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feat(package): Add biomed-multi-alignment (mammal) Nexus Package #204

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feat(package): Add biomed-multi-alignment (mammal) Nexus Package #204

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a7bfacc
feat(package): Add biomed-multi-alignment (mammal) Nexus Package
simona-rc Aug 6, 2026
181ac76
feat(package): updated mammal to release 0.2.5
simona-rc Aug 6, 2026
1b078c8
feat(package): removed the added md file
simona-rc Aug 18, 2026
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4 changes: 2 additions & 2 deletions .secrets.baseline
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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
}
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6 changes: 6 additions & 0 deletions packages/biomed-multi-alignment/models/biomed.omics.bl.sm.ma-ted-458m/model.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
model:
id: ibm-research/biomed.omics.bl.sm.ma-ted-458m
vllm:
enabled: true
plugins:
general: mammal
2 changes: 2 additions & 0 deletions packages/biomed-multi-alignment/nexus.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
package:
name: biomed-multi-alignment
3 changes: 3 additions & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -37,6 +38,7 @@ cli = [
"typer>=0.25.0",
]
ecosystem = [
"biomed-multi-alignment",
"bmfm-targets",
"gridfm-graphkit==0.8.1",
"terrakit>=0.2.0",
Expand Down Expand Up @@ -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
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736 changes: 696 additions & 40 deletions requirements-candidate.txt
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580 changes: 548 additions & 32 deletions requirements-ecosystem.txt
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4 changes: 1 addition & 3 deletions requirements-product.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -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 \
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105 changes: 52 additions & 53 deletions ruff.toml
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@christian-pinto christian-pinto Aug 18, 2026

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Please, revert these changes

Original file line number Diff line number Diff line change
@@ -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"

Expand All @@ -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/)
Expand Down
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