@platforma-open/milaboratories.3d-structure-prediction.software 1.0.7 → 1.1.1

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.
Files changed (13) hide show
  1. package/dist/artifacts/py-archive/archive.json +1 -1
  2. package/dist/artifacts/py-docker/docker_x64.json +1 -1
  3. package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
  4. package/package.json +9 -6
  5. package/.turbo/turbo-build.log +0 -425
  6. package/CHANGELOG.md +0 -53
  7. package/Dockerfile +0 -63
  8. package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.7.tgz +0 -0
  9. package/src_python/numbering.py +0 -103
  10. package/src_python/pdb_writer.py +0 -136
  11. package/src_python/requirements.txt +0 -5
  12. package/src_python/run_immunebuilder.py +0 -628
  13. package/src_python/sanitize.py +0 -150
package/dist/artifacts/py-archive/archive.json CHANGED
@@ -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/1.0.7.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.7.tgz"}
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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/1.1.1.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.1.tgz"}
package/dist/artifacts/py-docker/docker_x64.json CHANGED
@@ -1 +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-docker.fbb456fbfccc","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
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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.f3b1cc0122fe","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
package/dist/tengo/software/immunebuilder-predict.sw.json CHANGED
@@ -1 +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.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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+ {"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.f3b1cc0122fe","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/1.1.1.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 CHANGED
@@ -1,8 +1,15 @@
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  {
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  "name": "@platforma-open/milaboratories.3d-structure-prediction.software",
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- "version": "1.0.7",
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- "type": "module",
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+ "version": "1.1.1",
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  "description": "Block Software",
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+ "files": [
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+ "./dist/**/*"
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+ ],
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+ "type": "module",
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+ "devDependencies": {
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+ "@platforma-open/milaboratories.runenv-python-3": "1.8.6",
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+ "@platforma-sdk/package-builder": "3.13.0"
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+ },
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  "block-software": {
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  "artifacts": {
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  "py-archive": {
@@ -40,10 +47,6 @@
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  }
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  }
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  },
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- "devDependencies": {
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- "@platforma-open/milaboratories.runenv-python-3": "1.8.6",
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- "@platforma-sdk/package-builder": "3.12.0"
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- },
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  "scripts": {
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  "do-pack": "shx rm -f *.tgz && pl-pkg build && pnpm pack && shx mv platforma-open*.tgz package.tgz",
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  "changeset": "changeset",
package/.turbo/turbo-build.log DELETED
@@ -1,425 +0,0 @@
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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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-
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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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-
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- info: Building docker images...
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- info: Building docker image for 'py-docker'...
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- #0 building with "default" instance using docker driver
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- #1 transferring dockerfile: 2.53kB done
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- #1 DONE 0.0s
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- #3 DONE 1.2s
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- #4 DONE 0.6s
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- #5 [auth] mambaorg/micromamba:pull token for registry-1.docker.io
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- #5 DONE 0.0s
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- #6 [internal] load metadata for docker.io/mambaorg/micromamba:1.5.10
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- #6 DONE 8.2s
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- #9 [1/6] FROM docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d
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- #9 resolve docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d 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 15.95
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- #10 15.95 Transaction
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- #10 15.95 Prefix: /opt/conda
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- #10 15.95
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- #10 15.95 Updating specs:
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- #10 15.95 - python=3.12.10
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- #10 15.95 - anarci
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- #10 15.95 - hmmer
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- #10 15.95 - biopython=1.85
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- #10 15.95 - openmm=8.3.1
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- #10 15.95 - pdbfixer=1.12.0
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- #10 15.95 - numpy=2.4.3
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- #10 15.95 - scipy=1.17.1
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- #10 15.95 Install:
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- #10 15.95
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- #10 15.95 + python_abi 3.12 8_cp312 conda-forge 7kB
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- #10 15.95 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
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- #10 15.95 + libgomp 15.2.0 he0feb66_19 conda-forge 604kB
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- #10 15.95 + ocl-icd 2.3.4 hb03c661_1 conda-forge 110kB
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- #10 15.95 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
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- #10 15.95 + openmpi 4.1.6 hc5af2df_101 conda-forge 4MB
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- #10 15.95 + libblas 3.11.0 8_h4a7cf45_openblas conda-forge 19kB
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- #10 15.95 + libcblas 3.11.0 8_h0358290_openblas conda-forge 19kB
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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 + wheel 0.47.0 pyhd8ed1ab_0 conda-forge 33kB
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- #10 15.95 + pip 26.1.2 pyh8b19718_0 conda-forge 1MB
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- #10 15.95 + legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge 20kB
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- #10 15.95 + hmmer 3.4 hb6cb901_4 bioconda 12MB
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- #10 15.95 + numpy 2.4.3 py312h33ff503_0 conda-forge 9MB
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- #10 15.95 + scipy 1.17.1 py312h54fa4ab_1 conda-forge 17MB
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- #10 15.95 + biopython 1.85 py312h4c3975b_2 conda-forge 3MB
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- #10 15.95 + openmm 8.3.1 py312h50c43f0_0 conda-forge 13MB
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- #10 15.95 + anarci 2024.05.21 pyhdfd78af_0 bioconda 1MB
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- #10 21.31
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- #10 21.31 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
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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 mpiexec --mca opal_cuda_support 1 ...
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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 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
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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 mpiexec --mca pml ucx --mca osc ucx ...
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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 Or to execute a single command in this environment, use:
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- #10 22.50 micromamba run -n base mycommand
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- #10 22.92 libblas-3.11.0-8_h4a7cf45_openblas.conda 19kB
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- #10 22.92 mpi-1.0-openmpi.tar.bz2 4kB
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- #10 22.92 ncurses-6.6-hdb14827_0.conda 919kB
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- #10 22.92 numpy-2.4.3-py312h33ff503_0.conda 9MB
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- #10 22.92 ocl-icd-2.3.4-hb03c661_1.conda 110kB
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- #10 22.92 Total size: 353MB
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- #10 22.92 Cleaning tarballs..
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- #11 [3/6] COPY requirements.txt /tmp/requirements.txt
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- #11 DONE 0.0s
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-
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- #12 [4/6] RUN pip install --no-cache-dir --extra-index-url https://download.pytorch.org/whl/cpu -r /tmp/requirements.txt
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- #12 0.602 Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
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- #12 0.841 Collecting ImmuneBuilder==1.2 (from -r /tmp/requirements.txt (line 1))
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- #12 0.868 Downloading ImmuneBuilder-1.2-py3-none-any.whl.metadata (7.7 kB)
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- #12 1.001 Collecting torch==2.7.0 (from -r /tmp/requirements.txt (line 2))
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- #12 1.061 Downloading torch-2.7.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (27 kB)
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- #12 1.064 Requirement already satisfied: biopython==1.85 in /opt/conda/lib/python3.12/site-packages (from -r /tmp/requirements.txt (line 3)) (1.85)
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- #12 1.066 Requirement already satisfied: pdbfixer==1.12.0 in /opt/conda/lib/python3.12/site-packages (from -r /tmp/requirements.txt (line 5)) (1.12.0)
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- #12 1.066 Requirement already satisfied: numpy in /opt/conda/lib/python3.12/site-packages (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1)) (2.4.3)
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- #12 1.067 Requirement already satisfied: scipy>=1.6 in /opt/conda/lib/python3.12/site-packages (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1)) (1.17.1)
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- #12 1.085 Collecting einops>=0.3 (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
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- #12 1.089 Downloading einops-0.8.2-py3-none-any.whl.metadata (13 kB)
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- #12 1.158 Collecting requests (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
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- #12 1.162 Downloading requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
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- #12 1.216 Collecting filelock (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.220 Downloading filelock-3.29.0-py3-none-any.whl.metadata (2.0 kB)
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- #12 1.262 Collecting typing-extensions>=4.10.0 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.315 Collecting sympy>=1.13.3 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.450 Collecting jinja2 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.455 Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
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- #12 1.520 Collecting fsspec (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.524 Downloading fsspec-2026.4.0-py3-none-any.whl.metadata (10 kB)
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- #12 1.583 Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.587 Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
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- #12 1.665 Collecting MarkupSafe>=2.0 (from jinja2->torch==2.7.0->-r /tmp/requirements.txt (line 2))
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- #12 1.765 Collecting charset_normalizer<4,>=2 (from requests->ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
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- #12 2.790 Installing collected packages: mpmath, urllib3, typing-extensions, sympy, networkx, MarkupSafe, idna, fsspec, filelock, einops, charset_normalizer, certifi, requests, jinja2, torch, ImmuneBuilder
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- #12 17.73
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- #12 17.73 Successfully installed ImmuneBuilder-1.2 MarkupSafe-3.0.3 certifi-2026.5.20 charset_normalizer-3.4.7 einops-0.8.2 filelock-3.29.0 fsspec-2026.4.0 idna-3.18 jinja2-3.1.6 mpmath-1.3.0 networkx-3.6.1 requests-2.34.2 sympy-1.14.0 torch-2.7.0+cpu typing-extensions-4.15.0 urllib3-2.7.0
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- #12 17.73 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
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- #15 exporting layers 5.9s done
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- #15 naming to containers.pl-open.science/milaboratories/pl-containers:local-image.be0687a6bdf3 done
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- info: Docker image is built:
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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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- location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-docker/docker_x64.json'
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- info: Building package archives...
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- info: Building software package 'py-archive' for platform 'linux-x64'...
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- info: software archive is built:
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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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- info: Writing entrypoint descriptor to '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/tengo/software/immunebuilder-predict.sw.json'
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- info: Publishing docker images...
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- info: 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
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-
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- ## 1.0.7
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-
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- ### Patch Changes
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-
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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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-
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- ## 1.0.6
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-
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- ### Patch Changes
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- - 49b6d30: Update workflow version
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-
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- ## 1.0.5
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-
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- ### Patch Changes
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- - 4438d9d: Clarify NanoBodyBuilder2 usage in the settings panel: relabel the light chain dropdown as optional with a tooltip, and expand the mode-info alert to note that NanoBodyBuilder2 is camelid-VHH-trained, so for conventional heavy-only inputs (e.g. human bulk IGH-only) the produced structure has VHH-biased framework geometry.
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- Drop the user-facing CPU and memory inputs (per-batch resources are fixed). Each prediction batch now requests 4 CPU cores and 4 GiB of memory.
22
-
23
- Stop writing a wall-clock `prediction-date` REMARK into emitted PDBs. The timestamp made every PDB byte-different on every run, breaking the platforma backend's content-addressed caching — downstream nodes that consumed merged PDB ResourceMaps hit `CIDConflictError`. The other provenance REMARKs (immunebuilder version, torch seed, block version, numbering scheme) plus the seeded ensemble fully determine the prediction.
24
-
25
- Make the saved Python wrapper log byte-stable for identical inputs: drop the per-line UTC timestamp prefix and remove every wall-clock duration printed by `_log` (`predictor ready in Xs`, `predicted in Xs`, `elapsed=Xs`). The exec template saves stdout via `saveStdoutStream()` into the regular file output set, so its content hash flows into the resource CID; timestamped logs would re-introduce the same `CIDConflictError` failure mode as the PDB date.
26
-
27
- Set `stepCache: 30 * times.minute` on the `processColumn` call so per-batch outputs stay reachable for the dedup/recovery path across project re-renders, matching the convention used by mixcr-clonotyping and miltenyi-tcr-bcr-clonotyping.
28
-
29
- Add the species selector (spec R44): `human | mouse | camelid | rat | rabbit | other`, default `human`. Species is included in the block subtitle (R56) alongside the engine. The mode-info banner now splits into two cases: when the species is `camelid` and the light chain is unset we treat it as a true VHH input (informational); for any other species combined with heavy-only input we surface a warning that NanoBodyBuilder2's framework geometry is biased away from conventional VH. A separate warning fires for ABodyBuilder2 runs on species outside the training distribution (anything other than human or mouse). Species is held in `BlockData` only — the workflow does not consume it yet, so switching species does not invalidate cached predictions. Upstream clonotyping blocks do not propagate species through PColumn specs today, so the selector is user-supplied; once upstream wires `pl7.app/species` onto the clonotype-axis domain, this block can pre-fill the default.
30
-
31
- ## 1.0.4
32
-
33
- ### Patch Changes
34
-
35
- - 7a0fedd: Fix docker permissions
36
-
37
- ## 1.0.3
38
-
39
- ### Patch Changes
40
-
41
- - 53a03a1: Fix dependency resolution for docker
42
-
43
- ## 1.0.2
44
-
45
- ### Patch Changes
46
-
47
- - 4f126ee: Use custom Dockerfile
48
-
49
- ## 1.0.1
50
-
51
- ### Patch Changes
52
-
53
- - 9f63d06: Bump pdbfixer to dependencies
package/Dockerfile DELETED
@@ -1,63 +0,0 @@
1
- # syntax=docker/dockerfile:1
2
- #
3
- # Cloud-side image for the 3D-structure-prediction block.
4
- #
5
- # Why this exists: pl-pkg's auto-generated Dockerfile uses python:3.12-slim
6
- # and installs only requirements.txt deps. ImmuneBuilder relies at import
7
- # time on `anarci` and `pdbfixer`, neither of which are usable from PyPI
8
- # (anarci is yanked; pdbfixer is sdist-only and lacks several runtime
9
- # pieces). Locally the runenv ships hand-bundled anarci + HMMER + databases;
10
- # the cloud autogen ignores all that. This Dockerfile closes the gap by
11
- # pulling those packages from bioconda, then layering ImmuneBuilder + torch
12
- # via pip on top.
13
- #
14
- # pl-pkg invokes `docker build <context> -f Dockerfile`. Context is set to
15
- # `src_python` in package.json, so all COPY paths below are relative to
16
- # software/src_python/.
17
-
18
- FROM mambaorg/micromamba:1.5.10
19
-
20
- USER root
21
-
22
- # anarci and hmmer are deliberately left unpinned: bioconda's recipe builds
23
- # the HMM database at install time and the database depends on the HMMER
24
- # version, so locking the hash for both pkgs at once is fragile across
25
- # bioconda updates. After the first successful CI build, run
26
- # micromamba list -n base anarci hmmer
27
- # inside the image and copy the resulting build strings here if you need
28
- # bit-identical reproducibility.
29
- RUN micromamba install -y -n base -c bioconda -c conda-forge \
30
- python=3.12.10 \
31
- anarci \
32
- hmmer \
33
- biopython=1.85 \
34
- openmm=8.3.1 \
35
- pdbfixer=1.12.0 \
36
- numpy=2.4.3 \
37
- scipy=1.17.1 \
38
- && micromamba clean --all --yes
39
-
40
- # Activate the base env for every subsequent RUN/CMD layer so pip and
41
- # python resolve to /opt/conda/{bin,lib}.
42
- ARG MAMBA_DOCKERFILE_ACTIVATE=1
43
- ENV PATH=/opt/conda/bin:$PATH
44
-
45
- # Make conda's libstdc++ (and friends) win over the older system libs in
46
- # /lib/x86_64-linux-gnu. Pip-installed extension wheels (manylinux2014+)
47
- # expect a recent CXXABI; the base image's system libstdc++ predates it.
48
- ENV LD_LIBRARY_PATH=/opt/conda/lib
49
-
50
- # Layer pip-only deps (ImmuneBuilder + CPU torch). Anything bioconda
51
- # already provides is re-resolved by pip; pinned versions in
52
- # requirements.txt match the conda packages so this is a no-op for those.
53
- COPY requirements.txt /tmp/requirements.txt
54
- RUN pip install --no-cache-dir \
55
- --extra-index-url https://download.pytorch.org/whl/cpu \
56
- -r /tmp/requirements.txt
57
-
58
- # Block sources (everything in src_python/).
59
- WORKDIR /app
60
- COPY . /app/
61
- ENV PYTHONPATH=/app
62
-
63
- CMD ["python", "/app/run_immunebuilder.py"]