@platforma-open/milaboratories.3d-structure-prediction.software 1.0.1 → 1.0.2

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.
Files changed (10) hide show
  1. package/.turbo/turbo-build.log +403 -246
  2. package/CHANGELOG.md +6 -0
  3. package/Dockerfile +56 -0
  4. package/dist/artifacts/py-archive/archive.json +1 -1
  5. package/dist/artifacts/{py-archive → py-docker}/docker_x64.json +1 -1
  6. package/dist/tengo/software/immunebuilder-predict.sw.json +1 -1
  7. package/package.json +13 -1
  8. package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.2.tgz +0 -0
  9. package/dist/docker/Dockerfile-py-archive +0 -22
  10. package/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.1.tgz +0 -0
package/.turbo/turbo-build.log CHANGED
@@ -1,276 +1,433 @@
1
1
   WARN  Issue while reading "/home/runner/work/3d-structure-prediction/3d-structure-prediction/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
2
2
 
3
- > @platforma-open/milaboratories.3d-structure-prediction.software@1.0.1 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
3
+ > @platforma-open/milaboratories.3d-structure-prediction.software@1.0.2 build /home/runner/work/3d-structure-prediction/3d-structure-prediction/software
4
4
  > pl-pkg build
5
5
 
6
6
  info: Building docker images...
7
- info: Building docker image for 'py-archive'...
7
+ info: Building docker image for 'py-docker'...
8
8
  #0 building with "default" instance using docker driver
9
9
 
10
- #1 [internal] load build definition from Dockerfile-py-archive
11
- #1 transferring dockerfile: 539B done
10
+ #1 [internal] load build definition from Dockerfile
11
+ #1 transferring dockerfile: 2.23kB done
12
12
  #1 DONE 0.0s
13
13
 
14
- #2 [auth] library/python:pull token for registry-1.docker.io
15
- #2 DONE 0.0s
14
+ #2 resolve image config for docker-image://docker.io/docker/dockerfile:1
15
+ #2 ...
16
16
 
17
- #3 [internal] load metadata for docker.io/library/python:3.12-slim
18
- #3 DONE 0.5s
17
+ #3 [auth] docker/dockerfile:pull token for registry-1.docker.io
18
+ #3 DONE 0.0s
19
19
 
20
- #4 [internal] load .dockerignore
21
- #4 transferring context: 2B done
22
- #4 DONE 0.0s
20
+ #2 resolve image config for docker-image://docker.io/docker/dockerfile:1
21
+ #2 DONE 0.9s
23
22
 
24
- #5 [internal] load build context
25
- #5 transferring context: 36.40kB done
26
- #5 DONE 0.0s
23
+ #4 docker-image://docker.io/docker/dockerfile:1@sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769
24
+ #4 resolve docker.io/docker/dockerfile:1@sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769 done
25
+ #4 sha256:2780b5c3bab67f1f76c781860de469442999ed1a0d7992a5efdf2cffc0e3d769 8.43kB / 8.43kB done
26
+ #4 sha256:369c4e6584693f8e13d7a27755a6b10201798e229cdfad5eae04ea5f15a76412 1.13kB / 1.13kB done
27
+ #4 sha256:14cdce40ae0e938cf7d2d7fe6aa3dec2beb66aa066d6a54356c64fd8af6323c2 1.33kB / 1.33kB done
28
+ #4 sha256:bcb5d2ab7af67a669c932851c8bb8a26895dda6258900edfd7429d57bfd3592f 8.39MB / 14.11MB 0.1s
29
+ #4 sha256:bcb5d2ab7af67a669c932851c8bb8a26895dda6258900edfd7429d57bfd3592f 14.11MB / 14.11MB 0.1s done
30
+ #4 extracting sha256:bcb5d2ab7af67a669c932851c8bb8a26895dda6258900edfd7429d57bfd3592f 0.1s
31
+ #4 extracting sha256:bcb5d2ab7af67a669c932851c8bb8a26895dda6258900edfd7429d57bfd3592f 0.1s done
32
+ #4 DONE 0.3s
27
33
 
28
- #6 [1/6] FROM docker.io/library/python:3.12-slim@sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3
29
- #6 resolve docker.io/library/python:3.12-slim@sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3 done
30
- #6 sha256:46cb7cc2877e60fbd5e21a9ae6115c30ace7a077b9f8772da879e4590c18c2e3 10.37kB / 10.37kB done
31
- #6 sha256:4386a385d81dba9f72ed72a6fe4237755d7f5440c84b417650f38336bbc43117 1.75kB / 1.75kB done
32
- #6 sha256:7bf61a5ec2a4631b240bc8cf83404e2dd37fb06a4b4bbd34b2c36906a5fb4aee 5.66kB / 5.66kB done
33
- #6 sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 12.58MB / 29.78MB 0.1s
34
- #6 sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 0B / 1.29MB 0.1s
35
- #6 sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 0B / 12.10MB 0.1s
36
- #6 sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 29.78MB / 29.78MB 0.2s done
37
- #6 sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 1.29MB / 1.29MB 0.1s done
38
- #6 sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 5.24MB / 12.10MB 0.2s
39
- #6 sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357 248B / 248B 0.2s done
40
- #6 sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 12.10MB / 12.10MB 0.3s done
41
- #6 extracting sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd
42
- #6 extracting sha256:3531af2bc2a9c8883754652783cf96207d53189db279c9637b7157d034de7ecd 0.9s done
43
- #6 extracting sha256:cb8c0a9140ac107575972113eb5fd2e6c3cdddc592371a5ac31c4623dcb13d5d 0.1s done
44
- #6 extracting sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65
45
- #6 extracting sha256:4d873bcef452ab1c054b9a0f25ace04a446c558a7b925aed2fc5bc21533e0f65 1.8s done
46
- #6 extracting sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357
47
- #6 extracting sha256:3fc9d9ab5045181fbd49d1d30a2dbad144172d4c3c141f70117ddb0b918d8357 done
48
- #6 DONE 3.7s
34
+ #5 [internal] load metadata for docker.io/mambaorg/micromamba:1.5.10
35
+ #5 ...
49
36
 
50
- #7 [2/6] WORKDIR /app
37
+ #6 [auth] mambaorg/micromamba:pull token for registry-1.docker.io
38
+ #6 DONE 0.0s
39
+
40
+ #5 [internal] load metadata for docker.io/mambaorg/micromamba:1.5.10
41
+ #5 DONE 0.8s
42
+
43
+ #7 [internal] load .dockerignore
44
+ #7 transferring context: 2B done
51
45
  #7 DONE 0.0s
52
46
 
53
- #8 [3/6] RUN pip install --upgrade pip wheel setuptools
54
- #8 1.656 Requirement already satisfied: pip in /usr/local/lib/python3.12/site-packages (25.0.1)
55
- #8 1.717 Collecting pip
56
- #8 1.751 Downloading pip-26.1.1-py3-none-any.whl.metadata (4.6 kB)
57
- #8 1.779 Collecting wheel
58
- #8 1.784 Downloading wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
59
- #8 1.915 Collecting setuptools
60
- #8 1.920 Downloading setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
61
- #8 1.957 Collecting packaging>=24.0 (from wheel)
62
- #8 1.961 Downloading packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
63
- #8 1.973 Downloading pip-26.1.1-py3-none-any.whl (1.8 MB)
64
- #8 2.003 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 81.0 MB/s eta 0:00:00
65
- #8 2.008 Downloading wheel-0.47.0-py3-none-any.whl (32 kB)
66
- #8 2.015 Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
67
- #8 2.028 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 85.8 MB/s eta 0:00:00
68
- #8 2.034 Downloading packaging-26.2-py3-none-any.whl (100 kB)
69
- #8 2.081 Installing collected packages: setuptools, pip, packaging, wheel
70
- #8 2.734 Attempting uninstall: pip
71
- #8 2.737 Found existing installation: pip 25.0.1
72
- #8 2.769 Uninstalling pip-25.0.1:
73
- #8 2.777 Successfully uninstalled pip-25.0.1
74
- #8 3.640 Successfully installed packaging-26.2 pip-26.1.1 setuptools-82.0.1 wheel-0.47.0
75
- #8 3.641 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.
76
- #8 DONE 3.8s
47
+ #8 [internal] load build context
48
+ #8 transferring context: 36.40kB done
49
+ #8 DONE 0.0s
77
50
 
78
- #9 [4/6] COPY requirements.txt .
79
- #9 DONE 0.0s
51
+ #9 [1/6] FROM docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d
52
+ #9 resolve docker.io/mambaorg/micromamba:1.5.10@sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d done
53
+ #9 sha256:e3797091302382ea841498bc93a7b0a50f7c1448333d5e946d2d1608d0c5f43d 2.36kB / 2.36kB done
54
+ #9 sha256:30fe8036db79bfbab0cdf8d102dcfd22ee410944fed17b23851977246235b880 0B / 6.20MB 0.1s
55
+ #9 sha256:a2318d6c47ec9cac5acc500c47c79602bcf953cec711a18bc898911a0984365b 0B / 29.13MB 0.1s
56
+ #9 sha256:0d56d98386a9a231fee4dcf145a261d9d12da39f1c5a5d3bbe09a1aa727febf8 0B / 122.68kB 0.1s
57
+ #9 sha256:008e06cd8432eb558faa4738a092f30b38dd8db3137a5dd3fca57374a790825b 2.56kB / 2.56kB done
58
+ #9 sha256:c5ef7ca066aec9ae6b5a07ceca914beded0754d74f2006b33ee80cb661688f74 6.28kB / 6.28kB done
59
+ #9 sha256:a2318d6c47ec9cac5acc500c47c79602bcf953cec711a18bc898911a0984365b 29.13MB / 29.13MB 0.2s done
60
+ #9 sha256:0d56d98386a9a231fee4dcf145a261d9d12da39f1c5a5d3bbe09a1aa727febf8 122.68kB / 122.68kB 0.2s done
61
+ #9 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 0B / 32B 0.2s
62
+ #9 sha256:1b19c15ef8e221c4e8f2f5233ce6dcb27342ecf18997a0576cf301345df0b2ed 0B / 521B 0.2s
63
+ #9 sha256:30fe8036db79bfbab0cdf8d102dcfd22ee410944fed17b23851977246235b880 6.20MB / 6.20MB 0.3s done
64
+ #9 sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 32B / 32B 0.3s done
65
+ #9 sha256:1b19c15ef8e221c4e8f2f5233ce6dcb27342ecf18997a0576cf301345df0b2ed 521B / 521B 0.3s done
66
+ #9 extracting sha256:a2318d6c47ec9cac5acc500c47c79602bcf953cec711a18bc898911a0984365b 0.1s
67
+ #9 sha256:9a782d6d1eace15aadfa1d16eb83ad2abdea075c6c9e200247950571a3719e10 0B / 3.77kB 0.3s
68
+ #9 sha256:8b456163e45ffc9e8274e77e02d1a5a166f27e760db7314ea9ee89f5578090d6 0B / 215B 0.3s
69
+ #9 sha256:51b5951dad11c47781e0b67c512ab7f1b148983b42cb5b8cbfb3ea6e8d28a602 0B / 282B 0.3s
70
+ #9 sha256:9a782d6d1eace15aadfa1d16eb83ad2abdea075c6c9e200247950571a3719e10 3.77kB / 3.77kB 0.4s done
71
+ #9 sha256:51b5951dad11c47781e0b67c512ab7f1b148983b42cb5b8cbfb3ea6e8d28a602 282B / 282B 0.3s done
72
+ #9 sha256:c1d339bd3cdc8184904ef6ed4e4685a7551020e738a57e9b8c27edead08b3461 0B / 645B 0.4s
73
+ #9 sha256:e9e8562f12ed796758a0790bfccb45f2463190f4ba8696dac09a9f22b20e37e3 0B / 683B 0.4s
74
+ #9 sha256:8b456163e45ffc9e8274e77e02d1a5a166f27e760db7314ea9ee89f5578090d6 215B / 215B 0.4s done
75
+ #9 sha256:c1d339bd3cdc8184904ef6ed4e4685a7551020e738a57e9b8c27edead08b3461 645B / 645B 0.5s done
76
+ #9 sha256:e9e8562f12ed796758a0790bfccb45f2463190f4ba8696dac09a9f22b20e37e3 683B / 683B 0.4s done
77
+ #9 sha256:db3fc724910ed98f15e8511e8024faf769a34901595e617bd4c7ebd8b8b8fd29 345B / 345B 0.5s done
78
+ #9 extracting sha256:a2318d6c47ec9cac5acc500c47c79602bcf953cec711a18bc898911a0984365b 1.1s done
79
+ #9 extracting sha256:0d56d98386a9a231fee4dcf145a261d9d12da39f1c5a5d3bbe09a1aa727febf8 done
80
+ #9 extracting sha256:30fe8036db79bfbab0cdf8d102dcfd22ee410944fed17b23851977246235b880
81
+ #9 extracting sha256:30fe8036db79bfbab0cdf8d102dcfd22ee410944fed17b23851977246235b880 0.1s done
82
+ #9 extracting sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done
83
+ #9 extracting sha256:1b19c15ef8e221c4e8f2f5233ce6dcb27342ecf18997a0576cf301345df0b2ed done
84
+ #9 extracting sha256:51b5951dad11c47781e0b67c512ab7f1b148983b42cb5b8cbfb3ea6e8d28a602
85
+ #9 extracting sha256:51b5951dad11c47781e0b67c512ab7f1b148983b42cb5b8cbfb3ea6e8d28a602 done
86
+ #9 extracting sha256:9a782d6d1eace15aadfa1d16eb83ad2abdea075c6c9e200247950571a3719e10 done
87
+ #9 extracting sha256:8b456163e45ffc9e8274e77e02d1a5a166f27e760db7314ea9ee89f5578090d6 done
88
+ #9 extracting sha256:e9e8562f12ed796758a0790bfccb45f2463190f4ba8696dac09a9f22b20e37e3 done
89
+ #9 extracting sha256:c1d339bd3cdc8184904ef6ed4e4685a7551020e738a57e9b8c27edead08b3461 done
90
+ #9 extracting sha256:db3fc724910ed98f15e8511e8024faf769a34901595e617bd4c7ebd8b8b8fd29 done
91
+ #9 DONE 1.6s
80
92
 
81
- #10 [5/6] RUN pip install --no-cache-dir -r requirements.txt
82
- #10 0.642 Collecting ImmuneBuilder==1.2 (from -r requirements.txt (line 1))
83
- #10 0.682 Downloading ImmuneBuilder-1.2-py3-none-any.whl.metadata (7.7 kB)
84
- #10 0.749 Collecting torch==2.7.0 (from -r requirements.txt (line 2))
85
- #10 0.755 Downloading torch-2.7.0-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (29 kB)
86
- #10 0.807 Collecting biopython==1.85 (from -r requirements.txt (line 3))
87
- #10 0.815 Downloading biopython-1.85-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
88
- #10 0.854 Collecting openmm==8.3.1 (from -r requirements.txt (line 4))
89
- #10 0.859 Downloading openmm-8.3.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.0 kB)
90
- #10 0.868 Collecting pdbfixer==1.12.0 (from -r requirements.txt (line 5))
91
- #10 0.874 Downloading pdbfixer-1.12.0.tar.gz (665 kB)
92
- #10 0.893 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 665.9/665.9 kB 70.3 MB/s 0:00:00
93
- #10 0.940 Installing build dependencies: started
94
- #10 1.554 Installing build dependencies: finished with status 'done'
95
- #10 1.554 Getting requirements to build wheel: started
96
- #10 1.973 Getting requirements to build wheel: finished with status 'done'
97
- #10 1.974 Preparing metadata (pyproject.toml): started
98
- #10 2.168 Preparing metadata (pyproject.toml): finished with status 'done'
99
- #10 2.374 Collecting numpy (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
100
- #10 2.378 Downloading numpy-2.4.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
101
- #10 2.529 Collecting scipy>=1.6 (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
102
- #10 2.533 Downloading scipy-1.17.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
103
- #10 2.573 Collecting einops>=0.3 (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
104
- #10 2.578 Downloading einops-0.8.2-py3-none-any.whl.metadata (13 kB)
105
- #10 2.612 Collecting requests (from ImmuneBuilder==1.2->-r requirements.txt (line 1))
106
- #10 2.616 Downloading requests-2.33.1-py3-none-any.whl.metadata (4.8 kB)
107
- #10 2.644 Collecting filelock (from torch==2.7.0->-r requirements.txt (line 2))
108
- #10 2.648 Downloading filelock-3.29.0-py3-none-any.whl.metadata (2.0 kB)
109
- #10 2.666 Collecting typing-extensions>=4.10.0 (from torch==2.7.0->-r requirements.txt (line 2))
110
- #10 2.672 Downloading typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
111
- #10 2.676 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)
112
- #10 2.687 Collecting sympy>=1.13.3 (from torch==2.7.0->-r requirements.txt (line 2))
113
- #10 2.691 Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
114
- #10 2.707 Collecting networkx (from torch==2.7.0->-r requirements.txt (line 2))
115
- #10 2.712 Downloading networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
116
- #10 2.727 Collecting jinja2 (from torch==2.7.0->-r requirements.txt (line 2))
117
- #10 2.732 Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
118
- #10 2.746 Collecting fsspec (from torch==2.7.0->-r requirements.txt (line 2))
119
- #10 2.751 Downloading fsspec-2026.4.0-py3-none-any.whl.metadata (10 kB)
120
- #10 2.778 Collecting nvidia-cuda-nvrtc-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
121
- #10 2.781 Downloading nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
122
- #10 2.797 Collecting nvidia-cuda-runtime-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
123
- #10 2.803 Downloading nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
124
- #10 2.817 Collecting nvidia-cuda-cupti-cu12==12.6.80 (from torch==2.7.0->-r requirements.txt (line 2))
125
- #10 2.821 Downloading nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
126
- #10 2.841 Collecting nvidia-cudnn-cu12==9.5.1.17 (from torch==2.7.0->-r requirements.txt (line 2))
127
- #10 2.845 Downloading nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl.metadata (1.6 kB)
128
- #10 2.860 Collecting nvidia-cublas-cu12==12.6.4.1 (from torch==2.7.0->-r requirements.txt (line 2))
129
- #10 2.867 Downloading nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
130
- #10 2.877 Collecting nvidia-cufft-cu12==11.3.0.4 (from torch==2.7.0->-r requirements.txt (line 2))
131
- #10 2.885 Downloading nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
132
- #10 2.904 Collecting nvidia-curand-cu12==10.3.7.77 (from torch==2.7.0->-r requirements.txt (line 2))
133
- #10 2.908 Downloading nvidia_curand_cu12-10.3.7.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
134
- #10 2.923 Collecting nvidia-cusolver-cu12==11.7.1.2 (from torch==2.7.0->-r requirements.txt (line 2))
135
- #10 2.927 Downloading nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
136
- #10 2.938 Collecting nvidia-cusparse-cu12==12.5.4.2 (from torch==2.7.0->-r requirements.txt (line 2))
137
- #10 2.943 Downloading nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
138
- #10 2.953 Collecting nvidia-cusparselt-cu12==0.6.3 (from torch==2.7.0->-r requirements.txt (line 2))
139
- #10 2.958 Downloading nvidia_cusparselt_cu12-0.6.3-py3-none-manylinux2014_x86_64.whl.metadata (6.8 kB)
140
- #10 2.965 Collecting nvidia-nccl-cu12==2.26.2 (from torch==2.7.0->-r requirements.txt (line 2))
141
- #10 2.969 Downloading nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.0 kB)
142
- #10 2.984 Collecting nvidia-nvtx-cu12==12.6.77 (from torch==2.7.0->-r requirements.txt (line 2))
143
- #10 2.988 Downloading nvidia_nvtx_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
144
- #10 3.000 Collecting nvidia-nvjitlink-cu12==12.6.85 (from torch==2.7.0->-r requirements.txt (line 2))
145
- #10 3.004 Downloading nvidia_nvjitlink_cu12-12.6.85-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.5 kB)
146
- #10 3.014 Collecting nvidia-cufile-cu12==1.11.1.6 (from torch==2.7.0->-r requirements.txt (line 2))
147
- #10 3.018 Downloading nvidia_cufile_cu12-1.11.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
148
- #10 3.029 Collecting triton==3.3.0 (from torch==2.7.0->-r requirements.txt (line 2))
149
- #10 3.034 Downloading triton-3.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.5 kB)
150
- #10 3.069 Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch==2.7.0->-r requirements.txt (line 2))
151
- #10 3.073 Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
152
- #10 3.120 Collecting MarkupSafe>=2.0 (from jinja2->torch==2.7.0->-r requirements.txt (line 2))
153
- #10 3.125 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)
154
- #10 3.206 Collecting charset_normalizer<4,>=2 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
155
- #10 3.211 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)
156
- #10 3.221 Collecting idna<4,>=2.5 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
157
- #10 3.224 Downloading idna-3.13-py3-none-any.whl.metadata (8.0 kB)
158
- #10 3.240 Collecting urllib3<3,>=1.26 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
159
- #10 3.244 Downloading urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
160
- #10 3.255 Collecting certifi>=2023.5.7 (from requests->ImmuneBuilder==1.2->-r requirements.txt (line 1))
161
- #10 3.259 Downloading certifi-2026.4.22-py3-none-any.whl.metadata (2.5 kB)
162
- #10 3.268 Downloading ImmuneBuilder-1.2-py3-none-any.whl (32 kB)
163
- #10 3.272 Downloading torch-2.7.0-cp312-cp312-manylinux_2_28_x86_64.whl (865.0 MB)
164
- #10 5.616 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 865.0/865.0 MB 408.7 MB/s 0:00:02
165
- #10 5.623 Downloading biopython-1.85-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
166
- #10 5.633 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 423.8 MB/s 0:00:00
167
- #10 5.641 Downloading openmm-8.3.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (14.0 MB)
168
- #10 5.733 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.0/14.0 MB 157.6 MB/s 0:00:00
169
- #10 5.739 Downloading nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (393.1 MB)
170
- #10 6.411 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 393.1/393.1 MB 638.8 MB/s 0:00:00
171
- #10 6.417 Downloading nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.9 MB)
172
- #10 6.435 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.9/8.9 MB 567.2 MB/s 0:00:00
173
- #10 6.438 Downloading nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl (23.7 MB)
174
- #10 6.484 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 23.7/23.7 MB 542.5 MB/s 0:00:00
175
- #10 6.487 Downloading nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (897 kB)
176
- #10 6.490 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 897.7/897.7 kB 1.2 GB/s 0:00:00
177
- #10 6.494 Downloading nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl (571.0 MB)
178
- #10 7.821 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 571.0/571.0 MB 409.1 MB/s 0:00:01
179
- #10 7.826 Downloading nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (200.2 MB)
180
- #10 8.193 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 200.2/200.2 MB 548.4 MB/s 0:00:00
181
- #10 8.197 Downloading nvidia_cufile_cu12-1.11.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.1 MB)
182
- #10 8.200 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 1.1 GB/s 0:00:00
183
- #10 8.205 Downloading nvidia_curand_cu12-10.3.7.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (56.3 MB)
184
- #10 8.338 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 MB 427.8 MB/s 0:00:00
185
- #10 8.344 Downloading nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (158.2 MB)
186
- #10 8.644 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.2/158.2 MB 529.9 MB/s 0:00:00
187
- #10 8.648 Downloading nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (216.6 MB)
188
- #10 9.003 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 216.6/216.6 MB 613.3 MB/s 0:00:00
189
- #10 9.007 Downloading nvidia_cusparselt_cu12-0.6.3-py3-none-manylinux2014_x86_64.whl (156.8 MB)
190
- #10 9.444 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 156.8/156.8 MB 359.8 MB/s 0:00:00
191
- #10 9.449 Downloading nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (201.3 MB)
192
- #10 9.747 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 201.3/201.3 MB 684.7 MB/s 0:00:00
193
- #10 9.751 Downloading nvidia_nvjitlink_cu12-12.6.85-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (19.7 MB)
194
- #10 9.776 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.7/19.7 MB 846.2 MB/s 0:00:00
195
- #10 9.780 Downloading nvidia_nvtx_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (89 kB)
196
- #10 9.785 Downloading triton-3.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (156.5 MB)
197
- #10 10.17 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 156.5/156.5 MB 413.3 MB/s 0:00:00
198
- #10 10.17 Downloading einops-0.8.2-py3-none-any.whl (65 kB)
199
- #10 10.17 Downloading scipy-1.17.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.2 MB)
200
- #10 10.23 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 35.2/35.2 MB 648.8 MB/s 0:00:00
201
- #10 10.24 Downloading numpy-2.4.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
202
- #10 10.26 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.6/16.6 MB 798.0 MB/s 0:00:00
203
- #10 10.26 Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)
204
- #10 10.27 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 739.7 MB/s 0:00:00
205
- #10 10.28 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
206
- #10 10.28 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 998.2 MB/s 0:00:00
207
- #10 10.28 Downloading typing_extensions-4.15.0-py3-none-any.whl (44 kB)
208
- #10 10.29 Downloading filelock-3.29.0-py3-none-any.whl (39 kB)
209
- #10 10.29 Downloading fsspec-2026.4.0-py3-none-any.whl (203 kB)
210
- #10 10.29 Downloading jinja2-3.1.6-py3-none-any.whl (134 kB)
211
- #10 10.30 Downloading markupsafe-3.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
212
- #10 10.30 Downloading networkx-3.6.1-py3-none-any.whl (2.1 MB)
213
- #10 10.31 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 1.2 GB/s 0:00:00
214
- #10 10.31 Downloading requests-2.33.1-py3-none-any.whl (64 kB)
215
- #10 10.31 Downloading charset_normalizer-3.4.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (216 kB)
216
- #10 10.32 Downloading idna-3.13-py3-none-any.whl (68 kB)
217
- #10 10.32 Downloading urllib3-2.7.0-py3-none-any.whl (131 kB)
218
- #10 10.32 Downloading certifi-2026.4.22-py3-none-any.whl (135 kB)
219
- #10 13.22 Building wheels for collected packages: pdbfixer
220
- #10 13.22 Building wheel for pdbfixer (pyproject.toml): started
221
- #10 13.54 Building wheel for pdbfixer (pyproject.toml): finished with status 'done'
222
- #10 13.54 Created wheel for pdbfixer: filename=pdbfixer-1.12.0-py3-none-any.whl size=681766 sha256=d1e4f43402f6cbc1dfda11ad9c0a885847b65ab46dea394f9f32c835b0b24315
223
- #10 13.54 Stored in directory: /tmp/pip-ephem-wheel-cache-dhf0r3wh/wheels/79/ec/63/2ad240b7fac835f490bd1ecb748da87c99ae65618770c73a98
224
- #10 13.55 Successfully built pdbfixer
225
- #10 13.68 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, pdbfixer, nvidia-cusolver-cu12, torch, ImmuneBuilder
226
- #10 61.34
227
- #10 61.34 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 pdbfixer-1.12.0 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 urllib3-2.7.0
228
- #10 61.34 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.
229
- #10 DONE 64.6s
93
+ #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 && micromamba clean --all --yes
94
+ #10 16.13
95
+ #10 16.13 Transaction
96
+ #10 16.13
97
+ #10 16.13 Prefix: /opt/conda
98
+ #10 16.13
99
+ #10 16.13 Updating specs:
100
+ #10 16.13
101
+ #10 16.13 - python=3.12.10
102
+ #10 16.13 - anarci
103
+ #10 16.13 - hmmer
104
+ #10 16.13 - biopython=1.85
105
+ #10 16.13 - openmm=8.3.1
106
+ #10 16.13 - pdbfixer=1.12.0
107
+ #10 16.13
108
+ #10 16.13
109
+ #10 16.14 Package Version Build Channel Size
110
+ #10 16.14 ───────────────────────────────────────────────────────────────────────────────
111
+ #10 16.14 Install:
112
+ #10 16.14 ───────────────────────────────────────────────────────────────────────────────
113
+ #10 16.14
114
+ #10 16.14 + libzlib 1.3.2 h25fd6f3_2 conda-forge 64kB
115
+ #10 16.14 + libgomp 15.2.0 he0feb66_18 conda-forge 603kB
116
+ #10 16.14 + mpi 1.0 openmpi conda-forge 4kB
117
+ #10 16.14 + zlib 1.3.2 h25fd6f3_2 conda-forge 96kB
118
+ #10 16.14 + zstd 1.5.7 hb78ec9c_6 conda-forge 601kB
119
+ #10 16.14 + _openmp_mutex 4.5 20_gnu conda-forge 29kB
120
+ #10 16.14 + ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge 728kB
121
+ #10 16.14 + libgcc 15.2.0 he0feb66_18 conda-forge 1MB
122
+ #10 16.14 + tk 8.6.13 noxft_h366c992_103 conda-forge 3MB
123
+ #10 16.14 + libsqlite 3.53.1 h0c1763c_0 conda-forge 955kB
124
+ #10 16.14 + libgfortran5 15.2.0 h68bc16d_18 conda-forge 2MB
125
+ #10 16.14 + ncurses 6.6 hdb14827_0 conda-forge 919kB
126
+ #10 16.14 + libuuid 2.42 h5347b49_0 conda-forge 40kB
127
+ #10 16.14 + libnsl 2.0.1 hb9d3cd8_1 conda-forge 34kB
128
+ #10 16.14 + liblzma 5.8.3 hb03c661_0 conda-forge 113kB
129
+ #10 16.14 + libstdcxx 15.2.0 h934c35e_18 conda-forge 6MB
130
+ #10 16.14 + libgcc-ng 15.2.0 h69a702a_18 conda-forge 28kB
131
+ #10 16.14 + libffi 3.4.6 h2dba641_1 conda-forge 57kB
132
+ #10 16.14 + libexpat 2.8.0 hecca717_0 conda-forge 77kB
133
+ #10 16.14 + bzip2 1.0.8 hda65f42_9 conda-forge 260kB
134
+ #10 16.14 + libgfortran 15.2.0 h69a702a_18 conda-forge 28kB
135
+ #10 16.14 + readline 8.3 h853b02a_0 conda-forge 345kB
136
+ #10 16.14 + opencl-headers 2025.06.13 hecca717_0 conda-forge 56kB
137
+ #10 16.14 + libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge 28kB
138
+ #10 16.14 + libxcrypt 4.4.36 hd590300_1 conda-forge 100kB
139
+ #10 16.14 + libgfortran-ng 15.2.0 h69a702a_18 conda-forge 28kB
140
+ #10 16.14 + libopenblas 0.3.32 pthreads_h94d23a6_0 conda-forge 6MB
141
+ #10 16.14 + ocl-icd 2.3.3 hb9d3cd8_0 conda-forge 107kB
142
+ #10 16.14 + openmpi 4.1.6 hc5af2df_101 conda-forge 4MB
143
+ #10 16.14 + libblas 3.11.0 6_h4a7cf45_openblas conda-forge 19kB
144
+ #10 16.14 + ocl-icd-system 1.0.0 1 conda-forge 4kB
145
+ #10 16.14 + libcblas 3.11.0 6_h0358290_openblas conda-forge 19kB
146
+ #10 16.14 + liblapack 3.11.0 6_h47877c9_openblas conda-forge 19kB
147
+ #10 16.14 + gsl 2.7 he838d99_0 conda-forge 3MB
148
+ #10 16.14 + tzdata 2025c hc9c84f9_1 conda-forge 119kB
149
+ #10 16.14 + ca-certificates 2026.4.22 hbd8a1cb_0 conda-forge 131kB
150
+ #10 16.14 + cuda-version 12.9 h4f385c5_3 conda-forge 22kB
151
+ #10 16.14 + python_abi 3.12 8_cp312 conda-forge 7kB
152
+ #10 16.14 + hmmer 3.4 hb6cb901_4 bioconda 12MB
153
+ #10 16.14 + openssl 3.6.2 h35e630c_0 conda-forge 3MB
154
+ #10 16.14 + libcufft 11.4.1.4 hecca717_1 conda-forge 162MB
155
+ #10 16.14 + cuda-nvrtc 12.9.86 hecca717_1 conda-forge 67MB
156
+ #10 16.14 + python 3.12.10 h9e4cc4f_0_cpython conda-forge 31MB
157
+ #10 16.14 + packaging 26.2 pyhc364b38_0 conda-forge 92kB
158
+ #10 16.14 + setuptools 82.0.1 pyh332efcf_0 conda-forge 640kB
159
+ #10 16.14 + wheel 0.47.0 pyhd8ed1ab_0 conda-forge 33kB
160
+ #10 16.14 + pip 26.1.1 pyh8b19718_0 conda-forge 1MB
161
+ #10 16.14 + legacy-cgi 2.6.4 pyhcf101f3_0 conda-forge 20kB
162
+ #10 16.14 + numpy 2.4.3 py312h33ff503_0 conda-forge 9MB
163
+ #10 16.14 + scipy 1.17.1 py312h54fa4ab_0 conda-forge 17MB
164
+ #10 16.14 + biopython 1.85 py312h4c3975b_2 conda-forge 3MB
165
+ #10 16.14 + openmm 8.3.1 py312h50c43f0_0 conda-forge 13MB
166
+ #10 16.14 + anarci 2024.05.21 pyhdfd78af_0 bioconda 1MB
167
+ #10 16.14 + pdbfixer 1.12 pyhd8ed1ab_1 conda-forge 546kB
168
+ #10 16.14
169
+ #10 16.14 Summary:
170
+ #10 16.14
171
+ #10 16.14 Install: 54 packages
172
+ #10 16.14
173
+ #10 16.14 Total download: 353MB
174
+ #10 16.14
175
+ #10 16.14 ───────────────────────────────────────────────────────────────────────────────
176
+ #10 16.14
177
+ #10 16.14
178
+ #10 16.14
179
+ #10 16.14 Transaction starting
180
+ #10 21.20
181
+ #10 21.20 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
182
+ #10 21.20 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
183
+ #10 21.20 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
184
+ #10 21.20 mpiexec --mca opal_cuda_support 1 ...
185
+ #10 21.20
186
+ #10 21.20 In addition, the UCX support is also built but disabled by default.
187
+ #10 21.20 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
188
+ #10 21.20 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
189
+ #10 21.20 Equivalently, you can set the MCA parameters in the command line:
190
+ #10 21.20 mpiexec --mca pml ucx --mca osc ucx ...
191
+ #10 21.20 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
192
+ #10 21.20 Please consult UCX's documentation for detail.
193
+ #10 21.20
194
+ #10 21.20
195
+ #10 21.31
196
+ #10 21.31 For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
197
+ #10 21.31 To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
198
+ #10 21.31 launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
199
+ #10 21.31 mpiexec --mca opal_cuda_support 1 ...
200
+ #10 21.31
201
+ #10 21.31 In addition, the UCX support is also built but disabled by default.
202
+ #10 21.31 To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
203
+ #10 21.31 variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
204
+ #10 21.31 Equivalently, you can set the MCA parameters in the command line:
205
+ #10 21.31 mpiexec --mca pml ucx --mca osc ucx ...
206
+ #10 21.31 Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
207
+ #10 21.31 Please consult UCX's documentation for detail.
208
+ #10 21.31
209
+ #10 21.31
210
+ #10 22.65
211
+ #10 22.65 Transaction finished
212
+ #10 22.65
213
+ #10 22.65 To activate this environment, use:
214
+ #10 22.65
215
+ #10 22.65 micromamba activate base
216
+ #10 22.65
217
+ #10 22.65 Or to execute a single command in this environment, use:
218
+ #10 22.65
219
+ #10 22.65 micromamba run -n base mycommand
220
+ #10 22.65
221
+ #10 22.68 Collect information..
222
+ #10 22.68 Cleaning index cache..
223
+ #10 22.74 Cleaning lock files..
224
+ #10 22.74 Package file Size
225
+ #10 22.74 ───────────────────────────────────────────────────────────────
226
+ #10 22.74 /opt/conda/pkgs
227
+ #10 22.74 ───────────────────────────────────────────────────────────────
228
+ #10 22.74
229
+ #10 22.74 _openmp_mutex-4.5-20_gnu.conda 29kB
230
+ #10 22.74 anarci-2024.05.21-pyhdfd78af_0.tar.bz2 1MB
231
+ #10 22.74 biopython-1.85-py312h4c3975b_2.conda 3MB
232
+ #10 22.74 bzip2-1.0.8-hda65f42_9.conda 260kB
233
+ #10 22.74 ca-certificates-2026.4.22-hbd8a1cb_0.conda 131kB
234
+ #10 22.74 cuda-nvrtc-12.9.86-hecca717_1.conda 67MB
235
+ #10 22.74 cuda-version-12.9-h4f385c5_3.conda 22kB
236
+ #10 22.74 gsl-2.7-he838d99_0.tar.bz2 3MB
237
+ #10 22.74 hmmer-3.4-hb6cb901_4.tar.bz2 12MB
238
+ #10 22.74 ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda 728kB
239
+ #10 22.74 legacy-cgi-2.6.4-pyhcf101f3_0.conda 20kB
240
+ #10 22.74 libblas-3.11.0-6_h4a7cf45_openblas.conda 19kB
241
+ #10 22.74 libcblas-3.11.0-6_h0358290_openblas.conda 19kB
242
+ #10 22.74 libcufft-11.4.1.4-hecca717_1.conda 162MB
243
+ #10 22.74 libexpat-2.8.0-hecca717_0.conda 77kB
244
+ #10 22.74 libffi-3.4.6-h2dba641_1.conda 57kB
245
+ #10 22.74 libgcc-15.2.0-he0feb66_18.conda 1MB
246
+ #10 22.74 libgcc-ng-15.2.0-h69a702a_18.conda 28kB
247
+ #10 22.74 libgfortran-15.2.0-h69a702a_18.conda 28kB
248
+ #10 22.74 libgfortran-ng-15.2.0-h69a702a_18.conda 28kB
249
+ #10 22.74 libgfortran5-15.2.0-h68bc16d_18.conda 2MB
250
+ #10 22.74 libgomp-15.2.0-he0feb66_18.conda 603kB
251
+ #10 22.74 liblapack-3.11.0-6_h47877c9_openblas.conda 19kB
252
+ #10 22.74 liblzma-5.8.3-hb03c661_0.conda 113kB
253
+ #10 22.74 libnsl-2.0.1-hb9d3cd8_1.conda 34kB
254
+ #10 22.74 libopenblas-0.3.32-pthreads_h94d23a6_0.conda 6MB
255
+ #10 22.74 libsqlite-3.53.1-h0c1763c_0.conda 955kB
256
+ #10 22.74 libstdcxx-15.2.0-h934c35e_18.conda 6MB
257
+ #10 22.74 libstdcxx-ng-15.2.0-hdf11a46_18.conda 28kB
258
+ #10 22.74 libuuid-2.42-h5347b49_0.conda 40kB
259
+ #10 22.74 libxcrypt-4.4.36-hd590300_1.conda 100kB
260
+ #10 22.74 libzlib-1.3.2-h25fd6f3_2.conda 64kB
261
+ #10 22.74 mpi-1.0-openmpi.tar.bz2 4kB
262
+ #10 22.74 ncurses-6.6-hdb14827_0.conda 919kB
263
+ #10 22.74 numpy-2.4.3-py312h33ff503_0.conda 9MB
264
+ #10 22.74 ocl-icd-2.3.3-hb9d3cd8_0.conda 107kB
265
+ #10 22.74 ocl-icd-system-1.0.0-1.tar.bz2 4kB
266
+ #10 22.74 opencl-headers-2025.06.13-hecca717_0.conda 56kB
267
+ #10 22.74 openmm-8.3.1-py312h50c43f0_0.conda 13MB
268
+ #10 22.74 openmpi-4.1.6-hc5af2df_101.conda 4MB
269
+ #10 22.74 openssl-3.6.2-h35e630c_0.conda 3MB
270
+ #10 22.74 packaging-26.2-pyhc364b38_0.conda 92kB
271
+ #10 22.74 pdbfixer-1.12-pyhd8ed1ab_1.conda 546kB
272
+ #10 22.74 pip-26.1.1-pyh8b19718_0.conda 1MB
273
+ #10 22.74 python-3.12.10-h9e4cc4f_0_cpython.conda 31MB
274
+ #10 22.74 python_abi-3.12-8_cp312.conda 7kB
275
+ #10 22.74 readline-8.3-h853b02a_0.conda 345kB
276
+ #10 22.74 scipy-1.17.1-py312h54fa4ab_0.conda 17MB
277
+ #10 22.74 setuptools-82.0.1-pyh332efcf_0.conda 640kB
278
+ #10 22.74 tk-8.6.13-noxft_h366c992_103.conda 3MB
279
+ #10 22.74 tzdata-2025c-hc9c84f9_1.conda 119kB
280
+ #10 22.74 wheel-0.47.0-pyhd8ed1ab_0.conda 33kB
281
+ #10 22.74 zlib-1.3.2-h25fd6f3_2.conda 96kB
282
+ #10 22.74 zstd-1.5.7-hb78ec9c_6.conda 601kB
283
+ #10 22.74
284
+ #10 22.74 /root/.mamba/pkgs
285
+ #10 22.74 ───────────────────────────────────────────────────────────────
286
+ #10 22.74
287
+ #10 22.74
288
+ #10 22.74
289
+ #10 22.74 ───────────────────────────────────────────────────────────────
290
+ #10 22.74
291
+ #10 22.74 Total size: 353MB
292
+ #10 22.74 Cleaning tarballs..
293
+ #10 22.79 Cleaning packages..
294
+ #10 DONE 24.7s
230
295
 
231
- #11 [6/6] COPY . /app
296
+ #11 [3/6] COPY requirements.txt /tmp/requirements.txt
232
297
  #11 DONE 0.0s
233
298
 
234
- #12 exporting to image
235
- #12 exporting layers
236
- #12 exporting layers 11.6s done
237
- #12 writing image sha256:8ac7e5bdb1647f507409ad1289de6458c7531b92d919c45f4577ff1b5df486d9 done
238
- #12 naming to containers.pl-open.science/milaboratories/pl-containers:local-image.6af858c5c997 done
239
- #12 DONE 11.6s
299
+ #12 [4/6] RUN pip install --no-cache-dir --extra-index-url https://download.pytorch.org/whl/cpu -r /tmp/requirements.txt
300
+ #12 0.614 Looking in indexes: https://pypi.org/simple, https://download.pytorch.org/whl/cpu
301
+ #12 0.947 Collecting ImmuneBuilder==1.2 (from -r /tmp/requirements.txt (line 1))
302
+ #12 0.984 Downloading ImmuneBuilder-1.2-py3-none-any.whl.metadata (7.7 kB)
303
+ #12 1.153 Collecting torch==2.7.0 (from -r /tmp/requirements.txt (line 2))
304
+ #12 1.200 Downloading torch-2.7.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl.metadata (27 kB)
305
+ #12 1.203 Requirement already satisfied: biopython==1.85 in /opt/conda/lib/python3.12/site-packages (from -r /tmp/requirements.txt (line 3)) (1.85)
306
+ #12 1.204 Requirement already satisfied: openmm==8.3.1 in /opt/conda/lib/python3.12/site-packages (from -r /tmp/requirements.txt (line 4)) (8.3.1)
307
+ #12 1.205 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)
308
+ #12 1.205 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)
309
+ #12 1.206 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)
310
+ #12 1.285 Collecting einops>=0.3 (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
311
+ #12 1.287 Downloading einops-0.8.2-py3-none-any.whl.metadata (13 kB)
312
+ #12 1.402 Collecting requests (from ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
313
+ #12 1.405 Downloading requests-2.33.1-py3-none-any.whl.metadata (4.8 kB)
314
+ #12 1.578 Collecting filelock (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
315
+ #12 1.581 Downloading filelock-3.29.0-py3-none-any.whl.metadata (2.0 kB)
316
+ #12 1.678 Collecting typing-extensions>=4.10.0 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
317
+ #12 1.681 Downloading typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
318
+ #12 1.684 Requirement already satisfied: setuptools in /opt/conda/lib/python3.12/site-packages (from torch==2.7.0->-r /tmp/requirements.txt (line 2)) (82.0.1)
319
+ #12 1.841 Collecting sympy>=1.13.3 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
320
+ #12 1.843 Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
321
+ #12 2.075 Collecting networkx (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
322
+ #12 2.078 Downloading networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
323
+ #12 2.178 Collecting jinja2 (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
324
+ #12 2.181 Downloading jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
325
+ #12 2.291 Collecting fsspec (from torch==2.7.0->-r /tmp/requirements.txt (line 2))
326
+ #12 2.294 Downloading fsspec-2026.4.0-py3-none-any.whl.metadata (10 kB)
327
+ #12 2.529 Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch==2.7.0->-r /tmp/requirements.txt (line 2))
328
+ #12 2.531 Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
329
+ #12 2.858 Collecting MarkupSafe>=2.0 (from jinja2->torch==2.7.0->-r /tmp/requirements.txt (line 2))
330
+ #12 2.862 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)
331
+ #12 3.017 Collecting charset_normalizer<4,>=2 (from requests->ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
332
+ #12 3.019 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)
333
+ #12 3.248 Collecting idna<4,>=2.5 (from requests->ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
334
+ #12 3.250 Downloading idna-3.13-py3-none-any.whl.metadata (8.0 kB)
335
+ #12 3.489 Collecting urllib3<3,>=1.26 (from requests->ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
336
+ #12 3.492 Downloading urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
337
+ #12 3.708 Collecting certifi>=2023.5.7 (from requests->ImmuneBuilder==1.2->-r /tmp/requirements.txt (line 1))
338
+ #12 3.710 Downloading certifi-2026.4.22-py3-none-any.whl.metadata (2.5 kB)
339
+ #12 3.784 Downloading ImmuneBuilder-1.2-py3-none-any.whl (32 kB)
340
+ #12 3.791 Downloading torch-2.7.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl (175.8 MB)
341
+ #12 4.170 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 175.8/175.8 MB 470.9 MB/s 0:00:00
342
+ #12 4.172 Downloading einops-0.8.2-py3-none-any.whl (65 kB)
343
+ #12 4.175 Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)
344
+ #12 4.190 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 475.4 MB/s 0:00:00
345
+ #12 4.193 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
346
+ #12 4.196 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 664.2 MB/s 0:00:00
347
+ #12 4.199 Downloading typing_extensions-4.15.0-py3-none-any.whl (44 kB)
348
+ #12 4.201 Downloading filelock-3.29.0-py3-none-any.whl (39 kB)
349
+ #12 4.203 Downloading fsspec-2026.4.0-py3-none-any.whl (203 kB)
350
+ #12 4.207 Downloading jinja2-3.1.6-py3-none-any.whl (134 kB)
351
+ #12 4.210 Downloading markupsafe-3.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
352
+ #12 4.213 Downloading networkx-3.6.1-py3-none-any.whl (2.1 MB)
353
+ #12 4.218 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 514.3 MB/s 0:00:00
354
+ #12 4.221 Downloading requests-2.33.1-py3-none-any.whl (64 kB)
355
+ #12 4.223 Downloading charset_normalizer-3.4.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (216 kB)
356
+ #12 4.226 Downloading idna-3.13-py3-none-any.whl (68 kB)
357
+ #12 4.228 Downloading urllib3-2.7.0-py3-none-any.whl (131 kB)
358
+ #12 4.230 Downloading certifi-2026.4.22-py3-none-any.whl (135 kB)
359
+ #12 4.544 Installing collected packages: mpmath, urllib3, typing-extensions, sympy, networkx, MarkupSafe, idna, fsspec, filelock, einops, charset_normalizer, certifi, requests, jinja2, torch, ImmuneBuilder
360
+ #12 19.54
361
+ #12 19.55 Successfully installed ImmuneBuilder-1.2 MarkupSafe-3.0.3 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 requests-2.33.1 sympy-1.14.0 torch-2.7.0+cpu typing-extensions-4.15.0 urllib3-2.7.0
362
+ #12 19.55 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.
363
+ #12 DONE 21.1s
364
+
365
+ #13 [5/6] WORKDIR /app
366
+ #13 DONE 0.0s
367
+
368
+ #14 [6/6] COPY . /app/
369
+ #14 DONE 0.0s
370
+
371
+ #15 exporting to image
372
+ #15 exporting layers
373
+ #15 exporting layers 5.9s done
374
+ #15 writing image sha256:fe563ad24ee05256f21eef784c2d22133a721db4b45d1830575aba3812b4eed7 done
375
+ #15 naming to containers.pl-open.science/milaboratories/pl-containers:local-image.7ee41b17aacf done
376
+ #15 DONE 5.9s
240
377
  info: Docker image is built:
241
- tag: 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164'
242
- location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-archive/docker_x64.json'
378
+ tag: 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fe563ad24ee0'
379
+ location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-docker/docker_x64.json'
243
380
  info: Building package archives...
244
381
  info: Building software package 'py-archive' for platform 'linux-x64'...
245
382
  info: software archive is built:
246
- archive: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.1.tgz'
383
+ archive: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/pkg-platforma-open-milaboratories.3d-structure-prediction.software-py-archive-1.0.2.tgz'
247
384
  location file: '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/artifacts/py-archive/archive.json'
248
385
  info: Rendering entrypoint descriptors...
249
386
  info: Writing entrypoint descriptor to '/home/runner/work/3d-structure-prediction/3d-structure-prediction/software/dist/tengo/software/immunebuilder-predict.sw.json'
250
387
  info: Publishing docker images...
251
- info: Publishing docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164' using alternative tag 'quay.io/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164'
388
+ info: Publishing docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fe563ad24ee0' using alternative tag 'quay.io/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fe563ad24ee0'
252
389
  The push refers to repository [quay.io/milaboratories/pl-containers]
253
- aa48b9910849: Preparing
254
- e8ab1aff5214: Preparing
255
- 50319d7ec05a: Preparing
256
- 53d383103ae5: Preparing
257
- 9d135c42a506: Preparing
258
- 82f7b847f709: Preparing
259
- 3a9714186f75: Preparing
260
- e1ed8e09cf5d: Preparing
261
- 6d7c150df58d: Preparing
262
- 3a9714186f75: Waiting
263
- 6d7c150df58d: Waiting
264
- e1ed8e09cf5d: Waiting
265
- 82f7b847f709: Waiting
266
- 50319d7ec05a: Pushed
267
- aa48b9910849: Pushed
268
- 82f7b847f709: Layer already exists
269
- 3a9714186f75: Layer already exists
270
- 9d135c42a506: Pushed
271
- e1ed8e09cf5d: Layer already exists
272
- 53d383103ae5: Pushed
273
- 6d7c150df58d: Pushed
274
- e8ab1aff5214: Pushed
275
- platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164: digest: sha256:294661b2dd64108a9ed031eb0dd66c61e077af62d4e44db1e5cea0f0dfc3d6b2 size: 2207
276
- info: Docker image 'containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164' not exists locally but is already in remote registry. Skipping push...
390
+ bcec53b7f8ed: Preparing
391
+ d7baab739c4f: Preparing
392
+ e44845833786: Preparing
393
+ 8d2dc3b32579: Preparing
394
+ 9093b440cb78: Preparing
395
+ cc176b242a57: Preparing
396
+ 0f6514ac2db1: Preparing
397
+ 271be3d5c5cf: Preparing
398
+ f9926f359887: Preparing
399
+ 5f70bf18a086: Preparing
400
+ e3b1db6d44c6: Preparing
401
+ a818d59f8c76: Preparing
402
+ f8663d674596: Preparing
403
+ 5f70bf18a086: Preparing
404
+ c018a1aad765: Preparing
405
+ 438ed031efcc: Preparing
406
+ 8e2ab394fabf: Preparing
407
+ cc176b242a57: Waiting
408
+ 0f6514ac2db1: Waiting
409
+ 271be3d5c5cf: Waiting
410
+ f8663d674596: Waiting
411
+ f9926f359887: Waiting
412
+ 8e2ab394fabf: Waiting
413
+ c018a1aad765: Waiting
414
+ e3b1db6d44c6: Waiting
415
+ a818d59f8c76: Waiting
416
+ 438ed031efcc: Waiting
417
+ 8d2dc3b32579: Pushed
418
+ bcec53b7f8ed: Pushed
419
+ d7baab739c4f: Pushed
420
+ cc176b242a57: Layer already exists
421
+ 0f6514ac2db1: Layer already exists
422
+ 271be3d5c5cf: Layer already exists
423
+ f9926f359887: Layer already exists
424
+ e3b1db6d44c6: Layer already exists
425
+ 5f70bf18a086: Layer already exists
426
+ a818d59f8c76: Layer already exists
427
+ f8663d674596: Layer already exists
428
+ c018a1aad765: Layer already exists
429
+ 438ed031efcc: Layer already exists
430
+ 8e2ab394fabf: Layer already exists
431
+ e44845833786: Pushed
432
+ 9093b440cb78: Pushed
433
+ platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fe563ad24ee0: digest: sha256:3d0d1edef3c06543b24d60bb2f52f1ac32e20950e12b08d1930b3e483fb9a962 size: 3860
package/CHANGELOG.md CHANGED
@@ -1,5 +1,11 @@
1
1
  # @platforma-open/milaboratories.3d-structure-prediction.software
2
2
 
3
+ ## 1.0.2
4
+
5
+ ### Patch Changes
6
+
7
+ - 4f126ee: Use custom Dockerfile
8
+
3
9
  ## 1.0.1
4
10
 
5
11
  ### Patch Changes
package/Dockerfile ADDED
@@ -0,0 +1,56 @@
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
+ && micromamba clean --all --yes
37
+
38
+ # Activate the base env for every subsequent RUN/CMD layer so pip and
39
+ # python resolve to /opt/conda/{bin,lib}.
40
+ ARG MAMBA_DOCKERFILE_ACTIVATE=1
41
+ ENV PATH=/opt/conda/bin:$PATH
42
+
43
+ # Layer pip-only deps (ImmuneBuilder + CPU torch). Anything bioconda
44
+ # already provides is re-resolved by pip; pinned versions in
45
+ # requirements.txt match the conda packages so this is a no-op for those.
46
+ COPY requirements.txt /tmp/requirements.txt
47
+ RUN pip install --no-cache-dir \
48
+ --extra-index-url https://download.pytorch.org/whl/cpu \
49
+ -r /tmp/requirements.txt
50
+
51
+ # Block sources (everything in src_python/).
52
+ WORKDIR /app
53
+ COPY . /app/
54
+ ENV PYTHONPATH=/app
55
+
56
+ CMD ["python", "/app/run_immunebuilder.py"]
package/dist/artifacts/py-archive/archive.json CHANGED
@@ -1 +1 @@
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/1.0.1.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.1.tgz"}
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/1.0.2.tgz","uploadPath":"software/platforma-open/milaboratories.3d-structure-prediction.software/py-archive/1.0.2.tgz"}
package/dist/artifacts/{py-archive → py-docker}/docker_x64.json RENAMED
@@ -1 +1 @@
1
- {"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164","entrypoint":[]}
1
+ {"type":"docker","platform":"linux-x64","remoteArtifactLocation":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-docker.fe563ad24ee0","entrypoint":["/usr/local/bin/_entrypoint.sh"]}
package/dist/tengo/software/immunebuilder-predict.sw.json CHANGED
@@ -1 +1 @@
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/1.0.1.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"}},"docker":{"tag":"containers.pl-open.science/milaboratories/pl-containers:platforma-open.milaboratories.3d-structure-prediction.software.py-archive.8ac7e5bdb164","entrypoint":[],"cmd":["python","{pkg}/run_immunebuilder.py"],"pkg":"/app"}}
1
+ {"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.fe563ad24ee0","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/1.0.2.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
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@platforma-open/milaboratories.3d-structure-prediction.software",
3
- "version": "1.0.1",
3
+ "version": "1.0.2",
4
4
  "type": "module",
5
5
  "description": "Block Software",
6
6
  "block-software": {
@@ -14,6 +14,11 @@
14
14
  "requirements": "requirements.txt"
15
15
  },
16
16
  "root": "./src_python"
17
+ },
18
+ "py-docker": {
19
+ "type": "docker",
20
+ "context": "src_python",
21
+ "dockerfile": "Dockerfile"
17
22
  }
18
23
  },
19
24
  "entrypoints": {
@@ -24,6 +29,13 @@
24
29
  "python",
25
30
  "{pkg}/run_immunebuilder.py"
26
31
  ]
32
+ },
33
+ "docker": {
34
+ "artifact": "py-docker",
35
+ "cmd": [
36
+ "python",
37
+ "/app/run_immunebuilder.py"
38
+ ]
27
39
  }
28
40
  }
29
41
  }
package/dist/docker/Dockerfile-py-archive DELETED
@@ -1,22 +0,0 @@
1
- # Auto-generated Dockerfile for Python package
2
- FROM python:3.12-slim
3
-
4
- WORKDIR /app
5
-
6
-
7
-
8
- # Always keep basic python packaging tools fresh to avoid CVEs even in old python versions
9
- RUN pip install --upgrade pip wheel setuptools
10
-
11
- # Install dependencies to leverage Docker cache
12
- COPY requirements.txt .
13
- RUN pip install --no-cache-dir -r requirements.txt
14
-
15
- # Copy package source
16
- COPY . /app
17
-
18
- # Set Python path
19
- ENV PYTHONPATH=/app
20
-
21
- # Default command (will be overridden by entrypoint)
22
- CMD ["bash"]