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MILAB-6679: add the 3.12.10-antibody-design python run environment #108

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MILAB-6679: add the 3.12.10-antibody-design python run environment #108

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a82fae1
MILAB-6679: add the 3.12.10-antibody-design python run environment
popoffvg Sep 14, 2026
1e5433d
MILAB-6679: stop the antibody-design env vendoring a second numpy
popoffvg Sep 15, 2026
5053716
MILAB-6679: hold the antibody-design env to its own pins
popoffvg Sep 17, 2026
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22 changes: 22 additions & 0 deletions .changeset/antibody-design-runenv.md
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---
"@platforma-open/milaboratories.runenv-python-3.12.10-antibody-design": minor
"@platforma-open/milaboratories.runenv-python-3": minor
---

Add the `3.12.10-antibody-design` Python run environment for the Antibody Variant Designer block: AntiFold
inverse folding (`torch`, `torch_geometric`), Sapiens humanness (`transformers`), SASA exposure (`freesasa`)
and `promb`, with the whole runtime closure pinned flat.

Both of the block's software packages install this set with pip on every run today, about 2 GiB of it. Shipping
it as a run environment moves that cost to build time.

torch is declared per platform. linux-x64 takes `torch==2.2.2+cpu` from `https://download.pytorch.org/whl/cpu`,
because the PyPI wheel pulls twelve `nvidia-*` CUDA packages this block never uses; the other platforms take
the plain pin, whose PyPI wheels are CPU builds already.

`freesasa` is built on the runner for all five platforms — it publishes no cp312 wheel anywhere — following the
base `3.12.10` environment. `biotite` is built on the runner for linux-aarch64 only, which has no wheel for any
version.

`biotite` is pinned at 0.39.0, not the 0.38.\* the block currently asks for: 0.38 publishes no wheel usable
under Python 3.12, so the block's own bound has to move with this.
6 changes: 6 additions & 0 deletions .github/workflows/build.yaml
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Expand Up @@ -113,6 +113,12 @@ jobs:
{"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-amd64", "arch":"amd64", "selector":"./python-3.12.10-antibody-design"},
{"os":"ubuntu-large-arm64", "arch":"arm64", "selector":"./python-3.12.10-antibody-design"},
{"os":"macos-15", "arch":"arm64", "selector":"./python-3.12.10-antibody-design"},
{"os":"macos-15-large", "arch":"amd64", "selector":"./python-3.12.10-antibody-design"},
{"os":"windows-latest", "arch":"amd64", "selector":"./python-3.12.10-antibody-design"},

{"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"},
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6 changes: 5 additions & 1 deletion catalogue/package.json
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Expand Up @@ -50,6 +50,9 @@
},
"3.12.10-hilary": {
"reference": "@platforma-open/milaboratories.runenv-python-3.12.10-hilary/dist/tengo/software/main.sw.json"
},
"3.12.10-antibody-design": {
"reference": "@platforma-open/milaboratories.runenv-python-3.12.10-antibody-design/dist/tengo/software/main.sw.json"
}
}
},
Expand All @@ -70,7 +73,8 @@
"@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-3.12.10-hilary": "workspace:*"
"@platforma-open/milaboratories.runenv-python-3.12.10-hilary": "workspace:*",
"@platforma-open/milaboratories.runenv-python-3.12.10-antibody-design": "workspace:*"
},
"devDependencies": {
"@platforma-sdk/package-builder": "catalog:"
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29 changes: 29 additions & 0 deletions checker/whitelists/linux-aarch64.json
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Expand Up @@ -24,5 +24,34 @@
"torio.lib.libtorio_ffmpeg4": "libavutil.so.56: cannot open shared object file: No such file or directory",
"torio.lib.libtorio_ffmpeg5": "libavutil.so.57: cannot open shared object file: No such file or directory",
"torio.lib.libtorio_ffmpeg6": "libavutil.so.58: cannot open shared object file: No such file or directory"
},
"torch-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl": {
"functorch._C": "initialization failed"
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"biotite.sequence.phylo.upgma": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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"biotite.structure.io.pdb.hybrid36": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.sasa": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()"
}
}
29 changes: 29 additions & 0 deletions checker/whitelists/linux-x64.json
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Expand Up @@ -224,5 +224,34 @@
"ucxx._lib.libucxx": "libpython3.12.so.1.0: cannot open shared object file: No such file or directory",
"ucxx.examples.python_future_task_app": "libpython3.12.so.1.0: cannot open shared object file: No such file or directory",
"ucxx.lib64.libucxx_python": "libpython3.12.so.1.0: cannot open shared object file: No such file or directory"
},
"torch-2.2.2+cpu-cp312-cp312-linux_x86_64.whl": {
"functorch._C": "initialization failed"
},
"biotite-0.39.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl": {
"biotite.sequence.align.banded": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmeralphabet": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmersimilarity": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmertable": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.localgapped": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.localungapped": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.multiple": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.pairwise": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.permutation": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.selector": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.tracetable": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.codec": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.phylo.nj": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.phylo.tree": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.phylo.upgma": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.bonds": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.celllist": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.charges": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.convertarray": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.convertfile": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.decode": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.encode": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.pdb.hybrid36": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.sasa": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()"
}
}
29 changes: 29 additions & 0 deletions checker/whitelists/macosx-aarch64.json
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Expand Up @@ -34,5 +34,34 @@
"torio.lib.libtorio_ffmpeg4": "Reason: no LC_RPATH's found",
"torio.lib.libtorio_ffmpeg5": "Reason: no LC_RPATH's found",
"torio.lib.libtorio_ffmpeg6": "Reason: no LC_RPATH's found"
},
"torch-2.2.2-cp312-none-macosx_11_0_arm64.whl": {
"functorch._C": "initialization failed"
},
"biotite-0.39.0-cp312-cp312-macosx_11_0_arm64.whl": {
"biotite.sequence.align.banded": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmeralphabet": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmersimilarity": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.kmertable": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.localgapped": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.localungapped": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.multiple": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.pairwise": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.sequence.align.permutation": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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"biotite.sequence.codec": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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"biotite.structure.charges": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.convertarray": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.convertfile": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
"biotite.structure.io.mmtf.decode": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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}
}
26 changes: 26 additions & 0 deletions checker/whitelists/macosx-x64.json
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Expand Up @@ -23,5 +23,31 @@
},
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"biotite.sequence.align.kmeralphabet": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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"biotite.sequence.align.kmertable": "numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()",
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}
}
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