Remove redundant compression step

src/kg_bioportal/cli.py

@@ -209,22 +209,15 @@ def transform(input_dir, output_dir, compress) -> None:
     "--input_dir", "-i", default="data/transformed", type=click.Path(exists=True)
 )
 @click.option("--output_dir", "-o", default="data/merged")
-@click.option(
-    "--compress",
-    "-c",
-    is_flag=True,
-    default=True,
-    help="If true, compresses the output nodes and edges to tar.gz. Defaults to True.",
-)
 def merge(input_dir, output_dir, compress) -> None:
     """Merges all edges and nodes in the input directory to a single KGX graph.
 
+    Compresses all nodes and edges to tar.gz.
     Yields one log files: merged_graph_stats.yaml.
 
     Args:
         input_dir: A string pointing to the directory to import data from.
         output_dir: A string pointing to the directory to output data to.
-        compress: If true, compresses the output nodes and edges to tar.gz. Defaults to True.
 
     Returns:
         None.

src/kg_bioportal/merger.py

@@ -37,7 +37,7 @@ def __init__(
 
         return None
 
-    def merge_all(self, compress: bool) -> None:
+    def merge_all(self) -> None:
         """Merges all ontologies in the input directory to a single graph.
 
         Yields one log files: merged_graph_stats.yaml.
@@ -97,7 +97,7 @@ def merge_all(self, compress: bool) -> None:
 
         for filepath in filepaths:
             ontology_name = filepath[0]
-            success, nodecount, edgecount = self.merge(nodelist, edgelist, compress)
+            success, nodecount, edgecount = self.merge(nodelist, edgelist)
             if not success:
                 logging.error("Error in merging.")
                 status = False
@@ -108,7 +108,7 @@ def merge_all(self, compress: bool) -> None:
         return None
 
     def merge(
-        self, nodelist: List[str], edgelist: List[str], compress: bool
+        self, nodelist: List[str], edgelist: List[str]
     ) -> Tuple[bool, int, int]:
         """Merge graph files using cat_merge.
 
@@ -139,14 +139,6 @@ def merge(
             qc_report=True,
         )
 
-        if compress:
-            logging.info("Compressing merged graph.")
-            with tarfile.open(
-                os.path.join(self.output_dir, "merged_graph.tar.gz"), "w:gz"
-            ) as tar:
-                tar.add(os.path.join(self.output_dir, "kg_bioportal_nodes.tsv"))
-                tar.add(os.path.join(self.output_dir, "kg_bioportal_edges.tsv"))
-
         return status, nodecount, edgecount
 
     def decompress(