update pre-commit lint and format (#876)

* add & bump pre-commit, remove isort and black

* unsafe fixes

* rename and shorten line length

* add missing f-string

* typos

.pre-commit-config.yaml

@@ -20,29 +20,19 @@ repos:
         args: ['--fix=lf']
       - id: sort-simple-yaml
       - id: trailing-whitespace
-  - repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-      - id: black
-        additional_dependencies: [".[jupyter]"]
-        types_or: [python, pyi, jupyter]
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies: ["tomli"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.8.2'
+    rev: 'v0.9.4'
     hooks:
       - id: ruff
         args: ['--fix']
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.19
+    rev: 0.7.22
     hooks:
     - id: mdformat
       args: ["--wrap=80"]

examples/docs/04_metrics_and_plots.ipynb

@@ -623,9 +623,8 @@
     "    def run(self):\n",
     "        self.my_metric = {\"alpha\": 1.0, \"beta\": 0.00473}\n",
     "        self.my_plot = pd.DataFrame({\"val\": np.sin(np.linspace(0, 3.14, 100))})\n",
-    "        self.my_plot.index.name = (  # For DVC it is required that the index has a column name\n",
-    "            \"index\"\n",
-    "        )\n",
+    "        # For DVC it is required that the index has a column name\n",
+    "        self.my_plot.index.name = \"index\"\n",
     "\n",
     "\n",
     "with zntrack.Project() as project:\n",

examples/docs/09_lazy.ipynb

@@ -630,7 +630,7 @@
     "\n",
     "    add_one = AddOne(deps=random_number, name=\"AddOne_0\")\n",
     "    for index in range(10):\n",
-    "        add_one = AddOne(deps=add_one, name=f\"AddOne_{index+1}\")\n",
+    "        add_one = AddOne(deps=add_one, name=f\"AddOne_{index + 1}\")\n",
     "\n",
     "project.run()"
    ]

examples/docs/parameter_optimization.ipynb

@@ -45,10 +45,10 @@
    "source": [
     "# Setup temporary directory and initialize git and dvc\n",
     "from zntrack import config\n",
+    "from zntrack.utils import cwd_temp_dir\n",
     "\n",
     "config.nb_name = \"parameter_optimization.ipynb\"\n",
     "\n",
-    "from zntrack.utils import cwd_temp_dir\n",
     "\n",
     "temp_dir = cwd_temp_dir()\n",
     "\n",

pyproject.toml

@@ -37,6 +37,7 @@ dev = [
     "mlflow>=2.20.0",
     "nbsphinx>=0.9.6",
     "nbsphinx-link>=1.3.1",
+    "pre-commit>=4.1.0",
     "pytest>=8.3.4",
     "pytest-benchmark>=5.1.0",
     "sphinx>=8.1.3",
@@ -94,7 +95,7 @@ disable = [
 line-length = 90
 
 [tool.ruff.lint]
-select = ["E", "F", "D", "N", "C", "I"] #, "ANN"]
+select = ["E", "F", "N", "C", "I"] #, "ANN"]
 extend-ignore = [
     "D213", "D203",
     "D401",

tests/files/test_apply.py

@@ -13,12 +13,12 @@
 def test_apply(proj_path) -> None:
     project = zntrack.Project()
 
-    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")
+    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")  # noqa N806
 
     with project:
-        a = zntrack.examples.ParamsToOuts(params=["a", "b"])
-        b = JoinedParamsToOuts(params=["a", "b"])
-        c = zntrack.apply(zntrack.examples.ParamsToOuts, "join")(params=["a", "b", "c"])
+        zntrack.examples.ParamsToOuts(params=["a", "b"])
+        JoinedParamsToOuts(params=["a", "b"])
+        zntrack.apply(zntrack.examples.ParamsToOuts, "join")(params=["a", "b", "c"])
 
     project.build()
 

tests/files/test_custom_field.py

@@ -42,7 +42,7 @@ def run(self):
 
 def test_text_node(proj_path):
     with zntrack.Project() as project:
-        node = TextNode()
+        TextNode()
     project.build()
 
     assert json.loads(

tests/files/test_meta_params.py

@@ -19,7 +19,7 @@ def run(self) -> None:
 
 def test_node(proj_path):
     with zntrack.Project() as proj:
-        node = MyNode(name="some-node", always_changed=True)
+        MyNode(name="some-node", always_changed=True)
 
     proj.repro()
 

tests/files/test_metrics_deps.py

@@ -14,8 +14,8 @@ def test_metrics_as_deps(proj_path):
     with project:
         metrics_node = zntrack.examples.ParamsToMetrics(params={"loss": 0.01})
 
-        metrics_deps = zntrack.examples.DepsToMetrics(deps=metrics_node.metrics)
-        params_deps = zntrack.examples.DepsToMetrics(deps=metrics_node.params)
+        zntrack.examples.DepsToMetrics(deps=metrics_node.metrics)
+        zntrack.examples.DepsToMetrics(deps=metrics_node.params)
 
     project.build()
 

tests/files/test_user_config.py

@@ -16,7 +16,7 @@ def test_node(proj_path):
     assert zntrack.config.ALWAYS_CACHE is True
 
     # We define the node here, because the config has to be set
-    #  bevore calling zntrack.metrics()
+    #  before calling zntrack.metrics()
     class MyNode(zntrack.Node):
         """Some Node."""
 
@@ -27,7 +27,7 @@ def run(self) -> None:
             self.metric = {"a": 1, "b": 2}
 
     with zntrack.Project() as proj:
-        node = MyNode()
+        MyNode()
 
     proj.build()
 

tests/integration/skip_test_meta.py

@@ -18,9 +18,9 @@ class NodeWithEnv(zntrack.Node):
     def run(self):
         import os
 
-        assert (
-            os.environ["OMP_NUM_THREADS"] == self.OMP_NUM_THREADS
-        ), f'{os.environ["OMP_NUM_THREADS"]} != {self.OMP_NUM_THREADS}'
+        assert os.environ["OMP_NUM_THREADS"] == self.OMP_NUM_THREADS, (
+            f"{os.environ['OMP_NUM_THREADS']} != {self.OMP_NUM_THREADS}"
+        )
 
         self.result = os.environ["OMP_NUM_THREADS"]
 

tests/integration/test_apply_method.py

@@ -10,7 +10,7 @@ def test_apply(proj_path, eager) -> None:
     """Test the "zntrack.apply" function."""
     project = zntrack.Project()
 
-    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")
+    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")  # noqa N806
 
     with project:
         a = zntrack.examples.ParamsToOuts(params=["a", "b"])
@@ -33,7 +33,7 @@ def test_deps_apply(proj_path, eager, attribute):
     """Test connecting applied nodes to other nodes."""
     project = zntrack.Project()
 
-    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")
+    JoinedParamsToOuts = zntrack.apply(zntrack.examples.ParamsToOuts, "join")  # noqa N806
 
     assert issubclass(JoinedParamsToOuts, zntrack.Node)
 

tests/integration/test_build.py

@@ -13,7 +13,7 @@ def test_nodes_not_created(proj_path):
         b = zntrack.examples.ParamsToOuts(
             params=18,
         )
-        c = zntrack.examples.AddNodeAttributes(
+        zntrack.examples.AddNodeAttributes(
             a=a.outs,
             b=b.outs,
         )
@@ -25,7 +25,7 @@ def test_nodes_not_created(proj_path):
         e = zntrack.examples.ParamsToOuts(
             params=18,
         )
-        f = zntrack.examples.AddNodeAttributes(
+        zntrack.examples.AddNodeAttributes(
             a=d.outs,
             b=e.outs,
         )

tests/integration/test_dvc_outs.py

@@ -40,7 +40,7 @@ def run(self):
 def test_run_temp_path(proj_path):
     project = zntrack.Project()
     with project:
-        node = AssertTempPath()
+        AssertTempPath()
     project.repro()
 
 

tests/integration/test_node_node.py

@@ -21,7 +21,7 @@ def test_AddNodes(proj_path, eager):
         project.repro()
 
     assert add_numbers_a.c == 3
-    # TODO: Node status is not beind updated when not using from_rev
+    # TODO: Node status is not being updated when not using from_rev
     if eager:
         assert add_numbers_a.state.state == NodeStatusEnum.FINISHED
     assert add_numbers_b.c == 4

tests/integration/test_node_nwd_write.py

@@ -5,7 +5,8 @@
 
 import zntrack
 
-# TODO UNCLEAR ERROR, __file__ atribute is not the same as the test file we want to collect
+# TODO UNCLEAR ERROR, __file__ attribute is not the
+#  same as the test file we want to collect
 
 
 class WriteToNWD(zntrack.Node):

tests/integration/test_options_plots.py

@@ -101,7 +101,7 @@ def test_groups(proj_path):
 
 def test_autosave(proj_path):
     with zntrack.Project() as proj:
-        node = AutoSavePandasPlotNode(n=10)
+        AutoSavePandasPlotNode(n=10)
 
     proj.build()
     subprocess.run(["dvc", "repro"], cwd=proj_path, check=True)

tests/integration/test_plugins_aim.py

@@ -42,7 +42,7 @@ class RangePlotter(zntrack.Node):
     plots: pd.DataFrame = zntrack.plots(y="range")
 
     def run(self):
-        self.plots = pd.DataFrame({"idx": [idx for idx in range(self.start, self.stop)]})
+        self.plots = pd.DataFrame({"idx": list(range(self.start, self.stop))})
 
 
 # fixture to set the os.env before the test and remove if after the test
@@ -126,7 +126,7 @@ def test_aim_plotting(aim_proj_path):
         metrics = {}
         for metric in run.metrics():
             metrics[metric.name] = list(metric.data.values())[0]
-        npt.assert_array_equal(metrics["plots.idx"], [[idx for idx in range(10)]])
+        npt.assert_array_equal(metrics["plots.idx"], [list(range(10))])
 
     proj.finalize(msg="test")
     repo = git.Repo()
@@ -170,17 +170,26 @@ def test_multiple_nodes(aim_proj_path):
 
     aim_repo = aim.Repo(path=os.environ["AIM_TRACKING_URI"])
     for run_metrics_col in aim_repo.query_metrics(
-        f"run.dvc_stage_name == '{a.name}' and run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        (
+            f"run.dvc_stage_name == '{a.name}' and "
+            f"run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        )
     ).iter():
         assert "original_run_id" not in run_metrics_col.run.dataframe().columns
 
     for run_metrics_col in aim_repo.query_metrics(
-        f"run.dvc_stage_name == '{c.name}' and run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        (
+            f"run.dvc_stage_name == '{c.name}' and "
+            f"run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        )
     ).iter():
         assert "original_run_id" not in run_metrics_col.run.dataframe().columns
 
     for run_metrics_col in aim_repo.query_metrics(
-        f"run.dvc_stage_name == '{b.name}' and run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        (
+            f"run.dvc_stage_name == '{b.name}' and "
+            f"run.git_commit_hash == '{repo.head.commit.hexsha}'"
+        )
     ).iter():
         assert run_metrics_col.run.dataframe()["original_run_id"].tolist() == [b_run_id]
 
@@ -189,7 +198,7 @@ def test_project_tags(aim_proj_path):
     with zntrack.Project(tags={"lorem": "ipsum", "hello": "world"}) as proj:
         a = zntrack.examples.ParamsToOuts(params=3)
         b = zntrack.examples.ParamsToOuts(params=7)
-        c = zntrack.examples.SumNodeAttributesToMetrics(inputs=[a.outs, b.outs], shift=0)
+        zntrack.examples.SumNodeAttributesToMetrics(inputs=[a.outs, b.outs], shift=0)
 
     proj.repro()
 
@@ -234,5 +243,8 @@ def test_dataclass_deps(aim_proj_path):
     with md.from_rev().state.plugins["AIMPlugin"].get_aim_run() as run:
         df = run.dataframe()
         assert df["t"].tolist() == [
-            '[{"_cls": "test_plugins_aim.T1", "temperature": 1}, {"_cls": "test_plugins_aim.T2", "temperature": 1}]'
+            (
+                '[{"_cls": "test_plugins_aim.T1", "temperature": 1},'
+                ' {"_cls": "test_plugins_aim.T2", "temperature": 1}]'
+            )
         ]

tests/integration/test_plugins_mlflow.py

@@ -54,7 +54,7 @@ class RangePlotter(zntrack.Node):
     plots: pd.DataFrame = zntrack.plots(y="range")
 
     def run(self):
-        self.plots = pd.DataFrame({"idx": [idx for idx in range(self.start, self.stop)]})
+        self.plots = pd.DataFrame({"idx": list(range(self.start, self.stop))})
 
 
 @pytest.fixture
@@ -181,7 +181,7 @@ def test_multiple_nodes(mlflow_proj_path, skip_cached):
     assert c.metrics == {"value": 10.0}
 
     with a.state.plugins["MLFlowPlugin"]:
-        a_run = mlflow.get_run(a.state.plugins["MLFlowPlugin"].child_run_id)
+        mlflow.get_run(a.state.plugins["MLFlowPlugin"].child_run_id)
 
     with b.state.plugins["MLFlowPlugin"]:
         b_run = mlflow.get_run(b.state.plugins["MLFlowPlugin"].child_run_id)
@@ -210,14 +210,20 @@ def test_multiple_nodes(mlflow_proj_path, skip_cached):
         assert len(runs) == 4
 
     a_run_2 = mlflow.search_runs(
-        filter_string=f"tags.git_commit_hash = '{repo.head.commit.hexsha}' and tags.dvc_stage_name = '{a.name}'",
+        filter_string=(
+            f"tags.git_commit_hash = '{repo.head.commit.hexsha}' "
+            f"and tags.dvc_stage_name = '{a.name}'"
+        ),
         output_format="list",
     )
     assert len(a_run_2) == 1
     a_run_2 = a_run_2[0]
 
     b_run_2 = mlflow.search_runs(
-        filter_string=f"tags.git_commit_hash = '{repo.head.commit.hexsha}' and tags.dvc_stage_name = '{b.name}'",
+        filter_string=(
+            f"tags.git_commit_hash = '{repo.head.commit.hexsha}'"
+            f" and tags.dvc_stage_name = '{b.name}'"
+        ),
         output_format="list",
     )
     if skip_cached:
@@ -226,11 +232,15 @@ def test_multiple_nodes(mlflow_proj_path, skip_cached):
         assert len(b_run_2) == 1
         b_run_2 = b_run_2[0]
         assert b_run_2.data.tags["original_run_id"] == b_run.info.run_id
-        # original runs will not be updated with a new name to indicate that they are cached
+        # original runs will not be updated with a new name to
+        # indicate that they are cached
         assert b_run_2.data.tags[mlflow_tags.MLFLOW_RUN_NAME] == "ParamsToOuts_1"
 
     c_run_2 = mlflow.search_runs(
-        filter_string=f"tags.git_commit_hash = '{repo.head.commit.hexsha}' and tags.dvc_stage_name = '{c.name}'",
+        filter_string=(
+            f"tags.git_commit_hash = '{repo.head.commit.hexsha}'"
+            f" and tags.dvc_stage_name = '{c.name}'"
+        ),
         output_format="list",
     )
     assert len(c_run_2) == 1
@@ -302,7 +312,7 @@ def test_dataclass_deps(mlflow_proj_path):
     )
 
     proj.finalize(msg="run1 exp.")
-    repo = git.Repo()
+    git.Repo()
 
     mdx = MD.from_rev()
     assert mdx.__run_note__() != ""
@@ -338,9 +348,9 @@ def test_dataclass_deps(mlflow_proj_path):
     with md.state.plugins["MLFlowPlugin"]:
         run = mlflow.get_run(md.state.plugins["MLFlowPlugin"].child_run_id)
 
-    assert (
-        run.data.params["t"]
-        == "[{'temperature': 1, '_cls': 'test_plugins_mlflow.T1'}, {'temperature': 1, '_cls': 'test_plugins_mlflow.T2'}]"
+    assert run.data.params["t"] == (
+        "[{'temperature': 1, '_cls': 'test_plugins_mlflow.T1'},"
+        " {'temperature': 1, '_cls': 'test_plugins_mlflow.T2'}]"
     )
 
     md = zntrack.from_rev(md.name)