801 commits

Author	SHA1	Message	Date
Marco Ferrari	d43fcdc666	Sort environment variables when printing debug info	2020-09-26 00:51:53 +02:00
Marco Ferrari	31fd755fd7	Remove unneeded READ_ONLY_CHANGE_FLAG	2020-09-25 23:41:47 +02:00
Marco Ferrari	63f23368b8	Remove unneeded READ_ONLY_CHANGE_FLAG	2020-09-25 21:25:00 +02:00
kpj	9e7c84fbbb	Fix various Snakemake related variable names	2020-09-24 16:06:12 +02:00
kpj	40f995365b	Fix Snakefile regex	2020-09-24 15:55:47 +02:00
kpj	71ede6ccca	Add missing 'GetLinterRules' calls	2020-09-24 15:54:24 +02:00
Michael Shimokura	12543b369b	Lint all files with editorconfig-checker ... Since .editorconfig configuration files _could_ apply to any file, we should pass in the RAW_FILE_ARRAY to it. This ensures that files of all types are linted by editorconfig-checker.	2020-09-24 09:02:24 -04:00
Lukas Gravley	84c79a186b	Merge branch 'master' into master	2020-09-22 08:56:09 -05:00
Marco Ferrari	f24f52be11	Lint with Kubeval and fixes	2020-09-22 01:49:01 +02:00
Lukas Gravley	f290145dfa	Update linter.sh	2020-09-21 13:51:46 -05:00
Lukas Gravley	06cb2ebb6f	Update linter.sh	2020-09-21 13:50:58 -05:00
Marco Ferrari	6168112f61	Fix ERROR_ON_MISSING_EXEC_BIT initialization	2020-09-21 14:43:44 +02:00
kpj	6f6004275f	In anticipation of snakefmt 0.1.6, start using --check and --compact-diff	2020-09-18 16:32:01 +02:00
Marco Ferrari	5cefb9209f	Make bash-exec errors or warnings configurable	2020-09-15 22:40:12 +02:00
NicolasVuillamy	e470df5431	Fix file filters: Reorder arguments to LintCodeBase function	2020-09-15 08:15:53 +02:00
kpj	5b51c2bd92	Use '--compact-diff' instead of '--diff' for snakefmt	2020-09-14 09:36:33 +02:00
Joseph Marino	2698bdfbc3	Fixed a typo in code comments ... Replaced the term "CSS" with "HTML" in code comments for the HTML_LINTER_RULES variable.	2020-09-11 15:16:55 -04:00
kpj	11f437df4c	Fix usage of FILE_ARRAY_SNAKEMAKE	2020-09-11 13:51:15 +02:00
kpj	e1b2fd6085	Fix bug in Snakemake file regex	2020-09-11 13:49:05 +02:00
kpj	ec0577ae5b	Add Snakemake to language array	2020-09-11 13:31:57 +02:00
Lukas Gravley	79b055babe	Merge pull request #707 from ferrarimarco/fix-node-modules ... Fix list files function typos	2020-09-10 11:21:54 -05:00
Lucas Gravley	b232c5b970	this is the way./..	2020-09-10 10:34:04 -05:00
Lucas Gravley	f432ef2116	fix spaces	2020-09-10 10:25:56 -05:00
Marco Ferrari	ad9c0081f4	Fix list files function typos	2020-09-10 12:10:12 +02:00
NicolasVuillamy	27afc50d60	Set GROOVY Linter failure level to warning	2020-09-10 11:07:05 +02:00
NicolasVuillamy	c86e90b3d0	Solve conflicts + format	2020-09-09 20:22:32 +02:00
NicolasVuillamy	f072bc5c8d	Merge remote-tracking branch 'github/master'	2020-09-09 20:18:21 +02:00
Lukas Gravley	9f3eb7d454	Merge pull request #679 from Goryudyuma/just-filter-the-git-folder ... Just filter the .git folder	2020-09-09 10:53:19 -05:00
Lucas Gravley	b5d42bf181	this makes no sense	2020-09-09 10:37:02 -05:00
Lucas Gravley	880380d118	if i could only read	2020-09-09 10:18:12 -05:00
Lucas Gravley	dbd4cd673d	this has to be right	2020-09-09 10:04:21 -05:00
Lucas Gravley	eb67d9b9c6	fix that dumb action	2020-09-09 09:28:39 -05:00
Lucas Gravley	bae75b456b	more fix	2020-09-09 09:24:57 -05:00
Lucas Gravley	17c3ded695	i forgot how this works	2020-09-09 09:24:27 -05:00
Lukas Gravley	e9811c85d6	Update lib/worker.sh ... yes Co-authored-by: Goryudyuma(Kei.Matsumoto) <6211370+Goryudyuma@users.noreply.github.com>	2020-09-08 16:00:12 -05:00
Lucas Gravley	fd42f4b3fb	science...	2020-09-08 15:45:17 -05:00
Marco Ferrari	83666ffaba	Fix getting filename for hidden files	2020-09-08 19:20:49 +02:00
Lucas Gravley	0e5f996c3c	look at folders and not file names	2020-09-08 12:16:59 -05:00
Lucas Gravley	a0d4012b67	like this?	2020-09-08 12:01:17 -05:00
Lucas Gravley	53995952e0	Merge branch 'master' into just-filter-the-git-folder	2020-09-08 10:43:59 -05:00
Lucas Gravley	a6c9656015	fixing vars	2020-09-08 09:47:57 -05:00
kpj	6f6e6e9d03	[Snakemake] Remove wrong function argument	2020-09-08 11:26:48 +02:00
kpj	581f07a32b	[Snakemake] Fix 'LINTER_NAME'	2020-09-08 10:19:56 +02:00
kpj	8ac1c99a2e	[Snakemake] Support both formatting using 'snakefmt' and linting using 'snakemake --lint'	2020-09-08 09:38:48 +02:00
kpj	ad262196ba	[Snakemake] Also lint 'Snakefile' (without '.smk' suffix)	2020-09-08 09:11:54 +02:00
kpj	53f551c8b0	[Snakemake] Add '--config' parameter to 'snakefmt' calls	2020-09-07 17:26:58 +02:00
kpj	0c5029bf67	[Snakemake] Actually run 'snakefmt' tests	2020-09-07 17:20:56 +02:00
kpj	1e453be7fa	[Snakemake] Update codebase	2020-09-07 16:49:07 +02:00
NicolasVuillamy	04c93b4ff5	Add management of FILTER_REGEX_INCLUDE and FILTER_REGEX_EXCLUDE options	2020-09-05 12:25:44 +02:00
Lukas Gravley	828de134a9	this should be right	2020-09-04 13:22:01 -05:00
Goryudyuma(Kei.Matsumoto)	b31b696e00	Just filter the .git folder	2020-09-05 03:08:26 +09:00
Lukas Gravley	c58bab2627	Merge pull request #677 from v1v/feature/version ... Print version, date and revision	2020-09-04 10:35:38 -05:00
Lucas Gravley	b29eb851d3	make pretty	2020-09-04 10:14:47 -05:00
Lukas Gravley	a3fcb3ea7c	Merge pull request #675 from dmerrick/honoring-disable-errors ... Making MULTI_STATUS honor DISABLE_ERRORS setting	2020-09-04 09:15:06 -05:00
Lukas Gravley	eb36fb7d7c	Merge branch 'master' into master	2020-09-04 08:53:34 -05:00
NicolasVuillamy	21d75fb89e	Groovy traps .nf extension (nextflow) + upgrade npm-groovy-lint	2020-09-04 11:54:31 +02:00
Victor Martinez	d3c992bec7	Print version, date and revision	2020-09-04 09:09:20 +01:00
Dana Merrick	c64c5c8d60	Cleaner solution	2020-09-03 19:37:10 -04:00
Dana Merrick	dd84550d46	Honoring DISABLE_ERRORS	2020-09-03 19:23:24 -04:00
Lucas Gravley	c4bbf03935	fixing debug	2020-09-03 10:12:29 -05:00
Lucas Gravley	d78e707cba	no source needed	2020-09-03 09:57:20 -05:00
Lucas Gravley	a3c8b22e2c	fix duplicate names	2020-09-03 09:56:34 -05:00
Lucas Gravley	6ac933dc8c	fix print	2020-09-03 09:34:39 -05:00
Lucas Gravley	165b29cbe1	fix array	2020-09-03 09:21:22 -05:00
Lucas Gravley	8a51e59be7	even easier	2020-09-03 09:20:00 -05:00
Lucas Gravley	72fd3e3b87	super simple	2020-09-03 09:12:49 -05:00
Lukas Gravley	b012d72952	Merge pull request #662 from montyly/dev-black-config-file ... Add support for black config file	2020-09-02 09:57:44 -05:00
Lucas Gravley	f5e39e5aad	fix typo and add check	2020-09-02 09:26:01 -05:00
Lucas Gravley	a756e40157	typo	2020-09-02 09:07:39 -05:00
Lucas Gravley	6040030c8a	Adding more paths to ignore	2020-09-02 09:05:36 -05:00
Josselin	f34b084586	Add support for black config file	2020-09-02 11:28:57 +02:00
Marco Ferrari	de4b8a4fa0	Add shfmt and fixes back	2020-09-01 00:06:15 +02:00
Marco Ferrari	30763f2575	Streamline shell file list building	2020-08-31 23:47:48 +02:00
Lucas Gravley	98c2eec42a	small clean	2020-08-31 14:34:14 -05:00
Marco Ferrari	228a86e5c0	Remove duplicate output lines when checking for ZSH scripts	2020-08-31 19:56:49 +02:00
Marco Ferrari	798311822a	Add file path to ZSH warning messages	2020-08-31 19:47:05 +02:00
Marco Ferrari	833dcb8bd8	Don't check zsh files with shfmt	2020-08-31 19:31:22 +02:00
Marco Ferrari	f5331bdcd3	Skip shfmt if no .editorconfig file is present	2020-08-31 19:30:50 +02:00
Marco Ferrari	f90c3a289b	Check if report output folder exists before listing	2020-08-31 19:22:50 +02:00
Marco Ferrari	644e69131b	Fix shfmt test	2020-08-31 19:22:50 +02:00
Marco Ferrari	b3a980e06f	Fix bash-exec and terrascan versions	2020-08-31 19:22:49 +02:00
Marco Ferrari	0d849cd5e0	Lint shell files with shfmt	2020-08-31 19:22:49 +02:00
Lucas Gravley	13e87dd021	lots of cleanup	2020-08-31 11:51:03 -05:00
Lucas Gravley	958f70fe67	its real picky	2020-08-31 10:11:12 -05:00
Lucas Gravley	a32d0c1314	here	2020-08-28 14:08:08 -05:00
Lucas Gravley	a9bc2068f7	they come in pairs	2020-08-28 13:50:23 -05:00
Lucas Gravley	633418aa8a	fix var	2020-08-28 13:47:15 -05:00
Lucas Gravley	e9c3938982	fix tty issues	2020-08-28 13:44:11 -05:00
Lucas Gravley	b7781ba295	forgot quote	2020-08-28 11:54:31 -05:00
Lucas Gravley	9be83e0166	merge master	2020-08-28 11:46:11 -05:00
Lucas Gravley	345a6626e7	put it back	2020-08-28 11:42:14 -05:00
Lukas Gravley	10f44786ce	Merge pull request #641 from github/isExec ... adding bash-exec	2020-08-28 10:37:43 -05:00
Lucas Gravley	a35df1c943	its friday	2020-08-28 10:15:44 -05:00
Lucas Gravley	40fddbad79	get name even	2020-08-28 10:12:02 -05:00
Lucas Gravley	920f7b673b	adding warning	2020-08-28 10:08:21 -05:00
Lucas Gravley	0404c39203	adding exec	2020-08-28 09:56:53 -05:00
Lucas Gravley	d9f35b2af7	more cleanupo	2020-08-27 14:26:05 -05:00
Lucas Gravley	4bf0aee923	Make it happy	2020-08-27 14:12:24 -05:00
Lucas Gravley	94e03d50ac	better loop	2020-08-27 14:01:43 -05:00
Lucas Gravley	9cae4c7f6d	better	2020-08-27 09:00:54 -05:00
Cesar Rodriguez	815f8236dd	Updates scan command for Terrascan	2020-08-26 22:53:00 -04:00
Cesar Rodriguez	e060679ea8	Updates terrascan command	2020-08-26 22:53:00 -04:00
Eddy Nakamura	9c44d2d503	changing command - 2	2020-08-26 11:58:28 -03:00
Eddy Nakamura	b83e4c99ed	updating command	2020-08-26 11:42:05 -03:00
Lucas Gravley	454fa09b81	Fixed it?	2020-08-26 08:50:53 -05:00
Eddy Nakamura	6157d8a2ae	trying to solve command issue	2020-08-25 19:52:04 -03:00
Eddy Nakamura	a766e5f624	updating format command	2020-08-25 19:20:02 -03:00
Lucas Gravley	9b129f4873	fixed it again	2020-08-25 14:21:22 -05:00
Lukas Gravley	c2e207f643	Merge branch 'master' into feature/csharp-lint	2020-08-25 13:09:51 -05:00
Lucas Gravley	add83739a7	adding test folders	2020-08-25 13:07:44 -05:00
Lucas Gravley	ae9cb55eec	adding more folders to ignore	2020-08-25 10:32:05 -05:00
Lukas Gravley	fb70f94bd3	Merge branch 'master' into hadolintLinter	2020-08-25 10:06:43 -05:00
Lucas Gravley	ee3200654a	adding hadolint configuration	2020-08-25 09:55:30 -05:00
Lucas Gravley	cb41ae47fa	adding feature	2020-08-25 09:05:23 -05:00
Eddy Nakamura	79dccdf62b	updating command	2020-08-24 21:58:25 -03:00
Eddy Nakamura	efe1f95c87	updating linter script	2020-08-24 21:46:55 -03:00
Eddy Nakamura	accf805de4	adding files to buildFileList and linter	2020-08-24 21:43:50 -03:00
Eddy Nakamura	24ce47014d	Adding C# lint	2020-08-24 21:40:02 -03:00
Lucas Gravley	e7ff2d0e66	fixed it	2020-08-24 14:22:39 -05:00
Lucas Gravley	a1f76a8e2b	fix version	2020-08-24 14:17:44 -05:00
Lucas Gravley	254db11e08	better... faster... stronger...	2020-08-24 14:12:37 -05:00
Lucas Gravley	3fda83377a	add quotes	2020-08-24 13:56:09 -05:00
Lucas Gravley	6d7c89b7d7	fix struct	2020-08-24 11:16:22 -05:00
Lucas Gravley	bce238d392	adding some spaget	2020-08-24 11:11:10 -05:00
Lucas Gravley	815ff9d520	Adding more	2020-08-20 13:03:40 -05:00
Lucas Gravley	17a4bd2271	adding some dope code	2020-08-20 12:58:11 -05:00
Lucas Gravley	1f2c569c21	adding black	2020-08-20 09:44:11 -05:00
Lucas Gravley	b13ac9a14f	quotes	2020-08-19 14:18:49 -05:00
Lucas Gravley	54abac63b3	fix logic hole	2020-08-19 14:14:41 -05:00
Lukas Gravley	5970f28f6b	Merge pull request #588 from assignUser/chktex ... Add LaTeX support	2020-08-19 13:12:11 -05:00
assignUser	8224e9e6e5	fix exit code	2020-08-19 17:51:07 +00:00
assignUser	dcd81f09d0	fix global config warning	2020-08-19 14:28:41 +00:00
assignUser	bad32e6f53	adress review	2020-08-19 14:16:59 +00:00
assignUser	b42ba5c72a	quiet chktex	2020-08-19 01:11:34 +00:00
assignUser	e8db83e2dd	Update linter.sh	2020-08-19 01:03:12 +02:00
assignUser	e1bc1df9e7	add latex support	2020-08-18 22:54:32 +00:00
Lukas Gravley	308c1fd5aa	Merge pull request #569 from assignUser/master ... Add lintr support to super-lint	2020-08-18 16:08:35 -05:00
assignUser	cc903ad583	Adjust doc about exclusions	2020-08-18 16:11:26 +00:00
Lucas Gravley	f5752cfd45	adding the right var	2020-08-18 10:09:18 -05:00
Lucas Gravley	1f55b422da	fix folder for persistance	2020-08-18 09:51:38 -05:00
assignUser	3d4292f067	alphabetize	2020-08-17 19:47:03 +00:00
assignUser	c2f35fc0b3	Update lib/worker.sh ... Co-authored-by: Lukas Gravley <admiralawkbar@github.com>	2020-08-17 21:45:16 +02:00
assignUser	6372885cd0	relative exclusions work, adressed comments	2020-08-17 16:27:31 +00:00
assignUser	9ec761f61c	prereview	2020-08-17 15:34:55 +00:00
assignUser	727f982bf9	typo	2020-08-17 13:38:00 +00:00
assignUser	4f4784fd41	fix displayed lintr command	2020-08-17 13:30:39 +00:00
assignUser	f9b81243db	add quotes	2020-08-17 12:14:15 +00:00
assignUser	0f47f68445	add .lintr detection	2020-08-17 12:01:25 +00:00
Julie Garrone	1022ad20f5	Fix indentation in comment and table	2020-08-17 09:59:09 +02:00
assignUser	6bb65aaa2c	lowercase file_type	2020-08-16 13:31:23 +00:00
assignUser	7632f64664	ad lintr to TestCodebase	2020-08-16 12:44:37 +00:00
assignUser	527334883e	adjust lint command	2020-08-16 00:18:31 +00:00
assignUser	8baec3bc77	fix	2020-08-15 23:43:42 +00:00
assignUser	a745a38df9	add apks	2020-08-15 22:53:08 +00:00
assignUser	0933aebc7a	add R with edgecases	2020-08-15 19:29:22 +00:00
Julie Garrone	c043e87ef1	Fix VALIDATE variables name for Dockerfile linters	2020-08-14 10:38:26 +02:00
Lucas Gravley	0d3547c35b	more quotes	2020-08-13 12:48:00 -05:00
Lucas Gravley	c7f28b9b7f	backwards	2020-08-13 12:44:55 -05:00
Lucas Gravley	999413d224	adding more tests and cool logic	2020-08-13 12:40:21 -05:00
Lukas Gravley	f72cd683d7	Merge pull request #560 from GaboFDC/gf_sass ... Add sass and scss files to stylelint	2020-08-13 12:22:04 -05:00
Lukas Gravley	b63730f8fb	Merge pull request #555 from GaboFDC/gf_better_validate_logic ... Better VALIDATE_[LANGUAGE] vars logic	2020-08-13 12:21:08 -05:00
Lukas Gravley	118ab2ce5f	Merge pull request #563 from julie-garrone/fix-dockerfilelintrc-ignored-bug ... Fix .dockerfilelintrc is ignored bug	2020-08-13 12:20:47 -05:00
Julie Garrone	f289ebd074	Fix dockerfile linters FILE_NAME variable	2020-08-13 18:03:13 +02:00
Lucas Gravley	345862a029	smallFix	2020-08-13 10:06:11 -05:00
Gabo	50cf06f562	Add sass and scss	2020-08-13 07:58:06 -05:00
Gabo	d05f179506	Add logic to include/exclude linters	2020-08-11 21:05:01 -05:00
Gabo	cb2cf0eb49	Fix spell	2020-08-11 21:04:33 -05:00
Lucas Gravley	0f88a9ea5d	More verbose	2020-08-11 13:27:30 -05:00
Lucas Gravley	9856082087	add sql goods	2020-08-11 12:30:00 -05:00
Lukas Gravley	717f652dc9	super slick	2020-08-11 08:55:42 -05:00
Eric Nemchik	a4d7e4831a	Add missing editorconfig-checker to linter array	2020-08-10 09:45:40 -05:00
Ryan Moran	200f699c15	Adds --external-sources option for shellcheck ... Shellcheck supports a `--external-sources` option that allows directives like the follow to pass linting. ``` # shellcheck source=SCRIPTDIR/some/source/script.sh` source "$(dirname "${BASH_SOURCE[0]}")/some/source/script.sh" ``` Without this option, we will see lots of spurious errors from shellcheck like the following. ``` # shellcheck source=SCRIPTDIR/some/source/script.sh` source "$(dirname "${BASH_SOURCE[0]}")/some/source/script.sh" ^-- SC1091: Not following: SCRIPTDIR/some/source/script.sh: openBinaryFile: does not exist (No such file or directory) ``` It looks like it [may be possible](https://github.com/koalaman/shellcheck/issues/1818) to include this option in a future version of shellcheck through the .shellcheckrc configuration file, given that this issue is resolved, and that super-linter supports .shellcheckrc as a configuration file for shellcheck.	2020-08-07 15:18:40 -04:00
Lukas Gravley	1746012dab	Merge pull request #534 from marghidanu/master ... PerlCritic basic implementation	2020-08-07 11:56:09 -05:00
Lukas Gravley	d082f4f6e4	Merge pull request #529 from github/BetterTests ... Adding all codebase scan test	2020-08-07 09:22:17 -05:00
Lukas Gravley	9ea04e4012	Merge pull request #531 from GaboFDC/gf_improve_eslint ... Improve eslint	2020-08-07 08:34:13 -05:00
Tudor Marghidanu	523b14a2df	PerlCritic basic implementation	2020-08-07 14:58:40 +02:00
Gabo	9dc7afd67f	Allow to set markdownlint config file	2020-08-07 00:51:59 -05:00
Gabo	a186477c8b	Skip node_modules from finds	2020-08-06 19:56:36 -05:00
Lucas Gravley	f88db68011	remove space	2020-08-06 15:07:34 -05:00
Lucas Gravley	c9ef1fcb66	Saving it	2020-08-06 12:01:36 -05:00
Lukas Gravley	fc9654924f	Merge pull request #526 from github/fix-editorconfig ... Editorconfig error reporting fix	2020-08-06 11:27:47 -05:00
Lucas Gravley	5ffa5518db	fixed it real good	2020-08-06 10:56:06 -05:00
Lucas Gravley	f5532f9cd6	put them back lol	2020-08-06 10:53:42 -05:00
Lucas Gravley	2beb30e939	cleanup	2020-08-06 10:42:57 -05:00
Lucas Gravley	5b44f9d066	Adding secondary name	2020-08-06 10:30:10 -05:00
Eric Nemchik	e527b47e80	Update linter.sh	2020-08-06 10:25:45 -05:00
Lucas Gravley	54fe9b762b	Adding the look	2020-08-06 09:39:45 -05:00
Lucas Gravley	3a1535e413	fix typo	2020-08-05 14:53:48 -05:00
Lucas Gravley	c3e5cb0ef1	Fix the pathing	2020-08-05 14:37:38 -05:00
Lucas Gravley	3d7e7d1073	Fix checkstyle	2020-08-05 14:28:43 -05:00
Lucas Gravley	eaca27d508	Fix typo	2020-08-05 13:38:35 -05:00
Lucas Gravley	a216a6623a	adding some good code	2020-08-05 13:35:14 -05:00
Lucas Gravley	e638e3d8ac	Fix shell errors	2020-08-05 13:16:49 -05:00
Ishan Goel	f327a4dc5f	Merge branch 'master' into quackduck-pr	2020-08-05 20:10:30 +04:00
Ishan Goel	5527dab3fa	Fix some merge conflicts	2020-08-05 20:00:51 +04:00
Gabo	ad4ba7d492	Fix php var wrong default	2020-08-04 16:41:02 -05:00
Lukas Gravley	7d3ad70608	i made a mistake	2020-08-04 16:13:20 -05:00
Lucas Gravley	6a6bb77270	Fixing them rules	2020-08-04 14:41:10 -05:00
Lucas Gravley	c78f7f0ed8	adding better finder	2020-08-04 14:19:29 -05:00
Lucas Gravley	dee51753b0	now with connecting vars	2020-08-04 13:57:50 -05:00