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Project restructure WIP #13

Merged
merged 29 commits into from
Apr 25, 2024
Merged

Project restructure WIP #13

merged 29 commits into from
Apr 25, 2024

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mberacochea
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Some of the changes I think we need to do in the project:

  • Split code in different files (constants and ena should be enough at this point)
  • pyproject.toml for the requirements and other python packaging bits
  • Github Action test workflow
  • Using the python logger instead of print
  • Small fixes in the code (nothing big)

@mberacochea mberacochea requested a review from Ge94 January 25, 2024 13:44
@mberacochea mberacochea self-assigned this Jan 25, 2024
mberacochea and others added 20 commits January 25, 2024 13:50
@mberacochea
Fix arg parser and move exception to ena.py
56fa1be
@mberacochea
ENV loading prototype
22b5cb5
@mberacochea
Invert confitional in env loading
d298c7e
@mberacochea
Missing string interpolation f prefix
4f5388b
@Ge94
Add python-dotenv to requirements
3980454
@Ge94
ENA API refactor
ff723f3
@Ge94
Minor fixes - env variables
a2756d2
@Ge94
env name change
6a0c805
@Ge94
Solved bug in euks tax resolution
cbf1b68
@KateSakharova
conflicta in reqs
22e107f
@mberacochea
Pin python in the requirements.yml file
fb5d158
@KateSakharova
fix lon and lat digits
e5bc45c
@KateSakharova
rm print lineage
1eb12b9
@KateSakharova
Merge pull request #14 from EBI-Metagenomics/fix/geography
283391e 
Fix/geography
@KateSakharova
add check for missing collection date
6e5a08a
@KateSakharova
Merge pull request #15 from EBI-Metagenomics/fix/missing-collection-date
ce4b46b 
Fix/missing collection date
Fixed bugs for euks taxonomy
47cb39b
@Ge94
Minor bug fix test/live mode
9168315
@Ge94
Minor logic refactor
b9f3c71
@Ge94
Added e2e test support, minor code refactoring
abebc69
@Ge94 Ge94 marked this pull request as ready for review April 25, 2024 10:04
@Ge94 Ge94 merged commit 07361ac into main Apr 25, 2024
6 checks passed
@Ge94 Ge94 deleted the feature/code-review-mberacochea branch April 25, 2024 12:33
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@Ge94 Ge94 Ge94 approved these changes

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@mberacochea mberacochea

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3 participants
@mberacochea @Ge94 @KateSakharova