From 1cbb7fcd248168a1639feccb65f0254951a6c37e Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 08:59:16 -0400
Subject: [PATCH 01/27] increase CI sensitivity by testing both lowest-direct
 and highest dependency resolution strategy

---
 .github/workflows/testing.yml | 12 ++++++++----
 pyproject.toml                | 15 +++++++++++++++
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index d37830a4..671d9bc9 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -35,14 +35,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        version:
+          - { python: "3.9", resolution: highest, extras: strict }
+          - { python: "3.10", resolution: lowest-direct, extras: strict }
+          - { python: "3.11", resolution: highest, extras: non-strict }
+          - { python: "3.12", resolution: lowest-direct, extras: non-strict }
 
     steps:
       - uses: actions/checkout@v4
 
       - uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.version.python }}
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -52,13 +56,13 @@ jobs:
       - name: Install dependencies
         run: |
           pip install uv
-          uv pip install .[strict,tests] --system
+          uv pip install '.[tests,${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
 
       - name: Test
         run: pytest --cov=jobflow --cov-report=xml
 
       - uses: codecov/codecov-action@v1
-        if: matrix.python-version == '3.11' && github.repository == 'materialsproject/jobflow'
+        if: matrix.version.python == '3.11' && github.repository == 'materialsproject/jobflow'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
diff --git a/pyproject.toml b/pyproject.toml
index 797ec42d..31f326ab 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -65,6 +65,21 @@ strict = [
     "python-ulid==2.7.0",
     "typing-extensions==4.12.2",
 ]
+non-strict = [
+    "FireWorks>=2.0.3",
+    "PyYAML>=6.0.1",
+    "maggma>=0.69.0",
+    "matplotlib>=3.9.0",
+    "monty>=2024.5.24",
+    "moto>=4.2.13",
+    "networkx>=3.2.1",
+    "pydantic-settings>=2.3.4",
+    "pydantic>=2.8.0",
+    "pydash>=8.0.1",
+    "pydot>=2.0.0",
+    "python-ulid>=2.7.0",
+    "typing-extensions>=4.12.2",
+]
 
 [project.urls]
 homepage = "https://materialsproject.github.io/jobflow/"

From 737d4fd3b43411d8a31a4ecfcbf490177ef20d09 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:14:35 -0400
Subject: [PATCH 02/27] remove non-strict extra deps set

has the benefit of running CI with required deps only
---
 .github/workflows/testing.yml | 10 +++++-----
 pyproject.toml                | 21 +++------------------
 2 files changed, 8 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 671d9bc9..8c55751f 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -36,10 +36,10 @@ jobs:
     strategy:
       matrix:
         version:
-          - { python: "3.9", resolution: highest, extras: strict }
-          - { python: "3.10", resolution: lowest-direct, extras: strict }
-          - { python: "3.11", resolution: highest, extras: non-strict }
-          - { python: "3.12", resolution: lowest-direct, extras: non-strict }
+          - { python: "3.9", resolution: highest, extras: "tests,strict" }
+          - { python: "3.10", resolution: lowest-direct, extras: "tests,strict" }
+          - { python: "3.11", resolution: highest, extras: tests }
+          - { python: "3.12", resolution: lowest-direct, extras: tests }
 
     steps:
       - uses: actions/checkout@v4
@@ -56,7 +56,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install uv
-          uv pip install '.[tests,${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
+          uv pip install '.[${{ matrix.version.extras }}]' --system --resolution=${{ matrix.version.resolution }}
 
       - name: Test
         run: pytest --cov=jobflow --cov-report=xml
diff --git a/pyproject.toml b/pyproject.toml
index 31f326ab..6f858745 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -26,13 +26,13 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "PyYAML",
+    "PyYAML>=6.0.1",
     "maggma>=0.57.0",
     "monty>=2023.9.25",
-    "networkx",
+    "networkx>=3.2.1",
     "pydantic-settings>=2.0.3",
     "pydantic>=2.0.1",
-    "pydash",
+    "pydash>=8.0.1",
 ]
 
 [project.optional-dependencies]
@@ -65,21 +65,6 @@ strict = [
     "python-ulid==2.7.0",
     "typing-extensions==4.12.2",
 ]
-non-strict = [
-    "FireWorks>=2.0.3",
-    "PyYAML>=6.0.1",
-    "maggma>=0.69.0",
-    "matplotlib>=3.9.0",
-    "monty>=2024.5.24",
-    "moto>=4.2.13",
-    "networkx>=3.2.1",
-    "pydantic-settings>=2.3.4",
-    "pydantic>=2.8.0",
-    "pydash>=8.0.1",
-    "pydot>=2.0.0",
-    "python-ulid>=2.7.0",
-    "typing-extensions>=4.12.2",
-]
 
 [project.urls]
 homepage = "https://materialsproject.github.io/jobflow/"

From c0bed9e63a9ea29a3837747b1e9c2e090bfd6f98 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:22:23 -0400
Subject: [PATCH 03/27] skip tests that fail if optional deps not installed

---
 tests/core/test_store.py         | 2 ++
 tests/managers/test_fireworks.py | 2 ++
 tests/utils/test_graph.py        | 2 ++
 tests/utils/test_uid.py          | 2 ++
 4 files changed, 8 insertions(+)

diff --git a/tests/core/test_store.py b/tests/core/test_store.py
index 2ddd78a7..9ab9e4d7 100644
--- a/tests/core/test_store.py
+++ b/tests/core/test_store.py
@@ -32,6 +32,8 @@ def test_basic(memory_store):
 
 
 def test_additional(memory_store):
+    pytest.importorskip("moto")
+
     from copy import deepcopy
 
     import boto3
diff --git a/tests/managers/test_fireworks.py b/tests/managers/test_fireworks.py
index 71ae2c6b..35f51dd1 100644
--- a/tests/managers/test_fireworks.py
+++ b/tests/managers/test_fireworks.py
@@ -1,5 +1,7 @@
 import pytest
 
+pytest.importorskip("fireworks")
+
 
 def test_flow_to_workflow(
     memory_jobstore, simple_job, simple_flow, connected_flow, nested_flow
diff --git a/tests/utils/test_graph.py b/tests/utils/test_graph.py
index 0b831645..8398e494 100644
--- a/tests/utils/test_graph.py
+++ b/tests/utils/test_graph.py
@@ -71,6 +71,8 @@ def add(a, b):
 
 
 def test_to_pydot():
+    pytest.importorskip("pydot")
+
     from jobflow import Flow, Job
     from jobflow.utils.graph import to_pydot
 
diff --git a/tests/utils/test_uid.py b/tests/utils/test_uid.py
index 2e9e294e..b40c0eb0 100644
--- a/tests/utils/test_uid.py
+++ b/tests/utils/test_uid.py
@@ -2,6 +2,8 @@
 
 
 def test_uid():
+    pytest.importorskip("ulid")
+
     from uuid import UUID
 
     from ulid import ULID

From 4a1d1ec66f5720ae3534999524f025aeaadb7301 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:38:47 -0400
Subject: [PATCH 04/27] add pytest.importorskip("matplotlib") to all
 test_draw_graph

---
 tests/core/test_flow.py   | 4 ++++
 tests/utils/test_graph.py | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/tests/core/test_flow.py b/tests/core/test_flow.py
index 6f0d78f1..1e875ed6 100644
--- a/tests/core/test_flow.py
+++ b/tests/core/test_flow.py
@@ -354,6 +354,8 @@ def test_graph():
 
 
 def test_draw_graph():
+    pytest.importorskip("matplotlib")
+
     from jobflow import Flow, JobOrder
 
     # test unconnected graph
@@ -385,6 +387,8 @@ def test_draw_graph():
 
 @pytest.mark.usefixtures("no_pydot")
 def test_draw_graph_nopydot():
+    pytest.importorskip("matplotlib")
+
     from jobflow import Flow, JobOrder
 
     # test unconnected graph
diff --git a/tests/utils/test_graph.py b/tests/utils/test_graph.py
index 8398e494..8ade3f1f 100644
--- a/tests/utils/test_graph.py
+++ b/tests/utils/test_graph.py
@@ -33,6 +33,8 @@ def test_itergraph():
 
 
 def test_draw_graph():
+    pytest.importorskip("matplotlib")
+
     from networkx import DiGraph, planar_layout
 
     from jobflow.utils.graph import draw_graph
@@ -45,6 +47,8 @@ def test_draw_graph():
 
 @pytest.mark.usefixtures("no_pydot")
 def test_draw_graph_no_pydot():
+    pytest.importorskip("matplotlib")
+
     from networkx import DiGraph
 
     from jobflow.utils.graph import draw_graph

From 4d5070e57057190c0ae3208ef74b06f439dcffde Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:41:06 -0400
Subject: [PATCH 05/27] refactor

---
 tests/core/test_flow.py   | 3 +--
 tests/utils/test_graph.py | 6 ++----
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/tests/core/test_flow.py b/tests/core/test_flow.py
index 1e875ed6..25397aeb 100644
--- a/tests/core/test_flow.py
+++ b/tests/core/test_flow.py
@@ -385,8 +385,7 @@ def test_draw_graph():
     assert flow.draw_graph()
 
 
-@pytest.mark.usefixtures("no_pydot")
-def test_draw_graph_nopydot():
+def test_draw_graph_nopydot(no_pydot):
     pytest.importorskip("matplotlib")
 
     from jobflow import Flow, JobOrder
diff --git a/tests/utils/test_graph.py b/tests/utils/test_graph.py
index 8ade3f1f..c9e1d406 100644
--- a/tests/utils/test_graph.py
+++ b/tests/utils/test_graph.py
@@ -45,8 +45,7 @@ def test_draw_graph():
     assert draw_graph(graph, layout_function=planar_layout)
 
 
-@pytest.mark.usefixtures("no_pydot")
-def test_draw_graph_no_pydot():
+def test_draw_graph_no_pydot(no_pydot):
     pytest.importorskip("matplotlib")
 
     from networkx import DiGraph
@@ -57,8 +56,7 @@ def test_draw_graph_no_pydot():
     assert draw_graph(graph)
 
 
-@pytest.mark.usefixtures("no_matplotlib")
-def test_draw_graph_no_matplotlib():
+def test_draw_graph_no_matplotlib(no_matplotlib):
     from networkx import DiGraph
 
     import jobflow.utils.graph

From ddc65c61b29d67412cb3248654c296f8b5c6785d Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:48:55 -0400
Subject: [PATCH 06/27] maggma>=0.69

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6f858745..96a4d87b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ classifiers = [
 requires-python = ">=3.9"
 dependencies = [
     "PyYAML>=6.0.1",
-    "maggma>=0.57.0",
+    "maggma>=0.69.0",
     "monty>=2023.9.25",
     "networkx>=3.2.1",
     "pydantic-settings>=2.0.3",

From c3639b17a727398bf6b3172864291f32471e2509 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu, 4 Jul 2024 09:55:02 -0400
Subject: [PATCH 07/27] dropping 3.12 CI for now until maggma incompat is fixed

---
 .github/workflows/testing.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 8c55751f..0f13b76c 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -39,7 +39,9 @@ jobs:
           - { python: "3.9", resolution: highest, extras: "tests,strict" }
           - { python: "3.10", resolution: lowest-direct, extras: "tests,strict" }
           - { python: "3.11", resolution: highest, extras: tests }
-          - { python: "3.12", resolution: lowest-direct, extras: tests }
+          # python 3.12 CI failing due to maggma incompatible, see
+          # https://github.com/materialsproject/jobflow/pull/640#issuecomment-2209055692
+          # - { python: "3.12", resolution: lowest-direct, extras: tests }
 
     steps:
       - uses: actions/checkout@v4

From 700064405a87d1e75b04d41ab997d019892564df Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sat, 20 Jul 2024 15:54:50 -0400
Subject: [PATCH 08/27] fix typo

---
 .github/workflows/testing.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
index 0f13b76c..4edcb46d 100644
--- a/.github/workflows/testing.yml
+++ b/.github/workflows/testing.yml
@@ -37,7 +37,7 @@ jobs:
       matrix:
         version:
           - { python: "3.9", resolution: highest, extras: "tests,strict" }
-          - { python: "3.10", resolution: lowest-direct, extras: "tests,strict" }
+          - { python: "3.10", resolution: lowest-direct, extras: "tests" }
           - { python: "3.11", resolution: highest, extras: tests }
           # python 3.12 CI failing due to maggma incompatible, see
           # https://github.com/materialsproject/jobflow/pull/640#issuecomment-2209055692

From 3ee56d2c58e132845f968876350b1bb3e57a3629 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sat, 20 Jul 2024 15:58:04 -0400
Subject: [PATCH 09/27] fix ruff + mypy after update

---
 .pre-commit-config.yaml          |  8 ++++----
 src/jobflow/core/maker.py        |  2 +-
 tests/managers/test_fireworks.py | 12 ++++++------
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4f470b9f..5481fde5 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ default_language_version:
 exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.4.2
+    rev: v0.5.4
     hooks:
       - id: ruff
         args: [--fix]
@@ -17,7 +17,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
+    rev: 1.18.0
     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: v1.10.0
+    rev: v1.11.0
     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: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
diff --git a/src/jobflow/core/maker.py b/src/jobflow/core/maker.py
index 8344f67a..f45935d3 100644
--- a/src/jobflow/core/maker.py
+++ b/src/jobflow/core/maker.py
@@ -261,7 +261,7 @@ def recursive_call(
 
     if isinstance(class_filter, Maker):
         # Maker instance supplied rather than a Maker class
-        class_filter = class_filter.__class__
+        class_filter = class_filter.__class__  # type: ignore[assignment]
 
     def _filter(nested_obj: Maker):
         # Filter the Maker object
diff --git a/tests/managers/test_fireworks.py b/tests/managers/test_fireworks.py
index 35f51dd1..8b731e66 100644
--- a/tests/managers/test_fireworks.py
+++ b/tests/managers/test_fireworks.py
@@ -15,7 +15,7 @@ def test_flow_to_workflow(
     flow = simple_job()
     wf = flow_to_workflow(flow, memory_jobstore)
 
-    assert type(wf) == Workflow
+    assert type(wf) is Workflow
     assert wf.name == "Flow"
     assert len(wf.fws) == 1
     assert wf.fws[0].name == "func"
@@ -24,7 +24,7 @@ def test_flow_to_workflow(
     flow = simple_job()
     wf = flow_to_workflow(flow, name="custom_name")
 
-    assert type(wf) == Workflow
+    assert type(wf) is Workflow
     assert wf.name == "custom_name"
     assert len(wf.fws) == 1
     assert wf.fws[0].name == "func"
@@ -33,7 +33,7 @@ def test_flow_to_workflow(
     flow = simple_flow()
     wf = flow_to_workflow(flow, memory_jobstore)
 
-    assert type(wf) == Workflow
+    assert type(wf) is Workflow
     assert wf.name == "Flow"
     assert len(wf.fws) == 1
     assert wf.fws[0].name == "func"
@@ -42,7 +42,7 @@ def test_flow_to_workflow(
     flow = connected_flow()
     wf = flow_to_workflow(flow, memory_jobstore)
 
-    assert type(wf) == Workflow
+    assert type(wf) is Workflow
     assert wf.name == "Connected Flow"
     assert len(wf.fws) == 2
     assert wf.fws[0].name == "func"
@@ -83,7 +83,7 @@ def test_job_to_firework(
     job = simple_job()
     fw = job_to_firework(job, memory_jobstore)
 
-    assert type(fw) == Firework
+    assert type(fw) is Firework
     assert fw.name == "func"
 
     job2 = simple_job()
@@ -91,7 +91,7 @@ def test_job_to_firework(
         job2, memory_jobstore, parents=[job.uuid], parent_mapping={job.uuid: 1}
     )
 
-    assert type(fw) == Firework
+    assert type(fw) is Firework
     assert fw.name == "func"
 
     with pytest.raises(ValueError, match="Both or neither of"):

From 3b850161702c71423a12b1b39a03f07760cc74de Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sat, 20 Jul 2024 16:01:04 -0400
Subject: [PATCH 10/27] pin pydantic>=2.0.1->2.4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 96a4d87b..737f04ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,7 +31,7 @@ dependencies = [
     "monty>=2023.9.25",
     "networkx>=3.2.1",
     "pydantic-settings>=2.0.3",
-    "pydantic>=2.0.1",
+    "pydantic>=2.4",
     "pydash>=8.0.1",
 ]
 

From afcefe323112a1af6fcdd4265f50ecafe21b950e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 23 Sep 2024 23:18:41 +0000
Subject: [PATCH 11/27] Bump pydantic from 2.9.1 to 2.9.2 (#681)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.9.1 to 2.9.2.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v2.9.1...v2.9.2)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5390847e..3416ba17 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,7 +59,7 @@ strict = [
     "moto==4.2.13",
     "networkx==3.2.1",
     "pydantic-settings==2.5.2",
-    "pydantic==2.9.1",
+    "pydantic==2.9.2",
     "pydash==8.0.3",
     "pydot==2.0.0",
     "python-ulid==2.7.0",

From 7b6b1b4bc80d79b56688f821109cdfffbb3e2923 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 23:13:33 +0000
Subject: [PATCH 12/27] Bump maggma from 0.69.3 to 0.69.4 (#682)

Bumps [maggma](https://github.com/materialsproject/maggma) from 0.69.3 to 0.69.4.
- [Release notes](https://github.com/materialsproject/maggma/releases)
- [Changelog](https://github.com/materialsproject/maggma/blob/main/docs/CHANGELOG.md)
- [Commits](https://github.com/materialsproject/maggma/compare/v0.69.3...v0.69.4)

---
updated-dependencies:
- dependency-name: maggma
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3416ba17..8ce07a64 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ fireworks = ["FireWorks"]
 strict = [
     "FireWorks==2.0.3",
     "PyYAML==6.0.2",
-    "maggma==0.69.3",
+    "maggma==0.69.4",
     "matplotlib==3.9.2",
     "monty==2024.7.30",
     "moto==4.2.13",

From 77e23c578b43623089d833277ea5c7064a902e64 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed, 2 Oct 2024 17:53:26 -0400
Subject: [PATCH 13/27] bump commit hooks

---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5481fde5..765249a6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ default_language_version:
 exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.6.8
     hooks:
       - id: ruff
         args: [--fix]
@@ -43,7 +43,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.0
+    rev: v1.11.2
     hooks:
       - id: mypy
         files: ^src/

From d31b6142e0fec290fb83e6dbbc2dff68bd72e638 Mon Sep 17 00:00:00 2001
From: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed, 2 Oct 2024 18:03:32 -0400
Subject: [PATCH 14/27] ruff fixes + 1 mypy fix

---
 docs/tutorials/4-creating-flows.ipynb     |  2 +
 docs/tutorials/5-dynamic-flows.ipynb      | 79 ++++++++++++++---------
 docs/tutorials/6-makers.ipynb             | 20 +++---
 docs/tutorials/7-generalized-makers.ipynb |  4 +-
 pyproject.toml                            |  7 +-
 src/jobflow/core/flow.py                  |  2 +-
 tests/conftest.py                         | 10 +--
 tests/core/test_maker.py                  |  9 +--
 tests/core/test_schemas.py                |  2 +-
 tests/core/test_store.py                  |  2 +-
 10 files changed, 79 insertions(+), 58 deletions(-)

diff --git a/docs/tutorials/4-creating-flows.ipynb b/docs/tutorials/4-creating-flows.ipynb
index eba524b4..50c2ab91 100644
--- a/docs/tutorials/4-creating-flows.ipynb
+++ b/docs/tutorials/4-creating-flows.ipynb
@@ -51,10 +51,12 @@
    "source": [
     "from jobflow import job\n",
     "\n",
+    "\n",
     "@job\n",
     "def add(a, b, c=2):\n",
     "    return a + b + c\n",
     "\n",
+    "\n",
     "@job\n",
     "def mult(a, b):\n",
     "    return a * b"
diff --git a/docs/tutorials/5-dynamic-flows.ipynb b/docs/tutorials/5-dynamic-flows.ipynb
index 43844076..b97579de 100644
--- a/docs/tutorials/5-dynamic-flows.ipynb
+++ b/docs/tutorials/5-dynamic-flows.ipynb
@@ -42,12 +42,12 @@
    "execution_count": 1,
    "id": "78348798",
    "metadata": {
-    "nbsphinx": "hidden",
-    "tags": [],
     "ExecuteTime": {
      "end_time": "2023-11-23T22:55:01.113171569Z",
      "start_time": "2023-11-23T22:55:01.112486877Z"
-    }
+    },
+    "nbsphinx": "hidden",
+    "tags": []
    },
    "outputs": [],
    "source": [
@@ -98,26 +98,28 @@
    ],
    "source": [
     "from random import randint\n",
-    "from jobflow import job, Flow, Response\n",
+    "\n",
+    "from jobflow import Flow, Response, job\n",
     "from jobflow.managers.local import run_locally\n",
     "\n",
+    "\n",
     "@job\n",
     "def make_list(a):\n",
     "    return [a] * randint(2, 5)\n",
     "\n",
+    "\n",
     "@job\n",
     "def add(a, b):\n",
     "    return a + b\n",
     "\n",
+    "\n",
     "@job\n",
     "def add_distributed(list_a):\n",
-    "    jobs = []\n",
-    "    for val in list_a:\n",
-    "        jobs.append(add(val, 1))\n",
-    "    \n",
+    "    jobs = [add(val, 1) for val in list_a]\n",
     "    flow = Flow(jobs)\n",
     "    return Response(replace=flow)\n",
     "\n",
+    "\n",
     "job1 = make_list(2)\n",
     "job2 = add_distributed(job1.output)\n",
     "flow = Flow([job1, job2])\n",
@@ -215,14 +217,17 @@
    ],
    "source": [
     "@job\n",
-    "def add(a, b):\n",
+    "def add(a, b):  # noqa: F811\n",
     "    return a + b\n",
     "\n",
+    "\n",
     "@job\n",
     "def add_with_logic(a, b):\n",
     "    if a < 10:\n",
     "        return Response(addition=add(a, b))\n",
-    "    \n",
+    "    return None\n",
+    "\n",
+    "\n",
     "job1 = add(1, 2)\n",
     "job2 = add_with_logic(job1.output, 2)\n",
     "flow = Flow([job1, job2])\n",
@@ -294,11 +299,14 @@
     "def add(a, b):\n",
     "    return a + b\n",
     "\n",
+    "\n",
     "@job\n",
     "def add_with_logic(a, b):\n",
     "    if a < 10:\n",
     "        return Response(addition=add(a, b))\n",
-    "    \n",
+    "    return None\n",
+    "\n",
+    "\n",
     "job1 = add(1, 20)\n",
     "job2 = add_with_logic(job1.output, 20)\n",
     "flow = Flow([job1, job2])\n",
@@ -341,16 +349,25 @@
   },
   {
    "cell_type": "markdown",
-   "source": [
-    "In this way, one can also compute the Fibonacci numbers:"
-   ],
+   "id": "7fb27b941602401d91542211134fc71a",
    "metadata": {
     "collapsed": false
-   }
+   },
+   "source": [
+    "In this way, one can also compute the Fibonacci numbers:"
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 8,
+   "id": "acae54e37e7d407bbb7b55eff062a284",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-11-23T22:55:13.426518952Z",
+     "start_time": "2023-11-23T22:55:13.322421257Z"
+    },
+    "collapsed": false
+   },
    "outputs": [
     {
      "name": "stdout",
@@ -392,13 +409,12 @@
     }
    ],
    "source": [
-    "\"\"\"A dynamic workflow that calculates the Fibonacci sequence.\"\"\"\n",
-    "from jobflow import Response, job, run_locally\n",
+    "from jobflow import job, run_locally\n",
     "\n",
     "\n",
     "@job\n",
     "def fibonacci(smaller, larger, stop_point=1000):\n",
-    "    \"\"\"Calculate the next number in the Fibonacci sequence.\n",
+    "    \"\"\"A dynamic workflow that calculates the Fibonacci sequence.\n",
     "\n",
     "    If the number is larger than stop_point, the job will stop the workflow\n",
     "    execution, otherwise, a new job will be submitted to calculate the next number.\n",
@@ -415,15 +431,8 @@
     "fibonacci_job = fibonacci(1, 1)\n",
     "\n",
     "# run the job; responses will contain the output from all jobs\n",
-    "responses = run_locally(fibonacci_job)\n"
-   ],
-   "metadata": {
-    "collapsed": false,
-    "ExecuteTime": {
-     "end_time": "2023-11-23T22:55:13.426518952Z",
-     "start_time": "2023-11-23T22:55:13.322421257Z"
-    }
-   }
+    "responses = run_locally(fibonacci_job)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -472,11 +481,14 @@
     "def add(a, b):\n",
     "    return a + b\n",
     "\n",
+    "\n",
     "@job\n",
     "def add_with_logic(a, b):\n",
     "    if a < 10:\n",
     "        return Response(detour=add(a, b))\n",
-    "    \n",
+    "    return None\n",
+    "\n",
+    "\n",
     "job1 = add(1, 2)\n",
     "job2 = add_with_logic(job1.output, 2)\n",
     "flow = Flow([job1, job2])\n",
@@ -497,7 +509,12 @@
    "outputs": [
     {
      "data": {
-      "text/plain": "{'301d75f0-7042-494a-9f24-cab0428c2fd1': {1: Response(output=3, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)},\n '97be61a8-eec4-4e64-bf53-ba37621575e7': {1: Response(output=None, detour=Flow(name='Flow', uuid='0de995a5-1110-4200-b010-276cb2017474')\n  1. Job(name='add', uuid='d4c31f68-09ad-418a-ac52-89b303fc2a00'), addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)},\n 'd4c31f68-09ad-418a-ac52-89b303fc2a00': {1: Response(output=5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)}}"
+      "text/plain": [
+       "{'301d75f0-7042-494a-9f24-cab0428c2fd1': {1: Response(output=3, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)},\n",
+       " '97be61a8-eec4-4e64-bf53-ba37621575e7': {1: Response(output=None, detour=Flow(name='Flow', uuid='0de995a5-1110-4200-b010-276cb2017474')\n",
+       "  1. Job(name='add', uuid='d4c31f68-09ad-418a-ac52-89b303fc2a00'), addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)},\n",
+       " 'd4c31f68-09ad-418a-ac52-89b303fc2a00': {1: Response(output=5, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False)}}"
+      ]
      },
      "execution_count": 10,
      "metadata": {},
@@ -519,9 +536,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "name": "python3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "display_name": "Python 3 (ipykernel)"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
diff --git a/docs/tutorials/6-makers.ipynb b/docs/tutorials/6-makers.ipynb
index 93c25602..1c19a044 100644
--- a/docs/tutorials/6-makers.ipynb
+++ b/docs/tutorials/6-makers.ipynb
@@ -61,9 +61,11 @@
    ],
    "source": [
     "from dataclasses import dataclass\n",
-    "from jobflow import job, Flow, Maker\n",
+    "\n",
+    "from jobflow import Flow, Maker, job\n",
     "from jobflow.managers.local import run_locally\n",
     "\n",
+    "\n",
     "@dataclass\n",
     "class AddMaker(Maker):\n",
     "    name: str = \"Add Maker\"\n",
@@ -73,10 +75,9 @@
     "    def make(self, a, b):\n",
     "        if self.operation == \"add\":\n",
     "            return a + b\n",
-    "        elif self.operation == \"mult\":\n",
+    "        if self.operation == \"mult\":\n",
     "            return a * b\n",
-    "        else:\n",
-    "            raise ValueError(f\"Unknown operation: {self.operation}\")\n",
+    "        raise ValueError(f\"Unknown operation: {self.operation}\")\n",
     "\n",
     "\n",
     "job1 = AddMaker().make(a=2, b=3)\n",
@@ -122,9 +123,11 @@
    "outputs": [],
    "source": [
     "from dataclasses import dataclass\n",
-    "from jobflow import job, Flow, Maker\n",
+    "\n",
+    "from jobflow import Flow, Maker, job\n",
     "from jobflow.managers.local import run_locally\n",
     "\n",
+    "\n",
     "@dataclass\n",
     "class AddMaker(Maker):\n",
     "    name: str = \"Add Maker\"\n",
@@ -134,10 +137,10 @@
     "    def make(self, a, b):\n",
     "        if self.operation == \"add\":\n",
     "            return a + b\n",
-    "        elif self.operation == \"mult\":\n",
+    "        if self.operation == \"mult\":\n",
     "            return a * b\n",
-    "        else:\n",
-    "            raise ValueError(f\"Unknown operation: {self.operation}\")\n",
+    "        raise ValueError(f\"Unknown operation: {self.operation}\")\n",
+    "\n",
     "\n",
     "@dataclass\n",
     "class SubtractMaker(Maker):\n",
@@ -147,6 +150,7 @@
     "    def make(self, a, b):\n",
     "        return b - a\n",
     "\n",
+    "\n",
     "job1 = AddMaker().make(a=2, b=3)\n",
     "job2 = SubtractMaker().make(a=job1.output, b=4)\n",
     "flow = Flow([job1, job2])"
diff --git a/docs/tutorials/7-generalized-makers.ipynb b/docs/tutorials/7-generalized-makers.ipynb
index 4f9112a4..cd9353cc 100644
--- a/docs/tutorials/7-generalized-makers.ipynb
+++ b/docs/tutorials/7-generalized-makers.ipynb
@@ -46,7 +46,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from jobflow import Maker, job, Flow\n",
+    "from jobflow import Flow, Maker, job\n",
     "from jobflow.managers.local import run_locally"
    ]
   },
@@ -59,7 +59,7 @@
    "source": [
     "class BaseMaker(Maker):\n",
     "    def code_specific_func(self, arg1):\n",
-    "        raise NotImplementedError()\n",
+    "        raise NotImplementedError\n",
     "\n",
     "    def make(self):\n",
     "        return Flow([job1(self.code_specific_func, \"ARG1\")])\n",
diff --git a/pyproject.toml b/pyproject.toml
index 8ce07a64..02dd0865 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,13 +53,13 @@ fireworks = ["FireWorks"]
 strict = [
     "FireWorks==2.0.3",
     "PyYAML==6.0.2",
-    "maggma==0.69.4",
+    "maggma==0.69.3",
     "matplotlib==3.9.2",
     "monty==2024.7.30",
     "moto==4.2.13",
     "networkx==3.2.1",
     "pydantic-settings==2.5.2",
-    "pydantic==2.9.2",
+    "pydantic==2.9.1",
     "pydash==8.0.3",
     "pydot==2.0.0",
     "python-ulid==2.7.0",
@@ -121,6 +121,7 @@ exclude_lines = [
 
 [tool.ruff]
 target-version = "py39"
+output-format = "concise"
 
 [tool.ruff.lint]
 select = [
@@ -171,7 +172,6 @@ ignore = [
 ]
 pydocstyle.convention = "numpy"
 isort.known-first-party = ["jobflow"]
-ignore-init-module-imports = true
 
 [tool.ruff.lint.per-file-ignores]
 # F401: unused import
@@ -180,3 +180,4 @@ ignore-init-module-imports = true
 # PLR2004: magic-value-comparison
 # PT004: pytest-missing-fixture-name-underscore
 "**/tests/*" = ["ANN", "ARG001", "D", "PLR2004", "PT004", "S101"]
+"docs/tutorials/*" = ["D", "PLR2004"]
diff --git a/src/jobflow/core/flow.py b/src/jobflow/core/flow.py
index b2f47183..a74ffe4d 100644
--- a/src/jobflow/core/flow.py
+++ b/src/jobflow/core/flow.py
@@ -190,7 +190,7 @@ def __sub__(self, other: Flow | Job) -> Flow:
         if other not in self:
             raise ValueError(f"{other!r} not found in flow")
         new_flow = deepcopy(self)
-        new_flow.jobs = tuple([job for job in new_flow if job != other])
+        new_flow.jobs = tuple(job for job in new_flow if job != other)
         return new_flow
 
     def __repr__(self, level: int = 0, prefix: str = "") -> str:
diff --git a/tests/conftest.py b/tests/conftest.py
index 083d0b45..6bd17484 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -26,7 +26,7 @@ def mongo_jobstore(database):
     return store
 
 
-@pytest.fixture()
+@pytest.fixture
 def memory_jobstore():
     from maggma.stores import MemoryStore
 
@@ -38,7 +38,7 @@ def memory_jobstore():
     return store
 
 
-@pytest.fixture()
+@pytest.fixture
 def memory_data_jobstore():
     from maggma.stores import MemoryStore
 
@@ -50,7 +50,7 @@ def memory_data_jobstore():
     return store
 
 
-@pytest.fixture()
+@pytest.fixture
 def clean_dir():
     import os
     import shutil
@@ -85,7 +85,7 @@ def lpad(database, debug_mode):
             lpad.db[coll].drop()
 
 
-@pytest.fixture()
+@pytest.fixture
 def no_pydot(monkeypatch):
     import builtins
 
@@ -99,7 +99,7 @@ def mocked_import(name, *args, **kwargs):
     monkeypatch.setattr(builtins, "__import__", mocked_import)
 
 
-@pytest.fixture()
+@pytest.fixture
 def no_matplotlib(monkeypatch):
     import builtins
 
diff --git a/tests/core/test_maker.py b/tests/core/test_maker.py
index cd4f1979..ac5ecb81 100644
--- a/tests/core/test_maker.py
+++ b/tests/core/test_maker.py
@@ -116,8 +116,7 @@ def test_update_kwargs():
     from jobflow.core.maker import Maker
 
     # this is needed to get monty to deserialize them correctly
-    global AddMaker
-    global DetourMaker
+    global AddMaker, DetourMaker
 
     @dataclass
     class AddMaker(Maker):
@@ -183,8 +182,7 @@ def make(self, a, b):
     maker = maker.update_kwargs({"c": 10}, class_filter=AddMaker, nested=False)
     assert maker.add_maker.c == 5
 
-    global NotAMaker
-    global FakeDetourMaker
+    global NotAMaker, FakeDetourMaker
 
     @dataclass
     class NotAMaker(MSONable):
@@ -217,8 +215,7 @@ def test_recursive_call():
     from jobflow.core.maker import Maker, recursive_call
 
     # this is needed to get monty to deserialize them correctly
-    global AddMaker
-    global DetourMaker
+    global AddMaker, DetourMaker
 
     @dataclass
     class AddMaker(Maker):
diff --git a/tests/core/test_schemas.py b/tests/core/test_schemas.py
index 84af8ace..ef51e6a3 100644
--- a/tests/core/test_schemas.py
+++ b/tests/core/test_schemas.py
@@ -3,7 +3,7 @@
 import pytest
 
 
-@pytest.fixture()
+@pytest.fixture
 def sample_data():
     from jobflow.core.schemas import JobStoreDocument
 
diff --git a/tests/core/test_store.py b/tests/core/test_store.py
index 9ab9e4d7..d325b2df 100644
--- a/tests/core/test_store.py
+++ b/tests/core/test_store.py
@@ -6,7 +6,7 @@
     from jobflow.core.store import JobStore
 
 
-@pytest.fixture()
+@pytest.fixture
 def memory_store():
     from maggma.stores import MemoryStore
 

From 280aae1bb3226b2bc52f3aa7ab46e96f9d53cde1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 23:51:59 +0000
Subject: [PATCH 15/27] Bump maggma from 0.69.3 to 0.69.4 (#688)

Bumps [maggma](https://github.com/materialsproject/maggma) from 0.69.3 to 0.69.4.
- [Release notes](https://github.com/materialsproject/maggma/releases)
- [Changelog](https://github.com/materialsproject/maggma/blob/main/docs/CHANGELOG.md)
- [Commits](https://github.com/materialsproject/maggma/compare/v0.69.3...v0.69.4)

---
updated-dependencies:
- dependency-name: maggma
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 02dd0865..a83af575 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ fireworks = ["FireWorks"]
 strict = [
     "FireWorks==2.0.3",
     "PyYAML==6.0.2",
-    "maggma==0.69.3",
+    "maggma==0.69.4",
     "matplotlib==3.9.2",
     "monty==2024.7.30",
     "moto==4.2.13",

From f73ccc92591a8e24e85da79d212e3af33093cc43 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 23:52:02 +0000
Subject: [PATCH 16/27] Bump ipython from 8.27.0 to 8.28.0 (#687)

Bumps [ipython](https://github.com/ipython/ipython) from 8.27.0 to 8.28.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/compare/8.27.0...8.28.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a83af575..d3a4da03 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ ulid = ["python-ulid"]
 docs = [
     "autodoc_pydantic==2.1.0",
     "furo==2024.8.6",
-    "ipython==8.27.0",
+    "ipython==8.28.0",
     "myst_parser==4.0.0",
     "nbsphinx==0.9.5",
     "sphinx-copybutton==0.5.2",

From 4962f4dee129d91d6797f6f5be7f0ba03e0c1153 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2024 23:52:13 +0000
Subject: [PATCH 17/27] Bump pydantic from 2.9.1 to 2.9.2 (#689)

Bumps [pydantic](https://github.com/pydantic/pydantic) from 2.9.1 to 2.9.2.
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v2.9.1...v2.9.2)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index d3a4da03..9c1f095f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,7 +59,7 @@ strict = [
     "moto==4.2.13",
     "networkx==3.2.1",
     "pydantic-settings==2.5.2",
-    "pydantic==2.9.1",
+    "pydantic==2.9.2",
     "pydash==8.0.3",
     "pydot==2.0.0",
     "python-ulid==2.7.0",

From bf599bae8299b8ecd0ad88ee304e11441636a81d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 23:36:14 +0000
Subject: [PATCH 18/27] Bump sphinx from 8.0.2 to 8.1.3 (#692)

Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 8.0.2 to 8.1.3.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
- [Commits](https://github.com/sphinx-doc/sphinx/compare/v8.0.2...v8.1.3)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9c1f095f..7b11fef4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,7 +44,7 @@ docs = [
     "myst_parser==4.0.0",
     "nbsphinx==0.9.5",
     "sphinx-copybutton==0.5.2",
-    "sphinx==8.0.2",
+    "sphinx==8.1.3",
 ]
 dev = ["pre-commit>=2.12.1", "typing_extensions; python_version < '3.11'"]
 tests = ["moto==4.2.13", "pytest-cov==5.0.0", "pytest==8.3.3"]

From d4fd61596c5e5afbe1086be683b518801e2bf4e0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 23:36:25 +0000
Subject: [PATCH 19/27] Bump maggma from 0.69.4 to 0.70.0 (#693)

Bumps [maggma](https://github.com/materialsproject/maggma) from 0.69.4 to 0.70.0.
- [Release notes](https://github.com/materialsproject/maggma/releases)
- [Changelog](https://github.com/materialsproject/maggma/blob/main/docs/CHANGELOG.md)
- [Commits](https://github.com/materialsproject/maggma/compare/v0.69.4...v0.70.0)

---
updated-dependencies:
- dependency-name: maggma
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7b11fef4..03e999ed 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ fireworks = ["FireWorks"]
 strict = [
     "FireWorks==2.0.3",
     "PyYAML==6.0.2",
-    "maggma==0.69.4",
+    "maggma==0.70.0",
     "matplotlib==3.9.2",
     "monty==2024.7.30",
     "moto==4.2.13",

From bffc15f21fafccc617e75069027a5584c4e1de25 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 23:36:40 +0000
Subject: [PATCH 20/27] Bump python-ulid from 2.7.0 to 3.0.0 (#694)

Bumps [python-ulid](https://github.com/mdomke/python-ulid) from 2.7.0 to 3.0.0.
- [Release notes](https://github.com/mdomke/python-ulid/releases)
- [Changelog](https://github.com/mdomke/python-ulid/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/mdomke/python-ulid/compare/2.7.0...3.0.0)

---
updated-dependencies:
- dependency-name: python-ulid
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 03e999ed..53617031 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -62,7 +62,7 @@ strict = [
     "pydantic==2.9.2",
     "pydash==8.0.3",
     "pydot==2.0.0",
-    "python-ulid==2.7.0",
+    "python-ulid==3.0.0",
     "typing-extensions==4.12.2",
 ]
 

From 12f839cd162512ac9a1407130332680dc45c382b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Oct 2024 23:58:31 +0000
Subject: [PATCH 21/27] Bump pydantic-settings from 2.5.2 to 2.6.0 (#696)

Bumps [pydantic-settings](https://github.com/pydantic/pydantic-settings) from 2.5.2 to 2.6.0.
- [Release notes](https://github.com/pydantic/pydantic-settings/releases)
- [Commits](https://github.com/pydantic/pydantic-settings/compare/v2.5.2...v2.6.0)

---
updated-dependencies:
- dependency-name: pydantic-settings
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 53617031..a1ab6403 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ strict = [
     "monty==2024.7.30",
     "moto==4.2.13",
     "networkx==3.2.1",
-    "pydantic-settings==2.5.2",
+    "pydantic-settings==2.6.0",
     "pydantic==2.9.2",
     "pydash==8.0.3",
     "pydot==2.0.0",

From b97a9d4dc041fc43222ca31e2be11bf036350b99 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Oct 2024 23:58:45 +0000
Subject: [PATCH 22/27] Bump monty from 2024.7.30 to 2024.10.21 (#698)

Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2024.7.30 to 2024.10.21.
- [Release notes](https://github.com/materialsvirtuallab/monty/releases)
- [Changelog](https://github.com/materialsvirtuallab/monty/blob/master/docs/changelog.md)
- [Commits](https://github.com/materialsvirtuallab/monty/commits/v2024.10.21)

---
updated-dependencies:
- dependency-name: monty
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a1ab6403..5d58df96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,7 +55,7 @@ strict = [
     "PyYAML==6.0.2",
     "maggma==0.70.0",
     "matplotlib==3.9.2",
-    "monty==2024.7.30",
+    "monty==2024.10.21",
     "moto==4.2.13",
     "networkx==3.2.1",
     "pydantic-settings==2.6.0",

From 9cf327e6577d918dfcf515b556f41613c6596420 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 23:41:40 +0000
Subject: [PATCH 23/27] Bump ipython from 8.28.0 to 8.29.0 (#699)

Bumps [ipython](https://github.com/ipython/ipython) from 8.28.0 to 8.29.0.
- [Release notes](https://github.com/ipython/ipython/releases)
- [Commits](https://github.com/ipython/ipython/compare/8.28.0...8.29.0)

---
updated-dependencies:
- dependency-name: ipython
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5d58df96..979dd0f2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ ulid = ["python-ulid"]
 docs = [
     "autodoc_pydantic==2.1.0",
     "furo==2024.8.6",
-    "ipython==8.28.0",
+    "ipython==8.29.0",
     "myst_parser==4.0.0",
     "nbsphinx==0.9.5",
     "sphinx-copybutton==0.5.2",

From 88cc265e3ca5ac683528943d177a40782d9210ca Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 23:25:02 +0000
Subject: [PATCH 24/27] Bump pydash from 8.0.3 to 8.0.4 (#703)

Bumps [pydash](https://github.com/dgilland/pydash) from 8.0.3 to 8.0.4.
- [Changelog](https://github.com/dgilland/pydash/blob/develop/CHANGELOG.rst)
- [Commits](https://github.com/dgilland/pydash/compare/v8.0.3...v8.0.4)

---
updated-dependencies:
- dependency-name: pydash
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 979dd0f2..382e281d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -60,7 +60,7 @@ strict = [
     "networkx==3.2.1",
     "pydantic-settings==2.6.0",
     "pydantic==2.9.2",
-    "pydash==8.0.3",
+    "pydash==8.0.4",
     "pydot==2.0.0",
     "python-ulid==3.0.0",
     "typing-extensions==4.12.2",

From 278a15aacc282d4acf2531c8f0fb3c1b82f5eeaa Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 23:25:13 +0000
Subject: [PATCH 25/27] Bump pydantic-settings from 2.6.0 to 2.6.1 (#701)

Bumps [pydantic-settings](https://github.com/pydantic/pydantic-settings) from 2.6.0 to 2.6.1.
- [Release notes](https://github.com/pydantic/pydantic-settings/releases)
- [Commits](https://github.com/pydantic/pydantic-settings/compare/v2.6.0...v2.6.1)

---
updated-dependencies:
- dependency-name: pydantic-settings
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 382e281d..e0225015 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ strict = [
     "monty==2024.10.21",
     "moto==4.2.13",
     "networkx==3.2.1",
-    "pydantic-settings==2.6.0",
+    "pydantic-settings==2.6.1",
     "pydantic==2.9.2",
     "pydash==8.0.4",
     "pydot==2.0.0",

From fc4f1017cd1fd54d5b3ae4983cddc976d25f032e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 4 Nov 2024 23:25:22 +0000
Subject: [PATCH 26/27] Bump pytest-cov from 5.0.0 to 6.0.0 (#704)

Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 5.0.0 to 6.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v5.0.0...v6.0.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e0225015..9f5a2c47 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ docs = [
     "sphinx==8.1.3",
 ]
 dev = ["pre-commit>=2.12.1", "typing_extensions; python_version < '3.11'"]
-tests = ["moto==4.2.13", "pytest-cov==5.0.0", "pytest==8.3.3"]
+tests = ["moto==4.2.13", "pytest-cov==6.0.0", "pytest==8.3.3"]
 vis = ["matplotlib", "pydot"]
 fireworks = ["FireWorks"]
 strict = [

From ca778dbf0c20c1805a411bbb26e09a0f65234483 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Nov 2024 23:44:09 +0000
Subject: [PATCH 27/27] Update versioningit requirement from ~=1.0 to >=1,<4
 (#705)

Updates the requirements on [versioningit](https://github.com/jwodder/versioningit) to permit the latest version.
- [Release notes](https://github.com/jwodder/versioningit/releases)
- [Changelog](https://github.com/jwodder/versioningit/blob/master/CHANGELOG.md)
- [Commits](https://github.com/jwodder/versioningit/compare/v1.0.0...v3.1.2)

---
updated-dependencies:
- dependency-name: versioningit
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9f5a2c47..f29fa7cd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 42", "versioningit ~= 1.0", "wheel"]
+requires = ["setuptools >= 42", "versioningit >= 1,< 4", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]