Merge branch...

Merge branch '35-feature-add-support-or-document-how-to-connect-local-repo-to-remote-origin' into 'dev'

feature: added -r option to connect to a remote repo on publication. This is a...

Closes #35

See merge request meldb/concepts-processing!21

acmc/main.py

@@ -53,7 +53,7 @@ def phen_export(args):
 
 def phen_publish(args):
     """Handle the `phen publish` command."""
-    phen.publish(args.phen_dir)
+    phen.publish(args.phen_dir, args.remote_url)
 
 
 def phen_copy(args):
@@ -203,6 +203,9 @@ def main():
         default=str(phen.DEFAULT_PHEN_PATH.resolve()),
         help="Phenotype workspace directory",
     )
+    phen_publish_parser.add_argument(
+        "-r", "--remote_url", help="URL to remote git repository"
+    )
     phen_publish_parser.set_defaults(func=phen_publish)
 
     # phen copy

acmc/phen.py

@@ -285,6 +285,9 @@ def init(phen_dir, remote_url):
 # Ignore SQLite journal and metadata files
 *.db-journal
 *.sqlite3-journal
+
+# python
+.ipynb_checkpoints
  """
     ignore_path = phen_path / ".gitignore"
     with open(ignore_path, "w") as file:
@@ -749,7 +752,7 @@ def map_target_code_type(phen_path, phenotype, target_code_type):
     logger.info(f"Phenotype processed target code type {target_code_type}")
 
 
-def publish(phen_dir):
+def publish(phen_dir, remote_url):
     """Publishes updates to the phenotype by commiting all changes to the repo directory"""
 
     # Validate config
@@ -801,13 +804,24 @@ def publish(phen_dir):
     logger.info(f"New version: {version}")
 
     # push to origin if a remote repo
+    if remote_url is not None and "origin" not in repo.remotes:
+        repo.create_remote("origin", remote_url)
+
     try:
-        origin = repo.remotes.origin
-        origin.push("main")
-        origin.push(tags=True)
-        logger.debug("Changes pushed to 'origin'.")
-    except AttributeError:
-        logger.debug("No remote named 'origin' found, local repo.")
+        if "origin" in repo.remotes:
+            logger.debug(f"Remote 'origin' is already set {repo.remotes.origin.url}")
+            origin = repo.remotes.origin
+            logger.info(f"Pushing main branch to {repo.remotes.origin.url}")
+            origin.push("main")
+            logger.info(f"Pushing tags to {repo.remotes.origin.url}")
+            origin.push(tags=True)
+            logger.debug("Changes pushed to 'origin'")
+        else:
+            logger.debug("Remote 'origin' is not set")
+    except Exception as e:
+        repo.delete_tag(version)
+        repo.git.reset("--soft", "HEAD~1")
+        raise e
 
     logger.info(f"Phenotype published successfully")
 

docs/usage.md

@@ -108,6 +108,7 @@ The `phen` command is used phenotype-related operations.
   ```
 
   - `-d`, `--phen-dir`: (Optional) Directory of phenotype configuration (the default is ./build/phen).
+  - `-r`, `--remote_url`: (Optional) URL to a remote git repository, only supports an empty repo without existing commits
 
 - **Copy Phenotype Configuration**