Merge pull request #455 from OpenBioSim/backport_454

Author: lohedges

src/sire/mm/__init__.py

@@ -36,10 +36,6 @@
 
 from ..legacy import MM as _MM
 
-from .. import use_new_api as _use_new_api
-
-_use_new_api()
-
 AngleRestraint = _MM.AngleRestraint
 AngleRestraints = _MM.AngleRestraints
 
@@ -217,3 +213,18 @@ def _fix_siremm():
     _fix_siremm()
 except ImportError:
     pass
+
+# This must be called after _fix_siremm() above, not at the top of this
+# module (as in most other new-API submodules). use_new_api() eagerly loads
+# every other lazily-loaded new-API submodule, including sire.mol - and
+# sire.mol's own module-level code does 'from ..mm import _fix_siremm'. If
+# sire.mm is the first Sire submodule touched in a process, calling
+# use_new_api() before _fix_siremm is defined means that reentrant load of
+# sire.mol fails with 'cannot import name _fix_siremm from sire.mm', which
+# then cascades into 'sire.mm could not be loaded' via the lazy_import
+# wrapper. Nothing above this point depends on use_new_api() having run
+# (it only pythonizes names already pulled directly from the raw legacy
+# _MM module), so it is safe to defer to here.
+from .. import use_new_api as _use_new_api
+
+_use_new_api()

src/sire/restraints/_restraints.py

@@ -447,7 +447,7 @@ def boresch(
         b = BoreschRestraints(name, b)
 
     # Set the use_pbc flag.
-    b._use_pbc = use_pbc
+    b.set_uses_pbc(use_pbc)
 
     return b
 
@@ -876,7 +876,6 @@ def morse_potential(
         for bond in changed_bonds:
             bond_name, length0, length1, k0, k1 = bond
             if k1 == 0 or k0 == 0:
-
                 # If the bond is being created (k0 == 0), then we should
                 # use the parameters from the final state (length1, k1).
                 # If the bond is being annihilated (k1 == 0), then we don't

tests/restraints/test_boresch.py

@@ -1,6 +1,7 @@
+import pickle
+
 import pytest
 
-import sire as sr
 from sire.restraints import boresch
 
 # Valid Boresch restraint parameters.
@@ -203,6 +204,35 @@ def test_boresch_restraint_params(thrombin_complex):
     assert boresch_restraint.phi0()[2].value() == 1.4147
 
 
+def test_boresch_restraints_pickles_ok(thrombin_complex):
+    """
+    Regression test: sire.restraints.boresch() used to set a dynamic
+    '_use_pbc' Python attribute on the returned BoreschRestraints instead of
+    calling set_uses_pbc(), which broke pickling (fixed).
+    """
+    boresch_restraints = boresch(
+        thrombin_complex,
+        receptor=thrombin_complex["protein"][
+            BORESCH_PARAMS_DEFAULT["receptor_selection"]
+        ],
+        ligand=thrombin_complex["resname LIG"][
+            BORESCH_PARAMS_DEFAULT["ligand_selection"]
+        ],
+        kr=BORESCH_PARAMS_DEFAULT["kr"],
+        ktheta=BORESCH_PARAMS_DEFAULT["ktheta"],
+        kphi=BORESCH_PARAMS_DEFAULT["kphi"],
+        r0=BORESCH_PARAMS_DEFAULT["r0"],
+        theta0=BORESCH_PARAMS_DEFAULT["theta0"],
+        phi0=BORESCH_PARAMS_DEFAULT["phi0"],
+        name=BORESCH_PARAMS_DEFAULT["name"],
+    )
+
+    data = pickle.dumps(boresch_restraints)
+    reloaded = pickle.loads(data)
+
+    assert reloaded[0].kr().value() == boresch_restraints[0].kr().value()
+
+
 @pytest.mark.parametrize(
     (
         "receptor_selection",

tests/stream/test_pickle.py

@@ -0,0 +1,41 @@
+import pickle
+
+import pytest
+
+import sire as sr
+
+
+def test_dynamic_attribute_breaks_pickling():
+    """
+    General, still-open Sire issue: sire_pickle_suite<T> (wrapper/Qt/
+    qdatastream.hpp) never overrides pickle_suite::getstate_manages_dict(),
+    so any object using it that also has a dynamic Python attribute set on
+    it (populating __dict__) fails to pickle with 'Incomplete pickle support
+    (__getstate_manages_dict__ not set)', even though the object's own
+    QDataStream-based serialisation (sire.stream.save/load) is unaffected.
+    """
+    from sire.mm import BoreschRestraint, BoreschRestraints
+
+    b = BoreschRestraint(
+        receptor=[1574, 1554, 1576],
+        ligand=[4, 3, 5],
+        r0=sr.u("7.687 A"),
+        theta0=[sr.u("1.3031 rad"), sr.u("1.4777 rad")],
+        phi0=[sr.u("2.5569 rad"), sr.u("2.9359 rad"), sr.u("1.4147 rad")],
+        kr=sr.u("6.2012 kcal mol-1 A-2"),
+        ktheta=[sr.u("28.7685 kcal mol-1 rad-2"), sr.u("24.8204 kcal mol-1 rad-2")],
+        kphi=[
+            sr.u("59.8626 kcal mol-1 rad-2"),
+            sr.u("0.7923 kcal mol-1 rad-2"),
+            sr.u("55.1775 kcal mol-1 rad-2"),
+        ],
+    )
+    restraints = BoreschRestraints(b)
+
+    # Pickles fine before any dynamic attribute is set.
+    pickle.dumps(restraints)
+
+    restraints._some_dynamic_attribute = True
+
+    with pytest.raises(RuntimeError, match="Incomplete pickle support"):
+        pickle.dumps(restraints)