Drop Python 3.9 (#105)

* Drop Python 3.9

* Drop Python 3.9

* Lint, add CodeCov token

Author: mattwthompson

.github/workflows/CI.yml

@@ -22,8 +22,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.9"
           - "3.10"
+          - "3.11"
         os:
           - ubuntu-latest
           - macos-latest
@@ -36,13 +36,6 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Additional info about the build
-        shell: bash
-        run: |
-          uname -a
-          df -h
-          ulimit -a
-
       - name: Install dependencies
         if: ${{ matrix.toolkit == true }}
         uses: mamba-org/setup-micromamba@v1
@@ -61,10 +54,7 @@ jobs:
 
       - name: Install package
         run: |
-          micromamba remove --force openff-forcefields
           python -m pip install -e .
-          conda list
-          conda info --all
 
       - name: Run water model tests
         if: ${{ matrix.toolkit == true }}
@@ -100,5 +90,6 @@ jobs:
       - name: Codecov
         uses: codecov/codecov-action@v4
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           fail_ci_if_error: false

.github/workflows/canary.yaml

@@ -16,8 +16,8 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.9"
           - "3.10"
+          - "3.11"
         cfg:
           - os: ubuntu-latest
           - os: macOS-latest

.pre-commit-config.yaml

@@ -23,4 +23,4 @@ repos:
   rev: v3.15.2
   hooks:
   - id: pyupgrade
-    exclude: openforcefields/_version.py|setup.py
+    args: ["--py310-plus"]

openforcefields/_version.py

@@ -16,10 +16,11 @@
 import re
 import subprocess
 import sys
-from typing import Any, Callable, Dict, List, Optional, Tuple
+from collections.abc import Callable
+from typing import Any
 
 
-def get_keywords() -> Dict[str, str]:
+def get_keywords() -> dict[str, str]:
     """Get the keywords needed to look up the version information."""
     # these strings will be replaced by git during git-archive.
     # setup.py/versioneer.py will grep for the variable names, so they must
@@ -61,8 +62,8 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY: Dict[str, str] = {}
-HANDLERS: Dict[str, Dict[str, Callable]] = {}
+LONG_VERSION_PY: dict[str, str] = {}
+HANDLERS: dict[str, dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
@@ -79,18 +80,18 @@ def decorate(f: Callable) -> Callable:
 
 
 def run_command(
-    commands: List[str],
-    args: List[str],
-    cwd: Optional[str] = None,
+    commands: list[str],
+    args: list[str],
+    cwd: str | None = None,
     verbose: bool = False,
     hide_stderr: bool = False,
-    env: Optional[Dict[str, str]] = None,
-) -> Tuple[Optional[str], Optional[int]]:
+    env: dict[str, str] | None = None,
+) -> tuple[str | None, int | None]:
     """Call the given command(s)."""
     assert isinstance(commands, list)
     process = None
 
-    popen_kwargs: Dict[str, Any] = {}
+    popen_kwargs: dict[str, Any] = {}
     if sys.platform == "win32":
         # This hides the console window if pythonw.exe is used
         startupinfo = subprocess.STARTUPINFO()
@@ -119,7 +120,7 @@ def run_command(
             return None, None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(f"unable to find command, tried {commands}")
         return None, None
     stdout = process.communicate()[0].strip().decode()
     if process.returncode != 0:
@@ -134,7 +135,7 @@ def versions_from_parentdir(
     parentdir_prefix: str,
     root: str,
     verbose: bool,
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Try to determine the version from the parent directory name.
 
     Source tarballs conventionally unpack into a directory that includes both
@@ -165,15 +166,15 @@ def versions_from_parentdir(
 
 
 @register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
+def git_get_keywords(versionfile_abs: str) -> dict[str, str]:
     """Extract version information from the given file."""
     # the code embedded in _version.py can just fetch the value of these
     # keywords. When used from setup.py, we don't want to import _version.py,
     # so we do it with a regexp instead. This function is not used from
     # _version.py.
-    keywords: Dict[str, str] = {}
+    keywords: dict[str, str] = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs) as fobj:
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)
@@ -194,10 +195,10 @@ def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
 
 @register_vcs_handler("git", "keywords")
 def git_versions_from_keywords(
-    keywords: Dict[str, str],
+    keywords: dict[str, str],
     tag_prefix: str,
     verbose: bool,
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Get version information from git keywords."""
     if "refnames" not in keywords:
         raise NotThisMethod("Short version file found")
@@ -270,7 +271,7 @@ def git_versions_from_keywords(
 @register_vcs_handler("git", "pieces_from_vcs")
 def git_pieces_from_vcs(
     tag_prefix: str, root: str, verbose: bool, runner: Callable = run_command
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -318,7 +319,7 @@ def git_pieces_from_vcs(
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
 
-    pieces: Dict[str, Any] = {}
+    pieces: dict[str, Any] = {}
     pieces["long"] = full_out
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
@@ -383,7 +384,7 @@ def git_pieces_from_vcs(
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
+            pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format(
                 full_tag,
                 tag_prefix,
             )
@@ -417,14 +418,14 @@ def git_pieces_from_vcs(
     return pieces
 
 
-def plus_or_dot(pieces: Dict[str, Any]) -> str:
+def plus_or_dot(pieces: dict[str, Any]) -> str:
     """Return a + if we don't already have one, else return a ."""
     if "+" in pieces.get("closest-tag", ""):
         return "."
     return "+"
 
 
-def render_pep440(pieces: Dict[str, Any]) -> str:
+def render_pep440(pieces: dict[str, Any]) -> str:
     """Build up version string, with post-release "local version identifier".
 
     Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
@@ -448,7 +449,7 @@ def render_pep440(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+def render_pep440_branch(pieces: dict[str, Any]) -> str:
     """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
 
     The ".dev0" means not master branch. Note that .dev0 sorts backwards
@@ -477,7 +478,7 @@ def render_pep440_branch(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+def pep440_split_post(ver: str) -> tuple[str, int | None]:
     """Split pep440 version string at the post-release segment.
 
     Returns the release segments before the post-release and the
@@ -487,7 +488,7 @@ def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
     return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
 
 
-def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+def render_pep440_pre(pieces: dict[str, Any]) -> str:
     """TAG[.postN.devDISTANCE] -- No -dirty.
 
     Exceptions:
@@ -511,7 +512,7 @@ def render_pep440_pre(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_pep440_post(pieces: Dict[str, Any]) -> str:
+def render_pep440_post(pieces: dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]+gHEX] .
 
     The ".dev0" means dirty. Note that .dev0 sorts backwards
@@ -538,7 +539,7 @@ def render_pep440_post(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+def render_pep440_post_branch(pieces: dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
 
     The ".dev0" means not master branch.
@@ -567,7 +568,7 @@ def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_pep440_old(pieces: Dict[str, Any]) -> str:
+def render_pep440_old(pieces: dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
@@ -589,7 +590,7 @@ def render_pep440_old(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_git_describe(pieces: Dict[str, Any]) -> str:
+def render_git_describe(pieces: dict[str, Any]) -> str:
     """TAG[-DISTANCE-gHEX][-dirty].
 
     Like 'git describe --tags --dirty --always'.
@@ -609,7 +610,7 @@ def render_git_describe(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render_git_describe_long(pieces: Dict[str, Any]) -> str:
+def render_git_describe_long(pieces: dict[str, Any]) -> str:
     """TAG-DISTANCE-gHEX[-dirty].
 
     Like 'git describe --tags --dirty --always -long'.
@@ -629,7 +630,7 @@ def render_git_describe_long(pieces: Dict[str, Any]) -> str:
     return rendered
 
 
-def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
+def render(pieces: dict[str, Any], style: str) -> dict[str, Any]:
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
         return {
@@ -671,7 +672,7 @@ def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     }
 
 
-def get_versions() -> Dict[str, Any]:
+def get_versions() -> dict[str, Any]:
     """Get version information or return default if unable to do so."""
     # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
     # __file__, we can work backwards from there to the root. Some

openforcefields/tests/compare.py

@@ -1,13 +1,11 @@
-from typing import Dict
-
 import openmm
 import openmm.unit
 
 
 def _compare(
     system1: openmm.System,
     system2: openmm.System,
-    tolerances: Dict[str, openmm.unit.Quantity],
+    tolerances: dict[str, openmm.unit.Quantity],
 ):
     """Check that two OpenMM systems have the same parameters.
 
@@ -39,7 +37,7 @@ def _compare(
 def _compare_nonbonded_forces(
     force1: openmm.NonbondedForce,
     force2: openmm.NonbondedForce,
-    tolerances: Dict[str, openmm.unit.Quantity],
+    tolerances: dict[str, openmm.unit.Quantity],
 ):
     assert force1.getNumParticles() == force2.getNumParticles()
 

openforcefields/tests/test_water_models.py

@@ -1,5 +1,3 @@
-from typing import Dict
-
 import numpy
 import openmm
 import openmm.unit
@@ -62,7 +60,7 @@ def opc_positions() -> Molecule:
 def compare_water_systems(
     reference: openmm.System,
     system: openmm.System,
-    tolerances: Dict[str, openmm.unit.Quantity],
+    tolerances: dict[str, openmm.unit.Quantity],
 ):
     # OpenMM creates bond and angle forces despite each containing 0 parameters
     for index, force in enumerate(reference.getForces()):

scripts/write_tip3p.py

@@ -1,5 +1,3 @@
-from typing import Dict
-
 import pandas
 from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField
 from openff.toolkit.typing.engines.smirnoff.parameters import (
@@ -55,7 +53,7 @@
     }
 )
 
-element_to_atomic_number: Dict[str, int] = {
+element_to_atomic_number: dict[str, int] = {
     "Li": 3,
     "Na": 11,
     "K": 19,

setup.py

@@ -8,7 +8,7 @@
 
 short_description = __doc__.split("\n")
 
-with open("README.md", "r") as handle:
+with open("README.md") as handle:
     long_description = handle.read()