Merge pull request #66 from valentynbez/main

CI/CD fixes

mDeepFRI/pdb.py

@@ -37,7 +37,7 @@ def create_pdb_mmseqs():
                        "rb") as f_in, open(uncompressed_path, "wb") as f_out:
             f_out.write(f_in.read())
 
-        tabix_compress(uncompressed_path, compressed_path)
+        tabix_compress(uncompressed_path, compressed_path, force=True)
 
         # remove uncompressed
         uncompressed_path.unlink()
@@ -48,7 +48,7 @@ def create_pdb_mmseqs():
     # check if database exists
     if not pdb100_mmseqs.exists():
         logging.info("Creating MMSeqs2 database from PDB100.")
-        createdb(pdb100_path, pdb100_mmseqs)
+        createdb(compressed_path, pdb100_mmseqs)
         createindex(pdb100_mmseqs)
 
     pdb_db = Database(foldcomp_db=pdb100_path.stem,

mDeepFRI/pipeline.py

@@ -65,15 +65,15 @@ def predict_protein_function(
     # PDB100 database
     logger.info(
         "Creating PDB100 database. This may take a bit during a first run.")
-    try:
-        pdb100 = create_pdb_mmseqs()
-        deepfri_dbs.append(pdb100)
-        logger.info("PDB100 database created.")
-
-    except RuntimeError:
-        logger.warning(
-            "PDB100 server is not responding. Skipping PDB100 database creation."
-        )
+    # try:
+    pdb100 = create_pdb_mmseqs()
+    deepfri_dbs.append(pdb100)
+    logger.info("PDB100 database created.")
+
+    # except RuntimeError:
+    #     logger.warning(
+    #         "PDB100 server is not responding. Skipping PDB100 database creation."
+    #     )
 
     # design solution
     # database is built in the same directory

setup.py

@@ -147,7 +147,7 @@ def run(self):
 PACKAGES = [SRC_DIR]
 
 install_requires = ["cython", "numpy"]
-setup_requires = ["cython"]
+setup_requires = ["cython", "requests"]
 extra_compile_args = ["-std=c++17", "-O3"]
 
 EXTENSIONS = [