Update hictk to v2.0.0

recipes/hictk/build.sh

@@ -2,7 +2,7 @@
 
 export CONAN_NON_INTERACTIVE=1
 
-export CMAKE_BUILD_PARALLEL_LEVEL=1 # ${CPU_COUNT}
+export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
 export CTEST_PARALLEL_LEVEL=${CPU_COUNT}
 
 if [[ ${DEBUG_C} == yes ]]; then
@@ -19,23 +19,31 @@ trap "rm -rf '$scratch'" EXIT
 
 declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
+  # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+  export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
   CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
   conan_profile='apple-clang'
+
+  # https://github.com/conda/conda-build/issues/4392
+  for toolname in "otool" "install_name_tool"; do
+    tool=$(find "${BUILD_PREFIX}/bin/" -name "*apple*-$toolname")
+    mv "${tool}" "${tool}.bak"
+    ln -s "/Library/Developer/CommandLineTools/usr/bin/${toolname}" "$tool"
+  done
 else
   CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
-  conan_profile='gcc'
+  conan_profile='clang'
 fi
 
 # Remember to update these profiles when bioconda's compiler toolchains are updated
 mkdir -p "$CONAN_HOME/profiles/"
 ln -s "${RECIPE_DIR}/conan_profiles/$conan_profile" "$CONAN_HOME/profiles/$conan_profile"
 
-# Remove unnecessary dependencies from conanfile.txt
-patch conanfile.py < "${RECIPE_DIR}/conanfile.py.patch"
+# Remove unnecessary dependencies from conanfile.py
+patch conanfile.Dockerfile.py < "${RECIPE_DIR}/conanfile.Dockerfile.py.patch"
 
 # Install header-only deps
-conan install conanfile.py \
+conan install conanfile.Dockerfile.py \
        --build="*" \
        -pr:b "$conan_profile" \
        -pr:h "$conan_profile" \
@@ -52,6 +60,7 @@ cmake -DCMAKE_BUILD_TYPE="$CMAKE_BUILD_TYPE"   \
       -DBUILD_SHARED_LIBS=ON                   \
       -DENABLE_DEVELOPER_MODE=OFF              \
       -DHICTK_ENABLE_TESTING=ON                \
+      -DHICTK_ENABLE_FUZZY_TESTING=OFF         \
       -DHICTK_BUILD_EXAMPLES=OFF               \
       -DHICTK_BUILD_BENCHMARKS=OFF             \
       -DHICTK_BUILD_TOOLS=ON                   \
@@ -66,10 +75,9 @@ cmake -DCMAKE_BUILD_TYPE="$CMAKE_BUILD_TYPE"   \
 cmake --build build/
 
 ctest --test-dir build/   \
-      --schedule-random   \
       --output-on-failure \
       --no-tests=error    \
-      --timeout 100
+      --timeout 180
 
 cmake --install build/
 

recipes/hictk/conan_profiles/clang

@@ -0,0 +1,8 @@
+[settings]
+arch=x86_64
+build_type=Release
+compiler=clang
+compiler.cppstd=17
+compiler.libcxx=libstdc++11
+compiler.version=18
+os=Linux

recipes/hictk/conanfile.Dockerfile.py.patch

@@ -0,0 +1,66 @@
+diff --git a/conanfile.Dockerfile.py b/conanfile.Dockerfile.py
+index c9e6d177..b190d2df 100644
+--- a/conanfile.Dockerfile.py
++++ b/conanfile.Dockerfile.py
+@@ -36,26 +36,10 @@ class HictkConan(ConanFile):
+
+     def requirements(self):
+         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+-        self.requires("bzip2/1.0.8#d00dac990f08d991998d624be81a9526")
+-        self.requires("cli11/2.4.2#1b431bda2fb2cd3efed633899abcd8cc")
+         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+-        self.requires("fast_float/6.1.5#e067b96a6271d1b4c255858ca9805bdd")
+-        self.requires("fmt/11.0.2#5c7438ef4d5d69ab106a41e460ce11f3", force=True)
+-        self.requires("hdf5/1.14.4.3#df1467d7374938c231edbe10e83f2bb4", force=True)
+-        self.requires("highfive/2.10.0#3d1bd25944a57fa1bc30a0a22923d528")
+-        self.requires("libarchive/3.7.6#11e70b88b334f684eb9f6b65f287c81e")
+-        self.requires("libdeflate/1.22#f95aebe763153ccbc4cc76c023e42e5a")
+-        self.requires("lz4/1.10.0#68a01ece147a441b463d8cefea68d555", force=True)
+-        self.requires("lzo/2.10#5725914235423c771cb1c6b607109b45")
+-        self.requires("nlohmann_json/3.11.3#45828be26eb619a2e04ca517bb7b828d")
+         self.requires("parallel-hashmap/1.4.0#36ac84df77219748440cdb0f23624d56")
+         self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
+         self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
+-        self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
+-        self.requires("tomlplusplus/3.4.0#85dbfed71376fb8dc23cdcc0570e4727")
+-        self.requires("xz_utils/5.4.5#b885d1d79c9d30cff3803f7f551dbe66")
+-        self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+-        self.requires("zlib/1.3.1#f52e03ae3d251dec704634230cd806a2")
+
+     def validate(self):
+         if self.settings.get_safe("compiler.cppstd"):
+@@ -64,34 +48,3 @@ class HictkConan(ConanFile):
+     def configure(self):
+         if self.settings.compiler in ["clang", "gcc"]:
+             self.settings.compiler.libcxx = "libstdc++11"
+-
+-        self.options["fmt"].header_only = True
+-        self.options["hdf5"].enable_cxx = False
+-        self.options["hdf5"].hl = False
+-        self.options["hdf5"].threadsafe = False
+-        self.options["hdf5"].parallel = False
+-        self.options["highfive"].with_boost = False
+-        self.options["highfive"].with_eigen = False
+-        self.options["highfive"].with_opencv = False
+-        self.options["highfive"].with_xtensor = False
+-        self.options["libarchive"].with_acl = False
+-        self.options["libarchive"].with_zlib = True
+-        self.options["libarchive"].with_bzip2 = True
+-        self.options["libarchive"].with_libxml2 = False
+-        self.options["libarchive"].with_expat = False
+-        self.options["libarchive"].with_iconv = False
+-        self.options["libarchive"].with_acl = False
+-        self.options["libarchive"].with_pcreposix = False
+-        self.options["libarchive"].with_cng = False
+-        self.options["libarchive"].with_nettle = False
+-        self.options["libarchive"].with_openssl = False
+-        self.options["libarchive"].with_libb2 = False
+-        self.options["libarchive"].with_lz4 = True
+-        self.options["libarchive"].with_lzo = True
+-        self.options["libarchive"].with_lzma = True
+-        self.options["libarchive"].with_zstd = True
+-        self.options["libarchive"].with_mbedtls = False
+-        self.options["libarchive"].with_xattr = False
+-        self.options["libarchive"].with_pcre2 = False
+-        self.options["spdlog"].header_only = True
+-        self.options["zstd"].build_programs = False

recipes/hictk/conda_build_config.yaml

@@ -0,0 +1,8 @@
+c_compiler:             # [linux]
+  - clang               # [linux]
+c_compiler_version:     # [linux]
+  - 18                  # [linux]
+cxx_compiler:           # [linux]
+  - clangxx             # [linux]
+cxx_compiler_version:   # [linux]
+  - 18                  # [linux]

recipes/hictk/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "hictk" %}
-{% set version = "1.0.0" %}
-{% set sha256 = "e337f52658a257eb6265e211dd3cef6b73db40bdc5b5a6433b47ce4faa6006fb" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "714db992756867dd885581b58e61bad190cbd0f118168de69bc9714b18f9ad2f" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('hictk', max_pin='x') }}
 
@@ -22,24 +22,28 @@ requirements:
     - cmake >=3.25
     - conan >=2
     - make
-    - catch2 >=3.5
-    - cli11 >=2.3
+    - catch2 >=3.7
+    - cli11 >=2.4
     - eigen >=3.4
-    - fast_float >=5
-    - fmt >=10
-    - highfive >=2.8
-    - spdlog >=1.12
+    - fast_float >=6
+    - fmt >=11
+    - highfive >=2.9
+    - nlohmann_json >=3.11
+    - tomlplusplus >=3.3
+    - spdlog >=1.14
 
   host:
     - hdf5 >=1.12
+    - libarchive >=3
     - libarrow >=16
-    - libdeflate
+    - libdeflate >=1
     - zstd >=1.5
 
   run:
     - hdf5 >=1.12
+    - libarchive >=3
     - libarrow >=16
-    - libdeflate
+    - libdeflate >=1
     - zstd >=1.5
 
 about:
@@ -48,45 +52,18 @@ about:
   license_file: LICENSE
   summary: Blazing fast toolkit to work with .hic and .cool files
   dev_url: https://github.com/paulsengroup/{{ name }}
-  doc_url: https://github.com/paulsengroup/{{ name }}#readme
+  doc_url: https://{{ name }}.readthedocs.io/en/stable/
 
 test:
   requires:
+    - python >=3.11,<3.13
+    - pip
     - curl
-    - cooler>=0.9.3
     - perl-digest-sha1
-    - xz
+    - zstd
   source_files:
     - cmake/FetchTestDataset.cmake
-    - test/scripts/check_test_files_exist.sh
-    - test/scripts/compare_matrix_files.sh
-    - test/scripts/compare_plain_files.sh
-    - test/scripts/compare_weights.py
-    - test/scripts/hictk_balance_ice.sh
-    - test/scripts/hictk_balance_scale.sh
-    - test/scripts/hictk_balance_vc.sh
-    - test/scripts/hictk_convert_hic2cool.sh
-    - test/scripts/hictk_convert_cool2hic.sh
-    - test/scripts/hictk_dump_cells.sh
-    - test/scripts/hictk_dump_normalizations.sh
-    - test/scripts/hictk_dump_resolutions.sh
-    - test/scripts/hictk_dump_chroms.sh
-    - test/scripts/hictk_dump_bins.sh
-    - test/scripts/hictk_dump_gw.sh
-    - test/scripts/hictk_dump_cis.sh
-    - test/scripts/hictk_dump_trans.sh
-    - test/scripts/hictk_dump_balanced.sh
-    - test/scripts/hictk_fix_mcool.sh
-    - test/scripts/hictk_load_coo.sh
-    - test/scripts/hictk_load_bg2.sh
-    - test/scripts/hictk_load_4dn.sh
-    - test/scripts/hictk_merge.sh
-    - test/scripts/hictk_rename_chromosomes.sh
-    - test/scripts/hictk_validate.sh
-    - test/scripts/hictk_zoomify.sh
-    - test/scripts/nproc.sh
-    - test/scripts/readlink.sh
-    - test/scripts/shuffle.sh
+    - test/integration/
   commands:
     - hictk --help
     - hictk --version