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Build container images in workflow #7

Merged
merged 34 commits into from
Jun 19, 2024
Merged

Build container images in workflow #7

merged 34 commits into from
Jun 19, 2024

Commits on Jun 16, 2024

  1. add workflows

    @khiron
    khiron committed Jun 16, 2024
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  2. fir workflow in branch

    @khiron
    khiron committed Jun 16, 2024
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  3. log into GHCR first

    @khiron
    khiron committed Jun 16, 2024
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  4. set root as the context

    @khiron
    khiron committed Jun 16, 2024
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  5. case sensitive Dockerfile

    @khiron
    khiron committed Jun 16, 2024
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  6. renamed to force case change

    @khiron
    khiron committed Jun 16, 2024
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  7. update to Pascal case

    @khiron
    khiron committed Jun 16, 2024
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  8. force the base image to be built first

    @khiron
    khiron committed Jun 16, 2024
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  9. build just the base image

    @khiron
    khiron committed Jun 16, 2024
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  10. add prepopulated

    @khiron
    khiron committed Jun 16, 2024
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  11. prevent race conditions

    @khiron
    khiron committed Jun 16, 2024
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  12. add apse config

    @khiron
    khiron committed Jun 16, 2024
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  13. revert to python 3.11 for EnsemblLite and do not install conflicting … 

    …dev dependencies
    @khiron
    khiron committed Jun 16, 2024
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  14. rename image prepopulated to apes_112

    @khiron
    khiron committed Jun 16, 2024
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  15. force a refresh of the image from GHCR

    @khiron
    khiron committed Jun 16, 2024
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  16. copy apes_112.cfg relative to the local context

    @khiron
    khiron committed Jun 16, 2024
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  17. data is not necessarily in the root

    @khiron
    khiron committed Jun 16, 2024
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  18. pwd to find out where we are

    @khiron
    khiron committed Jun 16, 2024
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  19. set the workdir at the end of the process

    @khiron
    khiron committed Jun 16, 2024
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  20. copy the cfg filr to the ~/data folder

    @khiron
    khiron committed Jun 16, 2024
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  21. fix default python interpreter to 3.11 and update conda

    @khiron
    khiron committed Jun 16, 2024
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  22. change ensebml to develop branch and go back to python 3.12

    @khiron
    khiron committed Jun 16, 2024
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  23. determine how many procs are available to a workflow and set the cont… 

    …ainer to build using 2
    @khiron
    khiron committed Jun 16, 2024
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  24. use 2 cpus

    @khiron
    khiron committed Jun 16, 2024
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Commits on Jun 17, 2024

  1. disable processing of apes_112 to make sur ethe container has teh cfg… 

    … file copied
    @khiron
    khiron committed Jun 17, 2024
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  2. add workshop mount to ~ and explicitly locate data files for apes_112

    @khiron
    khiron committed Jun 17, 2024
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  3. concatenate both home environment variable so this works with mac.lin… 

    …ux&windows
    @khiron
    khiron committed Jun 17, 2024
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  4. make sure to activate conda before running elt

    @khiron
    khiron committed Jun 17, 2024
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  5. initialize conda in the apes_112 dockerfile

    @khiron
    khiron committed Jun 17, 2024
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  6. fully specify path to elt

    @khiron
    khiron committed Jun 17, 2024
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Commits on Jun 19, 2024

  1. copy the data directory to the base container

    = committed Jun 19, 2024
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  2. set user as owner of ~/data

    = committed Jun 19, 2024
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  3. comment out install and sample of data

    = committed Jun 19, 2024
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  4. chown needed sudo

    = committed Jun 19, 2024
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