Refactor function names and update build (#118)

* Update data dir location,refactor main function name,remove autoconf
and update INSTALL.txt.

* Also remove code coverage upload from workflow due to errors.

Author: srirampc

.github/workflows/main.yml

@@ -17,6 +17,7 @@ env:
 
 jobs:
   Build-Test:
+    permissions: write-all
     # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
     runs-on: ubuntu-latest
 
@@ -65,13 +66,13 @@ jobs:
       working-directory: ${{github.workspace}}/build
       run: make lcov2
     # Reporting code coverage
-    - name: Report code coverage
-      uses: zgosalvez/github-actions-report-lcov@v2
-      with:
-        working-directory: ${{github.workspace}}/build
-        coverage-files: ${{github.workspace}}/build/coverage.info
-        artifact-name: code-coverage-report
-        github-token: ${{ secrets.GITHUB_TOKEN }}
+    #- name: Report code coverage
+    #  uses: zgosalvez/github-actions-report-lcov@v3
+    #  with:
+    #    working-directory: ${{github.workspace}}/build
+    #    coverage-files: ${{github.workspace}}/build/coverage.info
+    #    artifact-name: code-coverage-report
+    #    github-token: ${{ secrets.GITHUB_TOKEN }}
     # Uploading to Codecov
     - name: Upload coverage reports to codecov.io
       uses: codecov/codecov-action@v3

CMakeLists.txt

@@ -9,7 +9,7 @@ add_executable(FastANI src/cgi/core_genome_identity.cpp src/cgi/main.cpp)
 target_include_directories(FastANI PUBLIC "src/")
 #
 # by default, static linking
-option(GSL_SHARED "Build using shared libraries" OFF)
+option(GSL_SHARED "Build using shared libraries" ON)
 option(BUILD_TESTING "Build tests" ON) # build tests
 #
 # zlib dependency
@@ -70,7 +70,7 @@ if(${BUILD_TESTING})
                           ${OpenMP_CXX_LIBRARIES}
                           gcov)
     catch_discover_tests(FastANITest)
-    file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    file(COPY tests/data DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
     add_custom_target(lcov lcov -c -d .. -o FastANITest.out
                         COMMAND genhtml -o ../lcov/ FastANITest.out
                         DEPENDS FastANITest)
@@ -81,6 +81,8 @@ if(${BUILD_TESTING})
                         DEPENDS FastANITest)
 endif(${BUILD_TESTING})
 
+install(TARGETS FastANI DESTINATION bin)
+
 set(CPACK_GENERATOR "TGZ")
 set(CPACK_SOURCE_GENERATOR "TGZ")
 set(CPACK_PACKAGE_DIRECTORY ${PROJECT_BINARY_DIR}/package)

INSTALL.txt

@@ -3,11 +3,11 @@ which is available in GCC >= 4.8 (on linux) and Clang >= 3.3 (on mac)
 
 Dependencies:
 -------------
-   - Autoconf ( http://www.gnu.org/software/autoconf/ )
+   - CMake 3.2 or above ( https://cmake.org/ )
    - either...
        GNU Scientific Library ( http://www.gnu.org/software/gsl/ )
      or..
-       Boost Library ( http://www.boost.org ) (see "-with-boost" below)
+       Boost Library ( http://www.boost.org ) (see "-DBOOST_ROOT" below)
    - Zlib ( included with OS X and most Linuxes, http://www.zlib.net ) *
    - C++ compiler with C++11 and openmp support
        Note for macOS users: Use "libomp" to link openmp with Clang
@@ -16,34 +16,32 @@ Dependencies:
 
 Steps:
 ------
-   ./bootstrap.sh
-   ./configure [--prefix=...] [--with-gsl=...] [--with-boost=...]
-   make
+   mkdir build 
+   cd build
+   cmake .. -DCMAKE_BUILD_TYPE=Release [--install-prefix ...  -DGSL_SHARED=... -DGSL_ROOT_DIR=... -DBOOST_ROOT=...]
+   cmake --build .
 
 
 Products:
 ---------
-   - Executable fastANI
+   - Executable fastANI built in the build directory
 
 
-
-Configure options:
-------------------
---prefix=</path/to/install>
+cmake configure options:
+-----------------------------
+--install-prefix </path/to/install>
   Installs binaries to bin/ and libraries to lib/ within this path. The default
   is /usr/local/, which will typically require sudo for make install. Must be
   absolute path.
---with-gsl=</path/to/gsl/>
+  lib/.
+-DGSL_ROOT_DIR=</path/to/gsl_dir>
   Where to find the GNU Scientific library install if not in the default
   location (/usr/local). Must be absolute path and should not include bin/ or
-  lib/.
---enable-static-gsl
+-DGSL_SHARED=OFF
   Statically link the GNU Scientific library instead of dynamically. Be mindful
   of licensure if distributing.
---with-boost=</path/to/boost/>
+-DBOOST_ROOT=</path/to/boost/>
   Use Boost from this location, instead of GSL. Must be absolute path and should
   not include bin/ or lib/. Will be statically linked. Be mindful of licensure
   if distributing.
 
-* If Zlib is not installed in a standard system location (it usually is),
-  CXXFLAGS and LDFLAGS will have to be modified before making.

src/cgi/core_genome_identity.cpp

@@ -24,7 +24,7 @@ inline bool file_exists (const std::string& name) {
     return f.good();
 }
 
-int cgi_main(int argc, char **argv)
+int core_genome_identity(int argc, char **argv)
 {
   /*
    * Make sure env variable MALLOC_ARENA_MAX is unset 

src/cgi/main.cpp

@@ -2,8 +2,8 @@
 // Created by srirampc on 11/30/22.
 //
 
-int cgi_main(int argc, char **argv);
+int core_genome_identity(int argc, char **argv);
 
 int main(int argc, char** argv) {
-    return cgi_main(argc, argv);
+    return core_genome_identity(argc, argv);
 }