algorithm-nexus 0.2.2__tar.gz → 0.3.0__tar.gz

{algorithm_nexus-0.2.2 → algorithm_nexus-0.3.0}/.secrets.baseline

@@ -3,7 +3,7 @@
     "files": "^.secrets$|^.secrets.baseline$",
     "lines": null
   },
-  "generated_at": "2026-07-16T22:04:38Z",
+  "generated_at": "2026-08-18T13:37:11Z",
   "plugins_used": [
     {
       "name": "AWSKeyDetector"
@@ -79,10 +79,10 @@
   "results": {
     "requirements-ecosystem.txt": [
       {
-        "hashed_secret": "07c7e5dca0db66092ee9e80cdb352d4f58a3d38a",
+        "hashed_secret": "52b44e0998fd3bcb1929ac25818191fae050cf1d",
         "is_secret": false,
         "is_verified": false,
-        "line_number": 666,
+        "line_number": 825,
         "type": "Secret Keyword",
         "verified_result": null
       }

{algorithm_nexus-0.2.2 → algorithm_nexus-0.3.0}/CHANGELOG.md

@@ -1,3 +1,26 @@
+## [0.2.3](https://github.com/ibm/algorithm-nexus/compare/36f3d99129ddf64de7f5098e4f1c290b991efa18..0.2.3) - 2026-08-25
+#### Features
+- (**dependencies**) Relaxed vllm dependency in product target (#214) - ([5926fdf](https://github.com/ibm/algorithm-nexus/commit/5926fdf6e38d8def91ab5ceed2a2b01b258d24c9)) - Christian Pinto
+- (**package**) Add biomed-multi-alignment (mammal) Nexus Package (#204) - ([d037a46](https://github.com/ibm/algorithm-nexus/commit/d037a460b9e6b610f86ef0cad59275ad4251337f)) - simona-rc
+#### Documentation
+- (**changelog**) add release notes for 0.2.2 (#197) - ([36f3d99](https://github.com/ibm/algorithm-nexus/commit/36f3d99129ddf64de7f5098e4f1c290b991efa18)) - DRL-NextGen
+#### Build system
+- (**deps**) update dependencies (#201) - ([1691af9](https://github.com/ibm/algorithm-nexus/commit/1691af97ea99bd1d0b22cf31578e4ebacae706aa)) - DRL-NextGen
+
+- - -
+
+## [0.2.2](https://github.com/ibm/algorithm-nexus/compare/240d5223c75c60c20cfaa45f18352ae59c5a7563..0.2.2) - 2026-07-27
+#### Features
+- (**package**) Add gridfm-graphkit Nexus package (#157) - ([b8e8b4a](https://github.com/ibm/algorithm-nexus/commit/b8e8b4a1218c60f1d2f34a47cfa6916150f788c4)) - Romeo Kienzler
+#### Documentation
+- (**changelog**) Added release notes for 0.2.1 (#187) - ([240d522](https://github.com/ibm/algorithm-nexus/commit/240d5223c75c60c20cfaa45f18352ae59c5a7563)) - Christian Pinto
+#### Build system
+- (**deps**) upgrade vllm to v0.26.0 in candidate and product (#196) - ([9bfc388](https://github.com/ibm/algorithm-nexus/commit/9bfc388c1f8a1e7155c297beb89a11442894a9cb)) - Christian Pinto
+- (**deps**) update dependencies (#189) - ([0e3815d](https://github.com/ibm/algorithm-nexus/commit/0e3815d353b1ce98888a065df95e8bf0007af732)) - DRL-NextGen
+- Migrate to uv-dynamic-versioning (#188) - ([7cf1ffb](https://github.com/ibm/algorithm-nexus/commit/7cf1ffbab6007eebbb6a9b5b3def0e19e52d62d9)) - Christian Pinto
+
+- - -
+
 ## [0.2.1](https://github.com/IBM/algorithm-nexus/compare/8ecb12699614fbe444ee9c03a49e42951a6a5563..0.2.1) - 2026-07-14
 
 #### Documentation

{algorithm_nexus-0.2.2 → algorithm_nexus-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: algorithm-nexus
-Version: 0.2.2
+Version: 0.3.0
 Summary: A comprehensive library for AI model delivery, testing, and benchmarking
 Project-URL: Homepage, https://github.com/IBM/algorithm-nexus
 Project-URL: Issues, https://github.com/IBM/algorithm-nexus/issues
@@ -10,6 +10,7 @@ Maintainer-email: Christian Pinto <christian.pinto@ibm.com>
 License-File: LICENSE
 Requires-Python: <3.14,>=3.12
 Provides-Extra: candidate
+Requires-Dist: biomed-multi-alignment[vllm]; extra == 'candidate'
 Requires-Dist: bmfm-targets[vllm]>=0.20.0; extra == 'candidate'
 Requires-Dist: opencv-python-headless!=5.0.0.93; extra == 'candidate'
 Requires-Dist: terrakit==0.2.0; extra == 'candidate'
@@ -22,6 +23,7 @@ Requires-Dist: pyyaml>=6.0.3; extra == 'cli'
 Requires-Dist: rich>=15.0.0; extra == 'cli'
 Requires-Dist: typer>=0.25.0; extra == 'cli'
 Provides-Extra: ecosystem
+Requires-Dist: biomed-multi-alignment; extra == 'ecosystem'
 Requires-Dist: bmfm-targets; extra == 'ecosystem'
 Requires-Dist: gridfm-graphkit==0.8.1; extra == 'ecosystem'
 Requires-Dist: terrakit>=0.2.0; extra == 'ecosystem'
@@ -30,8 +32,8 @@ Requires-Dist: tokamind; extra == 'ecosystem'
 Provides-Extra: product
 Requires-Dist: opencv-python-headless!=5.0.0.93; extra == 'product'
 Requires-Dist: terrakit==0.2.0; extra == 'product'
-Requires-Dist: terratorch[vllm]==1.2.10; extra == 'product'
-Requires-Dist: vllm==0.26.0; extra == 'product'
+Requires-Dist: terratorch[vllm]==1.2.13; extra == 'product'
+Requires-Dist: vllm<0.29.0,>=0.28.0; extra == 'product'
 Description-Content-Type: text/markdown
 
 # Algorithm Nexus

algorithm_nexus-0.3.0/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

algorithm_nexus-0.3.0/packages/biomed-multi-alignment/nexus.yaml

@@ -0,0 +1,2 @@
+package:
+  name: biomed-multi-alignment

{algorithm_nexus-0.2.2 → algorithm_nexus-0.3.0}/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",
@@ -51,8 +53,8 @@ product = [
   # This dependency is added by vLLM and TerraTorch
   "opencv-python-headless!=5.0.0.93",
   "terrakit==0.2.0",
-  "terratorch[vllm]==1.2.10",
-  "vllm==0.26.0",
+  "terratorch[vllm]==1.2.13",
+  "vllm>=0.28.0,<0.29.0",
 ]
 
 [dependency-groups]
@@ -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