Update pre-commit config (#216)

Bye nbqa

Author: martinkim0

.pre-commit-config.yaml

@@ -6,81 +6,40 @@ default_stages:
   - push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/psf/black
-    rev: 24.1.1
-    hooks:
-      - id: black
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
-    hooks:
-      - id: nbqa-pyupgrade
-        args: [--py38-plus]
-      - id: nbqa-black
-      - id: nbqa-isort
-      - id: nbqa-ruff
-        args: [--fix]
-      - id: nbqa
-        entry: nbqa blacken-docs
-        name: nbqa-blacken-docs
-        alias: nbqa-blacken-docs
-        additional_dependencies: [blacken-docs]
-        args: [--nbqa-md]
-      - id: nbqa
-        entry: nbqa mdformat
-        name: nbqa-mdformat
-        alias: nbqa-mdformat
-        additional_dependencies:
-          [
-            mdformat,
-            mdformat-black,
-            mdformat-frontmatter,
-            mdformat-web,
-            mdformat-myst,
-          ]
-        args: [--nbqa-md]
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+    rev: v3.1.0
     hooks:
       - id: prettier
-  - repo: https://github.com/asottile/blacken-docs
-    rev: 1.16.0
-    hooks:
-      - id: blacken-docs
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
-    hooks:
-      - id: isort
-  - repo: https://github.com/asottile/yesqa
-    rev: v1.5.0
-    hooks:
-      - id: yesqa
-        additional_dependencies:
-          - flake8-tidy-imports
-          - flake8-docstrings
-          - flake8-rst-docstrings
-          - flake8-comprehensions
-          - flake8-bugbear
-          - flake8-blind-except
+        # Newer versions of node don't work on systems that have an older version of GLIBC
+        # (in particular Ubuntu 18.04 and Centos 7)
+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+        # https://github.com/jupyterlab/jupyterlab/issues/12675
+        language_version: "17.9.1"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.11
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        types_or: [python, pyi, jupyter]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
       - id: detect-private-key
       - id: check-ast
+      - id: end-of-file-fixer
       - id: mixed-line-ending
         args: [--fix=lf]
       - id: trailing-whitespace
       - id: check-case-conflict
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.2.1
-    hooks:
-      - id: autoflake
-        args:
-          - --in-place
-          - --remove-all-unused-imports
-          - --remove-unused-variable
-          - --ignore-init-module-imports
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-      - id: pyupgrade
-        args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

atac/peakvi_in_R.ipynb

@@ -1937,4 +1937,4 @@
     },
     "nbformat": 4,
     "nbformat_minor": 4
-}
+}

figures/minification.svg

@@ -560,9 +560,9 @@
    "outputs": [],
    "source": [
     "adata = adata[:, adata.var[\"highly_variable\"]]  # focus on selected genes\n",
-    "adata.layers[\"counts\"] = (\n",
-    "    adata.X.copy().tocsr()\n",
-    ")  # converts to CSR format, preserve counts\n",
+    "adata.layers[\n",
+    "    \"counts\"\n",
+    "] = adata.X.copy().tocsr()  # converts to CSR format, preserve counts\n",
     "\n",
     "scvi.model.SCVI.setup_anndata(\n",
     "    adata, layer=\"counts\", batch_key=\"batch\"\n",