build: Update xlsxwriter due to compilation error with older version … #739
rust.yml
on: push
Formatting
28s
Linting
12m 54s
Testing
12m 21s
Annotations
43 warnings
Formatting
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Formatting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Formatting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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Formatting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Formatting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
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`filter_map()` will run forever if the iterator repeatedly produces an `Err`:
src/fastq/filter.rs#L44
warning: `filter_map()` will run forever if the iterator repeatedly produces an `Err`
--> src/fastq/filter.rs:44:48
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44 | HashSet::<String>::from_iter(f.lines().filter_map(Result::ok).collect::<Vec<String>>());
| ^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `map_while(Result::ok)`
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note: this expression returning a `std::io::Lines` may produce an infinite number of `Err` in case of a read error
--> src/fastq/filter.rs:44:38
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44 | HashSet::<String>::from_iter(f.lines().filter_map(Result::ok).collect::<Vec<String>>());
| ^^^^^^^^^
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#lines_filter_map_ok
= note: `#[warn(clippy::lines_filter_map_ok)]` on by default
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the borrowed expression implements the required traits:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L96
warning: the borrowed expression implements the required traits
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:96:41
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96 | str::from_utf8(&self.db.get(&Self::as_key(i as u64))?.unwrap()).unwrap(),
| ^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `Self::as_key(i as u64)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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the borrowed expression implements the required traits:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L88
warning: the borrowed expression implements the required traits
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:88:13
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88 | &Self::as_key(i as u64),
| ^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `Self::as_key(i as u64)`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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transmute from a `u64` to a `[u8; 8]`:
src/fastq/collapse_reads_to_fragments/pipeline.rs#L82
warning: transmute from a `u64` to a `[u8; 8]`
--> src/fastq/collapse_reads_to_fragments/pipeline.rs:82:18
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82 | unsafe { mem::transmute::<u64, [u8; 8]>(i) }
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: consider using `to_ne_bytes()`: `i.to_ne_bytes()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#transmute_num_to_bytes
= note: `#[warn(clippy::transmute_num_to_bytes)]` on by default
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iterating on a map's values:
src/csv/report.rs#L488
warning: iterating on a map's values
--> src/csv/report.rs:488:41
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488 | let unique_values: HashSet<_> = count_values.iter().map(|(_, v)| v).collect();
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: try: `count_values.values()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#iter_kv_map
= note: `#[warn(clippy::iter_kv_map)]` on by default
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this expression can be written more simply using `.retain()`:
src/bcf/report/table_report/static_reader.rs#L136
warning: this expression can be written more simply using `.retain()`
--> src/bcf/report/table_report/static_reader.rs:136:9
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136 | / matches_wr = matches_wr
137 | | .into_iter()
138 | | .filter(|b| random_rows.contains(&(b.row as u32)))
139 | | .collect();
| |______________________^ help: consider calling `.retain()` instead: `matches_wr.retain(|b| random_rows.contains(&(b.row as u32)))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_retain
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this expression can be written more simply using `.retain()`:
src/bcf/report/table_report/static_reader.rs#L132
warning: this expression can be written more simply using `.retain()`
--> src/bcf/report/table_report/static_reader.rs:132:9
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132 | / reads_wr = reads_wr
133 | | .into_iter()
134 | | .filter(|b| random_rows.contains(&(b.row as u32)))
135 | | .collect();
| |______________________^ help: consider calling `.retain()` instead: `reads_wr.retain(|b| random_rows.contains(&(b.row as u32)))`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#manual_retain
= note: `#[warn(clippy::manual_retain)]` on by default
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the borrowed expression implements the required traits:
src/bcf/report/table_report/create_report_table.rs#L472
warning: the borrowed expression implements the required traits
--> src/bcf/report/table_report/create_report_table.rs:472:25
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472 | &"\"Consequence annotations from Ensembl VEP. Format: ",
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: change this to: `"\"Consequence annotations from Ensembl VEP. Format: "`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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used consecutive `str::replace` call:
src/bcf/report/table_report/create_report_table.rs#L456
warning: used consecutive `str::replace` call
--> src/bcf/report/table_report/create_report_table.rs:456:11
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456 | hgvsg.replace('.', "_").replace('>', "_").replace(':', "_")
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `replace(['.', '>', ':'], "_")`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#collapsible_str_replace
= note: `#[warn(clippy::collapsible_str_replace)]` on by default
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the borrowed expression implements the required traits:
src/bcf/report/table_report/create_report_table.rs#L64
warning: the borrowed expression implements the required traits
--> src/bcf/report/table_report/create_report_table.rs:64:55
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64 | let mut vcf = rust_htslib::bcf::Reader::from_path(&vcf_path).unwrap();
| ^^^^^^^^^ help: change this to: `vcf_path`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L431
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bcf/report/table_report/alignment_reader.rs:431:20
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431 | let position = snip.pos as i64 + read_offset;
| ^^^^^^^^^^^^^^^ help: try: `snip.pos`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L367
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bcf/report/table_report/alignment_reader.rs:367:51
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367 | ... match_start = snip.pos as i64 + read_offset;
| ^^^^^^^^^^^^^^^ help: try: `snip.pos`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L308
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bcf/report/table_report/alignment_reader.rs:308:40
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308 | let position = snip.pos as i64 + read_offset;
| ^^^^^^^^^^^^^^^ help: try: `snip.pos`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`f64` -> `f64`):
src/bcf/report/table_report/alignment_reader.rs#L286
warning: casting to the same type is unnecessary (`f64` -> `f64`)
--> src/bcf/report/table_report/alignment_reader.rs:286:39
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286 | end_position: p as f64 + 1.3,
| ^^^^^^^^ help: try: `p`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`f64` -> `f64`):
src/bcf/report/table_report/alignment_reader.rs#L285
warning: casting to the same type is unnecessary (`f64` -> `f64`)
--> src/bcf/report/table_report/alignment_reader.rs:285:41
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285 | start_position: p as f64 + 0.7,
| ^^^^^^^^ help: try: `p`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bcf/report/table_report/alignment_reader.rs#L217
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bcf/report/table_report/alignment_reader.rs:217:51
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217 | ... match_start = snip.pos as i64 + read_offset;
| ^^^^^^^^^^^^^^^ help: try: `snip.pos`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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use of `char::is_digit` with literal radix of 10:
src/bcf/report/oncoprint.rs#L291
warning: use of `char::is_digit` with literal radix of 10
--> src/bcf/report/oncoprint.rs:291:60
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291 | ... ex_var.chars().filter(|c| !c.is_digit(10)).collect();
| ^^^^^^^^^^^^^^ help: try: `c.is_ascii_digit()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#is_digit_ascii_radix
= note: `#[warn(clippy::is_digit_ascii_radix)]` on by default
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called `unwrap` on `info` after checking its variant with `is_none`:
src/bcf/report/oncoprint.rs#L261
warning: called `unwrap` on `info` after checking its variant with `is_none`
--> src/bcf/report/oncoprint.rs:261:48
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245 | ... if info.is_none() {
| ----------------- help: try: `if let Some(..) = info`
...
261 | ... for val in info.unwrap() {
| ^^^^^^^^^^^^^
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_unwrap
= note: `#[warn(clippy::unnecessary_unwrap)]` on by default
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casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L247
warning: casting the result of `i32::abs()` to u32
--> src/bcf/match_variants.rs:247:24
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247 | if (l1 as i32 - l2 as i32).abs() as u32 <= max_len_diff && dist <= max_dist {
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `(l1 as i32 - l2 as i32).unsigned_abs()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned
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casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L238
warning: casting the result of `i32::abs()` to u32
--> src/bcf/match_variants.rs:238:24
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238 | let dist = (self.centerpoint(allele) as i32 - other.centerpoint(b) as i32).abs() as u32;
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: replace with: `(self.centerpoint(allele) as i32 - other.centerpoint(b) as i32).unsigned_abs()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned
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casting the result of `i32::abs()` to u32:
src/bcf/match_variants.rs#L131
warning: casting the result of `i32::abs()` to u32
--> src/bcf/match_variants.rs:131:40
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131 | Some(svlens.iter().map(|l| l.abs() as u32).collect_vec())
| ^^^^^^^^^^^^^^ help: replace with: `l.unsigned_abs()`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#cast_abs_to_unsigned
= note: `#[warn(clippy::cast_abs_to_unsigned)]` on by default
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the borrowed expression implements the required traits:
src/bcf/match_variants.rs#L73
warning: the borrowed expression implements the required traits
--> src/bcf/match_variants.rs:73:45
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73 | let mut outbcf = bcf::Writer::from_path(&"-", &header, false, Format::Bcf)?;
| ^^^^ help: change this to: `"-"`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
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the borrowed expression implements the required traits:
src/bcf/fix_iupac_alleles.rs#L26
warning: the borrowed expression implements the required traits
--> src/bcf/fix_iupac_alleles.rs:26:55
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26 | ... if valid_alphabet.is_word(&[*base]) {
| ^^^^^^^^ help: change this to: `[*base]`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
= note: `#[warn(clippy::needless_borrow)]` on by default
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bam/depth.rs#L79
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bam/depth.rs:79:13
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79 | start as i64 + (max_read_length * 2) as i64,
| ^^^^^^^^^^^^ help: try: `start`
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= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
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casting to the same type is unnecessary (`i64` -> `i64`):
src/bam/depth.rs#L78
warning: casting to the same type is unnecessary (`i64` -> `i64`)
--> src/bam/depth.rs:78:13
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78 | start as i64,
| ^^^^^^^^^^^^ help: try: `start`
|
= help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#unnecessary_cast
= note: `#[warn(clippy::unnecessary_cast)]` on by default
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Linting
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, actions-rs/clippy-check@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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Linting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Linting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Linting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Linting
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, actions-rs/toolchain@v1, Swatinem/[email protected]. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
|
Testing
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `save-state` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|
Testing
The `set-output` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/
|