Merge pull request #71 from oda-hub/pre-cleanup-galaxy-repo

Pre-cleanup tools repo

odabot/cli.py

@@ -714,21 +714,28 @@ def make_galaxy_tools(obj, dry_run, loop, force, pattern):
     with open(git_credentials) as fd:
         token = fd.read().split(':')[-1].split('@')[0]
 
-    def git_clone_or_update(local_path, remote, branch=None, origin='origin'):
+    def git_clone_or_update(local_path, remote, branch=None, origin='origin', pre_cleanup=False):
         if os.path.isdir(local_path) and os.listdir():
             os.chdir(local_path)
-            if branch is None:
-                # determine the default branch automatically
-                outp = sp.run(['git', 'remote', 'show', origin], check=True, capture_output=True)
-                m = re.search(r'^\s*(\w+ )*HEAD( \w+)*\s?:\s?(?P<branch>\w+)', outp.stdout.decode(), re.MULTILINE)
-                if m is None: 
-                    raise RuntimeError(f"Can't determine default branch for remote {remote}.")
-                branch = m.group('branch')
             try:
+                if branch is None:
+                    # determine the default branch automatically
+                    outp = sp.run(['git', 'remote', 'show', origin], check=True, capture_output=True)
+                    m = re.search(r'^\s*(\w+ )*HEAD( \w+)*\s?:\s?(?P<branch>\w+)', outp.stdout.decode(), re.MULTILINE)
+                    if m is None: 
+                        raise RuntimeError(f"Can't determine default branch for remote {remote}.")
+                    branch = m.group('branch')
+
                 res = sp.run(['git', 'remote', 'get-url', '--push', origin], 
                             check=True, capture_output=True, text=True)
                 if res.stdout.strip() != remote:
                     raise ValueError
+
+                if pre_cleanup:
+                    sp.run(['git', 'restore', '--staged', '.'], check=True)
+                    sp.run(['git', 'restore', '.'], check=True)
+                    sp.run(['git', 'clean', '-fd'], check=True)
+
                 sp.run(['git', 'checkout', branch], check=True)
                 sp.run(['git', 'pull', origin, branch], check=True)
                 sp.run(['git', 'remote', 'update', origin, '--prune'])
@@ -788,7 +795,7 @@ def make_pr(source_repo, source_branch, target_repo, target_branch, title='New P
         oda_bot_runtime["deployed_tools"] = {}
     deployed_tools = oda_bot_runtime["deployed_tools"]
 
-    git_clone_or_update(tools_repo_dir, tools_repo, target_branch)
+    git_clone_or_update(tools_repo_dir, tools_repo, target_branch, pre_cleanup=True)
     os.chdir(tools_repo_dir)
     sp.run(['git', 'config', 'user.name', git_name], check=True)
     sp.run(['git', 'config', 'user.email', git_email], check=True)