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Solve conflicts + format

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This commit is contained in:
NicolasVuillamy 2020-09-09 20:22:32 +02:00
parent f072bc5c8d
commit c86e90b3d0
1 changed files with 10 additions and 8 deletions
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18
lib/linter.sh
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@ -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
######################