Switch to the open-sourced brain-indexer

bluepysnap/edges/edge_population.py

@@ -612,15 +612,7 @@ def h5_filepath(self):
     @cached_property
     def spatial_synapse_index(self):
         """Access to edges spatial index."""
-        try:
-            from spatial_index import open_index
-        except ImportError as e:
-            raise BluepySnapError(
-                (
-                    "Spatial index is for now only available internally to BBP. "
-                    "It requires `spatial_index`, an internal package."
-                )
-            ) from e
+        from brain_indexer import open_index
 
         index_dir = self._properties.spatial_synapse_index_dir
         if not index_dir:

bluepysnap/nodes/node_population.py

@@ -648,15 +648,7 @@ def h5_filepath(self):
     @cached_property
     def spatial_segment_index(self):
         """Access to edges spatial index."""
-        try:
-            from spatial_index import open_index
-        except ImportError as e:
-            raise BluepySnapError(
-                (
-                    "Spatial index is for now only available internally to BBP. ",
-                    "It requires `spatial_index`, an internal package.",
-                )
-            ) from e
+        from brain_indexer import open_index
 
         index_dir = self._properties.spatial_segment_index_dir
         if not index_dir:

setup.py

@@ -43,6 +43,7 @@ def __init__(self, *args, **kwargs):
     name="bluepysnap",
     python_requires=">=3.8",
     install_requires=[
+        "brain-indexer>=3.0.0",
         "cached_property>=1.0",
         "h5py>=3.0.1,<4.0.0",
         "importlib_resources>=5.0.0",
@@ -58,7 +59,6 @@ def __init__(self, *args, **kwargs):
     extras_require={
         "docs": ["sphinx", "sphinx-bluebrain-theme"],
         "plots": ["matplotlib>=3.0.0"],
-        "spatial-index": ["spatial-index>=1.2.1"],
     },
     packages=find_packages(),
     package_data={

tests/test_edge_population.py

@@ -728,30 +728,13 @@ def test_iter_connection_unique(self):
     def test_h5_filepath_from_config(self):
         assert self.test_obj.h5_filepath == str(TEST_DATA_DIR / "edges.h5")
 
-    @pytest.mark.skip(reason="Until spatial-index is released publicly")
-    def test_spatial_synapse_index(self):
-        with mock.patch("spatial_index.open_index") as mock_open_index:
-            self.test_obj.spatial_synapse_index
-        mock_open_index.assert_called_once_with("path/to/edge/dir")
-
-    @mock.patch.dict(sys.modules, {"spatial_index": mock.Mock()})
     def test_spatial_synapse_index_call(self):
         with pytest.raises(
             BluepySnapError,
             match="It appears default does not have synapse indices",
         ):
             self.test_obj.spatial_synapse_index
 
-    def test_spatial_synapse_index_error(self):
-        with pytest.raises(
-            BluepySnapError,
-            match=(
-                "Spatial index is for now only available internally to BBP. "
-                "It requires `spatial_index`, an internal package."
-            ),
-        ):
-            self.test_obj.spatial_synapse_index
-
     def test_pickle(self, tmp_path):
         pickle_path = tmp_path / "pickle.pkl"
 
@@ -776,9 +759,9 @@ def setup_method(self):
             TEST_DATA_DIR / "circuit_config.json", "default2"
         )
 
-    @mock.patch.dict(sys.modules, {"spatial_index": mock.Mock()})
+    @mock.patch.dict(sys.modules, {"brain_indexer": mock.Mock()})
     def test_spatial_synapse_index_call(self):
         self.test_obj.spatial_synapse_index
-        mock = sys.modules["spatial_index"].open_index
+        mock = sys.modules["brain_indexer"].open_index
         assert mock.call_count == 1
         assert mock.call_args[0][0].endswith("path/to/edge/dir")

tests/test_node_population.py

@@ -625,23 +625,9 @@ def test_models(self):
     def test_h5_filepath_from_config(self):
         assert self.test_obj.h5_filepath == str(TEST_DATA_DIR / "nodes.h5")
 
-    @pytest.mark.skip(reason="Until spatial-index is released publicly")
-    def test_spatial_segment_index(self):
-        with mock.patch("spatial_index.open_index") as mock_open_index:
-            self.test_obj.spatial_segment_index
-        mock_open_index.assert_called_once_with("path/to/node/dir")
-
-    @mock.patch.dict(sys.modules, {"spatial_index": mock.Mock()})
-    def test_spatial_segment_index_call(self):
-        with pytest.raises(
-            BluepySnapError,
-            match="It appears default does not have segment indices",
-        ):
-            self.test_obj.spatial_segment_index
-
     def test_spatial_segment_index_error(self):
         with pytest.raises(
-            BluepySnapError, match="Spatial index is for now only available internally to BBP."
+            BluepySnapError, match="It appears default does not have segment indices"
         ):
             self.test_obj.spatial_segment_index
 
@@ -718,10 +704,10 @@ class TestNodePopulationSpatialIndex:
     def setup_method(self):
         self.test_obj = Circuit(str(TEST_DATA_DIR / "circuit_config.json")).nodes["default2"]
 
-    @mock.patch.dict(sys.modules, {"spatial_index": mock.Mock()})
+    @mock.patch.dict(sys.modules, {"brain_indexer": mock.Mock()})
     def test_spatial_segment_index_call(self):
         self.test_obj.spatial_segment_index
 
-        mock = sys.modules["spatial_index"].open_index
+        mock = sys.modules["brain_indexer"].open_index
         assert mock.call_count == 1
         assert mock.call_args[0][0].endswith("path/to/node/dir")

tests/utils.py

@@ -5,7 +5,6 @@
 import shutil
 import tempfile
 from contextlib import contextmanager
-from distutils.dir_util import copy_tree
 from pathlib import Path
 
 import numpy.testing as npt
@@ -24,7 +23,7 @@
 
 @contextmanager
 def setup_tempdir(cleanup=True):
-    temp_dir = str(Path(tempfile.mkdtemp()).resolve())
+    temp_dir = Path(tempfile.mkdtemp()).resolve()
     try:
         yield temp_dir
     finally:
@@ -41,7 +40,10 @@ def copy_test_data(config="circuit_config.json"):
         yields a path to the copy of the config file
     """
     with setup_tempdir() as tmp_dir:
-        copy_tree(str(TEST_DATA_DIR), tmp_dir)
+        # shutil.copytree expects the target to not exist
+        if tmp_dir.exists():
+            tmp_dir.rmdir()
+        shutil.copytree(str(TEST_DATA_DIR), tmp_dir)
         copied_path = Path(tmp_dir)
         yield copied_path, copied_path / config
 

tox.ini

@@ -4,7 +4,7 @@ name = bluepysnap
 [tox]
 envlist =
     lint
-    py{38,39,310,311}
+    py{39,310,311,312}
 
 ignore_basepython_conflict = true