Merge pull request #8 from chinwobble/remove-windows

Remove windows from CI

Author: sfchen

.github/workflows/ci-cmake.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-13, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-13, macos-14]
     env:
       # Indicates the location of the vcpkg as a Git submodule of the project repository.
       # Not using "VCPKG_ROOT" because a variable with the same name is defined in the VS's
@@ -105,7 +105,6 @@ jobs:
       - name: run benchmarks
         run: |
           ./builds/ninja-multi-vcpkg/Release/fastplong_benchmarks
-        if: runner.os != 'Windows'
 
       - name: run tests
         run: |

CMakeLists.txt

@@ -10,20 +10,21 @@ find_package(benchmark CONFIG REQUIRED)
 find_package(libdeflate CONFIG REQUIRED)
 
 if (MSVC)
-find_package(unofficial-isal CONFIG REQUIRED)
-set(
-    FASTPLONG_LIBS
-    hwy::hwy
-    unofficial::isal::isal
-    $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
-)
+    find_package(unofficial-isal CONFIG REQUIRED)
+    set(
+        FASTPLONG_LIBS
+        hwy::hwy
+        unofficial::isal::isal
+        $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
+    )
 else()
-set(
-    FASTPLONG_LIBS
-    hwy::hwy
-    $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
-    -lisal
-)
+    set(
+        FASTPLONG_LIBS
+        hwy::hwy
+        $<IF:$<TARGET_EXISTS:libdeflate::libdeflate_shared>,libdeflate::libdeflate_shared,libdeflate::libdeflate_static>
+        -lisal
+        -lpthread
+    )
 endif()
 
 if (CMAKE_CXX_COMPILER_ARCHITECTURE_ID MATCHES "x86_64")
@@ -74,48 +75,60 @@ set(
     test/sequence_test.cpp
 )
 include_directories(
+    # intel mac install location
     /usr/local/include
     # arm64 mac install location
     /opt/homebrew/include
 )
 link_directories(
+    # intel mac install location
     /usr/local/lib
     # arm64 mac install location
     /opt/homebrew/lib
 )
 
+add_library(fastplong_core ${FASTPLONG_SOURCES})
+target_link_libraries(
+    fastplong_core PRIVATE
+    ${FASTPLONG_LIBS}
+)
 
 if (NOT MSVC)
     # benchmark target
-    add_executable(fastplong_benchmarks)
-    target_sources(
-        fastplong_benchmarks PRIVATE
+    add_executable(fastplong_benchmarks
         benchmarks/sequence_benchmark.cpp
         test/globals.cpp
-        ${FASTPLONG_SOURCES}
     )
     target_link_libraries(
         fastplong_benchmarks PRIVATE
         ${FASTPLONG_LIBS}
+        fastplong_core
         benchmark::benchmark
         benchmark::benchmark_main
     )
 endif()
 # main target
-add_executable(fastplong src/main.cpp ${FASTPLONG_SOURCES})
+add_executable(fastplong src/main.cpp)
 target_link_libraries(
     fastplong PUBLIC
+    fastplong_core
     ${FASTPLONG_LIBS}
 )
 # tests target
 enable_testing()
 find_package(GTest CONFIG REQUIRED)
-add_executable(fastplong_tests ${FASTPLONG_SOURCES} ${FASTPLONG_TEST_SOURCES})
+add_executable(fastplong_tests ${FASTPLONG_TEST_SOURCES})
 target_link_libraries(
     fastplong_tests PRIVATE
     ${FASTPLONG_LIBS}
+    fastplong_core
     GTest::gtest
     GTest::gtest_main
-    -lpthread
 )
-add_test(fastplong_tests fastplong_tests)
+add_test(fastplong_tests fastplong_tests)
+
+install(TARGETS fastplong
+    CONFIGURATIONS Release
+    RUNTIME
+    DESTINATION bin
+)

CMakePresets.json

@@ -29,12 +29,6 @@
       "displayName": "Build (Release)",
       "description": "Build with Ninja/vcpkg (Release)",
       "configuration": "Release"
-    },
-    {
-      "name": "ninja-vcpkg",
-      "configurePreset": "ninja-multi-vcpkg",
-      "displayName": "Build",
-      "description": "Build with Ninja/vcpkg"
     }
   ],
   "testPresets": [

Makefile

@@ -18,14 +18,15 @@ else
   endef
 endif
 
-CMAKE_FLAGS := -DCMAKE_BUILD_TYPE=$(CMAKE_BUILD_TYPE)
-# Extra CMake flags which extend the default set
-CMAKE_EXTRA_FLAGS := -DCMAKE_TOOLCHAIN_FILE=vcpkg/scripts/buildsystems/vcpkg.cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+build: builds/ninja-multi-vcpkg/build.ninja
+	cmake --build --preset ninja-vcpkg-release
 
-all: build
+clean:
+	cmake --build --preset ninja-vcpkg-release --target clean
 
-build: builds/.ran-cmake
-	cmake --build --preset ninja-vcpkg-release
+install: build
+	cmake --install builds/ninja-multi-vcpkg
+	@echo "Installed."
 
 test: build
 	./builds/ninja-multi-vcpkg/Release/fastplong_tests
@@ -38,13 +39,12 @@ format:
 	find src -name "*.h" | xargs clang-format -i
 
 lint: builds/.ran-cmake
-	python3 scripts/run-clang-tidy.py -p builds/ninja-multi-vcpkg
+	run-clang-tidy -p builds/ninja-multi-vcpkg
 
 vcpkg/.vcpkg-root:
 	git submodule update --init --recursive
 
-builds/.ran-cmake: vcpkg/.vcpkg-root
-	$(CMAKE) -B builds/ninja-multi-vcpkg -G "Ninja Multi-Config" $(CMAKE_FLAGS) $(CMAKE_EXTRA_FLAGS) -S .
-	$(TOUCH) $@
+builds/ninja-multi-vcpkg/build.ninja: vcpkg/.vcpkg-root CMakeLists.txt CMakePresets.json
+	$(CMAKE) --preset "ninja-multi-vcpkg"
 
 .PHONY: lint build test format benchmark

README.md

@@ -1,17 +1,17 @@
 [![install with conda](
 https://anaconda.org/bioconda/fastplong/badges/version.svg)](https://anaconda.org/bioconda/fastplong)
 # fastplong
-Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).   
-If you're searching for tools to preprocess short reads (Illumina, MGI, etc.), please use [fastp](https://github.com/OpenGene/fastp)  
+Ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.).
+If you're searching for tools to preprocess short reads (Illumina, MGI, etc.), please use [fastp](https://github.com/OpenGene/fastp)
 
 - [simple usage](#simple-usage)
 - [examples of report](#examples-of-report)
 - [get fastplong](#get-fastplong)
   - [install with Bioconda](#install-with-bioconda)
   - [download the latest prebuilt binary for Linux users](#download-the-latest-prebuilt-binary-for-linux-users)
   - [or compile from source](#or-compile-from-source)
-    - [Step 1: install isa-l](#step-1-install-isa-l)
-    - [step 2: install libdeflate](#step-2-install-libdeflate)
+    - [Step 1: install build tools](#step-1-install-build-tools)
+    - [Step 2: install isa-l](#step-2-install-isa-l)
     - [Step 3: download and build fastplong](#step-3-download-and-build-fastplong)
 - [input and output](#input-and-output)
   - [output to STDOUT](#output-to-stdout)
@@ -37,7 +37,7 @@ If you're searching for tools to preprocess short reads (Illumina, MGI, etc.), p
 ```
 fastplong -i in.fq -o out.fq
 ```
-Both input and output can be gzip compressed. By default, the HTML report is saved to `fastplong.html` (can be specified with `-h` option), and the JSON report is saved to `fastplong.json` (can be specified with `-j` option). 
+Both input and output can be gzip compressed. By default, the HTML report is saved to `fastplong.html` (can be specified with `-h` option), and the JSON report is saved to `fastplong.json` (can be specified with `-j` option).
 
 # examples of report
 `fastplong` creates reports in both HTML and JSON format.
@@ -64,15 +64,22 @@ mv fastplong.0.2.2 fastplong
 chmod a+x ./fastplong
 ```
 ## or compile from source
-`fastplong` depends on `libdeflate` and `isa-l` for fast decompression and compression of zipped data.
+`fastplong` depends on `ninja-build` and `cmake` for building, and `isa-l` for fast decompression and compression of zipped data.
 
-### Step 1: install isa-l
+### Step 1: install build tools
+To build `fastplong` you will need some build tools.
+```bash
+sudo apt update && sudo apt install cmake make g++ gdb ninja-build curl zip unzip tar pkg-config
+```
+On Mac OSX
+```bash
+brew install ninja cmake make gdb zip unzip pkg-config
+```
+
+### Step 2: install isa-l
 It's recommended that to install it using your package manager, for example `apt install libisal-dev` on ubuntu, or `brew install isa-l` on Mac. Otherwise you can compile it from source. Please be noted that `isa-l` is not compatible with gcc 4.8 or older versions. See https://github.com/intel/isa-l
 `autoconf`, `automake`, `libtools`, `nasm (>=2.11.01)` and `yasm (>=1.2.0)` are required to build isa-l.
 
-### step 2: install libdeflate
-It's recommended that to install it using your package manager, for example `apt install libdeflate-dev` on ubuntu, or `brew install libdeflate` on Mac. Otherwise you can compile it from source. See https://github.com/ebiggers/libdeflate
-
 ### Step 3: download and build fastplong
 ```shell
 # get source (you can also use browser to download from master or releases)
@@ -186,7 +193,7 @@ Specify `--split_by_lines` to limit the lines of each file. The last files may h
 usage: fastplong -i <in> -o <out> [options...]
 fastplong: ultra-fast FASTQ preprocessing and quality control for long reads
 version 0.0.1
-usage: ./fastplong [options] ... 
+usage: ./fastplong [options] ...
 options:
   -i, --in                           read input file name (string [=])
   -o, --out                          read output file name (string [=])