Replace pkg_resources with importlib and add python 3.13 to test suite.

.github/workflows/CI.yaml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     defaults:
       run:
@@ -30,10 +30,12 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
-        uses: mamba-org/setup-micromamba@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-variant: Miniforge3
           environment-file: environment-dev.yml
-          create-args: python=${{ matrix.python-version }}
+          use-mamba: true
+          python-version: ${{ matrix.python-version }}
 
       - name: Install Package
         run: python -m pip install -e .
@@ -56,7 +58,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, macOS-13, ubuntu-latest, windows-latest]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
     defaults:
       run:
@@ -67,17 +69,21 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba (Linux)
-        uses: mamba-org/setup-micromamba@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-variant: Miniforge3
+          use-mamba: true
           environment-file: environment-dev.yml
-          create-args: python=${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
         if: runner.os != 'Windows'
 
       - name: Install Mamba (Windows)
-        uses: mamba-org/setup-micromamba@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-variant: Miniforge3
+          use-mamba: true
           environment-file: environment-dev-win.yml
-          create-args: python=${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
         if: runner.os == 'Windows'
 
       - name: Install Package
@@ -99,18 +105,20 @@ jobs:
         name: Checkout Branch / Pull Request
 
       - name: Install Mamba
-        uses: mamba-org/setup-micromamba@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
+          miniforge-variant: Miniforge3
+          use-mamba: true
           environment-file: environment-dev.yml
-          create-args: python=3.12
+          python-version: 3.13
 
       - name: Install Packages from Source
         run: |
           pip install -e .
 
       - name: Check environment
         run: |
-          micromamba list
+          conda list
 
       - name: Run Bleeding Edge Tests
         run: |

docs/docs-env.yml

@@ -14,6 +14,6 @@ dependencies:
     - sphinxcontrib-svg2pdfconverter
     - nbsphinx
     - networkx >=2.0
-    - lark-parser
+    - lark
     - requests
     - lxml

environment-dev.yml

@@ -2,7 +2,7 @@ name: foyer-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<=3.12
+  - python>=3.9,<=3.13
   - boltons
   - numpy=1.26.4
   - sympy

environment-win.yml

@@ -16,4 +16,4 @@ dependencies:
   - pytest-cov
   - pytest-timeout
   - pytest-xdist
-  - python>=3.9
+  - python>=3.10,<=3.13

environment.yml

@@ -10,4 +10,4 @@ dependencies:
   - parmed>=3.4.3
   - ele
   - requests
-  - python>=3.9
+  - python>=3.10,<=3.13

foyer/forcefield.py

@@ -2,12 +2,14 @@
 
 import collections
 import glob
+import importlib.resources as resources
 import itertools
 import os
 import re
 import warnings
 import xml.etree.ElementTree as ET
 from copy import copy
+from importlib.metadata import entry_points
 from tempfile import NamedTemporaryFile
 from typing import Callable, Iterable, List
 
@@ -31,7 +33,6 @@
     _convertParameterToNumber,
 )
 from parmed.gromacs.gromacstop import _Defaults
-from pkg_resources import iter_entry_points, resource_filename
 
 import foyer.element as custom_elem
 from foyer import smarts
@@ -133,7 +134,7 @@
 def get_available_forcefield_loaders() -> List[Callable]:
     """Get a list of available force field loader functions."""
     available_ff_paths = []
-    for entry_point in iter_entry_points(group="foyer.forcefields"):
+    for entry_point in entry_points(group="foyer.forcefields"):
         available_ff_paths.append(entry_point.load())
 
     return available_ff_paths
@@ -566,7 +567,7 @@
         if any(self._included_forcefields):
             return self._included_forcefields
 
-        ff_dir = resource_filename("foyer", "forcefields")
+        ff_dir = resources.files("foyer").joinpath("forcefields")
         ff_filepaths = set(glob.glob(os.path.join(ff_dir, "xml/*.xml")))
 
         for ff_filepath in ff_filepaths:

foyer/forcefields/__init__.py

@@ -1,6 +1,6 @@
 """Plugin support for forcefields."""
 
-from pkg_resources import iter_entry_points
+from importlib.metadata import entry_points
 
 
 class ForceFields:
@@ -11,5 +11,5 @@
 
 forcefields = ForceFields()
 
-for entry_point in iter_entry_points(group="foyer.forcefields", name=None):
+for entry_point in entry_points(group="foyer.forcefields"):
     setattr(forcefields, entry_point.name, entry_point.load())

foyer/forcefields/forcefields.py

@@ -1,18 +1,18 @@
 """Support user-created forcefield XML files."""
 
 import glob
+import importlib.resources as resources
 import os
 import warnings
 
-from pkg_resources import resource_filename
-
 from foyer import Forcefield
 from foyer.validator import ValidationWarning
 
 
 def get_ff_path():
     """Return path to forcefield locations."""
-    return [resource_filename("foyer", "forcefields")]
+    ff_dir = resources.files("foyer").joinpath("forcefields")
+    return [ff_dir]
 
 
 def get_forcefield_paths(forcefield_name=None):

foyer/tests/base_test.py

@@ -1,13 +1,15 @@
+import importlib.resources as resources
 from pathlib import Path
 
 import parmed as pmd
 import pytest
-from pkg_resources import resource_filename
 
 from foyer import forcefields
 from foyer.smarts import SMARTS
 
-OPLS_TEST_FILE_DIR = Path(resource_filename("foyer", "opls_validation")).resolve()
+OPLS_TEST_FILE_DIR = Path(
+    resources.files("foyer").joinpath("opls_validation")
+).resolve()
 
 
 class BaseTest:

foyer/tests/test_forcefield.py

@@ -1,13 +1,13 @@
 import difflib
 import glob
+import importlib.resources as resources
 import os
 from typing import List
 
 import parmed as pmd
 import pytest
 from lxml import etree as ET
 from parmed.gromacs.gromacstop import _Defaults
-from pkg_resources import resource_filename
 
 from foyer import Forcefield, forcefields
 from foyer.exceptions import (
@@ -23,7 +23,7 @@
 from foyer.tests.utils import get_fn, register_mock_request
 from foyer.utils.io import has_mbuild
 
-FF_DIR = resource_filename("foyer", "forcefields")
+FF_DIR = resources.files("foyer").joinpath("forcefields")
 FORCEFIELDS = glob.glob(os.path.join(FF_DIR, "xml/*.xml"))
 
 RESPONSE_BIB_ETHANE_JA962170 = """@article{Jorgensen_1996,

foyer/tests/test_opls.py

@@ -1,15 +1,15 @@
 import glob
+import importlib.resources as resources
 import itertools as it
 import os
 
 import parmed as pmd
 import pytest
-from pkg_resources import resource_filename
 
 from foyer.tests.base_test import BaseTest
 from foyer.tests.utils import atomtype
 
-OPLS_TESTFILES_DIR = resource_filename("foyer", "opls_validation")
+OPLS_TESTFILES_DIR = resources.files("foyer").joinpath("opls_validation")
 
 
 class TestOPLS(BaseTest):

foyer/tests/test_trappe.py

@@ -1,18 +1,17 @@
 import glob
+import importlib.resources as resources
 import itertools as it
 import os
 
 import parmed as pmd
 import pytest
-from pkg_resources import resource_filename
 
 from foyer import Forcefield
 from foyer.tests.base_test import BaseTest
 from foyer.tests.utils import atomtype
 
 TRAPPE_UA = Forcefield(name="trappe-ua")
-
-TRAPPE_TESTFILES_DIR = resource_filename("foyer", "trappe_validation")
+TRAPPE_TESTFILES_DIR = resources.files("foyer").joinpath("trappe_validation")
 
 
 class TestTraPPE(BaseTest):

foyer/tests/test_validator.py

@@ -1,9 +1,9 @@
 import glob
+import importlib.resources as resources
 import os
 
 import pytest
 from lxml.etree import DocumentInvalid, XMLSyntaxError
-from pkg_resources import resource_filename
 
 from foyer.exceptions import (
     MultipleValidationError,
@@ -21,7 +21,7 @@
     "documentinvalid": DocumentInvalid,
 }
 
-FF_DIR = resource_filename("foyer", "forcefields")
+FF_DIR = resources.files("foyer").joinpath("forcefields")
 FORCEFIELDS = glob.glob(os.path.join(FF_DIR, "xml/*.xml"))
 
 

pyproject.toml

@@ -29,7 +29,7 @@ classifiers=[
     "Operating System :: MacOS",
 ]
 urls = {Homepage = "https://github.com/mosdef-hub/foyer"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dynamic = ["version"]
 
 [tool.setuptools]