Update project to use uv + updating deps (#443)

* update workflow checkout version

* move all requirements to uv

* update workflows to use uv

Author: SkafteNicki

.github/dependabot.yaml

@@ -1,6 +1,6 @@
 version: 2
 updates:
-  - package-ecosystem: "pip"
+  - package-ecosystem: "uv"
     directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/check_docs.yaml

@@ -10,24 +10,20 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: 3.11
-          cache: 'pip'
-          cache-dependency-path: setup.py
+          enable-cache: true
 
-      - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
-          pip list
+      - name: Sync dependencies
+        run: uv sync
 
       - name: Build docs
-        run: mkdocs build -d build --strict
+        run: uv run mkdocs build -d build --strict
 
       - name: Upload docs
         uses: actions/upload-artifact@v4

.github/workflows/code_formatting.yml

@@ -14,22 +14,24 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip list
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+
+      - name: Sync dependencies
+        run: uv sync
 
       - name: ruff check
         run: |
-          ruff check .
+          uv run ruff check .
 
       - name: ruff format
         run: |
-          ruff format .
+          uv run ruff format .

.github/workflows/deploy_docs.yaml

@@ -13,21 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: 3.11
-          cache: 'pip'
-          cache-dependency-path: setup.py
+          enable-cache: true
 
-      - name: Install dependencies
-        run: |
-          pip install -r requirements.txt
-          pip list
+      - name: Sync dependencies
+        run: uv sync
 
       - name: Deploy docs
-        run: mkdocs gh-deploy --force
+        run: uv run mkdocs gh-deploy --force

.github/workflows/docs_formatting.yaml

@@ -13,7 +13,7 @@ jobs:
     name: Check Markdown formatting
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: xt0rted/markdownlint-problem-matcher@v3
       - run: npm install -g markdownlint-cli
       - run: markdownlint **/*.md --ignore node_modules -c .github/markdownlint.json

.github/workflows/linkcheck.yaml

@@ -13,7 +13,7 @@ jobs:
     name: Check Markdown links
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - uses: gaurav-nelson/github-action-markdown-link-check@master
         with:
           config-file: '.github/linkcheck_config.json'

.github/workflows/pre_commit.yaml

@@ -15,7 +15,7 @@ jobs:
 
     steps:
     - name: Checkout code
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Set up Python
       uses: actions/setup-python@v5

.github/workflows/repo_scraper.yml

@@ -10,25 +10,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: 3.11
-          cache: 'pip'
-          cache-dependency-path: setup.py
+          enable-cache: true
+
+      - name: Sync dependencies
+        run: uv sync
 
       - name: Auth with GCP
         uses: google-github-actions/auth@v2
         with:
           credentials_json: ${{ secrets.GCP_SA_KEY }}
 
-      - name: Install dependencies
-        run: |
-          pip install -r tools/repo_stats/requirements.txt
-          pip list
-
       - name: Run repo scraper
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/update_pre_commit.yaml

@@ -15,22 +15,18 @@ jobs:
   auto-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: 3.11
-          cache: 'pip'
+          enable-cache: true
 
-      - name: Upgrade pip
-        run: python -m pip install --upgrade pip
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Sync dependencies
+        run: uv sync
 
       - name: Run pre-commit autoupdate
-        run: pre-commit autoupdate
+        run: uv run pre-commit autoupdate
 
       - name: Create Pull Request
         uses: peter-evans/create-pull-request@v7

pyproject.toml

@@ -11,19 +11,63 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-  "codespell==2.4.1",
-  "invoke==2.2",
-  "ipython==9.0.2",
-  "markdown-exec[ansi]==1.10",
-  "mkdocs-exclude==1.0.2",
-  "mkdocs-git-revision-date-localized-plugin==1.4.5",
-  "mkdocs-glightbox==0.4",
-  "mkdocs-material==9.6.12",
-  "mkdocs-material-extensions==1.3.1",
-  "mkdocs-same-dir==0.1.3",
-  "pre-commit==4.1",
-  "pymdown-extensions==10.14.3",
-  "ruff==0.9.9",
+  "codespell>=2.4.1",
+  "invoke>=2.2",
+  "ipython>=9.0.2",
+  "markdown-exec[ansi]>=1.10",
+  "mkdocs-exclude>=1.0.2",
+  "mkdocs-git-revision-date-localized-plugin>=1.4.5",
+  "mkdocs-glightbox>=0.4",
+  "mkdocs-material>=9.7",
+  "mkdocs-material-extensions>=1.3.1",
+  "mkdocs-same-dir>=0.1.3",
+  "pre-commit>=4.1",
+  "pymdown-extensions>=10.14.3",
+  "ruff>=0.14.5",
+]
+
+[dependency-groups]
+exercises = [
+  "cookiecutter>=2.6",
+  "coverage>=7.11.3",
+  "datasets>=4.4.1",
+  "dvc>=3.64",
+  "dvc-gdrive>=3.0.1",
+  "dvc-gs>=3.0.2",
+  "evidently>=0.7.16",
+  "fastapi>=0.121.2",
+  "google-cloud-storage>=3.6",
+  "httpx>=0.28.1",
+  "hydra-core>=1.3.2",
+  "invoke>=2.2",
+  "locust>=2.42.3",
+  "mkdocs-material>=9.7",
+  "mypy>=1.18.2",
+  "nbconvert>=7.16.6",
+  "neural-compressor>=3.6",
+  "onnxruntime>=1.23.2",
+  "optuna>=4.6",
+  "pipreqs>=0.4.13",
+  "pre-commit>=4.1",
+  "prefect>=3.5",
+  "prometheus-fastapi-instrumentator>=7.1",
+  "ptflops>=0.7.5",
+  "pydantic>=2.11.10",
+  "pytest>=8.4.2",
+  "python-dotenv>=1.2.1",
+  "pytorch-lightning>=2.5.6",
+  "requests>=2.32.3",
+  "ruff>=0.14.5",
+  "scikit-learn>=1.7.2",
+  "snakeviz>=2.2.2",
+  "streamlit>=1.51",
+  "torch>=2.9.1",
+  "torch-tb-profiler>=0.4.3",
+  "torchvision>=0.24.1",
+  "transformers>=4.57.1",
+  "typer>=0.19.2",
+  "uvicorn>=0.38",
+  "wandb>=0.23",
 ]
 
 [tool.ruff]