MILAB-7089: Pin pgen runenv to the Generation Probability set

.changeset/pgen-polars-rtcompat.md

@@ -0,0 +1,11 @@
+---
+"@platforma-open/milaboratories.runenv-python-3.12.10-pgen": minor
+---
+
+Update the `3.12.10-pgen` run environment to the pins of the Generation Probability block: `numpy==2.4.6`, `numba==0.66.0`, `llvmlite==0.48.0`, `olga==1.3.0`, `polars==1.43.0`, `polars-runtime-32==1.43.0` and `polars-runtime-compat==1.43.0`.
+
+The block installs its `requirements.txt` with `pip --no-index --find-links <runenv packages>`. A pin that the run environment does not ship cannot resolve. The old set (`numpy==2.2.6`, `polars-lts-cpu==1.33.1`) did not match the block.
+
+`polars-lts-cpu` is removed. `polars[rtcompat]` replaces it upstream, and `polars-runtime-compat` is that runtime.
+
+`olga` and `numba` are declared under `noDeps`. Without it, their loose requirements pull the newest `numba`, `llvmlite` and `numpy` next to the pinned versions. `strictMissing` is on, so a missing wheel fails the build.

python-3.12.10-pgen/README.md

@@ -1,3 +1,7 @@
-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.
+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` for Parquet I/O.
 
-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.
+The set is pinned flat and matches the block's `requirements.txt`: `olga`, `numba`, `llvmlite`, `numpy`, `polars`, `polars-runtime-32` and `polars-runtime-compat`. The block installs it with `pip --no-index --find-links <runenv packages>`, so each pin in the block must exist here as a wheel. Change the pins here and in the block together.
+
+`polars-runtime-compat` is the `polars[rtcompat]` extra. It replaces `polars-lts-cpu`. `olga` and `numba` are declared under `noDeps`. Their loose requirements otherwise pull the newest `numba`, `llvmlite` and `numpy` next to the pinned versions.
+
+The block uses olga's `FastPgen`, which runs numba kernels. numpy 2.4.6 has only `manylinux_2_28` wheels on Linux, so the host needs glibc 2.28 or newer. macOS-Intel (`macosx-x64`) is intentionally not built — `llvmlite` ships no cp312 wheel for that platform.

python-3.12.10-pgen/config.json

@@ -2,12 +2,23 @@
   "packages": {
     "dependencies": [
       "olga==1.3.0",
-      "polars-lts-cpu==1.33.1",
-      "numpy==2.2.6"
+      "numba==0.66.0",
+      "llvmlite==0.48.0",
+      "numpy==2.4.6",
+      "polars==1.43.0",
+      "polars-runtime-32==1.43.0",
+      "polars-runtime-compat==1.43.0"
+    ],
+    "noDeps": [
+      "olga",
+      "numba"
     ],
     "skip": {},
     "overrides": {},
     "platformSpecific": {},
+    "resolution": {
+      "strictMissing": true
+    },
     "buildWheel": {}
   }
 }

python-3.12.10-pgen/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@platforma-open/milaboratories.runenv-python-3.12.10-pgen",
   "version": "0.2.0",
-  "description": "Python 3.12.10 run environment for the Generation Probability block (olga for CDR3 generation probability + numpy + polars-lts-cpu)",
+  "description": "Python 3.12.10 run environment for the Generation Probability block (olga for CDR3 generation probability + numpy + polars with the rtcompat runtime)",
   "scripts": {
     "cleanup": "rm -rf ./pkg-*.tgz ./pydist ./dist/ ./build/",
     "reset": "pnpm run cleanup && rm -rf ./node_modules ./.turbo",