mchernyshev/milab 6862 hilary

.changeset/hilary-runenv.md

@@ -0,0 +1,18 @@
+---
+"@platforma-open/milaboratories.runenv-python-3.12.10-hilary": minor
+"@platforma-open/milaboratories.runenv-python-3": minor
+---
+
+Add the `3.12.10-hilary` Python run environment: HILARy (`hilary`, invoked as `python -m hilary`) plus its
+runtime closure, for the Lineage Trees block's clonal-lineage clustering.
+
+`hilary` is declared under `noDeps`, following the `3.10.21-clustcr` precedent. The builder resolves each
+declared package's closure separately, so HILARy's loose requirements (`numpy<3`, `scipy<2,>1.11`,
+`pandas<3,>=2.2`) otherwise pulled the newest of each on top of the pinned versions and vendored duplicates.
+
+`hilary` ships a universal `py3-none-any` wheel, so nothing here compiles.
+
+There is no Linux ARM64 root, and the CI matrix omits it. `atriegc`, HILARy's trie-based CDR3 neighbour
+search, publishes no Linux ARM64 wheel for any Python version, and its 0.0.4 sdist cannot substitute: it
+ships `src/main.cpp` but omits the `trie_container.hpp` header that file includes, so a source build fails at
+the first compile.

.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-amd64", "arch":"amd64", "selector":"./python-3.12.10-hilary"},
+          {"os":"macos-15", "arch":"arm64", "selector":"./python-3.12.10-hilary"},
+          {"os":"macos-15-large", "arch":"amd64", "selector":"./python-3.12.10-hilary"},
+          {"os":"windows-latest", "arch":"amd64", "selector":"./python-3.12.10-hilary"},
+
           {"os":"ubuntu-large-arm64", "arch":"arm64", "selector":"./python-3.10.21-clustcr"},
           {"os":"ubuntu-large-amd64", "arch":"amd64", "selector":"./python-3.10.21-clustcr"},
           {"os":"macos-15", "arch":"arm64", "selector":"./python-3.10.21-clustcr"},

catalogue/package.json

@@ -47,6 +47,9 @@
       },
       "3.10.21-clustcr": {
         "reference": "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr/dist/tengo/software/main.sw.json"
+      },
+      "3.12.10-hilary": {
+        "reference": "@platforma-open/milaboratories.runenv-python-3.12.10-hilary/dist/tengo/software/main.sw.json"
       }
     }
   },
@@ -66,7 +69,8 @@
     "@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-pgen": "workspace:*",
-    "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr": "workspace:*"
+    "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr": "workspace:*",
+    "@platforma-open/milaboratories.runenv-python-3.12.10-hilary": "workspace:*"
   },
   "devDependencies": {
     "@platforma-sdk/package-builder": "catalog:"

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-hilary
   - python-3.10.21-clustcr
   - python-3.12.10-pgen
   - catalogue

python-3.12.10-hilary/README.md

@@ -0,0 +1,16 @@
+Run environment for the HILARy package used by the Lineage Trees block.
+
+Everything is pinned explicitly. A variant does not inherit the base environment's
+dependency list, so HILARy's whole runtime closure is named here.
+
+`hilary` is under `noDeps` because the builder resolves each declared package's
+closure separately, so HILARy's own loose requirements would vendor a second,
+newer copy of numpy, scipy, pandas, tqdm and setuptools alongside the pins. A
+consuming block should pin what it wants in its own requirements, since that is
+what decides the installed versions.
+
+There is no Linux ARM64 root. `atriegc`, HILARy's trie-based CDR3 neighbour search,
+publishes no Linux ARM64 wheel, and its 0.0.4 sdist cannot substitute: it ships
+`src/main.cpp` but omits the `trie_container.hpp` header that file includes, so a
+source build fails at the first compile. The other four platforms all have wheels
+for every pin, which is why `strictMissing` is on.

python-3.12.10-hilary/config.json

@@ -0,0 +1,28 @@
+{
+  "packages": {
+    "dependencies": [
+      "hilary==1.2.4",
+      "atriegc==0.0.4",
+      "structlog==22.3.0",
+      "textdistance==4.6.3",
+      "typer==0.27.2",
+      "tqdm==4.69.0",
+      "openpyxl==3.1.5",
+      "pandas==2.2.3",
+      "scipy==1.15.3",
+      "numpy==2.2.6",
+      "setuptools==83.0.0"
+    ],
+    "noDeps": [
+      "hilary"
+    ],
+    "skip": {},
+    "overrides": {},
+    "platformSpecific": {},
+    "resolution": {
+      "strictMissing": true
+    },
+    "forceSource": {},
+    "buildWheel": {}
+  }
+}

python-3.12.10-hilary/package.json

@@ -0,0 +1,42 @@
+{
+  "name": "@platforma-open/milaboratories.runenv-python-3.12.10-hilary",
+  "version": "0.1.0",
+  "description": "Python 3.12.10 run environment for the Lineage Trees block (HILARy clonal-lineage clustering and its numeric stack)",
+  "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",
+              "macosx-x64": "./pydist/macosx-x64",
+              "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:"
+  }
+}