
+    overlay: base
+    relstage: unstable
+    urls:
+      # repo is named qfit-3.0 but the tool/module is qfit (name/version guardrail)
+      - url: https://github.com/ExcitedStates/qfit-3.0/archive/refs/tags/v${V_PKG}.tar.gz
+        name: qfit-${V_PKG}.tar.gz
+        strip_dirs: 1
+  shasums:
+    qfit-3.2.2.tar.gz: b3c37a45598c31aabfb0a0024710b8e22ea6ffd49355ad69a17b93a7777e699d
+  versions:
+    3.2.2:
+      config:
+        relstage: unstable
+        # gcc for the small C extension (_extensions.c); plain C, so no runtime dep
+        build_requires: [gcc/12.3.0]

qfit/modulefile

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+#%Module1.0
+
+module-whatis       "qFit - automated multiconformer model building for X-ray and cryo-EM"
+module-url          "https://github.com/ExcitedStates/qfit-3.0"
+module-license      "MIT"
+module-maintainer   "MX Data <jiaxin.duan@psi.ch>"
+
+module-help     "
+qFit 3: qfit_protein, qfit_ligand, qfit_covalent_ligand, edia and
+friends, in a private Python venv with cvxopt + IBM CPLEX Community
+Edition as MIQP solvers. The post-refinement scripts
+(qfit_final_refine_xray.sh) expect phenix on PATH - load a phenix
+module for those.
+"
+
+setenv          QFIT_ENV    $PREFIX/venv
+prepend-path    PATH        $PREFIX/venv/bin