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helicalAI / helical

This repository contains the python package for Helical
https://www.helical-ai.com/
GNU Affero General Public License v3.0
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Dockerfile errors when building new image #106

Closed JesusGF1 closed 2 weeks ago

JesusGF1 commented 2 weeks ago

Hi team, I am trying to use the dockerfile image to containerize my analysis with Helical. When using the dockerfile that appears in the github repo I am unable to get it to completion. There seems to be a problem with the python and pytorch versions. Any help would be gladly appreciated. 

[+] Building 20.7s (8/9)                                                                                                                              
 => [internal] load build definition from dockerfile                                                                                             0.0s
 => => transferring dockerfile: 970B                                                                                                             0.0s
 => [internal] load .dockerignore                                                                                                                0.0s
 => => transferring context: 2B                                                                                                                  0.0s
 => [internal] load metadata for docker.io/library/python:3.10                                                                                   0.8s
 => [auth] library/python:pull token for registry-1.docker.io                                                                                    0.0s
 => [1/5] FROM docker.io/library/python:3.10@sha256:aaacc373f21abcbc67a22d203dab7fb797c016cc4c1daa7d2dec359dcbf4aea1                             0.0s
 => CACHED [2/5] RUN apt-get update -y     && apt-get upgrade -y     && apt-get -y install build-essential         wget         git         cur  0.0s
 => CACHED [3/5] RUN pip install --upgrade pip                                                                                                   0.0s
 => ERROR [4/5] RUN pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git                                        19.8s
------                                                                                                                                                
 > [4/5] RUN pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git:                                                    
#8 0.453 Collecting git+https://github.com/helicalAI/helical.git                                                                                      
#8 0.454   Cloning https://github.com/helicalAI/helical.git to /tmp/pip-req-build-q57euy5c                                                            
#8 0.456   Running command git clone --filter=blob:none --quiet https://github.com/helicalAI/helical.git /tmp/pip-req-build-q57euy5c                  
#8 3.207   Resolved https://github.com/helicalAI/helical.git to commit 77b32c05a3da22f3b123e3a46417d55a2ae29458                                       
#8 3.210   Installing build dependencies: started
#8 4.363   Installing build dependencies: finished with status 'done'
#8 4.364   Getting requirements to build wheel: started
#8 4.405   Getting requirements to build wheel: finished with status 'done'
#8 4.406   Preparing metadata (pyproject.toml): started
#8 4.587   Preparing metadata (pyproject.toml): finished with status 'done'
#8 4.650 Collecting accelerate==0.29.3 (from helical==0.0.1a2)
#8 4.694   Downloading accelerate-0.29.3-py3-none-any.whl.metadata (18 kB)
#8 4.731 Collecting anndata==0.10.7 (from helical==0.0.1a2)
#8 4.737   Downloading anndata-0.10.7-py3-none-any.whl.metadata (6.6 kB)
#8 4.770 Collecting azure-core==1.30.1 (from helical==0.0.1a2)
#8 4.781   Downloading azure_core-1.30.1-py3-none-any.whl.metadata (37 kB)
#8 4.811 Collecting azure-identity==1.16.0 (from helical==0.0.1a2)
#8 4.818   Downloading azure_identity-1.16.0-py3-none-any.whl.metadata (76 kB)
#8 4.849 Collecting azure-storage-blob==12.19.1 (from helical==0.0.1a2)
#8 4.856   Downloading azure_storage_blob-12.19.1-py3-none-any.whl.metadata (26 kB)
#8 4.886 Collecting datasets==2.20.0 (from helical==0.0.1a2)
#8 4.892   Downloading datasets-2.20.0-py3-none-any.whl.metadata (19 kB)
#8 4.926 Collecting einops==0.8.0 (from helical==0.0.1a2)
#8 4.933   Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
#8 4.961 Collecting gitpython==3.1.43 (from helical==0.0.1a2)
#8 4.968   Downloading GitPython-3.1.43-py3-none-any.whl.metadata (13 kB)
#8 4.991 Collecting hydra-core==1.3.2 (from helical==0.0.1a2)
#8 4.999   Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
#8 5.024 Collecting loompy==3.0.7 (from helical==0.0.1a2)
#8 5.040   Downloading loompy-3.0.7.tar.gz (4.8 MB)
#8 5.503      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 10.6 MB/s eta 0:00:00
#8 5.593   Preparing metadata (setup.py): started
#8 5.846   Preparing metadata (setup.py): finished with status 'done'
#8 5.880 Collecting louvain==0.8.2 (from helical==0.0.1a2)
#8 5.887   Downloading louvain-0.8.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (1.5 kB)
#8 6.013 Collecting numpy==1.26.4 (from helical==0.0.1a2)
#8 6.020   Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (62 kB)
#8 6.067 Collecting omegaconf==2.3.0 (from helical==0.0.1a2)
#8 6.075   Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)
#8 6.170 Collecting pandas==2.2.2 (from helical==0.0.1a2)
#8 6.178   Downloading pandas-2.2.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (19 kB)
#8 6.216 Collecting pyensembl (from helical==0.0.1a2)
#8 6.223   Downloading pyensembl-2.3.13-py3-none-any.whl.metadata (9.4 kB)
#8 6.268 Collecting requests==2.32.2 (from helical==0.0.1a2)
#8 6.278   Downloading requests-2.32.2-py3-none-any.whl.metadata (4.6 kB)
#8 6.296 Collecting scib==1.1.5 (from helical==0.0.1a2)
#8 6.303   Downloading scib-1.1.5-1-py3-none-any.whl.metadata (9.8 kB)
#8 6.369 Collecting scikit-learn>=1.2.2 (from helical==0.0.1a2)
#8 6.378   Downloading scikit_learn-1.5.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (13 kB)
#8 6.408 Collecting scikit-misc==0.3.1 (from helical==0.0.1a2)
#8 6.415   Downloading scikit_misc-0.3.1.tar.gz (302 kB)
#8 6.465   Installing build dependencies: started
#8 12.25   Installing build dependencies: finished with status 'done'
#8 12.25   Getting requirements to build wheel: started
#8 12.31   Getting requirements to build wheel: finished with status 'done'
#8 12.31   Installing backend dependencies: started
#8 13.12   Installing backend dependencies: finished with status 'done'
#8 13.12   Preparing metadata (pyproject.toml): started
#8 19.26   Preparing metadata (pyproject.toml): finished with status 'done'
#8 19.35 Collecting scipy==1.13.1 (from helical==0.0.1a2)
#8 19.35   Downloading scipy-1.13.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (113 kB)
#8 19.44 Collecting tensorflow==2.17.0 (from helical==0.0.1a2)
#8 19.45   Downloading tensorflow-2.17.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (4.1 kB)
#8 19.49 Collecting torch==2.3.0 (from helical==0.0.1a2)
#8 19.56   Downloading torch-2.3.0-cp310-cp310-manylinux2014_aarch64.whl.metadata (26 kB)
#8 19.60 INFO: pip is looking at multiple versions of helical to determine which version is compatible with other requirements. This could take a while.
#8 19.61 ERROR: Ignored the following yanked versions: 0.15.0
#8 19.61 ERROR: Ignored the following versions that require a different python version: 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10
#8 19.61 ERROR: Could not find a version that satisfies the requirement torchtext==0.18.0 (from helical) (from versions: 0.1.1, 0.2.0, 0.2.1, 0.2.3, 0.3.1, 0.4.0, 0.5.0, 0.6.0, 0.11.2, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.2)
#8 19.63 ERROR: No matching distribution found for torchtext==0.18.0
------
executor failed running [/bin/sh -c pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git]: exit code: 1
make[1]: *** [build] Error 1
make: *** [go] Error 2
mattwoodx commented 2 weeks ago

Hi @JesusGF1 ,

Thanks for bringing this to our attention. We have made changes to the dependencies and they are currently in our main branch.

If you want to make use of these changes until we merge into release, just change the run line in the Dockerfile to the following: RUN pip install --upgrade --force-reinstall git+https://github.com/helicalAI/helical.git@main

Please let us know if this solves your issue and thanks again for the feedback!

I am closing this ticket for now and we can reopen it if this problem persists 😁

JesusGF1 commented 2 weeks ago

Hi there, I changed the line of code but I was still getting an error when trying to dockerize the container. I am working with an M1 macbook pro. I had to setup the container's platform to linux to get it to completion. It seems to be running without any issue now. Thank you for your help