@platforma-open/milaboratories.3d-structure-prediction.software 1.0.0

package/.turbo/turbo-build.log

@@ -0,0 +1,265 @@
+ WARN  Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
+
+> @platforma-open/milaboratories.3d-structure-prediction.software@1.0.0 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
+> pl-pkg build
+
+info: Building docker images...
+info: Building docker image for 'py-archive'...
+#0 building with "default" instance using docker driver
+
+#1 [internal] load build definition from Dockerfile-py-archive
+#1 transferring dockerfile: 539B done
+#1 DONE 0.0s
+
+#2 [internal] load metadata for docker.io/library/python:3.12-slim
+#2 ...
+
+#3 [auth] library/python:pull token for registry-1.docker.io
+#3 DONE 0.0s
+
+#2 [internal] load metadata for docker.io/library/python:3.12-slim
+#2 DONE 1.0s
+
+#4 [internal] load .dockerignore
+#4 transferring context: 2B done
+#4 DONE 0.0s
+
+#5 [internal] load build context
+#5 transferring context: 36.38kB done
+#5 DONE 0.0s
+
+#6 [1/6] FROM docker.io/library/python:3.12-slim@sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3
+#6 resolve docker.io/library/python:3.12-slim@sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3 done
+#6 sha256:4386a385d81dba9f72ed72a6fe4237755d7f5440c84b417650f38336bbc43117 1.75kB / 1.75kB done
+#6 sha256:7bf61a5ec2a4631b240bc8cf83404e2dd37fb06a4b4bbd34b2c36906a5fb4aee 5.66kB / 5.66kB done
+#6 sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 0B / 29.78MB 0.1s
+#6 sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 0B / 1.29MB 0.1s
+#6 sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 0B / 12.10MB 0.1s
+#6 sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3 10.37kB / 10.37kB done
+#6 sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 29.78MB / 29.78MB 0.2s done
+#6 sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 1.29MB / 1.29MB 0.2s done
+#6 extracting sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 0.1s
+#6 sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357 0B / 248B 0.3s
+#6 sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 12.10MB / 12.10MB 0.4s done
+#6 sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357 248B / 248B 0.5s done
+#6 extracting sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 1.2s done
+#6 extracting sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 0.1s
+#6 extracting sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 0.1s done
+#6 extracting sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65
+#6 extracting sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 0.7s done
+#6 extracting sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357
+#6 extracting sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357 done
+#6 DONE 4.7s
+
+#7 [2/6] WORKDIR /app
+#7 DONE 0.0s
+
+#8 [3/6] RUN pip install --upgrade pip wheel setuptools
+#8 1.840 Requirement already satisfied: pip in /usr/local/lib/python3.12/site-packages (25.0.1)
+#8 1.896 Collecting pip
+#8 1.915   Downloading pip-26.1.1-py3-none-any.whl.metadata (4.6 kB)
+#8 1.945 Collecting wheel
+#8 1.949   Downloading wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
+#8 2.087 Collecting setuptools
+#8 2.090   Downloading setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
+#8 2.128 Collecting packaging>=24.0 (from wheel)
+#8 2.131   Downloading packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
+#8 2.143 Downloading pip-26.1.1-py3-none-any.whl (1.8 MB)
+#8 2.160    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 158.8 MB/s eta 0:00:00
+#8 2.164 Downloading wheel-0.47.0-py3-none-any.whl (32 kB)
+#8 2.170 Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
+#8 2.177    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 158.9 MB/s eta 0:00:00
+#8 2.180 Downloading packaging-26.2-py3-none-any.whl (100 kB)
+#8 2.211 Installing collected packages: setuptools, pip, packaging, wheel
+#8 2.820   Attempting uninstall: pip
+#8 2.825     Found existing installation: pip 25.0.1
+#8 2.882     Uninstalling pip-25.0.1:
+#8 2.892       Successfully uninstalled pip-25.0.1
+#8 4.076 Successfully installed packaging-26.2 pip-26.1.1 setuptools-82.0.1 wheel-0.47.0
+#8 4.076 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.
+#8 DONE 4.3s
+
+#9 [4/6] COPY requirements.txt .
+#9 DONE 0.0s
+
+#10 [5/6] RUN pip install --no-cache-dir -r requirements.txt
+#10 0.638 Collecting ImmuneBuilder==1.2 (from -r requirements.txt (line 1))
+#10 0.678   Downloading ImmuneBuilder-1.2-py3-none-any.whl.metadata (7.7 kB)
+#10 0.743 Collecting torch==2.7.0 (from -r requirements.txt (line 2))
+#10 0.746   Downloading torch-2.7.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (29 kB)
+#10 0.790 Collecting biopython==1.85 (from -r requirements.txt (line 3))
+#10 0.795   Downloading biopython-1.85-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
+#10 0.888 Collecting openmm==8.3.1 (from -r requirements.txt (line 4))
+#10 0.892   Downloading openmm-8.3.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.0 kB)
+#10 1.181 Collecting numpy (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 1.185   Downloading numpy-2.4.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
+#10 1.310 Collecting scipy>=1.6 (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 1.314   Downloading scipy-1.17.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
+#10 1.337 Collecting einops>=0.3 (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 1.340   Downloading einops-0.8.2-py3-none-any.whl.metadata (13 kB)
+#10 1.362 Collecting requests (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 1.365   Downloading requests-2.33.1-py3-none-any.whl.metadata (4.8 kB)
+#10 1.382 Collecting filelock (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.388   Downloading filelock-3.29.0-py3-none-any.whl.metadata (2.0 kB)
+#10 1.402 Collecting typing-extensions>=4.10.0 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.404   Downloading typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
+#10 1.407 Requirement already satisfied: setuptools in /usr/local/lib/python3.12/site-packages (from torch==2.7.0->-r requirements.txt (line 2)) (82.0.1)
+#10 1.419 Collecting sympy>=1.13.3 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.422   Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
+#10 1.443 Collecting networkx (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.446   Downloading networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
+#10 1.462 Collecting jinja2 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.466   Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
+#10 1.482 Collecting fsspec (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.485   Downloading fsspec-2026.4.0-py3-none-any.whl.metadata (10 kB)
+#10 1.514 Collecting nvidia-cuda-nvrtc-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.517   Downloading nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
+#10 1.531 Collecting nvidia-cuda-runtime-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.534   Downloading nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
+#10 1.550 Collecting nvidia-cuda-cupti-cu12==12.6.80 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.554   Downloading nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
+#10 1.568 Collecting nvidia-cudnn-cu12==9.5.1.17 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.571   Downloading nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl.metadata (1.6 kB)
+#10 1.580 Collecting nvidia-cublas-cu12==12.6.4.1 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.584   Downloading nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
+#10 1.598 Collecting nvidia-cufft-cu12==11.3.0.4 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.601   Downloading nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
+#10 1.614 Collecting nvidia-curand-cu12==10.3.7.77 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.617   Downloading nvidia_curand_cu12-10.3.7.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
+#10 1.631 Collecting nvidia-cusolver-cu12==11.7.1.2 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.635   Downloading nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
+#10 1.647 Collecting nvidia-cusparse-cu12==12.5.4.2 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.650   Downloading nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
+#10 1.664 Collecting nvidia-cusparselt-cu12==0.6.3 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.666   Downloading nvidia_cusparselt_cu12-0.6.3-py3-none-manylinux2014_x86_64.whl.metadata (6.8 kB)
+#10 1.680 Collecting nvidia-nccl-cu12==2.26.2 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.685   Downloading nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.0 kB)
+#10 1.700 Collecting nvidia-nvtx-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.705   Downloading nvidia_nvtx_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
+#10 1.718 Collecting nvidia-nvjitlink-cu12==12.6.85 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.721   Downloading nvidia_nvjitlink_cu12-12.6.85-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.5 kB)
+#10 1.730 Collecting nvidia-cufile-cu12==1.11.1.6 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.733   Downloading nvidia_cufile_cu12-1.11.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
+#10 1.746 Collecting triton==3.3.0 (from torch==2.7.0->-r requirements.txt (line 2))
+#10 1.750   Downloading triton-3.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.5 kB)
+#10 1.787 Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch==2.7.0->-r requirements.txt (line 2))
+#10 1.791   Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
+#10 1.876 Collecting MarkupSafe>=2.0 (from jinja2->torch==2.7.0->-r requirements.txt (line 2))
+#10 1.881   Downloading markupsafe-3.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
+#10 2.006 Collecting charset_normalizer<4,>=2 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 2.009   Downloading charset_normalizer-3.4.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (40 kB)
+#10 2.021 Collecting idna<4,>=2.5 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 2.024   Downloading idna-3.13-py3-none-any.whl.metadata (8.0 kB)
+#10 2.040 Collecting urllib3<3,>=1.26 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 2.043   Downloading urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
+#10 2.058 Collecting certifi>=2023.5.7 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
+#10 2.061   Downloading certifi-2026.4.22-py3-none-any.whl.metadata (2.5 kB)
+#10 2.070 Downloading ImmuneBuilder-1.2-py3-none-any.whl (32 kB)
+#10 2.073 Downloading torch-2.7.0-cp312-cp312-manylinux_2_28_x86_64.whl (865.0 MB)
+#10 11.73    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 865.0/865.0 MB 87.0 MB/s  0:00:09
+#10 11.73 Downloading biopython-1.85-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
+#10 11.75    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 223.5 MB/s  0:00:00
+#10 11.83 Downloading openmm-8.3.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (14.0 MB)
+#10 12.78    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.0/14.0 MB 14.5 MB/s  0:00:00
+#10 12.79 Downloading nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (393.1 MB)
+#10 15.98    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 393.1/393.1 MB 171.3 MB/s  0:00:03
+#10 15.99 Downloading nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.9 MB)
+#10 16.04    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.9/8.9 MB 173.9 MB/s  0:00:00
+#10 16.04 Downloading nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl (23.7 MB)
+#10 16.12    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.7/23.7 MB 307.3 MB/s  0:00:00
+#10 16.13 Downloading nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (897 kB)
+#10 16.13    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 897.7/897.7 kB 453.3 MB/s  0:00:00
+#10 16.14 Downloading nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl (571.0 MB)
+#10 22.98    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 571.0/571.0 MB 91.8 MB/s  0:00:06
+#10 22.99 Downloading nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (200.2 MB)
+#10 25.96    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 200.2/200.2 MB 67.2 MB/s  0:00:02
+#10 25.97 Downloading nvidia_cufile_cu12-1.11.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.1 MB)
+#10 25.98    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 60.2 MB/s  0:00:00
+#10 25.99 Downloading nvidia_curand_cu12-10.3.7.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB)
+#10 26.22    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 249.3 MB/s  0:00:00
+#10 26.22 Downloading nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (158.2 MB)
+#10 27.18    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.2/158.2 MB 164.5 MB/s  0:00:00
+#10 27.19 Downloading nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (216.6 MB)
+#10 29.27    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 216.6/216.6 MB 103.9 MB/s  0:00:02
+#10 29.28 Downloading nvidia_cusparselt_cu12-0.6.3-py3-none-manylinux2014_x86_64.whl (156.8 MB)
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+#10 33.59    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 201.3/201.3 MB 135.1 MB/s  0:00:01
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+#10 36.15 Downloading idna-3.13-py3-none-any.whl (68 kB)
+#10 36.15 Downloading urllib3-2.6.3-py3-none-any.whl (131 kB)
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+#10 38.60 Installing collected packages: nvidia-cusparselt-cu12, mpmath, urllib3, typing-extensions, triton, sympy, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufile-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, MarkupSafe, idna, fsspec, filelock, einops, charset_normalizer, certifi, scipy, requests, openmm, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, jinja2, biopython, nvidia-cusolver-cu12, torch, ImmuneBuilder
+#10 86.40 
+#10 86.40 Successfully installed ImmuneBuilder-1.2 MarkupSafe-3.0.3 biopython-1.85 certifi-2026.4.22 charset_normalizer-3.4.7 einops-0.8.2 filelock-3.29.0 fsspec-2026.4.0 idna-3.13 jinja2-3.1.6 mpmath-1.3.0 networkx-3.6.1 numpy-2.4.4 nvidia-cublas-cu12-12.6.4.1 nvidia-cuda-cupti-cu12-12.6.80 nvidia-cuda-nvrtc-cu12-12.6.77 nvidia-cuda-runtime-cu12-12.6.77 nvidia-cudnn-cu12-9.5.1.17 nvidia-cufft-cu12-11.3.0.4 nvidia-cufile-cu12-1.11.1.6 nvidia-curand-cu12-10.3.7.77 nvidia-cusolver-cu12-11.7.1.2 nvidia-cusparse-cu12-12.5.4.2 nvidia-cusparselt-cu12-0.6.3 nvidia-nccl-cu12-2.26.2 nvidia-nvjitlink-cu12-12.6.85 nvidia-nvtx-cu12-12.6.77 openmm-8.3.1 requests-2.33.1 scipy-1.17.1 sympy-1.14.0 torch-2.7.0 triton-3.3.0 typing-extensions-4.15.0 urllib3-2.6.3
+#10 86.40 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.
+#10 DONE 89.2s
+
+#11 [6/6] COPY . /app
+#11 DONE 0.0s
+
+#12 exporting to image
+#12 exporting layers
+#12 exporting layers 11.9s done
+#12 writing image sha256:a87395ddc3da5c6821dd753df4fe45af1b28236117f4a536419b511508a56421 done
+#12 naming to containers.pl-open.science/milaboratories/pl-containers:local-image.afeb28347e52 done
+#12 DONE 11.9s
+info: Docker image is built:
+        tag: 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da'
+        location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-archive/docker_x64.json'
+info: Building package archives...
+info: Building software package 'py-archive' for platform 'linux-x64'...
+info: software archive is built:
+        archive: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.0.tgz'
+        location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-archive/archive.json'
+info: Rendering entrypoint descriptors...
+info: Writing entrypoint descriptor to '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/tengo/software/immunebuilder-predict.sw.json'
+info: Publishing docker images...
+info: Publishing docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da' using alternative tag 'quay.io/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da'
+The push refers to repository [quay.io/milaboratories/pl-containers]
+0826d8e5c196: Preparing
+6478b4b624ed: Preparing
+0ad03b205566: Preparing
+153b8cd2ae3a: Preparing
+c23e35ce0d97: Preparing
+82f7b847f709: Preparing
+3a9714186f75: Preparing
+e1ed8e09cf5d: Preparing
+6d7c150df58d: Preparing
+82f7b847f709: Waiting
+3a9714186f75: Waiting
+e1ed8e09cf5d: Waiting
+6d7c150df58d: Waiting
+0ad03b205566: Pushed
+0826d8e5c196: Pushed
+82f7b847f709: Layer already exists
+c23e35ce0d97: Pushed
+3a9714186f75: Layer already exists
+e1ed8e09cf5d: Layer already exists
+153b8cd2ae3a: Pushed
+6d7c150df58d: Pushed
+6478b4b624ed: Pushed
+platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da: digest: sha256:034516fcbde67db5b936de6447ad9707cbc3323784480b8ada7015626c9942fb size: 2207
+info: Docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da' not exists locally but is already in remote registry. Skipping push...

package/dist/artifacts/py-archive/archive.json

@@ -0,0 +1 @@
+{"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/1.0.0.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.0.tgz"}

package/dist/artifacts/py-archive/docker_x64.json

@@ -0,0 +1 @@
+{"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da","entrypoint":[]}

package/dist/docker/Dockerfile-py-archive

@@ -0,0 +1,22 @@
+# Auto-generated Dockerfile for Python package
+FROM python:3.12-slim
+
+WORKDIR /app
+
+
+
+# Always keep basic python packaging tools fresh to avoid CVEs even in old python versions
+RUN pip install --upgrade pip wheel setuptools
+
+# Install dependencies to leverage Docker cache
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+# Copy package source
+COPY . /app
+
+# Set Python path
+ENV PYTHONPATH=/app
+
+# Default command (will be overridden by entrypoint)
+CMD ["bash"]

package/dist/tengo/software/immunebuilder-predict.sw.json

@@ -0,0 +1 @@
+{"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/1.0.0.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/1.2.4-{os}-{arch}.tgz","python-version":"3.12.10","envVars":[],"binDir":"bin"},"toolset":"pip","dependencies":{"requirements":"requirements.txt"}},"docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.a87395ddc3da","entrypoint":[],"cmd":["python","{pkg}/run_immunebuilder.py"],"pkg":"/app"}}

package/package.json

@@ -0,0 +1,41 @@
+{
+  "name": "@platforma-open/milaboratories.3d-structure-prediction.software",
+  "version": "1.0.0",
+  "type": "module",
+  "description": "Block Software",
+  "block-software": {
+    "artifacts": {
+      "py-archive": {
+        "type": "python",
+        "registry": "platforma-open",
+        "environment": "@platforma-open/milaboratories.runenv-python-3:3.12.10-atls",
+        "dependencies": {
+          "toolset": "pip",
+          "requirements": "requirements.txt"
+        },
+        "root": "./src_python"
+      }
+    },
+    "entrypoints": {
+      "immunebuilder-predict": {
+        "binary": {
+          "artifact": "py-archive",
+          "cmd": [
+            "python",
+            "{pkg}/run_immunebuilder.py"
+          ]
+        }
+      }
+    }
+  },
+  "devDependencies": {
+    "@platforma-open/milaboratories.runenv-python-3": "1.7.12",
+    "@platforma-sdk/package-builder": "3.12.0"
+  },
+  "scripts": {
+    "do-pack": "shx rm -f *.tgz && pl-pkg build && pnpm pack && shx mv platforma-open*.tgz package.tgz",
+    "changeset": "changeset",
+    "version-packages": "changeset version",
+    "build": "pl-pkg build"
+  }
+}

package/src_python/numbering.py

@@ -0,0 +1,103 @@
+"""IMGT numbering helpers.
+
+ImmuneBuilder runs ANARCI internally and exposes numbered residues on the
+Antibody object. Default scheme is typically Chothia unless configured. Until
+runtime testing confirms the scheme emitted by `antibody.numbered_sequences`,
+we trust what comes out and record the scheme in provenance; if a Chothia
+fallback is needed, switch to post-hoc renumbering via the `anarci` CLI here.
+
+IMGT CDR ranges (per spec R27):
+  CDRH1: 27-38   CDRH2: 56-65   CDRH3: 105-117
+  CDRL1: 27-38   CDRL2: 56-65   CDRL3: 105-117
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+IMGT_CDR_RANGES: dict[str, dict[str, tuple[int, int]]] = {
+    "H": {"CDR1": (27, 38), "CDR2": (56, 65), "CDR3": (105, 117)},
+    "L": {"CDR1": (27, 38), "CDR2": (56, 65), "CDR3": (105, 117)},
+}
+
+
+@dataclass
+class NumberedResidue:
+    chain: str  # "H" or "L"
+    pos: str  # IMGT position as string; may include insertion code (e.g. "111A").
+    aa: str
+
+    @property
+    def imgt_int(self) -> int:
+        digits = "".join(c for c in self.pos if c.isdigit())
+        return int(digits) if digits else 0
+
+    @property
+    def region(self) -> str:
+        ranges = IMGT_CDR_RANGES.get(self.chain, {})
+        n = self.imgt_int
+        for name, (lo, hi) in ranges.items():
+            if lo <= n <= hi:
+                return name
+        return "FR"
+
+
+def extract_numbered_residues(antibody) -> list[NumberedResidue]:
+    """Pull residue numbering out of an ImmuneBuilder Antibody.
+
+    `antibody.numbered_sequences` is {'H': [((pos, ins), aa), ...], 'L': ...}.
+    For VHH only 'H' is present. Residues are returned in N-to-C order per
+    chain, heavy first then light.
+    """
+    out: list[NumberedResidue] = []
+    numbered = getattr(antibody, "numbered_sequences", {}) or {}
+    for chain in ("H", "L"):
+        chain_data = numbered.get(chain, [])
+        for entry in chain_data:
+            (pos, ins), aa = entry
+            pos_str = f"{pos}{ins.strip()}" if ins and ins.strip() else str(pos)
+            out.append(NumberedResidue(chain=chain, pos=pos_str, aa=aa))
+    return out
+
+
+def cdr_ranges_in_pdb_notation(chain: str) -> dict[str, tuple[str, str]]:
+    """Return CDR ranges formatted for REMARK 99 CDR* records.
+
+    Example: {"CDR1": ("H27", "H38"), ...} for chain H.
+    """
+    ranges = IMGT_CDR_RANGES.get(chain, {})
+    return {
+        name: (f"{chain}{lo}", f"{chain}{hi}")
+        for name, (lo, hi) in ranges.items()
+    }
+
+
+def cdrh3_length(residues: list[NumberedResidue]) -> int:
+    """Count residues in CDRH3."""
+    return sum(1 for r in residues if r.chain == "H" and r.region == "CDR3")
+
+
+# IMGT 42/49/50/52 are the same four physical FR2 residues historically
+# described as Kabat 37/44/45/47. FR2 has no insertion-prone loops, so the
+# correspondence is canonical (Vincke et al. 2009; Mitchell & Colwell 2018).
+VHH_HALLMARKS_IMGT: dict[int, tuple[str, ...]] = {
+    42: ("F", "Y"),  # canonical VHH; conventional VH carries V
+    49: ("E",),      # canonical VHH; conventional VH carries G
+    50: ("R",),      # canonical VHH; conventional VH carries L
+    52: ("G",),      # canonical VHH; conventional VH carries W
+}
+
+
+def vhh_hallmarks_present(residues: list[NumberedResidue]) -> bool:
+    """R15 — return True when the heavy chain looks like a canonical VHH.
+
+    Reads IMGT-numbered residues already extracted from the predicted Antibody
+    (no second ANARCI call). Tolerates one humanized position: True iff at
+    least 2 of the 4 hallmark positions carry a canonical VHH residue.
+    """
+    by_pos = {r.imgt_int: r.aa for r in residues if r.chain == "H"}
+    matches = sum(
+        1 for pos, expected in VHH_HALLMARKS_IMGT.items()
+        if by_pos.get(pos) in expected
+    )
+    return matches >= 2

package/src_python/pdb_writer.py

@@ -0,0 +1,137 @@
+"""PDB writer that augments ImmuneBuilder output with REMARKs.
+
+ImmuneBuilder writes a standard PDB. Per spec R26/R28/R29 we need to:
+ - Clamp per-atom B-factor to [0.00, 99.99] to fit PDB `%6.2f` precision.
+ - Inject a TITLE line identifying the predictor.
+ - Inject REMARK 99 PROVENANCE block (version, seed, block version, ISO date).
+ - Inject REMARK 99 CDR* records with IMGT CDR ranges.
+
+The cleanest approach is: let ImmuneBuilder write a temp PDB, then post-
+process the lines — injecting REMARKs after TITLE and clamping B-factors on
+ATOM/HETATM lines in one pass.
+"""
+
+from __future__ import annotations
+
+from datetime import datetime, timezone
+from pathlib import Path
+
+from numbering import IMGT_CDR_RANGES, cdr_ranges_in_pdb_notation
+
+B_FACTOR_MIN = 0.00
+B_FACTOR_MAX = 99.99
+
+
+def _iso_now() -> str:
+    return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ")
+
+
+def _clamp_b_factor(line: str) -> tuple[str, bool]:
+    """Clamp B-factor column on ATOM/HETATM lines. Returns (new_line, clamped)."""
+    if not (line.startswith("ATOM") or line.startswith("HETATM")):
+        return line, False
+    if len(line) < 66:
+        return line, False
+    raw = line[60:66]
+    try:
+        value = float(raw)
+    except ValueError:
+        return line, False
+    clamped = max(B_FACTOR_MIN, min(B_FACTOR_MAX, value))
+    if clamped == value:
+        return line, False
+    return f"{line[:60]}{clamped:6.2f}{line[66:]}", True
+
+
+def _cdr_remark_lines(mode: str) -> list[str]:
+    """Emit REMARK 99 CDR* lines (IMGT ranges)."""
+    lines: list[str] = []
+    chains = ["H"] if mode == "NanoBodyBuilder2" else ["H", "L"]
+    for chain in chains:
+        for cdr_name, (lo, hi) in cdr_ranges_in_pdb_notation(chain).items():
+            # e.g. "REMARK 99 PLATFORMA CDRH1 H27-H38"
+            label = f"CDR{chain}{cdr_name[-1]}"  # CDR1 → CDRH1 / CDRL1
+            lines.append(f"REMARK  99 PLATFORMA {label} {lo}-{hi}")
+    return lines
+
+
+def _provenance_remark_lines(
+    *,
+    immunebuilder_version: str,
+    torch_seed: int,
+    block_version: str,
+    numbering_scheme: str,
+) -> list[str]:
+    return [
+        "REMARK  99 PROVENANCE",
+        f"REMARK  99 PROVENANCE immunebuilder-version={immunebuilder_version}",
+        f"REMARK  99 PROVENANCE torch-seed={torch_seed}",
+        f"REMARK  99 PROVENANCE block-version={block_version}",
+        f"REMARK  99 PROVENANCE prediction-date={_iso_now()}",
+        f"REMARK  99 PROVENANCE numbering-scheme={numbering_scheme}",
+    ]
+
+
+def _title_line(mode: str) -> str:
+    builder = "ABodyBuilder2" if mode == "ABodyBuilder2" else "NanoBodyBuilder2"
+    return f"TITLE     {builder} prediction (Platforma Structure Prediction block)"
+
+
+def augment_pdb(
+    source_path: Path,
+    dest_path: Path,
+    *,
+    mode: str,
+    immunebuilder_version: str,
+    torch_seed: int,
+    block_version: str,
+    numbering_scheme: str,
+) -> dict:
+    """Rewrite source_path → dest_path with TITLE + REMARK injections + B clamping.
+
+    Returns stats dict: {clamped_count: int, injected_remarks: int}.
+    """
+    with open(source_path, "r") as f:
+        src_lines = [line.rstrip("\n") for line in f]
+
+    title = _title_line(mode)
+    provenance = _provenance_remark_lines(
+        immunebuilder_version=immunebuilder_version,
+        torch_seed=torch_seed,
+        block_version=block_version,
+        numbering_scheme=numbering_scheme,
+    )
+    cdr = _cdr_remark_lines(mode)
+    injected = [title, *provenance, *cdr]
+
+    out_lines: list[str] = []
+    clamped = 0
+    header_done = False
+
+    for line in src_lines:
+        # Skip any existing TITLE that ImmuneBuilder might have put down.
+        if not header_done and line.startswith("TITLE"):
+            continue
+        if not header_done and line.startswith(("ATOM", "HETATM", "MODEL")):
+            # Inject our block before the coordinate section starts.
+            out_lines.extend(injected)
+            header_done = True
+
+        new_line, was_clamped = _clamp_b_factor(line)
+        out_lines.append(new_line)
+        if was_clamped:
+            clamped += 1
+
+    # If the PDB had no ATOM/HETATM/MODEL lines at all (shouldn't happen),
+    # still emit the REMARKs so downstream parsers don't break.
+    if not header_done:
+        out_lines = injected + out_lines
+
+    with open(dest_path, "w") as f:
+        f.write("\n".join(out_lines))
+        f.write("\n")
+
+    return {
+        "clamped_count": clamped,
+        "injected_remarks": len(injected),
+    }

package/src_python/requirements.txt

@@ -0,0 +1,4 @@
+ImmuneBuilder==1.2
+torch==2.7.0
+biopython==1.85
+openmm==8.3.1