abs file path fix + bin folder in package

aphylogeo/alignement.py

@@ -175,6 +175,7 @@ def __init__(self, sequences, makeDebugFiles=False):
             self.rate_similarity
             self.method_similarity
         """
+
         self.sequences = sequences
         self.makeDebugFiles = makeDebugFiles
 
@@ -316,8 +317,8 @@ def muscleAlign(self):
             Values: Aligned sequences
         """
         if sys.platform == "win32":
-            muscle_exe = r"bin/muscle5.1.win64.exe"
-            out_dir = r"bin/tmp/"
+            muscle_exe = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + "\\bin\\muscle5.1.win64.exe"
+            out_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + "\\bin\\tmp"
         elif (sys.platform == "linux1") | (sys.platform == "linux2") | (sys.platform == "linux") | (sys.platform == "darwin"):
             muscle_exe = r"bin/muscle5.1.linux_intel64"
             out_dir = r"bin/tmp/"

pyproject.toml

@@ -5,6 +5,8 @@ description = "A phylogenetic and geographic analysis tool"
 authors = ["'Tahiri Lab'"]
 license = "MIT"
 readme = "README.md"
+repository = "https://github.com/tahiri-lab/aPhyloGeo"
+include = ["bin/**"]
 
 [tool.poetry.dependencies]
 python = ">=3.9.0"
@@ -16,12 +18,12 @@ pyyaml = "^6.0.1"
 pytest = "^7.4.2"
 numpy = "^1.26.0"
 cython = "^3.0.2"
-#pymuscle5 = {git = "https://github.com/althonos/pymuscle5"}
 robinson-foulds = "^1.2"
 ete3 = "^3.1.3"
 dendropy = "^4.6.1"
 textdistance = "^4.6.0"
 
+
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.2"