[deps]: bump

.github/workflows/ci.yml

@@ -25,8 +25,8 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/ci.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -43,8 +43,8 @@ on:
   pull_request:
     paths:
       - ".github/workflows/ci.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -139,7 +139,7 @@ jobs:
         uses: actions/cache@v4
         id: restore-conan-cache
         with:
-          key: conan-cache-ci-${{ matrix.os }}-${{ hashFiles( 'configure', 'deps/conanfile.py', 'deps/generate_makevars.py') }}
+          key: conan-cache-ci-${{ matrix.os }}-${{ hashFiles( 'configure', 'tools/conanfile.py', 'tools/generate_makevars.py') }}
           path: ${{ env.HICTKR_CONAN_HOME }}/p
 
       - name: Build and test package

.github/workflows/pkgdown.yml

@@ -25,8 +25,8 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/pkgdown.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -44,8 +44,8 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/pkgdown.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -99,7 +99,7 @@ jobs:
         uses: actions/cache@v4
         id: restore-conan-cache
         with:
-          key: conan-cache-pkgdown-${{ hashFiles( 'configure', 'deps/conanfile.py', 'deps/generate_makevars.py') }}
+          key: conan-cache-pkgdown-${{ hashFiles( 'configure', 'tools/conanfile.py', 'tools/generate_makevars.py') }}
           path: ${{ env.HICTKR_CONAN_HOME }}/p
 
       - name: Add requirements

.github/workflows/r-build.yml

@@ -25,8 +25,8 @@ on:
     branches: [main]
     paths:
       - ".github/workflows/r-build.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -43,8 +43,8 @@ on:
   pull_request:
     paths:
       - ".github/workflows/r-build.yml"
-      - "deps/conanfile.py"
-      - "deps/generate_makevars.py"
+      - "tools/conanfile.py"
+      - "tools/generate_makevars.py"
       - "R/**"
       - "inst/extdata/**"
       - "man/**"
@@ -109,7 +109,7 @@ jobs:
         uses: actions/cache@v4
         id: restore-conan-cache
         with:
-          key: conan-cache-r-build-${{ hashFiles( 'configure', 'deps/conanfile.py', 'deps/generate_makevars.py') }}
+          key: conan-cache-r-build-${{ hashFiles( 'configure', 'tools/conanfile.py', 'tools/generate_makevars.py') }}
           path: ${{ env.HICTKR_CONAN_HOME }}/p
 
       - name: Build package

tools/conanfile.py

@@ -37,7 +37,7 @@
 
 class HictkConan(ConanFile):
     name = "hictk"
-    version = "2.1.4"
+    version = "2.2.0"
     description = "Blazing fast toolkit to work with .hic and .cool files"
     license = "MIT"
     url = "https://github.com/paulsengroup/hictkR"
@@ -52,38 +52,38 @@ def __init__(self, *args, **kwargs):
             "sources": {
                 HictkConan.version: {
                     "url": f"https://github.com/paulsengroup/hictk/archive/refs/tags/v{HictkConan.version}.tar.gz",
-                    "sha256": "3a0030425176dacc25c20afc6fedb5dfbbc3c1a67f773be11ac77d7fa6b7efde",
+                    "sha256": "989b6e84b967309d9822ee3274abf98daba66d3d6e6ae8c9abffcede07b24761",
                 },
             },
-            "patches": {
-                "2.1.4": [
-                    {
-                        "patch_file": "patches/hictk_v2.1.4_eigen_include.patch",
-                        "patch_type": "portability",
-                        "patch_description": "Support including Eigen headers located under eigen3/",
-                    }
-                ]
-            },
         }
 
     def layout(self):
         cmake_layout(self, src_folder="src")
 
+    def build_requirements(self):
+        self.requires("cmake/[>=3.25]")
+
     def requirements(self):
-        # Arrow 21.0.0 can't find certain kernels (e.g., sort_indices)
-        self.requires("arrow/20.0.0#6e04404a336dd16f08062f6923e6f8f1")
+        # re2
+        self.requires("abseil/20250814.0#4e0fdd34a888b97aca482e648fc27a3b", force=True)
+        # arrow
+        self.requires("re2/20251105#2eec620fc641f812a5837c642ecb7d66", force=True)
+        # hdf5
+        self.requires("zlib/1.3.1#b8bc2603263cf7eccbd6e17e66b0ed76", force=True)
+
+        self.requires("arrow/22.0.0#e46b173ba20adc478f7926495aeed142")
         self.requires("bshoshany-thread-pool/5.0.0#d94da300363f0c35b8f41b2c5490c94d")
         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
-        self.requires("eigen/3.4.90-unstable+git.2025.08.15#b407f03f085cdb246f6bcbadd84fe9db")
-        self.requires("fast_float/8.0.2#846ad0ebab16bc265c511095c3b490e9")
-        self.requires("fmt/11.2.0#579bb2cdf4a7607621beea4eb4651e0f", force=True)
-        self.requires("hdf5/1.14.6#6f1acd01d23d00735fe97300f4d5980c", force=True)
-        self.requires("highfive/2.10.0#75c849a0d940b2d4dae6055915132690")
-        self.requires("libdeflate/1.23#4994bea7cf7e93789da161fac8e26a53")
+        self.requires("eigen/5.0.0#f7561f543f4aafd6d2dc1f6d677e3075", force=True)
+        self.requires("fast_float/8.1.0#bbf67486bec084d167da0f3e13eee534")
+        self.requires("fmt/12.1.0#50abab23274d56bb8f42c94b3b9a40c7", force=True)
+        self.requires("hdf5/1.14.6#0b780319690d537e6cb0683244919955", force=True)
+        self.requires("highfive/3.1.1#d0c724526ebc8ce396ffa1bf7f3c7b64")
+        self.requires("libdeflate/1.25#49fcd3fe6c130c2ec5a01cabb0481ded")
         self.requires("parallel-hashmap/2.0.0#82acae64ffe2693fff5fb3f9df8e1746")
         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
-        self.requires("spdlog/1.15.3#3ca0e9e6b83af4d0151e26541d140c86")
+        self.requires("spdlog/1.16.0#942c2c39562ae25ba575d9c8e2bdf3b6")
         self.requires("zstd/1.5.7#fde461c0d847a22f16d3066774f61b11", force=True)
 
     def package_id(self):
@@ -95,9 +95,6 @@ def export_sources(self):
     def validate(self):
         check_min_cppstd(self, 17)
 
-    def build_requirements(self):
-        self.tool_requires("cmake/[>=3.25]")
-
     def source(self):
         get(self, **self.conan_data["sources"][self.version], strip_root=True)
 
@@ -145,6 +142,9 @@ def package_info(self):
 
         self.cpp_info.defines.append("HICTK_WITH_ARROW")
         self.cpp_info.defines.append("HICTK_WITH_EIGEN")
+        # TODO These should've been defined by the Arrow Conan recipe
+        self.cpp_info.defines.append("ARROW_STATIC")
+        self.cpp_info.defines.append("ARROW_COMPUTE_STATIC")
 
     def configure(self):
         self.options["arrow"].compute = True
@@ -154,6 +154,7 @@ def configure(self):
         self.options["arrow"].with_re2 = True
         self.options["arrow"].with_thrift = False
         self.options["arrow"].with_zlib = False
+        self.options["eigen"].MPL2_only = True
         self.options["fmt"].header_only = True
         self.options["hdf5"].enable_cxx = False
         self.options["hdf5"].hl = False

tools/generate_makevars.py

@@ -389,6 +389,8 @@ def run_conan_install(
         "--settings=build_type=Release",
         "--settings=compiler.cppstd=17",
         "--conf=tools.cmake.cmaketoolchain:generator=Ninja",
+        "--options",
+        "*/*:shared=False",
     ]
 
     if platform.system() != "Darwin":