Add OLGA runenv

.changeset/pgen-runenv.md

@@ -0,0 +1,6 @@
+---
+'@platforma-open/milaboratories.runenv-python-3.12.10-pgen': minor
+'@platforma-open/milaboratories.runenv-python-3': minor
+---
+
+Add Python 3.12.10 run environment for the Generation Probability block: olga (CDR3 generation probability + its bundled recombination models) with numpy and polars-lts-cpu. macOS-Intel is not built (no llvmlite cp312 wheel).

.github/workflows/build.yaml

@@ -108,6 +108,11 @@ jobs:
           {"os":"macos-15-large", "arch":"amd64", "selector":"./python-3.12.10-clustering"},
           {"os":"windows-latest", "arch":"amd64", "selector":"./python-3.12.10-clustering"},
 
+          {"os":"ubuntu-large-arm64", "arch":"arm64", "selector":"./python-3.12.10-pgen"},
+          {"os":"ubuntu-large-amd64", "arch":"amd64", "selector":"./python-3.12.10-pgen"},
+          {"os":"macos-15", "arch":"arm64", "selector":"./python-3.12.10-pgen"},
+          {"os":"windows-latest", "arch":"amd64", "selector":"./python-3.12.10-pgen"},
+
           {"os":"ubuntu-large-amd64", "arch":"amd64", "selector":"./python-3.12.10-torch-cuda"},
           {"os":"macos-15", "arch":"arm64", "selector":"./python-3.12.10-torch-cuda"}
         ]

catalogue/package.json

@@ -41,6 +41,9 @@
       },
       "3.12.10-clustering": {
         "reference": "@platforma-open/milaboratories.runenv-python-3.12.10-clustering/dist/tengo/software/main.sw.json"
+      },
+      "3.12.10-pgen": {
+        "reference": "@platforma-open/milaboratories.runenv-python-3.12.10-pgen/dist/tengo/software/main.sw.json"
       }
     }
   },
@@ -58,7 +61,8 @@
     "@platforma-open/milaboratories.runenv-python-3.12.10-scientific-slim": "workspace:*",
     "@platforma-open/milaboratories.runenv-python-3.12.10-humanness": "workspace:*",
     "@platforma-open/milaboratories.runenv-python-3.12.10-torch-cuda": "workspace:*",
-    "@platforma-open/milaboratories.runenv-python-3.12.10-clustering": "workspace:*"
+    "@platforma-open/milaboratories.runenv-python-3.12.10-clustering": "workspace:*",
+    "@platforma-open/milaboratories.runenv-python-3.12.10-pgen": "workspace:*"
   },
   "devDependencies": {
     "@platforma-sdk/package-builder": "catalog:"

checker/whitelists/macosx-aarch64.json

@@ -3,7 +3,7 @@
     "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
   },
   "numba-0.*-macosx_*_arm64.whl": {
-    "numba.np.ufunc.omppool": "'/Users/runner/miniconda3/envs/test/lib/libomp.dylib' (no such file)"
+    "numba.np.ufunc.omppool": "Reason: no LC_RPATH's found"
   },
   "numpy-1.26.4-cp312-cp312-macosx_11_0_arm64.whl": {
     "numpy.core._umath_tests": "cannot load _umath_tests module"

pnpm-workspace.yaml

@@ -11,6 +11,7 @@ packages:
   - python-3.12.10-humanness
   - python-3.12.10-torch-cuda
   - python-3.12.10-clustering
+  - python-3.12.10-pgen
   - catalogue
 
 catalog:

python-3.12.10-pgen/CHANGELOG.md

@@ -0,0 +1 @@
+# @platforma-open/milaboratories.runenv-python-3.12.10-pgen

python-3.12.10-pgen/README.md

@@ -0,0 +1,3 @@
+Python 3.12.10 run environment for the Generation Probability block (`generation-probability`): `olga` (V(D)J generation-probability computation for CDR3s, including its 10 bundled recombination models) plus `numpy` and `polars-lts-cpu` for Parquet I/O, and transitives.
+
+Note: olga declares `numba` as a hard dependency (pulling `llvmlite`/LLVM), so these are bundled even though the block only uses olga's pure-NumPy `compute_aa_CDR3_pgen` path, not olga's numba fast-path. macOS-Intel (`macosx-x64`) is intentionally not built — `llvmlite` ships no cp312 wheel for that platform.

python-3.12.10-pgen/config.json

@@ -0,0 +1,13 @@
+{
+  "packages": {
+    "dependencies": [
+      "olga==1.3.0",
+      "polars-lts-cpu==1.33.1",
+      "numpy==2.2.6"
+    ],
+    "skip": {},
+    "overrides": {},
+    "platformSpecific": {},
+    "buildWheel": {}
+  }
+}

python-3.12.10-pgen/package.json

@@ -0,0 +1,42 @@
+{
+  "name": "@platforma-open/milaboratories.runenv-python-3.12.10-pgen",
+  "version": "0.1.0",
+  "description": "Python 3.12.10 run environment for the Generation Probability block (olga for CDR3 generation probability + numpy + polars-lts-cpu)",
+  "scripts": {
+    "cleanup": "rm -rf ./pkg-*.tgz ./pydist ./dist/ ./build/",
+    "reset": "pnpm run cleanup && rm -rf ./node_modules ./.turbo",
+    "build": "pl-py-builder",
+    "after-prebuild": "pl-pkg publish packages",
+    "before-publish": "pl-pkg prepublish"
+  },
+  "files": [
+    "dist/"
+  ],
+  "block-software": {
+    "entrypoints": {
+      "main": {
+        "environment": {
+          "artifact": {
+            "type": "environment",
+            "runtime": "python",
+            "registry": "platforma-open",
+            "python-version": "3.12.10",
+            "roots": {
+              "linux-x64": "./pydist/linux-x64",
+              "linux-aarch64": "./pydist/linux-aarch64",
+              "macosx-aarch64": "./pydist/macosx-aarch64",
+              "windows-x64": "./pydist/windows-x64"
+            },
+            "binDir": "bin"
+          }
+        }
+      }
+    }
+  },
+  "license": "UNLICENSED",
+  "devDependencies": {
+    "@platforma-sdk/package-builder": "catalog:",
+    "runenv-python-builder": "workspace:*",
+    "tsx": "catalog:"
+  }
+}