Use ruff formatter instead of black formatter

Makefile

@@ -8,7 +8,7 @@ uninstall: FORCE
 
 lint: FORCE
 	ruff check .
-	black --check .
+	ruff format --check .
 
 docs: FORCE
 	cd docs && make html
@@ -18,7 +18,7 @@ license: FORCE
 
 format: license FORCE
 	ruff check --fix .
-	black .
+	ruff format .
 
 typecheck: FORCE
 	mypy cellarium tests

README.rst

@@ -25,11 +25,11 @@ To run the tests::
 
 To automatically format the code::
 
-   $ make format               # runs ruff and black formatters
+   $ make format               # runs ruff formatter and fixes linter errors
 
 To run the linters::
 
-   $ make lint                  # runs ruff and black checks
+   $ make lint                  # runs ruff linter and checks for formatter errors
 
 To build the documentation::
 

cellarium/ml/cli.py

@@ -247,7 +247,7 @@ def lightning_cli_factory(
                 "max_epochs": 1,  # one pass
                 "strategy": {
                     "class_path": "lightning.pytorch.strategies.DDPStrategy",
-                    "init_args": {"broadcast_buffers": False},
+                    "dict_kwargs": {"broadcast_buffers": False},
                 },
             },
         )
@@ -373,7 +373,7 @@ def incremental_pca(args: ArgsType = None) -> None:
             "max_epochs": 1,  # one pass
             "strategy": {
                 "class_path": "lightning.pytorch.strategies.DDPStrategy",
-                "init_args": {"broadcast_buffers": False},
+                "dict_kwargs": {"broadcast_buffers": False},
             },
         },
     )
@@ -455,7 +455,7 @@ def onepass_mean_var_std(args: ArgsType = None) -> None:
             "max_epochs": 1,  # one pass
             "strategy": {
                 "class_path": "lightning.pytorch.strategies.DDPStrategy",
-                "init_args": {"broadcast_buffers": False},
+                "dict_kwargs": {"broadcast_buffers": False},
             },
         },
     )

cellarium/ml/models/geneformer.py

@@ -134,7 +134,6 @@ def tokenize_with_perturbations(
         feature_deletion: list[str] | None = None,
         feature_map: dict[str, int] | None = None,
     ) -> tuple[torch.Tensor, torch.Tensor]:
-
         # activation and deletion happen before sorting
         if feature_deletion:
             if not all([g in self.var_names_g for g in feature_deletion]):

notebooks/geneformer_demo.ipynb

@@ -13,16 +13,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from cellarium.ml.models import Geneformer\n",
-    "from cellarium.ml.core import CellariumPipeline\n",
-    "from cellarium.ml.transforms import NormalizeTotal, DivideByScale\n",
+    "import os\n",
+    "import pickle\n",
+    "import tempfile\n",
     "\n",
     "import torch\n",
     "from transformers import AutoModel\n",
     "\n",
-    "import os\n",
-    "import pickle\n",
-    "import tempfile"
+    "from cellarium.ml.core import CellariumPipeline\n",
+    "from cellarium.ml.models import Geneformer\n",
+    "from cellarium.ml.transforms import DivideByScale, NormalizeTotal"
    ]
   },
   {
@@ -32,7 +32,6 @@
    "outputs": [],
    "source": [
     "def get_pretrained_geneformer_pipeline(device) -> CellariumPipeline:\n",
-    "\n",
     "    with tempfile.TemporaryDirectory() as tmpdir:\n",
     "        os.system(\n",
     "            f\"wget -O {os.path.join(tmpdir, 'token_dictionary.pkl')} https://huggingface.co/ctheodoris/Geneformer/resolve/main/geneformer/token_dictionary.pkl\"\n",

notebooks/mup_mlp.ipynb

@@ -18,17 +18,15 @@
    "outputs": [],
    "source": [
     "import math\n",
-    "from collections.abc import Callable, Iterator\n",
+    "from collections.abc import Callable\n",
     "from typing import Literal\n",
     "\n",
-    "import numpy as np\n",
-    "import pandas as pd\n",
+    "import matplotlib.pyplot as plt\n",
+    "import seaborn as sns\n",
     "import torch\n",
     "import torch.nn.functional as F\n",
     "from torch import nn\n",
     "from torchvision import datasets, transforms\n",
-    "import seaborn as sns\n",
-    "import matplotlib.pyplot as plt\n",
     "\n",
     "from cellarium.ml.models import MuLinear\n",
     "from cellarium.ml.utilities.testing import get_coord_data"

pyproject.toml

@@ -37,10 +37,7 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-lint = [
-    "black[jupyter]",
-    "ruff",
-]
+lint = ["ruff"]
 mypy = ["mypy", "types-PyYAML"]
 test = [
   "pytest-xdist",
@@ -78,10 +75,11 @@ dev_template = "{tag}.post{ccount}"
 
 [tool.ruff]
 line-length = 120
-select = ["E", "F", "I", "W"]
+extend-include = ["*.ipynb"]
+target-version = "py310"
 
-[tool.black]
-line-length = 120
+[tool.ruff.lint]
+select = ["E", "F", "I", "W"]
 
 [tool.mypy]
 ignore_missing_imports = true