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[automation] Auto-update linters version, help and documentation (#57)
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nvuillam authored Nov 13, 2020
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8 changes: 4 additions & 4 deletions docs/descriptors/c_cpplint.md
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Expand Up @@ -72,7 +72,7 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
suppresses errors of all categories on that line.

The files passed in will be linted; at least one file must be provided.
Default linted extensions are ['hxx', 'h++', 'h', 'cpp', 'cu', 'c++', 'cuh', 'hh', 'c', 'cxx', 'hpp', 'cc'].
Default linted extensions are ['cu', 'hh', 'hpp', 'cc', 'hxx', 'c++', 'cxx', 'cpp', 'h++', 'cuh', 'h', 'c'].
Other file types will be ignored.
Change the extensions with the --extensions flag.

Expand Down Expand Up @@ -188,7 +188,7 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
The allowed file extensions that cpplint will check
Examples:
--extensions=hxx,h++,h,cpp,cu,c++,cuh,hh,c,cxx,hpp,cc
--extensions=cu,hh,hpp,cc,hxx,c++,cxx,cpp,h++,cuh,h,c
includeorder=default|standardcfirst
For the build/include_order rule, the default is to blindly assume angle
Expand All @@ -202,10 +202,10 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
headers=x,y,...
The header extensions that cpplint will treat as .h in checks. Values are
automatically added to --extensions list.
(by default, only files with extensions {'hxx', 'h++', 'h', 'cuh', 'hh', 'hpp'} will be assumed to be headers)
(by default, only files with extensions {'hh', 'hpp', 'hxx', 'h++', 'cuh', 'h'} will be assumed to be headers)
Examples:
--headers=hxx,h++,h,cuh,hh,hpp
--headers=hh,hpp,hxx,h++,cuh,h
--headers=hpp,hxx
--headers=hpp
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8 changes: 4 additions & 4 deletions docs/descriptors/cpp_cpplint.md
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Expand Up @@ -81,7 +81,7 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
suppresses errors of all categories on that line.

The files passed in will be linted; at least one file must be provided.
Default linted extensions are ['hxx', 'h++', 'h', 'cpp', 'cu', 'c++', 'cuh', 'hh', 'c', 'cxx', 'hpp', 'cc'].
Default linted extensions are ['cu', 'hh', 'hpp', 'cc', 'hxx', 'c++', 'cxx', 'cpp', 'h++', 'cuh', 'h', 'c'].
Other file types will be ignored.
Change the extensions with the --extensions flag.

Expand Down Expand Up @@ -197,7 +197,7 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
The allowed file extensions that cpplint will check
Examples:
--extensions=hxx,h++,h,cpp,cu,c++,cuh,hh,c,cxx,hpp,cc
--extensions=cu,hh,hpp,cc,hxx,c++,cxx,cpp,h++,cuh,h,c
includeorder=default|standardcfirst
For the build/include_order rule, the default is to blindly assume angle
Expand All @@ -211,10 +211,10 @@ Syntax: cpplint.py [--verbose=#] [--output=emacs|eclipse|vs7|junit|sed|gsed]
headers=x,y,...
The header extensions that cpplint will treat as .h in checks. Values are
automatically added to --extensions list.
(by default, only files with extensions {'hxx', 'h++', 'h', 'cuh', 'hh', 'hpp'} will be assumed to be headers)
(by default, only files with extensions {'hh', 'hpp', 'hxx', 'h++', 'cuh', 'h'} will be assumed to be headers)
Examples:
--headers=hxx,h++,h,cuh,hh,hpp
--headers=hh,hpp,hxx,h++,cuh,h
--headers=hpp,hxx
--headers=hpp
Expand Down
1 change: 0 additions & 1 deletion docs/descriptors/css_scss_lint.md
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Expand Up @@ -38,7 +38,6 @@
### How are identified applicable files

- File extensions:
- `.css`
- `.scss`
- `.saas`

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4 changes: 2 additions & 2 deletions docs/descriptors/lua_luacheck.md
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Expand Up @@ -15,8 +15,8 @@

### Mega-linter configuration

- Enable luacheck by adding `LUA_LUACHECK` in [ENABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Disable luacheck by adding `LUA_LUACHECK` in [DISABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Enable luacheck by adding `LUA_LUACHECK` in [ENABLE_LINTERS variable](../index.md#activation-and-deactivation)
- Disable luacheck by adding `LUA_LUACHECK` in [DISABLE_LINTERS variable](../index.md#activation-and-deactivation)

| Variable | Description | Default value |
| ----------------- | -------------- | -------------- |
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15 changes: 15 additions & 0 deletions docs/descriptors/markdown_markdown_link_check.md
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Expand Up @@ -45,6 +45,21 @@ markdown-link-check -c .markdown-link-check.json myfile.md
```


### Help content

```shell
Usage: markdown-link-check [options] [filenameOrUrl]

Options:
-p, --progress show progress bar
-c, --config [config] apply a config file (JSON), holding e.g. url specific
header configuration
-q, --quiet displays errors only
-v, --verbose displays detailed error information
-h, --help display help for command

```

### Installation on mega-linter Docker image

- NPM packages (node.js):
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6 changes: 3 additions & 3 deletions docs/descriptors/php_psalm.md
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Expand Up @@ -3,7 +3,7 @@

<div align="center">
<a href="https://psalm.dev" target="blank" title="Visit linter Web Site">
<img src="https://i1.wp.com/phpmagazine.net/wp-content/uploads/2018/12/PsalmLogo.png?w=653&ssl=1" alt="psalm" height="150px">
<img src="https://i1.wp.com/phpmagazine.net/wp-content/uploads/2018/12/PsalmLogo.png?w=653&ssl=1" alt="psalm" height="150px" class="megalinter-banner">
</a>
</div>

Expand All @@ -22,8 +22,8 @@

### Mega-linter configuration

- Enable psalm by adding `PHP_PSALM` in [ENABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Disable psalm by adding `PHP_PSALM` in [DISABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Enable psalm by adding `PHP_PSALM` in [ENABLE_LINTERS variable](../index.md#activation-and-deactivation)
- Disable psalm by adding `PHP_PSALM` in [DISABLE_LINTERS variable](../index.md#activation-and-deactivation)

| Variable | Description | Default value |
| ----------------- | -------------- | -------------- |
Expand Down
4 changes: 2 additions & 2 deletions docs/descriptors/python_flake8.md
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Expand Up @@ -95,8 +95,8 @@ optional arguments:
of opening bracket's line.
--ignore errors Comma-separated list of errors and warnings to ignore
(or skip). For example, ``--ignore=E4,E51,W234``.
(Default: ['E226', 'E123', 'E24', 'E126', 'E121',
'E704', 'W503', 'W504'])
(Default: ['E121', 'W504', 'E704', 'E126', 'E226',
'E123', 'W503', 'E24'])
--extend-ignore errors
Comma-separated list of errors and warnings to add to
the list of ignored ones. For example, ``--extend-
Expand Down
4 changes: 2 additions & 2 deletions docs/descriptors/r_lintr.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@

### Mega-linter configuration

- Enable lintr by adding `R_LINTR` in [ENABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Disable lintr by adding `R_LINTR` in [DISABLE_LINTERS variable](https://github.com/nvuillam/mega-linter#activation-and-deactivation)
- Enable lintr by adding `R_LINTR` in [ENABLE_LINTERS variable](../index.md#activation-and-deactivation)
- Disable lintr by adding `R_LINTR` in [DISABLE_LINTERS variable](../index.md#activation-and-deactivation)

| Variable | Description | Default value |
| ----------------- | -------------- | -------------- |
Expand Down
2 changes: 1 addition & 1 deletion docs/descriptors/snakemake_snakefmt.md
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Expand Up @@ -3,7 +3,7 @@
# snakefmt

- Web Site: [**https://github.com/snakemake/snakefmt**](https://github.com/snakemake/snakefmt#readme)
- Version: **0.2.3**
- Version: **0.2.4**

## Configuration

Expand Down
13 changes: 10 additions & 3 deletions docs/descriptors/snakemake_snakemake.md
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Expand Up @@ -10,7 +10,7 @@
## Linter

- Web Site: [**https://snakemake.readthedocs.io/en/stable/**](https://snakemake.readthedocs.io/en/stable/)
- Version: **5.27.4**
- Version: **5.28.0**

## Configuration

Expand Down Expand Up @@ -69,7 +69,7 @@ usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]]
[--shadow-prefix DIR] [--scheduler [{ilp,greedy}]]
[--wms-monitor [WMS_MONITOR]]
[--scheduler-ilp-solver {PULP_CBC_CMD,PULP_CHOCO_CMD}]
[--groups GROUPS [GROUPS ...]]
[--no-subworkflows] [--groups GROUPS [GROUPS ...]]
[--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]]
[--report [FILE]] [--report-stylesheet CSSFILE]
[--edit-notebook TARGET] [--notebook-listen IP:PORT]
Expand Down Expand Up @@ -113,7 +113,7 @@ usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]]
[--google-lifesciences]
[--google-lifesciences-regions GOOGLE_LIFESCIENCES_REGIONS [GOOGLE_LIFESCIENCES_REGIONS ...]]
[--google-lifesciences-location GOOGLE_LIFESCIENCES_LOCATION]
[--google-lifesciences-keep-cache] [--use-conda]
[--google-lifesciences-keep-cache] [--tes URL] [--use-conda]
[--list-conda-envs] [--conda-prefix DIR]
[--conda-cleanup-envs]
[--conda-cleanup-pkgs [{tarballs,cache}]]
Expand Down Expand Up @@ -324,6 +324,9 @@ EXECUTION:
--scheduler-ilp-solver {PULP_CBC_CMD,PULP_CHOCO_CMD}
Specifies solver to be utilized when selecting ilp-
scheduler. (default: COIN_CMD)
--no-subworkflows, --nosw
Do not evaluate or execute subworkflows. (default:
False)

GROUPING:
--groups GROUPS [GROUPS ...]
Expand Down Expand Up @@ -809,6 +812,10 @@ GOOGLE_LIFE_SCIENCE:
deleted at the shutdown step of the workflow.
(default: False)

TES:
--tes URL Send workflow tasks to GA4GH TES server specified by
url. (default: None)

CONDA:
--use-conda If defined in the rule, run job in a conda
environment. If this flag is not set, the conda
Expand Down
35 changes: 27 additions & 8 deletions linter-helps.json
Original file line number Diff line number Diff line change
Expand Up @@ -460,7 +460,7 @@
" suppresses errors of all categories on that line.",
"",
" The files passed in will be linted; at least one file must be provided.",
" Default linted extensions are ['hxx', 'h++', 'h', 'cpp', 'cu', 'c++', 'cuh', 'hh', 'c', 'cxx', 'hpp', 'cc'].",
" Default linted extensions are ['cu', 'hh', 'hpp', 'cc', 'hxx', 'c++', 'cxx', 'cpp', 'h++', 'cuh', 'h', 'c'].",
" Other file types will be ignored.",
" Change the extensions with the --extensions flag.",
"",
Expand Down Expand Up @@ -576,7 +576,7 @@
" The allowed file extensions that cpplint will check",
"",
" Examples:",
" --extensions=hxx,h++,h,cpp,cu,c++,cuh,hh,c,cxx,hpp,cc",
" --extensions=cu,hh,hpp,cc,hxx,c++,cxx,cpp,h++,cuh,h,c",
"",
" includeorder=default|standardcfirst",
" For the build/include_order rule, the default is to blindly assume angle",
Expand All @@ -590,10 +590,10 @@
" headers=x,y,...",
" The header extensions that cpplint will treat as .h in checks. Values are",
" automatically added to --extensions list.",
" (by default, only files with extensions {'hxx', 'h++', 'h', 'cuh', 'hh', 'hpp'} will be assumed to be headers)",
" (by default, only files with extensions {'hh', 'hpp', 'hxx', 'h++', 'cuh', 'h'} will be assumed to be headers)",
"",
" Examples:",
" --headers=hxx,h++,h,cuh,hh,hpp",
" --headers=hh,hpp,hxx,h++,cuh,h",
" --headers=hpp,hxx",
" --headers=hpp",
"",
Expand Down Expand Up @@ -1061,8 +1061,8 @@
" of opening bracket's line.",
" --ignore errors Comma-separated list of errors and warnings to ignore",
" (or skip). For example, ``--ignore=E4,E51,W234``.",
" (Default: ['E226', 'E123', 'E24', 'E126', 'E121',",
" 'E704', 'W503', 'W504'])",
" (Default: ['E121', 'W504', 'E704', 'E126', 'E226',",
" 'E123', 'W503', 'E24'])",
" --extend-ignore errors",
" Comma-separated list of errors and warnings to add to",
" the list of ignored ones. For example, ``--extend-",
Expand Down Expand Up @@ -1860,6 +1860,18 @@
" Luacheck documentation: https://luacheck.readthedocs.org",
""
],
"markdown-link-check": [
"Usage: markdown-link-check [options] [filenameOrUrl]",
"",
"Options:",
" -p, --progress show progress bar",
" -c, --config [config] apply a config file (JSON), holding e.g. url specific",
" header configuration",
" -q, --quiet displays errors only",
" -v, --verbose displays detailed error information",
" -h, --help display help for command",
""
],
"markdownlint": [
"",
" Usage: markdownlint [options] <files|directories|globs>",
Expand Down Expand Up @@ -3263,7 +3275,7 @@
" [--shadow-prefix DIR] [--scheduler [{ilp,greedy}]]",
" [--wms-monitor [WMS_MONITOR]]",
" [--scheduler-ilp-solver {PULP_CBC_CMD,PULP_CHOCO_CMD}]",
" [--groups GROUPS [GROUPS ...]]",
" [--no-subworkflows] [--groups GROUPS [GROUPS ...]]",
" [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]]",
" [--report [FILE]] [--report-stylesheet CSSFILE]",
" [--edit-notebook TARGET] [--notebook-listen IP:PORT]",
Expand Down Expand Up @@ -3307,7 +3319,7 @@
" [--google-lifesciences]",
" [--google-lifesciences-regions GOOGLE_LIFESCIENCES_REGIONS [GOOGLE_LIFESCIENCES_REGIONS ...]]",
" [--google-lifesciences-location GOOGLE_LIFESCIENCES_LOCATION]",
" [--google-lifesciences-keep-cache] [--use-conda]",
" [--google-lifesciences-keep-cache] [--tes URL] [--use-conda]",
" [--list-conda-envs] [--conda-prefix DIR]",
" [--conda-cleanup-envs]",
" [--conda-cleanup-pkgs [{tarballs,cache}]]",
Expand Down Expand Up @@ -3518,6 +3530,9 @@
" --scheduler-ilp-solver {PULP_CBC_CMD,PULP_CHOCO_CMD}",
" Specifies solver to be utilized when selecting ilp-",
" scheduler. (default: COIN_CMD)",
" --no-subworkflows, --nosw",
" Do not evaluate or execute subworkflows. (default:",
" False)",
"",
"GROUPING:",
" --groups GROUPS [GROUPS ...]",
Expand Down Expand Up @@ -4003,6 +4018,10 @@
" deleted at the shutdown step of the workflow.",
" (default: False)",
"",
"TES:",
" --tes URL Send workflow tasks to GA4GH TES server specified by",
" url. (default: None)",
"",
"CONDA:",
" --use-conda If defined in the rule, run job in a conda",
" environment. If this flag is not set, the conda",
Expand Down
5 changes: 3 additions & 2 deletions linter-versions.json
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
"kubeval": "dev",
"lintr": "2.0.1.9000",
"luacheck": "0.23.0",
"markdown-link-check": "0.0.0",
"markdownlint": "0.24.0",
"npm-groovy-lint": "7.6.4",
"perlcritic": "1.138",
Expand All @@ -46,8 +47,8 @@
"scss-lint": "0.59.0",
"shellcheck": "0.7.1",
"shfmt": "3.2.0",
"snakefmt": "0.2.3",
"snakemake": "5.27.4",
"snakefmt": "0.2.4",
"snakemake": "5.28.0",
"spectral": "5.6.0",
"sql-lint": "0.0.15",
"standard": "15.0.1",
Expand Down
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