Merge pull request #685 from materialsproject/lint

Update commit hooks and fix new `ruff` and `mypy` issues

.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: v0.6.8
     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: v1.11.2
     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]

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"

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": {

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])"

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",

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"]

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:

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