Merge pull request #26580 from pavelToman/patch-42

add patch to fix DistGeomHelpers test in RDKit v2026.03.4

Author: boegel

easybuild/easyconfigs/r/RDKit/RDKit-2026.03.4-foss-2026.1.eb

@@ -67,13 +67,16 @@ sources = [
         ),
     },
 ]
+patches = ['RDKit-2026.03.4_relax-DistGeomHelpers-tests.patch']
 checksums = [
     {'Release_2026_03_4.tar.gz': 'a8bff65bdf13dd47a01f707f7759dd59124a8742f8c50952c2ceae9523b4fd2b'},
     {'INCHI-1-SRC.zip': 'b42d828b5d645bd60bc43df7e0516215808d92e5a46c28e12b1f4f75dfaae333'},
     {'freesasa-2.0.3.tar.gz': 'ba1d4f7e9dd51ae2452b5c3a80ac34039d51da4826dae1dbe173cd7a1d6aca94'},
     {'RingDecomposerLib-1.1.3_rdkit.tar.gz': '944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715'},
     {'pubchem-align3d-daefab3.tar.gz': '4871a08104c660890015f27d32a0147fc32df69a8962ca5cd1fe54ef6319c779'},
     {'chemdraw-1.0.14.tar.gz': 'bedd75643b9bfaee1663fc41814370ac9329c8d0934e970179929cb355a82aff'},
+    {'RDKit-2026.03.4_relax-DistGeomHelpers-tests.patch':
+     '9762a3a7f2c089aaf1e4d8de0ae327fde1618a54f8ad1838a277e08b48680284'},
 ]
 
 _boost_version = '1.90.0'
@@ -125,14 +128,13 @@ buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./'
 # Specify path for libraries so that they are found during the tests when the module is built with --rpath flag
 pretestopts = 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && '
 pretestopts += 'export RDBASE=$PWD && '
-pretestopts += 'export PYTHONPATH=$PWD:$PYTHONPATH &&'
+pretestopts += 'export PYTHONPATH=$PWD:$PYTHONPATH && '
 
 runtest = True
 
 testopts = (
     "-j %(parallel)s -E "
     "'pythonSourceTests|"  # skip test with known issues
-    "testDistGeomHelpers|"  # platform-sensitive ETKDG/distance-geometry regression checks
     "moldraw2DTestCatch'"  # strict MolDraw2D SVG/PNG rendering-regression checks that are sensitive to font/rendering
     " || ctest --rerun-failed --output-on-failure -j 1"  # rerun failed tests serially to catch flaky failures
 )

easybuild/easyconfigs/r/RDKit/RDKit-2026.03.4_relax-DistGeomHelpers-tests.patch

@@ -0,0 +1,33 @@
+Relax platform-sensitive DistGeomHelpers test expectations.
+
+RDKit 2026.03.4's testDistGeomHelpers can fail on native CPU-optimized
+builds because small platform-dependent numerical differences affect both
+the ETKDGv3 reference-coordinate comparison and RMS-based conformer
+pruning. Relax the compareConfs coordinate tolerance from 0.05 to 0.1 and
+accept either 7 or 8 retained conformers in the AIO symmetry-pruning test.
+These changes affect the test suite only and do not modify installed RDKit
+functionality.
+See https://github.com/rdkit/rdkit/issues/9406
+
+Author: Pavel Tomanek (Inuits/UGent) with help from ChatGPT5.6
+diff --git a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
+--- a/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
++++ b/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
+@@ -125,7 +125,7 @@ void compareConfs(const RWMol *m, const RWMol *expected, int molConfId = -1,
+             expected->getAtomWithIdx(i)->getAtomicNum());
+     RDGeom::Point3D pt1i = conf1.getAtomPos(i);
+     RDGeom::Point3D pt2i = conf2.getAtomPos(i);
+-    CHECK((pt1i - pt2i).length() < 0.05);
++    CHECK((pt1i - pt2i).length() < 0.1);
+   }
+ }
+ }  // namespace
+@@ -1706,7 +1706,7 @@ TEST_CASE("testSymmetryPruningAIO") {
+   CHECK(cids.size() == 3);
+   params.useSymmetryForPruning = false;
+   cids = DGeomHelpers::EmbedMultipleConfs(*mol, 50, params);
+-  CHECK(cids.size() == 8);
++  CHECK((cids.size() == 7 || cids.size() == 8));
+ }
+ 
+ TEST_CASE("testMissingHsWarning") {