Migrate pkg_resources to importlib_resources (#139)

bluepyemodel/data/utils.py

@@ -17,9 +17,9 @@
 """
 
 import csv
+from importlib import resources
 
 import numpy as np
-import pkg_resources
 
 
 def get_dendritic_data_filepath(data_type):
@@ -32,11 +32,12 @@ def get_dendritic_data_filepath(data_type):
         ValueError if data_type is not 'ISI_CV' nor 'rheobase'
     """
     if data_type == "ISI_CV":
-        return pkg_resources.resource_filename(__name__, "ISI_CV_Shai2015.csv")
+        return resources.files("bluepyemodel").joinpath("data", "ISI_CV_Shai2015.csv")
     if data_type == "rheobase":
-        return pkg_resources.resource_filename(
-            __name__, "spike_rheobase_pA_BeaulieuLaroche2021.csv"
+        return resources.files("bluepyemodel").joinpath(
+            "data", "spike_rheobase_pA_BeaulieuLaroche2021.csv"
         )
+
     raise ValueError(f"read_data expects 'ISI_CV' or 'rheobase' but got {data_type}")
 
 

bluepyemodel/ecode/noiseou3.py

@@ -17,9 +17,9 @@
 """
 
 import logging
+from importlib import resources
 
 import numpy
-import pkg_resources
 
 from bluepyemodel.ecode.noise import NoiseMixin
 
@@ -55,8 +55,9 @@ def __init__(self, location, **kwargs):
         if data_filepath is not None:
             series = numpy.loadtxt(data_filepath)
         else:
-            series_file = pkg_resources.resource_filename(__name__, "data/NoiseOU3.txt")
-            series = numpy.loadtxt(series_file)
+            resource = resources.files("bluepyemodel").joinpath("ecode", "data", "NoiseOU3.txt")
+            with open(resource, "r") as f:
+                series = numpy.loadtxt(f)
 
         self.current_series = series[:, 1]
         self.time_series = series[:, 0]

bluepyemodel/ecode/subwhitenoise.py

@@ -17,9 +17,9 @@
 """
 
 import logging
+from importlib import resources
 
 import numpy
-import pkg_resources
 
 from bluepyemodel.ecode.stimulus import BPEM_stimulus
 
@@ -62,8 +62,11 @@ def __init__(self, location, **kwargs):
         if data_filepath is not None:
             series = numpy.loadtxt(data_filepath)
         else:
-            series_file = pkg_resources.resource_filename(__name__, "data/SubWhiteNoise.txt")
-            series = numpy.loadtxt(series_file)
+            resource = resources.files("bluepyemodel").joinpath(
+                "ecode", "data", "SubWhiteNoise.txt"
+            )
+            with open(resource, "r") as f:
+                series = numpy.loadtxt(f)
 
         self.current_series = series[:, 1]
         self.time_series = series[:, 0]

bluepyemodel/ecode/whitenoise.py

@@ -17,9 +17,9 @@
 """
 
 import logging
+from importlib import resources
 
 import numpy
-import pkg_resources
 
 from bluepyemodel.ecode.noise import NoiseMixin
 
@@ -55,8 +55,9 @@ def __init__(self, location, **kwargs):
         if data_filepath is not None:
             series = numpy.loadtxt(data_filepath)
         else:
-            series_file = pkg_resources.resource_filename(__name__, "data/WhiteNoise.txt")
-            series = numpy.loadtxt(series_file)
+            resource = resources.files("bluepyemodel").joinpath("ecode", "data", "WhiteNoise.txt")
+            with open(resource, "r") as f:
+                series = numpy.loadtxt(f)
 
         self.current_series = series[:, 1]
         self.time_series = series[:, 0]

bluepyemodel/model/model.py

@@ -68,6 +68,7 @@ def define_distributions(distributions_definition, morphology=None):
     Args:
         distributions_definition (list): definitions of the distributions
     """
+    hotspot_begin, hotspot_end = None, None
     if any(definition.name == "step" for definition in distributions_definition):
         hotspot_begin, hotspot_end = get_hotspot_location(morphology.morphology_path)
     distributions = collections.OrderedDict()

bluepyemodel/tools/utils.py

@@ -93,6 +93,8 @@ def parse_legacy_checkpoint_path(path):
             "iteration": None,
             "ttype": None,
         }
+    else:
+        raise ValueError(f"Invalid checkpoint path: {path}")
 
     return checkpoint_metadata
 

doc/source/conf.py

@@ -15,7 +15,7 @@
 
 sys.path.insert(0, os.path.abspath("../../."))
 
-from pkg_resources import get_distribution
+from importlib.metadata import version
 
 
 # -- Project information -----------------------------------------------------
@@ -24,7 +24,7 @@
 author = "Blue Brain Project/EPFL"
 
 # The short X.Y version
-version = get_distribution("bluepyemodel").version
+version = version("bluepyemodel")
 
 # The full version, including alpha/beta/rc tags
 release = version