renamed C++ tool to aligncount from Aligncount

Author: vr1087

.github/workflows/cpp_standalone.yml

@@ -37,4 +37,4 @@ jobs:
         run: cmake --build build -j4
 
       - name: run
-        run: ./build/Aligncount --help
+        run: ./build/aligncount --help

cli/entrypoint.py

@@ -33,12 +33,12 @@ def main():
         sys.exit(1)
 
     try:
-        raw = subprocess.check_output(["Aligncount", "-a", args.alignments])
+        raw = subprocess.check_output(["aligncount", "-a", args.alignments])
     except FileNotFoundError:
-        print("Error: C++ binary 'Aligncount' not found in PATH.", file=sys.stderr)
+        print("Error: C++ binary 'aligncount' not found in PATH.", file=sys.stderr)
         sys.exit(1)
     except subprocess.CalledProcessError as e:
-        print(f"Error: 'Aligncount' failed (exit {e.returncode}).", file=sys.stderr)
+        print(f"Error: 'aligncount' failed (exit {e.returncode}).", file=sys.stderr)
         sys.exit(e.returncode)
 
     # Use our new helper to produce the final string to print

conda-recipe/meta.yaml

@@ -1,8 +1,8 @@
-{% set REPO_NAME   = environ.get('REPO_NAME',  'aligncount') %}
-{% set VERSION     = environ.get('VERSION',    '0.2.81') %}
-{% set TAR_URL     = environ.get('TAR_URL',    'https://github.com/vr1087/cpp-python-tool-template/archive/refs/tags/v0.2.81.tar.gz') %}
-{% set SHA256      = environ.get('SHA256',     'b1e10ade2ae4b183d45a554ae9753b925d601aa56cfad797a6a143e873303105') %}
-{% set REPO_HOME   = environ.get('REPO_HOME',  'https://github.com/vr1087/cpp-python-tool-template') %}
+{% set REPO_NAME   = environ.get('REPO_NAME',  '') %}
+{% set VERSION     = environ.get('VERSION',    '') %}
+{% set TAR_URL     = environ.get('TAR_URL',    '') %}
+{% set SHA256      = environ.get('SHA256',     '') %}
+{% set REPO_HOME   = environ.get('REPO_HOME',  '') %}
 
 package:
   name: {{ REPO_NAME }}
@@ -18,12 +18,14 @@ build:
     - CFLAGS
     - CXXFLAGS
   script: |
+    
     # On Linux aarch64 builds we saw undefined pthread symbols (e.g. pthread_join)
     # unless we compile and link with -pthread. Autotools (HTSlib) only picks up
     # Conda headers and flags if CFLAGS/CXXFLAGS and LDFLAGS are exported.
     # On macOS x86 (SDK < 10.15), Clang’s availability annotations block newer
     # libc++ symbols (std::filesystem::path, etc.), so we disable those checks
     # with -D_LIBCPP_DISABLE_AVAILABILITY
+    
     export CFLAGS="-pthread -I${PREFIX}/include $CFLAGS"
     export CXXFLAGS="-pthread -I${PREFIX}/include $CXXFLAGS -D_LIBCPP_DISABLE_AVAILABILITY"
     export LDFLAGS="-pthread ${LDFLAGS}"

cpp/standalone/CMakeLists.txt

@@ -24,7 +24,7 @@ file(GLOB sources CONFIGURE_DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/source/*.cpp)
 
 add_executable(${PROJECT_NAME} ${sources})
 
-set_target_properties(${PROJECT_NAME} PROPERTIES CXX_STANDARD 20 OUTPUT_NAME "Aligncount")
+set_target_properties(${PROJECT_NAME} PROPERTIES CXX_STANDARD 20 OUTPUT_NAME "aligncount")
 
 target_link_libraries(${PROJECT_NAME} Aligncount::Aligncount cxxopts)