fixed compilation and dependency issues on linux

pyproject.toml

@@ -17,7 +17,6 @@ dependencies = [
     "numpy==1.26.3",
     "networkx==3.1",
     "ete3==3.1.2",
-    "glpk",
     "pyomo==6.7.3",
     "pygraphviz>=1.10",
     "pandas==2.1.1",

tribal.yml

@@ -1,17 +1,17 @@
-name: tribal
+name: test
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python==3.9.19
-  - numpy==1.26.3
-  - pandas==2.1.1
-  - networkx==3.1
-  - pygraphviz==1.10
-  - ete3==3.1.2
+  - python==3.9
+  - numpy>=1.26.3
+  - pandas>=2.1.1
+  - networkx>=3.1
+  - pygraphviz
+  - ete3>=3.1.2
   - pip>=22.3.1
-  - conda-forge::mafft>=7.526
-  - glpk==5.0
+  - conda-forge::mafft==7.526
+  - glpk>=5.0
   - pip:
     - biopython==1.81
 

tribal/backend.py

@@ -17,7 +17,7 @@ def compile_dnapars(self):
             subprocess.run(["cc", "-c", source, "-o", obj], check=True)
 
         # Link the object files to create the executable
-        subprocess.run(["cc", *object_files, "-o", executable], check=True)
+        subprocess.run(["cc", *object_files, "-o", executable, "-lm"], check=True)
 
         # Make the executable globally accessible (optional)
         os.chmod(executable, 0o755)