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🔖 release v0.4.3 #36

Merged
merged 29 commits into from
Nov 11, 2021
Merged

🔖 release v0.4.3 #36

merged 29 commits into from
Nov 11, 2021

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bunop
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@bunop bunop commented Nov 10, 2021 •
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Description

SMARTER database release v0.4.3:

  • Track database status and constants
  • Add foreground/background type attribute in SampleSpecies
  • Update dependencies
  • Add make rule to pack results and make checksum
  • Move greek foreground metadata to a custom phenotypes dataset
  • Update greek foreground metadata
  • Import phenotypes from Uruguay
  • Import phenotypes using alias
  • Allow phenotypes for ambiguous sex animals
  • Import french goat foreground dataset
  • Pin plinkio to support extra-chroms in plink binary files
  • Import 5 Sweden Sheep background genotypes
  • Force half-missing SNPs to be MISSING
  • Add the README.txt.ftp
  • Bug fixed in importing multibreed reportfile (setting FID properly in output)

Related Issue

closes #32
closes #11

Motivation and Context

This PR will model the latest datasets submitted, fix an issue in assigning FID from illumina reports and model other little feature.

How Has This Been Tested?

Code was tested with CI and by generating the genotypes files with database updates

Types of changes

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Refactoring (non-breaking change which improve code itself)
  • Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

  • My code follows the code style of this project.
  • My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • All new and existing tests passed.

bunop and others added 21 commits September 30, 2021 17:55
@bunop
🔖 Bump version: 0.4.2 → 0.4.3.dev0
678d8c9
@bunop
✅ test FID in import illumina multibreed report
d6822f9
@bunop
🐛 bug fixed in importing multibreed reportfile
1209a34
@bunop
🔀 Merge pull request #33 from cnr-ibba/issue-32
4f33af4 
🐛 imported illumina report multi breeds file have the same FID in output
@bunop
📝 add readme for FTP
7d8c38e
@bunop
♻️ plot image for SMARTER notebook/results
88d56f8
@bunop
✨ deal with half-missing SNPs in genotypes
113b1e5 
Forcing half-missing SNPs to MISSING
@bunop
✨ import sweden background sheep dataset
8168917
@bunop
📌 pin to a custum version of plinkio
197eb9f 
using a custom plinkio version in order to open plink binary files with extra chromosomes
@bunop
✨ import french goat foreground dataset
c2598fc
@bunop
🔧 allow phenotypes for ambigous sex animals
6ef2717
@bunop
✨ import phenotypes using alias
6263e09
@bunop
✨ import phenotypes from Uruguay
46be740
@bunop
🧐 update smarter results notebook
56732bb
@bunop
♻️ update greek metadata
7b2ceca
@bunop
🐛 fix greek metadata
a4b5c21
@bunop
♻️ load greek metadata from phenotypes dataset
c40cead
@bunop
🔧 pack and checksum merged genotypes
de27534
@dependabot @bunop
⬆️ Bump babel from 2.9.0 to 2.9.1
215be1f 
Bumps [babel](https://github.com/python-babel/babel) from 2.9.0 to 2.9.1.
- [Release notes](https://github.com/python-babel/babel/releases)
- [Changelog](https://github.com/python-babel/babel/blob/master/CHANGES)
- [Commits](python-babel/babel@v2.9.0...v2.9.1)

---
updated-dependencies:
- dependency-name: babel
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot @bunop
⬆️ Bump dask from 2021.2.0 to 2021.10.0
dd9218c 
Bumps [dask](https://github.com/dask/dask) from 2021.2.0 to 2021.10.0.
- [Release notes](https://github.com/dask/dask/releases)
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](dask/dask@2021.02.0...2021.10.0)

---
updated-dependencies:
- dependency-name: dask
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
@bunop
♻️ update requirements.txt
62096f8
@bunop bunop added bug Something isn't working enhancement New feature or request performance Improve the performance or better resource management dependencies Pull requests that update a dependency file labels Nov 10, 2021
@bunop bunop added this to the SMARTER database v1.0.0 milestone Nov 10, 2021
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coveralls commented Nov 10, 2021 •
edited
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Coverage Status

Coverage increased (+0.09%) to 91.707% when pulling a6ed1ab on devel into 540e24d on master.

@bunop bunop merged commit f5519d2 into master Nov 11, 2021
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bug Something isn't working dependencies Pull requests that update a dependency file enhancement New feature or request performance Improve the performance or better resource management
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