From e0a0a31dff28081fa329749bd9061847e87b96b3 Mon Sep 17 00:00:00 2001
From: faranm-stack <318811131+faranm-stack@users.noreply.github.com>
Date: Fri, 23 Oct 2026 15:57:20 -0400
Subject: [PATCH 1/3] Fix certifi advisory and release smoke import path in
 nvidia-alchemi

- Bump certifi to 2026.10.19 (GHSA-6q48-6c7w-9gw2, critical), which
  dependency review flagged after the previous fixes merged.
- Let the checkpoint downloader tests locate /app/build themselves, so
  `python /app/release_smoke.py` runs unchanged in the deployed image.
  Image-build tests now run with the runtime PYTHONPATH to catch this.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 agents/nvidia-alchemi/CHANGELOG.md                        | 6 +++++-
 agents/nvidia-alchemi/README.md                           | 6 +++---
 agents/nvidia-alchemi/tools/nvidia-alchemi/Dockerfile     | 2 +-
 .../tools/nvidia-alchemi/requirements-build.txt           | 2 +-
 .../nvidia-alchemi/tests/test_download_checkpoints.py     | 8 ++++++++
 5 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/agents/nvidia-alchemi/CHANGELOG.md b/agents/nvidia-alchemi/CHANGELOG.md
index adbb4e3..4c9a49a 100644
--- a/agents/nvidia-alchemi/CHANGELOG.md
+++ b/agents/nvidia-alchemi/CHANGELOG.md
@@ -14,6 +14,8 @@ checkpoint bytes are unchanged from 1.1.1.
 
 - Updated GitPython, hydra-core, multidict and urllib3 to patched versions after
   dependency review identified published advisories.
+- Updated certifi to 2026.10.19 to remove the compromised emSign root CAs
+  (GHSA-6q48-6c7w-9gw2).
 - Checkpoints are downloaded, size/hash verified, and only then deserialized.
 - Runtime learned-model aliases resolve only to hash-verified checkpoints baked
   into the image; explicit existing local paths remain available for training
@@ -36,7 +38,9 @@ checkpoint bytes are unchanged from 1.1.1.
 ### Fixed
 
 - Image-build tests can import the checkpoint downloader from `/app/build`
-  without adding that directory to the runtime import path.
+  without adding that directory to the runtime import path, so
+  `python /app/release_smoke.py` runs unchanged in the deployed image. Image-build
+  tests now run with the runtime `PYTHONPATH` to catch import-path regressions.
 - Screening validation tests explicitly use the selected test device, and the
   release-manifest test checks the shared AIMNet cache under `/opt/cache/aimnet`.
 
diff --git a/agents/nvidia-alchemi/README.md b/agents/nvidia-alchemi/README.md
index e52dfef..1b8ea8f 100644
--- a/agents/nvidia-alchemi/README.md
+++ b/agents/nvidia-alchemi/README.md
@@ -139,11 +139,11 @@ cannot alone prove logical independence; callers must retain real observations.
 
 Tests are in [tools/nvidia-alchemi/tests](tools/nvidia-alchemi/tests). Run them using
 Python's `unittest` discovery with the tool directory on `PYTHONPATH`; no pytest
-dependency is required. Inside the image, include `/app/build` for the checkpoint
-downloader tests:
+dependency is required. Inside the image, the runtime `PYTHONPATH` is sufficient; the
+checkpoint downloader tests locate `/app/build` themselves:
 
 ```bash
-PYTHONPATH=/app:/app/build python -B -m unittest discover -s /app/tests -v
+python -B -m unittest discover -s /app/tests -v
 ```
 
 Image-build tests explicitly use the CPU test path. Set `ALCHEMI_TEST_GPU=1` on
diff --git a/agents/nvidia-alchemi/tools/nvidia-alchemi/Dockerfile b/agents/nvidia-alchemi/tools/nvidia-alchemi/Dockerfile
index 8e281c6..5e074ac 100644
--- a/agents/nvidia-alchemi/tools/nvidia-alchemi/Dockerfile
+++ b/agents/nvidia-alchemi/tools/nvidia-alchemi/Dockerfile
@@ -54,6 +54,6 @@ ENV PYTHONPATH="/app" \
     ALCHEMI_AGENT_RELEASE="1.1.2" \
     ALCHEMI_BASE_IMAGE="${BASE_IMAGE}"
 RUN python /app/build_release_manifest.py \
-    && PYTHONPATH="/app:/app/build" python -B -m unittest discover -s /app/tests -v
+    && python -B -m unittest discover -s /app/tests -v
 WORKDIR /app/workdir
 CMD ["/bin/bash"]
diff --git a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
index d971563..30f818a 100644
--- a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
+++ b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
@@ -19,7 +19,7 @@ beartype==0.22.9
 bibtexparser==1.4.4
 botocore==1.43.56
 cachetools==7.1.7
-certifi==2026.7.22
+certifi==2026.10.19
 cftime==1.6.5
 charset-normalizer==3.5.1
 click==8.4.2
diff --git a/agents/nvidia-alchemi/tools/nvidia-alchemi/tests/test_download_checkpoints.py b/agents/nvidia-alchemi/tools/nvidia-alchemi/tests/test_download_checkpoints.py
index c15fd5f..399cb48 100644
--- a/agents/nvidia-alchemi/tools/nvidia-alchemi/tests/test_download_checkpoints.py
+++ b/agents/nvidia-alchemi/tools/nvidia-alchemi/tests/test_download_checkpoints.py
@@ -3,10 +3,18 @@
 import hashlib
 import json
 from pathlib import Path
+import sys
 import tempfile
 import unittest
 from unittest.mock import patch
 
+# The downloader lives beside the tests in the repository and in /app/build in
+# the image, which is deliberately not on the runtime PYTHONPATH.
+_TOOL_DIR = Path(__file__).resolve().parents[1]
+for _candidate in (_TOOL_DIR, _TOOL_DIR / "build"):
+    if (_candidate / "download_checkpoints.py").is_file() and str(_candidate) not in sys.path:
+        sys.path.append(str(_candidate))
+
 import download_checkpoints as downloader
 
 

From 366533025e601af33960ac0512bb5bc5db38ef1e Mon Sep 17 00:00:00 2001
From: faranm-stack <318811131+faranm-stack@users.noreply.github.com>
Date: Tue, 27 Oct 2026 18:10:08 -0400
Subject: [PATCH 2/3] Update nvidia-alchemi dependencies for newly reviewed
 advisories

Dependency Review fails on high or critical advisories. These were reviewed
after the previous update and affect the pinned versions:

- Pillow 12.3.0 -> 13.0.0 (28 high/critical, including 5 critical)
- GitPython 3.1.62 -> 3.2.1 (5 high)
- aiohttp 3.14.3 -> 3.14.4 (3 high)
- filelock 3.32.3 -> 4.2.1 (1 high)
- hydra-core 1.3.7 -> 1.3.8 (1 high)
- setuptools 84.0.0 -> 84.1.0 (1 low)

No pinned package declares a conflict with these versions, and none of them
has a known advisory.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 agents/nvidia-alchemi/CHANGELOG.md                   |  3 +++
 .../tools/nvidia-alchemi/requirements-build.txt      | 12 ++++++------
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/agents/nvidia-alchemi/CHANGELOG.md b/agents/nvidia-alchemi/CHANGELOG.md
index 4c9a49a..304eb90 100644
--- a/agents/nvidia-alchemi/CHANGELOG.md
+++ b/agents/nvidia-alchemi/CHANGELOG.md
@@ -16,6 +16,9 @@ checkpoint bytes are unchanged from 1.1.1.
   dependency review identified published advisories.
 - Updated certifi to 2026.10.19 to remove the compromised emSign root CAs
   (GHSA-6q48-6c7w-9gw2).
+- Updated aiohttp 3.14.4, filelock 4.2.1, GitPython 3.2.1, hydra-core 1.3.8 and
+  Pillow 13.0.0 for high and critical advisories reviewed after the previous
+  update, and setuptools 84.1.0 for a low-severity advisory.
 - Checkpoints are downloaded, size/hash verified, and only then deserialized.
 - Runtime learned-model aliases resolve only to hash-verified checkpoints baked
   into the image; explicit existing local paths remain available for training
diff --git a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
index 30f818a..b4be5dc 100644
--- a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
+++ b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
@@ -6,7 +6,7 @@ absl-py==2.5.0
 aimnet==0.2.0
 aiobotocore==3.9.0
 aiohappyeyeballs==2.7.1
-aiohttp==3.14.3
+aiohttp==3.14.4
 aioitertools==0.13.0
 aiosignal==1.4.0
 annotated-types==0.8.0
@@ -44,13 +44,13 @@ donfig==0.8.1.post1
 e3nn==0.4.4
 einops==0.8.2
 fastrlock==0.8.3
-filelock==3.32.3
+filelock==4.2.1
 fonttools==4.63.0
 frozenlist==1.8.0
 fsspec==2026.7.0
 gast==0.7.0
 gitdb==4.0.12
-GitPython==3.1.62
+GitPython==3.2.1
 google-crc32c==1.8.0
 h11==0.16.0
 h5py==3.16.0
@@ -58,7 +58,7 @@ hf-xet==1.6.0
 httpcore==1.0.9
 httpx==0.28.1
 huggingface_hub==1.28.0
-hydra-core==1.3.7
+hydra-core==1.3.8
 idna==3.19
 importlib_metadata==9.0.0
 jaxtyping==0.3.11
@@ -136,7 +136,7 @@ packaging==26.2
 palettable==3.3.3
 pandas==2.3.3
 periodictable==2.0.2
-pillow==12.3.0
+pillow==13.0.0
 pip==26.2.1
 platformdirs==4.11.3
 plotext==5.3.2
@@ -169,7 +169,7 @@ safetensors==0.8.0
 scikit-learn==1.9.0
 scipy==1.18.0
 seaborn==0.13.2
-setuptools==84.0.0
+setuptools==84.1.0
 six==1.17.0
 smmap==5.0.3
 spglib==2.7.0

From cee6af3891f435fbe6a1d53dddfc0015a8ed022d Mon Sep 17 00:00:00 2001
From: faranm-stack <318811131+faranm-stack@users.noreply.github.com>
Date: Tue, 27 Oct 2026 18:18:51 -0400
Subject: [PATCH 3/3] Pin yarl 1.25.1 for aiohttp 3.14.4

aiohttp 3.14.4 requires yarl>=1.25.1; the image build's pip check rejected
yarl 1.24.5. An offline pip-check of all 198 pins finds no other violations,
and yarl 1.25.1 has no known advisories.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
---
 agents/nvidia-alchemi/CHANGELOG.md                             | 3 ++-
 .../nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/agents/nvidia-alchemi/CHANGELOG.md b/agents/nvidia-alchemi/CHANGELOG.md
index 304eb90..5b0e41f 100644
--- a/agents/nvidia-alchemi/CHANGELOG.md
+++ b/agents/nvidia-alchemi/CHANGELOG.md
@@ -18,7 +18,8 @@ checkpoint bytes are unchanged from 1.1.1.
   (GHSA-6q48-6c7w-9gw2).
 - Updated aiohttp 3.14.4, filelock 4.2.1, GitPython 3.2.1, hydra-core 1.3.8 and
   Pillow 13.0.0 for high and critical advisories reviewed after the previous
-  update, and setuptools 84.1.0 for a low-severity advisory.
+  update, and setuptools 84.1.0 for a low-severity advisory. yarl moves to 1.25.1,
+  the minimum aiohttp 3.14.4 requires.
 - Checkpoints are downloaded, size/hash verified, and only then deserialized.
 - Runtime learned-model aliases resolve only to hash-verified checkpoints baked
   into the image; explicit existing local paths remain available for training
diff --git a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
index b4be5dc..c050370 100644
--- a/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
+++ b/agents/nvidia-alchemi/tools/nvidia-alchemi/requirements-build.txt
@@ -197,6 +197,6 @@ warp-lang==1.16.0
 wcwidth==0.8.2
 wheel==0.48.0
 wrapt==2.3.0
-yarl==1.24.5
+yarl==1.25.1
 zarr==3.3.0
 zipp==4.1.0