Merge pull request #104 from paulsengroup/bump/hictk

Bump hictk to v2.0.1

CMakeLists.txt

@@ -35,8 +35,8 @@ FetchContent_Declare(
 FetchContent_Declare(
   hictk
   URL
-    "${CMAKE_CURRENT_SOURCE_DIR}/external/hictk-312d83ec.tar.xz"
-  URL_HASH "SHA256=a47b1088de6650179715db17337e09c44729f8e86b4457848e306f028d0b5878"
+    "${CMAKE_CURRENT_SOURCE_DIR}/external/hictk-v2.0.1.tar.xz"
+  URL_HASH "SHA256=9282f7f4e978c71970f07627b360c3a4cf2bce4670ce3bd12e040c51c691ec3c"
   EXCLUDE_FROM_ALL
   OVERRIDE_FIND_PACKAGE
   SYSTEM

src/include/hictkpy/bin_table.hpp

@@ -68,12 +68,6 @@ class BinTable {
   [[nodiscard]] std::vector<std::string> chrom_names(bool include_ALL = false) const;
 };
 
-// TODO remove after merging https://github.com/paulsengroup/hictk/pull/298
-template <typename T>
-inline hictkpy::BinTable get_bins_from_sc_file(const T& obj) {
-  return hictkpy::BinTable(obj.bins());
-}
-
 template <typename T>
 inline hictkpy::BinTable get_bins_from_object(const T& obj) {
   return hictkpy::BinTable(obj.bins_ptr());

src/singlecell_file.cpp

@@ -114,7 +114,7 @@ void declare_singlecell_file_class(nb::module_& m) {
   scell_file.def("chromosomes", &get_chromosomes_from_object<hictk::cooler::SingleCellFile>,
                  nb::arg("include_ALL") = false,
                  "Get chromosomes sizes as a dictionary mapping names to sizes.");
-  scell_file.def("bins", &get_bins_from_sc_file<hictk::cooler::SingleCellFile>,
+  scell_file.def("bins", &get_bins_from_object<hictk::cooler::SingleCellFile>,
                  nb::sig("def bins(self) -> hictkpy.BinTable"), "Get table of bins.");
   scell_file.def("attributes", &singlecell_file::get_attrs, "Get file attributes as a dictionary.");
   scell_file.def("cells", &singlecell_file::get_cells, "Get the list of available cells.");