Clinical-Genomics / housekeeper

File data orchestrator
MIT License
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feat(docker): Use Poetry #205

Closed henrikstranneheim closed 1 month ago

henrikstranneheim commented 1 month ago

Description

Added

-

Changed

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Fixed

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Testing

How to prepare for test

housekeeper-test-deploy use-poetry-instead-of-pip
housekeeper-test --help

Any migrations need to be applied manually with alembic against the stage database.

How to test

Expected test outcome

Review

This version is a:

henrikstranneheim commented 1 month ago

Only using Poetry and locking container to only executing HK, 👍


    Setup the database.
[henrik.stranneheim@hasta:~] [base] $ housekeeper-test-deploy use-poetry-instead-of-pip
Pulling image for feature branch: use-poetry-instead-of-pip...
WARNING: Authentication token file not found : Only pulls of public images will succeed
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:6533c3eba3f3cd4c840877f9245b26929fc8c22a39f42c872aa314c32c6d654b
Skipping fetch of repeat blob sha256:d69c32f98917901c7b942c9884e7d8e04916a6c6c45938e8c389f8412546bb6b
Skipping fetch of repeat blob sha256:9e3a3447a656117614d9a6ccd9b487f88f52049611a47028899ebcc9ef2c96d3
Skipping fetch of repeat blob sha256:6cb66b05ec9b9c63a0e8feb327380c48b19ec4438ebcd903fd9ead2eb54b02d7
Copying blob sha256:6abc681e39a2bb8cfb03d457b51ef965dcb727df2be84dff5d5ecd9dcbc42852
 93 B / 93 B [==============================================================] 0s
Copying blob sha256:c6977ce5bc3334f0c1b7b161bd914d4fff360df62fee912fb86c5f979667da14
 452.82 KiB / 452.82 KiB [==================================================] 0s
Copying blob sha256:aac40169957bc36789e0bfafed017484fcbf3787017943070c51548ab23cca78
 65.30 MiB / 65.30 MiB [====================================================] 1s
Copying config sha256:37183bb4f3d7bd9cca1d639006c162f67381fd562c35708f47986d2605055508
 5.97 KiB / 5.97 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/proj/stage/singularity_containers/housekeeper_use-poetry-instead-of-pip.sif
You can now run 'housekeeper-test --help' to test the feature branch: use-poetry-instead-of-pip.
[henrik.stranneheim@hasta:~] [base] $ housekeeper-test --help
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Skipping fetch of repeat blob sha256:6533c3eba3f3cd4c840877f9245b26929fc8c22a39f42c872aa314c32c6d654b
Skipping fetch of repeat blob sha256:d69c32f98917901c7b942c9884e7d8e04916a6c6c45938e8c389f8412546bb6b
Skipping fetch of repeat blob sha256:9e3a3447a656117614d9a6ccd9b487f88f52049611a47028899ebcc9ef2c96d3
Skipping fetch of repeat blob sha256:6cb66b05ec9b9c63a0e8feb327380c48b19ec4438ebcd903fd9ead2eb54b02d7
Skipping fetch of repeat blob sha256:6abc681e39a2bb8cfb03d457b51ef965dcb727df2be84dff5d5ecd9dcbc42852
Skipping fetch of repeat blob sha256:c6977ce5bc3334f0c1b7b161bd914d4fff360df62fee912fb86c5f979667da14
Skipping fetch of repeat blob sha256:aac40169957bc36789e0bfafed017484fcbf3787017943070c51548ab23cca78
Copying config sha256:37183bb4f3d7bd9cca1d639006c162f67381fd562c35708f47986d2605055508
 5.97 KiB / 5.97 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: /home/henrik.stranneheim/.singularity/cache/oci-tmp/b06193c3f17ea2964ac5bad19f8a138af8380b997b859104c4be2eb0b02e2398/housekeeper_use-poetry-instead-of-pip.sif
INFO:    Image cached as SIF at /home/henrik.stranneheim/.singularity/cache/oci-tmp/b06193c3f17ea2964ac5bad19f8a138af8380b997b859104c4be2eb0b02e2398/housekeeper_use-poetry-instead-of-pip.sif
Usage: housekeeper [OPTIONS] COMMAND [ARGS]...

  Housekeeper - Access your files!

Options:
  -c, --config FILENAME
  -d, --database TEXT    path/URI of the SQL database
  -r, --root PATH        Housekeeper root dir
  -l, --log-level TEXT
  --version              Show the version and exit.
  --help                 Show this message and exit.

Commands:
  add      Add things to the store.
  delete   Delete things in the database.
  get      Get info from database
  include  Include a bundle of files into the internal space.
  init     Setup the database.
sonarcloud[bot] commented 1 month ago

Quality Gate Failed Quality Gate failed

Failed conditions
1 Security Hotspot

See analysis details on SonarCloud