Use importlib-resources to load data in older Python versions

mini3di/encoder.py

@@ -4,13 +4,17 @@
 import functools
 import struct
 import typing
-import importlib.resources
 
 import numpy
 
 from .utils import normalize
 from ._unkerasify import KerasifyParser, Layer
 
+try:
+    from importlib.resources import files as resource_files
+except ImportError:
+    from importlib_resources import files as resource_files
+
 if typing.TYPE_CHECKING:
     from Bio.PDB import Chain
     from .utils import ArrayN, ArrayNx2, ArrayNx3, ArrayNx10
@@ -109,8 +113,8 @@ def calc_conformation_descriptors(
 
 class FeatureEncoder:
     @classmethod
-    def load(cls):
-        path = importlib.resources.files(__package__).joinpath("encoder_weights_3di.kerasify")
+    def load(cls) -> FeatureEncoder:
+        path = resource_files(__package__).joinpath("encoder_weights_3di.kerasify")
         with path.open("rb") as f:
             parser = KerasifyParser(f)
             layers = list(parser)

setup.cfg

@@ -44,6 +44,8 @@ python_requires = >=3.7
 test_suite = tests
 include_package_data = true
 setup_requires = setuptools >=46.4
+install_requires =
+    importlib-resources >=1.3 ; python_version < '3.8'
 
 [options.package_data]
 mini3di = py.typed, *.kerasify

tests/__init__.py

@@ -1,9 +1,13 @@
 import unittest
-import importlib.resources
 
 import Bio.PDB
 from mini3di import Encoder
 
+try:
+    from importlib.resources import files as resource_files
+except ImportError:
+    from importlib_resources import files as resource_files
+
 
 class TestEncoder(unittest.TestCase):
     @classmethod
@@ -13,7 +17,7 @@ def setUpClass(cls):
 
     @classmethod
     def get_structure(cls, name):
-        path = importlib.resources.files(__package__).joinpath("data", name).with_suffix(".pdb")
+        path = resource_files(__package__).joinpath("data", name).with_suffix(".pdb")
         return cls.parser.get_structure(name, path)
 
     def test_encode_3bww(self):
@@ -58,4 +62,4 @@ def test_encode_8crb(self):
             "DPCVLVVLVLQLVLVVLLLVVVVVVLVVCVVVLFKDWQDPVHDWQLACVSPDHDCPDCCSVPGSNN"
             "VQQCPKPLDDVTATNQSVQQIDDGDLDHDDDDDTIQGCPPPVRCSVVVVVVSVVSVVVSVVSCVVS"
             "VVVVVVD",
-        )
+        )

tests/test_encoder.py

@@ -1,5 +1,65 @@
 import unittest
 
-import numpy
+import Bio.PDB
+from mini3di import Encoder
 
-import mini3di
+try:
+    from importlib.resources import files as resource_files
+except ImportError:
+    from importlib_resources import files as resource_files
+
+
+class TestEncoder(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.encoder = Encoder()
+        cls.parser = Bio.PDB.PDBParser(QUIET=True)
+
+    @classmethod
+    def get_structure(cls, name):
+        path = resource_files(__package__).joinpath("data", name).with_suffix(".pdb")
+        return cls.parser.get_structure(name, path)
+
+    def test_encode_3bww(self):
+        structure = self.get_structure("3bww")
+        states = self.encoder.encode_chain(structure[0]["A"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DKDFFEAAEDDLVCLVVLLPPPACPQRQAYEDALVVQVPDDPVSVVSVVNSLVHHAYAYEYEAQQL"
+            "LDDPQGDVVSLVSVLVCCVVSVPQEYEYENDPPDADALDVVSLVSSLVSQLVSCVSSVGAYAYEDA"
+            "ADQDHDPRHPDDVLVSRQSNCVSNVHAHAYELVRLVRCCVRPVPDDSLVSLVRHPLQRHQHYEYQV"
+            "VSVVSVLVNLVDHQAHHYYYHDYPDDVVVNSVVRVVSRVSNVVSCVVVVHYIDMD",
+        )
+
+    def test_encode_8crb(self):
+        structure = self.get_structure("8crb")
+
+        states = self.encoder.encode_chain(structure[0]["A"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DWAKDKDWADEDAAQAKTKIKMATPPDLLQDFFKFKWFDAPPDDIDGQAPGACPSPPLADDVHHHH"
+            "GKGWHDDSVRRMIMIMGGNDDQVVFGKMKMFTADDADPQVVVPDGDDTDDMHDIDTYGHPPDDFFA"
+            "WDKDKDQDDPVPCPVQKPKIKMKTDDGDDDDKDKAWLVNPGDPQKDDFDWDADPVRGIIDMIIGMD"
+            "GNVCFQVGFTKIWMAGVVVRDIDIDGGHD",
+        )
+
+        states = self.encoder.encode_chain(structure[0]["B"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DAAKDFDQQEEEAAQAKDKGWIFAADVPPVPDAFWKWWDAPPDDIDTAADPNQAGDPVDHSQKGWD"
+            "ADHGITIIMGGRDDNSRQGFIWRAQPDDPDHNGHTDDTHGYYHCPDDQDDKDKDWDDAAVVVLVVL"
+            "FGKTKIKIDDGDDPPKDKFKDLQNHTDDAQWDWDDWDLDPVRTIMTMIIRRDGVVSCVVSQKMKMW"
+            "IDDDVHTDIDMDGNVVHD",
+        )
+
+        states = self.encoder.encode_chain(structure[0]["C"])
+        sequence = self.encoder.build_sequence(states)
+        self.assertEqual(
+            sequence,
+            "DPCVLVVLVLQLVLVVLLLVVVVVVLVVCVVVLFKDWQDPVHDWQLACVSPDHDCPDCCSVPGSNN"
+            "VQQCPKPLDDVTATNQSVQQIDDGDLDHDDDDDTIQGCPPPVRCSVVVVVVSVVSVVVSVVSCVVS"
+            "VVVVVVD",
+        )