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kojix2 · Aug 23, 2024 · 716387c · 716387c
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commit 716387c
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Showing 4 changed files with 76 additions and 56 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -6,7 +6,7 @@ jobs:
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
-        os: ["ubuntu"]
+        os: ["ubuntu", "macos"]
         ruby: ["3.3"]
     steps:
       - uses: actions/checkout@v4
@@ -17,12 +17,14 @@ jobs:
           ruby-version: ${{ matrix.ruby }}
           bundler-cache: true
       - if: matrix.os == 'ubuntu'
-        run: sudo apt-get update -yq && sudo apt upgrade -yq && sudo apt-get upgrade # libjemalloc-dev
+        run: sudo apt-get update -yq && sudo apt upgrade -yq # && sudo apt-get upgrade libjemalloc-dev
       - if: matrix.os == 'macos'
-        run: brew update && brew install jemalloc
+        run: brew update && brew install llvm libomp #jemalloc
       - if: matrix.os == 'ubuntu'
         run: bundle exec rake jemalloc:build && bundle exec rake odgi:build
       - if: matrix.os == 'macos'
-        run: CC=/opt/homebrew/opt/llvm/bin/clang CXX=/opt/homebrew/opt/llvm/bin/clang++ LDFLAGS=-L/opt/homebrew/lib bundle exec rake odgi:build
+        run: |
+          CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ LDFLAGS=-L/opt/homebrew/lib bundle exec rake jemalloc:build
+          CC=$(brew --prefix llvm)/bin/clang CXX=$(brew --prefix llvm)/bin/clang++ LDFLAGS=-L/opt/homebrew/lib bundle exec rake jemalloc:build
       - run: bundle exec rake compile
       - run: bundle exec rake test
diff --git a/Rakefile b/Rakefile
@@ -1,36 +1,36 @@
-require "bundler/gem_tasks"
-require "rake/testtask"
+require 'bundler/gem_tasks'
+require 'rake/testtask'
 
 Rake::TestTask.new(:test) do |t|
-  t.libs << "test"
-  t.libs << "lib"
-  t.test_files = FileList["test/**/*_test.rb"]
+  t.libs << 'test'
+  t.libs << 'lib'
+  t.test_files = FileList['test/**/*_test.rb']
 end
 
-require "rake/extensiontask"
+require 'rake/extensiontask'
 
 task build: :compile
 
-Rake::ExtensionTask.new("odgi") do |ext|
-  ext.lib_dir = "lib/odgi"
+Rake::ExtensionTask.new('odgi') do |ext|
+  ext.lib_dir = 'lib/odgi'
 end
 
 namespace :jemalloc do
-  desc "Building jemalloc"
+  desc 'Building jemalloc'
   task :build do
-    Dir.chdir("jemalloc") do
-      sh "./autogen.sh"
-      sh "./configure --disable-initial-exec-tls"
+    Dir.chdir('jemalloc') do
+      sh './autogen.sh'
+      sh './configure --disable-initial-exec-tls'
       sh "make -j #{Etc.nprocessors}"
     end
   end
 end
 
 namespace :odgi do
-  desc "Building odgi"
+  desc 'Building odgi'
   task :build do
-    jemalloc_lib_dir = File.expand_path("jemalloc/lib", __dir__)
-    Dir.chdir("odgi") do
+    jemalloc_lib_dir = File.expand_path('jemalloc/lib', __dir__)
+    Dir.chdir('odgi') do
       sh "cmake -H. -Bbuild -DJEMALLOC_LIBRARY=#{jemalloc_lib_dir}"
       sh "cmake --build build -- -j #{Etc.nprocessors}"
     end

diff --git a/ext/odgi/extconf.rb b/ext/odgi/extconf.rb
@@ -2,39 +2,57 @@
 
 require 'mkmf-rice'
 
-handlegraph_include_dir = File.expand_path('../../odgi/deps/libhandlegraph/src/include', __dir__)
-hopscotchmap_include_dir = File.expand_path('../../odgi/deps/hopscotch-map/include', __dir__)
-dynamic_include_dir = File.expand_path('../../odgi/deps/DYNAMIC/include', __dir__)
-sparsepp_include_dir = File.expand_path('../../odgi/deps/sparsepp/sparsepp', __dir__)
-flat_hash_map_include_dir = File.expand_path('../../odgi/deps/flat_hash_map', __dir__)
-atomicbitvector_include_dir = File.expand_path('../../odgi/deps/atomicbitvector/include', __dir__)
-
-odgi_include_dir = File.expand_path('../../odgi/src', __dir__)
-odgi_library_dir = File.expand_path('../../odgi/lib', __dir__)
-
-find_header('handlegraph/types.hpp', handlegraph_include_dir)
-find_header('handlegraph/iteratee.hpp', handlegraph_include_dir)
-find_header('handlegraph/util.hpp', handlegraph_include_dir)
-find_header('handlegraph/handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/path_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/mutable_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/mutable_path_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/mutable_path_mutable_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/deletable_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/mutable_path_deletable_handle_graph.hpp', handlegraph_include_dir)
-find_header('handlegraph/serializable_handle_graph.hpp', handlegraph_include_dir)
-
-find_header('tsl/hopscotch_map.h', hopscotchmap_include_dir)
-
-find_header('dynamic.hpp', dynamic_include_dir)
-
-find_header('spp.h', sparsepp_include_dir)
-
-find_header('bytell_hash_map.hpp', flat_hash_map_include_dir)
-
-find_header('atomic_bitvector.hpp', atomicbitvector_include_dir)
-
-find_header('odgi-api.h', odgi_include_dir)
+ODGI_DIR = Pathname(__dir__) / '../../odgi'
+odgi_library_dir = (ODGI_DIR / 'lib').to_s
+
+# if macOS
+if RUBY_PLATFORM =~ /darwin/
+  (`brew --prefix libomp`.strip + '/include').tap do |dir|
+    find_header 'omp.h', dir
+  end
+end
+
+(ODGI_DIR / 'deps/libhandlegraph/src/include').tap do |dir|
+  find_header 'handlegraph/types.hpp', dir
+  find_header 'handlegraph/iteratee.hpp', dir
+  find_header 'handlegraph/util.hpp', dir
+  find_header 'handlegraph/handle_graph.hpp', dir
+  find_header 'handlegraph/path_handle_graph.hpp', dir
+  find_header 'handlegraph/mutable_handle_graph.hpp', dir
+  find_header 'handlegraph/mutable_path_handle_graph.hpp', dir
+  find_header 'handlegraph/mutable_path_mutable_handle_graph.hpp', dir
+  find_header 'handlegraph/deletable_handle_graph.hpp', dir
+  find_header 'handlegraph/mutable_path_deletable_handle_graph.hpp', dir
+  find_header 'handlegraph/serializable_handle_graph.hpp', dir
+end
+
+(ODGI_DIR / 'deps/hopscotch-map/include').tap do |dir|
+  find_header 'tsl/hopscotch_map.h', dir
+end
+
+(ODGI_DIR / 'deps/DYNAMIC/include').tap do |dir|
+  find_header 'dynamic.hpp', dir
+end
+
+(ODGI_DIR / 'src').tap do |dir|
+  find_header 'atomic_bitvector.hpp', dir
+end
+
+(ODGI_DIR / 'deps/sparsepp/sparsepp').tap do |dir|
+  find_header 'spp.h', dir
+end
+
+(ODGI_DIR / 'deps/flat_hash_map').tap do |dir|
+  find_header 'bytell_hash_map.hpp', dir
+end
+
+(ODGI_DIR / 'deps/atomicbitvector/include').tap do |dir|
+  find_header 'atomic_bitvector.hpp', dir
+end
+
+(ODGI_DIR / 'src').tap do |dir|
+  find_header 'odgi-api.h', dir
+end
 
 find_library('odgi', nil, odgi_library_dir)
 

diff --git a/test/odgi_test.rb b/test/odgi_test.rb
@@ -1,4 +1,4 @@
-require_relative "test_helper"
+require_relative 'test_helper'
 
 class OdgiTest < Minitest::Test
   def test_that_it_has_a_version_number
@@ -10,9 +10,9 @@ def test_odgi_version
   end
 
   def test_odgi_load_graph
-    graph =  ODGI::FFI.odgi_load_graph(
-      File.join(File.dirname(__dir__), "odgi", "test", "DRB1-3123_sorted.og")
-      )
+    graph = ODGI::FFI.odgi_load_graph(
+      File.join(File.dirname(__dir__), 'odgi', 'test', 'DRB1-3123_sorted.og')
+    )
     assert_kind_of ODGI::FFI::Graph, graph
   end
 end