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Merge pull request #713 from kpj/master

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Fix file detection issues of Snakemake linter/formatter
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Lukas Gravley 2020-09-22 09:16:21 -05:00 committed by GitHub
commit 23fca80de7
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4 changed files with 73 additions and 53 deletions
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@ -16,6 +16,13 @@
] ]
}, },
"default": { "default": {
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"sha256:6e5d53af62772790ba82a989a3de72b8ce5c1cd809613c06f7cb061f7ec34dc8",
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],
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},
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@ -35,6 +42,7 @@
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}, },
"attrs": { "attrs": {
@ -42,37 +50,38 @@
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"version": "==20.2.0" "version": "==20.2.0"
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@ -83,11 +92,11 @@
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@ -101,6 +110,7 @@
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"version": "==7.1.2" "version": "==7.1.2"
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@ -137,6 +147,7 @@
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@ -148,11 +159,11 @@
}, },
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"version": "==0.16"
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@ -167,6 +178,7 @@
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@ -174,6 +186,7 @@
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@ -181,6 +194,7 @@
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@ -188,6 +202,7 @@
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}, },
"ipython-genutils": { "ipython-genutils": {
@ -199,16 +214,18 @@
}, },
"isort": { "isort": {
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"jmespath": { "jmespath": {
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@ -224,6 +241,7 @@
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@ -244,6 +262,7 @@
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@ -270,6 +289,7 @@
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@ -284,15 +304,9 @@
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@ -322,19 +336,22 @@
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@ -342,6 +359,7 @@
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"version": "==2.2.0" "version": "==2.2.0"
}, },
"pylint": { "pylint": {
@ -354,15 +372,17 @@
}, },
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"version": "==0.17.3" "version": "==0.17.3"
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"python-dateutil": { "python-dateutil": {
@ -370,6 +390,7 @@
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@ -427,6 +448,7 @@
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], ],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==2.24.0" "version": "==2.24.0"
}, },
"s3transfer": { "s3transfer": {
@ -441,6 +463,7 @@
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259", "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced" "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
], ],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==1.15.0" "version": "==1.15.0"
}, },
"smmap": { "smmap": {
@ -448,23 +471,24 @@
"sha256:54c44c197c819d5ef1991799a7e30b662d1e520f2ac75c9efbeb54a742214cf4", "sha256:54c44c197c819d5ef1991799a7e30b662d1e520f2ac75c9efbeb54a742214cf4",
"sha256:9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24" "sha256:9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24"
], ],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==3.0.4" "version": "==3.0.4"
}, },
"snakefmt": { "snakefmt": {
"hashes": [ "hashes": [
"sha256:a394a202311c3f244f7f822f4ffa262972f97d117bd290faa3815065896fd923", "sha256:6dfd5f82ae9799c359776079fef37f2dfb582ff1653ca25095c6a4083338dc51",
"sha256:e50c09202bab30451dc459df15da8254f26c7829572eca2831025593385467fa" "sha256:ec3f97feb69df2dcda2d63de145e561db9a3be97ae015b7159332560e13a1e9b"
], ],
"index": "pypi", "index": "pypi",
"version": "==0.1.5" "version": "==0.2.0"
}, },
"snakemake": { "snakemake": {
"hashes": [ "hashes": [
"sha256:9925451c5a1f5ab080a5827bef727d05e4f03f91f0b7ffc4cc3f2a7328572379", "sha256:6e9ba39038c0d64a6bba492e1646dda10f4826bd905a8b2aa93b18a6793b098b",
"sha256:a4608447bf14a1e224a2732ec97ab6608a6d74650fcfd3a4b7a3c5ce8208ae47" "sha256:b3060be5a7a88bf9e1b39e62315e8c06a831706f1a8a8883f83a49de0ab2c767"
], ],
"index": "pypi", "index": "pypi",
"version": "==5.24.1" "version": "==5.25.0"
}, },
"toml": { "toml": {
"hashes": [ "hashes": [
@ -485,6 +509,7 @@
"sha256:86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b", "sha256:86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b",
"sha256:9664ec0c526e48e7b47b7d14cd6b252efa03e0129011de0a9c1d70315d4309c3" "sha256:9664ec0c526e48e7b47b7d14cd6b252efa03e0129011de0a9c1d70315d4309c3"
], ],
"markers": "python_version >= '3.7'",
"version": "==5.0.4" "version": "==5.0.4"
}, },
"typed-ast": { "typed-ast": {
@ -513,14 +538,6 @@
], ],
"version": "==1.4.1" "version": "==1.4.1"
}, },
"typing-extensions": {
"hashes": [
"sha256:7cb407020f00f7bfc3cb3e7881628838e69d8f3fcab2f64742a5e76b2f841918",
"sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c",
"sha256:dafc7639cde7f1b6e1acc0f457842a83e722ccca8eef5270af2d74792619a89f"
],
"version": "==3.7.4.3"
},
"urllib3": { "urllib3": {
"hashes": [ "hashes": [
"sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a", "sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a",
@ -563,6 +580,7 @@
"sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b", "sha256:aa36550ff0c0b7ef7fa639055d797116ee891440eac1a56f378e2d3179e0320b",
"sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96" "sha256:c599e4d75c98f6798c509911d08a22e6c021d074469042177c8c86fb92eefd96"
], ],
"markers": "python_version >= '3.6'",
"version": "==3.1.0" "version": "==3.1.0"
} }
}, },

2
lib/buildFileList.sh
View file

@ -487,7 +487,7 @@ function BuildFileList() {
########################### ###########################
# Get the SNAKEMAKE files # # Get the SNAKEMAKE files #
########################### ###########################
elif [ "${FILE_TYPE}" == "smk" ]; then elif [ "${FILE_TYPE}" == "smk" ] || [ "${BASE_FILE}" == "Snakefile" ]; then
################################ ################################
# Append the file to the array # # Append the file to the array #
################################ ################################

6
lib/linter.sh
View file

@ -144,7 +144,7 @@ LANGUAGE_ARRAY=('ANSIBLE' 'ARM' 'BASH' 'BASH_EXEC' 'CLOUDFORMATION' 'CLOJURE' 'C
'DART' 'DOCKERFILE' 'DOCKERFILE_HADOLINT' 'EDITORCONFIG' 'ENV' 'GO' 'GROOVY' 'HTML' 'DART' 'DOCKERFILE' 'DOCKERFILE_HADOLINT' 'EDITORCONFIG' 'ENV' 'GO' 'GROOVY' 'HTML'
'JAVA' 'JAVASCRIPT_ES' 'JAVASCRIPT_STANDARD' 'JSON' 'JSX' 'KUBERNETES_KUBEVAL' 'KOTLIN' 'LATEX' 'LUA' 'MARKDOWN' 'JAVA' 'JAVASCRIPT_ES' 'JAVASCRIPT_STANDARD' 'JSON' 'JSX' 'KUBERNETES_KUBEVAL' 'KOTLIN' 'LATEX' 'LUA' 'MARKDOWN'
'OPENAPI' 'PERL' 'PHP_BUILTIN' 'PHP_PHPCS' 'PHP_PHPSTAN' 'PHP_PSALM' 'POWERSHELL' 'OPENAPI' 'PERL' 'PHP_BUILTIN' 'PHP_PHPCS' 'PHP_PHPSTAN' 'PHP_PSALM' 'POWERSHELL'
'PROTOBUF' 'PYTHON_BLACK' 'PYTHON_PYLINT' 'PYTHON_FLAKE8' 'R' 'RAKU' 'RUBY' 'SHELL_SHFMT' 'STATES' 'SQL' 'TERRAFORM' 'PROTOBUF' 'PYTHON_BLACK' 'PYTHON_PYLINT' 'PYTHON_FLAKE8' 'R' 'RAKU' 'RUBY' 'SHELL_SHFMT' 'SNAKEMAKE_LINT' 'SNAKEMAKE_SNAKEFMT' 'STATES' 'SQL' 'TERRAFORM'
'TERRAFORM_TERRASCAN' 'TSX' 'TYPESCRIPT_ES' 'TYPESCRIPT_STANDARD' 'XML' 'YAML') 'TERRAFORM_TERRASCAN' 'TSX' 'TYPESCRIPT_ES' 'TYPESCRIPT_STANDARD' 'XML' 'YAML')
############################################ ############################################
@ -317,6 +317,7 @@ FILE_ARRAY_PYTHON_FLAKE8=() # Array of files to check
FILE_ARRAY_R=() # Array of files to check FILE_ARRAY_R=() # Array of files to check
FILE_ARRAY_RAKU=() # Array of files to check FILE_ARRAY_RAKU=() # Array of files to check
FILE_ARRAY_RUBY=() # Array of files to check FILE_ARRAY_RUBY=() # Array of files to check
FILE_ARRAY_SNAKEMAKE=() # Array of files to check
FILE_ARRAY_STATES=() # Array of files to check FILE_ARRAY_STATES=() # Array of files to check
FILE_ARRAY_SQL=() # Array of files to check FILE_ARRAY_SQL=() # Array of files to check
FILE_ARRAY_TERRAFORM=() # Array of files to check FILE_ARRAY_TERRAFORM=() # Array of files to check
@ -1934,6 +1935,7 @@ if [ "${VALIDATE_SNAKEMAKE_LINT}" == "true" ]; then
################################ ################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY" # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}" LintCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi fi
###################### ######################
@ -1944,7 +1946,7 @@ if [ "${VALIDATE_SNAKEMAKE_SNAKEFMT}" == "true" ]; then
# Lint the files with snakefmt # # Lint the files with snakefmt #
################################ ################################
# LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY" # LintCodebase "FILE_TYPE" "LINTER_NAME" "LINTER_CMD" "FILE_TYPES_REGEX" "FILTER_REGEX_INCLUDE" "FILTER_REGEX_EXCLUDE" "FILE_ARRAY"
LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}" LintCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" "\(Snakefile|.*\.smk\)\$" "${FILTER_REGEX_INCLUDE}" "${FILTER_REGEX_EXCLUDE}" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi fi
###################### ######################

2
lib/worker.sh
View file

@ -727,7 +727,7 @@ function RunTestCases() {
TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby" TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby"
TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt" TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt"
TestCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\.\(smk\)\$" "snakemake" TestCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\.\(smk\)\$" "snakemake"
TestCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" ".*\.\(smk\)\$" "snakemake" TestCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --check --compact-diff" ".*\.\(smk\)\$" "snakemake"
TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states" TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states"
TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql" TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql"
TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform" TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform"