Resolve Ruff issues

.devcontainer/Dockerfile

@@ -10,7 +10,7 @@ ARG USER_GID=$USER_UID
 # https://code.visualstudio.com/remote/advancedcontainers/add-nonroot-user
 RUN groupadd --gid $USER_GID $USERNAME \
   && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME \
-  && usermod -a -G video user \ 
+  && usermod -a -G video user \
   && apt-get update \
   && apt-get install -y sudo \
   && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \

.devcontainer/devcontainer.json

@@ -1,5 +1,3 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.238.1/containers/python-3
 {
 	"name": "Python 3",
 	"build": {
@@ -12,46 +10,6 @@
 		"--gpus",
 		"all"
 	],
-	// Configure tool-specific properties.
-	"customizations": {
-		// Configure properties specific to VS Code.
-		"vscode": {
-			// Set *default* container specific settings.json values on container create.
-			"settings": {
-				"mypy.dmypyExecutable": "dmypy"
-			},
-			// Add the IDs of extensions you want installed when the container is created.
-			"extensions": [
-				"christian-kohler.path-intellisense",
-				"davidanson.vscode-markdownlint",
-				"donjayamanne.githistory",
-				"donjayamanne.python-extension-pack",
-				"github.copilot",
-				"github.vscode-github-actions",
-				"github.vscode-pull-request-github",
-				"ionutvmi.path-autocomplete",
-				"matangover.mypy",
-				"mikoz.autoflake-extension",
-				"ms-python.black-formatter",
-				"ms-python.isort",
-				"ms-python.pylint",
-				"ms-python.python",
-				"ms-python.vscode-pylance",
-				"ms-toolsai.jupyter-keymap",
-				"ms-toolsai.jupyter-renderers",
-				"ms-toolsai.jupyter",
-				"ms-vsliveshare.vsliveshare-pack",
-				"njpwerner.autodocstring",
-				"richie5um2.vscode-sort-json",
-				"stkb.rewrap",
-				"streetsidesoftware.code-spell-checker-british-english",
-				"streetsidesoftware.code-spell-checker",
-				"tushortz.python-extended-snippets",
-				"yzhang.markdown-all-in-one"
-			]
-		}
-	},
 	"containerUser": "user",
-	// Install any dependencies
 	"postCreateCommand": "poetry env use 3.11 && poetry install --with dev,jupyter"
-}
+}

.github/workflows/checks.yml

@@ -2,15 +2,15 @@ name: Checks
 
 on:
   push:
-    branches: 
+    branches:
       - main
     paths-ignore:
       - '.devcontainer/**'
       - '.vscode/**'
       - '.gitignore'
       - 'README.md'
   pull_request:
-    branches: 
+    branches:
       - main
     paths-ignore:
       - '.devcontainer/**'
@@ -35,21 +35,24 @@ jobs:
           - "3.10"
           - "3.11"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Install Poetry
       uses: snok/install-poetry@v1
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'poetry'
+        allow-prereleases: true
     - name: Install dependencies
       run: poetry install --with dev
-    - name: Pytest
-      run: poetry run pytest
     - name: Pyright type check
       run: poetry run pyright
-    - name: Ruff (lint & format)
-      run: poetry run ruff --check sparse_autoencoder
+    - name: Ruff lint
+      run: poetry run ruff check sparse_autoencoder --output-format=github
+    - name: Ruff format
+      run: poetry run ruff format sparse_autoencoder --check
+    - name: Pytest
+      run: poetry run pytest
     - name: Build check
-      run: poetry build
+      run: poetry build

.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
      - name: Parse semver string
-       id: semver_parser 
+       id: semver_parser
        uses: booxmedialtd/[email protected]
        with:
          input_string: ${{ github.event.release.tag_name }}
@@ -51,4 +51,4 @@ jobs:
       - name: Publish
         run: poetry publish
         env:
-          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.POETRY_PYPI_TOKEN }}
+          POETRY_PYPI_TOKEN_PYPI: ${{ secrets.POETRY_PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.5.0
+      hooks:
+          - id: trailing-whitespace
+          - id: end-of-file-fixer
+          - id: check-yaml
+          - id: check-toml
+          - id: check-json
+          - id: check-added-large-files
+          - id: check-merge-conflict
+          - id: check-symlinks
+          - id: destroyed-symlinks
+          - id: detect-private-key
+    - repo: local
+      hooks:
+          - id: ruff_lint
+            name: Ruff Lint
+            entry: poetry run ruff check sparse_autoencoder
+            language: system
+            types: [python]
+            require_serial: true
+          - id: ruff_format
+            name: Ruff Format
+            entry: poetry run ruff format sparse_autoencoder --check
+            language: system
+            types: [python]
+            require_serial: true
+          - id: typecheck
+            name: Pyright Type Check
+            entry: poetry run pyright
+            language: system
+            types: [python]
+            require_serial: true

.vscode/cspell.json

@@ -2,23 +2,28 @@
     "language": "en,en-GB",
     "words": [
         "allclose",
+        "astroid",
         "autocast",
-        "Autoencoder",
+        "autoencoder",
         "categoricalwprobabilities",
         "circuitsvis",
         "colab",
         "cuda",
         "cudnn",
+        "davidanson",
         "devcontainer",
         "devel",
+        "dmypy",
         "docstrings",
+        "donjayamanne",
         "dtype",
         "dunder",
         "earlyterminate",
         "einops",
         "endoftext",
         "gelu",
-        "Hobbhahn",
+        "githistory",
+        "hobbhahn",
         "hyperband",
         "imageuri",
         "imputewhilerunning",
@@ -41,6 +46,7 @@
         "nelement",
         "numel",
         "optim",
+        "penality",
         "polysemantic",
         "polysemantically",
         "pyproject",
@@ -59,6 +65,7 @@
         "sharded",
         "tqdm",
         "transformer_lens",
+        "typecheck",
         "uncopyrighted",
         "unsqueeze",
         "venv",

.vscode/extensions.json

@@ -21,4 +21,4 @@
         "kevinrose.vsc-python-indent",
         "donjayamanne.python-environment-manager"
     ]
-}
+}

.vscode/settings.json

@@ -1,14 +1,44 @@
 {
-  "rewrap.autoWrap.enabled": true,
+  "[jsonc]": {
+    "editor.defaultFormatter": "vscode.json-language-features"
+  },
+  "[python]": {
+    "editor.defaultFormatter": "charliermarsh.ruff"
+  },
+  "[toml]": {
+    "editor.defaultFormatter": "tamasfe.even-better-toml"
+  },
   "editor.codeActionsOnSave": {
     "source.fixAll.eslint": true,
     "source.organizeImports": true
   },
-  "rewrap.reformat": false,
   "editor.formatOnSave": true,
-  "python.testing.pytestEnabled": true,
-  "rewrap.wrappingColumn": 100,
+  "evenBetterToml.formatter.alignComments": true,
+  "evenBetterToml.formatter.alignEntries": true,
+  "evenBetterToml.formatter.allowedBlankLines": 2,
+  "evenBetterToml.formatter.arrayAutoCollapse": true,
+  "evenBetterToml.formatter.arrayAutoExpand": true,
+  "evenBetterToml.formatter.arrayTrailingComma": true,
+  "evenBetterToml.formatter.columnWidth": 100,
+  "evenBetterToml.formatter.compactArrays": true,
+  "evenBetterToml.formatter.compactEntries": true,
+  "evenBetterToml.formatter.compactInlineTables": true,
+  "evenBetterToml.formatter.indentEntries": true,
+  "evenBetterToml.formatter.indentTables": true,
+  "evenBetterToml.formatter.inlineTableExpand": false,
+  "evenBetterToml.formatter.reorderArrays": true,
+  "evenBetterToml.formatter.reorderKeys": true,
+  "evenBetterToml.formatter.trailingNewline": true,
   "notebook.formatOnCellExecution": true,
   "notebook.formatOnSave.enabled": true,
-  "editor.defaultFormatter": "charliermarsh.ruff",
-}
+  "python.analysis.autoFormatStrings": true,
+  "python.analysis.autoImportCompletions": true,
+  "python.analysis.inlayHints.functionReturnTypes": false,
+  "python.analysis.typeCheckingMode": "basic",
+  "python.languageServer": "Pylance",
+  "python.terminal.activateEnvInCurrentTerminal": true,
+  "python.testing.pytestEnabled": true,
+  "rewrap.autoWrap.enabled": true,
+  "rewrap.reformat": true,
+  "rewrap.wrappingColumn": 100
+}