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[Cloud Deployment IV]: Simple neuroconv deployment #393

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CodyCBakerPhD
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Introduces the one-line helper function deploy_conversion_from_yaml_and_upload_to_dandi to perform the entire cloud deployment stack, along with necessary changes to the batch submission utility introduced in the base of this PR.

Note the one-liner isn't working yet, but I attached detailed instructions for running the utility function in separate stand-alone scripts which is still much easier than doing the entire thing manually.

@bendichter
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@CodyCBakerPhD thanks for sharing this. Would you like to convert it to a Draft PR?

@CodyCBakerPhD CodyCBakerPhD marked this pull request as draft April 3, 2023 14:49
@CodyCBakerPhD CodyCBakerPhD changed the title [WIP]: Simple neuroconv deployment [Cloud Deployment - WIP]: Simple neuroconv deployment Apr 24, 2023
@CodyCBakerPhD CodyCBakerPhD changed the title [Cloud Deployment - WIP]: Simple neuroconv deployment [WIP - Cloud Deployment IIb]: Simple neuroconv deployment Feb 19, 2024
@CodyCBakerPhD CodyCBakerPhD changed the title [WIP - Cloud Deployment IIb]: Simple neuroconv deployment [WIP - Cloud Deployment IId]: Simple neuroconv deployment Jun 12, 2024
@CodyCBakerPhD CodyCBakerPhD changed the title [WIP - Cloud Deployment IId]: Simple neuroconv deployment [WIP - Cloud Deployment IV]: Simple neuroconv deployment Jul 15, 2024
@CodyCBakerPhD CodyCBakerPhD changed the title [WIP - Cloud Deployment IV]: Simple neuroconv deployment [Cloud Deployment IV]: Simple neuroconv deployment Jul 15, 2024
@CodyCBakerPhD
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TODO

  • add optional status table updates to YAML conversion side (needs to run in docker image after upload to DANDI)
  • CI tests

@CodyCBakerPhD CodyCBakerPhD self-assigned this Jul 24, 2024
Comment on lines +4 to +5
schedule:
- cron: "0 16 * * 1" # Weekly at noon EST on Monday
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Set to trigger on github release

@CodyCBakerPhD
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TODO - add cosideration for ctrl-C based termination of job submission - how is cleanup handled?

Example: EFS is created but CLI terminates before jobs are submitted. Ensure EFS gets cleaned up in that case

Base automatically changed from batch_helper to main August 8, 2024 19:40
@h-mayorquin
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I am closing this one as all the PRs have been merged and the future TODO is here:
#1103

@h-mayorquin h-mayorquin deleted the simple_neuroconv_deployment branch December 13, 2024 21:47
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codecov bot commented Dec 13, 2024

Codecov Report

Attention: Patch coverage is 88.05373% with 418 lines in your changes missing coverage. Please review.

Project coverage is 89.30%. Comparing base (648dffc) to head (4491a7f).
Report is 2099 commits behind head on main.

Files with missing lines Patch % Lines
src/neuroconv/tools/data_transfers/_aws.py 10.65% 109 Missing ⚠️
...v/datainterfaces/behavior/deeplabcut/_dlc_utils.py 58.08% 57 Missing ⚠️
src/neuroconv/tools/data_transfers/_dandi.py 21.42% 33 Missing ⚠️
.../ecephys/cellexplorer/cellexplorerdatainterface.py 84.27% 25 Missing ⚠️
...nterfaces/ecephys/basesortingextractorinterface.py 71.83% 20 Missing ⚠️
...nv/tools/nwb_helpers/_metadata_and_file_helpers.py 86.66% 20 Missing ⚠️
...aces/ophys/scanimage/scanimageimaginginterfaces.py 94.68% 15 Missing ⚠️
...nterfaces/behavior/fictrac/fictracdatainterface.py 91.60% 12 Missing ⚠️
..._helpers/_configuration_models/_hdf5_dataset_io.py 68.57% 11 Missing ⚠️
...atainterfaces/behavior/video/videodatainterface.py 91.73% 10 Missing ⚠️
... and 34 more
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #393      +/-   ##
==========================================
- Coverage   91.96%   89.30%   -2.66%     
==========================================
  Files          88      129      +41     
  Lines        4055     7633    +3578     
==========================================
+ Hits         3729     6817    +3088     
- Misses        326      816     +490     
Flag Coverage Δ
unittests 89.30% <88.05%> (-2.66%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
src/neuroconv/__init__.py 100.00% <100.00%> (ø)
src/neuroconv/baseextractorinterface.py 100.00% <100.00%> (ø)
src/neuroconv/converters/__init__.py 100.00% <100.00%> (ø)
src/neuroconv/datainterfaces/__init__.py 100.00% <100.00%> (ø)
...ces/behavior/deeplabcut/deeplabcutdatainterface.py 92.50% <100.00%> (+2.75%) ⬆️
...onv/datainterfaces/behavior/medpc/medpc_helpers.py 100.00% <100.00%> (ø)
...faces/behavior/miniscope/miniscopedatainterface.py 100.00% <100.00%> (ø)
...aces/ecephys/alphaomega/alphaomegadatainterface.py 100.00% <100.00%> (ø)
...atainterfaces/ecephys/baselfpextractorinterface.py 100.00% <100.00%> (ø)
...tainterfaces/ecephys/biocam/biocamdatainterface.py 100.00% <100.00%> (ø)
... and 111 more

... and 1 file with indirect coverage changes

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3 participants