Merge branch 'materialsproject:main' into hiphive

.github/workflows/testing.yml

@@ -3,9 +3,9 @@ name: testing
 on:
   push:
     branches: [main]
-    tags: ['v*']
+    tags: ["v*"]
   pull_request:
-    branches: [main]
+  workflow_dispatch:
 
 jobs:
   lint:
@@ -43,9 +43,16 @@ jobs:
           cache-dependency-path: pyproject.toml
 
       - name: Install dependencies
+        # ERROR: Cannot install atomate2 and atomate2[strict,tests]==0.0.1 because these package versions have conflicting dependencies.
+        # The conflict is caused by:
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen>=2023.10.4
+        #   atomate2[strict,tests] 0.0.1 depends on pymatgen==2023.10.4; extra == "strict"
+        # ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
+        #   chgnet 0.2.1 depends on pymatgen>=2023.5.31
+        #   emmet-core 0.70.0 depends on pymatgen>=2023.10.11
         run: |
           python -m pip install --upgrade pip
-            pip install .[strict,tests]
+          pip install .[strict,tests]
 
       - name: Test
         env:

.github/workflows/update-precommit.yml

@@ -8,7 +8,7 @@ on:
 jobs:
   auto-update:
     runs-on: ubuntu-latest
-    
+
     steps:
       - uses: actions/checkout@v3
 

.pre-commit-config.yaml

@@ -1,22 +1,21 @@
 default_language_version:
   python: python3
-exclude: '^.github/'
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.287
+  rev: v0.1.1
   hooks:
   - id: ruff
     args: [--fix]
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.10.0
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
@@ -46,7 +45,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.5.1
+  rev: v1.6.1
   hooks:
   - id: mypy
     files: ^src/
@@ -55,9 +54,9 @@ repos:
     - types-pkg_resources==0.1.2
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.5
+  rev: v2.2.6
   hooks:
   - id: codespell
     stages: [commit, commit-msg]
-    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te,atomate']
     types_or: [python, rst, markdown]

ADMIN.md

@@ -2,6 +2,7 @@
 
 Version releases on Pypi and GitHub are handled automatically through GitHub
 actions. The steps to push a new release are:
+
 1. Update `CHANGELOG.md` with a new version and release notes.
 2. Create a tagged Git commit with the above changes: `git tag v0.0.1`
 3. Push the commit and tags to GitHub using: `git push origin --tags`

README.md

@@ -120,9 +120,8 @@ Atomate2 is released under a modified BSD license; the full text can be found [h
 
 ## Acknowledgements
 
-Atomate2 was designed and developed by Alex Ganose.
-
-A full list of all contributors can be found [here][contributors].
+The development of atomate2 has benefited from many people across several research groups.
+A full list of contributors can be found [here][contributors].
 
 [pymatgen]: https://pymatgen.org
 [fireworks]: https://materialsproject.github.io/fireworks/

docs/about/contributors.md

@@ -3,12 +3,12 @@
 [gh]: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg
 [orc]: ../_static/orcid.svg
 
-atomate2 was designed and developed by **Alex Ganose** [![gh]][utf] [![orc]][0000-0002-4486-3321].
+The first version of atomate2 was designed and developed by **Alex Ganose** [![gh]][utf] [![orc]][0000-0002-4486-3321].
 
 [utf]: https://github.com/utf
 [0000-0002-4486-3321]: https://orcid.org/0000-0002-4486-3321
 
-Additional contributions have been provided by:
+Further substantial contributions have been provided by:
 
 **Andrew Rosen** [![gh]][Andrew-S-Rosen] [![orc]][0000-0002-0141-7006] \
 Assistant Professor of Chemical & Biological Engineering \
@@ -95,3 +95,24 @@ University of California, Berkeley
 
 [mattmcdermott]: https://github.com/mattmcdermott
 [0000-0002-4071-3000]: https://orcid.org/0000-0002-4071-3000
+
+**Thomas Purcell** [![gh]][tpurcell90] [![orc]][0000-0003-4564-7206] \
+Assistant Professor of Chemistry \
+University of Arizona
+
+[tpurcell90]: https://github.com/tpurcell90
+[0000-0003-4564-7206]: https://orcid.org/0000-0003-4564-7206
+
+**Alexander Bonkowski** [![gh]][ab5424] [![orc]][0000-0002-0525-4742] \
+PhD student in Chemistry \
+RWTH Aachen University
+
+[ab5424]: https://github.com/ab5424
+[0000-0002-0525-4742]: https://orcid.org/0000-0002-0525-4742
+
+**Matthew Kuner** [![gh]][matthewkuner] [![orc]][0000-0002-8218-8558] \
+PhD student in Materials Science and Engineering \
+University of California, Berkeley
+
+[matthewkuner]: https://github.com/matthewkuner
+[0000-0002-8218-8558]: https://orcid.org/0000-0002-8218-8558

pyproject.toml

@@ -17,8 +17,8 @@ classifiers = [
     "Intended Audience :: System Administrators",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.9",
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
@@ -28,54 +28,56 @@ dependencies = [
     "PyYAML",
     "click",
     "custodian>=2023.3.10",
-    "emmet-core>=0.65.0",
+    "emmet-core>=0.70.5",
     "jobflow>=0.1.11",
-    "monty",
+    "monty>=2023.9.25",
     "numpy",
-    "pydantic",
-    "pymatgen>=2023.1.9",
+    "pydantic-settings>=2.0.3",
+    "pydantic>=2.0.1",
+    "pymatgen>=2023.10.11",
 ]
 
 [project.optional-dependencies]
 amset = ["amset>=0.4.15", "pydash"]
 cclib = ["cclib"]
-mp = ["mp-api>=0.27.5"]
+mp = ["mp-api>=0.37.5"]
 phonons = ["phonopy>=1.10.8", "seekpath"]
-lobster = ["lobsterpy>=0.3.1"]
+lobster = ["lobsterpy>=0.3.2"]
 defects = ["dscribe>=1.2.0", "pymatgen-analysis-defects>=2022.11.30"]
-forcefields = ["chgnet==0.2.0", "matgl==0.8.3", "quippy-ase==0.9.14"]
+forcefields = ["chgnet>=0.2.2", "matgl>=0.8.3", "quippy-ase>=0.9.14"]
 docs = [
     "FireWorks==2.0.3",
-    "autodoc_pydantic==1.9.0",
+    "autodoc_pydantic==2.0.1",
     "furo==2023.9.10",
-    "ipython==8.16.0",
+    "ipython==8.16.1",
     "jsonschema[format]",
     "myst_parser==2.0.0",
     "numpydoc==1.6.0",
-    "sphinx==7.2.6",
     "sphinx-copybutton==0.5.2",
+    "sphinx==7.2.6",
     "sphinx_design==0.5.0",
 ]
 dev = ["pre-commit>=2.12.1"]
 tests = ["FireWorks==2.0.3", "pytest-cov==4.1.0", "pytest==7.4.2"]
 strict = [
     "PyYAML==6.0.1",
     "cclib==1.8",
-    "chgnet==0.2.0",
+    "chgnet==0.2.2",
     "click==8.1.7",
-    "custodian==2023.7.22",
+    "custodian==2023.10.9",
     "dscribe==2.1.0",
-    "emmet-core==0.68.0",
-    "jobflow==0.1.13",
-    "lobsterpy==0.3.1",
+    "emmet-core==0.70.5",
+    "jobflow==0.1.14",
+    "lobsterpy==0.3.2",
     "matgl==0.8.3",
-    "monty==2023.9.5",
-    "mp-api==0.35.1",
+    "monty==2023.9.25",
+    "mp-api==0.37.5",
     "numpy",
     "phonopy==2.20.0",
-    "pydantic==1.10.9",
+    "pydantic-settings==2.0.3",
+    "pydantic==2.4.2",
     "pymatgen-analysis-defects==2023.8.22",
-    "pymatgen==2023.9.10",
+    "pymatgen==2023.10.11",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
     "typing-extensions==4.8.0",
@@ -114,6 +116,7 @@ ignore_missing_imports = true
 no_strict_optional = true
 
 [tool.pytest.ini_options]
+addopts = "-p no:warnings --import-mode=importlib"
 filterwarnings = [
     "ignore:.*POTCAR.*:UserWarning",
     "ignore:.*input structure.*:UserWarning",
@@ -140,36 +143,37 @@ exclude_lines = [
 ]
 
 [tool.ruff]
-target-version = "py38"
+target-version = "py39"
 select = [
-    "B",    # flake8-bugbear
-    "C4",   # flake8-comprehensions
-    "D",    # pydocstyle
-    "E",    # pycodestyle error
-    "EXE",  # flake8-executable
-    "F",    # pyflakes
-    "FLY",  # flynt
-    "I",    # isort
-    "ICN",  # flake8-import-conventions
-    "ISC",  # flake8-implicit-str-concat
-    "PD",   # pandas-vet
-    "PERF", # perflint
-    "PIE",  # flake8-pie
-    "PL",   # pylint
-    "PT",   # flake8-pytest-style
-    "PYI",  # flakes8-pyi
-    "Q",    # flake8-quotes
-    "RET",  # flake8-return
-    "RSE",  # flake8-raise
-    "RUF",  # Ruff-specific rules
-    "SIM",  # flake8-simplify
-    "SLOT", # flake8-slots
-    "TCH",  # flake8-type-checking
-    "TID",  # tidy imports
-    "TID",  # flake8-tidy-imports
-    "UP",   # pyupgrade
-    "W",    # pycodestyle warning
-    "YTT",  # flake8-2020
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "D",      # pydocstyle
+    "E",      # pycodestyle error
+    "EXE",    # flake8-executable
+    "F",      # pyflakes
+    "FA",     # flake8-future-annotations
+    "FBT003", # boolean-positional-value-in-call
+    "FLY",    # flynt
+    "I",      # isort
+    "ICN",    # flake8-import-conventions
+    "ISC",    # flake8-implicit-str-concat
+    "PD",     # pandas-vet
+    "PERF",   # perflint
+    "PIE",    # flake8-pie
+    "PL",     # pylint
+    "PT",     # flake8-pytest-style
+    "PYI",    # flakes8-pyi
+    "Q",      # flake8-quotes
+    "RET",    # flake8-return
+    "RSE",    # flake8-raise
+    "RUF",    # Ruff-specific rules
+    "SIM",    # flake8-simplify
+    "SLOT",   # flake8-slots
+    "TCH",    # flake8-type-checking
+    "TID",    # flake8-tidy-imports
+    "UP",     # pyupgrade
+    "W",      # pycodestyle warning
+    "YTT",    # flake8-2020
 ]
 ignore = [
     "PD011",   # pandas-use-of-dot-values
@@ -190,5 +194,7 @@ isort.known-first-party = ["atomate2"]
 "**/tests/*" = ["D"]
 # flake8-type-checking (TCH): things inside TYPE_CHECKING aren't available
 #     at runtime and so can't be used by pydantic models
-# flake8-future-annotations (FA): future annotations only work in pydantic models in python 3.10+
-"**/schemas/*" = ["FA", "TCH"]
+# flake8-future-annotations (FA): pipe operator for type unions only work in pydantic models in python 3.10+
+"**/schemas/*" = ["FA", "TCH", "UP007"]
+"**/schemas.py" = ["FA", "TCH", "UP007"]
+"**/settings.py" = ["FA", "TCH", "UP007"]

src/atomate2/amset/files.py

@@ -24,7 +24,7 @@ def copy_amset_files(
     src_dir: Path | str,
     src_host: str | None = None,
     file_client: FileClient = None,
-):
+) -> None:
     """
     Copy AMSET files to current directory.
 
@@ -78,7 +78,7 @@ def copy_amset_files(
     logger.info("Finished copying inputs")
 
 
-def write_amset_settings(settings_updates: dict, from_prev: bool = False):
+def write_amset_settings(settings_updates: dict, from_prev: bool = False) -> None:
     """
     Write AMSET settings to file.
 

src/atomate2/amset/jobs.py

@@ -46,7 +46,7 @@ def make(
         wavefunction_dir: str | Path = None,
         deformation_dir: str | Path = None,
         bandstructure_dir: str | Path = None,
-    ):
+    ) -> Response:
         """
         Run an AMSET calculation.
 

src/atomate2/amset/run.py

@@ -12,7 +12,7 @@
 _CONVERGENCE_PROPERTIES = ("mobility.overall", "seebeck")
 
 
-def run_amset():
+def run_amset() -> None:
     """Run amset in the current directory."""
     # Run AMSET using the command line as calling from python can cause issues
     # with multiprocessing