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feat: Consolidate CLI #1482

feat: Consolidate CLI

feat: Consolidate CLI #1482

GitHub Actions / clippy succeeded Jan 2, 2025 in 0s

clippy

21 warnings

Details

Results

Message level Amount
Internal compiler error 0
Error 0
Warning 21
Note 0
Help 0

Versions

  • rustc 1.83.0 (90b35a623 2024-11-26)
  • cargo 1.83.0 (5ffbef321 2024-10-29)
  • clippy 0.1.83 (90b35a6 2024-11-26)

Annotations

Check warning on line 37 in src/verify/seqvars.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

empty line after doc comment

warning: empty line after doc comment
  --> src/verify/seqvars.rs:36:5
   |
36 | /     /// Path to output TSV file.
37 | |
   | |_
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments
   = help: if the empty line is unintentional remove it

Check warning on line 33 in src/verify/seqvars.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

empty line after doc comment

warning: empty line after doc comment
  --> src/verify/seqvars.rs:32:5
   |
32 | /     /// Path to the reference FASTA file.
33 | |
   | |_
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#empty_line_after_doc_comments
   = note: `#[warn(clippy::empty_line_after_doc_comments)]` on by default
   = help: if the empty line is unintentional remove it

Check warning on line 1755 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1755:22
     |
1755 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |                      ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1755 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1755 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 1637 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1637:14
     |
1637 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |              ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1637 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1637 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 1536 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1536:22
     |
1536 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |                      ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1536 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1536 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 1442 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1442:14
     |
1442 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |              ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1442 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1442 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 1266 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1266:22
     |
1266 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |                      ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1266 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1266 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 1089 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
    --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:1089:14
     |
1089 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
     |              ^^^                     ^^^
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
     |
1089 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
1089 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
     |

Check warning on line 964 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:964:22
    |
964 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
964 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
964 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 830 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:830:14
    |
830 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |              ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
830 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
830 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 729 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:729:22
    |
729 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
729 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
729 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 627 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:627:14
    |
627 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |              ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
627 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
627 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 498 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:498:22
    |
498 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
498 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
498 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 331 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:331:22
    |
331 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
331 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
331 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 158 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:158:22
    |
158 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
158 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
158 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 29 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
  --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.txs.serde.rs:29:14
   |
29 |         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
   |              ^^^                     ^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
   |
29 -         impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
29 +         impl serde::de::Visitor<'_> for GeneratedVisitor {
   |

Check warning on line 199 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.server.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
   --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.server.serde.rs:199:22
    |
199 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
    |                      ^^^                     ^^^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
help: elide the lifetimes
    |
199 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
199 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
    |

Check warning on line 70 in /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.server.serde.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

the following explicit lifetimes could be elided: 'de

warning: the following explicit lifetimes could be elided: 'de
  --> /home/runner/work/mehari/mehari/target/debug/build/mehari-149f7224d7193971/out/mehari.server.serde.rs:70:22
   |
70 |                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
   |                      ^^^                     ^^^
   |
   = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_lifetimes
   = note: `#[warn(clippy::needless_lifetimes)]` on by default
help: elide the lifetimes
   |
70 -                 impl<'de> serde::de::Visitor<'de> for GeneratedVisitor {
70 +                 impl serde::de::Visitor<'_> for GeneratedVisitor {
   |

Check warning on line 241 in src/db/subset/mod.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

writing `&Vec` instead of `&[_]` involves a new object where a slice will do

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
   --> src/db/subset/mod.rs:241:19
    |
241 |     gene_symbols: &Vec<String>,
    |                   ^^^^^^^^^^^^ help: change this to: `&[String]`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

Check warning on line 228 in src/db/subset/mod.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

writing `&Vec` instead of `&[_]` involves a new object where a slice will do

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
   --> src/db/subset/mod.rs:228:21
    |
228 |     transcript_ids: &Vec<String>,
    |                     ^^^^^^^^^^^^ help: change this to: `&[String]`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg

Check warning on line 2119 in src/annotate/seqvars/mod.rs

See this annotation in the file changed.

@github-actions github-actions / clippy

writing `&Vec` instead of `&[_]` involves a new object where a slice will do

warning: writing `&Vec` instead of `&[_]` involves a new object where a slice will do
    --> src/annotate/seqvars/mod.rs:2119:17
     |
2119 |     tx_sources: &Vec<String>,
     |                 ^^^^^^^^^^^^ help: change this to: `&[String]`
     |
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#ptr_arg
     = note: `#[warn(clippy::ptr_arg)]` on by default