v0.7.3: merge with colour option added

* upgraded github workflow dependencies

Author: Paul K. Korir, PhD

.github/workflows/python-package.yml

@@ -18,9 +18,9 @@ jobs:
         python-version: [ 3.6, 3.7, 3.8, 3.9, '3.10' ]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -41,7 +41,7 @@ jobs:
           # pytest --cov=./sfftkrw ./sfftkrw/unittests
           coverage run --rcfile=.coveragerc -m pytest
       - name: Upload Coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
         with:
           verbose: true
 

CHANGELOG.md

@@ -1,5 +1,9 @@
 #Changes by release
 
+## [0.7.3] - 2023-01-27 Option to include source EMDB-SFF colours when merging
+
+* In EMDB-SFF `v0.8.0.dev1` `SFFSegmentation.merge_annotation(other_seg, include_colour=False)` (*do not* merge colour by default)
+
 ## [0.7.2] - 2022-04-26
 
 add Python3.10 support

setup.py

@@ -36,6 +36,7 @@
     u"Programming Language :: Python :: 3.8",
     u"Programming Language :: Python :: 3.9",
     u"Programming Language :: Python :: 3.10",
+    u"Programming Language :: Python :: 3.11",
     u"Topic :: Software Development :: Libraries :: Python Modules",
     u"Topic :: Terminals",
     u"Topic :: Text Processing",

sfftkrw/conf.py

@@ -1,2 +1,2 @@
-SFFTKRW_VERSION = 'v0.7.2'
+SFFTKRW_VERSION = 'v0.7.3'
 SFFTKRW_ENTRY_POINT = 'sff'

sfftkrw/schema/adapter_v0_8_0_dev1.py

@@ -2518,10 +2518,11 @@ def to_file(self, *args, **kwargs):
         """Alias for :py:meth:`.export` method. Passes all args and kwargs onto :py:meth:`.export`"""
         return super(SFFSegmentation, self).export(*args, **kwargs)
 
-    def merge_annotation(self, other_seg):
+    def merge_annotation(self, other_seg, include_colour=False):
         """Merge the annotation from another sff_seg to this one
 
         :param other_seg: segmentation to get annotations from
+        :param bool include_colour: copy the colours from the source (useful if you want control over the colours)
         :type other_seg: :py:class:`sfftkrw.SFFSegmentation`
         """
         _assert_or_raise(other_seg, SFFSegmentation)
@@ -2534,6 +2535,8 @@ def merge_annotation(self, other_seg):
         for segment in self.segments:
             other_segment = other_seg.segments.get_by_id(segment.id)
             segment.biological_annotation = other_segment.biological_annotation
+            if include_colour:
+                segment.colour = other_segment.colour
 
     def copy_annotation(self, from_id, to_id):
         """Copy annotation across segments

sfftkrw/test_data/sff/v0.8/emd_1014.json

@@ -574,6 +574,21 @@ def test_hff(self):
         with h5py.File(self.test_hdf5_fn, u'r') as h:
             ee2 = adapter.SFFExternalReferenceList.from_hff(h[u'container'])
 
+    def test_create_from_list(self):
+        """Test that we can create an SFFExternalReferenceList from a literal list"""
+        ee = [adapter.SFFExternalReference(
+            resource=self.rr[i],
+            url=self.uu[i],
+            accession=self.aa[i],
+            label=self.ll[i],
+            description=self.dd[i]
+        ) for i in _xrange(self._no_items)]
+        E = adapter.SFFExternalReferenceList()
+        print(ee)
+        print(E)
+        ES = adapter.SFFExternalReferenceList(new_obj=True, )
+        print(ES)
+
 
 class TestSFFGlobalExternalReferenceList(Py23FixTestCase):
     """Test the SFFGlobalExternalReferenceList class"""
@@ -948,7 +963,8 @@ def test_hff(self):
             self.assertIn(u'description', group[u'biological_annotation'])
             self.assertEqual(_decode(group[u'biological_annotation/description'][()], 'utf-8'), b_full.description)
             self.assertIn(u'number_of_instances', group[u'biological_annotation'])
-            self.assertEqual(_decode(group[u'biological_annotation/number_of_instances'][()], 'utf-8'), b_full.number_of_instances)
+            self.assertEqual(_decode(group[u'biological_annotation/number_of_instances'][()], 'utf-8'),
+                             b_full.number_of_instances)
             self.assertIn(u'external_references', group[u'biological_annotation'])
             self.assertEqual(len(group[u'biological_annotation/external_references']),
                              len(b_full.external_references))
@@ -5301,6 +5317,14 @@ def test_merge_annotation(self):
             other_segment = seg2.segment_list.get_by_id(segment.id)
             self.assertEqual(segment.biological_annotation.external_references,
                              other_segment.biological_annotation.external_references)
+            self.assertNotEqual(segment.colour, other_segment.colour)
+        # test that we can merge colours too!
+        seg1.merge_annotation(seg2, include_colour=True)
+        for segment in seg1.segment_list:
+            other_segment = seg2.segment_list.get_by_id(segment.id)
+            self.assertEqual(segment.biological_annotation.external_references,
+                             other_segment.biological_annotation.external_references)
+            self.assertEqual(segment.colour, other_segment.colour)
 
     def test_copy_annotation(self):
         """Test that we can copy annotations: global and local"""

sfftkrw/unittests/test_adapter_v0_8_0_dev1.py

@@ -1,5 +1,5 @@
 [tox]
-envlist = py36, py37, py38, py39, py310
+envlist = py36, py37, py38, py39, py310, py311
 
 [testenv]
 deps =