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pinellolab / DNA-Diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨
https://pinellolab.github.io/DNA-Diffusion/
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357 stars 49 forks source link

add workflow cli #274

Open cameronraysmith opened 9 months ago

cameronraysmith commented 9 months ago
review-notebook-app[bot] commented 9 months ago

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codecov[bot] commented 9 months ago

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 ```diff @@ 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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cameronraysmith commented 9 months ago

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

```sh 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: dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:

We couldn't respond to your request in time.

dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:

Sorry about that. Please try refreshing and contact us if the problem persists.

dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:
dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845: Contact Support — dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845: GitHub Status — dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845: @githubstatus dna-diffusion-build-37492b9-rczsw-kaniko-build-push-1064953845:
```

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.