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Feature/pass recipe to docker #285

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merged 10 commits into from
Nov 15, 2024

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ascibisz
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@ascibisz ascibisz commented Aug 22, 2024

Problem

Cleaning up docker code so we are actually passing the recipe / config parameters specified in the commandline / as ENV variables into the docker container.
Link to story or ticket

Solution

  • Updated docker-entrypoint.sh to actually read provided recipe and config file paths and pass them to the pack script
  • Added .dockerignore file so we aren't copying unneeded files into the docker image
  • Added an optional boolean docker for when we want to default to pointing to staging for firebase without prompting the user via commandline. To use, we can call the pack script from the commandline with the -d flag, i.e. pack -r my_recipe.json -c my_config.json -d

Type of change

  • New feature (non-breaking change which adds functionality)

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github-actions bot commented Aug 22, 2024

Packing analysis report

Analysis for packing results located at cellpack/tests/outputs/test_spheres/spheresSST

Ingredient name Encapsulating radius Average number packed
ext_A 25 236.0

Packing image

Packing image

Distance analysis

Expected minimum distance: 50.00
Actual minimum distance: 50.01

Ingredient key Pairwise distance distribution
ext_A Distance distribution ext_A

Base automatically changed from feature/aws-cli-in-docker to staging/cellpack-server August 22, 2024 18:24
@ascibisz ascibisz force-pushed the feature/pass-recipe-to-docker branch from 9d74276 to 3480a55 Compare August 26, 2024 20:15
@ascibisz ascibisz marked this pull request as ready for review September 18, 2024 20:21
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@rugeli rugeli left a comment

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LGTM! We can update the documentation for triggering batch jobs once the gateway api is in place. If we want to rename variables like use_docker, we can handle that in a cleanup pr before merging into main from staging.

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@mogres mogres left a comment

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I was able to build the image but could not run it on the on-site dgx machines due to docker being unable to access my home directory. However, the implementation looks good to me!

@@ -392,13 +392,13 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
return sphere_data


def load_file(filename, destination="", cache="geometries", force=None):
def load_file(filename, destination="", cache="geometries", force=None, use_docker=False):
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Could we make this argument name more generic? Seeing as this flag decides the database to use, maybe it could be renamed to skip_database_check or something equivalent?

@meganrm meganrm removed their request for review September 23, 2024 22:42
* retrieve job id

* formatting

* add a bucket for batch jobs

* formatting

* remove print statement and add comments
@rugeli rugeli merged commit b5e4fa0 into staging/cellpack-server Nov 15, 2024
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@rugeli rugeli deleted the feature/pass-recipe-to-docker branch November 15, 2024 19:26
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3 participants