Merge branch 'master' into public

refresh-bio · Mar 21, 2023 · bcf7ad0 · bcf7ad0
2 parents 91d70e9 + b206029
commit bcf7ad0
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Showing 21 changed files with 50 additions and 2,495 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -24,7 +24,10 @@ jobs:
       CLR_LOSSY: ./test/A.thaliana.fastq.quan
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Checkout repository and submodules
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
     - name: make
       run: make -j2
 
@@ -109,10 +112,13 @@ jobs:
 
   macos-remote:
     name: macOS build (remote)
-    runs-on: macOS-latest
+    runs-on: macOS-11
 
     steps:
-    - uses: actions/checkout@v2
+    - name: Checkout repository and submodules
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
     - name: make
       run: make -j2
 

diff --git a/.github/workflows/self-hosted.yml b/.github/workflows/self-hosted.yml
@@ -15,7 +15,10 @@ jobs:
     env: 
       EXE: ./bin/colord
     steps:
-    - uses: actions/checkout@v2
+    - name: Checkout repository and submodules
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
 
     - name: make (g++ 9)
       run: |

diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "src/colord/libs/mimalloc"]
+	path = src/colord/libs/mimalloc
+	url = https://github.com/microsoft/mimalloc
diff --git a/Makefile b/Makefile
@@ -56,11 +56,12 @@ $(SRC)/reference_genome.o
 COBJS = \
 $(SRC)/libs/md5/md5.o
 
+MIMALLOC_OBJ=$(SRC)/libs/mimalloc/mimalloc.o
+
 ifeq ($(UNAME_S),Darwin)
 	LIB_ZLIB = $(SRC)/../common/libs/zlib/libz.mac.a
     LIBS = \
 	$(SRC)/../common/libs/zlib/libz.mac.a \
-	$(SRC)/libs/mimalloc/libmimalloc.mac.a \
 	$(SRC)/libs/count_kmers/libfiltering_kmc.mac.a \
 	$(SRC)/libs/count_kmers/libbz2.1.0.5.dylib
 
@@ -69,7 +70,6 @@ else
 	LIB_ZLIB = $(SRC)/../common/libs/zlib/libz.a
 	LIBS = \
 	$(SRC)/../common/libs/zlib/libz.a \
-	$(SRC)/libs/mimalloc/libmimalloc.a \
 	$(SRC)/libs/count_kmers/libfiltering_kmc.a \
 	$(SRC)/libs/count_kmers/libbz2.a
 
@@ -78,7 +78,11 @@ endif
 
 all: $(BIN_DIR)/colord $(BIN_DIR)/libcolord_api.a $(BIN_DIR)/api_example
 
-$(BIN_DIR)/colord: $(OBJS) $(COBJS) $(OBJS_COMMON) $(LIB_FILTERING_KMC)
+$(MIMALLOC_OBJ):
+	$(CXX) -DMI_MALLOC_OVERRIDE -O3 -DNDEBUG -fPIC -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -ftls-model=initial-exec -fno-builtin-malloc -c -I $(SRC)/libs/mimalloc/include $(SRC)/libs/mimalloc/src/static.c -o $(MIMALLOC_OBJ)
+
+
+$(BIN_DIR)/colord: $(MIMALLOC_OBJ) $(OBJS) $(COBJS) $(OBJS_COMMON) $(LIB_FILTERING_KMC)
 	-mkdir -p $(BIN_DIR)
 	$(CXX) $(CLINK) -o $@ $^ $(LIBS)
 

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ A versatile compressor of third generation sequencing reads.
 ## Quick start
 
 ```bash
-git clone https://github.com/refresh-bio/colord
+git clone --recurse-submodules https://github.com/refresh-bio/colord
 cd colord && make
 cd bin
 

diff --git a/src/API/API.vcxproj b/src/API/API.vcxproj
@@ -29,26 +29,26 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>StaticLibrary</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>StaticLibrary</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>StaticLibrary</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>StaticLibrary</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>

diff --git a/src/API_example/API_example.vcxproj b/src/API_example/API_example.vcxproj
@@ -29,26 +29,26 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>

diff --git a/src/colord/colord.vcxproj b/src/colord/colord.vcxproj
@@ -28,26 +28,26 @@
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>Application</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
-    <PlatformToolset>v142</PlatformToolset>
+    <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
   </PropertyGroup>
@@ -75,15 +75,15 @@
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
     <LinkIncremental>true</LinkIncremental>
-    <IncludePath>../common/libs/zlib;libs/CLI11/;libs/kmc_api/;libs/edlib/;libs/mimalloc/;$(VC_IncludePath);$(WindowsSDK_IncludePath);</IncludePath>
+    <IncludePath>../common/libs/zlib;libs/CLI11/;libs/kmc_api/;libs/edlib/;libs/mimalloc/include;$(VC_IncludePath);$(WindowsSDK_IncludePath);</IncludePath>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
     <LinkIncremental>false</LinkIncremental>
     <IncludePath>libs/CLI11/;libs/zlib/;libs/kmc_api/;libs/edlib/;libs/mimalloc/;$(VC_IncludePath);$(WindowsSDK_IncludePath);</IncludePath>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
     <LinkIncremental>false</LinkIncremental>
-    <IncludePath>libs/CLI11/;../common/libs/zlib/;libs/kmc_api/;libs/edlib/;libs/mimalloc/;$(VC_IncludePath);$(WindowsSDK_IncludePath);</IncludePath>
+    <IncludePath>libs/CLI11/;../common/libs/zlib/;libs/kmc_api/;libs/edlib/;libs/mimalloc/include;$(VC_IncludePath);$(WindowsSDK_IncludePath);</IncludePath>
   </PropertyGroup>
   <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
     <ClCompile>
@@ -186,6 +186,7 @@
     <ClCompile Include="libs\kmc_api\kmer_api.cpp" />
     <ClCompile Include="libs\kmc_api\mmer.cpp" />
     <ClCompile Include="libs\md5\md5.c" />
+    <ClCompile Include="libs\mimalloc\src\static.c" />
     <ClCompile Include="main.cpp" />
     <ClCompile Include="override-new-delete.cpp" />
     <ClCompile Include="pooled_threads.cpp" />
@@ -246,14 +247,6 @@
   </ItemGroup>
   <ItemGroup>
     <Library Include="..\common\libs\zlib\zlibstat.lib" />
-    <Library Include="libs\mimalloc\mimalloc-static-debug.lib">
-      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild>
-      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</ExcludedFromBuild>
-    </Library>
-    <Library Include="libs\mimalloc\mimalloc-static.lib">
-      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild>
-      <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</ExcludedFromBuild>
-    </Library>
   </ItemGroup>
   <ItemGroup>
     <ProjectReference Include="..\filtering-KMC\kmer_counter.vcxproj">

diff --git a/src/colord/colord.vcxproj.filters b/src/colord/colord.vcxproj.filters
@@ -37,6 +37,9 @@
     <Filter Include="libs\md5">
       <UniqueIdentifier>{13e7a6b7-2caf-409c-8619-d18be35be574}</UniqueIdentifier>
     </Filter>
+    <Filter Include="libs\mimalloc">
+      <UniqueIdentifier>{eb946dda-8c53-4c13-a57e-86f122dfc350}</UniqueIdentifier>
+    </Filter>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="main.cpp">
@@ -126,6 +129,9 @@
     <ClCompile Include="decompression_common.cpp">
       <Filter>Source Files</Filter>
     </ClCompile>
+    <ClCompile Include="libs\mimalloc\src\static.c">
+      <Filter>libs\mimalloc</Filter>
+    </ClCompile>
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="params.h">
@@ -265,8 +271,6 @@
     </ClInclude>
   </ItemGroup>
   <ItemGroup>
-    <Library Include="libs\mimalloc\mimalloc-static.lib" />
-    <Library Include="libs\mimalloc\mimalloc-static-debug.lib" />
     <Library Include="..\common\libs\zlib\zlibstat.lib" />
   </ItemGroup>
 </Project>
diff --git a/src/colord/libs/mimalloc b/src/colord/libs/mimalloc
diff --git a/src/colord/libs/mimalloc/libmimalloc.a b/src/colord/libs/mimalloc/libmimalloc.a
diff --git a/src/colord/libs/mimalloc/libmimalloc.mac.a b/src/colord/libs/mimalloc/libmimalloc.mac.a