hictkpy: add v1.0.0 (#51561)

* Update Conan profiles

* Update build config to be in line with hictk's recipe

* Update patch files

* Update build script

* Bump version

* Update about section

* Update requirements

* Update test requirements

* Update package version pinning

* Make tests verbose

* Enable parallel builds

* Ensure the correct sysroot is used when building on macOS

* Ensure the correct sysroot is used when building on Linux

* Help CMake find NumPy headers

* Export env variables in build script

* Update checksum

recipes/hictkpy/build.sh

@@ -1,40 +1,54 @@
 #!/bin/bash
 
-# export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
+CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
 
 scratch=$(mktemp -d)
 export CONAN_HOME="$scratch/conan"
 
 # shellcheck disable=SC2064
 trap "rm -rf '$scratch'" EXIT
 
-declare -a CMAKE_PLATFORM_FLAGS
 if [[ ${HOST} =~ .*darwin.* ]]; then
-  export MACOSX_DEPLOYMENT_TARGET=10.15  # Required to use std::filesystem
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_OSX_SYSROOT="${CONDA_BUILD_SYSROOT}")
+  if [[ "$OSX_ARCH" == 'x86_64' ]]; then
+    # https://conda-forge.org/docs/maintainer/knowledge_base/#newer-c-features-with-old-sdk
+    CFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+    CXXFLAGS+=' -D_LIBCPP_DISABLE_AVAILABILITY'
+  fi
+  CMAKE_ARGS+=" -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}"
   conan_profile='apple-clang'
 else
-  CMAKE_PLATFORM_FLAGS+=(-DCMAKE_TOOLCHAIN_FILE="${RECIPE_DIR}/cross-linux.cmake")
-  conan_profile='gcc'
+  # Workaround missing LLVMgold.so on Linux
+  CMAKE_ARGS+=' -DCMAKE_LINKER_TYPE=LLD'
+  CMAKE_ARGS+=" -DCMAKE_TOOLCHAIN_FILE=${RECIPE_DIR}/cross-linux.cmake"
+  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/default"
 
-# explicitly set CMAKE_OSX_DEPLOYMENT_TARGET
-patch CMakeLists.txt < "${RECIPE_DIR}/CMakeLists.txt.patch"
-
-# Remove unnecessary dependencies from conanfile.txt
-patch conanfile.txt < "${RECIPE_DIR}/conanfile.txt.patch"
+# Remove unnecessary dependencies from conanfile.py
+patch conanfile.py < "${RECIPE_DIR}/conanfile.py.patch"
 
 # Build hictkpy as a shared library
 patch pyproject.toml < "${RECIPE_DIR}/pyproject.toml.patch"
 
-CMAKE_ARGS+=" -DPython_EXECUTABLE=$PYTHON"
+# See https://github.com/conda-forge/conda-forge.github.io/pull/2321
+Python_INCLUDE_DIR="$("$PYTHON" -c 'import sysconfig; print(sysconfig.get_path("include"))')"
+Python_NumPy_INCLUDE_DIR="$("$PYTHON" -c 'import numpy; print(numpy.get_include())')"
+
+CMAKE_ARGS+=" -DPython_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_EXECUTABLE:PATH=${PYTHON}"
+CMAKE_ARGS+=" -DPython3_INCLUDE_DIR:PATH=${Python_INCLUDE_DIR}"
+CMAKE_ARGS+=" -DPython3_NumPy_INCLUDE_DIR=${Python_NumPy_INCLUDE_DIR}"
+
+echo "CFLAGS='$CFLAGS'"
+echo "CXXFLAGS='$CXXFLAGS'"
+echo "CMAKE_ARGS='$CMAKE_ARGS'"
 
-echo "$CMAKE_ARGS"
-export CMAKE_ARGS
+export CMAKE_ARGS CMAKE_BUILD_PARALLEL_LEVEL CFLAGS CXXFLAGS
 
 SETUPTOOLS_SCM_PRETEND_VERSION="$PKG_VERSION" \
 "$PYTHON" -m pip install "$SRC_DIR" -vv

recipes/hictkpy/conan_profiles/gcc → recipes/hictkpy/conan_profiles/clang

@@ -1,8 +1,8 @@
 [settings]
 arch=x86_64
 build_type=Release
-compiler=gcc
+compiler=clang
 compiler.cppstd=17
 compiler.libcxx=libstdc++11
-compiler.version=13
+compiler.version=18
 os=Linux

recipes/hictkpy/conanfile.py.patch

@@ -0,0 +1,90 @@
+diff --git a/conanfile.py b/conanfile.py
+index a7d5c74..c08b356 100644
+--- a/conanfile.py
++++ b/conanfile.py
+@@ -35,21 +35,11 @@ class HictkpyConan(ConanFile):
+         return 17
+
+     def requirements(self):
+-        self.requires("arrow/17.0.0#81be2aa6c49800df8cc163adf4b99e9f")
+-        self.requires("boost/1.86.0#cd839a2082585255010f9e82eea94c7f", force=True)
+         self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
+         self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
+-        self.requires("eigen/3.4.0#2e192482a8acff96fe34766adca2b24c")
+-        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("libdeflate/1.22#f95aebe763153ccbc4cc76c023e42e5a")
+         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("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b", force=True)
+
+     def validate(self):
+         if self.settings.get_safe("compiler.cppstd"):
+@@ -58,63 +48,3 @@ class HictkpyConan(ConanFile):
+     def configure(self):
+         if self.settings.compiler in ["clang", "gcc"]:
+             self.settings.compiler.libcxx = "libstdc++11"
+-
+-        self.options["arrow"].compute = True
+-        self.options["arrow"].parquet = False
+-        self.options["arrow"].with_boost = True
+-        self.options["arrow"].with_re2 = True
+-        self.options["arrow"].with_thrift = False
+-        self.options["boost"].system_no_deprecated = True
+-        self.options["boost"].asio_no_deprecated = True
+-        self.options["boost"].filesystem_no_deprecated = True
+-        self.options["boost"].filesystem_version = 4
+-        self.options["boost"].zlib = False
+-        self.options["boost"].bzip2 = False
+-        self.options["boost"].lzma = False
+-        self.options["boost"].zstd = False
+-        self.options["boost"].without_atomic = False
+-        self.options["boost"].without_charconv = True
+-        self.options["boost"].without_chrono = True
+-        self.options["boost"].without_cobalt = True
+-        self.options["boost"].without_container = True
+-        self.options["boost"].without_context = True
+-        self.options["boost"].without_contract = True
+-        self.options["boost"].without_coroutine = True
+-        self.options["boost"].without_date_time = True
+-        self.options["boost"].without_exception = True
+-        self.options["boost"].without_fiber = True
+-        self.options["boost"].without_filesystem = False
+-        self.options["boost"].without_graph = True
+-        self.options["boost"].without_graph_parallel = True
+-        self.options["boost"].without_iostreams = True
+-        self.options["boost"].without_json = True
+-        self.options["boost"].without_locale = True
+-        self.options["boost"].without_log = True
+-        self.options["boost"].without_math = True
+-        self.options["boost"].without_mpi = True
+-        self.options["boost"].without_nowide = True
+-        self.options["boost"].without_process = False
+-        self.options["boost"].without_program_options = True
+-        self.options["boost"].without_python = True
+-        self.options["boost"].without_random = True
+-        self.options["boost"].without_regex = True
+-        self.options["boost"].without_serialization = True
+-        self.options["boost"].without_stacktrace = True
+-        self.options["boost"].without_system = False
+-        self.options["boost"].without_test = True
+-        self.options["boost"].without_thread = True
+-        self.options["boost"].without_timer = True
+-        self.options["boost"].without_type_erasure = True
+-        self.options["boost"].without_url = True
+-        self.options["boost"].without_wave = True
+-        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["spdlog"].header_only = True
+-        self.options["zstd"].build_programs = False

recipes/hictkpy/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/hictkpy/meta.yaml

@@ -1,61 +1,68 @@
 {% set name = "hictkpy" %}
-{% set version = "0.0.5" %}
-{% set sha256 = "e9576a1a719ce378873da15b76e9f7e699748c0486901607e4d7e87c3f0c6556" %}
+{% set version = "1.0.0" %}
+{% set sha256 = "a12c05cba9395ce39eb742b5d1e1a6e0cc0179a5b6981ae8a828ff9aee2c64ce" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   skip: True  # [py < 39]
   run_exports:
-    - {{ pin_subpackage('hictkpy', max_pin='x.x') }}
+    - {{ pin_subpackage('hictkpy', max_pin='x') }}
 
 source:
-  url: https://github.com/paulsengroup/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  url: https://pypi.python.org/packages/source/h/{{ name }}/{{ name }}-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - cmake >=3.25
+    - cmake >=3.29
     - conan >=2
     - make
-    - fast_float >=5
-    - fmt >=10
-    - highfive >=2.7
-    - spdlog >=1.12
+    - eigen >=3.4
+    - fast_float >=6
+    - fmt >=11
+    - highfive >=2.9
+    - spdlog >=1.14
+
   host:
     - python
     - pip
     - hdf5 >=1.12
-    - libdeflate
-    - scikit-build-core
+    - libarrow >=16
+    - libdeflate >=1
+    - lld  # [linux]
+    - nanobind >=2
+    - numpy
+    - scikit-build-core >=0.10
     - setuptools_scm
     - zstd >=1.5
 
   run:
     - python
-    - hdf5 >=1.12
-    - libdeflate
-    - numpy
-    - pandas
-    - scipy
-    - zstd >=1.5
+    - {{ pin_compatible('hdf5', min_pin='1.12') }}
+    - {{ pin_compatible('libdeflate', min_pin='1') }}
+    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('pandas', min_pin='2.1') }}
+    - {{ pin_compatible('pyarrow', min_pin='16') }}
+    - {{ pin_compatible('scipy') }}
+    - {{ pin_compatible('zstd', min_pin='1.5') }}
 
 about:
   home: https://github.com/paulsengroup/{{ name }}
   license: MIT
   license_file: LICENSE
-  summary: Python bindings for hictk
+  summary: "Python bindings for hictk: read and write .cool and .hic files directly from Python"
   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:
-     - pytest>=6
+     - pytest>=8
    source_files:
      - test/*
    imports:

recipes/hictkpy/pyproject.toml.patch

@@ -1,13 +1,13 @@
 diff --git a/pyproject.toml b/pyproject.toml
-index 1a03623..36102d0 100644
+index 5ded5b9..fe8d305 100644
 --- a/pyproject.toml
 +++ b/pyproject.toml
-@@ -49,7 +49,7 @@ HICTK_BUILD_EXAMPLES = "OFF"
- HICTK_BUILD_BENCHMARKS = "OFF"
- HICTK_BUILD_TOOLS = "OFF"
- HICTK_ENABLE_GIT_VERSION_TRACKING = "OFF"
+@@ -74,7 +74,7 @@ wheel.expand-macos-universal-tags = true
+ cmake.build-type = "Release"
+
+ [tool.scikit-build.cmake.define]
 -BUILD_SHARED_LIBS = "OFF"
 +BUILD_SHARED_LIBS = "ON"
- CONAN_INSTALL_ARGS = "--settings=compiler.cppstd=17;--build=missing;--update;--options=*/*:shared=False"
-
- [tool.setuptools_scm]
+ CMAKE_OSX_DEPLOYMENT_TARGET = "10.15"
+ CMAKE_PROJECT_TOP_LEVEL_INCLUDES = { env="HICTKPY_PROJECT_TOP_LEVEL_INCLUDES", default="cmake/conan_provider.cmake" }
+ CONAN_INSTALL_ARGS = { env="HICTKPY_CONAN_INSTALL_ARGS", default="--settings=compiler.cppstd=17;--settings=build_type=Release;--build=missing;--update;--options=*/*:shared=False" }

recipes/hictkpy/run_test.sh

@@ -1,4 +1,4 @@
 #!/usr/bin/env bash
 
 "$PYTHON" -c 'import hictkpy; print(hictkpy.__version__)'
-"$PYTHON" -m pytest test
+"$PYTHON" -m pytest test -v