From 06121fdfda1b13899d6484efd35f37e69716deff Mon Sep 17 00:00:00 2001 From: Julen Mendieta Date: Wed, 24 Jun 2026 13:08:01 +0200 Subject: [PATCH 1/2] Include dependencies needed for the new sequence embedding models --- .changeset/torch-cuda-ablang2-sceptr.md | 11 +++++++++++ python-3.12.10-torch-cuda/config.json | 5 ++++- 2 files changed, 15 insertions(+), 1 deletion(-) create mode 100644 .changeset/torch-cuda-ablang2-sceptr.md diff --git a/.changeset/torch-cuda-ablang2-sceptr.md b/.changeset/torch-cuda-ablang2-sceptr.md new file mode 100644 index 0000000..ea5ec39 --- /dev/null +++ b/.changeset/torch-cuda-ablang2-sceptr.md @@ -0,0 +1,11 @@ +--- +'@platforma-open/milaboratories.runenv-python-3.12.10-torch-cuda': minor +--- + +Add antibody (AbLang2) and TCR (SCEPTR) specialist embedding libraries plus rdkit to the torch-cuda run environment. + +- `ablang2==0.2.1` — AbLang2 antibody language model (pulls einops + rotary-embedding-torch) +- `sceptr==1.2.0` — SCEPTR paired-chain TCR model (pulls libtcrlm + tidytcells + pandas + blosum) +- `rdkit==2026.3.3` — cheminformatics toolkit for the PeptideCLM-2 amino-acid→SMILES conversion (pulls Pillow) + +All install conflict-free on top of the existing pins (transformers 4.53.2, polars-lts-cpu 1.33.1, numpy 2.2.6, pyarrow 21.0.0, torch 2.7.0); `pip check` clean. diff --git a/python-3.12.10-torch-cuda/config.json b/python-3.12.10-torch-cuda/config.json index e50636f..8ae2b23 100644 --- a/python-3.12.10-torch-cuda/config.json +++ b/python-3.12.10-torch-cuda/config.json @@ -9,7 +9,10 @@ "transformers==4.53.2", "polars-lts-cpu==1.33.1", "numpy==2.2.6", - "pyarrow==21.0.0" + "pyarrow==21.0.0", + "ablang2==0.2.1", + "sceptr==1.2.0", + "rdkit==2026.3.3" ], "platformSpecific": { "linux-x64": { From d4487b129ce7e3510749cb71c8d7aab65c36483d Mon Sep 17 00:00:00 2001 From: Julen Mendieta Date: Wed, 24 Jun 2026 14:55:56 +0200 Subject: [PATCH 2/2] Solve CI issue --- checker/whitelists/linux-x64.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/checker/whitelists/linux-x64.json b/checker/whitelists/linux-x64.json index 9841b80..af558ce 100644 --- a/checker/whitelists/linux-x64.json +++ b/checker/whitelists/linux-x64.json @@ -185,6 +185,9 @@ "pynvjitlink_cu12-0.7.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl": { "pynvjitlink._nvjitlinklib": "libcuda.so.1: cannot open shared object file: No such file or directory" }, + "rdkit-2026.3.3-cp312-cp312-manylinux_2_28_x86_64.whl": { + "rdkit.Chem.Draw.rdMolDraw2D": "libXrender.so.1: cannot open shared object file: No such file or directory" + }, "scipy-1.*.whl": { "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module", "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'" @@ -202,6 +205,10 @@ "torch-2.9.1+cpu-cp312-cp312-manylinux_2_28_x86_64.whl": { "functorch._C": "initialization failed" }, + "torch-2.12.1+cu126-cp312-cp312-manylinux_2_28_x86_64.whl": { + "functorch._C": "initialization failed", + "torch.lib.libcaffe2_nvrtc": "libcuda.so.1: cannot open shared object file" + }, "torchaudio-2.7.0+cpu-cp312-cp312-manylinux_2_28_x86_64.whl": { "torchaudio.lib._torchaudio_sox": "libtorchaudio_sox.so: cannot open shared object file: No such file or directory", "torchaudio.lib.libtorchaudio_sox": "libsox.so: cannot open shared object file: No such file or directory",