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Ci cd build #85

Merged
merged 294 commits into from
Jan 31, 2021
Merged

Ci cd build #85

merged 294 commits into from
Jan 31, 2021
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jan 19, 2021

  1. adding flush

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    callahantiff committed Jan 19, 2021
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  2. trying sysout

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  3. adding logginfg

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    callahantiff committed Jan 19, 2021
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  4. fixing directory structure

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    callahantiff committed Jan 19, 2021
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  5. repairing file_loc default

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  6. fixing bad filepath

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  7. adding owltools

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  8. sub subprocess

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  9. fixing owltoolsdownload link

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    callahantiff committed Jan 19, 2021
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  10. adding memory

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  11. adding cpu

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  12. fixing memory spec

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  13. trying 7.99G

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  14. adding gib

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  15. adding backslash

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  16. increasing timeout

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    callahantiff committed Jan 19, 2021
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  17. updated all build scripts

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    callahantiff committed Jan 19, 2021
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  18. commenting gce workflow

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  19. switching to beta for longer timeout

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  20. adding quiet

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  21. adding line wrap

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  22. preparing for pypi release

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  23. updating docs for pypi pub prac

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  24. silencing build workflow

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  25. updating workflow

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  26. removing unused workflow line

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  27. refreshing docker container

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  28. removing tagline

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  29. testing build

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  30. fixing owltools link

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    callahantiff committed Jan 19, 2021
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Commits on Jan 20, 2021

  1. fixing filepath error

    @callahantiff
    callahantiff committed Jan 20, 2021
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  2. updating github actions

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  3. removing dash in job name

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    callahantiff committed Jan 20, 2021
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  4. removing colon from job name

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  5. adding another step

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  6. testing wait

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  7. adding job monitoring

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  8. take 2

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  9. adding file directory

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    callahantiff committed Jan 20, 2021
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  10. adding credential

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  11. fixing parameter name

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    callahantiff committed Jan 20, 2021
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  12. writing file

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  13. write key

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  14. wrapping secret

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    callahantiff committed Jan 20, 2021
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  15. passing file

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  16. setting python env var

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  17. removed google dep

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  18. adding python back

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  19. combining monitoring and run steps

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    callahantiff committed Jan 20, 2021
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  20. updating builds

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  21. updating workflow

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  22. removing uneeded file

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  23. adding pypi push

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  24. fixing import

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  25. updating package publish

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  26. fixing import error

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  27. testing phase 2

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  28. finalized workflow 1

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  29. adding print statements

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  30. fixing yml error

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    callahantiff committed Jan 20, 2021
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  31. removing typo in build name

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    callahantiff committed Jan 20, 2021
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  32. fixing directory issue

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    callahantiff committed Jan 20, 2021
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  33. adding missing library

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  34. only testing remaining methods

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  35. extending owltools memory

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  36. bumping memory

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  37. memory bump

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  38. updating download logic

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  39. updating bucket search criteria

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Commits on Jan 21, 2021

  1. fixing file reading error

    @callahantiff
    callahantiff committed Jan 21, 2021
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  2. updating download logic

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    callahantiff committed Jan 21, 2021
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  3. updated metdata logic

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  4. adding missing return statement

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    callahantiff committed Jan 21, 2021
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  5. adding owltools path

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    callahantiff committed Jan 21, 2021
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  6. removing directory

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  7. updating merge func with owl_tools

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  8. adding merge method

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  9. updating merge func

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  10. fixing typo

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    callahantiff committed Jan 21, 2021
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  11. adding missing gene key

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    callahantiff committed Jan 21, 2021
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  12. catching errors

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  13. cleaning up work flow

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    callahantiff committed Jan 21, 2021
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  14. testing final part of phase 2

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    callahantiff committed Jan 21, 2021
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  15. updating logic

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  16. added missing argument

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  17. updating workflow

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  18. renaming endpoint script

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  19. finalizing file

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  20. adding phase 3

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  21. addingmissing argument

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  22. adding startup script

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  23. specifying zone

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  24. not stopping

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  25. testing ssh

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  26. calling startup from ssh command

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Commits on Jan 22, 2021

  1. adding curly braces

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    callahantiff committed Jan 22, 2021
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  2. changing container name

    @callahantiff
    callahantiff committed Jan 22, 2021
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  3. switch to image

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    callahantiff committed Jan 22, 2021
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  4. fixing end of line error

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    callahantiff committed Jan 22, 2021
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  5. adding auth to bash script

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    callahantiff committed Jan 22, 2021
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  6. trying different strategy

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  7. fixinf typo

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  8. changing instance name

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  9. adding image

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  10. fixinf syntax

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  11. syntax again...

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  12. chaining arguments

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  13. trying another approach

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  14. changing approach

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  15. adding missing file

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  16. adding missing files

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  17. fixing errors

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  18. adding scope arg

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  19. changing job name

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  20. renamed and moved files

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  21. adding logging

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  22. updated file

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  23. testing phases 1-2

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  24. fixing logging error

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  25. dup code removed

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  26. uncommenting code

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  27. logging error

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  28. fixing write path

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  29. adding logging library

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  30. adding formal logging

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  31. adding missing module

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  32. fixing filepath

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  33. updating filepath

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  34. removing duplicate resource

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Commits on Jan 23, 2021

  1. moved entry point

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  2. updated documentation

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  3. testing job monitoring

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  4. moving import

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  5. installing pkt_kg

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  6. updating logic

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  7. test phase 3 monitoring

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  8. adding missing module

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  9. adding ga workflow jobs

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  10. updating code

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  11. Merge branch 'ci_cd_build' of github.com:callahantiff/PheKnowLator in… 

    …to ci_cd_build
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  12. testing phase 1 console log

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  13. updating yml

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  14. adding missing module

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  15. phase 3 test

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  16. adding note about finding build logs

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  17. updating logging

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  18. Merge branch 'ci_cd_build' of github.com:callahantiff/PheKnowLator in… 

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  19. fixing logger call

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  20. take 2

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  21. testing step 3

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  22. test both steps

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  23. updating logging

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  24. moving timestamp

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  25. fixing log naming issue

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  26. adding container restart policy

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Commits on Jan 24, 2021

  1. testing env vars

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  2. removing needs

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  3. changing syntax

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  4. exp 2

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  5. fixing value error

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  6. exp3

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  7. testing build with env vars

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  8. remove uneeded scripts

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  9. updating env

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  10. exp5

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  11. undoing formatting

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  12. fixing EOF error

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  13. editing job name var

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  14. again ...

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  15. again .... 2

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  16. again ... 3

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  17. rolling back job_name env

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  18. changing defaults

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  19. fixing missing filename

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  20. fixing missing log reference

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  21. fixing queueing

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  22. fixing logic

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  23. adding addiitonal logging

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  24. adding log pushing method

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  25. uncommenting methods

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  26. removing untracked files

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  27. testing overhaul for directory re-org

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  28. updating build directory structure

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  29. updating flawed logic

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  30. Merge branch 'ci_cd_build' of github.com:callahantiff/PheKnowLator in… 

    …to ci_cd_build
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  31. cleaning logs dir before run

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Commits on Jan 25, 2021

  1. updated file paths

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  2. adding build utilities

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  3. testing p1/p2

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  4. updating env path

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  5. adding missing library

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  6. changing filepath

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  7. updating dockerfile

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  8. adding log files

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  9. fixing path issues

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  10. fixing pythonpath

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  11. removed uneeded script

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  12. updating owltools loc

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  13. re-running job

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  14. fixing removed file

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  15. fixing logic

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  16. verified workflow

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  17. adding google api exceptions

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  18. simlifying downloader

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  19. removing redundant func

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  20. reordering method

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  21. adding logging steps

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  22. adding missing info

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  23. updating curated data path

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  24. adding command to delete existing logs

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  25. evaluation args

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  26. forcce std out to message

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  27. adding phase 1 back

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  28. making exit more explicit

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  29. fixing broken method

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  30. fixing broken links

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  31. patching dl

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  32. dedup github action stdout

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Commits on Jan 26, 2021

  1. fixing owltools ref

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  2. fixing owltools

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  3. removing comments

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  4. testing exit method

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  5. testing quit method

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  6. reverse commenting

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  7. update yml to test step 3

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  8. adding async process runner

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  9. adding timer

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  10. fixing docker spec and script name

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  11. adding logging 

    addresses issue #53
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  12. test kg build

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  13. repairing line wrap

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  14. adding missing module

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Commits on Jan 27, 2021

  1. specifying boot disc for instance

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  2. fixing container specs

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  3. fixing docker curl calls

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  4. removed extra carriage return

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  5. adding kg stats to logging

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  6. fixing docker dl

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  7. extending functionality

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  8. Jan kg build stats

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  9. blocked yml for all kg builds

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  10. fixing download assumption

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  11. updating stats function

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  12. re-arranged funcs

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  13. adding additional logging

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Commits on Jan 28, 2021

  1. updating github workflow

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  2. adding note to documentation for clarification

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Commits on Jan 29, 2021

  1. adding logo

    @callahantiff
    callahantiff authored Jan 29, 2021
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Commits on Jan 30, 2021

  1. finalizing draft build

    @callahantiff
    callahantiff committed Jan 30, 2021
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Commits on Jan 31, 2021

  1. Merge branch 'master' into ci_cd_build

    @callahantiff
    callahantiff authored Jan 31, 2021
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