fix: added version message to publish

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, args.remote_url)
+    phen.publish(args.phen_dir, args.msg, 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(
+        "-m", "--msg", help="Message to include with the published version"
+    )
     phen_publish_parser.add_argument(
         "-r", "--remote_url", help="URL to remote git repository"
     )

acmc/phen.py

@@ -766,7 +766,7 @@ 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, remote_url):
+def publish(phen_dir, msg, remote_url):
     """Publishes updates to the phenotype by commiting all changes to the repo directory"""
 
     # Validate config
@@ -821,7 +821,9 @@ def publish(phen_dir, remote_url):
     # Create and push the tag
     if version in repo.tags:
         raise Exception(f"Tag {version} already exists in repo {phen_path}")
-    repo.create_tag(version, message=f"Release {version}")
+    if msg is None:
+        msg = f"Release {version}"
+    repo.create_tag(version, message=msg)
     logger.info(f"New version: {version}")
 
     # push to origin if a remote repo

docs/usage.md

@@ -108,7 +108,8 @@ 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
+  - `-m`, `--msg`: (Optional) Message to include with the published version- 
+  - `-r`, `--remote_url`: (Optional) URL to a remote git repository, only supports an empty repo without existing commits.
 
 - **Copy Phenotype Configuration**
 

tests/test_acmc.py

@@ -109,10 +109,20 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
             main.main()
         assert "Phenotype processed successfully" in caplog.text
 
-    # publish phenotype
+    # publish phenotype with version message
     with caplog.at_level(logging.DEBUG):
         monkeypatch.setattr(
-            sys, "argv", ["main.py", "phen", "publish", "-d", str(phen_path.resolve())]
+            sys,
+            "argv",
+            [
+                "main.py",
+                "phen",
+                "publish",
+                "-d",
+                str(phen_path.resolve()),
+                "-m",
+                "version message",
+            ],
         )
         main.main()
     assert "Phenotype published successfully" in caplog.text