Try to workaround macOS build failures

CMakeLists.txt

@@ -23,11 +23,12 @@ project(
   HOMEPAGE_URL https://github.com/paulsengroup/hictkpy
   DESCRIPTION "High-performance C++ library to read and write .cool files.")
 
+# include(cmake/FetchExternalDeps.cmake)
 include(FetchContent)
 FetchContent_Declare(
   hictk
   GIT_REPOSITORY "https://github.com/paulsengroup/hictk.git"
-  GIT_TAG        "6e9d46efc3cd3a4efa06db9d05b9af9fe91df4fe"
+  GIT_TAG        "1c2ec57446d1485e16958bc611016548329b6620"
   SYSTEM)
 
 set(BUILD_SHARED_LIBS ON)
@@ -37,6 +38,7 @@ set(HICTK_BUILD_BENCHMARKS OFF)
 set(HICTK_BUILD_PYTHON_BINDINGS OFF)
 set(HICTK_WITH_EIGEN OFF)
 set(HICTK_BUILD_TOOLS OFF)
+set(HICTK_INSTALL OFF)
 FetchContent_MakeAvailable(hictk)
 
 add_library(hictkpy_project_options INTERFACE)

cmake/FetchExternalDeps.cmake

@@ -0,0 +1,105 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+include(FetchContent)
+
+FetchContent_Declare(
+  FastFloat
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/fast_float-v5.2.0.tar.xz
+  URL_HASH SHA256=4c46c081d2098d1d39f70a003e0ada92959b305c121addab60a92de1cfffaae2
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  fmt
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/fmt-v10.0.0.tar.xz
+  URL_HASH SHA256=8570604ab8bc1c4cf70c3eecd278c88be3acf941373374c4908ddf9e7ae84288
+  EXCLUDE_FROM_ALL
+  SYSTEM
+  FIND_PACKAGE_ARGS
+  NAMES
+  FMT)
+
+FetchContent_Declare(
+  HDF5
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/hdf5-v1.14.1.tar.xz
+  URL_HASH SHA256=61af1d1412160d2369c44b0ef7a5e92269f596de03d1c47f6d2680af29b0bbd6
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  HighFive
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/highfive-v2.7.1.tar.xz
+  URL_HASH SHA256=951596d3e85bbc8c6ea00cd73ee76e2af203dd29febdce827016378d2f0925e8
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  libdeflate
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/libdeflate-v1.18.tar.xz
+  URL_HASH SHA256=f1e1e2432f9329a5f53939527afb46c417c843520bd526be7f777ab270eb65a0
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  phmap
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/parallel-hashmap-v1.3.11.tar.xz
+  URL_HASH SHA256=f8f672e9fefdaa5fba555a77ff1037d9003401344dd651e71c98212e3eaad8cc
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  spdlog
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/spdlog-v1.12.0.tar.xz
+  URL_HASH SHA256=a37bb250032861c468716861f76aa97192a31107308aea8bf21cb0ad23e8693a
+  EXCLUDE_FROM_ALL SYSTEM FIND_PACKAGE_ARGS)
+
+FetchContent_Declare(
+  zlib
+  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/zlib-v1.2.13.tar.xz
+  URL_HASH SHA256=da09190636bdd21d1fbe90edb78c7ede68fdac4db7549f8d4521667d552db262
+  EXCLUDE_FROM_ALL
+  SYSTEM
+  FIND_PACKAGE_ARGS
+  NAMES
+  ZLIB)
+
+# Setup libdeflate
+set(LIBDEFLATE_BUILD_SHARED_LIB ${BUILD_SHARED_LIBS})
+set(LIBDEFLATE_BUILD_STATIC_LIB NOT ${BUILD_SHARED_LIBS})
+set(LIBDEFLATE_COMPRESSION_SUPPORT OFF)
+set(LIBDEFLATE_BUILD_GZIP OFF)
+
+# Setup HDF5
+set(BUILD_STATIC_LIBS NOT ${BUILD_SHARED_LIBS})
+set(ONLY_SHARED_LIBS ${BUILD_SHARED_LIBS})
+set(HDF5_ENABLE_THREADSAFE OFF)
+set(BUILD_TESTING OFF)
+set(HDF5_BUILD_TOOLS OFF)
+set(HDF5_BUILD_EXAMPLES OFF)
+set(HDF5_BUILD_HL_LIB OFF)
+set(HDF5_BUILD_FORTRAN OFF)
+set(HDF5_BUILD_CPP_LIB OFF)
+set(HDF5_ENABLE_Z_LIB_SUPPORT ON)
+
+# Setup HighFive
+set(HIGHFIVE_PARALLEL_HDF5 OFF)
+set(HIGHFIVE_USE_BOOST OFF)
+set(HIGHFIVE_USE_EIGEN OFF)
+set(HIGHFIVE_USE_XTENSOR OFF)
+set(HIGHFIVE_USE_OPENCV OFF)
+set(HIGHFIVE_EXAMPLES OFF)
+set(HIGHFIVE_UNIT_TESTS OFF)
+set(HIGHFIVE_BUILD_DOCS OFF)
+set(HIGHFIVE_USE_INSTALL_DEPS OFF)
+
+# Setup phmap
+set(PHMAP_INSTALL ON)
+
+find_package(ZLIB REQUIRED)
+
+FetchContent_MakeAvailable(
+  FastFloat
+  fmt
+  HDF5
+  HighFive
+  libdeflate
+  phmap
+  spdlog
+  zlib)

conanfile.txt

@@ -16,6 +16,10 @@ spdlog/1.12.0
 CMakeDeps
 
 [options]
+hdf5*:enable_cxx=False
+hdf5*:hl=False
+hdf5*:threadsafe=False
+hdf5*:parallel=False
 highfive*:with_boost=False
 highfive*:with_eigen=False
 highfive*:with_opencv=False

devel/cibw/linux/cibw_setup_deps.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2023 Roberto Rossini ([email protected])
+# SPDX-License-Identifier: MIT
+
+set -e
+set -u
+
+# readlink -f is not available on macos...
+function readlink_py {
+  set -eu
+  python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+}
+
+install_prefix="$(readlink_py "${1-/usr/local}")"
+
+conan install conanfile.txt \
+  -s build_type=Release \
+  -s compiler.cppstd=17 \
+  --output-folder "$install_prefix/share/cmake/" \
+  -o '*/*:shared=True' \
+  --build="missing"

devel/cibw/linux/conanfile.txt

@@ -0,0 +1,26 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+[requires]
+fast_float/5.2.0
+fmt/10.0.0
+hdf5/1.14.0
+highfive/2.7.1
+libdeflate/1.18
+parallel-hashmap/1.3.11
+pybind11/2.10.4
+spdlog/1.12.0
+
+[generators]
+CMakeDeps
+
+[options]
+hdf5*:enable_cxx=False
+hdf5*:hl=False
+hdf5*:threadsafe=False
+hdf5*:parallel=False
+highfive*:with_boost=False
+highfive*:with_eigen=False
+highfive*:with_opencv=False
+highfive*:with_xtensor=False

devel/cibw/macos/cibw_setup_deps.sh

@@ -0,0 +1,141 @@
+#!/usr/bin/env bash
+
+# Copyright (C) 2023 Roberto Rossini ([email protected])
+# SPDX-License-Identifier: MIT
+
+set -e
+set -u
+
+# readlink -f is not available on macos...
+function readlink_py {
+  set -eu
+  python3 -c 'import os, sys; print(os.path.realpath(sys.argv[1]))' "$1"
+}
+
+export MACOSX_DEPLOYMENT_TARGET='10.15'
+CMAKE_BUILD_PARALLEL_LEVEL="$(python3 -c 'import multiprocessing; multiprocessing.cpu_count()')"
+export CMAKE_BUILD_PARALLEL_LEVEL
+
+install_prefix="$(readlink_py "${1-/usr/local}")"
+wd="$(mktemp -d)"
+
+conan install conanfile.txt \
+  -s build_type=Release \
+  -s compiler.cppstd=17 \
+  --output-folder "$install_prefix/share/cmake/" \
+  -o '*/*:shared=True' \
+  --build="missing"
+
+# shellcheck disable=SC2064
+trap "cd '$PWD'; rm -rf '$wd'" EXIT
+
+data_dir="$(readlink_py ../../../external)"
+cd "$wd"
+
+
+# tar -xf "$data_dir/fast_float-v5.2.0.tar.xz"
+# cmake -DCMAKE_BUILD_TYPE=Release \
+#       -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+#       -S fast_float* \
+#       -B fast_float_build
+# cmake --build fast_float_build
+# cmake --install fast_float_build
+
+
+tar -xf "$data_dir/fmt-v10.0.0.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -DFMT_TEST=OFF \
+      -DFMT_LIB_DIR="lib" \
+      -DFMT_INSTALL=ON \
+      -S fmt* \
+      -B fmt_build
+cmake --build fmt_build
+cmake --install fmt_build
+
+
+tar -xf "$data_dir/spdlog-v1.12.0.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DSPDLOG_FMT_EXTERNAL_HO=ON \
+      -DSPDLOG_INSTALL=ON \
+      -DSPDLOG_BUILD_SHARED=OFF \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -S spdlog* \
+      -B spdlog_build
+cmake --build spdlog_build
+cmake --install spdlog_build
+
+
+tar -xf "$data_dir/zlib-v1.2.13.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -DSKIP_INSTALL_FILES=ON \
+      -S zlib* \
+      -B zlib_build
+cmake --build zlib_build
+cmake --install zlib_build
+
+
+tar -xf "$data_dir/hdf5-v1.14.1.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -DBUILD_STATIC_LIBS=OFF \
+      -DONLY_SHARED_LIBS=ON \
+      -DHDF5_ENABLE_THREADSAFE=OFF \
+      -DBUILD_TESTING=OFF \
+      -DHDF5_BUILD_TOOLS=OFF \
+      -DHDF5_BUILD_EXAMPLES=OFF \
+      -DHDF5_BUILD_HL_LIB=OFF \
+      -DHDF5_BUILD_FORTRAN=OFF \
+      -DHDF5_BUILD_CPP_LIB=OFF \
+      -DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
+      -DHDF5_ENABLE_SZIP_SUPPORT=OFF \
+      -DHDF5_PACKAGE_EXTLIBS=OFF \
+      -DZLIB_ROOT=staging \
+      -S hdf5* \
+      -B hdf5_build
+cmake --build hdf5_build
+cmake --install hdf5_build
+
+tar -xf "$data_dir/highfive-v2.7.1.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -DHIGHFIVE_PARALLEL_HDF5=OFF \
+      -DHIGHFIVE_USE_BOOST=OFF \
+      -DHIGHFIVE_USE_EIGEN=OFF \
+      -DHIGHFIVE_USE_XTENSOR=OFF \
+      -DHIGHFIVE_USE_OPENCV=OFF \
+      -DHIGHFIVE_EXAMPLES=OFF \
+      -DHIGHFIVE_UNIT_TESTS=OFF \
+      -DHIGHFIVE_BUILD_DOCS=OFF \
+      -DHIGHFIVE_USE_INSTALL_DEPS=OFF \
+      -DHDF5_C_LIBRARIES="$install_prefix/lib/libhdf5.so" \
+      -DHDF5_NO_FIND_PACKAGE_CONFIG_FILE=ON \
+      -S HighFive* \
+      -B HighFive_build
+cmake --build HighFive_build
+cmake --install HighFive_build
+
+
+tar -xf "$data_dir/libdeflate-v1.18.tar.xz"
+cmake -DCMAKE_BUILD_TYPE=Release \
+      -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+      -DLIBDEFLATE_BUILD_STATIC_LIB=OFF \
+      -DLIBDEFLATE_BUILD_SHARED_LIB=ON \
+      -DLIBDEFLATE_BUILD_GZIP=OFF \
+      -S libdeflate* \
+      -B libdeflate_build
+cmake --build libdeflate_build
+cmake --install libdeflate_build
+
+
+# tar -xf "$data_dir/parallel-hashmap-v1.3.11.tar.xz"
+# cmake -DCMAKE_BUILD_TYPE=Release \
+#       -DCMAKE_INSTALL_PREFIX="$install_prefix" \
+#       -DPHMAP_INSTALL=ON \
+#       -DPHMAP_BUILD_TESTS=OFF \
+#       -DPHMAP_BUILD_EXAMPLES=OFF \
+#       -S parallel-hashmap* \
+#       -B parallel-hashmap_build
+# cmake --build parallel-hashmap_build
+# cmake --install parallel-hashmap_build

devel/cibw/macos/conanfile.txt

@@ -0,0 +1,17 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+[requires]
+fast_float/5.2.0
+parallel-hashmap/1.3.11
+pybind11/2.10.4
+
+[generators]
+CMakeDeps
+
+[options]
+highfive*:with_boost=False
+highfive*:with_eigen=False
+highfive*:with_opencv=False
+highfive*:with_xtensor=False

external/licenses/fast_float.LICENSE-MIT

@@ -0,0 +1,27 @@
+MIT License
+
+Copyright (c) 2021 The fast_float authors
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.