Merge pull request #387 from materialsproject/fix-mutable-dataclass-f…

…ield

Fix ValueError: mutable default for field `add_maker` is not allowed: use default_factory

.pre-commit-config.yaml

@@ -1,63 +1,63 @@
 default_language_version:
   python: python3
-exclude: '^src/atomate2/vasp/schemas/calc_types/'
+exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
-- repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.250
-  hooks:
-  - id: ruff
-    args: [--fix]
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
-  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: 22.12.0
-  hooks:
-  - id: black
-- repo: https://github.com/asottile/blacken-docs
-  rev: v1.12.1
-  hooks:
-  - id: blacken-docs
-    additional_dependencies: [black]
-    exclude: README.md
-- repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    entry: pflake8
-    files: ^src/
-    additional_dependencies:
-    - pyproject-flake8==6.0.0
-    - flake8-bugbear==22.12.6
-    - flake8-typing-imports==1.14.0
-    - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.3.0
-    - flake8-rst==0.8.0
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
-  hooks:
-  - id: python-use-type-annotations
-  - id: rst-backticks
-  - id: rst-directive-colons
-  - id: rst-inline-touching-normal
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.991
-  hooks:
-  - id: mypy
-    files: ^src/
-    additional_dependencies:
-    - tokenize-rt==4.1.0
-    - types-pkg_resources==0.1.2
-    - types-paramiko
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.2.2
-  hooks:
-    - id: codespell
-      stages: [commit, commit-msg]
-      args: [--ignore-words-list, 'titel,statics,ba,nd,te']
-      types_or: [python, rst, markdown]
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.0.282
+    hooks:
+      - id: ruff
+        args: [--fix]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    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: 22.12.0
+    hooks:
+      - id: black
+  - repo: https://github.com/asottile/blacken-docs
+    rev: v1.12.1
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black]
+        exclude: README.md
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        entry: pflake8
+        files: ^src/
+        additional_dependencies:
+          - pyproject-flake8==6.0.0
+          - flake8-bugbear==22.12.6
+          - flake8-typing-imports==1.14.0
+          - flake8-docstrings==1.6.0
+          - flake8-rst-docstrings==0.3.0
+          - flake8-rst==0.8.0
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.991
+    hooks:
+      - id: mypy
+        files: ^src/
+        additional_dependencies:
+          - tokenize-rt==4.1.0
+          - types-pkg_resources==0.1.2
+          - types-paramiko
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.2
+    hooks:
+      - id: codespell
+        stages: [commit, commit-msg]
+        args: [--ignore-words-list, "titel,statics,ba,nd,te"]
+        types_or: [python, rst, markdown]

examples/schema.py

@@ -22,5 +22,5 @@ def compute(a: float, b: float):
 print(compute_job.output.total)
 # OutputReference(8ff2a94e-7633-42e9-8aa0-8479801347d5, .total)
 
-compute_job.output.not_in_schema
+_ = compute_job.output.not_in_schema
 # AttributeError: ComputeSchema does not have property 'not_in_schema'.

pyproject.toml

@@ -11,54 +11,54 @@ license = { text = "modified BSD" }
 authors = [{ name = "Alex Ganose", email = "alexganose@gmail.com" }]
 dynamic = ["version"]
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
     "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Information Technology",
     "Intended Audience :: Science/Research",
     "Intended Audience :: System Administrators",
-    "Intended Audience :: Information Technology",
     "Operating System :: OS Independent",
-    "Topic :: Other/Nonlisted Topic",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
     "Topic :: Database :: Front-Ends",
+    "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
 ]
 requires-python = ">=3.8"
 dependencies = [
+    "PyYAML",
+    "maggma>=0.38.1",
     "monty>=2021.5.9",
-    "pydash",
     "networkx",
-    "maggma>=0.38.1",
     "pydantic",
-    "PyYAML",
+    "pydash",
 ]
 
 [project.optional-dependencies]
 docs = [
-    "sphinx==7.1.1",
+    "autodoc_pydantic==1.9.0",
     "furo==2023.7.26",
-    "myst_parser==2.0.0",
     "ipython==8.14.0",
+    "myst_parser==2.0.0",
     "nbsphinx==0.9.2",
-    "autodoc_pydantic==1.9.0",
     "sphinx-copybutton==0.5.2",
+    "sphinx==7.1.1",
 ]
 dev = ["pre-commit>=2.12.1"]
-tests = ["pytest==7.4.0", "pytest-cov==4.1.0"]
+tests = ["pytest-cov==4.1.0", "pytest==7.4.0"]
 vis = ["matplotlib", "pydot"]
 fireworks = ["FireWorks"]
 strict = [
+    "FireWorks==2.0.3",
+    "PyYAML==6.0.1",
+    "maggma==0.51.24",
+    "matplotlib==3.7.2",
     "monty==2023.5.8",
+    "moto==4.1.14",
     "networkx==3.1",
-    "pydash==7.0.6",
-    "maggma==0.51.24",
     "pydantic==1.10.9",
-    "PyYAML==6.0.1",
-    "FireWorks==2.0.3",
-    "matplotlib==3.7.2",
+    "pydash==7.0.6",
     "pydot==1.4.2",
-    "moto==4.1.14",
     "typing-extensions==4.7.1",
 ]
 
@@ -91,9 +91,9 @@ no_strict_optional = true
 [tool.pytest.ini_options]
 filterwarnings = [
     "ignore:.*POTCAR.*:UserWarning",
-    "ignore:.*magmom.*:UserWarning",
-    "ignore:.*is not gzipped.*:UserWarning",
     "ignore:.*input structure.*:UserWarning",
+    "ignore:.*is not gzipped.*:UserWarning",
+    "ignore:.*magmom.*:UserWarning",
     "ignore::DeprecationWarning",
 ]
 
@@ -109,9 +109,9 @@ source = ["src/"]
 skip_covered = true
 show_missing = true
 exclude_lines = [
+    '^\s*@overload( |$)',
     '^\s*assert False(,|$)',
     'if typing.TYPE_CHECKING:',
-    '^\s*@overload( |$)',
 ]
 
 [tool.ruff]
@@ -134,6 +134,7 @@ select = [
     "W",   # pycodestyle
     "YTT", # flake8-2020
 ]
+ignore = ["B028", "PLW0603", "RUF013"]
 pydocstyle.convention = "numpy"
 isort.known-first-party = ["jobflow"]
 

src/jobflow/core/flow.py

@@ -121,11 +121,11 @@ class Flow(MSONable):
     def __init__(
         self,
         jobs: list[Flow | jobflow.Job] | jobflow.Job | Flow,
-        output: Any | None = None,
+        output: Any = None,
         name: str = "Flow",
         order: JobOrder = JobOrder.AUTO,
         uuid: str = None,
-        hosts: list[str] | None = None,
+        hosts: list[str] = None,
     ):
         from jobflow.core.job import Job
 
@@ -336,8 +336,8 @@ def iterflow(self):
     def update_kwargs(
         self,
         update: dict[str, Any],
-        name_filter: str | None = None,
-        function_filter: Callable | None = None,
+        name_filter: str = None,
+        function_filter: Callable = None,
         dict_mod: bool = False,
     ):
         """
@@ -392,8 +392,8 @@ def update_kwargs(
     def update_maker_kwargs(
         self,
         update: dict[str, Any],
-        name_filter: str | None = None,
-        class_filter: type[jobflow.Maker] | None = None,
+        name_filter: str = None,
+        class_filter: type[jobflow.Maker] = None,
         nested: bool = True,
         dict_mod: bool = False,
     ):
@@ -511,8 +511,8 @@ def append_name(self, append_str: str, prepend: bool = False):
     def update_metadata(
         self,
         update: dict[str, Any],
-        name_filter: str | None = None,
-        function_filter: Callable | None = None,
+        name_filter: str = None,
+        function_filter: Callable = None,
         dict_mod: bool = False,
         dynamic: bool = True,
     ):
@@ -634,7 +634,7 @@ def update_config(
             )
 
     def add_hosts_uuids(
-        self, hosts_uuids: str | list[str] | None = None, prepend: bool = False
+        self, hosts_uuids: str | list[str] = None, prepend: bool = False
     ):
         """
         Add a list of UUIDs to the internal list of hosts.