@platforma-open/milaboratories.3d-structure-prediction.software 1.0.5 → 1.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/.turbo/turbo-build.log +336 -349
- package/CHANGELOG.md +12 -0
- package/Dockerfile +0 -9
- package/dist/artifacts/py-archive/archive.json +1 -1
- package/dist/artifacts/py-docker/docker_x64.json +1 -1
- package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
- package/package.json +1 -1
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.7.tgz +0 -0
- package/src_python/run_immunebuilder.py +16 -29
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.5.tgz +0 -0
package/.turbo/turbo-build.log
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@@ -1,6 +1,6 @@
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WARN Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.
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> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.7 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
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[32minfo[39m: Building docker images...
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#0 building with "default" instance using docker driver
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#10 [2/6] RUN micromamba install -y -n base -c bioconda -c conda-forge python=3.12.10 anarci hmmer biopython=1.85 openmm=8.3.1 pdbfixer=1.12.0 numpy=2.4.3 scipy=1.17.1 && micromamba clean --all --yes
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#10 15.95 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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#10 15.95 + ca-certificates 2026.5.20 hbd8a1cb_0 conda-forge 130kB
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#10 15.95 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
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#10 15.95 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
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#10 15.95 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
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#10 15.95 + packaging 26.2 pyhc364b38_0 conda-forge 92kB
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#10 15.95 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 15.95 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
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#10 15.95 Install: 54 packages
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#10 15.95 Total download: 353MB
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#10 21.17
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#10 21.31
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#10 21.31 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
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#10 21.31 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
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#10 21.31 In addition, the UCX support is also built but disabled by default.
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#10 21.31 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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#10 21.31 Equivalently, you can set the MCA parameters in the command line:
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#10 21.31 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
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#10 21.31 Please consult UCX's documentation for detail.
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#10 22.50 To activate this environment, use:
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#10 22.50 micromamba activate base
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#10 22.50 micromamba run -n base mycommand
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#10 22.53 Collect information..
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#10 22.53 Cleaning index cache..
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#10 22.92 Cleaning lock files..
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#10 22.92 Package file Size
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#10 22.92 ───────────────────────────────────────────────────────────────
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#10 22.92 /opt/conda/pkgs
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#10 22.92 ───────────────────────────────────────────────────────────────
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#10 22.92
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#10 22.92 _openmp_mutex-4.5-20_gnu.conda 29kB
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#10 22.92 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
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#10 22.92 biopython-1.85-py312h4c3975b_2.conda 3MB
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#10 22.92 bzip2-1.0.8-hda65f42_9.conda 260kB
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#10 22.92 cuda-nvrtc-12.9.86-hecca717_1.conda 67MB
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#10 22.92 ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda 728kB
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#10 22.92 libblas-3.11.0-8_h4a7cf45_openblas.conda 19kB
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#10 22.92 libcblas-3.11.0-8_h0358290_openblas.conda 19kB
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#10 22.92 libcufft-11.4.1.4-hecca717_1.conda 162MB
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#10 22.92 libexpat-2.8.1-hecca717_0.conda 77kB
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#10 22.92 libffi-3.4.6-h2dba641_1.conda 57kB
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#10 22.92 libgcc-15.2.0-he0feb66_19.conda 1MB
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#10 22.92 libgcc-ng-15.2.0-h69a702a_19.conda 28kB
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#10 22.92 libgfortran-15.2.0-h69a702a_19.conda 28kB
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tag: 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc'
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archive: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.7.tgz'
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[32minfo[39m: Publishing docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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[32minfo[39m: Publishing docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc' using alternative tag 'quay.io/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc'
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc: digest: sha256:98396c40c2a63bad68708457c032a5d7474686a8ebd79a23f3162ef5f6fa3cd6 size: 3860
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package/CHANGELOG.md
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# @platforma-open/milaboratories.3d-structure-prediction.software
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## 1.0.7
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### Patch Changes
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- 8aeaff0: Load ImmuneBuilder model weights from a published Platforma asset (`immunebuilder-weights-assets`) instead of downloading them from Zenodo at runtime. The matching per-mode asset is mounted into each batch workdir and passed to ImmuneBuilder via `--weights-dir`. Removes the pre-warmup step, the per-batch warmup sentinel wiring, and the Docker image weight bake.
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## 1.0.6
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### Patch Changes
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## 1.0.5
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package/Dockerfile
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@@ -55,15 +55,6 @@ RUN pip install --no-cache-dir \
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--extra-index-url https://download.pytorch.org/whl/cpu \
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-r /tmp/requirements.txt
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# Pre-download model weights into the image. ImmuneBuilder otherwise writes
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# them into its own site-packages dir (/opt/conda/.../ImmuneBuilder/trained_model/)
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# on first use. That works locally because we're root, but cloud runtimes
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# run as a non-root user and hit PermissionError. Doing the download at
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# build time bakes ~400 MB of weights into the image and the runtime is
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# read-only there, which is what we want.
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RUN python -c "from ImmuneBuilder import ABodyBuilder2, NanoBodyBuilder2; ABodyBuilder2(); NanoBodyBuilder2()" \
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&& chmod -R a+rX /opt/conda/lib/python3.12/site-packages/ImmuneBuilder/trained_model
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{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.
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{"type":"python","platform":"linux-x64","registryURL":"https://bin.pl-open.science/","registryName":"platforma-open","remoteArtifactLocation":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.7.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.7.tgz"}
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{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
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{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.
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{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fbb456fbfccc","entrypoint":["/usr/local/bin/_entrypoint.sh"],"cmd":["python","/app/run_immunebuilder.py"],"pkg":"/app"},"binary":{"type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.7.tgz","cmd":["python","{pkg}/run_immunebuilder.py"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-python-3:3.12.10-atls","type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.runenv-python-3.12.10-atls/main/1.2.7-{os}-{arch}.tgz","python-version":"3.12.10","envVars":[],"binDir":"bin"},"toolset":"pip","dependencies":{"requirements":"requirements.txt"}}}
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def _load_predictor(mode: str):
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def _load_predictor(mode: str, weights_dir: str | None = None):
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# weights_dir points at the asset mounted into the workdir (see
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# predict-batch.tpl.tengo). ImmuneBuilder loads `<weights_dir>/<model_file>`
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# asset present, never happens. weights_dir=None preserves upstream
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# download-to-site-packages behaviour for local/manual runs.
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weights_dir: str | None = None,
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) -> None:
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pdb_dir.mkdir(parents=True, exist_ok=True)
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_set_seed(seed)
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predictor = _load_predictor(mode, weights_dir)
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"""
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if sentinel is not None:
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sentinel.write_text(
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)
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parser = argparse.ArgumentParser()
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parser.add_argument("--mode", choices=["ABodyBuilder2", "NanoBodyBuilder2"], required=True)
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help="
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parser.add_argument("--weights-dir", default=None,
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help="Directory holding the ImmuneBuilder model weights "
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"(mounted from the weights asset). When omitted, "
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"ImmuneBuilder downloads them on first use.")
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parser.add_argument("--input", help="Batch TSV with clonotypeKey, heavyChain[, lightChain]")
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parser.add_argument("--output-dir", help="Directory for per-clonotype PDB files")
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parser.add_argument("--manifest", help="Path to manifest.tsv")
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help="Confidence threshold (Å) used to derive confidentCount in summary.json")
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warmup(args.mode, Path(args.sentinel) if args.sentinel else None)
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return
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missing = [
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("--input", args.input),
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parser.error(f"the following arguments are required: {', '.join(missing)}")
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process_batch(
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