update ci

Author: kamil271e

.github/actions/setup/action.yml

@@ -1,7 +1,18 @@
+name: 'Setup Python Environment'
+description: 'Install uv, create venv, and install project dependencies'
 runs:
-  using: composite
+  using: "composite"
   steps:
-    - name: "Install UV"
+    - name: "Install UV and add to PATH"
       shell: bash
       run: |
-        curl -LsSf https://astral.sh/uv/install.sh | sh
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+    - name: "Create Virtual Environment"
+      shell: bash
+      run: uv venv
+
+    - name: "Install Python Dependencies"
+      shell: bash
+      run: uv sync

.github/workflows/code-quality.yml

@@ -1,10 +1,10 @@
 name: Python Code Quality
 
 on:
-    pull_request:
-    push:
-      branches:
-        - main
+  pull_request:
+  push:
+    branches:
+      - main
 
 jobs:
   lock_file:
@@ -20,26 +20,26 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/setup
-      - run: uvx ruff check src/
+      - run: make check_format
 
   formatting:
     runs-on: ubuntu-latest
     needs: [lock_file]
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/setup
-      - run: uvx ruff format --check src/
+      - run: make check_formatting
 
   type_consistency:
     runs-on: ubuntu-latest
     needs: [lock_file]
     steps:
       - uses: actions/checkout@v4
       - uses: ./.github/actions/setup
-      - run: uv run mypy src/
+      - run: make mypy
 
   build:
-    runs-on: [ubuntu-latest]
+    runs-on: ubuntu-latest
     needs: [linting, formatting, type_consistency]
     steps:
       - uses: actions/checkout@v4

Makefile

@@ -5,6 +5,9 @@ format:
 check_format:
 	uv run ruff check src
 
+check_formatting:
+	uv run ruff format --check src/
+
 mypy:
 	uv run mypy src/ --exclude "src/research"
 

pyproject.toml

@@ -17,6 +17,7 @@ dependencies = [
     "scipy>=1.15.2",
     "sentence-transformers>=4.1.0",
     "stubs>=1.0.0",
+    "ruff>=0.9.3",
     "torch>=2.6.0",
     "transformers>=4.48.3",
 ]

src/models/autoencoder.py

@@ -138,4 +138,4 @@ def _initialize_weights(
 
     def forward(self, x: torch.Tensor) -> torch.Tensor:
         x = self.encoder(x)
-        return self.decoder(x) # type: ignore[no-any-return]
+        return self.decoder(x)  # type: ignore[no-any-return]

src/recovery/utils.py

@@ -5,7 +5,7 @@
 import numpy as np
 import torch
 from numpy.typing import NDArray
-from scipy.optimize import linear_sum_assignment # type: ignore[import-untyped]
+from scipy.optimize import linear_sum_assignment  # type: ignore[import-untyped]
 from torch import Tensor, nn, optim
 
 from .reconstruction_stats import compare_H

src/spectra/run.py

@@ -172,7 +172,7 @@ def full_extraction(
             coef = 2**iteration
 
             layer_idx = 4 - (iteration - 1)
-            pre, post = get_layer_outputs(autoencoder, inputs, layer_idx)
+            pre, _ = get_layer_outputs(autoencoder, inputs, layer_idx)
             pre_restored = inverse_activation_dict[str(activation.activation_fun)](pre)
 
             if torch.device("cuda") == DEVICE and svd_driver == "gesvd":