@platforma-open/milaboratories.3d-structure-prediction.software 1.0.3 → 1.0.4
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 +344 -316
- package/CHANGELOG.md +6 -0
- package/Dockerfile +9 -0
- 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-1.0.4.tgz +0 -0
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.3.tgz +0 -0
package/.turbo/turbo-build.log
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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@1.0.4 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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#1 [internal] load build definition from Dockerfile
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#10 DONE
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#10 [2/7] 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 16.06 + python_abi 3.12 8_cp312 conda-forge 7kB
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#10 16.06 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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#10 16.06 + ca-certificates 2026.4.22 hbd8a1cb_0 conda-forge 131kB
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#10 16.06 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
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#10 16.06 + libzlib 1.3.2 h25fd6f3_2 conda-forge 64kB
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#10 16.06 + libgomp 15.2.0 he0feb66_18 conda-forge 603kB
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#10 16.06 + zlib 1.3.2 h25fd6f3_2 conda-forge 96kB
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#10 16.06 + zstd 1.5.7 hb78ec9c_6 conda-forge 601kB
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#10 16.06 + ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge 728kB
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#10 16.06 + libgcc 15.2.0 he0feb66_18 conda-forge 1MB
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#10 16.06 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
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#10 16.06 + libsqlite 3.53.1 h0c1763c_0 conda-forge 955kB
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#10 16.06 + openssl 3.6.2 h35e630c_0 conda-forge 3MB
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#10 16.06 + ncurses 6.6 hdb14827_0 conda-forge 919kB
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#10 16.06 + libuuid 2.42 h5347b49_0 conda-forge 40kB
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#10 16.06 + libnsl 2.0.1 hb9d3cd8_1 conda-forge 34kB
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#10 16.06 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
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#10 16.06 + libgfortran5 15.2.0 h68bc16d_18 conda-forge 2MB
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#10 16.06 + readline 8.3 h853b02a_0 conda-forge 345kB
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#10 16.06 + opencl-headers 2025.06.13 hecca717_0 conda-forge 56kB
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#10 16.06 + libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge 28kB
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#10 16.06 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
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#10 16.06 + cuda-nvrtc 12.9.86 hecca717_1 conda-forge 67MB
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#10 16.06 + libxcrypt 4.4.36 hd590300_1 conda-forge 100kB
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#10 16.06 + libgfortran 15.2.0 h69a702a_18 conda-forge 28kB
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#10 16.06 + ocl-icd 2.3.3 hb9d3cd8_0 conda-forge 107kB
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#10 16.06 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
|
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#10 16.06 + libgfortran-ng 15.2.0 h69a702a_18 conda-forge 28kB
|
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#10 16.06 + openmpi 4.1.6 hc5af2df_101 conda-forge 4MB
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154
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#10 16.06 + libblas 3.11.0 6_h4a7cf45_openblas conda-forge 19kB
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#10 16.06 + libcblas 3.11.0 6_h0358290_openblas conda-forge 19kB
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#10 16.06 + packaging 26.2 pyhc364b38_0 conda-forge 92kB
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159
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#10 16.06 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 16.06 + wheel 0.47.0 pyhd8ed1ab_0 conda-forge 33kB
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#10 16.06 + pip 26.1.1 pyh8b19718_0 conda-forge 1MB
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#10 16.06 + legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge 20kB
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#10 16.06 + hmmer 3.4 hb6cb901_4 bioconda 12MB
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#10 16.06 + numpy 2.4.3 py312h33ff503_0 conda-forge 9MB
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#10 16.06 + biopython 1.85 py312h4c3975b_2 conda-forge 3MB
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#10 16.06 + anarci 2024.05.21 pyhdfd78af_0 bioconda 1MB
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#10 16.06 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
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#10 16.06
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#10 16.06 Summary:
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#10 16.06 Install: 54 packages
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#10 16.06
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#10 16.06 Total download: 353MB
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#10 16.06 ───────────────────────────────────────────────────────────────────────────────
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#10 16.06 Transaction starting
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#10 21.51
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#10 21.65
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#10 21.65 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
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#10 21.65 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
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#10 21.65 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
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#10 21.65 mpiexec --mca opal_cuda_support 1 ...
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#10 21.65 In addition, the UCX support is also built but disabled by default.
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#10 21.65 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
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#10 21.65 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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#10 21.65 Equivalently, you can set the MCA parameters in the command line:
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#10 21.65 mpiexec --mca pml ucx --mca osc ucx ...
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#10 21.65 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
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#10 21.65 Please consult UCX's documentation for detail.
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#10 21.65
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#10 22.75
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#10 22.75 Transaction finished
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#10 22.75
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#10 22.75 To activate this environment, use:
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#10 22.75
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#10 22.75 micromamba activate base
|
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#10 22.75
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#10 22.75 Or to execute a single command in this environment, use:
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#10 22.75
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#10 22.75 micromamba run -n base mycommand
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#10 22.75
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#10 22.78 Collect information..
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#10 22.78 Cleaning index cache..
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#10 22.84 Cleaning lock files..
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#10 22.84 Package file Size
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#10 22.84 ───────────────────────────────────────────────────────────────
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#10 22.84 /opt/conda/pkgs
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#10 22.84 ───────────────────────────────────────────────────────────────
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#10 22.84
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#10 22.84 _openmp_mutex-4.5-20_gnu.conda 29kB
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#10 22.84 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
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#10 22.84 biopython-1.85-py312h4c3975b_2.conda 3MB
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#10 22.84 bzip2-1.0.8-hda65f42_9.conda 260kB
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#10 22.84 ca-certificates-2026.4.22-hbd8a1cb_0.conda 131kB
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#10 22.84 cuda-nvrtc-12.9.86-hecca717_1.conda 67MB
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#10 22.84 cuda-version-12.9-h4f385c5_3.conda 22kB
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#10 22.84 gsl-2.7-he838d99_0.tar.bz2 3MB
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#10 22.84 hmmer-3.4-hb6cb901_4.tar.bz2 12MB
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#10 22.84 ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda 728kB
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#10 22.84 legacy-cgi-2.6.4-pyhcf101f3_0.conda 20kB
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#10 22.84 libblas-3.11.0-6_h4a7cf45_openblas.conda 19kB
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#10 22.84 libcblas-3.11.0-6_h0358290_openblas.conda 19kB
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#10 22.84 libcufft-11.4.1.4-hecca717_1.conda 162MB
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#10 22.84 libexpat-2.8.0-hecca717_0.conda 77kB
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#10 22.84 libffi-3.4.6-h2dba641_1.conda 57kB
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#10 22.84 libgcc-15.2.0-he0feb66_18.conda 1MB
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#10 22.84 libgcc-ng-15.2.0-h69a702a_18.conda 28kB
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#10 22.84 libgfortran-15.2.0-h69a702a_18.conda 28kB
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#10 22.84 libgfortran-ng-15.2.0-h69a702a_18.conda 28kB
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#10 22.84 libgfortran5-15.2.0-h68bc16d_18.conda 2MB
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#10 22.84 libgomp-15.2.0-he0feb66_18.conda 603kB
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#10 22.84 liblapack-3.11.0-6_h47877c9_openblas.conda 19kB
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#10 22.84 liblzma-5.8.3-hb03c661_0.conda 113kB
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#10 22.84 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
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242
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#10 22.84 libopenblas-0.3.32-pthreads_h94d23a6_0.conda 6MB
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#10 22.84 libsqlite-3.53.1-h0c1763c_0.conda 955kB
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#10 22.84 libstdcxx-15.2.0-h934c35e_18.conda 6MB
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#10 22.84 libstdcxx-ng-15.2.0-hdf11a46_18.conda 28kB
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#10 22.84 libuuid-2.42-h5347b49_0.conda 40kB
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#10 22.84 libxcrypt-4.4.36-hd590300_1.conda 100kB
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#10 22.84 libzlib-1.3.2-h25fd6f3_2.conda 64kB
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#10 22.84 mpi-1.0-openmpi.tar.bz2 4kB
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#10 22.84 ncurses-6.6-hdb14827_0.conda 919kB
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#10 22.84 numpy-2.4.3-py312h33ff503_0.conda 9MB
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#10 22.84 ocl-icd-2.3.3-hb9d3cd8_0.conda 107kB
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#10 22.84 ocl-icd-system-1.0.0-1.tar.bz2 4kB
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#10 22.84 opencl-headers-2025.06.13-hecca717_0.conda 56kB
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#10 22.84 openmm-8.3.1-py312h50c43f0_0.conda 13MB
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256
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#10 22.84 openmpi-4.1.6-hc5af2df_101.conda 4MB
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257
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#10 22.84 openssl-3.6.2-h35e630c_0.conda 3MB
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#10 22.84 packaging-26.2-pyhc364b38_0.conda 92kB
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#10 22.84 pdbfixer-1.12-pyhd8ed1ab_1.conda 546kB
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260
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#10 22.84 pip-26.1.1-pyh8b19718_0.conda 1MB
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#10 22.84 python-3.12.10-h9e4cc4f_0_cpython.conda 31MB
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#10 22.84 python_abi-3.12-8_cp312.conda 7kB
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#10 22.84 readline-8.3-h853b02a_0.conda 345kB
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#10 22.84 scipy-1.17.1-py312h54fa4ab_0.conda 17MB
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#10 22.84 setuptools-82.0.1-pyh332efcf_0.conda 640kB
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#10 22.84 tk-8.6.13-noxft_h366c992_103.conda 3MB
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platforma-open.milaboratories.3d-structure-prediction.software.py-docker.a834563f25d9: digest: sha256:fd8a4cbd41b953004faa0fc70c9ad2ac92e0a41db2ace8a3eedc94c3f84f6780 size: 4073
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package/CHANGELOG.md
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package/Dockerfile
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@@ -55,6 +55,15 @@ 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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# Block sources (everything in src_python/).
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WORKDIR /app
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COPY . /app/
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@@ -1 +1 @@
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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/1.0.4.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.4.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.a834563f25d9","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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1
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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.a834563f25d9","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/1.0.4.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"}}}
|
package/package.json
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