error[E0277]: the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied --> src/seq_analysis.rs:51:41 | 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<'_, '_>` | = 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 | 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`

error[E0277]: the trait bound `std::vec::Vec<&[u8]>: pyo3::FromPyObject<'_>` is not satisfied --> src/seq_analysis.rs:51:23 | 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<'_, '_>` | = 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 | 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`

Clippy had exited with the 101 exit code

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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 | 34 | let sys = PyModule::import(py, "sys")?; | ^^^^^^

warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument --> src/lib.rs:25:25 | 25 | fn bioforma(py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 118 | let sys = PyModule::import(py, "sys")?; | ^^^^^^

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 | 114 | pub fn seq_analysis(py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 107 | fn gc(_py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 100 | fn orf(_py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 248 | let sys = PyModule::import(py, "sys")?; | ^^^^^^

warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument --> src/alphabets.rs:240:30 | 240 | pub fn alphabets(py: Python, m: &PyModule) -> PyResult<()> { | ^

warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument --> src/alphabets.rs:230:21 | 230 | fn rna(_py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 226 | PyBytes::new(py, _rna_revcomp(text).as_slice()) | ^^^

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 | 220 | Ok(PyBytes::new(py, arr.as_slice())) | ^^^

warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument --> src/alphabets.rs:193:25 | 193 | fn protein(_py: Python, m: &PyModule) -> PyResult<()> { | ^

warning: use of deprecated method `pyo3::deprecations::GilRefs::<T>::function_arg`: use `&Bound<'_, T>` instead for this function argument --> src/alphabets.rs:173:21 | 173 | fn dna(_py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 169 | PyBytes::new(py, _dna_revcomp(text).as_slice()) | ^^^

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 | 163 | Ok(PyBytes::new(py, arr.as_slice())) | ^^^

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 | 125 | res.into_py_dict(py) | ^^^^^^^^^^^^

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 | 50 | PyBytes::new(py, v.as_slice()) | ^^^

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 | 27 | let sys = PyModule::import(py, "sys")?; | ^^^^^^

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 | 10 | pub fn alignment(py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 84 | _cls: &PyType, | ^

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 | 48 | pub fn distance(_py: Python, m: &PyModule) -> PyResult<()> { | ^

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 | 213 | PyCell::new(py, Yclip::new(y)).ok().map(|o| o.to_object(py)) | ^^^

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 | 210 | PyCell::new(py, Xclip::new(x)).ok().map(|o| o.to_object(py)) | ^^^

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 | 208 | _AlignmentOperation::Ins => PyCell::new(py, Ins::new()).ok().map(|o| o.to_object(py)), | ^^^

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 | 207 | _AlignmentOperation::Del => PyCell::new(py, Del::new()).ok().map(|o| o.to_object(py)), | ^^^

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 | 206 | _AlignmentOperation::Subst => PyCell::new(py, Subst::new()).ok().map(|o| o.to_object(py)), | ^^^

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 | 205 | _AlignmentOperation::Match => PyCell::new(py, Match::new()).ok().map(|o| o.to_object(py)), | ^^^

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 | 234 | operations: Vec<&PyCell<AlignmentOperation>>, | ^^^^^^

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 | 213 | PyCell::new(py, Yclip::new(y)).ok().map(|o| o.to_object(py)) | ^^^^^^

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 | 210 | PyCell::new(py, Xclip::new(x)).ok().map(|o| o.to_object(py)) | ^^^^^^

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 | 208 | _AlignmentOperation::Ins => PyCell::new(py, Ins::new()).ok().map(|o| o.to_object(py)), | ^^^^^^

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 | 207 | _AlignmentOperation::Del => PyCell::new(py, Del::new()).ok().map(|o| o.to_object(py)), | ^^^^^^

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 | 206 | _AlignmentOperation::Subst => PyCell::new(py, Subst::new()).ok().map(|o| o.to_object(py)), | ^^^^^^

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 | 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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