Replace imports of distutils.

As reported in [Debian bug #1083070], the Python module distutils is
going to be removed entirely from the upcoming Debian release,
following the deprecation on Python side of the distutils module.
Removal of distutils is causing test failures in bmtk though:

	Traceback:
	/usr/lib/python3.12/importlib/__init__.py:90: in import_module
	    return _bootstrap._gcd_import(name[level:], package, level)
	tests/simulator/filternet/test_filternet_movies.py:5: in <module>
	    from bmtk.utils.sim_setup import build_env_filternet
	/usr/lib/python3/dist-packages/bmtk/utils/sim_setup.py:32: in <module>
	    from distutils.dir_util import copy_tree
	E   ModuleNotFoundError: No module named 'distutils'

These changes replace copy_tree invocations by shutil.copytree, with
the option to clobber existing directories by default, as otherwise
the refusal of erasing the target directory will cause other test
regressions.  The version sort invocation perusing LooseVersion is
replaced by invocations of the bare packaging.version.Version.

[Debian bug #1083070]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1083070

Signed-off-by: Étienne Mollier <[email protected]>

Author: emollier

bmtk/analyzer/spikes_analyzer.py

@@ -24,8 +24,8 @@
 import numpy as np
 
 try:
-    from distutils.version import LooseVersion
-    use_sort_values = LooseVersion(pd.__version__) >= LooseVersion('0.19.0')
+    from packaging.version import Version
+    use_sort_values = Version(pd.__version__) >= Version('0.19.0')
 
 except:
     use_sort_values = False

bmtk/utils/compile_mechanisms/compile_mechanisms.py

@@ -1,7 +1,7 @@
 import os
 import logging
 from subprocess import call
-from distutils.dir_util import copy_tree
+from shutil import copytree
 
 
 logger = logging.getLogger(__name__)
@@ -28,4 +28,4 @@ def copy_modfiles(mechanisms_dir, cached_dir=None):
         cached_dir = os.path.join(local_path, '..', 'scripts/bionet/mechanisms')
 
     logger.info('Copying mod files from {} to {}'.format(cached_dir, mechanisms_dir))
-    copy_tree(cached_dir, mechanisms_dir)
+    copytree(cached_dir, mechanisms_dir, dirs_exist_ok=True)

bmtk/utils/create_environment/env_builder.py

@@ -27,7 +27,7 @@
 from subprocess import call
 from collections import OrderedDict
 import logging
-from distutils.dir_util import copy_tree
+from shutil import copytree
 
 from bmtk.utils.compile_mechanisms import copy_modfiles, compile_mechanisms
 
@@ -270,7 +270,7 @@ def _create_components_dir(self, components_dir, with_examples=True):
 
             if with_examples:
                 logger.info('  Copying files from {}.'.format(src_dir))
-                copy_tree(src_dir, trg_dir)
+                copytree(src_dir, trg_dir, dirs_exist_ok=True)
 
         # return components_config
         self._circuit_config['components'] = components_config

bmtk/utils/sim_setup.py

@@ -29,7 +29,7 @@
 from optparse import OptionParser
 from collections import OrderedDict
 import logging
-from distutils.dir_util import copy_tree
+from shutil import copytree
 
 
 logger = logging.getLogger(__name__)
@@ -248,7 +248,7 @@ def _create_components_dir(self, components_dir, with_examples=True):
 
             if with_examples:
                 logger.info('  Copying files from {}.'.format(src_dir))
-                copy_tree(src_dir, trg_dir)
+                copytree(src_dir, trg_dir, dirs_exist_ok=True)
 
         # return components_config
         self._circuit_config['components'] = components_config
@@ -852,4 +852,4 @@ def membrane_report_parser(option, opt, value, parser):
     elif target_sim == 'filternet':
         build_env_filternet(base_dir=base_dir, network_dir=options.network_dir, tstop=options.tstop,
                             include_examples=options.include_examples,
-                            config_file=options.config_file)
+                            config_file=options.config_file)