From f48ff6253d8b6a80778c7546d1ad0c47d5aa28aa Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Wed, 14 Feb 2024 09:57:56 +0100
Subject: [PATCH] Update dependencies

Update all dependencies to latest versions. This might be necessary to support
Windows.
---
 Cargo.toml     | 13 +++++--------
 pyproject.toml |  2 +-
 src/lib.rs     | 33 +++++++++++++++++----------------
 3 files changed, 23 insertions(+), 25 deletions(-)

diff --git a/Cargo.toml b/Cargo.toml
index 26dfff7..de56b7c 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -12,11 +12,8 @@ name = "pycoverm"
 crate-type = ["cdylib"]
 
 [dependencies]
-coverm = "0.6.0"
-ndarray = "0.13.1"
-numpy = "0.12.1"
-pyo3 = { version = "0.12.4", features = ["extension-module"] }
-rust-htslib = "0.36.0"
-
-[package.metadata.maturin]
-requires-dist = ["numpy"]
+coverm = "0.7.0"
+ndarray = "0.15.6"
+numpy = "0.20.0"
+pyo3 = { version = "0.20", features = ["extension-module"] }
+rust-htslib = "0.45.0"
diff --git a/pyproject.toml b/pyproject.toml
index 9a2f56d..28236c1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["maturin>=0.10,<0.11"]
+requires = ["maturin>=1.4.0,<2.0", "numpy==0.20.0"]
 build-backend = "maturin"
diff --git a/src/lib.rs b/src/lib.rs
index 22cd7cf..92e856e 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -3,7 +3,8 @@ use coverm::{
     FlagFilter,
 };
 use ndarray::Array;
-use numpy::convert::ToPyArray;
+use numpy::pyo3::IntoPy;
+use numpy::ToPyArray;
 use pyo3::{prelude::*, wrap_pyfunction};
 use rust_htslib::{bam, bam::Read};
 use std::collections::HashSet;
@@ -83,14 +84,16 @@ fn is_bam_sorted(bam_file: &str) -> PyResult<bool> {
 /// tuple
 ///     A tuple whose fist element is a list of the contig names and the second
 ///     one is a numpy matrix of contig coverages in the input BAM files.
-#[pyfunction(
-    contig_end_exclusion = "75",
-    min_identity = "0.97",
-    trim_lower = "0.",
-    trim_upper = "0.",
-    contig_set = "None",
-    threads = "1"
-)]
+#[pyfunction]
+#[pyo3(signature = (
+    bam_list,
+    contig_end_exclusion = 75,
+    min_identity = 0.97,
+    trim_lower = 0.,
+    trim_upper = 0.,
+    contig_set = None,
+    threads = 1
+))]
 fn get_coverages_from_bam(
     py: Python,
     bam_list: Vec<&str>,
@@ -99,7 +102,7 @@ fn get_coverages_from_bam(
     trim_lower: f32,
     trim_upper: f32,
     contig_set: Option<HashSet<&str>>,
-    threads: usize,
+    threads: u16,
 ) -> (PyObject, PyObject) {
     let trim_upper = 1. - trim_upper;
     let min_fraction_covered_bases = 0.;
@@ -166,7 +169,7 @@ fn get_coverages_from_bam(
         &mut estimators_and_taker.taker,
         &mut estimators_and_taker.estimators,
         true,
-        filter_params.flag_filters,
+        &filter_params.flag_filters,
         threads,
     );
 
@@ -200,9 +203,7 @@ fn get_coverages_from_bam(
     }
     (
         headers.into_py(py),
-        matrix
-            .to_pyarray(Python::acquire_gil().python())
-            .into_py(py),
+        matrix.to_pyarray(py).into()
     )
 }
 
@@ -210,8 +211,8 @@ fn default_return_value(py: Python, n_files: usize) -> (Py<PyAny>, Py<PyAny>) {
     (
         Vec::<String>::new().into_py(py),
         Array::from_elem((0, n_files), 0f32)
-            .to_pyarray(Python::acquire_gil().python())
-            .into_py(py),
+            .to_pyarray(py)
+            .into(),
     )
 }