Bump min supported Python to 3.10 (#992)

* obj.__class__.__name__ -> type(maker).__name__

* bump ruff target-version to py310 and fix errors

* pyproject bump requires-python = ">=3.9", testing.yml drop 3.9 CI, README.md add badge showing min supported Python version

* missed some python-version: 3.9 in GH wfs

* fix outdated docs saying atomate2 supports py3.8+

* add Python 3.12 to supported versions and test in CI

* fix multiple level 1 headings in docs/user/codes/openmm.md

* quippy-ase==0.9.14; python_version < '3.12'

* "tblite>=0.3.0; python_version < '3.12'"

* try zip(strict=True) everywhere

* ruff

---------

Co-authored-by: Alex Ganose <utf@users.noreply.github.com>

Author: janosh

.github/workflows/testing.yml

@@ -17,7 +17,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.10"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -36,7 +36,7 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - name: Check out repo
@@ -103,7 +103,7 @@ jobs:
         shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - name: Check out repo

.github/workflows/update-precommit.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install pre-commit
         run: pip install pre-commit

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.6.1
+  rev: v0.6.7
   hooks:
   - id: ruff
     args: [--fix]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.11.1
+  rev: v1.11.2
   hooks:
   - id: mypy
     files: ^src/

README.md

@@ -5,6 +5,7 @@
 [![pypi version](https://img.shields.io/pypi/v/atomate2?color=blue)](https://pypi.org/project/atomate2)
 ![supported python versions](https://img.shields.io/pypi/pyversions/atomate2)
 [![Zenodo](https://img.shields.io/badge/DOI-10.5281/zenodo.10677081-blue?logo=Zenodo&logoColor=white)](https://zenodo.org/records/10677081)
+[![This project supports Python 3.10+](https://img.shields.io/badge/Python-3.10+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
 
 [Documentation][docs] | [PyPI][pypi] | [GitHub][github]
 
@@ -85,7 +86,7 @@ atomate2 workflows can be run using the [FireWorks] software. See the
 
 ## Installation
 
-Atomate2 is a Python 3.8+ library and can be installed using pip. Full installation
+Atomate2 is a Python 3.10+ library and can be installed using pip. Full installation
 and configuration instructions are provided in the [installation tutorial][installation].
 
 ## Tutorials

docs/conf.py

@@ -169,7 +169,7 @@
 
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3.8", None),
+    "python": ("https://docs.python.org/3.10", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
     "jobflow": ("https://materialsproject.github.io/jobflow", None),

docs/user/codes/openmm.md

@@ -6,7 +6,7 @@
 >>> conda activate atomate2
 
 # installing atomate2
->>> pip install git+https://github.com/orionarcher/atomate2.git
+>>> pip install git+https://github.com/orionarcher/atomate2
 
 # installing classical_md dependencies
 >>> conda install -c conda-forge --file .github/classical_md_requirements.txt
@@ -18,7 +18,7 @@ you can clone the repository and install from source.
 
 ``` bash
 # installing atomate2
->>> git clone https://github.com/orionarcher/atomate2.git
+>>> git clone https://github.com/orionarcher/atomate2
 >>> cd atomate2
 >>> git branch openff
 >>> git checkout openff
@@ -33,7 +33,7 @@ you intend to run on GPU, make sure that the tests are passing for CUDA.
 >>> python -m openmm.testInstallation
 ```
 
-# Understanding Atomate2 OpenMM
+## Understanding Atomate2 OpenMM
 
 Atomate2 is really just a collection of jobflow workflows relevant to
 materials science. In all the workflows, we pass our system of interest
@@ -55,7 +55,6 @@ The first job we need to create generates the `Interchange` object.
 To specify the system of interest, we use give it the SMILES strings,
 counts, and names (optional) of the molecules we want to include.
 
-
 ```python
 from atomate2.openff.core import generate_interchange
 
@@ -73,7 +72,6 @@ out the `create_mol_spec` function in the `atomate2.openff.utils`
 module. Under the hood, this is being called on each mol_spec dict.
 Meaning the code below is functionally identical to the code above.
 
-
 ```python
 from atomate2.openff.utils import create_mol_spec
 
@@ -90,7 +88,6 @@ object, which we can pass to the next stage of the simulation.
 NOTE: It's actually mandatory to include partial charges
 for PF6- here, the built in partial charge method fails.
 
-
 ```python
 import numpy as np
 from pymatgen.core.structure import Molecule
@@ -205,13 +202,13 @@ Awesome! At this point, we've run a workflow and could start analyzing
 our data. Before we get there though, let's go through some of the
 other simulation options available.
 
-# Digging Deeper
+## Digging Deeper
 
 Atomate2 OpenMM supports running a variety of workflows with different
 configurations. Below we dig in to some of the more advanced options.
 
-
 ### Configuring the Simulation
+
 <details>
 <summary>Learn more about the configuration of OpenMM simulations</summary>
 
@@ -228,14 +225,13 @@ once and have it apply to all stages of the simulation. The value inheritance
 is as follows: 1) any explicitly set value, 2) the value from the previous
 maker, 3) the default value (as shown below).
 
-
 ```python
 from atomate2.openmm.jobs.base import OPENMM_MAKER_DEFAULTS
 
 print(OPENMM_MAKER_DEFAULTS)
 ```
 
-```
+```py
 {
     "step_size": 0.001,
     "temperature": 298,
@@ -339,7 +335,6 @@ Rather than use `jobflow.yaml`, you could also create the stores in
 Python and pass the stores to the `run_locally` function. This is a bit
 more code, so usually the prior method is preferred.
 
-
 ```python
 from jobflow import run_locally, JobStore
 from maggma.stores import MongoStore, S3Store
@@ -374,19 +369,18 @@ run_locally(
     ensure_success=True,
 )
 ```
+
 </details>
 
 ### Running on GPUs
 
 <details>
 <summary>Learn to accelerate MD simulations with GPUs</summary>
 
-
 Running on a GPU is nearly as simple as running on a CPU. The only difference
 is that you need to specify the `platform_properties` argument in the
 `EnergyMinimizationMaker` with the `DeviceIndex` of the GPU you want to use.
 
-
 ```python
 production_maker = OpenMMFlowMaker(
     name="test_production",
@@ -414,7 +408,6 @@ First you'll need to install mpi4py.
 
 Then you can modify and run the following script to distribute the work across the GPUs.
 
-
 ```python
 # other imports
 
@@ -457,15 +450,16 @@ for i in range(4):
 # this script will run four times, each with a different rank, thus distributing the work across the four GPUs.
 run_locally(flows[rank], ensure_success=True)
 ```
+
 </details>
 
-# Analysis with Emmet
+## Analysis with Emmet
 
 For now, you'll need to make sure you have a particular emmet branch installed.
 Later the builders will be integrated into `main`.
 
 ```bash
-pip install git+https://github.com/orionarcher/emmet.git@md_builders
+pip install git+https://github.com/orionarcher/emmet@md_builders
 ```
 
 ### Analyzing Local Data
@@ -498,6 +492,7 @@ u = create_universe(
 
 solute = create_solute(u, solute_name="Li", networking_solvents=["PF6"])
 ```
+
 </details>
 
 ### Setting up builders
@@ -556,6 +551,7 @@ builder.connect()
 <summary>Here are some more convenient queries.</summary>
 
 Here are some more convenient queries we could use!
+
 ```python
 # query jobs from a specific day
 april_16 = {"completed_at": {"$regex": "^2024-04-16"}}
@@ -570,6 +566,7 @@ job_uuids = [
 ]
 my_specific_jobs = {"uuid": {"$in": job_uuids}}
 ```
+
 </details>
 
 </details>
@@ -611,6 +608,7 @@ solute = create_solute(
     fallback_radius=3,
 )
 ```
+
 </details>
 
 ### Automated analysis with builders

docs/user/install.md

@@ -136,8 +136,8 @@ atomate2
 ## Create a conda environment
 
 ```{note}
-Make sure to create a Python 3.8+ environment as recent versions of atomate2 only
-support Python 3.8 and higher.
+Make sure to create a Python 3.10+ environment as recent versions of atomate2 only
+support Python 3.10 and higher.
 ```
 
 We highly recommend that you organize your installation of the atomate2 and the other

pyproject.toml

@@ -19,11 +19,11 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "PyYAML",
     "click",
@@ -54,21 +54,19 @@ forcefields = [
     "calorine<=2.2.1",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
-    "torchdata<=0.7.1", # TODO: remove when issue fixed
     "matgl>=1.1.3",
-    "quippy-ase>=0.9.14",
+    # quippy-ase support for py3.12 tracked in https://github.com/libAtoms/QUIP/issues/645
+    "quippy-ase>=0.9.14; python_version < '3.12'",
     "sevenn>=0.9.3",
+    "torchdata<=0.7.1",                            # TODO: remove when issue fixed
 ]
-ase = [
-    "ase>=3.23.0",
-]
-ase-ext = [
-    "tblite>=0.3.0",
-]
+ase = ["ase>=3.23.0"]
+# tblite py3.12 support tracked in https://github.com/tblite/tblite/issues/198
+ase-ext = ["tblite>=0.3.0; python_version < '3.12'"]
 openmm = [
     "mdanalysis>=2.7.0",
-    "openmm>=8.1.0",
     "openmm-mdanalysis-reporter>=0.1.0",
+    "openmm>=8.1.0",
 ]
 docs = [
     "FireWorks==2.0.3",
@@ -101,31 +99,31 @@ strict = [
     "ijson==3.3.0",
     "jobflow==0.1.18",
     "lobsterpy==0.4.5",
+    "mdanalysis==2.7.0",
     "monty==2024.7.30",
     "mp-api==0.42.2",
     "numpy",
+    "openmm-mdanalysis-reporter==0.1.0",
+    "openmm==8.1.1",
     "phonopy==2.27.0",
     "pydantic-settings==2.5.2",
     "pydantic==2.9.2",
     "pymatgen-analysis-defects==2024.7.19",
     "pymatgen==2024.6.10",
     "python-ulid==2.7.0",
     "seekpath==2.1.0",
-    "tblite==0.3.0",
+    "tblite==0.3.0; python_version < '3.12'",
     "typing-extensions==4.12.2",
-    "mdanalysis==2.7.0",
-    "openmm==8.1.1",
-    "openmm-mdanalysis-reporter==0.1.0",
 ]
 strict-forcefields = [
     "calorine==2.2.1",
     "chgnet==0.3.8",
     "mace-torch>=0.3.3",
-    "torchdata==0.7.1", # TODO: remove when issue fixed
     "matgl==1.1.3",
-    "quippy-ase==0.9.14",
+    "quippy-ase==0.9.14; python_version < '3.12'",
     "sevenn==0.9.3.post1",
     "torch==2.2.1",
+    "torchdata==0.7.1",                            # TODO: remove when issue fixed
 ]
 
 [project.scripts]
@@ -179,7 +177,8 @@ exclude_lines = [
 ]
 
 [tool.ruff]
-target-version = "py39"
+target-version = "py310"
+output-format = "concise"
 
 [tool.ruff.lint]
 select = ["ALL"]

src/atomate2/abinit/sets/base.py

@@ -8,7 +8,7 @@
 import os
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from abipy.abio.inputs import AbinitInput, MultiDataset
@@ -39,7 +39,7 @@
 )
 
 if TYPE_CHECKING:
-    from collections.abc import Iterable, Sequence
+    from collections.abc import Callable, Iterable, Sequence
 
     from pymatgen.core.structure import Structure
 
@@ -394,7 +394,7 @@ def check_format_prev_dirs(
         """Check and format the prev_dirs (restart or dependency)."""
         if prev_dirs is None:
             return None
-        if isinstance(prev_dirs, (str, Path)):
+        if isinstance(prev_dirs, str | Path):
             return [str(prev_dirs)]
         return [str(prev_dir) for prev_dir in prev_dirs]
 

src/atomate2/abinit/sets/core.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import TYPE_CHECKING, Callable
+from typing import TYPE_CHECKING
 
 import numpy as np
 from abipy.abio.factories import (
@@ -18,6 +18,8 @@
 from atomate2.abinit.sets.base import AbinitInputGenerator
 
 if TYPE_CHECKING:
+    from collections.abc import Callable
+
     from abipy.abio.inputs import AbinitInput
     from pymatgen.core import Structure
     from pymatgen.io.abinit import PseudoTable