@platforma-open/milaboratories.3d-structure-prediction.software 1.0.6 → 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 +334 -347
- package/CHANGELOG.md +6 -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-1.0.6.tgz +0 -0
package/.turbo/turbo-build.log
CHANGED
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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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> pl-pkg build
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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 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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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 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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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 22.53 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 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 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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#10 22.92 libgfortran-ng-15.2.0-h69a702a_19.conda 28kB
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#10 22.92 libgfortran5-15.2.0-h68bc16d_19.conda 2MB
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#10 22.92 libgomp-15.2.0-he0feb66_19.conda 604kB
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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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# @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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package/Dockerfile
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--extra-index-url https://download.pytorch.org/whl/cpu \
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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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|
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help="
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|
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return
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|
missing = [
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|
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process_batch(
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