From c86e90b3d0b06a7c6af362607db5a9327b66f8f4 Mon Sep 17 00:00:00 2001
From: NicolasVuillamy <nicolas.vuillamy@gmail.com>
Date: Wed, 9 Sep 2020 20:22:32 +0200
Subject: [PATCH] Solve conflicts + format
---
lib/linter.sh | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/lib/linter.sh b/lib/linter.sh
index c3a65a41..6c282cf4 100755
--- a/lib/linter.sh
+++ b/lib/linter.sh
@@ -119,8 +119,8 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}" # Path to the R lint r
RUBY_FILE_NAME="${RUBY_CONFIG_FILE:-.ruby-lint.yml}" # Name of the file
RUBY_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${RUBY_FILE_NAME}" # Path to the ruby lint rules
# Snakemake Vars
-SNAKEMAKE_FILE_NAME="${SNAKEMAKE_CONFIG_FILE:-.snakefmt.toml}" # Name of the file
-SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}" # Path to the snakemake lint rules
+SNAKEMAKE_FILE_NAME="${SNAKEMAKE_CONFIG_FILE:-.snakefmt.toml}" # Name of the file
+SNAKEMAKE_SNAKEFMT_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SNAKEMAKE_FILE_NAME}" # Path to the snakemake lint rules
# SQL Vars
SQL_FILE_NAME=".sql-config.json" # Name of the file
SQL_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${SQL_FILE_NAME}" # Path to the SQL lint rules
@@ -1019,7 +1019,8 @@ CallStatusAPI() {
##############################################
# Call the status API to create status check #
##############################################
- SEND_STATUS_CMD=$(curl -f -s -X POST \
+ SEND_STATUS_CMD=$(
+ curl -f -s -X POST \
--url "${GITHUB_API_URL}/repos/${GITHUB_REPOSITORY}/statuses/${GITHUB_SHA}" \
-H 'accept: application/vnd.github.v3+json' \
-H "authorization: Bearer ${GITHUB_TOKEN}" \
@@ -1027,7 +1028,8 @@ CallStatusAPI() {
-d "{ \"state\": \"${STATUS}\",
\"target_url\": \"https://github.com/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}\",
\"description\": \"${MESSAGE}\", \"context\": \"--> Linted: ${LANGUAGE}\"
- }" 2>&1)
+ }" 2>&1
+ )
#######################
# Load the error code #
@@ -1866,8 +1868,8 @@ if [ "${VALIDATE_SNAKEMAKE_LINT}" == "true" ]; then
################################
# Lint the files with snakefmt #
################################
- # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY"
- LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
+ # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE"
+ LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}"
fi
######################
@@ -1877,8 +1879,8 @@ if [ "${VALIDATE_SNAKEMAKE_SNAKEFMT}" == "true" ]; then
################################
# Lint the files with snakefmt #
################################
- # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY"
- LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
+ # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILE_ARRAY" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE"
+ LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}"
fi
######################