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Merge pull request #187 from paulsengroup/fix/build-system
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Various fixes to the build system and CI
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@robomics
robomics authored Jun 17, 2024
2 parents 0d3b21d + 8b66461 commit 60cbdbf
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Showing 9 changed files with 74 additions and 58 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/codecov.yml
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Expand Up @@ -175,7 +175,7 @@ jobs:
apt-get update
apt-get install -y --no-install-recommends python3-pip xz-utils
python3 -m pip install 'cooler>=0.9.3'
python3 -m pip install 'cooler==0.10.0' 'numpy<2'
- name: Run integration tests
run: |
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2 changes: 1 addition & 1 deletion .github/workflows/fuzzy-testing.yml
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Expand Up @@ -195,7 +195,7 @@ jobs:
run: |
apt-get update
apt-get install -y curl zstd
pip install --no-cache-dir 'cooler>=0.9.3'
pip install --no-cache-dir 'cooler==0.10.0' 'numpy<2'
- name: Detect CI type
id: ci-type
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14 changes: 8 additions & 6 deletions .github/workflows/macos-ci.yml
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Expand Up @@ -61,11 +61,11 @@ jobs:
var includes = []
includes.push({ compiler_name: 'apple-clang', compiler_version: '14', os: 'macos-12', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.1.*', cmake: '3.28.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.1.*', cmake: '3.28.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.1.*', cmake: '3.28.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '14', os: 'macos-12', conan: '2.4.*', cmake: '3.29.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.4.*', cmake: '3.29.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.4.*', cmake: '3.29.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-13', conan: '2.4.*', cmake: '3.29.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler_name: 'apple-clang', compiler_version: '15', os: 'macos-14', conan: '2.4.*', cmake: '3.29.*', build_type: 'Debug', developer_mode: 'OFF' })
return { include: includes }
Expand Down Expand Up @@ -318,7 +318,9 @@ jobs:
chown -R $(id -u):$(id -g) $PWD
- name: Generate requirements.txt for pip
run: echo 'cooler>=0.9.3' > requirements.txt
run: |
echo 'cooler==0.10.0' > requirements.txt
echo 'numpy<2' >> requirements.txt
- uses: actions/setup-python@v5
with:
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76 changes: 38 additions & 38 deletions .github/workflows/ubuntu-ci.yml
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Expand Up @@ -71,57 +71,57 @@ jobs:
var includes = []
// Debug builds (short CI)
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'ON' })
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'ON' })
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' })
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'ON' })
// Release builds (short CI)
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'ON' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'ON' })
includes.push({ compiler: 'gcc-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'ON' })
if (ci_short) {
return { include: includes }
}
// Debug builds (long CI)
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Debug', developer_mode: 'OFF' })
// Release builds (long CI)
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-9', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-10', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-11', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-12', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'gcc-13', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-8', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-9', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-10', os: 'ubuntu-20.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-11', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-12', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-13', os: 'ubuntu-22.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-14', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-15', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-16', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-17', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
// Make sure project builds with CMake 3.25
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.25.2', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Ninja', cmake: '3.25.2', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
// Make sure project builds with make
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Unix Makefiles', cmake: '3.29.*', conan: '2.3.*', build_type: 'Release', developer_mode: 'OFF' })
includes.push({ compiler: 'clang-18', os: 'ubuntu-24.04', generator: 'Unix Makefiles', cmake: '3.29.*', conan: '2.4.*', build_type: 'Release', developer_mode: 'OFF' })
return { include: includes }
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5 changes: 3 additions & 2 deletions .github/workflows/windows-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,8 @@ jobs:
fail-fast: false
matrix:
include:
- { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.1.*', cmake-ver: '3.28.*', build_type: Debug, developer_mode: OFF }
- { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.1.*', cmake-ver: '3.28.*', build_type: Release, developer_mode: OFF }
- { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.4.*', cmake-ver: '3.29.*', build_type: Debug, developer_mode: OFF }
- { compiler-name: msvc, os: 'windows-2022', conan-ver: '2.4.*', cmake-ver: '3.29.*', build_type: Release, developer_mode: OFF }


steps:
Expand Down Expand Up @@ -136,6 +136,7 @@ jobs:
run: |
conan install . \
--build=missing \
--build="b2/*" \
--build="catch2/*" \
-pr:h default \
-pr:b default \
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2 changes: 1 addition & 1 deletion Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ ENV CC="$C_COMPILER"
ENV CXX="$CXX_COMPILER"

# Install b2 using Conan
RUN printf '[requires]\nb2/4.10.1\n[options]\nb2*:toolset=%s' \
RUN printf '[requires]\nb2/5.2.1\n[options]\nb2*:toolset=%s' \
"$(basename "$(which "$CC")")" | cut -f 1 -d - > /tmp/conanfile.txt

RUN conan install /tmp/conanfile.txt \
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8 changes: 8 additions & 0 deletions cmake/hictkConfig.cmake.in
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,14 @@ set(HICTK_WITH_EIGEN @HICTK_WITH_EIGEN@)

include(CMakeFindDependencyMacro)

if(HICTK_WITH_ARROW)
find_dependency(
Arrow
CONFIG
QUIET
REQUIRED)
endif()

find_dependency(
bshoshany-thread-pool
CONFIG
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16 changes: 8 additions & 8 deletions conanfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,23 +36,23 @@ def _min_cppstd(self):
return 17

def requirements(self):
self.requires("arrow/16.0.0#c0b940c80fddf319983165f7588c279d")
self.requires("boost/1.85.0#7926babdab0a9779cc164d0af6c28d5e", force=True)
self.requires("arrow/16.1.0#f484da4c4c27c1eb3ead5d61b70635cd")
self.requires("boost/1.85.0#d9ae7996a5b917e0cfd4b738aa976dee", force=True)
self.requires("bshoshany-thread-pool/4.1.0#be1802a8768416a6c9b1393cf0ce5e9c")
self.requires("catch2/3.5.4#d346ca291f8f62040fd9c1a891654711")
self.requires("cli11/2.4.1#afacffd31f631bbb8b7c7d6425fe7a66")
self.requires("catch2/3.6.0#819bc5a82c2cb626916fc18ee1dbc45f")
self.requires("cli11/2.4.2#1b431bda2fb2cd3efed633899abcd8cc")
self.requires("concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502")
self.requires("eigen/3.4.0#2e192482a8acff96fe34766adca2b24c")
self.requires("fast_float/6.1.1#e29acaa3d0543dee343abe3f6815346e")
self.requires("fmt/10.2.1#9199a7a0611866dea5c8849a77467b25")
self.requires("hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1")
self.requires("highfive/2.9.0#c57477beed8b0110fadeb6da8f48bcc5")
self.requires("libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602")
self.requires("parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7")
self.requires("libdeflate/1.20#3bd86e0160becf992346aa68b4938c40")
self.requires("parallel-hashmap/1.3.12#dc7755096d8a1fac7792fdd85760b6ca")
self.requires("readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83")
self.requires("span-lite/0.11.0#519fd49fff711674cfed8cd17d4ed422")
self.requires("spdlog/1.13.0#8e88198fd5b9ee31d329431a6d0ccaa2")
self.requires("zstd/1.5.6#67383dae85d33f43823e7751a6745ea1", force=True)
self.requires("spdlog/1.14.1#972bbf70be1da4bc57ea589af0efde03")
self.requires("zstd/1.5.6#afefe79a309bc2a7b9f56c2093504c8b")

def validate(self):
if self.settings.get_safe("compiler.cppstd"):
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