[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.pre-commit-config.yaml

@@ -1,79 +1,79 @@
 fail_fast: false
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - commit
-    - push
+  - commit
+  - push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: 23.3.0
-      hooks:
-          - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.6
-      hooks:
-          - id: prettier
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.13.0
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.4.0
-      hooks:
-          - id: yesqa
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      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: v2.0.2
-      hooks:
-          - id: autoflake
-            args:
-                - --in-place
-                - --remove-all-unused-imports
-                - --remove-unused-variable
-                - --ignore-init-module-imports
-    - repo: https://github.com/PyCQA/flake8
-      rev: 6.0.0
-      hooks:
-          - id: flake8
-            additional_dependencies:
-                - flake8-tidy-imports
-                - flake8-docstrings
-                - flake8-rst-docstrings
-                - flake8-comprehensions
-                - flake8-bugbear
-                - flake8-blind-except
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.3.1
-      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$'
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.6
+    hooks:
+      - id: prettier
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.13.0
+    hooks:
+      - id: blacken-docs
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.4.0
+    hooks:
+      - id: yesqa
+        additional_dependencies:
+          - flake8-tidy-imports
+          - flake8-docstrings
+          - flake8-rst-docstrings
+          - flake8-comprehensions
+          - flake8-bugbear
+          - flake8-blind-except
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    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: v2.0.2
+    hooks:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-all-unused-imports
+          - --remove-unused-variable
+          - --ignore-init-module-imports
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies:
+          - flake8-tidy-imports
+          - flake8-docstrings
+          - flake8-rst-docstrings
+          - flake8-comprehensions
+          - flake8-bugbear
+          - flake8-blind-except
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    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$'

.readthedocs.yaml

@@ -1,16 +1,16 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-    os: ubuntu-20.04
-    tools:
-        python: "3.10"
+  os: ubuntu-20.04
+  tools:
+    python: "3.10"
 sphinx:
-    configuration: docs/conf.py
-    # disable this for more lenient docs builds
-    fail_on_warning: false
+  configuration: docs/conf.py
+  # disable this for more lenient docs builds
+  fail_on_warning: false
 python:
-    install:
-        - method: pip
-          path: .
-          extra_requirements:
-              - doc
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

src/simple_scvi/_mymodel.py

@@ -4,12 +4,8 @@
 from anndata import AnnData
 from scvi import REGISTRY_KEYS
 from scvi.data import AnnDataManager
-from scvi.data.fields import (
-    CategoricalJointObsField,
-    CategoricalObsField,
-    LayerField,
-    NumericalJointObsField,
-)
+from scvi.data.fields import (CategoricalJointObsField, CategoricalObsField,
+                              LayerField, NumericalJointObsField)
 from scvi.model._utils import _init_library_size
 from scvi.model.base import BaseModelClass, UnsupervisedTrainingMixin, VAEMixin
 from scvi.utils import setup_anndata_dsp

src/simple_scvi/_mypyromodel.py

@@ -6,12 +6,8 @@
 from anndata import AnnData
 from scvi import REGISTRY_KEYS
 from scvi.data import AnnDataManager
-from scvi.data.fields import (
-    CategoricalJointObsField,
-    CategoricalObsField,
-    LayerField,
-    NumericalJointObsField,
-)
+from scvi.data.fields import (CategoricalJointObsField, CategoricalObsField,
+                              LayerField, NumericalJointObsField)
 from scvi.dataloaders import DataSplitter
 from scvi.model.base import BaseModelClass
 from scvi.train import PyroTrainingPlan, TrainRunner