@platforma-open/milaboratories.3d-structure-prediction.software 1.0.1 → 1.0.3
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 +375 -243
- package/CHANGELOG.md +12 -0
- package/Dockerfile +63 -0
- package/dist/artifacts/py-archive/archive.json +1 -1
- package/dist/artifacts/{py-archive → py-docker}/docker_x64.json +1 -1
- package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
- package/package.json +13 -1
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.3.tgz +0 -0
- package/dist/docker/Dockerfile-py-archive +0 -22
- package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.1.tgz +0 -0
package/.turbo/turbo-build.log
CHANGED
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@@ -1,276 +1,408 @@
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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@1.0.3 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
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[32minfo[39m: Building docker image for 'py-
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[32minfo[39m: Building docker image for 'py-docker'...
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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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#1 transferring dockerfile: 2.53kB done
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#4 docker-image://docker.io/docker/dockerfile:1@sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769
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#4 resolve docker.io/docker/dockerfile:1@sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769 done
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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 15.41 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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#10 15.41 + libsqlite 3.53.1 h0c1763c_0 conda-forge 955kB
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#10 15.41 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
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#10 15.41 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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#10 15.41 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
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#10 15.41 Install: 54 packages
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#10 15.41 Total download: 353MB
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#10 21.24
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#10 21.39 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
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#10 21.39 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
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#10 21.39 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
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#10 21.39 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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#10 21.39 Please consult UCX's documentation for detail.
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#10 22.51 Transaction finished
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#10 22.51 To activate this environment, use:
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#10 22.51 micromamba activate base
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#10 22.51 Or to execute a single command in this environment, use:
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#10 22.51 micromamba run -n base mycommand
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#10 22.51
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#10 22.54 Collect information..
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#10 22.54 Cleaning index cache..
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#10 22.70 Cleaning lock files..
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#10 22.70 Package file Size
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#10 22.70 ───────────────────────────────────────────────────────────────
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#10 22.70 /opt/conda/pkgs
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#10 22.70 ───────────────────────────────────────────────────────────────
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#10 22.70
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#10 22.70 _openmp_mutex-4.5-20_gnu.conda 29kB
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#10 22.70 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
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#10 22.70 biopython-1.85-py312h4c3975b_2.conda 3MB
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#10 22.70 bzip2-1.0.8-hda65f42_9.conda 260kB
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#10 22.70 libcblas-3.11.0-6_h0358290_openblas.conda 19kB
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#10 22.70 libcufft-11.4.1.4-hecca717_1.conda 162MB
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#10 22.70 libffi-3.4.6-h2dba641_1.conda 57kB
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#10 22.70 libgcc-15.2.0-he0feb66_18.conda 1MB
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#10 22.70 libgcc-ng-15.2.0-h69a702a_18.conda 28kB
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#10 22.70 libgfortran5-15.2.0-h68bc16d_18.conda 2MB
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#10 22.70 libgomp-15.2.0-he0feb66_18.conda 603kB
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#10 22.70 liblapack-3.11.0-6_h47877c9_openblas.conda 19kB
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#10 22.70 liblzma-5.8.3-hb03c661_0.conda 113kB
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#10 22.70 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
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#10 22.70 libopenblas-0.3.32-pthreads_h94d23a6_0.conda 6MB
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#10 22.70 libsqlite-3.53.1-h0c1763c_0.conda 955kB
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#10 22.70 libstdcxx-15.2.0-h934c35e_18.conda 6MB
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#10 22.70 libstdcxx-ng-15.2.0-hdf11a46_18.conda 28kB
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#10 22.70 libuuid-2.42-h5347b49_0.conda 40kB
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#10 22.70 libxcrypt-4.4.36-hd590300_1.conda 100kB
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#10 22.70 libzlib-1.3.2-h25fd6f3_2.conda 64kB
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#10 22.70 mpi-1.0-openmpi.tar.bz2 4kB
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#10 22.70 ncurses-6.6-hdb14827_0.conda 919kB
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#10 22.70 numpy-2.4.3-py312h33ff503_0.conda 9MB
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#10 22.70 ocl-icd-2.3.3-hb9d3cd8_0.conda 107kB
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#10 22.70 ocl-icd-system-1.0.0-1.tar.bz2 4kB
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#10 22.70 opencl-headers-2025.06.13-hecca717_0.conda 56kB
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#10 22.70 openmm-8.3.1-py312h50c43f0_0.conda 13MB
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#10 22.70 openmpi-4.1.6-hc5af2df_101.conda 4MB
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#10 22.70 openssl-3.6.2-h35e630c_0.conda 3MB
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#10 22.70 packaging-26.2-pyhc364b38_0.conda 92kB
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#10 22.70 pdbfixer-1.12-pyhd8ed1ab_1.conda 546kB
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#10 22.70 pip-26.1.1-pyh8b19718_0.conda 1MB
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#10 22.70 python-3.12.10-h9e4cc4f_0_cpython.conda 31MB
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#10 22.70 python_abi-3.12-8_cp312.conda 7kB
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#10 22.70 readline-8.3-h853b02a_0.conda 345kB
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#10 22.70 scipy-1.17.1-py312h54fa4ab_0.conda 17MB
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# @platforma-open/milaboratories.3d-structure-prediction.software
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### Patch Changes
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package/Dockerfile
ADDED
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@@ -0,0 +1,63 @@
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1
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+
# syntax=docker/dockerfile:1
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2
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#
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# Cloud-side image for the 3D-structure-prediction block.
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#
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# Why this exists: pl-pkg's auto-generated Dockerfile uses python:3.12-slim
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# and installs only requirements.txt deps. ImmuneBuilder relies at import
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# time on `anarci` and `pdbfixer`, neither of which are usable from PyPI
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# (anarci is yanked; pdbfixer is sdist-only and lacks several runtime
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# pieces). Locally the runenv ships hand-bundled anarci + HMMER + databases;
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# the cloud autogen ignores all that. This Dockerfile closes the gap by
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# pulling those packages from bioconda, then layering ImmuneBuilder + torch
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# via pip on top.
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#
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# pl-pkg invokes `docker build <context> -f Dockerfile`. Context is set to
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# `src_python` in package.json, so all COPY paths below are relative to
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# software/src_python/.
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FROM mambaorg/micromamba:1.5.10
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USER root
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# anarci and hmmer are deliberately left unpinned: bioconda's recipe builds
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# the HMM database at install time and the database depends on the HMMER
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# version, so locking the hash for both pkgs at once is fragile across
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# bioconda updates. After the first successful CI build, run
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# micromamba list -n base anarci hmmer
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# inside the image and copy the resulting build strings here if you need
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# bit-identical reproducibility.
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RUN micromamba install -y -n base -c bioconda -c conda-forge \
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python=3.12.10 \
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anarci \
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hmmer \
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biopython=1.85 \
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openmm=8.3.1 \
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pdbfixer=1.12.0 \
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numpy=2.4.3 \
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scipy=1.17.1 \
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&& micromamba clean --all --yes
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# Activate the base env for every subsequent RUN/CMD layer so pip and
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# python resolve to /opt/conda/{bin,lib}.
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ARG MAMBA_DOCKERFILE_ACTIVATE=1
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ENV PATH=/opt/conda/bin:$PATH
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# Make conda's libstdc++ (and friends) win over the older system libs in
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# /lib/x86_64-linux-gnu. Pip-installed extension wheels (manylinux2014+)
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# expect a recent CXXABI; the base image's system libstdc++ predates it.
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ENV LD_LIBRARY_PATH=/opt/conda/lib
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# Layer pip-only deps (ImmuneBuilder + CPU torch). Anything bioconda
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# already provides is re-resolved by pip; pinned versions in
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# requirements.txt match the conda packages so this is a no-op for those.
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COPY requirements.txt /tmp/requirements.txt
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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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# Block sources (everything in src_python/).
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WORKDIR /app
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COPY . /app/
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ENV PYTHONPATH=/app
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CMD ["python", "/app/run_immunebuilder.py"]
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@@ -1 +1 @@
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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/1.0.3.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.3.tgz"}
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@@ -1 +1 @@
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1
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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-
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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.e8cc067379a9","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
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@@ -1 +1 @@
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1
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-
{"name":"@platforma-open/milaboratories.3d-structure-prediction.software:immunebuilder-predict","binary":{"type":"python","registry":"platforma-open","package":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.
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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.e8cc067379a9","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/1.0.3.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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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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1
1
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{
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"name": "@platforma-open/milaboratories.3d-structure-prediction.software",
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"version": "1.0.
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"version": "1.0.3",
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"type": "module",
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"description": "Block Software",
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"block-software": {
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@@ -14,6 +14,11 @@
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"requirements": "requirements.txt"
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},
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"root": "./src_python"
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},
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"py-docker": {
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"type": "docker",
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"context": "src_python",
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"dockerfile": "Dockerfile"
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}
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},
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"entrypoints": {
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@@ -24,6 +29,13 @@
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"python",
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"{pkg}/run_immunebuilder.py"
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]
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},
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"docker": {
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"artifact": "py-docker",
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"cmd": [
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"python",
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"/app/run_immunebuilder.py"
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]
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}
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}
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}
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package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.3.tgz
ADDED
|
Binary file
|
|
@@ -1,22 +0,0 @@
|
|
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1
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-
# Auto-generated Dockerfile for Python package
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2
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FROM python:3.12-slim
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-
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WORKDIR /app
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-
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-
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-
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# Always keep basic python packaging tools fresh to avoid CVEs even in old python versions
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RUN pip install --upgrade pip wheel setuptools
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-
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# Install dependencies to leverage Docker cache
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COPY requirements.txt .
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RUN pip install --no-cache-dir -r requirements.txt
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-
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# Copy package source
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COPY . /app
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-
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# Set Python path
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ENV PYTHONPATH=/app
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-
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# Default command (will be overridden by entrypoint)
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CMD ["bash"]
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