@platforma-open/milaboratories.3d-structure-prediction.software 1.1.0 → 1.1.2

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.
@@ -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/1.1.0.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.0.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/1.1.2.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.1.2.tgz"}
@@ -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.c57294107f92","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.bac5da929a65","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
@@ -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.c57294107f92","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/1.1.0.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.bac5da929a65","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/1.1.2.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": "1.1.0",
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- "type": "module",
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+ "version": "1.1.2",
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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/block-tools": "2.14.3"
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+ },
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  "block-software": {
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  "artifacts": {
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  "py-archive": {
@@ -40,14 +47,10 @@
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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": "3.13.0"
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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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+ "do-pack": "shx rm -f *.tgz && block-tools software build && pnpm pack && shx mv platforma-open*.tgz package.tgz",
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  "changeset": "changeset",
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  "version-packages": "changeset version",
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- "build": "pl-pkg build"
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+ "build": "block-tools software build"
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  }
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  }
@@ -1,423 +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@1.1.0 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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-
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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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- #1 DONE 0.0s
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- #2 [auth] docker/dockerfile:pull token for registry-1.docker.io
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- #2 DONE 0.0s
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- #3 resolve image config for docker-image://docker.io/docker/dockerfile:1
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- #3 DONE 0.5s
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-
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- #4 docker-image://docker.io/docker/dockerfile:1@sha256:87999aa3d42bdc6bea60565083ee17e86d1f3339802f543c0d03998580f9cb89
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- #4 resolve docker.io/docker/dockerfile:1@sha256:87999aa3d42bdc6bea60565083ee17e86d1f3339802f543c0d03998580f9cb89 done
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- #4 sha256:e82bbc85c3cb06cf2a5a27b058208b43984448acbcd6a832cd1491933d4376dd 1.13kB / 1.13kB done
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- #4 extracting sha256:50ba52cd6a2c01eaf1a9efbedc7c75b5da5e3965c1586001c722980487a73fd7
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- #4 sha256:50ba52cd6a2c01eaf1a9efbedc7c75b5da5e3965c1586001c722980487a73fd7 14.36MB / 14.36MB 0.3s done
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- #4 extracting sha256:50ba52cd6a2c01eaf1a9efbedc7c75b5da5e3965c1586001c722980487a73fd7 0.1s done
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- #4 DONE 0.4s
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-
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- #5 [internal] load metadata for docker.io/mambaorg/micromamba:1.5.10
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- #5 ...
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- #9 transferring context: 38.79kB done
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- #8 [1/6] FROM docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d
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- #8 resolve docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d done
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-
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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 16.69
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- #10 16.69 Transaction
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- #10 16.69
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- #10 16.69 Prefix: /opt/conda
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- #10 16.69
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- #10 16.69 Updating specs:
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- #10 16.69
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- #10 16.69 - python=3.12.10
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- #10 16.69 - anarci
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- #10 16.69 - hmmer
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- #10 16.69 - biopython=1.85
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- #10 16.69 - openmm=8.3.1
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- #10 16.69 - pdbfixer=1.12.0
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- #10 16.69 - numpy=2.4.3
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- #10 16.69 - scipy=1.17.1
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- #10 16.69
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- #10 16.69
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- #10 16.69 Package Version Build Channel Size
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- #10 16.69 ───────────────────────────────────────────────────────────────────────────────
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- #10 16.69 Install:
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- #10 16.69 ───────────────────────────────────────────────────────────────────────────────
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- #10 16.69
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- #10 16.69 + python_abi 3.12 8_cp312 conda-forge 7kB
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- #10 16.69 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
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- #10 16.69 + ca-certificates 2026.5.20 hbd8a1cb_0 conda-forge 130kB
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- #10 16.69 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
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- #10 16.69 + libzlib 1.3.2 h25fd6f3_2 conda-forge 64kB
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- #10 16.69 + libgomp 15.2.0 he0feb66_19 conda-forge 604kB
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- #10 16.69 + mpi 1.0 openmpi conda-forge 4kB
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- #10 16.69 + zlib 1.3.2 h25fd6f3_2 conda-forge 96kB
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- #10 16.69 + zstd 1.5.7 hb78ec9c_6 conda-forge 601kB
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- #10 16.69 + _openmp_mutex 4.5 20_gnu conda-forge 29kB
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- #10 16.69 + ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge 728kB
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- #10 16.69 + libgcc 15.2.0 he0feb66_19 conda-forge 1MB
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- #10 16.69 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
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- #10 16.69 + libsqlite 3.53.2 h0c1763c_0 conda-forge 958kB
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- #10 16.69 + openssl 3.6.3 h35e630c_0 conda-forge 3MB
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- #10 16.69 + ncurses 6.6 hdb14827_0 conda-forge 919kB
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- #10 16.69 + libuuid 2.42.1 h5347b49_0 conda-forge 40kB
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- #10 16.69 + libnsl 2.0.1 hb9d3cd8_1 conda-forge 34kB
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- #10 16.69 + liblzma 5.8.3 hb03c661_0 conda-forge 113kB
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- #10 16.69 + libffi 3.4.6 h2dba641_1 conda-forge 57kB
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- #10 16.69 + libexpat 2.8.1 hecca717_0 conda-forge 77kB
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- #10 16.69 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
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- #10 16.69 + libstdcxx 15.2.0 h934c35e_19 conda-forge 6MB
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- #10 16.69 + libgcc-ng 15.2.0 h69a702a_19 conda-forge 28kB
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- #10 16.69 + libgfortran5 15.2.0 h68bc16d_19 conda-forge 2MB
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- #10 16.69 + readline 8.3 h853b02a_0 conda-forge 345kB
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- #10 16.69 + opencl-headers 2025.06.13 hecca717_0 conda-forge 56kB
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- #10 16.69 + libstdcxx-ng 15.2.0 hdf11a46_19 conda-forge 28kB
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- #10 16.69 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
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- #10 16.69 + cuda-nvrtc 12.9.86 hecca717_1 conda-forge 67MB
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- #10 16.69 + libxcrypt 4.4.36 hd590300_1 conda-forge 100kB
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- #10 16.69 + libgfortran 15.2.0 h69a702a_19 conda-forge 28kB
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- #10 16.69 + ocl-icd 2.3.4 hb03c661_1 conda-forge 110kB
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- #10 16.69 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
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- #10 16.69 + libgfortran-ng 15.2.0 h69a702a_19 conda-forge 28kB
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- #10 16.69 + libopenblas 0.3.33 pthreads_h94d23a6_0 conda-forge 6MB
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- #10 16.69 + ocl-icd-system 1.0.0 1 conda-forge 4kB
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- #10 16.69 + openmpi 4.1.6 hc5af2df_101 conda-forge 4MB
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- #10 16.69 + libblas 3.11.0 8_h4a7cf45_openblas conda-forge 19kB
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- #10 16.69 + libcblas 3.11.0 8_h0358290_openblas conda-forge 19kB
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- #10 16.69 + liblapack 3.11.0 8_h47877c9_openblas conda-forge 19kB
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- #10 16.69 + gsl 2.7 he838d99_0 conda-forge 3MB
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- #10 16.69 + packaging 26.2 pyhc364b38_0 conda-forge 92kB
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- #10 16.69 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
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- #10 16.69 + wheel 0.47.0 pyhd8ed1ab_0 conda-forge 33kB
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- #10 16.69 + pip 26.1.2 pyh8b19718_0 conda-forge 1MB
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- #10 16.69 + legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge 20kB
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- #10 16.69 + hmmer 3.4 hb6cb901_4 bioconda 12MB
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- #10 16.69 + numpy 2.4.3 py312h33ff503_0 conda-forge 9MB
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- #10 16.69 + scipy 1.17.1 py312h54fa4ab_1 conda-forge 17MB
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- #10 16.69 + biopython 1.85 py312h4c3975b_2 conda-forge 3MB
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- #10 16.69 + openmm 8.3.1 py312h50c43f0_0 conda-forge 13MB
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- #10 16.69 + anarci 2024.05.21 pyhdfd78af_0 bioconda 1MB
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- #10 16.69 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
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- #10 16.69 Summary:
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- #10 16.69
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- #10 16.69 Install: 54 packages
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- #10 16.69
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- #10 16.69 Total download: 353MB
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- #10 16.69 ───────────────────────────────────────────────────────────────────────────────
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- #10 16.69 Transaction starting
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- #10 22.01
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- #10 22.17
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- #10 22.17 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
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- #10 22.17 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
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- #10 22.17 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
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- #10 22.17 mpiexec --mca opal_cuda_support 1 ...
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- #10 22.17
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- #10 22.17 In addition, the UCX support is also built but disabled by default.
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- #10 22.17 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
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- #10 22.17 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
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- #10 22.17 Equivalently, you can set the MCA parameters in the command line:
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- #10 22.17 mpiexec --mca pml ucx --mca osc ucx ...
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- #10 22.17 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
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- #10 22.17 Please consult UCX's documentation for detail.
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- #10 23.29
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- #10 23.29 Transaction finished
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- # @platforma-open/milaboratories.3d-structure-prediction.software
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-
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- ## 1.1.0
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- ### Minor Changes
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- - 37da856: Export only confident structures. The PDB ResourceMap now contains only confident clonotypes — prediction succeeded AND the selected error metric is within threshold — and the `confident` / `predictionSuccessful` subset filter columns are no longer exported. Downstream blocks consume confident structures directly, with no all-vs-confident selection to make. The results table still shows every clonotype and every column (confidence values, failure reasons, warnings); failed and unconfident clonotypes simply have no downloadable PDB. Confident filtering is applied once, in the Python wrapper's manifest, so the PDB map is built by the existing stable path (no post-hoc rebuild).
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- Clonotypes whose prediction succeeded but whose error exceeds the confidence threshold now carry a failure reason — "Prediction confidence above threshold (<value> Å)" — so the table explains why they have no downloadable structure (their error values remain visible).
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- Output column traces are now rooted in the Lead Selection filter when present, so predictions off the same dataset with different filters carry distinguishable provenance (dataset → lead selection → prediction) in downstream labels.
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- The error-distribution histogram now shows the confidence threshold as a dashed vertical line (via a `pl7.app/graph/thresholds` annotation on the selected-metric column) — on the CDR-H3 page for the `cdrh3Mean` metric, or the Mean page for `overallMean`.
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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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- - 49b6d30: Update workflow version
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- ## 1.0.5
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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.
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- 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.
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-
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- 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.
38
-
39
- 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.
40
-
41
- 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.
42
-
43
- ## 1.0.4
44
-
45
- ### Patch Changes
46
-
47
- - 7a0fedd: Fix docker permissions
48
-
49
- ## 1.0.3
50
-
51
- ### Patch Changes
52
-
53
- - 53a03a1: Fix dependency resolution for docker
54
-
55
- ## 1.0.2
56
-
57
- ### Patch Changes
58
-
59
- - 4f126ee: Use custom Dockerfile
60
-
61
- ## 1.0.1
62
-
63
- ### Patch Changes
64
-
65
- - 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"]