Squashed 'modules/core/dependency/python-ihm/' changes from 78f278840…

…0..5c7c382a41

5c7c382a41 Prepare for 1.5 release
4df39c4d83 Don't duplicate struct_ref.id, closes ihmwg/python-ihm#149

git-subtree-dir: modules/core/dependency/python-ihm
git-subtree-split: 5c7c382a415580b1999d743c3fd119668fcd79ee

modules/core/dependency/python-ihm/ChangeLog.rst

@@ -1,3 +1,12 @@
+1.5 - 2024-09-06
+================
+  - Trying to create a :class:`ihm.Residue`, :class:`ihm.EntityRange`, or
+    :class:`ihm.AsymUnitRange` that references out-of-range residues (i.e.
+    ``seq_id`` less than 1 or beyond the length of the :class:`ihm.Entity`
+    sequence) will now raise an error.
+  - Bugfix: :class:`ihm.reference.Reference` objects are no longer given
+    erroneous duplicate IDs on output (#149).
+
 1.4 - 2024-08-30
 ================
   - :class:`ihm.metadata.CIFParser` now extracts metadata from mmCIF starting

modules/core/dependency/python-ihm/MANIFEST.in

@@ -4,4 +4,4 @@ include examples/*
 include util/make-mmcif.py
 include src/ihm_format.h
 include src/ihm_format.i
-include src/ihm_format_wrap_1.4.c
+include src/ihm_format_wrap_1.5.c

modules/core/dependency/python-ihm/ihm/__init__.py

@@ -20,7 +20,7 @@
 import json
 from . import util
 
-__version__ = '1.4'
+__version__ = '1.5'
 
 
 class __UnknownValue(object):

modules/core/dependency/python-ihm/ihm/dumper.py

@@ -422,19 +422,21 @@ def _prettyprint_seq(seq, width):
 
 class _StructRefDumper(Dumper):
     def finalize(self, system):
-        self._refs_by_id = {}
+        # List of (entity, ref) by ID
+        self._refs_by_id = []
+        seen_refs = {}
         align_id = itertools.count(1)
         for e in system.entities:
             for r in e.references:
                 util._remove_id(r)
 
         for e in system.entities:
-            seen_refs = {}
             # Two refs are not considered duplicated if they relate to
-            # different entities, so keep list per entity
-            self._refs_by_id[id(e)] = by_id = []
+            # different entities, so add entity to reference signature
             for r in e.references:
-                util._assign_id(r, seen_refs, by_id, seen_obj=r._signature())
+                sig = (id(e), r._signature())
+                util._assign_id(r, seen_refs, self._refs_by_id, seen_obj=sig,
+                                by_id_obj=(e, r))
                 for a in r._get_alignments():
                     a._id = next(align_id)
 
@@ -520,23 +522,21 @@ def dump(self, system, writer):
                 ["id", "entity_id", "db_name", "db_code", "pdbx_db_accession",
                  "pdbx_align_begin", "pdbx_seq_one_letter_code",
                  "details"]) as lp:
-            for e in system.entities:
-                for r in self._refs_by_id[id(e)]:
-                    self._check_reference_sequence(e, r)
-                    db_begin = min(a.db_begin for a in r._get_alignments())
-                    lp.write(id=r._id, entity_id=e._id, db_name=r.db_name,
-                             db_code=r.db_code, pdbx_db_accession=r.accession,
-                             pdbx_align_begin=db_begin, details=r.details,
-                             pdbx_seq_one_letter_code=self._get_sequence(r))
+            for e, r in self._refs_by_id:
+                self._check_reference_sequence(e, r)
+                db_begin = min(a.db_begin for a in r._get_alignments())
+                lp.write(id=r._id, entity_id=e._id, db_name=r.db_name,
+                         db_code=r.db_code, pdbx_db_accession=r.accession,
+                         pdbx_align_begin=db_begin, details=r.details,
+                         pdbx_seq_one_letter_code=self._get_sequence(r))
         self.dump_seq(system, writer)
         self.dump_seq_dif(system, writer)
 
     def dump_seq(self, system, writer):
         def _all_alignments():
-            for e in system.entities:
-                for r in self._refs_by_id[id(e)]:
-                    for a in r._get_alignments():
-                        yield e, r, a
+            for e, r in self._refs_by_id:
+                for a in r._get_alignments():
+                    yield e, r, a
         with writer.loop(
                 "_struct_ref_seq",
                 ["align_id", "ref_id", "seq_align_beg", "seq_align_end",
@@ -557,15 +557,14 @@ def dump_seq_dif(self, system, writer):
                 "_struct_ref_seq_dif",
                 ["pdbx_ordinal", "align_id", "seq_num", "db_mon_id", "mon_id",
                  "details"]) as lp:
-            for e in system.entities:
-                for r in self._refs_by_id[id(e)]:
-                    for a in r._get_alignments():
-                        for sd in a.seq_dif:
-                            lp.write(pdbx_ordinal=next(ordinal),
-                                     align_id=a._id, seq_num=sd.seq_id,
-                                     db_mon_id=sd.db_monomer.id
-                                     if sd.db_monomer else ihm.unknown,
-                                     mon_id=sd.monomer.id, details=sd.details)
+            for e, r in self._refs_by_id:
+                for a in r._get_alignments():
+                    for sd in a.seq_dif:
+                        lp.write(pdbx_ordinal=next(ordinal),
+                                 align_id=a._id, seq_num=sd.seq_id,
+                                 db_mon_id=sd.db_monomer.id
+                                 if sd.db_monomer else ihm.unknown,
+                                 mon_id=sd.monomer.id, details=sd.details)
 
 
 class _EntityPolyDumper(Dumper):

modules/core/dependency/python-ihm/ihm/util/__init__.py

@@ -27,13 +27,16 @@ def _remove_id(obj, attr='_id'):
         delattr(obj, attr)
 
 
-def _assign_id(obj, seen_objs, obj_by_id, attr='_id', seen_obj=None):
+def _assign_id(obj, seen_objs, obj_by_id, attr='_id', seen_obj=None,
+               by_id_obj=None):
     """Assign a unique ID to obj, and track all ids in obj_by_id."""
     if seen_obj is None:
         seen_obj = obj
+    if by_id_obj is None:
+        by_id_obj = obj
     if seen_obj not in seen_objs:
         if not hasattr(obj, attr):
-            obj_by_id.append(obj)
+            obj_by_id.append(by_id_obj)
             setattr(obj, attr, len(obj_by_id))
         seen_objs[seen_obj] = getattr(obj, attr)
     else:

modules/core/dependency/python-ihm/setup.py

@@ -7,7 +7,7 @@
 import sys
 import os
 
-VERSION = "1.4"
+VERSION = "1.5"
 
 copy_args = sys.argv[1:]
 

modules/core/dependency/python-ihm/test/test_dumper.py

@@ -606,6 +606,15 @@ def test_struct_ref(self):
 
         system.entities.append(ihm.Entity('LSPT', references=[r1, r2, r3, r4,
                                                               r5]))
+
+        # Duplicate reference, but should be included as it pertains to a
+        # different Entity
+        r3a = ihm.reference.UniProtSequence(
+            db_code='testcode2', accession='testacc2', sequence=None)
+        r3a.alignments.append(ihm.reference.Alignment(
+            db_begin=4, db_end=5, entity_begin=2, entity_end=3))
+        system.entities.append(ihm.Entity('LSPTW', references=[r3a]))
+
         dumper = ihm.dumper._EntityDumper()
         dumper.finalize(system)  # Assign entity IDs
 
@@ -626,6 +635,7 @@ def test_struct_ref(self):
 2 1 UNP testcode testacc 4 SPTYQT test2
 3 1 UNP testcode2 testacc2 4 . .
 4 1 UNP testcode3 testacc3 4 ? .
+5 2 UNP testcode2 testacc2 4 . .
 #
 #
 loop_
@@ -640,6 +650,7 @@ def test_struct_ref(self):
 3 2 4 4 9 9
 4 3 2 3 4 5
 5 4 2 3 4 5
+7 5 2 3 4 5
 #
 #
 loop_

modules/core/dependency/python-ihm/util/debian/changelog

@@ -1,3 +1,9 @@
+python-ihm (1.5-1~@CODENAME@) @CODENAME@; urgency=low
+
+  * python-ihm 1.5 release
+
+ -- Ben Webb <[email protected]>  Fri, 06 Sep 2024 14:15:12 -0700
+
 python-ihm (1.4-1~@CODENAME@) @CODENAME@; urgency=low
 
   * python-ihm 1.4 release

modules/core/dependency/python-ihm/util/python-ihm.spec

@@ -1,7 +1,7 @@
 Name:          python3-ihm
 License:       MIT
 Group:         Applications/Engineering
-Version:       1.4
+Version:       1.5
 Release:       1%{?dist}
 Summary:       Package for handling IHM mmCIF and BinaryCIF files
 Packager:      Ben Webb <[email protected]>
@@ -36,6 +36,9 @@ sed -i -e "s/install_requires=\['msgpack'\]/#/" setup.py
 %defattr(-,root,root)
 
 %changelog
+* Fri Sep 06 2024 Ben Webb <[email protected]>   1.5-1
+- Update to latest upstream.
+
 * Fri Aug 30 2024 Ben Webb <[email protected]>   1.4-1
 - Update to latest upstream.