fix: workaround for docker compose bugs. #295
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manasaV3
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* Updating tomograms * updates to tomogram processing * updates to tomogram key photo filename * updates to tomogram neuroglance filepath * cleaning up tomogram and related entities * Updating tiltseries with identifiers * Updating alignment for tomogram relations * Adding alignment metadatapath to annotations and tomograms * Updating the paths * Updating the paths * Updating failed tests * Working tests clean up needed * fix: workaround for docker compose bugs. (#295) * fix: support filtering entities by related object id's (#296) * fix: support filtering entities by related object id's * chore: add seed script. (#297) * feat: Updates to the alignment entity (#298) * Updates to schema and template * Fixing tests * Adding files to alignments metadata * Update the alignment configs method type * Fixing typo * Adding undefined alignment_method_type * chore: Documenting the Jensen config generation (#293) * Adds comments to jensen config generation * Adding guardrails * Clean up * fix: method_name * chore: Update footer of release please PR's. (#299) * Adding tests * cleaning up the paths * Cleaning up paths * fix tests * Updating tomogram id generation * Updating viz_config generation * Making id directories * Making id directories * Making annotation id directory * Cleaning up paths with id * Updating neuroglancer precompute for dir structure * Updating neuroglancer config for dir structure * Updating raw tilt import to tiltseries_id directory * Fixing dependency on existing metadata * Adding documentation comment --------- Co-authored-by: Jessica Gadling <jgadling@chanzuckerberg.com>
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Oct 21, 2024
* Updating tomograms * updates to tomogram processing * updates to tomogram key photo filename * updates to tomogram neuroglance filepath * cleaning up tomogram and related entities * Updating tiltseries with identifiers * Updating alignment for tomogram relations * Adding alignment metadatapath to annotations and tomograms * Updating the paths * Updating the paths * Updating failed tests * Working tests clean up needed * fix: workaround for docker compose bugs. (#295) * fix: support filtering entities by related object id's (#296) * fix: support filtering entities by related object id's * chore: add seed script. (#297) * feat: Updates to the alignment entity (#298) * Updates to schema and template * Fixing tests * Adding files to alignments metadata * Update the alignment configs method type * Fixing typo * Adding undefined alignment_method_type * chore: Documenting the Jensen config generation (#293) * Adds comments to jensen config generation * Adding guardrails * Clean up * fix: method_name * chore: Update footer of release please PR's. (#299) * Adding tests * cleaning up the paths * Cleaning up paths * fix tests * Updating tomogram id generation * Updating viz_config generation * Making id directories * Making id directories * Making annotation id directory * Cleaning up paths with id * Updating neuroglancer precompute for dir structure * Updating neuroglancer config for dir structure * Updating raw tilt import to tiltseries_id directory * Migration script * Update for tomograms * Adding support for alignments * Migrating annotation precompute * Migrating collection_metadata * Migrating rawtilt and gains * Clean up * Clean up * Clean up * Enabling the move * Adding metadata updates * Uncommenting deletion * Adding check before move * Adding wdl * minor fixes * Updating enqueue script * Updating annotation file names * Updating the tomogram key photo path * Fixing tests * Fix key_photo migration * Handling default alignments * fix path standardization when bucket name not in path * Lint. --------- Co-authored-by: Jessica Gadling <jgadling@chanzuckerberg.com>
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Docker compose has had a variety of issues (spanning several years!) with recreating containers in situations where it shouldn't, especially when executing
docker compose run. I've had problems launching the apiv2 dev environment in some cases, wheremake alembic-upgradewill erroneously tear down the db container and recreate it from scratch, but since we're reliant on an additional DB being added to postgres before running alembic upgrades, this db container recreate causes the startup of the dev environment to fail. Adding this--no-depsflag seems to fix the problem on my laptop, so I'm hoping it doesn't break anything in CI.