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Merge pull request #689 from kpj/master

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Add `snakemake --lint`/`snakefmt` support to super-linter
This commit is contained in:
Lukas Gravley 2020-09-08 10:31:19 -05:00 committed by GitHub
commit 1d46677b4f
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13 changed files with 318 additions and 17 deletions
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19
.automation/test/snakemake/README.md Normal file
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@ -0,0 +1,19 @@
# Snakemake test cases
This folder holds the test cases for **Snakemake**.
## Additional Docs
No Additional information is needed for this test case.
## Good Test Cases
The test cases denoted: `LANGUAGE_good_FILE.EXTENSION` are all valid, and should pass successfully when linted.
- **Note:** They are linted utilizing the default linter rules.
## Bad Test Cases
The test cases denoted: `LANGUAGE_bad_FILE.EXTENSION` are **NOT** valid, and should trigger errors when linted.
- **Note:** They are linted utilizing the default linter rules.

11
.automation/test/snakemake/snakemake_bad_1.smk Normal file
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@ -0,0 +1,11 @@
rule all:
input:
file1='result.txt',
rule simulation:
output:
file1="result.txt"
shell:
"""
touch {output}
"""

16
.automation/test/snakemake/snakemake_good_1.smk Normal file
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@ -0,0 +1,16 @@
rule all:
input:
file1="result.txt",
rule simulation:
output:
file1="result.txt",
log:
"logs/simulation.log",
conda:
"envs/simulation.yml"
shell:
"""
touch {output}
"""

0
.github/linters/.snakefmt.toml vendored Normal file
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4
Dockerfile
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@ -91,6 +91,7 @@ RUN apk add --update --no-cache \
krb5-libs \
libc-dev libxml2-dev libxml2-utils libgcc \
libcurl libintl libssl1.1 libstdc++ \
linux-headers \
make \
musl-dev \
npm nodejs-current \
@ -338,6 +339,7 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
OUTPUT_FOLDER=${OUTPUT_FOLDER} \
OUTPUT_FORMAT=${OUTPUT_FORMAT} \
RUN_LOCAL=${RUN_LOCAL} \
SNAKEMAKE_CONFIG_FILE=${SNAKEMAKE_CONFIG_FILE} \
TEST_CASE_RUN=${TEST_CASE_RUN} \
VALIDATE_ALL_CODEBASE=${VALIDATE_ALL_CODEBASE} \
VALIDATE_ANSIBLE=${VALIDATE_ANSIBLE} \
@ -381,6 +383,8 @@ ENV ACTIONS_RUNNER_DEBUG=${ACTIONS_RUNNER_DEBUG} \
VALIDATE_RAKU=${VALIDATE_RAKU} \
VALIDATE_RUBY=${VALIDATE_RUBY} \
VALIDATE_SHELL_SHFMT=${VALIDATE_SHELL_SHFMT} \
VALIDATE_SNAKEMAKE_LINT=${VALIDATE_SNAKEMAKE_LINT} \
VALIDATE_SNAKEMAKE_SNAKEFMT=${VALIDATE_SNAKEMAKE_SNAKEFMT} \
VALIDATE_STATES=${VALIDATE_STATES} \
VALIDATE_SQL=${VALIDATE_SQL} \
VALIDATE_TERRAFORM=${VALIDATE_TERRAFORM} \

6
README.md
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@ -74,6 +74,7 @@ Developers on **GitHub** can call the **GitHub Action** to lint their code base
| **Raku** | [Raku](https://raku.org) |
| **Ruby** | [RuboCop](https://github.com/rubocop-hq/rubocop) |
| **Shell** | [Shellcheck](https://github.com/koalaman/shellcheck) / [executable bit check] / [shfmt](https://github.com/mvdan/sh) |
| **Snakemake** | [snakefmt](https://github.com/snakemake/snakefmt/) / [snakemake --lint](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#best-practices) |
| **SQL** | [sql-lint](https://github.com/joereynolds/sql-lint) |
| **Terraform** | [tflint](https://github.com/terraform-linters/tflint) / [terrascan](https://github.com/accurics/terrascan) |
| **TypeScript** | [eslint](https://eslint.org/) / [standard js](https://standardjs.com/) |
@ -193,6 +194,7 @@ But if you wish to select or exclude specific linters, we give you full control
| **PYTHON_FLAKE8_CONFIG_FILE** | `.flake8` | Filename for [flake8 configuration](https://flake8.pycqa.org/en/latest/user/configuration.html) (ex: `.flake8`, `tox.ini`) |
| **PYTHON_BLACK_CONFIG_FILE** | `.python-black` | Filename for [black configuration](https://github.com/psf/black/blob/master/docs/compatible_configs.md) (ex: `.isort.cfg`, `pyproject.toml`) |
| **RUBY_CONFIG_FILE** | `.ruby-lint.yml` | Filename for [rubocop configuration](https://docs.rubocop.org/rubocop/configuration.html) (ex: `.ruby-lint.yml`, `.rubocop.yml`) |
| **SNAKEMAKE_CONFIG_FILE** | `.snakefmt.toml` | Filename for [Snakemake configuration](https://github.com/snakemake/snakefmt#configuration) (ex: `pyproject.toml`, `.snakefmt.toml`) |
| **TYPESCRIPT_ES_CONFIG_FILE** | `.eslintrc.yml` | Filename for [eslint configuration](https://eslint.org/docs/user-guide/configuring#configuration-file-formats) (ex: `.eslintrc.yml`, `.eslintrc.json`) |
| **VALIDATE_ALL_CODEBASE** | `true` | Will parse the entire repository and find all files to validate across all types. **NOTE:** When set to `false`, only **new** or **edited** files will be parsed for validation. |
| **VALIDATE_ANSIBLE** | `true` | Flag to enable or disable the linting process of the Ansible language. |
@ -238,10 +240,12 @@ But if you wish to select or exclude specific linters, we give you full control
| **VALIDATE_RAKU** | `true` | Flag to enable or disable the linting process of the Raku language. |
| **VALIDATE_RUBY** | `true` | Flag to enable or disable the linting process of the Ruby language. |
| **VALIDATE_SHELL_SHFMT** | `true` | Flag to enable or disable the linting process of Shell scripts. (Utilizing: shfmt) |
| **VALIDATE_SNAKEMAKE_LINT** | `true` | Flag to enable or disable the linting process of Snakefiles. (Utilizing: snakemake --lint) |
| **VALIDATE_SNAKEMAKE_SNAKEFMT** | `true` | Flag to enable or disable the linting process of Snakefiles. (Utilizing: snakefmt) |
| **VALIDATE_STATES** | `true` | Flag to enable or disable the linting process for AWS States Language. |
| **VALIDATE_SQL** | `true` | Flag to enable or disable the linting process of the SQL language. |
| **VALIDATE_TERRAFORM** | `true` | Flag to enable or disable the linting process of the Terraform language. |
| **VALIDATE_TERRAFORM_TERRASCAN** | `true` | Flag to enable or disable the linting process of the Terraform language for security related issues. |
| **VALIDATE_TERRAFORM_TERRASCAN** | `true` | Flag to enable or disable the linting process of the Terraform language for security related issues. |
| **VALIDATE_TSX** | `true` | Flag to enable or disable the linting process for tsx files (Utilizing: eslint) |
| **VALIDATE_TYPESCRIPT_ES** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: eslint) |
| **VALIDATE_TYPESCRIPT_STANDARD** | `true` | Flag to enable or disable the linting process of the Typescript language. (Utilizing: standard) |

0
TEMPLATES/.snakefmt.toml Normal file
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2
dependencies/Pipfile vendored
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@ -10,6 +10,8 @@ black = "*"
cfn-lint = "*"
flake8 = "*"
pylint = "*"
snakefmt = "*"
snakemake = "*"
yamllint = "*"
yq = "*"

219
dependencies/Pipfile.lock generated vendored
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@ -1,7 +1,7 @@
{
"_meta": {
"hash": {
"sha256": "1f2a4e188bcf058f78905dbe7c959b9a801148e39a69e86d6a795b45a65b7af9"
"sha256": "db425ed57eee9f33aae7341acbde447b5170e9cbdb3bd360794c4ce4f3944c5c"
},
"pipfile-spec": 6,
"requires": {
@ -16,6 +16,13 @@
]
},
"default": {
"amply": {
"hashes": [
"sha256:6e5d53af62772790ba82a989a3de72b8ce5c1cd809613c06f7cb061f7ec34dc8",
"sha256:c93da6113cac809487abc6565f41e37b9b8a5d469dcfaf4443d8d35befb181af"
],
"version": "==0.1.2"
},
"appdirs": {
"hashes": [
"sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41",
@ -35,6 +42,7 @@
"sha256:2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703",
"sha256:bc58d83eb610252fd8de6363e39d4f1d0619c894b0ed24603b881c02e64c7386"
],
"markers": "python_version >= '3.5'",
"version": "==2.4.2"
},
"attrs": {
@ -42,6 +50,7 @@
"sha256:26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594",
"sha256:fce7fc47dfc976152e82d53ff92fa0407700c21acd20886a13777a0d20e655dc"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==20.2.0"
},
"aws-sam-translator": {
@ -54,11 +63,11 @@
},
"black": {
"hashes": [
"sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea",
"sha256:70b62ef1527c950db59062cda342ea224d772abdf6adc58b86a45421bab20a6b"
"sha256:1b30e59be925fafc1ee4565e5e08abef6b03fe455102883820fe5ee2e4734e0b",
"sha256:c2edb73a08e9e0e6f65a0e6af18b059b8b1cdd5bef997d7a0b181df93dc81539"
],
"index": "pypi",
"version": "==20.8b1"
"version": "==19.10b0"
},
"boto3": {
"hashes": [
@ -74,6 +83,13 @@
],
"version": "==1.17.56"
},
"certifi": {
"hashes": [
"sha256:5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3",
"sha256:8fc0819f1f30ba15bdb34cceffb9ef04d99f420f68eb75d901e9560b8749fc41"
],
"version": "==2020.6.20"
},
"cfn-lint": {
"hashes": [
"sha256:98c7e2c2846df779f1a878e76f3eb7a3f40dd7b7dd316e5673c4923cf2ed121e",
@ -82,13 +98,58 @@
"index": "pypi",
"version": "==0.35.1"
},
"chardet": {
"hashes": [
"sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae",
"sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15460124c106691"
],
"version": "==3.0.4"
},
"click": {
"hashes": [
"sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a",
"sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==7.1.2"
},
"configargparse": {
"hashes": [
"sha256:edd17be986d5c1ba2e307150b8e5f5107aba125f3574dddd02c85d5cdcfd37dc"
],
"version": "==1.2.3"
},
"datrie": {
"hashes": [
"sha256:0e3b76676abbae2368cce6bf605bb0ba7cfd11f2c420b96d67959f353d5d423f",
"sha256:25e9e07ecfceaef78d23bde8d7278e4d6f63e1e3dc5ac00ccb4bec3062f0a8e0",
"sha256:2de594d84a2f43a09ddc15316a8afd48aae0fdc456f9279d0940aa59c473d9d5",
"sha256:31e316ba305cdd7b8a42f8e4af5a0a15a628aee270d2f392c41329a709eeda6d",
"sha256:327d9c17efaebc66d1956dca047b76fdd0e5b989d63cb55b9038ec09d8769089",
"sha256:3a3e360a765cc95410898dc222f8585ea1b1bba0538a1af4d8630a5bc3ad6ee7",
"sha256:525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d",
"sha256:53969643e2794c37f024d5edaa42d5e6e2627d9937ddcc18d99128e9df700e4c",
"sha256:651c63325056347b86c5de7ffeea8529230a5787c61ee6dcabc5b6c644bd3252",
"sha256:67603594f5db5c0029b1cf86a08e89cde015fe64cf0c4ae4e539c61114396729",
"sha256:6c9b333035312b79e6e9a10356d033e3d29aadbae6365007f706c854b3a94674",
"sha256:89ff3d41df4f899387aa07b4b066f5da36e3a10b67b8aeae631c950502ff4503",
"sha256:b07bd5fdfc3399a6dab86d6e35c72b1dbd598e80c97509c7c7518ab8774d3fda",
"sha256:b2d80fa687173cb8f8bae224ef00d1ad6bda8f8597bbb1a63f85182c7d91aeb3",
"sha256:b6fd6c7c149b410a87d46072c1c98f6e87ec557802e1d0e09db7b858746e8550",
"sha256:bf5c956c0a9a9d0f07e3c8923746279171096de18a8a51685e22d9817f8755a6",
"sha256:bf9f34f7c63797219b32713b561c4f94e777ff6c22beecfcd6bdf6b6c25b8518",
"sha256:c783e2c1e28964b2b045a951eb9606833a188c4bd4a780da68d22f557e03e429",
"sha256:dbe04704eb41b8440ca61416d3670ca6ddeea847d19731cf121889bac2962d07",
"sha256:e0582435a4adef1a2fce53aeedb656bf769b0f113b524f98be51d3e3d40720cb",
"sha256:e1d704ee4fdc03f02d7dacc4d92052dbd490dba551509fccfd8ee52c9039d4ad",
"sha256:ee7cd8470a982356e104e62148f2dbe2d3e17545cafaa3ada29f2548984f1e89",
"sha256:f61cf2726f04c08828bfb4e7af698b0b16bdf2777c3993d042f2898b8e118f21",
"sha256:f826e843138698501cbf1a21233f724b851b1e475fad532b638ac5904e115f10",
"sha256:fa9f39ac88dc6286672b9dd286fe459646da48133c877a927af24803eaea441e"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==0.8.2"
},
"decorator": {
"hashes": [
"sha256:41fa54c2a0cc4ba648be4fd43cff00aedf5b9465c9bf18d64325bc225f08f760",
@ -102,6 +163,7 @@
"sha256:9e4d7ecfc600058e07ba661411a2b7de2fd0fafa17d1a7f7361cd47b1175c827",
"sha256:a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'",
"version": "==0.15.2"
},
"flake8": {
@ -112,11 +174,43 @@
"index": "pypi",
"version": "==3.8.3"
},
"gitdb": {
"hashes": [
"sha256:91f36bfb1ab7949b3b40e23736db18231bf7593edada2ba5c3a174a7b23657ac",
"sha256:c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9"
],
"markers": "python_version >= '3.4'",
"version": "==4.0.5"
},
"gitpython": {
"hashes": [
"sha256:080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912",
"sha256:1858f4fd089abe92ae465f01d5aaaf55e937eca565fb2c1fce35a51b5f85c910"
],
"markers": "python_version >= '3.4'",
"version": "==3.1.8"
},
"idna": {
"hashes": [
"sha256:b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6",
"sha256:b97d804b1e9b523befed77c48dacec60e6dcb0b5391d57af6a65a312a90648c0"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.10"
},
"ipython-genutils": {
"hashes": [
"sha256:72dd37233799e619666c9f639a9da83c34013a73e8bbc79a7a6348d93c61fab8",
"sha256:eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8"
],
"version": "==0.2.0"
},
"isort": {
"hashes": [
"sha256:92533892058de0306e51c88f22ece002a209dc8e80288aa3cec6d443060d584f",
"sha256:a200d47b7ee8b7f7d0a9646650160c4a51b6a91a9413fd31b1da2c4de789f5d3"
],
"markers": "python_version >= '3.6' and python_version < '4.0'",
"version": "==5.5.1"
},
"jmespath": {
@ -124,6 +218,7 @@
"sha256:b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9",
"sha256:cdf6525904cc597730141d61b36f2e4b8ecc257c420fa2f4549bac2c2d0cb72f"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'",
"version": "==0.10.0"
},
"jsonpatch": {
@ -139,6 +234,7 @@
"sha256:c192ba86648e05fdae4f08a17ec25180a9aef5008d973407b581798a83975362",
"sha256:ff379fa021d1b81ab539f5ec467c7745beb1a5671463f9dcc2b2d458bd361c1e"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.0"
},
"jsonschema": {
@ -154,6 +250,14 @@
],
"version": "==1.9"
},
"jupyter-core": {
"hashes": [
"sha256:394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e",
"sha256:a4ee613c060fe5697d913416fc9d553599c05e4492d58fac1192c9a6844abb21"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==4.6.3"
},
"lazy-object-proxy": {
"hashes": [
"sha256:0c4b206227a8097f05c4dbdd323c50edf81f15db3b8dc064d08c62d37e1a504d",
@ -178,6 +282,7 @@
"sha256:efa1909120ce98bbb3777e8b6f92237f5d5c8ea6758efea36a473e1d38f7d3e4",
"sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==1.4.3"
},
"mccabe": {
@ -187,12 +292,13 @@
],
"version": "==0.6.1"
},
"mypy-extensions": {
"nbformat": {
"hashes": [
"sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d",
"sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"
"sha256:54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340",
"sha256:ea55c9b817855e2dfcd3f66d74857342612a60b1f09653440f4a5845e6e3523f"
],
"version": "==0.4.3"
"markers": "python_version >= '3.5'",
"version": "==5.0.7"
},
"networkx": {
"hashes": [
@ -209,11 +315,36 @@
],
"version": "==0.8.0"
},
"psutil": {
"hashes": [
"sha256:0ee3c36428f160d2d8fce3c583a0353e848abb7de9732c50cf3356dd49ad63f8",
"sha256:10512b46c95b02842c225f58fa00385c08fa00c68bac7da2d9a58ebe2c517498",
"sha256:4080869ed93cce662905b029a1770fe89c98787e543fa7347f075ade761b19d6",
"sha256:5e9d0f26d4194479a13d5f4b3798260c20cecf9ac9a461e718eb59ea520a360c",
"sha256:66c18ca7680a31bf16ee22b1d21b6397869dda8059dbdb57d9f27efa6615f195",
"sha256:68d36986ded5dac7c2dcd42f2682af1db80d4bce3faa126a6145c1637e1b559f",
"sha256:90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb",
"sha256:a5b120bb3c0c71dfe27551f9da2f3209a8257a178ed6c628a819037a8df487f1",
"sha256:d8a82162f23c53b8525cf5f14a355f5d1eea86fa8edde27287dd3a98399e4fdf",
"sha256:f2018461733b23f308c298653c8903d32aaad7873d25e1d228765e91ae42c3f2",
"sha256:ff1977ba1a5f71f89166d5145c3da1cea89a0fdb044075a12c720ee9123ec818"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==5.7.2"
},
"pulp": {
"hashes": [
"sha256:1953894015ed3b9dfefea14a2fba1deef4b47138ef847d05c66ef9806f9fc3b4",
"sha256:9d8ecf532868cc31fa9ff59ee5d5b2049600c5c902c18c794a2bad677c1f92e5"
],
"version": "==2.3"
},
"pycodestyle": {
"hashes": [
"sha256:2295e7b2f6b5bd100585ebcb1f616591b652db8a741695b3d8f5d28bdc934367",
"sha256:c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.6.0"
},
"pyflakes": {
@ -221,6 +352,7 @@
"sha256:0d94e0e05a19e57a99444b6ddcf9a6eb2e5c68d3ca1e98e90707af8152c90a92",
"sha256:35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==2.2.0"
},
"pylint": {
@ -231,6 +363,14 @@
"index": "pypi",
"version": "==2.6.0"
},
"pyparsing": {
"hashes": [
"sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1",
"sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"
],
"markers": "python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2'",
"version": "==2.4.7"
},
"pyrsistent": {
"hashes": [
"sha256:28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3"
@ -242,6 +382,7 @@
"sha256:73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c",
"sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==2.8.1"
},
"pyyaml": {
@ -261,6 +402,13 @@
"markers": "python_version != '3.4'",
"version": "==5.3.1"
},
"ratelimiter": {
"hashes": [
"sha256:5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7",
"sha256:a52be07bc0bb0b3674b4b304550f10c769bbb00fead3072e035904474259809f"
],
"version": "==1.2.0.post0"
},
"regex": {
"hashes": [
"sha256:0dc64ee3f33cd7899f79a8d788abfbec168410be356ed9bd30bbd3f0a23a7204",
@ -287,6 +435,14 @@
],
"version": "==2020.7.14"
},
"requests": {
"hashes": [
"sha256:b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b",
"sha256:fe75cc94a9443b9246fc7049224f75604b113c36acb93f87b80ed42c44cbb898"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'",
"version": "==2.24.0"
},
"s3transfer": {
"hashes": [
"sha256:2482b4259524933a022d59da830f51bd746db62f047d6eb213f2f8855dcb8a13",
@ -299,8 +455,32 @@
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
"version": "==1.15.0"
},
"smmap": {
"hashes": [
"sha256:54c44c197c819d5ef1991799a7e30b662d1e520f2ac75c9efbeb54a742214cf4",
"sha256:9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24"
],
"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'",
"version": "==3.0.4"
},
"snakefmt": {
"hashes": [
"sha256:550b893d0b115adf73e3fc0acee5960f047b5e2c3ca5bbda31ba83f9d594c931",
"sha256:e6612968c3cb98e204449a5d7ad01359ef46da3e1c41bffbda39fe0e253c0c5e"
],
"index": "pypi",
"version": "==0.1.4"
},
"snakemake": {
"hashes": [
"sha256:d8bbde85fa8d93bd6312cae5d39247b316ead0589022aa7b48760374b1994b79"
],
"index": "pypi",
"version": "==5.23.0"
},
"toml": {
"hashes": [
"sha256:926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f",
@ -308,6 +488,21 @@
],
"version": "==0.10.1"
},
"toposort": {
"hashes": [
"sha256:d80128b83b411d503b0cdb4a8f172998bc1d3b434b6402a349b8ebd734d51a80",
"sha256:dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd"
],
"version": "==1.5"
},
"traitlets": {
"hashes": [
"sha256:86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b",
"sha256:9664ec0c526e48e7b47b7d14cd6b252efa03e0129011de0a9c1d70315d4309c3"
],
"markers": "python_version >= '3.7'",
"version": "==5.0.4"
},
"typed-ast": {
"hashes": [
"sha256:0666aa36131496aed8f7be0410ff974562ab7eeac11ef351def9ea6fa28f6355",
@ -334,14 +529,6 @@
],
"version": "==1.4.1"
},
"typing-extensions": {
"hashes": [
"sha256:7cb407020f00f7bfc3cb3e7881628838e69d8f3fcab2f64742a5e76b2f841918",
"sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c",
"sha256:dafc7639cde7f1b6e1acc0f457842a83e722ccca8eef5270af2d74792619a89f"
],
"version": "==3.7.4.3"
},
"urllib3": {
"hashes": [
"sha256:91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a",

16
docs/disabling-linters.md
View file

@ -48,6 +48,7 @@ For some linters it is also possible to override rules on a case by case level w
- [Raku](#raku)
- [Ruby](#ruby)
- [Shell](#shell)
- [Snakemake](#snakemake)
- [SQL](#sql)
- [Terraform](#terraform)
- [Typescript eslint](#typescript-eslint)
@ -1120,6 +1121,21 @@ shfmt [supports EditorConfig files for configuration](https://github.com/mvdan/s
---
## Snakemake
- [snakemake --lint](https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html#best-practices)
- [snakefmt](https://github.com/snakemake/snakefmt/)
### snakemake's configuration
- Check the repository's README
### snakefmt configuration
- Check the repository's README
---
## SQL
- [SQL](https://www.npmjs.com/package/sql-lint)

13
lib/buildFileList.sh
View file

@ -484,6 +484,19 @@ function BuildFileList() {
##########################################################
READ_ONLY_CHANGE_FLAG=1
###########################
# Get the SNAKEMAKE files #
###########################
elif [ "${FILE_TYPE}" == "smk" ]; then
################################
# Append the file to the array #
################################
FILE_ARRAY_SNAKEMAKE+=("${FILE}")
##########################################################
# Set the READ_ONLY_CHANGE_FLAG since this could be exec #
##########################################################
READ_ONLY_CHANGE_FLAG=1
#####################
# Get the SQL files #
#####################

27
lib/linter.sh
View file

@ -118,6 +118,9 @@ R_LINTER_RULES="${DEFAULT_RULES_LOCATION}/${R_FILE_NAME}"
# Ruby Vars
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
# 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
@ -207,6 +210,8 @@ VALIDATE_RAKU="${VALIDATE_RAKU}" # Boolean t
VALIDATE_RUBY="${VALIDATE_RUBY}" # Boolean to validate language
VALIDATE_STATES="${VALIDATE_STATES}" # Boolean to validate language
VALIDATE_SHELL_SHFMT="${VALIDATE_SHELL_SHFMT}" # Boolean to check Shell files against editorconfig
VALIDATE_SNAKEMAKE_LINT="${VALIDATE_SNAKEMAKE_LINT}" # Boolean to validate Snakefiles
VALIDATE_SNAKEMAKE_SNAKEFMT="${VALIDATE_SNAKEMAKE_SNAKEFMT}" # Boolean to validate Snakefiles
VALIDATE_SQL="${VALIDATE_SQL}" # Boolean to validate language
VALIDATE_TERRAFORM="${VALIDATE_TERRAFORM}" # Boolean to validate language
VALIDATE_TERRAFORM_TERRASCAN="${VALIDATE_TERRAFORM_TERRASCAN}" # Boolean to validate language
@ -1846,6 +1851,28 @@ if [ "${VALIDATE_SHELL_SHFMT}" == "true" ]; then
fi
fi
##################
# SNAKEMAKE LINT #
##################
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" "\(Snakefile|.*\.smk\)\$" "${FILE_ARRAY_SNAKEMAKE[@]}"
fi
######################
# SNAKEMAKE SNAKEFMT #
######################
if [ "${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[@]}"
fi
######################
# AWS STATES LINTING #
######################

2
lib/worker.sh
View file

@ -702,6 +702,8 @@ function RunTestCases() {
TestCodebase "RAKU" "raku" "raku -c" ".*\.\(raku\|rakumod\|rakutest\|pm6\|pl6\|p6\)\$" "raku"
TestCodebase "RUBY" "rubocop" "rubocop -c ${RUBY_LINTER_RULES}" ".*\.\(rb\)\$" "ruby"
TestCodebase "SHELL_SHFMT" "shfmt" "shfmt -d" ".*\.\(sh\|bash\|dash\|ksh\)\$" "shell_shfmt"
TestCodebase "SNAKEMAKE_LINT" "snakemake" "snakemake --lint -s" ".*\.\(smk\)\$" "snakemake"
TestCodebase "SNAKEMAKE_SNAKEFMT" "snakefmt" "snakefmt --config ${SNAKEMAKE_SNAKEFMT_LINTER_RULES} --diff" ".*\.\(smk\)\$" "snakemake"
TestCodebase "STATES" "asl-validator" "asl-validator --json-path" ".*\.\(json\)\$" "states"
TestCodebase "SQL" "sql-lint" "sql-lint --config ${SQL_LINTER_RULES}" ".*\.\(sql\)\$" "sql"
TestCodebase "TERRAFORM" "tflint" "tflint -c ${TERRAFORM_LINTER_RULES}" ".*\.\(tf\)\$" "terraform"