EBISPOT/gwas-sumstats-validator issues and pull requests

#72 - TypeError: read_csv() got an unexpected keyword argument 'error_bad_lines'

Issue - State: open - Opened by carbocation over 1 year ago - 1 comment

#71 - bug fix for exiting rather than breaking

Pull Request - State: closed - Opened by jdhayhurst over 1 year ago

#70 - investigate the use of Pandera

Issue - State: closed - Opened by jdhayhurst over 1 year ago - 1 comment

#69 - Bump certifi from 2020.6.20 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#68 - Bump py from 1.10.0 to 1.11.0

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#67 - Dev

Pull Request - State: closed - Opened by jdhayhurst almost 2 years ago

#66 - update bumpversion conf, add get version, add ref allele

Pull Request - State: closed - Opened by jdhayhurst almost 2 years ago

#65 - reimplement with csv validator lib

Issue - State: open - Opened by jdhayhurst about 2 years ago - 1 comment

#64 - add duplication and autosome check to validator

Issue - State: open - Opened by jdhayhurst about 2 years ago

#63 - Schema update v1.0

Pull Request - State: closed - Opened by jdhayhurst about 2 years ago

#62 - Bump numpy from 1.17.0 to 1.22.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#61 - Dev

Pull Request - State: closed - Opened by jdhayhurst over 2 years ago

#60 - Build and deploy to pypi is failing

Issue - State: closed - Opened by jdhayhurst over 2 years ago - 2 comments

#59 - Dev

Pull Request - State: closed - Opened by jdhayhurst over 2 years ago

#58 - Bump numpy from 1.17.0 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#57 - Gwas sumstats validator#54

Pull Request - State: closed - Opened by jdhayhurst over 2 years ago

#56 - validator update so OR should be positive

Issue - State: closed - Opened by jdhayhurst over 2 years ago - 3 comments

#55 - update readme

Pull Request - State: closed - Opened by jdhayhurst over 2 years ago

#54 - option to drop bad lines isn't working

Issue - State: closed - Opened by jdhayhurst over 2 years ago - 3 comments

#53 - Update schema to meet the recommendations from the working groups

Issue - State: closed - Opened by jdhayhurst almost 3 years ago - 1 comment

#52 - Enable schema versioning

Issue - State: closed - Opened by jdhayhurst almost 3 years ago - 1 comment

#51 - Documentation should clarify how to run the validator script for non-Python users

Issue - State: open - Opened by dpanyard about 3 years ago - 4 comments

#50 - conda env for ss-validate not working

Issue - State: closed - Opened by jdhayhurst about 3 years ago - 1 comment

#49 - Validator should catch error when file is blank

Issue - State: closed - Opened by jdhayhurst about 3 years ago - 1 comment

#48 - Report a useful error message if the file is not a table

Issue - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#47 - Bump urllib3 from 1.25.10 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#46 - changing sonar coverage config

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#45 - Sonar integration

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#44 - Bump py from 1.8.0 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#43 - Dev

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#42 - drop invalid lines arg not having expected outcome

Issue - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#41 - Bump pygments from 2.6.1 to 2.7.4

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#40 - bug when there are no pvalues in scientific notation

Issue - State: closed - Opened by jdhayhurst over 3 years ago

#39 - Handle no scientific notation

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#38 - relaxing so p-values can equal 1

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#37 - p-values of 1 should pass

Issue - State: closed - Opened by jdhayhurst over 3 years ago

#36 - change build to before_script

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#35 - Dev

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#34 - Bump bleach from 3.1.5 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#33 - Dev

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#32 - deploy to pypi

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#31 - deploy to test pypi

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#30 - gitlab-ci

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#29 - Ci cd

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#28 - Small floats

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#27 - validator should not pass date where quotations are given in fields

Issue - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#26 - catch NULL byte error

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#25 - changed log level so info goes to logfile by default

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#24 - adding pbar

Pull Request - State: closed - Opened by jdhayhurst over 3 years ago

#23 - Make the validator more portable/user friendly

Issue - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#22 - sumstats validator improvements

Issue - State: open - Opened by jdhayhurst over 3 years ago - 1 comment
Labels: Epic

#21 - spit the schema out into version controlled schema

Issue - State: closed - Opened by jdhayhurst over 3 years ago - 1 comment

#20 - handle null bytes in the file

Issue - State: closed - Opened by jdhayhurst over 3 years ago

#19 - Mock validate option

Issue - State: closed - Opened by jdhayhurst over 3 years ago

#18 - pip install error

Issue - State: closed - Opened by anglixue over 3 years ago - 2 comments

#17 - when valid, say so in the log file

Issue - State: closed - Opened by jdhayhurst almost 4 years ago

#16 - Add progress bar

Issue - State: closed - Opened by jdhayhurst almost 4 years ago

#15 - Validator fails when numerical values are smaller than the system limits

Issue - State: closed - Opened by jdhayhurst almost 4 years ago - 5 comments

#14 - Smaller chunks

Pull Request - State: closed - Opened by jdhayhurst almost 4 years ago

#13 - import ss-validate pacakge

Issue - State: closed - Opened by zqsha almost 4 years ago - 1 comment

#12 - workaround for overflow error

Pull Request - State: closed - Opened by jdhayhurst about 4 years ago

#11 - enable compatibility for windows users

Issue - State: closed - Opened by jdhayhurst about 4 years ago

#10 - Set up CI/CD

Issue - State: closed - Opened by jdhayhurst about 4 years ago - 2 comments

#9 - Min line req

Pull Request - State: closed - Opened by jdhayhurst about 4 years ago

#8 - Add minimum number of SNPs to validator

Issue - State: closed - Opened by ljwh2 about 4 years ago - 6 comments

#7 - Stop at n bad rows

Pull Request - State: closed - Opened by jdhayhurst almost 5 years ago

#6 - gzip handling

Pull Request - State: closed - Opened by jdhayhurst about 5 years ago

#5 - Feature/gwas sumstats validator/#3

Pull Request - State: closed - Opened by jdhayhurst about 5 years ago

#3 - rows are valid if specific combinations of fields are present

Issue - State: closed - Opened by jdhayhurst about 5 years ago

#2 - validator should have another option for user uploaded sumstats file

Issue - State: closed - Opened by jdhayhurst about 5 years ago

#1 - validator should inform user which headers it has found/not found in the file

Issue - State: closed - Opened by jdhayhurst about 5 years ago

GitHub / EBISPOT/gwas-sumstats-validator issues and pull requests