Merge for 2.20.1 release

salilab · Jan 10, 2024 · c959ef1 · c959ef1
2 parents dcb2ac4 + 1423e5d
commit c959ef1
Show file tree

Hide file tree

Showing 16 changed files with 80 additions and 75 deletions.
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,6 +1,12 @@
 ChangeLog {#changelog}
 =========
 
+# 2.20.1 - 2024-01-16 # {#changelog_2_20_1}
+- Bugfix: fix `soap_score` crash when scoring multiple models with an
+  orientation-dependent SOAP score.
+- Bugfix: allow building with SWIG 4.2.
+- Bugfix: various fixes for Python 3.12.
+
 # 2.20.0 - 2023-12-21 # {#changelog_2_20_0}
 - The Windows .exe installer now supports Python 3.7 through 3.12.
 - RPM packages for IMP for RedHat Linux (and clones such as Alma or Rocky)

diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ new shell.
 Copyright and License information
 =================================
 
-IMP is Copyright 2007-2023 IMP Inventors. The IMP Inventors are
+IMP is Copyright 2007-2024 IMP Inventors. The IMP Inventors are
 Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman,
 Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan,
 Seung Joong Kim, Yannick Spill, Riccardo Pellarin.

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.20.0
+2.20.1
diff --git a/doc/manual/licenses.md b/doc/manual/licenses.md
@@ -1,7 +1,7 @@
 Copyright and licenses {#licenses}
 ======================
 
-%IMP is Copyright 2007-2023 %IMP Inventors. The %IMP Inventors are
+%IMP is Copyright 2007-2024 %IMP Inventors. The %IMP Inventors are
 Andrej Sali, Ben Webb, Daniel Russel, Keren Lasker, Dina Schneidman,
 Javier Velázquez-Muriel, Friedrich Förster, Elina Tjioe, Hao Fan,
 Seung Joong Kim, Yannick Spill, Riccardo Pellarin.

diff --git a/modules/algebra/pyext/IMP_algebra.vector.i b/modules/algebra/pyext/IMP_algebra.vector.i
@@ -103,21 +103,21 @@ IMP_SWIG_ALGEBRA_VALUE_D(IMP::algebra,  Vector);
 
 %extend IMP::algebra::VectorD<-1> {
   double __getitem__(int index) const {
-    int D = self->get_dimension();
-    if (index >= 0 && index < D) {
+    int dim = self->get_dimension();
+    if (index >= 0 && index < dim) {
       return self->operator[](index);
-    } else if (index <= -1 && index >= -(D)) {
-      return self->operator[](index + D);
+    } else if (index <= -1 && index >= -(dim)) {
+      return self->operator[](index + dim);
     } else {
       throw IMP::IndexException("VectorD index out of range");
     }
   }
   void __setitem__(int index, double val) {
-    int D = self->get_dimension();
-    if (index >= 0 && index < D) {
+    int dim = self->get_dimension();
+    if (index >= 0 && index < dim) {
       self->operator[](index) = val;
-    } else if (index <= -1 && index >= -(D)) {
-      self->operator[](index + D) = val;
+    } else if (index <= -1 && index >= -(dim)) {
+      self->operator[](index + dim) = val;
     } else {
       throw IMP::IndexException("VectorD assignment index out of range");
     }

diff --git a/modules/algebra/pyext/swig.i-in b/modules/algebra/pyext/swig.i-in
@@ -235,21 +235,17 @@ IMP_SWIG_ALGEBRA_FUNCTION_DS_D(Vector, get_vertices, UnitSimplex);
 IMP_SWIG_ALGEBRA_FUNCTION_D_DD(Vector, get_increasing_from_embedded, UnitSimplex, Vector);
 IMP_SWIG_ALGEBRA_FUNCTION_D_DD(Vector, get_embedded_from_increasing, UnitSimplex, Vector);
 
-namespace IMP {
- namespace algebra {
-   %template(_AxisAnglePair) ::std::pair<IMP::algebra::VectorD<3>,double>;
+%template(_AxisAnglePair) std::pair<IMP::algebra::VectorD<3>,double>;
 
-   %template(get_transformation_aligning_first_to_second) get_transformation_aligning_first_to_second<IMP::Vector<IMP::algebra::VectorD<3> >, IMP::Vector<IMP::algebra::VectorD<3> > >;
-   // rotation operations
+%template(get_transformation_aligning_first_to_second) IMP::algebra::get_transformation_aligning_first_to_second<IMP::Vector<IMP::algebra::VectorD<3> >, IMP::Vector<IMP::algebra::VectorD<3> > >;
 
-   %template(_RotatedVector3DAdjoint) ::std::pair<IMP::algebra::VectorD<3>,IMP::algebra::VectorD<4> >;
-   %template(_ComposeRotation3DAdjoint) ::std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<4> >;
+// rotation operations
+%template(_RotatedVector3DAdjoint) std::pair<IMP::algebra::VectorD<3>,IMP::algebra::VectorD<4> >;
+%template(_ComposeRotation3DAdjoint) std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<4> >;
 
-   %template(_Transformation3DAdjoint) ::std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> >;
-   %template(_TransformedVector3DAdjoint) ::std::pair<IMP::algebra::VectorD<3>,std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> > >;
-   %template(_ComposeTransformation3DAdjoint) ::std::pair<std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> >,std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> > >;
- }
-}
+%template(_Transformation3DAdjoint) std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> >;
+%template(_TransformedVector3DAdjoint) std::pair<IMP::algebra::VectorD<3>,std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> > >;
+%template(_ComposeTransformation3DAdjoint) std::pair<std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> >,std::pair<IMP::algebra::VectorD<4>,IMP::algebra::VectorD<3> > >;
 
 %inline %{
 double get_rmsd_transforming_first(IMP::algebra::Transformation3D tr,

diff --git a/modules/atom/pyext/swig.i-in b/modules/atom/pyext/swig.i-in
@@ -247,24 +247,17 @@ IMP_SWIG_NESTED_SEQUENCE_TYPEMAP(IMP::atom::AtomType, IMP::atom::AtomTypes, IMP:
 %template(_ALoopStatisticalBase) IMP::score_functor::DistancePairScore<IMP::score_functor::LoopStatistical>;
 %template(_BLoopStatisticalBase) IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::LoopStatisticalType,false,true,false > >;
 %template(_OrientedSoapBase) IMP::score_functor::DistancePairScoreWithCache<IMP::score_functor::OrientedSoap>;
-namespace IMP {
-  namespace atom {
-   %template(_SPSFTB) ::IMP::score_functor::DistancePairScore<score_functor::Statistical< IMP::atom::ProteinLigandType, true, false> >;
-   %template(_SPSTF) ::IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType, true, false>;
-   %template(_SPSFT) ::IMP::core::StatisticalPairScore< IMP::atom::DopeType, false, true>;
-   %template(_SPSFTL) ::IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType, false, true>;
-  }
-}
+%template(_SPSFTB) ::IMP::score_functor::DistancePairScore<score_functor::Statistical< IMP::atom::ProteinLigandType, true, false> >;
+%template(_SPSTF) ::IMP::core::StatisticalPairScore< IMP::atom::ProteinLigandType, true, false>;
+%template(_SPSFT) ::IMP::core::StatisticalPairScore< IMP::atom::DopeType, false, true>;
+%template(_SPSFTL) ::IMP::core::StatisticalPairScore< IMP::atom::LoopStatisticalType, false, true>;
 %include "IMP/atom/protein_ligand_score.h"
 
-namespace IMP {
-  namespace atom {
-   // swig has random, perplexing issues if these are higher in the file
-   %template(AtomType) ::IMP::Key<IMP_ATOM_TYPE_INDEX>;
-   %template(ResidueType) ::IMP::Key<IMP_RESIDUE_TYPE_INDEX>;
-   %template(ChainType) ::IMP::Key<IMP_CHAIN_TYPE_INDEX>;
-  }
-}
+// swig has random, perplexing issues if these are higher in the file
+%template(AtomType) ::IMP::Key<IMP_ATOM_TYPE_INDEX>;
+%template(ResidueType) ::IMP::Key<IMP_RESIDUE_TYPE_INDEX>;
+%template(ChainType) ::IMP::Key<IMP_CHAIN_TYPE_INDEX>;
+
 %include "IMP/atom/element.h"
 %include "IMP/atom/Atom.h"
 %include "IMP/atom/Residue.h"

diff --git a/modules/core/pyext/swig.i-in b/modules/core/pyext/swig.i-in
@@ -379,17 +379,12 @@ IMP::Restraint *create_restraint(IMP::PairScore *ps, IMP::ParticlePair pp) {
 }
 %}
 
-namespace IMP {
-  namespace core {
-    %template(TruncatedHarmonicLowerBound) ::IMP::core::TruncatedHarmonic<LOWER>;
-    %template(TruncatedHarmonicUpperBound) ::IMP::core::TruncatedHarmonic<UPPER>;
-    %template(TruncatedHarmonicBound) ::IMP::core::TruncatedHarmonic<BOTH>;
-    // swig screws up on scopes, I can't be bothered to fix it
-    //%template(show_named_hierarchy) show<::IMP::core::Name>;
-   %template(ParticleType) ::IMP::Key<IMP_PARTICLE_TYPE_INDEX>;
-
-  }
-}
+%template(TruncatedHarmonicLowerBound) ::IMP::core::TruncatedHarmonic<IMP::core::LOWER>;
+%template(TruncatedHarmonicUpperBound) ::IMP::core::TruncatedHarmonic<IMP::core::UPPER>;
+%template(TruncatedHarmonicBound) ::IMP::core::TruncatedHarmonic<IMP::core::BOTH>;
+// swig screws up on scopes, I can't be bothered to fix it
+//%template(show_named_hierarchy) show<::IMP::core::Name>;
+%template(ParticleType) ::IMP::Key<IMP_PARTICLE_TYPE_INDEX>;
 
 IMP_SWIG_GENERIC_OBJECT_TEMPLATE(IMP::core, AttributeSingletonScore, generic_attribute_singleton_score, UnaryFunction);
 IMP_SWIG_GENERIC_OBJECT_TEMPLATE(IMP::core, BoundingBox3DSingletonScore, bounding_box_3d_singleton_score, UnaryFunction);

diff --git a/modules/em2d/pyext/swig.i-in b/modules/em2d/pyext/swig.i-in
@@ -99,22 +99,18 @@ IMP_SWIG_DECORATOR(IMP::em2d, ProjectionParameters, ProjectionParametersList);
 
 // %include "IMP/em2d/TemplateFinder.h"
 
-namespace IMP {
-  namespace em2d {
-    %template(ResultAlign2D)
-            ::std::pair< IMP::algebra::Transformation2D,double >;
+%template(ResultAlign2D)
+        ::std::pair< IMP::algebra::Transformation2D,double >;
 
 //    %template(VectorOfInts)   ::std::vector< IMP::Ints >;
 //    %template(VectorOfFloats) ::std::vector< IMP::Floats >;
 
-   %template(_do_hierarchical_clustering_single_linkage)
-          ::IMP::em2d::do_hierarchical_agglomerative_clustering<SingleLinkage>;
-   %template(_do_hierarchical_clustering_complete_linkage)
-           ::IMP::em2d::do_hierarchical_agglomerative_clustering<CompleteLinkage>;
-   %template(_do_hierarchical_clustering_average_distance_linkage)
-           ::IMP::em2d::do_hierarchical_agglomerative_clustering<AverageDistanceLinkage>;
-  }
-}
+%template(_do_hierarchical_clustering_single_linkage)
+      ::IMP::em2d::do_hierarchical_agglomerative_clustering<IMP::em2d::SingleLinkage>;
+%template(_do_hierarchical_clustering_complete_linkage)
+       ::IMP::em2d::do_hierarchical_agglomerative_clustering<IMP::em2d::CompleteLinkage>;
+%template(_do_hierarchical_clustering_average_distance_linkage)
+       ::IMP::em2d::do_hierarchical_agglomerative_clustering<IMP::em2d::AverageDistanceLinkage>;
 
 %pythoncode %{
   do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage

diff --git a/modules/integrative_docking/src/internal/soap_score.cpp b/modules/integrative_docking/src/internal/soap_score.cpp
@@ -81,6 +81,9 @@ double oriented_soap_score(const IMP::score_functor::OrientedSoap* soap_score,
     grid[grid_index].push_back(j);
   }
 
+  // Since we are not using a ScoringFunction we must update the Model
+  // ourselves so that everything is up to date (e.g. caches)
+  model->update();
   // score
   soap_score->check_cache_valid(model);
   double score = 0.0;
@@ -122,6 +125,10 @@ double oriented_soap_score(const IMP::score_functor::OrientedSoap* soap_score,
     coordinates.push_back(IMP::core::XYZ(model, pis[i]).get_coordinates());
   }
 
+  // Since we are not using a ScoringFunction we must update the Model
+  // ourselves so that everything is up to date (e.g. caches)
+  model->update();
+
   soap_score->check_cache_valid(model);
   float distance_threshold = soap_score->get_distance_threshold();
   float distance_threshold2 = distance_threshold * distance_threshold;

diff --git a/modules/kernel/src/utility.cpp b/modules/kernel/src/utility.cpp
@@ -2,7 +2,7 @@
  *  \file utility.cpp
  *  \brief Various general useful functions for IMP.
  *
- *  Copyright 2007-2023 IMP Inventors. All rights reserved.
+ *  Copyright 2007-2024 IMP Inventors. All rights reserved.
  *
  */
 
@@ -37,7 +37,7 @@ std::string get_unique_name(std::string name) {
 }
 
 std::string get_copyright() {
-  return "Copyright 2007-2023 IMP Inventors";
+  return "Copyright 2007-2024 IMP Inventors";
 }
 
 IMPKERNEL_END_NAMESPACE
diff --git a/modules/sampcon b/modules/sampcon
diff --git a/modules/test/pyext/src/__init__.py b/modules/test/pyext/src/__init__.py
@@ -801,14 +801,20 @@ def startTest(self, test):
         test.start_time = datetime.datetime.now()
 
     def _test_finished(self, test, state, detail=None):
-        delta = datetime.datetime.now() - test.start_time
-        try:
-            pv = delta.total_seconds()
-        except AttributeError:
-            pv = (float(delta.microseconds)
-                  + (delta.seconds + delta.days * 24 * 3600) * 10**6) / 10**6
-        if pv > 1:
-            self.stream.write("in %.3fs ... " % pv)
+        if hasattr(test, 'start_time'):
+            delta = datetime.datetime.now() - test.start_time
+            try:
+                pv = delta.total_seconds()
+            except AttributeError:
+                pv = (float(delta.microseconds)
+                      + (delta.seconds
+                         + delta.days * 24 * 3600) * 10**6) / 10**6
+            if pv > 1:
+                self.stream.write("in %.3fs ... " % pv)
+        else:
+            # If entire test was skipped, startTest() may not have been
+            # called, in which case start_time won't be set
+            pv = 0
         if detail is not None and not isinstance(detail, str):
             detail = self._exc_info_to_string(detail, test)
         test_doc = self.getDescription(test)

diff --git a/tools/debian/copyright b/tools/debian/copyright
@@ -2,7 +2,7 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: imp
 Source: https://integrativemodeling.org/
 
-Copyright: 2007-2023 IMP Inventors
+Copyright: 2007-2024 IMP Inventors
 License: LGPL-2+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU Lesser General Public License as published by

diff --git a/tools/rpm/IMP-copr.spec.in b/tools/rpm/IMP-copr.spec.in
@@ -82,7 +82,7 @@ BuildRequires: cmake >= 2.8
 %global our_cmake cmake
 %endif
 BuildRequires: boost-devel >= 1.53
-BuildRequires: RMF-devel
+BuildRequires: RMF-devel >= 1.6
 %if 0%{?with_python3}
 BuildRequires: python3-ihm
 Requires: python3-ihm
@@ -514,6 +514,9 @@ export PYTHONPATH=%{buildroot}%{_libdir}/python${py2_ver}/site-packages
 %endif
 
 %changelog
+* Tue Jan 16 2024 Ben Webb <[email protected]>   2.20.1-1
+- 2.20.1 release.
+
 * Thu Dec 21 2023 Ben Webb <[email protected]>   2.20.0-1
 - 2.20.0 release.
 

diff --git a/tools/rpm/IMP.spec.in b/tools/rpm/IMP.spec.in
@@ -539,6 +539,9 @@ find ${RPM_BUILD_ROOT}%{_prefix}/share/IMP/tools -name '*.py' -exec perl -pi -e
 %endif
 
 %changelog
+* Tue Jan 16 2024 Ben Webb <[email protected]>   2.20.1-1
+- 2.20.1 release.
+
 * Thu Dec 21 2023 Ben Webb <[email protected]>   2.20.0-1
 - 2.20.0 release.
+1 −1		.github/workflows/build.yml
+11 −0		test/test_precision_rmsd.py
+8 −0		test/test_rmsd_calculation.py
+4 −1		tools/setup_ci.sh