update config for flake8 linter by espenhgn · Pull Request #126 · comorment/containers

espenhgn · 2023-02-08T15:06:52Z

Fixes #125

Changes proposed in this pull request:

flake8 should complain for line lengths > 120 chars (E501)
flake8 should ignore number of newlines between functions altogether (E302)

Before submitting

I've read and followed all steps in the Making a pull request
section of the CONTRIBUTING docs.

commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output

commit 4f7a26a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon Feb 20 09:29:28 2023 +0000 added pROC library commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output

* install LDAK * W.I.P. * not implemented LDAK test * add missing .eigenvec file * add some R scripts * PGS using prsice2 * backup w.i.p. * backing up files * work in progress * work in progress * rebuild gwas.sif including ldak tool * rebuild r.sif with PRSice_linux binary * backup * hidden functions return strings * work in progress * Work in progress * w.i.p. * w.i.p. * w.i.p. * script updates + config.yaml file * w.i.p. * simplify notebook * w.i.p. * w.i.p. * linting * linting * linting * fuck * post_run using python container * add runtime script for interactive use * some flexibility w Eigenvec_file * add option for bash and slurm jobs * ldpred2.R script from main branch * BasePGRS->BasePGS * backin up * fixed application with synthetic data * cleanup * backing up * don't use log object from outer scope * fix parallelization * code that should run on TSD * remove Data_postfix arg in main classes * adapting PGS/pgs as common term * PRS -> PGS etc. * renamed file * updating pgs_exec w. example * some user example script updates * subparser added for method specific * updates to usage * Input_dir/Data_prefix to Geno_file * rebuilt container, tee build logs * linting * suppress some CI warnings * setup-python@v4 * add R script for evaluating model fit * make Phenotype mandatory arg * sep * df.merge stuff * backup * add some example on MoBa * fit lm model <pheno>~PGS+PC1+...+PCN+<cov> * move R scripts to Rscripts dir * write results to "results" * get rid of semiredundant kwargs * do not autoasses #cores * use env variables * fixes * disgusting * path things * chromosomes * minor formatting * w.i.p. * reformatting env setup * paths * clump and a2->a0 fixes * minifixes * Squashed commit of the following: commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output * revert gwas.py to main branch * multithreading * multithreading * fixes * fix action * Squashed commit of the following: commit 4f7a26a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Mon Feb 20 09:29:28 2023 +0000 added pROC library commit 2dd1c58 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:28:28 2023 +0000 updated md5sum commit 6ceaaf5 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:26:21 2023 +0000 rebuild r.sif container commit 021e333 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 17 07:23:52 2023 +0000 +PRSice_linux, revise R package repo commit b984ff6 Merge: 3666140 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 15:33:25 2023 +0100 Merge branch 'deepchocolate/ldpred2_ld' commit 99d7c0e Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:50:16 2023 +0100 Added note on filtering commit f4f7e06 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:40:51 2023 +0100 Renamed --file-keep-snps to --extract commit 27413a6 Author: deepchocolate <andreas@systerdyster.se> Date: Fri Feb 10 13:27:51 2023 +0100 Removed --sumstats-sep from test script commit a94a18a Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Fri Feb 10 10:12:33 2023 +0000 removed redundant --sumstats-sep arg commit 3666140 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:57:39 2023 +0100 fix flake8 for combine_figures.py commit f8f904e Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:54:05 2023 +0100 noqa: W605 commit 5e3ff1d Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 22:51:45 2023 +0100 manually edit to clear most errors commit c89ac5b Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Thu Feb 9 21:56:37 2023 +0100 autopep8 --max-line-length 119 --ignore E302 commit 246ad6b Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Thu Feb 9 23:01:35 2023 +0100 update config for flake8 linter (#126) * test flake8_args * Node.js 12 actions are deprecated * nonsensical edit that should trigger E501 * flake8_args * bad style * check if flake8 is reporting * check E302 nontrigger * check E302 nontrigger * revert things * revert gwas.py * updated changelog commit 8f0f2b5 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Feb 9 16:04:15 2023 +0100 Added threshold filtering parameter commit 92fc902 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Wed Feb 8 11:05:04 2023 +0100 Allow custom name for IID columns (#123) * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * clarify comments * allow IID column in .pheno file to have a custom name (as defined in .dict file) * fix rename_iid_column * add tests for identical FIDs and custom IIDs * also rename pheno.dict iid_column_name --------- Co-authored-by: ttfiliz <110425985+ttfiliz@users.noreply.github.com> commit 814db96 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 14:52:05 2023 +0000 some markdown stuff commit 05f520f Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:57:38 2023 +0000 sensible score values. Use plink from container commit e653381 Author: Espen Hagen <2492641+espenhgn@users.noreply.github.com> Date: Wed Feb 1 10:42:39 2023 +0000 add --sumstats-sep option etc. commit 5673a1f Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 31 09:58:49 2023 +0100 throw an error if --variance-standardize is applied to a continuous variable without variation (#121) commit e70c033 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:58 2023 +0100 Updated changelog commit 9ece1f8 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 31 09:47:38 2023 +0100 Updated LDpred2 README commit 6e06f24 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 17:55:33 2023 +0100 Renamed --geno-file argument commit 00e8d35 Author: deepchocolate <andreas@systerdyster.se> Date: Thu Jan 26 13:56:02 2023 +0100 Added readme in folder for testdata commit b6da1a3 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 24 13:22:59 2023 +0100 Added auto mode to tests commit 7c1bbf4 Author: Oleksandr Frei <oleksandr.frei@gmail.com> Date: Tue Jan 24 09:11:15 2023 +0100 Update README.md commit 0bb5f1a Author: ttfiliz <110425985+ttfiliz@users.noreply.github.com> Date: Tue Jan 24 09:06:18 2023 +0100 unit tests for gwas.py (#119) * Added unit tests for gwas.py * change cwd back to original cwd after each test * updated changelog * set environment variables in test script * Update README.md * removed unnecessary singularity bind path * update README.md Co-authored-by: Espen Hagen <2492641+espenhgn@users.noreply.github.com> commit 31036f8 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 15:22:51 2023 +0100 Added sampling of individuals commit bb8f80d Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:45:18 2023 +0100 Removed redundant code, fixed chr2use argument commit ea54fff Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:26:07 2023 +0100 Cleanup, fixed arguments to --sumstats commit 82d39c1 Author: deepchocolate <andreas@systerdyster.se> Date: Wed Jan 11 14:25:35 2023 +0100 Reorganized tests commit 896eadf Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 20:39:57 2023 +0100 Added test runs commit 304f19a Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 17:24:22 2023 +0100 Working version commit 6b47b30 Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:55 2023 +0100 Added test runs commit 087d50f Author: deepchocolate <andreas@systerdyster.se> Date: Tue Jan 10 10:55:25 2023 +0100 Trimmed some output * ncores * split in two scripts * fixes * add clump_field parameter to PGS_plink * disable sorting while merging * remove use of --pheno-file and --col-pheno * fixes * notebooks * newline * added gtsummary r package * added R flextable * added R parameters * cleanup merge * better r lib test, PR cleanup * formatting * added R2 calcs * removed outdated ldpred2 files * renaming params * renaming variable nems etc. * clean up variable names * eigenvec file stuff * fixes * moving files * updated .gitignore * nPCs * cleanup * comment * misc updates * posit cran clone, new R libraries * fixing build * rebuilt r.sif container * linting * linting * add more R stuff * docs * plink score_args -> score_columns * cleanup * limit PLINK cpu usage * wrap up R packages * updated r.sif build procedure and scripts * update R build recipes and test * rebuilt r.sif * hadolint * better crash handling, explicit args w. createBackingFile.R * docs, deal with prsice2 bar-levels/fastscore * updated MoBa scripts * added lm/glm fits/stats w.o. covariates; ORs * details on output * string formatting * MplusAutomation/PredictABEL added to r.sif * rebuilt r.sif * roll back install_minimac4.sh script to main * removed non-lfs file (will re-add) * prep add EUR.eigenvec file * Add missing PRSice2 tutorial file * updated changelog w. main changes * github markdown math * typo * better math formatting w. sphinx * got rid of a myst-parser warning * flake8 fix * fixed broken test of createBackingFile.R

test flake8_args

7c2bce8

espenhgn marked this pull request as draft February 8, 2023 15:06

espenhgn changed the title ~~test flake8_args~~ update config for flake8 linter Feb 8, 2023

espenhgn added 10 commits February 8, 2023 15:11

Node.js 12 actions are deprecated

e9f3c8d

nonsensical edit that should trigger E501

d291a33

flake8_args

a26bb1e

bad style

6dc63e2

check if flake8 is reporting

80ad162

check E302 nontrigger

552b5fb

check E302 nontrigger

10c9b6b

revert things

b57aa2b

revert gwas.py

eba6cb4

updated changelog

e63fc79

espenhgn marked this pull request as ready for review February 8, 2023 15:53

espenhgn requested a review from ofrei February 8, 2023 15:54

ofrei approved these changes Feb 9, 2023

View reviewed changes

ofrei merged commit 246ad6b into main Feb 9, 2023

ofrei mentioned this pull request Feb 9, 2023

Reformat gwas.py and combine_figures.py #128

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espenhgn deleted the fix-125 branch February 10, 2023 08:17

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update config for flake8 linter#126

update config for flake8 linter#126
ofrei merged 11 commits intomainfrom
fix-125

espenhgn commented Feb 8, 2023 •

edited

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espenhgn commented Feb 8, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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espenhgn commented Feb 8, 2023 •

edited

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