Merge branch 'main' into splits

.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
 
@@ -39,7 +39,7 @@ 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"]
         split: [1, 2, 3]
 
     steps:
@@ -95,7 +95,7 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           name: coverage${{ matrix.split }}
           file: ./coverage.xml
-  
+
   test-notebooks-and-ase:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/atomate2'
@@ -117,7 +117,7 @@ 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/

CHANGELOG.md

@@ -1,5 +1,35 @@
 # Change log
 
+## v0.0.16
+
+This release brings lots of new workflows and support for all ASE calculators.
+
+### New Features 🎉
+
+* Anharmonicity Quantification workflow by @4kevinbeck5 in https://github.com/materialsproject/atomate2/pull/901
+* Workflow for Quasi-harmonic approximation (forcefields and VASP) by @JaGeo in https://github.com/materialsproject/atomate2/pull/903
+* Atomate2 OpenMM integration & broader classical MD framework by @orionarcher in https://github.com/materialsproject/atomate2/pull/782
+* Frequency Flattening Optimizer by @rohithsrinivaas in https://github.com/materialsproject/atomate2/pull/863
+* Including VASP surface adsorption flow by @itsduowang in https://github.com/materialsproject/atomate2/pull/691
+* Generalize forcefields for generic ASE calculator support by @esoteric-ephemera in https://github.com/materialsproject/atomate2/pull/940
+
+### Documentation 📖
+
+* Input set tutorial by @JonathanSchmidt1 in https://github.com/materialsproject/atomate2/pull/780
+
+### House-Keeping 🧹
+
+* Remove emmet `==` pin in `pyproject.toml` and update version in `strict` by @Andrew-S-Rosen in https://github.com/materialsproject/atomate2/pull/988
+
+### New Contributors
+
+* @4kevinbeck5 made their first contribution in https://github.com/materialsproject/atomate2/pull/901
+* @orionarcher made their first contribution in https://github.com/materialsproject/atomate2/pull/782
+* @rohithsrinivaas made their first contribution in https://github.com/materialsproject/atomate2/pull/863
+* @itsduowang made their first contribution in https://github.com/materialsproject/atomate2/pull/691
+
+**Full Changelog**: https://github.com/materialsproject/atomate2/compare/v0.0.15...v0.0.16
+
 ## v0.0.15
 
 **NOTE**: This version updates the VASP workflows to use input sets defined in pymatgen. Please make sure your pymatgen version is updated accordingly.
@@ -72,7 +102,7 @@
 * `ruff` fixes by @janosh in https://github.com/materialsproject/atomate2/pull/894
 * `ruff` fixes by @janosh in https://github.com/materialsproject/atomate2/pull/946
 
-## New Contributors
+### New Contributors
 
 * @rul048 made their first contribution in https://github.com/materialsproject/atomate2/pull/775
 * @davidwaroquiers made their first contribution in https://github.com/materialsproject/atomate2/pull/183
@@ -127,7 +157,7 @@
 * Update lobsterpy version by @naik-aakash in https://github.com/materialsproject/atomate2/pull/683
 * Fix all ruff PT011 (not checking error message when testing exceptions) by @janosh in https://github.com/materialsproject/atomate2/pull/698
 
-## New Contributors
+### New Contributors
 
 * @JonathanSchmidt1 made their first contribution in https://github.com/materialsproject/atomate2/pull/648
 * @rdguha1995 made their first contribution in https://github.com/materialsproject/atomate2/pull/161
@@ -235,7 +265,7 @@ The API of `Maker.maker` for all workflows (VASP, CP2K, force fields) have been
 * Future type annotations by @janosh in https://github.com/materialsproject/atomate2/pull/580
 * Use `numpy.testing.assert_allclose` over assert `np.(all|is)close` by @janosh in https://github.com/materialsproject/atomate2/pull/582
 
-## New Contributors
+### New Contributors
 
 * @mattmcdermott made their first contribution in https://github.com/materialsproject/atomate2/pull/506
 * @tpurcell90 made their first contribution in https://github.com/materialsproject/atomate2/pull/568
@@ -353,7 +383,7 @@ reciprocal_density_metal` instead of `reciprocal_density` for metallic systems.
 * Simplify: `dict.get(key, None)` -> `dict.get(key)` by @janosh in https://github.com/materialsproject/atomate2/pull/429
 * `dict.setdefault` instead of `if key not in dict: dict[key] = ...` by @janosh in https://github.com/materialsproject/atomate2/pull/452
 
-## New Contributors
+### New Contributors
 
 * @naik-aakash made their first contribution in https://github.com/materialsproject/atomate2/pull/279
 * @matthewkuner made their first contribution in https://github.com/materialsproject/atomate2/pull/322

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