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Published 20 hours ago • verified publisher icon pinellolab

add workflow cli

Open cameronraysmith opened this issue 1 year ago • 3 comments

  • [x] resolves #272
  • [x] adds support for hydra-zen but not #299

cameronraysmith avatar Dec 01 '23 19:12 cameronraysmith

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review-notebook-app[bot] avatar Dec 02 '23 13:12 review-notebook-app[bot]

Codecov Report

Attention: 526 lines in your changes are missing coverage. Please review.

Comparison is base (2096882) 37.00% compared to head (7a6e4f2) 29.48%.

:exclamation: Current head 7a6e4f2 differs from pull request most recent head 4d23772. Consider uploading reports for the commit 4d23772 to get more accurate results

Files Patch % Lines
src/dnadiffusion/hydra/execution_utils.py 0.00% 142 Missing :warning:
src/dnadiffusion/hydra/execute.py 0.00% 125 Missing :warning:
src/dnadiffusion/workflows/lrwine.py 0.00% 42 Missing :warning:
src/dnadiffusion/hydra/execution_config.py 0.00% 35 Missing :warning:
src/dnadiffusion/constants.py 0.00% 25 Missing :warning:
src/dnadiffusion/data/validation_preprocessing.py 18.18% 18 Missing :warning:
src/dnadiffusion/utils/data_util.py 28.00% 18 Missing :warning:
src/dnadiffusion/data/preprocessing.py 23.80% 16 Missing :warning:
src/dnadiffusion/models/diffusion.py 0.00% 16 Missing :warning:
src/dnadiffusion/logging.py 0.00% 15 Missing :warning:
... and 12 more
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #274      +/-   ##
==========================================
- Coverage   37.00%   29.48%   -7.52%     
==========================================
  Files          23       31       +8     
  Lines        1481     1896     +415     
  Branches      202      252      +50     
==========================================
+ Hits          548      559      +11     
- Misses        925     1325     +400     
- Partials        8       12       +4

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codecov[bot] avatar Dec 02 '23 20:12 codecov[bot]

All three images built successfully on the CI run associated to 91b4b9d114ca44d50ec2a2a854bc19c44458b1ab; however, the push of the conda image to ghcr failed in isolation with

ghcr conda image push API request failure 

dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845: error pushing image: failed to push to destination ghcr.io/pinellolab/dna-diffusion-conda:37492b9: PUT https://ghcr.io/v2/pinellolab/dna-diffusion-conda/blobs/upload/53e3c757-19b5-4b36-b597-bb9552fec94a?digest=sha256%3Acf6896c4ddc5baab24171de32edfd856c9351464232169cd5b6a8ca571e16182: unexpected status code 504 Gateway Timeout: <!DOCTYPE html>
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:       <p><strong>We couldn't respond to your request in time.</strong></p>
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:       <p>Sorry about that. Please try refreshing and contact us if the problem persists.</p>
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:       <div id="suggestions">
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:         <a href="https://github.com/contact">Contact Support</a> &mdash;
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:         <a href="https://www.githubstatus.com/">GitHub Status</a> &mdash;
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:         <a href="https://twitter.com/githubstatus">@githubstatus</a>
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:       </div>

The push to gcr succeeded without issue. This may have been transient; however, as we do not in general require or even want to utilize this conda-based image in workflows and it is the most bloated of the three approaching 15GB when decompressed, we may disable its automatic build while retaining the specification files required to build it.

cameronraysmith avatar Dec 08 '23 13:12 cameronraysmith