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build: Docker builds without Conda #103

Merged
merged 10 commits into from
Dec 31, 2022
Merged

build: Docker builds without Conda #103

merged 10 commits into from
Dec 31, 2022

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BorisYourich
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Description

Previously the Image used conda to install dependencies, now only apt-get and pip are used. The image is built from python:3.9-slim, which shaves off about 1.3GB in size. The image is 416MB compared to 1.77GB previously, builds in seconds compared to minutes, and also alleviates some overhead as repeatedly the htsinfer called on the test files paired adapters was half a second faster than the previous image.

Fixes #96

This PR depends on #102 and should be merged after that one.

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

  • I have performed a self-review of my own code
  • My code follows the existing coding style, lints and generates no new
    warnings
  • I have added type annotations to all function/method signatures, and I
    have added type annotations for any local variables that are non-trivial,
    potentially ambiguous or might otherwise benefit from explicit typing.
  • I have commented my code in hard-to-understand areas
  • I have added ["Google-style docstrings"] to all new modules, classes,
    methods/functions or updated previously existing ones
  • I have added tests that prove my fix is effective or that my feature
    works
  • New and existing unit tests pass locally with my changes and I have not
    reduced the code coverage relative to the previous state
  • I have updated any sections of the app's documentation that are affected
    by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

@codecov-commenter
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Codecov Report

Base: 99.78% // Head: 99.78% // Increases project coverage by +0.00% 🎉

Coverage data is based on head (cfe5430) compared to base (656baa6).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@           Coverage Diff           @@
##              dev     #103   +/-   ##
=======================================
  Coverage   99.78%   99.78%           
=======================================
  Files          12       12           
  Lines         929      948   +19     
=======================================
+ Hits          927      946   +19     
  Misses          2        2           
Impacted Files Coverage Δ
htsinfer/exceptions.py 100.00% <100.00%> (ø)
htsinfer/get_read_layout.py 100.00% <100.00%> (ø)
htsinfer/models.py 100.00% <100.00%> (ø)

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Dockerfile Show resolved Hide resolved
@uniqueg uniqueg merged commit d22d165 into dev Dec 31, 2022
@uniqueg uniqueg deleted the docker_image branch December 31, 2022 19:21
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Docker image for the htsinfer project
3 participants