Squashed 'modules/core/dependency/python-ihm/' changes from 993cfebf3…

…4..487413476a

487413476a Read/write alternate locations, closes ihmwg/python-ihm#146
82370afc0b Support ihm_modeling_protocol.details, relates ihmwg/python-ihm#145
de381f0969 Remove obsolete file
5dbceb7772 Use latest codecov action with token
f584b404b9 Render numpy 2 ints correctly in output mmCIF

git-subtree-dir: modules/core/dependency/python-ihm
git-subtree-split: 487413476a38edab220c97590887532a51c55fa5

modules/core/dependency/python-ihm/.codecov.yml

@@ -1,4 +1,3 @@
 ignore:
   - test
   - util
-  - **/_compat_collections.py

modules/core/dependency/python-ihm/.github/workflows/testpy.yml

@@ -49,4 +49,6 @@ jobs:
         else
           flake8 --ignore E402,W503,W504,N816
         fi
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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

@@ -1358,10 +1358,12 @@ def dump(self, system, writer):
 
     def dump_summary(self, system, writer):
         with writer.loop("_ihm_modeling_protocol",
-                         ["id", "protocol_name", "num_steps"]) as lp:
+                         ["id", "protocol_name", "num_steps",
+                          "details"]) as lp:
             for p in system._all_protocols():
                 lp.write(id=p._id,
-                         protocol_name=p.name, num_steps=len(p.steps))
+                         protocol_name=p.name, num_steps=len(p.steps),
+                         details=p.details)
 
     def dump_details(self, system, writer):
         ordinal = itertools.count(1)
@@ -1657,6 +1659,7 @@ def dump_atoms(self, system, writer, add_ihm=True):
                              type_symbol=atom.type_symbol,
                              group_PDB='HETATM' if atom.het else 'ATOM',
                              label_atom_id=atom.atom_id,
+                             label_alt_id=atom.alt_id,
                              label_comp_id=comp.id,
                              label_asym_id=atom.asym_unit._id,
                              label_entity_id=atom.asym_unit.entity._id,

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

@@ -228,8 +228,10 @@ def _repr(self, obj):
         # which isn't valid mmCIF syntax. _long_type = long only on Python 2.
         elif isinstance(obj, _long_type):
             return "%d" % obj
-        else:
+        elif isinstance(obj, str):
             return repr(obj)
+        else:
+            return str(obj)
 
 
 # Acceptable 'whitespace' characters in CIF

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

@@ -56,20 +56,23 @@ class Atom(object):
        :param float biso: Temperature factor or equivalent (if applicable)
        :param float occupancy: Fraction of the atom type present
               (if applicable)
+       :param float alt_id: Alternate conformation indicator
+              (if applicable)
     """
 
     # Reduce memory usage
     __slots__ = ['asym_unit', 'seq_id', 'atom_id', 'type_symbol',
-                 'x', 'y', 'z', 'het', 'biso', 'occupancy']
+                 'x', 'y', 'z', 'het', 'biso', 'occupancy', 'alt_id']
 
     def __init__(self, asym_unit, seq_id, atom_id, type_symbol, x, y, z,
-                 het=False, biso=None, occupancy=None):
+                 het=False, biso=None, occupancy=None, alt_id=None):
         self.asym_unit = asym_unit
         self.seq_id, self.atom_id = seq_id, atom_id
         self.type_symbol = type_symbol
         self.x, self.y, self.z = x, y, z
         self.het, self.biso = het, biso
         self.occupancy = occupancy
+        self.alt_id = alt_id
 
 
 class Model(object):

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

@@ -65,9 +65,13 @@ class Protocol(object):
        Normally a protocol is passed to one or more :class:`~ihm.model.Model`
        objects, although unused protocols can still be included in the file
        if desired by adding them to :attr:`~ihm.System.orphan_protocols`.
+
+       :param str name: Optional name for the protocol
+       :param str details: Additional text describing the protocol
     """
-    def __init__(self, name=None):
+    def __init__(self, name=None, details=None):
         self.name = name
+        self.details = details
 
         #: All modeling steps (:class:`Step` objects)
         self.steps = []

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

@@ -1738,9 +1738,10 @@ class _ProtocolHandler(Handler):
     category = '_ihm_modeling_protocol'
     ignored_keywords = ['ordinal_id', 'struct_assembly_description']
 
-    def __call__(self, id, protocol_name, num_steps):
+    def __call__(self, id, protocol_name, num_steps, details):
         p = self.sysr.protocols.get_by_id(id)
-        self.copy_if_present(p, locals(), mapkeys={'protocol_name': 'name'})
+        self.copy_if_present(p, locals(), mapkeys={'protocol_name': 'name'},
+                             keys=['details'])
 
 
 class _ProtocolDetailsHandler(Handler):
@@ -2136,7 +2137,7 @@ def _get_seq_id_from_auth(self, auth_seq_id, pdbx_pdb_ins_code, asym):
     def __call__(self, pdbx_pdb_model_num, label_asym_id, b_iso_or_equiv,
                  label_seq_id, label_atom_id, type_symbol, cartn_x, cartn_y,
                  cartn_z, occupancy, group_pdb, auth_seq_id,
-                 pdbx_pdb_ins_code, auth_asym_id, label_comp_id):
+                 pdbx_pdb_ins_code, auth_asym_id, label_comp_id, label_alt_id):
         # seq_id can be None for non-polymers (HETATM)
         seq_id = self.get_int(label_seq_id)
         # todo: handle fields other than those output by us
@@ -2164,7 +2165,7 @@ def __call__(self, pdbx_pdb_model_num, label_asym_id, b_iso_or_equiv,
             asym_unit=asym, seq_id=our_seq_id, atom_id=label_atom_id,
             type_symbol=type_symbol, x=float(cartn_x), y=float(cartn_y),
             z=float(cartn_z), het=group != 'ATOM', biso=biso,
-            occupancy=occupancy)
+            occupancy=occupancy, alt_id=label_alt_id)
         model.add_atom(a)
 
         # Note any residues that have different seq_id and auth_seq_id

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

@@ -1762,7 +1762,7 @@ class MockObject(object):
             num_models_end=2000, multi_scale=True, ensemble=False))
         system.orphan_protocols.append(p1)
 
-        p2 = ihm.protocol.Protocol('sampling')
+        p2 = ihm.protocol.Protocol('sampling', details='extra details')
         p2.steps.append(ihm.protocol.Step(
             assembly=assembly, dataset_group=dsg2,
             method='Replica exchange', num_models_begin=2000,
@@ -1779,8 +1779,9 @@ class MockObject(object):
 _ihm_modeling_protocol.id
 _ihm_modeling_protocol.protocol_name
 _ihm_modeling_protocol.num_steps
-1 equilibration 2
-2 sampling 1
+_ihm_modeling_protocol.details
+1 equilibration 2 .
+2 sampling 1 'extra details'
 #
 #
 loop_
@@ -2357,7 +2358,7 @@ def test_model_dumper_atoms(self):
                                        het=True),
                         ihm.model.Atom(asym_unit=asym, seq_id=2, atom_id='N',
                                        type_symbol='N', x=4.0, y=5.0, z=6.0,
-                                       biso=42.0, occupancy=0.2)]
+                                       biso=42.0, occupancy=0.2, alt_id='A')]
 
         dumper = ihm.dumper._ModelDumper()
         dumper.finalize(system)  # assign model/group IDs
@@ -2410,7 +2411,7 @@ def test_model_dumper_atoms(self):
 _atom_site.ihm_model_id
 ATOM 1 C C . ALA 1 1 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1
 HETATM 2 C CA . ALA 1 1 ? X 10.000 20.000 30.000 . 9 X ALA . 1 1
-ATOM 3 N N . CYS 2 2 ? X 4.000 5.000 6.000 0.200 9 X CYS 42.000 1 1
+ATOM 3 N N A CYS 2 2 ? X 4.000 5.000 6.000 0.200 9 X CYS 42.000 1 1
 #
 #
 loop_
@@ -2431,7 +2432,7 @@ def test_model_dumper_atoms(self):
         self.assertEqual(
             out.split('\n')[44:47:2],
             ["ATOM 1 C C . ALA 1 0 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1",
-             "ATOM 3 N N . CYS 2 1 ? X 4.000 5.000 6.000 "
+             "ATOM 3 N N A CYS 2 1 ? X 4.000 5.000 6.000 "
              "0.200 9 X CYS 42.000 1 1"])
 
         # With auth_seq_id map
@@ -2440,7 +2441,7 @@ def test_model_dumper_atoms(self):
         self.assertEqual(
             out.split('\n')[44:47:2],
             ["ATOM 1 C C . ALA 1 42 ? X 1.000 2.000 3.000 . 9 X ALA . 1 1",
-             "ATOM 3 N N . CYS 2 99 ? X 4.000 5.000 6.000 "
+             "ATOM 3 N N A CYS 2 99 ? X 4.000 5.000 6.000 "
              "0.200 9 X CYS 42.000 1 1"])
 
     def test_model_dumper_water_atoms(self):

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

@@ -41,7 +41,7 @@ def test_simple_docking_example(self):
             # can read it
             with open(os.path.join(tmpdir, 'output.cif')) as fh:
                 contents = fh.readlines()
-            self.assertEqual(len(contents), 318)
+            self.assertEqual(len(contents), 319)
             with open(os.path.join(tmpdir, 'output.cif')) as fh:
                 s, = ihm.reader.read(fh)
 
@@ -70,7 +70,7 @@ def test_ligands_water_example(self):
         # can read it
         with open(out) as fh:
             contents = fh.readlines()
-        self.assertEqual(len(contents), 254)
+        self.assertEqual(len(contents), 255)
         with open(out) as fh:
             s, = ihm.reader.read(fh)
         # Make sure that resulting Python objects are picklable

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

@@ -2,6 +2,10 @@
 import os
 import unittest
 import sys
+try:
+    import numpy
+except ImportError:
+    numpy = None
 
 if sys.version_info[0] >= 3:
     from io import StringIO
@@ -226,6 +230,11 @@ def test_repr(self):
         # Literal . must be quoted to distinguish from the omitted value
         self.assertEqual(w._repr('.foo'), ".foo")
         self.assertEqual(w._repr('.'), "'.'")
+        # Make sure that numpy ints are treated like plain ints,
+        # not rendered as "np.int32(42)" or similar
+        if numpy is not None:
+            self.assertEqual(w._repr(numpy.int32(42)), '42')
+            self.assertEqual(w._repr(numpy.int64(42)), '42')
 
     def test_reader_base(self):
         """Test Reader base class"""

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

@@ -1320,12 +1320,14 @@ def test_protocol_handler(self):
 _ihm_modeling_protocol.id
 _ihm_modeling_protocol.protocol_name
 _ihm_modeling_protocol.num_steps
-1 Prot1 5
+_ihm_modeling_protocol.details
+1 Prot1 5 'extra details'
 """
         for fh in cif_file_handles(cif):
             s, = ihm.reader.read(fh)
             p1, = s.orphan_protocols
             self.assertEqual(p1.name, "Prot1")
+            self.assertEqual(p1.details, "extra details")
             # no step objects read yet, num_steps ignored
             self.assertEqual(len(p1.steps), 0)
 
@@ -1987,7 +1989,7 @@ def test_atom_site_handler(self):
 _atom_site.pdbx_PDB_model_num
 _atom_site.ihm_model_id
 ATOM 1 N N . SER 1 A 54.401 -49.984 -35.287 . 1 A . 1 1
-HETATM 2 C CA . SER . B 54.452 -48.492 -35.210 0.200 1 A 42.0 1 1
+HETATM 2 C CA A SER . B 54.452 -48.492 -35.210 0.200 1 A 42.0 1 1
 """)
         s, = ihm.reader.read(fh)
         m = s.state_groups[0][0][0][0]
@@ -2002,6 +2004,7 @@ def test_atom_site_handler(self):
         self.assertEqual(a1.het, False)
         self.assertIsNone(a1.biso)
         self.assertIsNone(a1.occupancy)
+        self.assertIsNone(a1.alt_id)
 
         self.assertEqual(a2.asym_unit._id, 'B')
         self.assertEqual(a2.seq_id, 1)
@@ -2010,6 +2013,7 @@ def test_atom_site_handler(self):
         self.assertEqual(a2.het, True)
         self.assertAlmostEqual(a2.biso, 42.0, delta=1.0)
         self.assertAlmostEqual(a2.occupancy, 0.2, delta=0.1)
+        self.assertEqual(a2.alt_id, 'A')
 
     def test_atom_site_handler_auth_seq_id(self):
         """Test AtomSiteHandler handling of auth_seq_id and ins_code"""