diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 0402c423..910b014b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -13,43 +13,49 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.12']
-    
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y build-essential libffi-dev libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev libncurses5-dev libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev libjpeg-dev libpng-dev libtiff-dev libwebp-dev libopenjp2-7-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libpoppler-cpp-dev libpoppler-dev libhdf5-dev libnetcdf-dev libgl1 libglib2.0-0 libsm6 libxext6 libxrender-dev libgomp1 libcairo2-dev libpango1.0-dev libpangocairo-1.0-0 libgdk-pixbuf2.0-dev libffi-dev shared-mime-info graphviz libgraphviz-dev
-      
+
       - name: Cache dependencies
         uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
-      
+
       - name: Cache SDK generation
         uses: actions/cache@v3
         with:
           path: src/tooluniverse/tools
           key: ${{ runner.os }}-sdk-${{ hashFiles('scripts/build_tools.py', 'src/tooluniverse/data/*.json') }}
-      
+
       - name: Install uv
         uses: astral-sh/setup-uv@v3
-      
+
       - name: Install project with dev extras
         run: |
           uv pip install -e .[dev] --system
-      
+
+      - name: Check code formatting/linting requirements
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "latest"
+        run: ruff check
+
       - name: Generate SDK
         run: python scripts/build_tools.py
-      
+
       - name: Run fast tests (excluding tools, examples, and api)
         run: |
           pytest tests/ -v \
@@ -61,30 +67,28 @@ jobs:
             --ignore=tests/tools \
             --ignore=tests/examples \
             --ignore=tests/api
-      
+
       - name: Test doctor CLI tool
         run: |
           python -m src.tooluniverse.doctor
-      
+
       - name: Run tools, examples, and api tests (optional, requires network)
         if: github.event.inputs.run_tools_tests == 'true' || github.event_name == 'workflow_dispatch'
         run: |
           pytest tests/tools/ tests/examples/ tests/api/ -v \
             --tb=short \
             -m "not slow and not require_api_keys"
-      
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         if: github.ref == 'refs/heads/main'
         with:
           file: ./coverage.xml
           fail_ci_if_error: false
-      
+
       - name: Upload test results
         if: always()
         uses: actions/upload-artifact@v4
         with:
           name: test-results-${{ matrix.python-version }}
-          path: coverage.xml
-
-
+          path: coverage.xml
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 638b9251..c66ec777 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,38 +8,19 @@ exclude: |
   )
 
 repos:
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: check-ast
       - id: check-yaml
       - id: check-toml
 
-  - repo: https://github.com/psf/black
-    rev: 25.9.0
-    hooks:
-      - id: black
-        args: ["--line-length=88"]
-        language_version: python3
-
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        args: ["--remove-all-unused-imports", "--remove-unused-variables", "--in-place"]
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
-    hooks:
-      - id: flake8
-        additional_dependencies: ["flake8-bugbear"]
-        args: ["--max-line-length=88", "--extend-ignore=E501,F401,F541,E203,W503"]
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.4
+    rev: v0.14.5
     hooks:
-      - id: ruff
-        args: ["--fix", "--line-length=88", "--ignore=E203"]
\ No newline at end of file
+      # Run the linter.
+      - id: ruff-check
+        args: [ --fix ] # automatically fix linting issues
+      # Run the formatter.
+      - id: ruff-format
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index e4cc5799..d58cf090 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ authors = [
 dependencies = [
     "requests>=2.32.0",
     "numpy>=2.2.0",
-    "sympy>=1.12.0",  # Symbolic mathematics for Python executor
+    "sympy>=1.12.0", # Symbolic mathematics for Python executor
     "graphql-core>=3.2.0",
     "fastapi>=0.116.0",
     "uvicorn>=0.35.0",
@@ -31,7 +31,7 @@ dependencies = [
     "rcsb-api>=1.4.0",
     "fitz>=0.0.1.dev2",
     "pandas>=2.2.3",
-    "setuptools>=70.0.0,<81.0.0",  # Fix pkg_resources deprecation warnings
+    "setuptools>=70.0.0,<81.0.0", # Fix pkg_resources deprecation warnings
     "pdfplumber>=0.11.0",
     "playwright>=1.55.0",
     "faiss-cpu>=1.12.0",
@@ -58,12 +58,11 @@ dev = [
     "pytest-timeout>=2.3.1",
     "pytest-mock>=3.14.0",
     "pytest-asyncio>=0.21.0",
-    "requests-mock>=1.12.1",
-    "black>=22.0",
-    "flake8>=4.0",
     "pre-commit>=2.0",
     "pytest-xdist>=3.0",
     "pytest-html>=3.0",
+    "requests-mock>=1.12.1",
+    "ruff>=0.14.5",
 ]
 docs = [
     "sphinx>=4.0",
@@ -155,4 +154,16 @@ dev = [
 ]
 
 [tool.uv.sources]
-tooluniverse = { workspace = true }
\ No newline at end of file
+tooluniverse = { workspace = true }
+
+[tool.ruff]
+line-length = 88
+exclude = [
+    ".venv",
+    "docs",
+    "examples",
+]
+unsafe-fixes = true
+
+[tool.ruff.lint]
+ignore = ["E203", "E402", "E501", "F401", "F541"]
\ No newline at end of file
diff --git a/uv.lock b/uv.lock
index 39a98a14..62c5ee02 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
 version = 1
-revision = 2
+revision = 3
 requires-python = ">=3.10"
 resolution-markers = [
     "python_full_version < '3.11'",
@@ -363,40 +363,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/94/fe/3aed5d0be4d404d12d36ab97e2f1791424d9ca39c2f754a6285d59a3b01d/beautifulsoup4-4.14.2-py3-none-any.whl", hash = "sha256:5ef6fa3a8cbece8488d66985560f97ed091e22bbc4e9c2338508a9d5de6d4515", size = 106392, upload-time = "2025-09-29T10:05:43.771Z" },
 ]
 
-[[package]]
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-version = "25.1.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "click" },
-    { name = "mypy-extensions" },
-    { name = "packaging" },
-    { name = "pathspec" },
-    { name = "platformdirs" },
-    { name = "tomli", marker = "python_full_version < '3.11'" },
-    { name = "typing-extensions", marker = "python_full_version < '3.11'" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/94/49/26a7b0f3f35da4b5a65f081943b7bcd22d7002f5f0fb8098ec1ff21cb6ef/black-25.1.0.tar.gz", hash = "sha256:33496d5cd1222ad73391352b4ae8da15253c5de89b93a80b3e2c8d9a19ec2666", size = 649449, upload-time = "2025-01-29T04:15:40.373Z" }
-wheels = [
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-    { url = "https://files.pythonhosted.org/packages/09/71/54e999902aed72baf26bca0d50781b01838251a462612966e9fc4891eadd/black-25.1.0-py3-none-any.whl", hash = "sha256:95e8176dae143ba9097f351d174fdaf0ccd29efb414b362ae3fd72bf0f710717", size = 207646, upload-time = "2025-01-29T04:15:38.082Z" },
-]
-
 [[package]]
 name = "brotli"
 version = "1.1.0"
@@ -1015,7 +981,7 @@ version = "3.24.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "attrs" },
-    { name = "docstring-parser", marker = "python_full_version < '4.0'" },
+    { name = "docstring-parser", marker = "python_full_version < '4'" },
     { name = "rich" },
     { name = "rich-rst" },
     { name = "typing-extensions", marker = "python_full_version < '3.11'" },
@@ -1309,20 +1275,6 @@ wheels = [
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 ]
 
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-name = "flake8"
-version = "7.3.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "mccabe" },
-    { name = "pycodestyle" },
-    { name = "pyflakes" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/9b/af/fbfe3c4b5a657d79e5c47a2827a362f9e1b763336a52f926126aa6dc7123/flake8-7.3.0.tar.gz", hash = "sha256:fe044858146b9fc69b551a4b490d69cf960fcb78ad1edcb84e7fbb1b4a8e3872", size = 48326, upload-time = "2025-06-20T19:31:35.838Z" }
-wheels = [
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-
 [[package]]
 name = "flask"
 version = "2.1.3"
@@ -2760,15 +2712,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/16/53/8d8fa0ea32a8c8239e04d022f6c059ee5e1b77517769feccd50f1df43d6d/matplotlib-3.10.6-pp311-pypy311_pp73-manylinux2014_x86_64.manylinux_2_17_x86_64.whl", hash = "sha256:4d6ca6ef03dfd269f4ead566ec6f3fb9becf8dab146fb999022ed85ee9f6b3eb", size = 8693933, upload-time = "2025-08-30T00:14:22.942Z" },
 ]
 
-[[package]]
-name = "mccabe"
-version = "0.7.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/e7/ff/0ffefdcac38932a54d2b5eed4e0ba8a408f215002cd178ad1df0f2806ff8/mccabe-0.7.0.tar.gz", hash = "sha256:348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325", size = 9658, upload-time = "2022-01-24T01:14:51.113Z" }
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-
 [[package]]
 name = "mcp"
 version = "1.14.0"
@@ -3568,15 +3511,6 @@ wheels = [
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 ]
 
-[[package]]
-name = "pathspec"
-version = "0.12.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/ca/bc/f35b8446f4531a7cb215605d100cd88b7ac6f44ab3fc94870c120ab3adbf/pathspec-0.12.1.tar.gz", hash = "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712", size = 51043, upload-time = "2023-12-10T22:30:45Z" }
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-
 [[package]]
 name = "pdfminer-six"
 version = "20250506"
@@ -3999,15 +3933,6 @@ wheels = [
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 ]
 
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     { name = "ddgs", specifier = ">=9.0.0" },
     { name = "epam-indigo", specifier = ">=1.34.0" },
     { name = "faiss-cpu", specifier = ">=1.12.0" },
@@ -5857,7 +5772,6 @@ requires-dist = [
     { name = "fastapi", specifier = ">=0.116.0" },
     { name = "fastmcp", specifier = ">=2.12.0" },
     { name = "fitz", specifier = ">=0.0.1.dev2" },
-    { name = "flake8", marker = "extra == 'dev'", specifier = ">=4.0" },
     { name = "flask", specifier = ">=2.0.0" },
     { name = "flask", marker = "extra == 'graph'", specifier = ">=2.0.0" },
     { name = "furo", marker = "extra == 'docs'", specifier = ">=2024.8.6" },
@@ -5903,6 +5817,7 @@ requires-dist = [
     { name = "pytest-mock", marker = "extra == 'dev'", specifier = ">=3.14.0" },
     { name = "pytest-timeout", marker = "extra == 'dev'", specifier = ">=2.3.1" },
     { name = "pytest-xdist", marker = "extra == 'dev'", specifier = ">=3.0" },
+    { name = "python-dotenv", specifier = ">=1.0.0" },
     { name = "pyyaml", specifier = ">=6.0.0" },
     { name = "pyyaml", marker = "extra == 'space'", specifier = ">=6.0.0" },
     { name = "rcsb-api", specifier = ">=1.4.0" },
@@ -5910,6 +5825,7 @@ requires-dist = [
     { name = "requests", specifier = ">=2.32.0" },
     { name = "requests", marker = "extra == 'space'", specifier = ">=2.32.0" },
     { name = "requests-mock", marker = "extra == 'dev'", specifier = ">=1.12.1" },
+    { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.14.5" },
     { name = "scipy", marker = "extra == 'graph'", specifier = ">=1.7.0" },
     { name = "scipy", marker = "extra == 'visualization'", specifier = ">=1.7.0" },
     { name = "sentence-transformers", marker = "extra == 'embedding'", specifier = ">=5.1.0" },
@@ -5925,6 +5841,7 @@ requires-dist = [
     { name = "sphinx-notfound-page", marker = "extra == 'docs'", specifier = ">=0.8" },
     { name = "sphinx-rtd-theme", marker = "extra == 'docs'", specifier = ">=1.0" },
     { name = "sphinx-tabs", marker = "extra == 'docs'", specifier = ">=3.2.0" },
+    { name = "sympy", specifier = ">=1.12.0" },
     { name = "tooluniverse", extras = ["dev", "docs", "graph", "visualization", "space", "embedding", "ml"], marker = "extra == 'all'", editable = "." },
     { name = "uvicorn", specifier = ">=0.35.0" },
     { name = "werkzeug", marker = "extra == 'graph'", specifier = ">=2.0.0" },