From f748558fe498a0c437e5cfc2285e007cfc8e6c89 Mon Sep 17 00:00:00 2001
From: Dawn <jiaxin.duan@psi.ch>
Date: Wed, 2 Sep 2026 10:02:19 +0200
Subject: [PATCH] update qfit to include missing package

---
 qfit/README.md |  7 +++++--
 qfit/build     | 10 +++++++++-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/qfit/README.md b/qfit/README.md
index 13f6df7..695b555 100644
--- a/qfit/README.md
+++ b/qfit/README.md
@@ -13,7 +13,10 @@ follows the name/version rule as `qfit/<version>`.
 - **2025.3** (Dec 2025) — current. Post-2024-paper qFit-ligand
   (RDKit `-sm SMILES` route, `-em` flag). Python 3.12, solvers
   cvxpy + pyscipopt (SCIP) declared in `install_requires` — no
-  extras, no CPLEX size cap.
+  CPLEX size cap. One extra: `cctbx-base` (structure I/O imports
+  iotbx/scitbx/cctbx/mmtbx but upstream lists it only in conda's
+  `environment.yml`; the PyPI manylinux_2_28 wheel works on Ra
+  RHEL8 — no conda involved, anaconda repo is unreachable from Ra).
 - **3.2.2** (Aug 2022) — legacy, pre-paper qfit_ligand algorithm.
   Python 3.10 (`numpy<1.22`), cvxopt + CPLEX Community Edition
   pip-installed as extras. Last upstream tag with the `v` prefix —
@@ -54,7 +57,7 @@ module use MX unstable && module load qfit/2025.3
 which qfit_protein                     # -> .../qfit/2025.3/venv/bin/qfit_protein
 qfit_protein --help                    # argparse usage, no traceback
 qfit_ligand --help                     # should list -sm/--smiles (2024.3+)
-"$QFIT_ENV/bin/python" -c "import qfit, pyscipopt, cvxpy; print(qfit.__version__)"
+"$QFIT_ENV/bin/python" -c "import qfit, iotbx, pyscipopt, cvxpy; print(qfit.__version__)"
 ```
 
 The post-refinement scripts (`qfit_final_refine_xray.sh`) call phenix:
diff --git a/qfit/build b/qfit/build
index 3972e99..36268ba 100755
--- a/qfit/build
+++ b/qfit/build
@@ -8,7 +8,10 @@
 #   (>=81 removed pkg_resources entirely).
 # - 2024.3+ : numpy relaxed to <2 -> Python 3.12; solvers switched to
 #   cvxpy+pyscipopt and moved into install_requires (no CPLEX size cap);
-#   pkg_resources import removed -> no extras needed at all.
+#   pkg_resources import removed. BUT structure I/O now imports
+#   iotbx/scitbx/cctbx/mmtbx, and cctbx-base is only in environment.yml,
+#   not install_requires (same conda-only trap as the old solvers)
+#   -> pip cctbx-base explicitly (manylinux_2_28 wheel, Ra RHEL8 = glibc 2.28).
 # - both eras: use_scm_version needs git metadata the tarball lacks
 #   -> SETUPTOOLS_SCM_PRETEND_VERSION
 
@@ -38,9 +41,14 @@ pbuild::install() {
         # cplex is the IBM Community Edition pip wheel (problem-size limited);
         # full CPLEX needs an academic license, see README.
         3.*) extras=('setuptools<81' cvxopt cplex) ;;
+        # cctbx-base: conda-only dep upstream forgot in install_requires;
+        # PyPI wheel (not conda - anaconda repo is unreachable from Ra)
+        *)   extras=(cctbx-base) ;;
     esac
     "$UV" pip install --python "$PREFIX/venv/bin/python" \
         "${extras[@]}" "$SRC_DIR" || \
         std::die 42 "qfit install failed - check build log above"
     [[ -x "$PREFIX/venv/bin/qfit_protein" ]] || std::die 42 "qfit_protein missing from venv"
+    # full import chain (hits iotbx, solvers, ...) - catches forgotten runtime deps at build time
+    "$PREFIX/venv/bin/python" -c "import qfit" || std::die 42 "qfit import failed - missing runtime dep?"
 }