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openworm / OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
http://openworm.org
MIT License
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Docker build failing with latest owmeta #312

Closed pgleeson closed 3 years ago

pgleeson commented 3 years ago

Docker file here: https://github.com/openworm/OpenWorm/blob/c5bb24b396804256a2b0018e38224fc9a511046e/Dockerfile#L77 is failing when installing owmeta & core from latest on pypi.

$ ./rebuild.sh 

[+] Building 400.0s (15/26)                                                                                                                                                                                                                 
 => [internal] load build definition from Dockerfile                                                                                                                                                                                   0.0s
 => => transferring dockerfile: 37B                                                                                                                                                                                                    0.0s
 => [internal] load .dockerignore                                                                                                                                                                                                      0.0s
 => => transferring context: 96B                                                                                                                                                                                                       0.0s
 => [internal] load metadata for docker.io/library/ubuntu:18.04                                                                                                                                                                        0.0s
 => CACHED [ 1/22] FROM docker.io/library/ubuntu:18.04                                                                                                                                                                                 0.0s
 => [internal] load build context                                                                                                                                                                                                      0.0s
 => => transferring context: 40B                                                                                                                                                                                                       0.0s
 => [ 2/22] RUN apt-get update &&   apt-get upgrade -y &&   apt-get dist-upgrade -y                                                                                                                                                   22.0s
 => [ 3/22] RUN mkdir -p /etc/sudoers.d &&   export uid=1000 gid=1000 &&   mkdir -p /home/ow &&   echo "ow:x:${uid}:${gid}:ow,,,:/home/ow:/bin/bash" >> /etc/passwd &&   echo "ow:x:${uid}:" >> /etc/group &&   echo "ow ALL=(ALL) NO  0.4s
 => [ 4/22] RUN apt-get update && apt-get install -y --no-install-recommends apt-utils   wget nano htop build-essential make git automake autoconf   g++ rpm libtool libncurses5-dev zlib1g-dev bison flex lsb-core   sudo xorg ope  301.5s 
 => [ 5/22] RUN sudo usermod -a -G video ow                                                                                                                                                                                            0.7s 
 => [ 6/22] WORKDIR /home/ow                                                                                                                                                                                                           0.1s 
 => [ 7/22] RUN sudo pip3 install neuron==7.8.1                                                                                                                                                                                        7.0s 
 => [ 8/22] RUN git clone https://github.com/NeuroML/pyNeuroML.git &&   cd pyNeuroML &&   git checkout master  &&   sudo python3 setup.py install                                                                                     40.6s 
 => [ 9/22] RUN sudo pip3 install owmeta_core==0.13.2 owmeta==0.12.3                                                                                                                                                                  21.5s 
 => [10/22] RUN owm bundle  remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'                                                                                                         1.9s 
 => ERROR [11/22] RUN owm clone https://github.com/openworm/OpenWormData.git                                                                                                                                                           4.1s 
------                                                                                                                                                                                                                                      
 > [11/22] RUN owm clone https://github.com/openworm/OpenWormData.git:                                                                                                                                                                      
#14 1.673 Cloning...                                                                                                                                                                                                                        
100%|##########| 806.0/806.0 [00:02<00:00, 379.55objects/s]                                                                                                                                                                                 
#14 3.836 WARNING:owmeta_core.bundle:Unable to read remote 343af67c5830b1eec791738c590a076fe5025fac5be2bea2bcb255ff.remote                                                                                                                  
#14 3.836 Traceback (most recent call last):                                                                                                                                                                                                
#14 3.836   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 1173, in retrieve_remotes
#14 3.836     rem = Remote.read(inp)
#14 3.836   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 149, in read
#14 3.836     res = yaml.unsafe_load(inp)
#14 3.836 AttributeError: module 'yaml' has no attribute 'unsafe_load'
#14 3.867 WARNING:owmeta_core.bundle:Unable to read remote 343af67c5830b1eec791738c590a076fe5025fac5be2bea2bcb255ff.remote
#14 3.867 Traceback (most recent call last):
#14 3.867   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 706, in _gather_dependency_configs
#14 3.867     bundle_directory = find_bundle_directory(self.bundles_directory, dep_ident, dep_version)
#14 3.867   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/common.py", line 135, in find_bundle_directory
#14 3.867     f'Bundle directory, "{res}", does not exist for the specified version', version)
#14 3.867 owmeta_core.bundle.exceptions.BundleNotFound: Missing bundle "openworm/owmeta-core" at version 1: Bundle directory, "/home/ow/.owmeta/bundles/openworm%2Fowmeta-core/1", does not exist for the specified version
#14 3.867 
#14 3.867 During handling of the above exception, another exception occurred:
#14 3.867 
#14 3.867 Traceback (most recent call last):
#14 3.867   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 1173, in retrieve_remotes
#14 3.867     rem = Remote.read(inp)
#14 3.867   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 149, in read
#14 3.867     res = yaml.unsafe_load(inp)
#14 3.867 AttributeError: module 'yaml' has no attribute 'unsafe_load'
#14 3.986 Traceback (most recent call last):
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 706, in _gather_dependency_configs
#14 3.986     bundle_directory = find_bundle_directory(self.bundles_directory, dep_ident, dep_version)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/common.py", line 135, in find_bundle_directory
#14 3.986     f'Bundle directory, "{res}", does not exist for the specified version', version)
#14 3.986 owmeta_core.bundle.exceptions.BundleNotFound: Missing bundle "openworm/owmeta-core" at version 1: Bundle directory, "/home/ow/.owmeta/bundles/openworm%2Fowmeta-core/1", does not exist for the specified version
#14 3.986 
#14 3.986 During handling of the above exception, another exception occurred:
#14 3.986 
#14 3.986 Traceback (most recent call last):
#14 3.986   File "/usr/local/bin/owm", line 11, in <module>
#14 3.986     sys.exit(main())
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli.py", line 170, in main
#14 3.986     _helper(p)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli.py", line 266, in _helper
#14 3.986     argument_namespace_callback=ns_handler)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli_command_wrapper.py", line 512, in main
#14 3.986     return self.mapper.apply(self.runner)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli_command_wrapper.py", line 129, in apply
#14 3.986     return continuation()
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli_command_wrapper.py", line 117, in continuation
#14 3.986     return runmethod(*(tuple(args) + tuple(nargs)), **kwargs)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/cli_command_wrapper.py", line 42, in _f
#14 3.986     return method(*args, **kwargs)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/command.py", line 1375, in clone
#14 3.986     self._init_store()
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/command.py", line 1329, in _conf
#14 3.986     store_name, store_conf = cfg_builder.build(store_conf, deps)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 672, in build
#14 3.986     read_only=self.read_only)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 683, in _construct_store_config
#14 3.986     dependency_configs = self._gather_dependency_configs(dependencies, current_path, paths, bundle_directory)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/utils.py", line 37, in wrapper
#14 3.986     return list(fun(*args, **kwargs))
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 711, in _gather_dependency_configs
#14 3.986     bundle_directory = self._fetch_bundle(dep_ident, dep_version)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 729, in _fetch_bundle
#14 3.986     return f.fetch(bundle_ident, version, self.remotes)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 919, in fetch
#14 3.986     loaders_list = list(loaders)
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 986, in _get_bundle_loaders
#14 3.986     for rem in self._get_remotes(remotes):
#14 3.986   File "/usr/local/lib/python3.6/dist-packages/owmeta_core/bundle/__init__.py", line 849, in _get_remotes
#14 3.986     raise NoRemoteAvailable()
#14 3.986 owmeta_core.bundle.exceptions.NoRemoteAvailable
------
executor failed running [/bin/sh -c owm clone https://github.com/openworm/OpenWormData.git]: exit code: 1

Any idea @mwatts15?

mwatts15 commented 3 years ago

@pgleeson I'm guessing the version of pyyaml is too low. I added a constraint to pyyaml>=5.1 for owmeta-core 0.13.3, but I see an install of python3-yaml before that which I suspect is below that. I'm trying a build now.

mwatts15 commented 3 years ago

@pgleeson looks like that worked. Please try with owmeta-core 0.13.3

pgleeson commented 3 years ago

Great, thanks @mwatts15 , that solved my problem. Looking into some other issues now.