Remove deprecated pkg_resources (#1166)

* Replace `pkg_resources` with `importlib`

* Update requirements

* Add test to make sure we can read examples from README

nmodl/ast.py

@@ -1,5 +1,23 @@
+"""
+Module for vizualization of NMODL abstract syntax trees (ASTs).
+"""
+import getpass
+import json
+import os
+import sys
+import tempfile
+import webbrowser
+from shutil import copytree
+
+
+if sys.version_info >= (3, 9):
+    from importlib.resources import files
+else:
+    from importlib_resources import files
+
+from ._nmodl import to_json
 from ._nmodl.ast import *  # noqa
-from pkg_resources import *
+
 
 def view(nmodl_ast):
     """Visualize given NMODL AST in web browser
@@ -14,31 +32,21 @@ def view(nmodl_ast):
     Returns:
         None
     """
-    from ._nmodl import to_json
-    from distutils.dir_util import copy_tree
-    import getpass
-    import json
-    import os
-    import tempfile
-    import webbrowser
-
-    resource = "ext/viz"
-    if resource_exists(__name__, resource) and resource_isdir(__name__, resource):
-        installed_viz_tool = resource_filename(__name__, resource)
-    else:
+
+    path = files("nmodl") / "ext/viz"
+    if not path.is_dir():
         raise FileNotFoundError("Could not find sample mod files")
 
     work_dir = os.path.join(tempfile.gettempdir(), getpass.getuser(), "nmodl")
 
     # first copy necessary files to temp work directory
-    copy_tree(installed_viz_tool, work_dir)
+    copytree(path, work_dir, dirs_exist_ok=True)
 
     # prepare json data
-    with open(os.path.join(work_dir, 'ast.js'), 'w') as outfile:
-        json_data = json.loads(to_json(nmodl_ast, True, True, True))
-        outfile.write('var astRoot = %s;' % json.dumps(json_data))
+    json_data = json.loads(to_json(nmodl_ast, True, True, True))
+    with open(os.path.join(work_dir, "ast.js"), "w", encoding="utf-8") as outfile:
+        outfile.write(f"var astRoot = {json.dumps(json_data)};")
 
     # open browser with ast
-    url = 'file://' + os.path.join(work_dir, "index.html")
+    url = "file://" + os.path.join(work_dir, "index.html")
     webbrowser.open(url, new=1, autoraise=True)
-

nmodl/dsl.py

@@ -1,10 +1,15 @@
-import os.path as osp
-from pkg_resources import *
+import sys
+
+if sys.version_info >= (3, 9):
+    from importlib.resources import files
+else:
+    from importlib_resources import files
 
 from ._nmodl import *
 
 RESOURCE_DIR = "ext/example"
 
+
 def list_examples():
     """Returns a list of examples available
 
@@ -13,10 +18,11 @@ def list_examples():
     Returns:
         List of available examples
     """
-    if resource_exists(__name__, RESOURCE_DIR) and resource_isdir(__name__, RESOURCE_DIR):
-        return resource_listdir(__name__, RESOURCE_DIR)
-    else:
-        raise FileNotFoundError("Could not find sample directory")
+    path = files("nmodl") / RESOURCE_DIR
+    if path.exists() and path.is_dir():
+        return [result.name for result in path.glob("*.mod")]
+
+    raise FileNotFoundError("Could not find sample directory")
 
 
 def load_example(example):
@@ -29,10 +35,10 @@ def load_example(example):
     Args:
         example: Filename of an example as provided by `list_examples()`
     Returns:
-        List of available examples
+        An path to the example as a string
     """
-    resource =  osp.join(RESOURCE_DIR, example)
-    if resource_exists(__name__, resource):
-        return resource_string(__name__, resource)
-    else:
-        raise FileNotFoundError("Could not find sample mod files")
+    path = files("nmodl") / RESOURCE_DIR / example
+    if path.exists():
+        return path.read_text()
+
+    raise FileNotFoundError(f"Could not find sample mod file {example}")

pywheel/shim/_binwrapper.py

@@ -3,39 +3,44 @@
 A generic wrapper to access nmodl binaries from a python installation
 Please create a softlink with the binary name to be called.
 """
-
 import os
-import sys
 import stat
-from pkg_resources import working_set
+import sys
+
+
+if sys.version_info >= (3, 9):
+    from importlib.metadata import metadata, PackageNotFoundError
+    from importlib.resources import files
+else:
+    from importlib_metadata import metadata, PackageNotFoundError
+    from importlib_resources import files
+
 from find_libpython import find_libpython
 
 
 def _config_exe(exe_name):
     """Sets the environment to run the real executable (returned)"""
 
-    package_name = "nmodl"
-
-    if package_name not in working_set.by_key:
-        print ("INFO : Using nmodl-nightly Package (Developer Version)")
-        package_name = 'nmodl-nightly'
-
-    assert (
-        package_name in working_set.by_key
-    ), "NMODL package not found! Verify PYTHONPATH"
+    try:
+        metadata("nmodl-nightly")
+        print("INFO : Using nmodl-nightly Package (Developer Version)")
+    except PackageNotFoundError:
+        pass
 
-    NMODL_PREFIX = os.path.join(working_set.by_key[package_name].location, "nmodl")
-    NMODL_HOME = os.path.join(NMODL_PREFIX, ".data")
-    NMODL_BIN = os.path.join(NMODL_HOME, "bin")
+    NMODL_PREFIX = files("nmodl")
+    NMODL_HOME = NMODL_PREFIX / ".data"
+    NMODL_BIN = NMODL_HOME / "bin"
 
     # add libpython*.so path to environment
     os.environ["NMODL_PYLIB"] = find_libpython()
 
     # add nmodl home to environment (i.e. necessary for nrnunits.lib)
-    os.environ["NMODLHOME"] = NMODL_HOME
+    os.environ["NMODLHOME"] = str(NMODL_HOME)
 
     # set PYTHONPATH for embedded python to properly find the nmodl module
-    os.environ["PYTHONPATH"] = working_set.by_key[package_name].location + ':' + os.environ.get("PYTHONPATH", "")
+    os.environ["PYTHONPATH"] = (
+        str(NMODL_PREFIX.parent) + ":" + os.environ.get("PYTHONPATH", "")
+    )
 
     return os.path.join(NMODL_BIN, exe_name)
 

requirements.txt

@@ -6,4 +6,5 @@ sympy
 numpy
 find_libpython
 scikit-build
-importlib_resources;python_version<"3.9"
+importlib_resources;python_version<'3.9'
+importlib_metadata;python_version<'3.9'

setup.py

@@ -16,7 +16,6 @@
 Please create a softlink with the binary name to be called.
 """
 import stat
-from pkg_resources import working_set
 from find_libpython import find_libpython
 
 
@@ -78,6 +77,7 @@ def run(self, *args, **kwargs):
     "sympy>=1.3",
     "find_libpython",
     "importlib_resources;python_version<'3.9'",
+    "importlib_metadata;python_version<'3.9'",
 ]
 
 

test/unit/pybind/test_examples.py

@@ -0,0 +1,21 @@
+from json import loads
+from pathlib import Path
+
+from nmodl import dsl
+
+
+def test_example():
+    """
+    Test for the Python API from example
+    """
+
+    examples = dsl.list_examples()
+
+    # ordering may be off so we use a set
+    assert set(examples) == {"exp2syn.mod", "expsyn.mod", "hh.mod", "passive.mod"}
+
+    driver = dsl.NmodlDriver()
+    for example in examples:
+        nmodl_string = dsl.load_example(example)
+        # make sure we can parse the string
+        assert driver.parse_string(nmodl_string)