Set the new env for clusTCR

.changeset/clustcr-runenv.md

@@ -0,0 +1,17 @@
+---
+"@platforma-open/milaboratories.runenv-python-3.10.21-clustcr": minor
+"@platforma-open/milaboratories.runenv-python-3": minor
+---
+
+Add the `3.10.21-clustcr` Python run environment: clusTCR (`immunewatch-clustcr`, module `imw_clustcr`)
+plus its runtime closure, faiss-cpu and polars-lts-cpu, for the clusTCR Clustering block.
+
+Python 3.10 rather than the repo's usual 3.12.10, deliberately: clusTCR requires SciPy 1.8, which no
+Python 3.11+ release supports, and that requirement is load-bearing — on SciPy 1.8 a sparse array is still
+an `spmatrix`, which is what makes clusTCR's Markov-clustering step work, while newer SciPy breaks it and
+NumPy 2 breaks its FAISS-backed paths. Targeting 3.10 lets the package be installed and used unmodified:
+no dependency metadata skipped, no numpy ceiling, and no runtime patching in the consuming block. Intended
+to be temporary — see the package README. Python 3.10 is EOL 2026-10-31.
+
+`python-louvain` ships no wheel for any version and is built on the runner via `buildWheel` with an
+explicit setuptools backend, since pip's build isolation cannot reach an index for one.

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

catalogue/package.json

@@ -44,6 +44,9 @@
       },
       "3.12.10-pgen": {
         "reference": "@platforma-open/milaboratories.runenv-python-3.12.10-pgen/dist/tengo/software/main.sw.json"
+      },
+      "3.10.21-clustcr": {
+        "reference": "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr/dist/tengo/software/main.sw.json"
       }
     }
   },
@@ -62,9 +65,10 @@
     "@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-pgen": "workspace:*"
+    "@platforma-open/milaboratories.runenv-python-3.12.10-pgen": "workspace:*",
+    "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr": "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-3.10.21-clustcr
   - python-3.12.10-pgen
   - catalogue
 

python-3.10.21-clustcr/README.md

@@ -0,0 +1,3 @@
+Python **3.10.21** run environment for the **clusTCR Clustering** block (`tcr-clustering-clusttcr`):
+clusTCR (`immunewatch-clustcr`, importable as `imw_clustcr`) plus its runtime closure and faiss-cpu, with
+polars-lts-cpu for the block runner's own I/O.

python-3.10.21-clustcr/config.json

@@ -0,0 +1,59 @@
+{
+  "packages": {
+    "dependencies": [
+      "immunewatch-clustcr==1.0.1",
+      "scipy==1.8.0",
+      "numpy==1.24.4",
+      "pandas==2.3.3",
+      "networkx==3.4.2",
+      "scikit-learn==1.7.2",
+      "markov_clustering==0.0.6.dev0",
+      "parmap==1.7.0",
+      "python-louvain==0.16",
+      "matplotlib==3.10.9",
+      "faiss-cpu==1.8.0.post1",
+      "polars-lts-cpu==1.33.1"
+    ],
+    "noDeps": [
+      "immunewatch-clustcr"
+    ],
+    "skip": {},
+    "overrides": {},
+    "platformSpecific": {},
+    "resolution": {
+      "strictMissing": true
+    },
+    "buildWheel": {
+      "python-louvain": {
+        "linux-x64": {
+          "reason": "python-louvain ships NO wheel for any version (0.1-0.16 are all sdist), so it must be built on the runner. It is pure Python, so no compiler is needed - but pip's build isolation tries to fetch the setuptools backend, and the build runs with --find-links pointing only at the local package dir, so that fetch fails. Pre-installing the backend via buildRequires makes the builder pass --no-build-isolation, which avoids the isolated env entirely.",
+          "buildRequires": [
+            "setuptools>=40.8.0",
+            "wheel"
+          ]
+        },
+        "linux-aarch64": {
+          "reason": "python-louvain ships NO wheel for any version (0.1-0.16 are all sdist), so it must be built on the runner. It is pure Python, so no compiler is needed - but pip's build isolation tries to fetch the setuptools backend, and the build runs with --find-links pointing only at the local package dir, so that fetch fails. Pre-installing the backend via buildRequires makes the builder pass --no-build-isolation, which avoids the isolated env entirely.",
+          "buildRequires": [
+            "setuptools>=40.8.0",
+            "wheel"
+          ]
+        },
+        "macosx-x64": {
+          "reason": "python-louvain ships NO wheel for any version (0.1-0.16 are all sdist), so it must be built on the runner. It is pure Python, so no compiler is needed - but pip's build isolation tries to fetch the setuptools backend, and the build runs with --find-links pointing only at the local package dir, so that fetch fails. Pre-installing the backend via buildRequires makes the builder pass --no-build-isolation, which avoids the isolated env entirely.",
+          "buildRequires": [
+            "setuptools>=40.8.0",
+            "wheel"
+          ]
+        },
+        "macosx-aarch64": {
+          "reason": "python-louvain ships NO wheel for any version (0.1-0.16 are all sdist), so it must be built on the runner. It is pure Python, so no compiler is needed - but pip's build isolation tries to fetch the setuptools backend, and the build runs with --find-links pointing only at the local package dir, so that fetch fails. Pre-installing the backend via buildRequires makes the builder pass --no-build-isolation, which avoids the isolated env entirely.",
+          "buildRequires": [
+            "setuptools>=40.8.0",
+            "wheel"
+          ]
+        }
+      }
+    }
+  }
+}

python-3.10.21-clustcr/package.json

@@ -0,0 +1,42 @@
+{
+  "name": "@platforma-open/milaboratories.runenv-python-3.10.21-clustcr",
+  "version": "0.1.0",
+  "description": "Python 3.10.21 run environment for the clusTCR Clustering block (immunewatch-clustcr on the SciPy 1.8 generation it requires)",
+  "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": "3.10.21",
+            "roots": {
+              "linux-x64": "./pydist/linux-x64",
+              "linux-aarch64": "./pydist/linux-aarch64",
+              "macosx-x64": "./pydist/macosx-x64",
+              "macosx-aarch64": "./pydist/macosx-aarch64"
+            },
+            "binDir": "bin"
+          }
+        }
+      }
+    }
+  },
+  "license": "UNLICENSED",
+  "devDependencies": {
+    "@platforma-sdk/package-builder": "catalog:",
+    "runenv-python-builder": "workspace:*",
+    "tsx": "catalog:"
+  }
+}