Conditionally skip tests requiring bluepy (#5)

pyproject.toml

@@ -38,7 +38,6 @@ dynamic = ["version"]
 [project.optional-dependencies]
 extra = [
     # extra requirements that may be dropped at some point
-#    "bluepy>=2.5.2",
     "fastparquet>=0.8.3,!=2023.1.0", # needed by pandas to read and write parquet files
     "orjson", # faster json decoder used by fastparquet
     "tables>=3.6.1", # needed by pandas to read and write hdf files
@@ -117,13 +116,15 @@ source = [
 branch = true
 parallel = false
 omit = [
-    "src/blueetl/_version.py",
+    "*/blueetl/_version.py",
+    "*/blueetl/adapters/bluepy/*.py",
+    "*/blueetl/external/**/*.py",
 ]
 
 [tool.coverage.report]
 show_missing = true
 precision = 0
-fail_under = 80
+fail_under = 70
 
 [tool.pydocstyle]
 # D413: no blank line after last section
@@ -140,6 +141,8 @@ extension-pkg-allow-list = ["numpy", "lxml", "pydantic"]
 # List of plugins (as comma separated values of python module names) to load,
 # usually to register additional checkers.
 load-plugins = ["pylint_pydantic"]
+# List of module names for which member attributes should not be checked.
+ignored-modules = ["bluepy"]
 
 [tool.pylint.design]
 # Maximum number of arguments for function / method.

src/blueetl/adapters/bluepy/__init__.py

@@ -1 +1,5 @@
 """Bluepy implementation."""
+from blueetl.utils import import_optional_dependency
+
+# Immediately raise an error with a custom message if the submodule is imported
+import_optional_dependency("bluepy")

src/blueetl/adapters/bluepy/circuit.py

@@ -2,13 +2,13 @@
 from collections.abc import Mapping
 from typing import Optional
 
-import bluepy
+from bluepy import Circuit
 
 from blueetl.adapters.interfaces.circuit import CircuitInterface, NodePopulationInterface
 from blueetl.utils import checksum_json
 
 
-class CircuitImpl(CircuitInterface[bluepy.Circuit]):
+class CircuitImpl(CircuitInterface[Circuit]):
     """Bluepy circuit implementation."""
 
     def checksum(self) -> str:

src/blueetl/adapters/bluepy/simulation.py

@@ -4,8 +4,8 @@
 from functools import cached_property
 from typing import Optional, Union
 
-import bluepy
 import pandas as pd
+from bluepy import Simulation
 from bluepy.exceptions import BluePyError
 from bluepy.impl.compartment_report import CompartmentReport, SomaReport
 from bluepy.impl.spike_report import SpikeReport
@@ -53,7 +53,7 @@ def get(self, group=None, t_start=None, t_stop=None, t_step=None) -> pd.DataFram
 class ReportCollection(UserDict):
     """Collection of reports as: name -> population -> report."""
 
-    def __init__(self, simulation: bluepy.Simulation) -> None:
+    def __init__(self, simulation: Simulation) -> None:
         """Init the report collection with the specified simulation."""
         super().__init__()
         self._simulation = simulation
@@ -68,7 +68,7 @@ def __getitem__(self, name) -> Mapping[Optional[str], PopulationReportInterface]
         return self.data[name]
 
 
-class SimulationImpl(SimulationInterface[bluepy.Simulation]):
+class SimulationImpl(SimulationInterface[Simulation]):
     """Bluepy simulation implementation."""
 
     def is_complete(self) -> bool:

src/blueetl/adapters/bluepysnap/circuit.py

@@ -2,13 +2,13 @@
 from collections.abc import Mapping
 from typing import Optional
 
-import bluepysnap
+from bluepysnap import Circuit
 
 from blueetl.adapters.interfaces.circuit import CircuitInterface, NodePopulationInterface
 from blueetl.utils import checksum_json
 
 
-class CircuitImpl(CircuitInterface[bluepysnap.Circuit]):
+class CircuitImpl(CircuitInterface[Circuit]):
     """Bluepysnap circuit implementation."""
 
     def checksum(self) -> str:

src/blueetl/adapters/bluepysnap/simulation.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Optional
 
-import bluepysnap
+from bluepysnap import Simulation
 
 from blueetl.adapters.bluepysnap.circuit import CircuitImpl
 from blueetl.adapters.interfaces.circuit import CircuitInterface
@@ -15,7 +15,7 @@
 )
 
 
-class SimulationImpl(SimulationInterface[bluepysnap.Simulation]):
+class SimulationImpl(SimulationInterface[Simulation]):
     """Bluepysnap simulation implementation."""
 
     def is_complete(self) -> bool:

src/blueetl/adapters/circuit.py

@@ -17,13 +17,9 @@ def _load_impl(self, config: str) -> Optional[CircuitInterface]:
             return None
         CircuitImpl: type[CircuitInterface]
         if config.endswith(".json"):
-            from bluepysnap import Circuit
-
-            from blueetl.adapters.bluepysnap.circuit import CircuitImpl
+            from blueetl.adapters.bluepysnap.circuit import Circuit, CircuitImpl
         else:
-            from bluepy import Circuit
-
-            from blueetl.adapters.bluepy.circuit import CircuitImpl
+            from blueetl.adapters.bluepy.circuit import Circuit, CircuitImpl
         return CircuitImpl(Circuit(config))
 
     def checksum(self) -> str:

src/blueetl/adapters/simulation.py

@@ -22,13 +22,9 @@ def _load_impl(self, config: str) -> Optional[SimulationInterface]:
             return None
         SimulationImpl: type[SimulationInterface]
         if config.endswith(".json"):
-            from bluepysnap import Simulation
-
-            from blueetl.adapters.bluepysnap.simulation import SimulationImpl
+            from blueetl.adapters.bluepysnap.simulation import Simulation, SimulationImpl
         else:
-            from bluepy import Simulation
-
-            from blueetl.adapters.bluepy.simulation import SimulationImpl
+            from blueetl.adapters.bluepy.simulation import Simulation, SimulationImpl
         return SimulationImpl(Simulation(config))
 
     def is_complete(self) -> bool:

src/blueetl/utils.py

@@ -1,5 +1,6 @@
 """Common utilities."""
 import hashlib
+import importlib
 import itertools
 import json
 import logging
@@ -8,7 +9,6 @@
 from collections.abc import Iterable, Iterator
 from contextlib import contextmanager
 from functools import cache, cached_property
-from importlib import import_module
 from pathlib import Path
 from typing import Any, Callable, Optional, Union
 
@@ -123,7 +123,7 @@ def import_by_string(full_name: str) -> Callable:
         The imported function.
     """
     module_name, _, func_name = full_name.rpartition(".")
-    return getattr(import_module(module_name), func_name)
+    return getattr(importlib.import_module(module_name), func_name)
 
 
 def resolve_path(*paths: StrOrPath, symlinks: bool = False) -> Path:
@@ -269,3 +269,24 @@ def all_equal(iterable: Iterable) -> bool:
             return False
         prev = item
     return True
+
+
+def import_optional_dependency(name: str) -> Any:
+    """Import an optional dependency.
+
+    If a dependency is missing, an ImportError with a custom message is raised. Based on:
+    https://github.com/pandas-dev/pandas/blob/0d853e77/pandas/compat/_optional.py#L85
+
+    Args:
+        name: The module name.
+
+    Returns:
+        ModuleType: The imported module, if found.
+    """
+    try:
+        module = importlib.import_module(name)
+    except ImportError as ex:
+        msg = f"Missing optional dependency {name!r}. Use pip to install it."
+        raise ImportError(msg) from ex
+
+    return module

tests/unit/adapters/test_circuit.py

@@ -1,13 +1,10 @@
 import pickle
 
-import bluepy
-import bluepysnap
 import pytest
-import bluepysnap.nodes
+
 from blueetl.adapters import circuit as test_module
 from blueetl.adapters.base import AdapterError
-from tests.unit.utils import TEST_DATA_PATH
-import bluepy.cells
+from tests.unit.utils import BLUEPY_AVAILABLE, TEST_DATA_PATH, assert_isinstance
 
 
 @pytest.mark.parametrize(
@@ -18,8 +15,8 @@
                 "sonata/circuit_config.json",
                 "default",
                 {
-                    "circuit": bluepysnap.Circuit,
-                    "population": bluepysnap.nodes.NodePopulation,
+                    "circuit": "bluepysnap.Circuit",
+                    "population": "bluepysnap.nodes.NodePopulation",
                 },
                 id="snap",
             )
@@ -29,10 +26,11 @@
                 "bbp/CircuitConfig",
                 None,
                 {
-                    "circuit": bluepy.Circuit,
-                    "population": bluepy.cells.CellCollection,
+                    "circuit": "bluepy.Circuit",
+                    "population": "bluepy.cells.CellCollection",
                 },
                 id="bluepy",
+                marks=pytest.mark.skipif(not BLUEPY_AVAILABLE, reason="bluepy not available"),
             )
         ),
     ],
@@ -42,11 +40,11 @@ def test_circuit_adapter(path, population, expected_classes, monkeypatch):
     # enter the circuit dir to resolve relative paths in bluepy
     monkeypatch.chdir(path.parent)
     obj = test_module.CircuitAdapter(TEST_DATA_PATH / path)
-    assert isinstance(obj.instance, expected_classes["circuit"])
+    assert_isinstance(obj.instance, expected_classes["circuit"])
 
     # access methods and properties
     pop = obj.nodes[population]
-    assert isinstance(pop, expected_classes["population"])
+    assert_isinstance(pop, expected_classes["population"])
 
     checksum = obj.checksum()
     assert isinstance(checksum, str)
@@ -56,7 +54,7 @@ def test_circuit_adapter(path, population, expected_classes, monkeypatch):
     loaded = pickle.loads(dumped)
 
     assert isinstance(loaded, test_module.CircuitAdapter)
-    assert isinstance(loaded.instance, expected_classes["circuit"])
+    assert_isinstance(loaded.instance, expected_classes["circuit"])
     # no cached_properties should be loaded after unpickling
     assert sorted(loaded.__dict__) == ["_impl"]
     assert sorted(loaded._impl.__dict__) == ["_circuit"]

tests/unit/adapters/test_simulation.py

@@ -1,17 +1,10 @@
 import pickle
 
-import bluepy.cells
-import bluepy.impl.compartment_report
-import bluepy.impl.spike_report
-import bluepysnap.frame_report
-import bluepysnap.nodes
-import bluepysnap.spike_report
 import pytest
 
 from blueetl.adapters import simulation as test_module
 from blueetl.adapters.base import AdapterError
-from blueetl.adapters.bluepy.simulation import PopulationReportImpl, PopulationSpikesReportImpl
-from tests.unit.utils import TEST_DATA_PATH
+from tests.unit.utils import BLUEPY_AVAILABLE, TEST_DATA_PATH, assert_isinstance
 
 
 @pytest.mark.parametrize(
@@ -23,11 +16,11 @@
                 "default",
                 ["soma_report", "section_report"],
                 {
-                    "simulation": bluepysnap.Simulation,
-                    "population": bluepysnap.nodes.NodePopulation,
-                    "spikes": bluepysnap.spike_report.PopulationSpikeReport,
-                    "soma_report": bluepysnap.frame_report.PopulationSomaReport,
-                    "section_report": bluepysnap.frame_report.PopulationCompartmentReport,
+                    "simulation": "bluepysnap.Simulation",
+                    "population": "bluepysnap.nodes.NodePopulation",
+                    "spikes": "bluepysnap.spike_report.PopulationSpikeReport",
+                    "soma_report": "bluepysnap.frame_report.PopulationSomaReport",
+                    "section_report": "bluepysnap.frame_report.PopulationCompartmentReport",
                 },
                 id="snap",
             )
@@ -38,13 +31,14 @@
                 None,
                 ["soma", "AllCompartments"],
                 {
-                    "simulation": bluepy.Simulation,
-                    "population": bluepy.cells.CellCollection,
-                    "spikes": PopulationSpikesReportImpl,
-                    "soma": PopulationReportImpl,
-                    "AllCompartments": PopulationReportImpl,
+                    "simulation": "bluepy.Simulation",
+                    "population": "bluepy.cells.CellCollection",
+                    "spikes": "blueetl.adapters.bluepy.simulation.PopulationSpikesReportImpl",
+                    "soma": "blueetl.adapters.bluepy.simulation.PopulationReportImpl",
+                    "AllCompartments": "blueetl.adapters.bluepy.simulation.PopulationReportImpl",
                 },
                 id="bluepy",
+                marks=pytest.mark.skipif(not BLUEPY_AVAILABLE, reason="bluepy not available"),
             )
         ),
     ],
@@ -54,28 +48,28 @@ def test_simulation_adapter(path, population, reports, expected_classes, monkeyp
     # enter the circuit dir to resolve relative paths in bluepy
     monkeypatch.chdir(path.parent)
     obj = test_module.SimulationAdapter(TEST_DATA_PATH / path)
-    assert isinstance(obj.instance, expected_classes["simulation"])
+    assert_isinstance(obj.instance, expected_classes["simulation"])
 
     assert obj.exists() is True
     assert obj.is_complete() is True
 
     # access methods and properties
     pop = obj.circuit.nodes[population]
-    assert isinstance(pop, expected_classes["population"])
+    assert_isinstance(pop, expected_classes["population"])
 
     spikes = obj.spikes[population]
-    assert isinstance(spikes, expected_classes["spikes"])
+    assert_isinstance(spikes, expected_classes["spikes"])
 
     for report_name in reports:
         report = obj.reports[report_name][population]
-        assert isinstance(report, expected_classes[report_name])
+        assert_isinstance(report, expected_classes[report_name])
 
     # test pickle roundtrip
     dumped = pickle.dumps(obj)
     loaded = pickle.loads(dumped)
 
     assert isinstance(loaded, test_module.SimulationAdapter)
-    assert isinstance(loaded.instance, expected_classes["simulation"])
+    assert_isinstance(loaded.instance, expected_classes["simulation"])
     # no cached_properties should be loaded after unpickling
     assert sorted(loaded.__dict__) == ["_impl"]
     assert sorted(loaded._impl.__dict__) == ["_simulation"]

tests/unit/utils.py

@@ -1,9 +1,17 @@
+import importlib
 from pathlib import Path
 
 import pandas as pd
 import pydantic
 import xarray as xr
 
+try:
+    import bluepy
+
+    BLUEPY_AVAILABLE = True
+except ImportError:
+    BLUEPY_AVAILABLE = False
+
 TEST_DATA_PATH = Path(__file__).parent / "data"
 
 
@@ -34,9 +42,16 @@ def iterallvalues(obj):
 
 
 def assert_not_duplicates(obj):
-    # verify that obj doesn't contain duplicate instances
+    """Verify that obj doesn't contain duplicate instances."""
     ids = set()
     for v in iterallvalues(obj):
         if isinstance(v, (dict, list, tuple)):
             assert id(v) not in ids, f"Duplicate {type(v).__name__}: {v}"
             ids.add(id(v))
+
+
+def assert_isinstance(instance, class_name):
+    """Verify that instance is an instance of class_name (given as string)."""
+    module_name, _, class_name = class_name.rpartition(".")
+    cls = getattr(importlib.import_module(module_name), class_name)
+    assert isinstance(instance, cls)

tox.ini

@@ -43,6 +43,7 @@ deps =
     {[base]testdeps}
     brion;platform_system=='Linux'
     elephant>=0.10.0,<0.13.0  # CPDF output changed in 0.13.0
+    bluepy>=2.5.2
 commands = python -m pytest -vs tests/functional {posargs}
 
 [testenv:check-packaging]