update the setup scripts

MANIFEST.in

@@ -1,6 +1,7 @@
 # Include C++ source files
 include src/cpp/*.cpp
 include src/cpp/*.hpp
+include src/cpp/*.h
 
 # Include other necessary files
 include LICENSE.txt

Makefile

@@ -7,14 +7,14 @@ SRC_DIR = src/cpp
 BIN_DIR = src/yacht
 
 # Source files
-SRC_FILES = $(SRC_DIR)/yacht_train_core.cpp $(SRC_DIR)/utils.cpp $(SRC_DIR)/compute_similarity.cpp
+SRC_FILES = $(SRC_DIR)/yacht_train_core.cpp $(SRC_DIR)/utils.cpp $(SRC_DIR)/yacht_run_compute_similarity.cpp
 
 # Object files
 OBJ_FILES = $(SRC_FILES:.cpp=.o)
 
 # target executable
-TARGET1 = $(BIN_DIR)/run_yacht_train_core
-TARGET2 = $(BIN_DIR)/run_compute_similarity
+TARGET1 = $(BIN_DIR)/yacht_train_core
+TARGET2 = $(BIN_DIR)/yacht_run_compute_similarity
 
 # Build rules
 all: $(TARGET1) $(TARGET2)
@@ -23,7 +23,7 @@ $(TARGET1): $(OBJ_FILES)
 	$(CXX) $(CXXFLAGS) $(SRC_DIR)/yacht_train_core.cpp $(SRC_DIR)/utils.cpp -o $(TARGET1)
 
 $(TARGET2): $(OBJ_FILES)
-	$(CXX) $(CXXFLAGS) $(SRC_DIR)/compute_similarity.cpp $(SRC_DIR)/utils.cpp -o $(TARGET2)
+	$(CXX) $(CXXFLAGS) $(SRC_DIR)/yacht_run_compute_similarity.cpp $(SRC_DIR)/utils.cpp -o $(TARGET2)
 
 %.o: %.cpp
 	$(CXX) $(CXXFLAGS) -c $< -o $@

build_windows.bat

@@ -1,21 +1,41 @@
 @echo off
+setlocal enabledelayedexpansion
 
-REM Set up paths for directories
+rem Set up paths for directories
 set SRC_DIR=src\cpp
 set BIN_DIR=src\yacht
 
-REM Create bin directory if it doesn't exist
+rem Create bin directory if it doesn't exist
 if not exist %BIN_DIR% (
     mkdir %BIN_DIR%
 )
 
-REM Compile the main.cpp file using g++ from MinGW or another suitable compiler
-g++ -std=c++17 -Wsign-compare -Wall -O3 -o %BIN_DIR%\run_yacht_train_core.exe %SRC_DIR%\main.cpp
+rem Compile source files into object files
+set OBJ_FILES=
+for %%f in (%SRC_DIR%\*.cpp) do (
+    g++ -std=c++17 -Wall -O3 -Wsign-compare -c %%f -o %%~nf.o
+    if %errorlevel% neq 0 (
+        echo Compilation failed for %%f!
+        exit /b %errorlevel%
+    )
+    set OBJ_FILES=!OBJ_FILES! %%~nf.o
+)
+
+rem Create yacht_train_core.exe
+g++ %OBJ_FILES% -o %BIN_DIR%\yacht_train_core.exe
+if %errorlevel% neq 0 (
+    echo Linking failed for yacht_train_core.exe!
+    exit /b %errorlevel%
+)
 
-REM Check if compilation succeeded
+rem Create yacht_run_compute_similarity.exe
+g++ %OBJ_FILES% -o %BIN_DIR%\yacht_run_compute_similarity.exe
 if %errorlevel% neq 0 (
-    echo Compilation failed!
+    echo Linking failed for yacht_run_compute_similarity.exe!
     exit /b %errorlevel%
 )
 
-echo Compilation successful. Executable created at %BIN_DIR%\run_yacht_train_core.exe
+rem Clean up object files
+del *.o
+
+echo Compilation successful. Executables created in %BIN_DIR%.

env/yacht_env.yml

@@ -20,7 +20,6 @@ dependencies:
   - pytaxonkit
   - requests
   - pip
-  - sourmash_plugin_branchwater
   - pip:
     - openpyxl
     - ruff

setup.py

@@ -30,15 +30,24 @@ def run(self):
                 print(f"Error during Unix compilation: {e}")
                 raise e
 
-        # Move the compiled binary to the correct location for packaging
-        compiled_binary = os.path.join('src', 'yacht', 'run_yacht_train_core')
-        if os.path.exists(compiled_binary):
+        # Move the compiled binary files to the correct location for packaging
+        compiled_binary1 = os.path.join('src', 'yacht', 'yacht_train_core')
+        compiled_binary2 = os.path.join('src', 'yacht', 'yacht_run_compute_similarity')
+        if os.path.exists(compiled_binary1):
             destination = os.path.join(self.build_lib, 'yacht')
             os.makedirs(destination, exist_ok=True)
-            shutil.move(compiled_binary, destination)
+            shutil.move(compiled_binary1, destination)
         else:
             print("Compiled binary not found after build step.")
-            raise FileNotFoundError("The executable 'run_yacht_train_core' was not generated successfully.")
+            raise FileNotFoundError("The executable 'yacht_train_core' was not generated successfully.")
+
+        if os.path.exists(compiled_binary2):
+            destination = os.path.join(self.build_lib, 'yacht')
+            os.makedirs(destination, exist_ok=True)
+            shutil.move(compiled_binary2, destination)
+        else:
+            print("Compiled binary not found after build step.")
+            raise FileNotFoundError("The executable 'yacht_run_compute_similarity' was not generated successfully.")
 
         # Run the usual build_ext logic (necessary to continue with setuptools)
         super().run()