IBM · simona-rc · Aug 6, 2026 · Aug 6, 2026
diff --git a/.secrets.baseline b/.secrets.baseline
@@ -3,7 +3,7 @@
     "files": "^.secrets$|^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2026-08-05T13:33:24Z",
+  "generated_at": "2026-08-06T17:18:31Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -82,7 +82,7 @@
         "hashed_secret": "52b44e0998fd3bcb1929ac25818191fae050cf1d",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 662,
+        "line_number": 829,
         "type": "Secret Keyword",
         "verified_result": null
       }

diff --git a/add-biomed-multi-alignment-report.md b/add-biomed-multi-alignment-report.md
@@ -0,0 +1,51 @@
+---
+name: New Nexus Package
+about: Submit a new Nexus package to Algorithm Nexus
+title: "feat(package): Add biomed-multi-alignment Nexus package"
+labels: "nexus-package"
+---
+
+## Description
+
+Adds the [biomed-multi-alignment](https://github.com/BiomedSciAI/biomed-multi-alignment)
+package as a new Nexus package. This package provides MAMMAL (Molecular Aligned
+Multi-Modal Architecture and Language), a 458M-parameter T5-style biomedical
+foundation model trained on over 2 billion biological samples across proteins,
+small molecules, and single-cell gene expression data.
+
+### Changes made
+
+- Created `packages/biomed-multi-alignment/nexus.yaml` with the Nexus package
+  definition.
+- Created `packages/biomed-multi-alignment/models/biomed.omics.bl.sm.ma-ted-458m/model.yaml`
+  with the HuggingFace model ID (`ibm-research/biomed.omics.bl.sm.ma-ted-458m`)
+  and vLLM plugin configuration (general plugin: `mammal`).
+- Added `biomed-multi-alignment` as a dependency to both the `ecosystem` and
+  `candidate` variants in `pyproject.toml`, pinned to release `0.2.5`
+  (`git+https://github.com/BiomedSciAI/biomed-multi-alignment@0.2.5`).
+  The package is **vllm-agnostic** (vLLM is an optional dependency via the
+  `[vllm]` extra), so it is added without extras for `ecosystem` and with
+  `[vllm]` for `candidate`.
+- Updated `uv.lock` and exported updated `requirements-ecosystem.txt` and
+  `requirements-candidate.txt`.
+
+### Variant classification
+
+The package declares `vllm` as an **optional** dependency (via the `[vllm]`
+extra in its `pyproject.toml`). It therefore belongs to both the **ecosystem**
+and **candidate** variants per the Variant Association Rules.
+
+## Additional Information
+
+The vLLM plugin (`vllm_mammal_plugin`) is located under the `mammal_vllm/`
+subdirectory of the repository and is included when installing with the `[vllm]`
+extra. The plugin is registered via the `vllm.general_plugins` entry point and
+exposes the MAMMAL model as a pooling-runner embedding model in vLLM.
+
+## I need help with this PR
+
+N/A — all steps completed successfully.
+
+## Related Issues
+
+N/A
diff --git a/packages/biomed-multi-alignment/models/biomed.omics.bl.sm.ma-ted-458m/model.yaml b/packages/biomed-multi-alignment/models/biomed.omics.bl.sm.ma-ted-458m/model.yaml
@@ -0,0 +1,6 @@
+model:
+  id: ibm-research/biomed.omics.bl.sm.ma-ted-458m
+  vllm:
+    enabled: true
+    plugins:
+      general: mammal
diff --git a/packages/biomed-multi-alignment/nexus.yaml b/packages/biomed-multi-alignment/nexus.yaml
@@ -0,0 +1,2 @@
+package:
+  name: biomed-multi-alignment
diff --git a/pyproject.toml b/pyproject.toml
@@ -18,6 +18,7 @@ nexus = "algorithm_nexus.cli:main"
 
 [project.optional-dependencies]
 candidate = [
+  "biomed-multi-alignment[vllm]",
   "bmfm-targets[vllm]>=0.20.0",
   # CP 02/07/2026
   # Scanners are flagging opencv-python-headless==5.0.0.93 as
@@ -37,6 +38,7 @@ cli = [
   "typer>=0.25.0",
 ]
 ecosystem = [
+  "biomed-multi-alignment",
   "bmfm-targets",
   "gridfm-graphkit==0.8.1",
   "terrakit>=0.2.0",
@@ -88,6 +90,7 @@ conflicts = [
 [tool.uv.sources]
 bmfm-targets = { git = "https://github.com/BiomedSciAI/biomed-multi-omic.git" }
 tokamind = { git = "https://github.com/UKAEA-IBM-STFC-Fusion-FMs/tokamind", tag = "OS_v2.0" }
+biomed-multi-alignment = { git = "https://github.com/BiomedSciAI/biomed-multi-alignment", rev = "0.2.5" }
 
 [tool.uv-dynamic-versioning]
 enable = true

diff --git a/requirements-candidate.txt b/requirements-candidate.txt
diff --git a/requirements-ecosystem.txt b/requirements-ecosystem.txt
diff --git a/requirements-product.txt b/requirements-product.txt
@@ -1630,9 +1630,7 @@ nvidia-cuda-nvrtc==13.3.33 ; sys_platform == 'darwin' \
     --hash=sha256:7b05ecda494c6dabc44231a608b060a71008a730d9dfda932cc508e6d29159e0 \
     --hash=sha256:7d2af818851c0c224d5f92221e9226e51ee23c236df4b51f9194563979c888be \
     --hash=sha256:82530788b8c6164a54d3fd9ae8bcca8893d397c4aeb998861982a03bbe41e204
-    # via
-    #   humming-kernels
-    #   nvidia-cublas
+    # via humming-kernels
 nvidia-cuda-runtime==13.0.96 ; sys_platform != 'darwin' \
     --hash=sha256:7f82250d7782aa23b6cfe765ecc7db554bd3c2870c43f3d1821f1d18aebf0548 \
     --hash=sha256:ef9bcbe90493a2b9d810e43d249adb3d02e98dd30200d86607d8d02687c43f55 \

diff --git a/ruff.toml b/ruff.toml
@@ -1,34 +1,33 @@
 # Exclude a variety of commonly ignored directories.
 exclude = [
-    ".bzr",
-    ".direnv",
-    ".eggs",
-    ".git",
-    ".git-rewrite",
-    ".hg",
-    ".ipynb_checkpoints",
-    ".mypy_cache",
-    ".nox",
-    ".pants.d",
-    ".pyenv",
-    ".pytest_cache",
-    ".pytype",
-    ".ruff_cache",
-    ".svn",
-    ".tox",
-    ".venv",
-    ".vscode",
-    "__pypackages__",
-    "_build",
-    "buck-out",
-    "build",
-    "dist",
-    "node_modules",
-    "site-packages",
-    "venv",
+  ".bzr",
+  ".direnv",
+  ".eggs",
+  ".git",
+  ".git-rewrite",
+  ".hg",
+  ".ipynb_checkpoints",
+  ".mypy_cache",
+  ".nox",
+  ".pants.d",
+  ".pyenv",
+  ".pytest_cache",
+  ".pytype",
+  ".ruff_cache",
+  ".svn",
+  ".tox",
+  ".venv",
+  ".vscode",
+  "__pypackages__",
+  "_build",
+  "buck-out",
+  "build",
+  "dist",
+  "node_modules",
+  "site-packages",
+  "venv",
 ]
 
-
 # Assume Python 3.10
 target-version = "py310"
 
@@ -37,32 +36,32 @@ target-version = "py310"
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
 select = [
-    # "D",
-    "E",     # pycodestyle errors
-    "F",     # Pyflakes
-    "FA",    # flake8-future-annotations
-    "FAST",  # FastAPI
-    "FLY",   # flynt
-    "FURB",  # refurb
-    "I",     # isort
-    "ICN",   # flake8-import-conventions
-    "INT",   # flake8-gettext
-    "ISC",   # flake8-implicit-str-concat
-    "NPY",   # NumPy-specific rules
-    "PERF",  # Perflint
-    "PGH",   # pygrep-hooks
-    "PIE",   # flake8-pie
-    "PT",    # flake8-pytest-style
-    "RUF",   # Ruff-specific rules
-    "S",     # flake8-bandit
-    "S608",  # SQL injection
-    "SIM",   # flake8-simplify
-    "SLOT",  # flake8-slots
-    "T10",   # flake8-debugger
-    "TID",   # flake8-tidy-imports
-    "UP",    # pyupgrade
-    "W",     # pycodestyle warnings
-    "YTT",   # flake8-2020
+  # "D",
+  "E",  # pycodestyle errors
+  "F",  # Pyflakes
+  "FA",  # flake8-future-annotations
+  "FAST",  # FastAPI
+  "FLY",  # flynt
+  "FURB",  # refurb
+  "I",  # isort
+  "ICN",  # flake8-import-conventions
+  "INT",  # flake8-gettext
+  "ISC",  # flake8-implicit-str-concat
+  "NPY",  # NumPy-specific rules
+  "PERF",  # Perflint
+  "PGH",  # pygrep-hooks
+  "PIE",  # flake8-pie
+  "PT",  # flake8-pytest-style
+  "RUF",  # Ruff-specific rules
+  "S",  # flake8-bandit
+  "S608",  # SQL injection
+  "SIM",  # flake8-simplify
+  "SLOT",  # flake8-slots
+  "T10",  # flake8-debugger
+  "TID",  # flake8-tidy-imports
+  "UP",  # pyupgrade
+  "W",  # pycodestyle warnings
+  "YTT",  # flake8-2020
 ]
 
 # E501 - line too long (https://docs.astral.sh/ruff/rules/line-too-long/)