Bump pyo3-build-config from 0.20.3 to 0.21.0 (#34) #54
SKY-ALINci.yml
on: push
Matrix: Linux -> build & test
Matrix: MacOS -> build & test
Matrix: Windows -> build & test
Release
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Annotations
3 errors and 46 warnings
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the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied:
src/seq_analysis.rs#L51
error[E0277]: the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied
--> src/seq_analysis.rs:51:41
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51 | pub fn new(start: Vec<&[u8]>, stop: Vec<&[u8]>, min_len: usize) -> PyResult<Self> {
| ^^^ the trait `pyo3::FromPyObject<'_>` is not implemented for `std::vec::Vec<&[u8]>`, which is required by `std::vec::Vec<&[u8]>: pyo3::impl_::extract_argument::PyFunctionArgument<'_, '_>`
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= help: the trait `pyo3::FromPyObject<'py>` is implemented for `std::vec::Vec<T>`
= note: required for `std::vec::Vec<&[u8]>` to implement `pyo3::conversion::FromPyObjectBound<'_, '_>`
= note: required for `std::vec::Vec<&[u8]>` to implement `pyo3::impl_::extract_argument::PyFunctionArgument<'_, '_>`
note: required by a bound in `pyo3::impl_::extract_argument::extract_argument`
--> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyo3-0.21.0/src/impl_/extract_argument.rs:119:8
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113 | pub fn extract_argument<'a, 'py, T>(
| ---------------- required by a bound in this function
...
119 | T: PyFunctionArgument<'a, 'py>,
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^ required by this bound in `extract_argument`
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the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied:
src/seq_analysis.rs#L51
error[E0277]: the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied
--> src/seq_analysis.rs:51:23
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51 | pub fn new(start: Vec<&[u8]>, stop: Vec<&[u8]>, min_len: usize) -> PyResult<Self> {
| ^^^ the trait `pyo3::FromPyObject<'_>` is not implemented for `std::vec::Vec<&[u8]>`, which is required by `std::vec::Vec<&[u8]>: pyo3::impl_::extract_argument::PyFunctionArgument<'_, '_>`
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= help: the trait `pyo3::FromPyObject<'py>` is implemented for `std::vec::Vec<T>`
= note: required for `std::vec::Vec<&[u8]>` to implement `pyo3::conversion::FromPyObjectBound<'_, '_>`
= note: required for `std::vec::Vec<&[u8]>` to implement `pyo3::impl_::extract_argument::PyFunctionArgument<'_, '_>`
note: required by a bound in `pyo3::impl_::extract_argument::extract_argument`
--> /home/runner/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyo3-0.21.0/src/impl_/extract_argument.rs:119:8
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113 | pub fn extract_argument<'a, 'py, T>(
| ---------------- required by a bound in this function
...
119 | T: PyFunctionArgument<'a, 'py>,
| ^^^^^^^^^^^^^^^^^^^^^^^^^^^ required by this bound in `extract_argument`
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Clippy check
Clippy had exited with the 101 exit code
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use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version:
src/lib.rs#L34
warning: use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version
--> src/lib.rs:34:25
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34 | let sys = PyModule::import(py, "sys")?;
| ^^^^^^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/lib.rs#L25
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/lib.rs:25:25
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25 | fn bioforma(py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version:
src/seq_analysis.rs#L118
warning: use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version
--> src/seq_analysis.rs:118:25
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118 | let sys = PyModule::import(py, "sys")?;
| ^^^^^^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/seq_analysis.rs#L114
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/seq_analysis.rs:114:33
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114 | pub fn seq_analysis(py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/seq_analysis.rs#L107
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/seq_analysis.rs:107:20
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107 | fn gc(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/seq_analysis.rs#L100
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/seq_analysis.rs:100:21
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100 | fn orf(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version:
src/alphabets.rs#L248
warning: use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version
--> src/alphabets.rs:248:25
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248 | let sys = PyModule::import(py, "sys")?;
| ^^^^^^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alphabets.rs#L240
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alphabets.rs:240:30
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240 | pub fn alphabets(py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alphabets.rs#L230
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alphabets.rs:230:21
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230 | fn rna(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version:
src/alphabets.rs#L226
warning: use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version
--> src/alphabets.rs:226:14
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226 | PyBytes::new(py, _rna_revcomp(text).as_slice())
| ^^^
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use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version:
src/alphabets.rs#L220
warning: use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version
--> src/alphabets.rs:220:21
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220 | Ok(PyBytes::new(py, arr.as_slice()))
| ^^^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alphabets.rs#L193
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alphabets.rs:193:25
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193 | fn protein(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alphabets.rs#L173
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alphabets.rs:173:21
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173 | fn dna(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version:
src/alphabets.rs#L169
warning: use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version
--> src/alphabets.rs:169:14
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169 | PyBytes::new(py, _dna_revcomp(text).as_slice())
| ^^^
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use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version:
src/alphabets.rs#L163
warning: use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version
--> src/alphabets.rs:163:21
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163 | Ok(PyBytes::new(py, arr.as_slice()))
| ^^^
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use of deprecated method `pyo3::types::IntoPyDict::into_py_dict`: `IntoPyDict::into_py_dict` will be replaced by `IntoPyDict::into_py_dict_bound` in a future PyO3 version:
src/alphabets.rs#L125
warning: use of deprecated method `pyo3::types::IntoPyDict::into_py_dict`: `IntoPyDict::into_py_dict` will be replaced by `IntoPyDict::into_py_dict_bound` in a future PyO3 version
--> src/alphabets.rs:125:13
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125 | res.into_py_dict(py)
| ^^^^^^^^^^^^
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use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version:
src/alphabets.rs#L50
warning: use of deprecated associated function `pyo3::types::PyBytes::new`: `PyBytes::new` will be replaced by `PyBytes::new_bound` in a future PyO3 version
--> src/alphabets.rs:50:18
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50 | PyBytes::new(py, v.as_slice())
| ^^^
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use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version:
src/alignment/mod.rs#L27
warning: use of deprecated associated function `pyo3::prelude::PyModule::import`: `PyModule::import` will be replaced by `PyModule::import_bound` in a future PyO3 version
--> src/alignment/mod.rs:27:25
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27 | let sys = PyModule::import(py, "sys")?;
| ^^^^^^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alignment/mod.rs#L10
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alignment/mod.rs:10:30
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10 | pub fn alignment(py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alignment/scoring.rs#L84
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alignment/scoring.rs:84:15
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84 | _cls: &PyType,
| ^
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use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument:
src/alignment/distance.rs#L48
warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument
--> src/alignment/distance.rs:48:30
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48 | pub fn distance(_py: Python, m: &PyModule) -> PyResult<()> {
| ^
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L213
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:213:21
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213 | PyCell::new(py, Yclip::new(y)).ok().map(|o| o.to_object(py))
| ^^^
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L210
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:210:21
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210 | PyCell::new(py, Xclip::new(x)).ok().map(|o| o.to_object(py))
| ^^^
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L208
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:208:45
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208 | _AlignmentOperation::Ins => PyCell::new(py, Ins::new()).ok().map(|o| o.to_object(py)),
| ^^^
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L207
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:207:45
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207 | _AlignmentOperation::Del => PyCell::new(py, Del::new()).ok().map(|o| o.to_object(py)),
| ^^^
|
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L206
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:206:47
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206 | _AlignmentOperation::Subst => PyCell::new(py, Subst::new()).ok().map(|o| o.to_object(py)),
| ^^^
|
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use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`:
src/alignment/alignment_type.rs#L205
warning: use of deprecated associated function `pyo3::PyCell::<T>::new`: use `Bound::new(py, value)` or `Py::new(py, value)` instead of `PyCell::new(py, value)`
--> src/alignment/alignment_type.rs:205:47
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205 | _AlignmentOperation::Match => PyCell::new(py, Match::new()).ok().map(|o| o.to_object(py)),
| ^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L234
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:234:26
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234 | operations: Vec<&PyCell<AlignmentOperation>>,
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L213
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:213:13
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213 | PyCell::new(py, Yclip::new(y)).ok().map(|o| o.to_object(py))
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L210
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:210:13
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210 | PyCell::new(py, Xclip::new(x)).ok().map(|o| o.to_object(py))
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L208
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:208:37
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208 | _AlignmentOperation::Ins => PyCell::new(py, Ins::new()).ok().map(|o| o.to_object(py)),
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L207
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:207:37
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207 | _AlignmentOperation::Del => PyCell::new(py, Del::new()).ok().map(|o| o.to_object(py)),
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L206
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:206:39
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206 | _AlignmentOperation::Subst => PyCell::new(py, Subst::new()).ok().map(|o| o.to_object(py)),
| ^^^^^^
|
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use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info:
src/alignment/alignment_type.rs#L205
warning: use of deprecated struct `pyo3::PyCell`: `PyCell` was merged into `Bound`, use that instead; see the migration guide for more info
--> src/alignment/alignment_type.rs:205:39
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205 | _AlignmentOperation::Match => PyCell::new(py, Match::new()).ok().map(|o| o.to_object(py)),
| ^^^^^^
|
= note: `#[warn(deprecated)]` on by default
|
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Rustfmt check
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/toolchain@v1, actions-rs/cargo@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Rustfmt check
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/cargo@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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Rustfmt check
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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Rustfmt check
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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Rustfmt check
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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Rustfmt check
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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Clippy check
Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, actions-rs/toolchain@v1, actions-rs/clippy-check@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.
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Clippy check
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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Clippy check
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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Clippy check
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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Clippy check
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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Clippy check
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/
|