also check for presence of assembly.py before waiving clone of viral-…

…core

docs/conf.py

@@ -44,12 +44,17 @@ def _git_version():
 # -- Obtain upstream viral-core module: this is super hacky and not pinned to any version
 def _get_viral_core():
     viral_core_dir = os.path.abspath('viral-core')
-    if not os.path.isdir(viral_core_dir):
-        cmd = ['git', 'clone', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
-        subprocess.check_call(cmd)
-    else: # else fetch latest
+
+    # if the viral-core dir and its file exist, pull the latest
+    if os.path.exists(os.path.join(viral_core_dir,"assembly.py")): # ToDo: check if empty instead
         cmd = ['git', '-C', viral_core_dir, 'pull', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
         subprocess.check_call(cmd)
+    # otherwise clone viral-core, removing the viral-core directory if present
+    else:
+        if os.path.isdir(viral_core_dir):
+            os.remove(viral_core_dir, missing_ok=True)
+            cmd = ['git', 'clone', '--depth=1', 'https://github.com/broadinstitute/viral-core.git']
+            subprocess.check_call(cmd)
 
     viral_core_parent_dir = os.path.dirname(os.path.abspath('viral-core'))
     if viral_core_parent_dir not in sys.path: