Python 3.12 compatibility

.github/workflows/CI.yaml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest] #, windows-latest] # AmberTools is not currently installable on Windows
-        python-version: ["3.11"] #, "3.12"] # intend to support more recent Python version eventually, but tooling is built around 3.11 only for now
+        python-version: ["3.11", "3.12"] # intend to support more recent Python version eventually, but tooling is built around 3.11 only for now
       fail-fast: false
 
     steps:

devtools/conda-envs/docs-env.yml

@@ -4,7 +4,7 @@ channels:
     - openeye
 dependencies:
     # Basic Python dependencies
-    - python=3.11.0
+    - python>=3.11
     - pip
 
     # Unit testing

devtools/conda-envs/release-build.yml

@@ -4,9 +4,9 @@ channels:
     - openeye
 dependencies:
     # Basic Python dependencies
-    - python=3.11.0
+    - python>=3.11.0
     - pip
-    - setuptools<82 # to avoid ImportErrors from pkg_resources deprecation
+    - setuptools
 
     # Unit testing
     - pytest
@@ -35,7 +35,7 @@ dependencies:
     - rdkit
     - mbuild
     - openbabel
-    - packmol<=20.15.1 # DEVNOTE: have no idea why, but versions tested later than this release (at least 20.16.1 and 21.0.4) introduce PDB CONECT errors where there were previously none
+    - packmol
     - openeye-toolkits # TODO: consider making this optional?
 
     # MD engines

devtools/conda-envs/test-env.yml

@@ -4,9 +4,9 @@ channels:
     - openeye
 dependencies:
     # Basic Python dependencies
-    - python=3.11.0
+    - python>=3.11.0
     - pip
-    - setuptools<82 # to avoid ImportErrors from pkg_resources deprecation
+    - setuptools
 
     # Unit testing
     - pytest
@@ -28,7 +28,8 @@ dependencies:
     - rdkit
     - mbuild
     - openbabel
-    - packmol<=20.15.1 # DEVNOTE: have no idea why, but versions tested later than this release (at least 20.16.1 and 21.0.4) introduce PDB CONECT errors where there were previously none
+    # - packmol<=20.15.1 # DEVNOTE: have no idea why, but versions tested later than this release (at least 20.16.1 and 21.0.4) introduce PDB CONECT errors where there were previously none
+    - packmol
     - openeye-toolkits # TODO: consider making this optional?
 
     # MD engines

polymerist/genutils/importutils/pkginspect.py

@@ -11,29 +11,36 @@
     Package,
     files as get_package_path
 )
-from importlib.resources._common import get_package, from_package, resolve
+from importlib.resources._common import resolve
+
+ModuleLike = Union[str, ModuleType, Package]
 
 
 # CHECKING PACKAGE AND MODULE STATUS
-def is_module(module : Package) -> bool:
+def is_module(module : ModuleLike) -> bool:
     '''Determine whether a given Package-like (i.e. str or ModuleType) is a valid Python module
     This will return True for packages, bottom-level modules (i.e. *.py) and Python scripts'''
     try:
-        resolve(module)
-        return True
+        module_loaded : ModuleType = resolve(module)
+        return True # enough to check that module is loadable as ModuleType
     except ModuleNotFoundError:
         return False
 
-def is_package(package : Package) -> bool:
+def is_package(package : ModuleLike) -> bool:
     '''Determine whether a given Package-like (i.e. str or ModuleType) is a valid Python package'''
     try:
-        get_package(package)
-        return True
-    except (ModuleNotFoundError, TypeError):
+        module_loaded : ModuleType = resolve(package)
+        if (module_spec := module_loaded.__spec__) is None:
+            return False
+        return (module_spec.submodule_search_locations is not None)
+        # per importlib docs : "[submodule_search_locations] should be set to None for non-package modules"
+        # (https://docs.python.org/3/library/importlib.html#importlib.machinery.ModuleSpec.submodule_search_locations)
+    except (ModuleNotFoundError):
+        # DEV 05/15/2026 - removed TypeError, as this was only raised by the deprecated _common.get_package function
         return False
 
 # EXTRACTING MODULE NAMING INFO
-def flexible_module_pass(module : Union[str, Path, ModuleType]) -> ModuleType: # TODO: extend this to decorator
+def flexible_module_pass(module : ModuleLike | Path) -> ModuleType: # TODO: extend this to decorator
     '''Flexible interface for supplying a ModuleType object as an argument
     Allows for passing a name (either module name or string path), Path location, or a module proper'''
     if isinstance(module, (str, ModuleType)):

polymerist/polymers/building/sequencing.py

@@ -7,7 +7,7 @@
 LOGGER = logging.getLogger(__name__)
 
 from typing import Iterable, Optional
-from dataclasses import dataclass, field, asdict
+from dataclasses import dataclass, asdict
 
 from ...genutils.textual.substrings import shortest_repeating_substring, repeat_string_to_length
 from ...genutils.fileutils.jsonio.jsonify import make_jsonifiable
@@ -174,7 +174,7 @@ def describe_order(self, end_group_names : Optional[Iterable[str]]=None, default
         if (num_names_provided := len(end_group_names)) != self.n_repeat_units_terminal: # DEV: consider supporting filling in missing names with default in future
             raise IndexError(f'Defined sequence info with {self.n_repeat_units_terminal} end groups, but only provided names for {num_names_provided}')
 
-        # Insert middle omnomer parts as necessary
+        # Insert middle monomer parts as necessary
         sequence_middle = []
         if self.n_full_periods != 0: ## Whole sequence strings
             sequence_middle.append(f'{self.n_full_periods}*[{self.sequence_kernel}]')

polymerist/tests/genutils/importutils/test_pkginspect.py

@@ -4,6 +4,7 @@
 __email__ = '[email protected]'
 
 from types import ModuleType
+from dataclasses import dataclass
 
 import pytest
 from pathlib import Path
@@ -16,64 +17,66 @@
 from polymerist import tests
 
 
-
 # TABULATED EXPECTED TESTS OUTPUTS
-non_module_types = [ # types that are obviously not modules OR packages, and which should fail
-    bool, int, float, complex, tuple, list, dict, set, # str, Path # str and Path need to be tested separately
-]
-
-are_modules = [
-    ('--not_a_module--', False), # deliberately weird to ensure this never accidentally clashes with a legit module name
-    (math, True),
-    ('math', True), # test that the string -> module resolver also works as intended
-    (json, True),
-    ('json', True),
-    (json.decoder, True),
-    ('json.decoder', True),
-    (polymerist, True),
-    ('polymerist.polymerist', True),
-    (genutils, True),
-    ('polymerist.genutils', True),
-]
-
-are_packages = [
-    ('--not_a_package--', False), # deliberately weird to ensure this never accidentally clashes with a legit module name
-    (math, False),
-    ('math', False), # test that the string -> module resolver also works as intended
-    (json, True),
-    ('json', True),
-    (json.decoder, False),
-    ('json.decoder', False),
-    (polymerist, False),
-    ('polymerist.polymerist', False),
-    (genutils, True),
-    ('polymerist.genutils', True),
-]
+def non_module_types() ->list[type]:
+    '''Types that are obviously not modules OR packages, and which should fail'''
+    return [
+        bool, int, float, complex, tuple, list, dict, set, 
+        # str, Path # str and Path need to be tested separately
+    ]
+
+@dataclass(frozen=True)
+class ModuleExample:
+    '''For encapsulating package and module check tests'''
+    resource : str | ModuleType
+    is_module : bool
+    is_package : bool
+
+def module_examples() -> tuple[ModuleExample, ...]:
+    '''
+    Module-like objects labelled with whether they
+    are modules and whether they are packages
+    '''
+    return (
+        # deliberately weird to ensure this never accidentally clashes with a legit module name
+        ModuleExample('--not_a_module--', False, False), 
+        ModuleExample(math, True, False),
+        # test that the string -> module resolver also works as intended
+        ModuleExample('math', True, False), 
+        ModuleExample(json, True, True),
+        ModuleExample('json', True, True),
+        ModuleExample(json.decoder, True, False),
+        ModuleExample('json.decoder', True, False),
+        ModuleExample(polymerist, True, False),
+        ModuleExample('polymerist.polymerist', True, False),
+        ModuleExample(genutils, True, True),
+        ModuleExample('polymerist.genutils', True, True),
+    )
 
 
 # MODULE AND PACKAGE PERCEPTION
-@pytest.mark.parametrize('module, expected_output', are_modules)
-def test_is_module(module : ModuleType, expected_output : bool) -> None:
+@pytest.mark.parametrize('module_example', module_examples())
+def test_is_module(module_example : ModuleExample) -> None:
     '''See if Python module perception behaves as expected'''
-    assert pkginspect.is_module(module) == expected_output
+    assert pkginspect.is_module(module_example.resource) == module_example.is_module
 
-@pytest.mark.parametrize('non_module_type', non_module_types)
+@pytest.mark.parametrize('non_module_type', non_module_types())
 def test_is_module_fail_on_invalid_types(non_module_type : type) -> None:
     '''check that module perception fails on invalid inputs'''
     with pytest.raises(AttributeError) as err_info:
         instance = non_module_type() # create a default instance
         _ = pkginspect.is_module(instance)
 
-@pytest.mark.parametrize('module, expected_output', are_packages)
-def test_is_package(module : ModuleType, expected_output : bool) -> None:
+@pytest.mark.parametrize('module_example', module_examples())
+def test_is_package(module_example : ModuleExample) -> None:
     '''See if Python package perception behaves as expected'''
-    assert pkginspect.is_package(module) == expected_output
+    assert pkginspect.is_package(module_example.resource) == module_example.is_package
 
-@pytest.mark.parametrize('non_module_type', non_module_types) # NOTE: these args are in fact deliberately NOT renamed to ".*package" from ".*module"
-def test_is_module_fail_on_invalid_types(non_module_type : type) -> None:
+@pytest.mark.parametrize('non_package_type', non_module_types())
+def test_is_package_fail_on_invalid_types(non_package_type : type) -> None:
     '''check that package perception fails on invalid inputs'''
     with pytest.raises(AttributeError) as err_info:
-        instance = non_module_type() # create a default instance
+        instance = non_package_type() # create a default instance
         _ = pkginspect.is_package(instance)
 
 # FETCHING DATA FROM PACKAGES

pyproject.toml

@@ -18,12 +18,12 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
 ]
-requires-python = "~=3.11"
+requires-python = ">=3.11"
 # Declare any run-time dependencies that should be installed with the package.
 dependencies = [
     "importlib-resources", # added to allow incorporation of `data` later on
-    "setuptools<82.0.0",   # added to avoid CI errors due to pkg_resources deprecation
-    "numpy<2.0.0", # DEV: pinning this, as leaving it unpinned causes errors when importing mbuild (deprecated numpy.vecdot function)
+    "setuptools",   # added to avoid CI errors due to pkg_resources deprecation
+    "numpy>=2.0.0", # DEV: pinning this, as leaving it unpinned causes errors when importing mbuild (deprecated numpy.vecdot function)
     "scipy",
     "pandas",
     "rich",
@@ -36,7 +36,8 @@ dependencies = [
     "openmm",
     # DEV: as of 08/18/2025, latest stable version of lammps shipped w/ binaries on conda 
     # lammps-dependent code is unrunnable (citing MPI OSError) for more recent builds (i.e. 2025.MM.DD) 
-    "lammps<=2024.08.29", 
+    # "lammps<=2024.08.29", 
+    "lammps", 
 ]
 
 # Update the urls once the hosting is set up.