From a97706a97407d0a4c6b5adb44c6f66164a4a2e56 Mon Sep 17 00:00:00 2001
From: AdrianSosic <adrian.sosic@gmail.com>
Date: Mon, 30 Mar 2026 09:45:18 +0200
Subject: [PATCH 1/5] Switch from pip-audit to uv audit

---
 .github/workflows/ci.yml      |   2 +-
 .github/workflows/regular.yml |   2 +-
 CONTRIBUTING.md               |   2 +-
 pyproject.toml                |   3 +-
 tox.ini                       |  17 +--
 uv.lock                       | 216 ----------------------------------
 6 files changed, 9 insertions(+), 233 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index b794452031..b920d02a17 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -114,7 +114,7 @@ jobs:
         id: setup-python
         with:
           python-version: ${{ matrix.py-version.semantic }}
-      - name: Run pip-audit
+      - name: Run uv audit
         run: |
           pip install tox-uv
           tox -e audit-${{ matrix.py-version.tox }}
diff --git a/.github/workflows/regular.yml b/.github/workflows/regular.yml
index 6b97a49c79..60ed7f9c37 100644
--- a/.github/workflows/regular.yml
+++ b/.github/workflows/regular.yml
@@ -104,7 +104,7 @@ jobs:
         id: setup-python
         with:
           python-version: ${{ matrix.py-version.semantic }}
-      - name: Run pip-audit
+      - name: Run uv audit
         run: |
           pip install tox-uv
           tox -e audit-${{ matrix.py-version.tox }}
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 1524084b15..2ae466db0f 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -117,7 +117,7 @@ If you have questions or problems, simply ask for advice.
 | [pytest](https://docs.pytest.org/)                                                              | testing                                   |
 | [pytest-cov](https://pytest-cov.readthedocs.io/)                                                | measuring test coverage                   |
 | [sphinx](https://www.sphinx-doc.org/)                                                           | generating our documentation              |
-| [pip-audit](https://github.com/pypa/pip-audit)                                                  | detecting vulnerabilities in dependencies |
+| [uv audit](https://docs.astral.sh/uv/reference/cli/#uv-audit)                                   | detecting vulnerabilities in dependencies |
 | [tox](https://tox.wiki/)                                                                        | orchestrating all the above               |
 
 Executing a specific one of these tools is easiest by using the corresponding
diff --git a/pyproject.toml b/pyproject.toml
index d634aa5fb1..0736a4fed0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,7 @@ Issues = "https://github.com/emdgroup/baybe/issues/"
 
 # AUDIT NOTE: The marked packages are secondary dependencies but their versions are
 # set explicitly because the otherwise installed default versions have been flagged
-# for vulnerabilities by pip-audit
+# for vulnerabilities by uv audit
 
 [project.optional-dependencies]
 extras = [
@@ -93,7 +93,6 @@ dev = [
     "baybe[mypy]",
     "baybe[test]",
     "baybe[benchmarking]",
-    "pip-audit>=2.5.5",
     "setuptools-scm>=7.1.0",
     "tox-uv>=1.7.0",
     "uv>=0.11.3",
diff --git a/tox.ini b/tox.ini
index d828ce4940..1355265372 100644
--- a/tox.ini
+++ b/tox.ini
@@ -66,25 +66,18 @@ commands =
     mypy
 
 [testenv:audit,audit-py{310,311,312,313}]
-description = Run pip-audit
-extras = dev # audit entire environment
-setenv =
-    # Add pip-audit exceptions here, like:
-    # EXCLUDES=--ignore-vuln EXCEPTION_ID1 --ignore-vuln EXCEPTION_ID2 ...
+description = Run uv audit
+extras = dev  # audit entire environment
 commands =
     python --version
-    pip-audit {env:EXCLUDES:}
+    uv audit
 
 # This is separated from the other audit block because in 3.14 only core deps are tested
 [testenv:audit-py314]
-description = Run pip-audit
-deps = pip-audit
-setenv =
-    # Add pip-audit exceptions here, like:
-    # EXCLUDES=--ignore-vuln EXCEPTION_ID1 --ignore-vuln EXCEPTION_ID2 ...
+description = Run uv audit
 commands =
     python --version
-    pip-audit {env:EXCLUDES:}
+    uv audit
 
 [testenv:docs-py310]
 description = Build documentation, passing posargs to control what should be built
diff --git a/uv.lock b/uv.lock
index 302729623e..052c20111f 100644
--- a/uv.lock
+++ b/uv.lock
@@ -258,7 +258,6 @@ dev = [
     { name = "openpyxl" },
     { name = "pandas-stubs" },
     { name = "pillow" },
-    { name = "pip-audit" },
     { name = "plotly" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "pre-commit" },
@@ -433,7 +432,6 @@ requires-dist = [
     { name = "pandas", specifier = ">=1.4.2,<3" },
     { name = "pandas-stubs", marker = "extra == 'mypy'", specifier = ">=2.2.2.240603" },
     { name = "pillow", marker = "extra == 'examples'", specifier = ">=10.0.1" },
-    { name = "pip-audit", marker = "extra == 'dev'", specifier = ">=2.5.5" },
     { name = "plotly", marker = "extra == 'examples'", specifier = ">=5.10.0" },
     { name = "polars", extras = ["pyarrow"], marker = "extra == 'polars'", specifier = ">=0.19.19,<2" },
     { name = "pre-commit", marker = "extra == 'lint'", specifier = "==4.2.0" },
@@ -511,15 +509,6 @@ wheels = [
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 ]
 
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-sdist = { url = "https://files.pythonhosted.org/packages/c4/cf/85379f13b76f3a69bca86b60237978af17d6aa0bc5998978c3b8cf05abb2/boolean_py-5.0.tar.gz", hash = "sha256:60cbc4bad079753721d32649545505362c754e121570ada4658b852a3a318d95", size = 37047, upload-time = "2025-04-03T10:39:49.734Z" }
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-
 [[package]]
 name = "boto3"
 version = "1.42.27"
@@ -569,24 +558,6 @@ wheels = [
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-source = { registry = "https://pypi.org/simple" }
-dependencies = [
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-    { name = "requests" },
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-]
-
-[package.optional-dependencies]
-filecache = [
-    { name = "filelock" },
-]
-
 [[package]]
 name = "cachetools"
 version = "6.2.4"
@@ -1130,22 +1101,6 @@ wheels = [
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-version = "11.6.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "license-expression" },
-    { name = "packageurl-python" },
-    { name = "py-serializable" },
-    { name = "sortedcontainers" },
-    { name = "typing-extensions", marker = "python_full_version < '3.13'" },
-]
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 [[package]]
 name = "dask"
 version = "2025.12.0"
@@ -2419,18 +2374,6 @@ wheels = [
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-name = "license-expression"
-version = "30.4.4"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
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 [[package]]
 name = "lifelines"
 version = "0.30.0"
@@ -2933,67 +2876,6 @@ wheels = [
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-source = { registry = "https://pypi.org/simple" }
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-    { url = "https://files.pythonhosted.org/packages/54/d0/d04f1d1e064ac901439699ee097f58688caadea42498ec9c4b4ad2ef84ab/pip_requirements_parser-32.0.1-py3-none-any.whl", hash = "sha256:4659bc2a667783e7a15d190f6fccf8b2486685b6dba4c19c3876314769c57526", size = 35648, upload-time = "2022-12-21T15:25:21.046Z" },
-]
-
 [[package]]
 name = "platformdirs"
 version = "4.5.1"
@@ -4131,18 +3949,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/8e/37/efad0257dc6e593a18957422533ff0f87ede7c9c6ea010a2177d738fb82f/pure_eval-0.2.3-py3-none-any.whl", hash = "sha256:1db8e35b67b3d218d818ae653e27f06c3aa420901fa7b081ca98cbedc874e0d0", size = 11842, upload-time = "2024-07-21T12:58:20.04Z" },
 ]
 
-[[package]]
-name = "py-serializable"
-version = "2.1.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "defusedxml" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/73/21/d250cfca8ff30c2e5a7447bc13861541126ce9bd4426cd5d0c9f08b5547d/py_serializable-2.1.0.tar.gz", hash = "sha256:9d5db56154a867a9b897c0163b33a793c804c80cee984116d02d49e4578fc103", size = 52368, upload-time = "2025-07-21T09:56:48.07Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/9b/bf/7595e817906a29453ba4d99394e781b6fabe55d21f3c15d240f85dd06bb1/py_serializable-2.1.0-py3-none-any.whl", hash = "sha256:b56d5d686b5a03ba4f4db5e769dc32336e142fc3bd4d68a8c25579ebb0a67304", size = 23045, upload-time = "2025-07-21T09:56:46.848Z" },
-]
-
 [[package]]
 name = "pyarrow"
 version = "22.0.0"
@@ -4694,19 +4500,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/7e/71/44ce230e1b7fadd372515a97e32a83011f906ddded8d03e3c6aafbdedbb7/rfc3987_syntax-1.1.0-py3-none-any.whl", hash = "sha256:6c3d97604e4c5ce9f714898e05401a0445a641cfa276432b0a648c80856f6a3f", size = 8046, upload-time = "2025-07-18T01:05:03.843Z" },
 ]
 
-[[package]]
-name = "rich"
-version = "14.2.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "markdown-it-py" },
-    { name = "pygments" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/fb/d2/8920e102050a0de7bfabeb4c4614a49248cf8d5d7a8d01885fbb24dc767a/rich-14.2.0.tar.gz", hash = "sha256:73ff50c7c0c1c77c8243079283f4edb376f0f6442433aecb8ce7e6d0b92d1fe4", size = 219990, upload-time = "2025-10-09T14:16:53.064Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/25/7a/b0178788f8dc6cafce37a212c99565fa1fe7872c70c6c9c1e1a372d9d88f/rich-14.2.0-py3-none-any.whl", hash = "sha256:76bc51fe2e57d2b1be1f96c524b890b816e334ab4c1e45888799bfaab0021edd", size = 243393, upload-time = "2025-10-09T14:16:51.245Z" },
-]
-
 [[package]]
 name = "roman-numerals"
 version = "4.1.0"
@@ -5877,15 +5670,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/23/d1/136eb2cb77520a31e1f64cbae9d33ec6df0d78bdf4160398e86eec8a8754/tomli-2.4.0-py3-none-any.whl", hash = "sha256:1f776e7d669ebceb01dee46484485f43a4048746235e683bcdffacdf1fb4785a", size = 14477, upload-time = "2026-01-11T11:22:37.446Z" },
 ]
 
-[[package]]
-name = "tomli-w"
-version = "1.2.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/19/75/241269d1da26b624c0d5e110e8149093c759b7a286138f4efd61a60e75fe/tomli_w-1.2.0.tar.gz", hash = "sha256:2dd14fac5a47c27be9cd4c976af5a12d87fb1f0b4512f81d69cce3b35ae25021", size = 7184, upload-time = "2025-01-15T12:07:24.262Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/c7/18/c86eb8e0202e32dd3df50d43d7ff9854f8e0603945ff398974c1d91ac1ef/tomli_w-1.2.0-py3-none-any.whl", hash = "sha256:188306098d013b691fcadc011abd66727d3c414c571bb01b1a174ba8c983cf90", size = 6675, upload-time = "2025-01-15T12:07:22.074Z" },
-]
-
 [[package]]
 name = "toolz"
 version = "1.1.0"

From 28414f10ccddf8ffbb939fe07a3c35d8ea447e92 Mon Sep 17 00:00:00 2001
From: AdrianSosic <adrian.sosic@gmail.com>
Date: Wed, 8 Apr 2026 10:26:07 +0200
Subject: [PATCH 2/5] Re-enable audit ignore mechanism

---
 tox.ini | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tox.ini b/tox.ini
index 1355265372..a9e71ff8f3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -68,16 +68,22 @@ commands =
 [testenv:audit,audit-py{310,311,312,313}]
 description = Run uv audit
 extras = dev  # audit entire environment
+setenv =
+    # Add uv audit exceptions here using --ignore/--ignore-until-fixed, like:
+    # EXCLUDES=--ignore EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
 commands =
     python --version
-    uv audit
+    uv audit {env:EXCLUDES:}
 
 # This is separated from the other audit block because in 3.14 only core deps are tested
 [testenv:audit-py314]
 description = Run uv audit
+setenv =
+    # Add uv audit exceptions here using --ignore/--ignore-until-fixed, like:
+    # EXCLUDES=--ignore EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
 commands =
     python --version
-    uv audit
+    uv audit {env:EXCLUDES:}
 
 [testenv:docs-py310]
 description = Build documentation, passing posargs to control what should be built

From 0a697f7150cbe69cbc41bfc3d6813e5d62307478 Mon Sep 17 00:00:00 2001
From: AdrianSosic <adrian.sosic@gmail.com>
Date: Wed, 8 Apr 2026 12:23:56 +0200
Subject: [PATCH 3/5] Only fail on direct dependency vulnerabilities

---
 pyproject.toml |   4 -
 tools/audit.py | 194 +++++++++++++++++++++++++++++++++++++++++++++++++
 tox.ini        |  16 ++--
 uv.lock        | 194 ++++++++++++++++++++++++-------------------------
 4 files changed, 299 insertions(+), 109 deletions(-)
 create mode 100644 tools/audit.py

diff --git a/pyproject.toml b/pyproject.toml
index 0736a4fed0..727b9a4ab2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,10 +54,6 @@ Issues = "https://github.com/emdgroup/baybe/issues/"
 # DEV TOOLS NOTE: The versions of all dev tools should be consistent everywhere
 # (pre-commit, environment.yml, requirements.txt, pyproject.toml, ...)
 
-# AUDIT NOTE: The marked packages are secondary dependencies but their versions are
-# set explicitly because the otherwise installed default versions have been flagged
-# for vulnerabilities by uv audit
-
 [project.optional-dependencies]
 extras = [
     "baybe[chem]",
diff --git a/tools/audit.py b/tools/audit.py
new file mode 100644
index 0000000000..ba5f877688
--- /dev/null
+++ b/tools/audit.py
@@ -0,0 +1,194 @@
+"""Wrapper around ``uv audit`` that only fails on direct dependency vulnerabilities.
+
+This script runs ``uv audit`` with any extra arguments forwarded, parses its output
+to determine which packages are flagged, and cross-references them against the
+project's direct dependencies (from ``pyproject.toml``). The output is reorganized
+into clearly separated sections for direct vs. transitive vulnerabilities, and the
+exit code only reflects whether *direct* dependencies are affected.
+"""
+
+from __future__ import annotations
+
+import re
+import subprocess
+import sys
+from pathlib import Path
+
+try:
+    import tomllib
+except ModuleNotFoundError:  # Python < 3.11
+    import tomli as tomllib  # type: ignore[no-redef]
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+# PEP 503 normalization: lowercase, runs of [-_.] become a single dash
+_NORMALIZE_RE = re.compile(r"[-_.]+")
+
+
+def _normalize(name: str) -> str:
+    return _NORMALIZE_RE.sub("-", name).lower()
+
+
+def _extract_package_name(spec: str) -> str:
+    """Return the bare package name from a PEP 508 dependency string."""
+    return re.split(r"[\[><=!~;\s]", spec, maxsplit=1)[0].strip()
+
+
+def _get_direct_dependencies(pyproject_path: Path) -> set[str]:
+    """Collect all direct dependency names from ``pyproject.toml``.
+
+    This includes core ``dependencies`` as well as every entry listed under
+    ``[project.optional-dependencies]``.  Self-references (e.g. ``baybe[chem]``)
+    are excluded.
+    """
+    with open(pyproject_path, "rb") as f:
+        data = tomllib.load(f)
+
+    project = data.get("project", {})
+    project_name = _normalize(project.get("name", ""))
+
+    deps: set[str] = set()
+
+    # Core dependencies
+    for spec in project.get("dependencies", []):
+        name = _normalize(_extract_package_name(spec))
+        if name != project_name:
+            deps.add(name)
+
+    # Optional dependencies (all extras)
+    for group_deps in project.get("optional-dependencies", {}).values():
+        for spec in group_deps:
+            name = _normalize(_extract_package_name(spec))
+            if name != project_name:
+                deps.add(name)
+
+    return deps
+
+
+# Regex matching the header line for each vulnerable package in ``uv audit``
+# output, e.g. ``requests 2.32.5 has 1 known vulnerability:``
+_VULN_HEADER_RE = re.compile(
+    r"^(\S+)\s+\S+\s+has\s+\d+\s+known\s+vulnerabilit", re.MULTILINE
+)
+
+
+def _parse_vulnerability_blocks(output: str) -> list[tuple[str, str]]:
+    """Parse ``uv audit`` output into (package_name, block_text) pairs.
+
+    Each block starts with a header like ``requests 2.32.5 has 1 known
+    vulnerability:`` and includes all subsequent lines until the next header
+    or end of output.
+    """
+    # Find all header positions
+    headers = list(_VULN_HEADER_RE.finditer(output))
+    if not headers:
+        return []
+
+    blocks: list[tuple[str, str]] = []
+    for i, match in enumerate(headers):
+        start = match.start()
+        end = headers[i + 1].start() if i + 1 < len(headers) else len(output)
+        pkg_name = _normalize(match.group(1))
+        block_text = output[start:end].rstrip()
+        blocks.append((pkg_name, block_text))
+
+    return blocks
+
+
+def _count_vulns(blocks: list[tuple[str, str]]) -> int:
+    """Count the total number of individual vulnerabilities across blocks."""
+    total = 0
+    for _, text in blocks:
+        # Each vulnerability entry starts with "- GHSA-" or "- CVE-" etc.
+        total += len(re.findall(r"^- \S+", text, re.MULTILINE))
+    return total
+
+
+# ---------------------------------------------------------------------------
+# Main
+# ---------------------------------------------------------------------------
+
+_SEPARATOR = "=" * 72
+
+
+def main() -> int:
+    """Run ``uv audit`` and only fail on direct dependency vulnerabilities."""
+    # Locate pyproject.toml relative to this script (repo root)
+    repo_root = Path(__file__).resolve().parent.parent
+    pyproject_path = repo_root / "pyproject.toml"
+
+    if not pyproject_path.exists():
+        print(f"ERROR: {pyproject_path} not found", file=sys.stderr)
+        return 1
+
+    direct_deps = _get_direct_dependencies(pyproject_path)
+
+    # Run uv audit, forwarding any extra CLI arguments (e.g. --ignore-until-fixed)
+    result = subprocess.run(
+        ["uv", "audit", *sys.argv[1:]],
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
+    # Forward stderr (warnings, progress, etc.)
+    if result.stderr:
+        print(result.stderr, end="", file=sys.stderr)
+
+    # If uv audit passed, we pass too
+    if result.returncode == 0:
+        if result.stdout:
+            print(result.stdout, end="")
+        return 0
+
+    # Parse vulnerability blocks and classify them
+    blocks = _parse_vulnerability_blocks(result.stdout)
+    direct_blocks = [(name, text) for name, text in blocks if name in direct_deps]
+    transitive_blocks = [
+        (name, text) for name, text in blocks if name not in direct_deps
+    ]
+
+    n_direct = _count_vulns(direct_blocks)
+    n_transitive = _count_vulns(transitive_blocks)
+
+    # Print transitive vulnerabilities (informational)
+    if transitive_blocks:
+        print(_SEPARATOR)
+        names = ", ".join(sorted({n for n, _ in transitive_blocks}))
+        print(
+            f"TRANSITIVE dependency vulnerabilities ({n_transitive} total, "
+            f"not causing failure): {names}"
+        )
+        print(_SEPARATOR)
+        for _, text in transitive_blocks:
+            print()
+            print(text)
+        print()
+
+    # Print direct vulnerabilities (these cause failure)
+    if direct_blocks:
+        print(_SEPARATOR)
+        names = ", ".join(sorted({n for n, _ in direct_blocks}))
+        print(
+            f"DIRECT dependency vulnerabilities ({n_direct} total, "
+            f"CAUSING FAILURE): {names}"
+        )
+        print(_SEPARATOR)
+        for _, text in direct_blocks:
+            print()
+            print(text)
+        print()
+        return 1
+
+    print(_SEPARATOR)
+    print(
+        f"All {n_transitive} vulnerabilities are in transitive dependencies -- passing."
+    )
+    print(_SEPARATOR)
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
diff --git a/tox.ini b/tox.ini
index a9e71ff8f3..3ad935833f 100644
--- a/tox.ini
+++ b/tox.ini
@@ -66,24 +66,24 @@ commands =
     mypy
 
 [testenv:audit,audit-py{310,311,312,313}]
-description = Run uv audit
+description = Run uv audit (only direct dependency vulnerabilities cause failure)
 extras = dev  # audit entire environment
 setenv =
-    # Add uv audit exceptions here using --ignore/--ignore-until-fixed, like:
-    # EXCLUDES=--ignore EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
+    # Add uv audit exceptions here, like:
+    # EXCLUDES=--ignore-until-fixed EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
 commands =
     python --version
-    uv audit {env:EXCLUDES:}
+    python tools/audit.py {env:EXCLUDES:}
 
 # This is separated from the other audit block because in 3.14 only core deps are tested
 [testenv:audit-py314]
-description = Run uv audit
+description = Run uv audit (only direct dependency vulnerabilities cause failure)
 setenv =
-    # Add uv audit exceptions here using --ignore/--ignore-until-fixed, like:
-    # EXCLUDES=--ignore EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
+    # Add uv audit exceptions here, like:
+    # EXCLUDES=--ignore-until-fixed EXCEPTION_ID1 --ignore-until-fixed EXCEPTION_ID2 ...
 commands =
     python --version
-    uv audit {env:EXCLUDES:}
+    python tools/audit.py {env:EXCLUDES:}
 
 [testenv:docs-py310]
 description = Build documentation, passing posargs to control what should be built
diff --git a/uv.lock b/uv.lock
index 052c20111f..eb97b4ac63 100644
--- a/uv.lock
+++ b/uv.lock
@@ -3691,100 +3691,100 @@ wheels = [
 
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 ]
 
 [[package]]
@@ -5481,7 +5481,7 @@ wheels = [
 
 [[package]]
 name = "streamlit"
-version = "1.52.2"
+version = "1.56.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "altair" },
@@ -5504,9 +5504,9 @@ dependencies = [
     { name = "typing-extensions" },
     { name = "watchdog", marker = "sys_platform != 'darwin'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/43/20/434aaceccc6e1912671d869926103051330437adba72d538d787a07727ef/streamlit-1.52.2.tar.gz", hash = "sha256:64a4dda8bc5cdd37bfd490e93bb53da35aaef946fcfc283a7980dacdf165108b", size = 8584178, upload-time = "2025-12-17T17:07:59.642Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/03/85/7c669b3a1336d34ef39fa9760fbd343185f3b15db2ad0838fd78423d1c7f/streamlit-1.56.0.tar.gz", hash = "sha256:1176acfa89ae1318b79078e8efe689a9d02e8d58e325c00fc0e55fa2f3fe8d6a", size = 8559239, upload-time = "2026-03-31T22:29:38.59Z" }
 wheels = [
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 [[package]]

From 88c643f1a0457b273e3b69d2906d6d178f07f8bc Mon Sep 17 00:00:00 2001
From: AdrianSosic <adrian.sosic@gmail.com>
Date: Wed, 8 Apr 2026 12:25:45 +0200
Subject: [PATCH 4/5] Adjust version pins

Drop all pins related to secondary dependency vulnerabilities
---
 pyproject.toml |  5 +----
 uv.lock        | 17 -----------------
 2 files changed, 1 insertion(+), 21 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 727b9a4ab2..1af59c80dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -76,7 +76,6 @@ chem = [
 # for onnxruntime to <1.24 for Python 3.10.
 # See https://github.com/microsoft/onnxruntime/pull/27354 for more details.
 onnx = [
-    "onnx>=1.16.0", # see AUDIT NOTE, required by skl2onnx
     "onnxruntime>=1.15.1,<1.24; python_version < '3.11'",
     "onnxruntime>=1.15.1; python_version >= '3.11'",   
     "skl2onnx>=1.19.1",
@@ -117,11 +116,9 @@ examples = [
     "baybe[extras]",
     "matplotlib>=3.7.3,!=3.9.1",
     "openpyxl>=3.0.9",
-    "pillow>=10.0.1", # Necessary due to vulnerability
     "plotly>=5.10.0",
     "seaborn>=0.12.2",
-    "streamlit>=1.37.0", # Necessary due to vulnerability
-    "tornado>=6.3.3", # see AUDIT NOTE, required by streamlit
+    "streamlit>=1.37.0",
 ]
 
 lint = [
diff --git a/uv.lock b/uv.lock
index eb97b4ac63..5fda7762fe 100644
--- a/uv.lock
+++ b/uv.lock
@@ -221,10 +221,8 @@ benchmarking = [
     { name = "gitpython" },
     { name = "matplotlib" },
     { name = "ngboost" },
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "openpyxl" },
-    { name = "pillow" },
     { name = "plotly" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "psutil" },
@@ -234,7 +232,6 @@ benchmarking = [
     { name = "skl2onnx" },
     { name = "streamlit" },
     { name = "torch" },
-    { name = "tornado" },
     { name = "xyzpy" },
 ]
 chem = [
@@ -253,11 +250,9 @@ dev = [
     { name = "mypy" },
     { name = "myst-parser" },
     { name = "ngboost" },
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "openpyxl" },
     { name = "pandas-stubs" },
-    { name = "pillow" },
     { name = "plotly" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "pre-commit" },
@@ -283,7 +278,6 @@ dev = [
     { name = "streamlit" },
     { name = "tenacity" },
     { name = "torch" },
-    { name = "tornado" },
     { name = "tox-uv" },
     { name = "tqdm" },
     { name = "types-psutil" },
@@ -300,10 +294,8 @@ docs = [
     { name = "matplotlib" },
     { name = "myst-parser" },
     { name = "ngboost" },
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "openpyxl" },
-    { name = "pillow" },
     { name = "plotly" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "scikit-fingerprints" },
@@ -319,7 +311,6 @@ docs = [
     { name = "sphinx-paramlinks" },
     { name = "sphinxcontrib-bibtex" },
     { name = "streamlit" },
-    { name = "tornado" },
     { name = "tqdm" },
     { name = "xyzpy" },
 ]
@@ -327,10 +318,8 @@ examples = [
     { name = "fpsample" },
     { name = "matplotlib" },
     { name = "ngboost" },
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "openpyxl" },
-    { name = "pillow" },
     { name = "plotly" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "scikit-fingerprints" },
@@ -338,13 +327,11 @@ examples = [
     { name = "shap", extra = ["others"] },
     { name = "skl2onnx" },
     { name = "streamlit" },
-    { name = "tornado" },
     { name = "xyzpy" },
 ]
 extras = [
     { name = "fpsample" },
     { name = "ngboost" },
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "polars", extra = ["pyarrow"] },
     { name = "scikit-fingerprints" },
@@ -370,7 +357,6 @@ mypy = [
     { name = "types-tqdm" },
 ]
 onnx = [
-    { name = "onnx" },
     { name = "onnxruntime" },
     { name = "skl2onnx" },
 ]
@@ -425,13 +411,11 @@ requires-dist = [
     { name = "myst-parser", marker = "extra == 'docs'", specifier = ">=4.0.0" },
     { name = "ngboost", marker = "extra == 'extras'", specifier = ">=0.3.12,<1" },
     { name = "numpy", specifier = ">=1.24.1,<3" },
-    { name = "onnx", marker = "extra == 'onnx'", specifier = ">=1.16.0" },
     { name = "onnxruntime", marker = "python_full_version >= '3.11' and extra == 'onnx'", specifier = ">=1.15.1" },
     { name = "onnxruntime", marker = "python_full_version < '3.11' and extra == 'onnx'", specifier = ">=1.15.1,<1.24" },
     { name = "openpyxl", marker = "extra == 'examples'", specifier = ">=3.0.9" },
     { name = "pandas", specifier = ">=1.4.2,<3" },
     { name = "pandas-stubs", marker = "extra == 'mypy'", specifier = ">=2.2.2.240603" },
-    { name = "pillow", marker = "extra == 'examples'", specifier = ">=10.0.1" },
     { name = "plotly", marker = "extra == 'examples'", specifier = ">=5.10.0" },
     { name = "polars", extras = ["pyarrow"], marker = "extra == 'polars'", specifier = ">=0.19.19,<2" },
     { name = "pre-commit", marker = "extra == 'lint'", specifier = "==4.2.0" },
@@ -458,7 +442,6 @@ requires-dist = [
     { name = "tenacity", marker = "extra == 'test'", specifier = ">=8.5.0" },
     { name = "torch", specifier = ">=1.13.1,<3" },
     { name = "torch", marker = "extra == 'benchmarking'", specifier = ">=2.4.0" },
-    { name = "tornado", marker = "extra == 'examples'", specifier = ">=6.3.3" },
     { name = "tox-uv", marker = "extra == 'dev'", specifier = ">=1.7.0" },
     { name = "tqdm", marker = "extra == 'docs'" },
     { name = "types-psutil", marker = "extra == 'mypy'", specifier = ">=7.0.0.20250801" },

From 65ddbf1ba3d96c4e188c8322e322272fa9bd7cde Mon Sep 17 00:00:00 2001
From: AdrianSosic <adrian.sosic@gmail.com>
Date: Wed, 8 Apr 2026 12:27:41 +0200
Subject: [PATCH 5/5] Update CHANGELOG.md

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d9931d0d0e..6fc57def2d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   for determining the Pareto front
 - Interpoint constraints for continuous search spaces
 
+### Changed
+- Switched from `pip-audit` to `uv audit`, checking only direct dependencies
+
 ### Breaking Changes
 - `ContinuousLinearConstraint.to_botorch` now returns a collection of constraint tuples
   instead of a single tuple (needed for interpoint constraints)