Update lint and deps

.github/workflows/deploy.yml

@@ -17,7 +17,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: '3.12'
 
       - name: Build
         run: |

.github/workflows/docs.yml

@@ -26,7 +26,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
+          python-version: "3.12"
           cache: pip
           cache-dependency-path: pyproject.toml
 

.github/workflows/link-check.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |

.github/workflows/testing.yml

@@ -16,7 +16,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -35,7 +35,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v4
@@ -58,7 +58,7 @@ jobs:
         run: pytest --cov=jobflow --cov-report=xml
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/jobflow'
+        if: matrix.python-version == '3.12' && github.repository == 'materialsproject/jobflow'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -74,7 +74,7 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
           cache: pip
           cache-dependency-path: pyproject.toml
 

.github/workflows/update-precommit.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v3
         with:
-          python-version: 3.9
+          python-version: 3.10
 
       - name: Install pre-commit
         run: pip install pre-commit

.pre-commit-config.yaml

@@ -3,21 +3,21 @@ default_language_version:
 exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.6.8
+    rev: v0.11.12
     hooks:
       - id: ruff
         args: [--fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: fix-encoding-pragma
         args: [--remove]
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.18.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
         additional_dependencies: [black]
@@ -43,7 +43,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.16.0
     hooks:
       - id: mypy
         files: ^src/
@@ -52,7 +52,7 @@ repos:
           - types-pkg_resources==0.1.2
           - types-paramiko
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         stages: [commit, commit-msg]

pyproject.toml

@@ -19,12 +19,13 @@ 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",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Database :: Front-Ends",
     "Topic :: Other/Nonlisted Topic",
     "Topic :: Scientific/Engineering",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "PyYAML",
     "maggma>=0.57.0",
@@ -40,28 +41,28 @@ ulid = ["python-ulid"]
 docs = [
     "autodoc_pydantic==2.2.0",
     "furo==2024.8.6",
-    "ipython==9.0.2",
+    "ipython==9.3.0",
     "myst_parser==4.0.1",
-    "nbsphinx==0.9.6",
+    "nbsphinx==0.9.7",
     "sphinx-copybutton==0.5.2",
-    "sphinx==8.2.3",
+    "sphinx==8.1.3",
 ]
 dev = ["pre-commit>=2.12.1", "typing_extensions; python_version < '3.11'"]
-tests = ["moto==4.2.13", "pytest-cov==6.1.1", "pytest==8.4.0"]
+tests = ["moto==5.1.5", "pytest-cov==6.1.1", "pytest==8.4.0"]
 vis = ["matplotlib", "pydot"]
 fireworks = ["FireWorks"]
 strict = [
     "FireWorks==2.0.4",
     "PyYAML==6.0.2",
     "maggma==0.71.5",
-    "matplotlib==3.9.4",
+    "matplotlib==3.10.3",
     "monty==2025.3.3",
-    "moto==4.2.13",
-    "networkx==3.2.1",
+    "moto==5.1.5",
+    "networkx==3.4.2",
     "pydantic-settings==2.9.1",
     "pydantic==2.11.5",
     "pydash==8.0.5",
-    "pydot==2.0.0",
+    "pydot==4.0.0",
     "python-ulid==3.0.0",
     "typing-extensions==4.13.2",
 ]
@@ -84,7 +85,7 @@ max-line-length = 88
 max-doc-length = 88
 select = "C, E, F, W, B"
 extend-ignore = "E203, W503, E501, F401, RST21"
-min-python-version = "3.9.0"
+min-python-version = "3.10.0"
 docstring-convention = "numpy"
 rst-roles = "class, func, ref, obj"
 

src/jobflow/core/job.py

@@ -1265,7 +1265,7 @@ def from_job_returns(
                 job_returns.output = apply_schema(job_returns.output, output_schema)
 
             job_returns.job_dir = job_dir
-            return cast(Self, job_returns)
+            return cast("Self", job_returns)
 
         if isinstance(job_returns, (list, tuple)):
             # check that a Response object is not given as one of many outputs

src/jobflow/utils/graph.py

@@ -170,7 +170,7 @@ def add_cluster(nested_flow, outer_graph):
             if isinstance(job, Flow):
                 add_cluster(job, cluster)
             else:
-                cluster.add_node(pydot_graph.get_node(f'"{job.uuid}"')[0])
+                cluster.add_node(pydot_graph.get_node(f"{job.uuid}")[0])
 
         outer_graph.add_subgraph(cluster)
 

tests/core/test_reference.py

@@ -515,6 +515,6 @@ def test_not_iterable():
     with pytest.raises(TypeError):
         next(ref)
 
-    with pytest.raises(TypeError):  # noqa: PT012
+    with pytest.raises(TypeError):
         for _ in ref:
             pass

tests/core/test_store.py

@@ -36,11 +36,11 @@ def test_additional(memory_store):
 
     import boto3
     from maggma.stores import MemoryStore, S3Store
-    from moto import mock_s3
+    from moto import mock_aws
 
     from jobflow import JobStore
 
-    with mock_s3():
+    with mock_aws():
         conn = boto3.resource("s3", region_name="us-east-1")
         conn.create_bucket(Bucket="bucket1")
         index = MemoryStore("index", key="blob_uuid")