Update v2 migration logic. (#856)

* Standardize upgrade command message.

* Fix issue with input prompt disappearing.

* Use _mkdir_p, os.path.join.

* Don't use _mkdir_p. Raise if .signac already exists.

* Update signac/common/config.py

Co-authored-by: Vyas Ramasubramani <vyas.ramasubramani@gmail.com>

signac/contrib/migration/v1_to_v2.py

@@ -47,8 +47,6 @@ def _migrate_v1_to_v2(root_directory):
     """Migrate from schema version 1 to version 2."""
     # Load the v1 config.
     cfg = _load_config_v1(root_directory)
-    fn_doc = os.path.join(root_directory, Project.FN_DOCUMENT)
-    doc = BufferedJSONAttrDict(filename=fn_doc, write_concern=True)
 
     # Try to migrate a custom workspace directory if one exists.
     current_workspace_name = cfg.get("workspace_dir")
@@ -66,8 +64,12 @@ def _migrate_v1_to_v2(root_directory):
             os.replace(current_workspace, new_workspace)
         del cfg["workspace_dir"]
 
-    # Delete project name from config and store in project doc.
-    doc["signac_project_name"] = cfg["project"]
+    # Delete project name from config and store in project doc if non-default.
+    # For default names, no modifications to the project document should be made.
+    if cfg["project"] != "None":
+        fn_doc = os.path.join(root_directory, Project.FN_DOCUMENT)
+        doc = BufferedJSONAttrDict(filename=fn_doc, write_concern=True)
+        doc["signac_project_name"] = cfg["project"]
     del cfg["project"]
     cfg.write()
 
@@ -79,12 +81,10 @@ def _migrate_v1_to_v2(root_directory):
 
     # Now move all other files.
     files_to_move = {
-        ".signac_shell_history": os.sep.join((".signac", "shell_history")),
-        ".signac_sp_cache.json.gz": os.sep.join(
-            (".signac", "statepoint_cache.json.gz")
-        ),
+        ".signac_shell_history": os.path.join(".signac", "shell_history"),
+        ".signac_sp_cache.json.gz": os.path.join(".signac", "statepoint_cache.json.gz"),
     }
     for src, dst in files_to_move.items():
-        src = os.sep.join((root_directory, src))
+        src = os.path.join(root_directory, src)
         if os.path.isfile(src):
-            os.replace(src, os.sep.join((root_directory, dst)))
+            os.replace(src, os.path.join(root_directory, dst))

signac/contrib/project.py

@@ -232,7 +232,7 @@ def _check_schema_compatibility(self):
         elif config_schema_version < schema_version:
             raise IncompatibleSchemaVersion(
                 "The signac schema version used by this project is '{}', but signac {} "
-                "requires schema version '{}'. Please use '$ signac migrate' to "
+                "requires schema version '{}'. Please use 'python -m signac migrate' to "
                 "irreversibly migrate this project's schema to the supported "
                 "version.".format(config_schema_version, __version__, schema_version)
             )

signac/contrib/utility.py

@@ -56,14 +56,13 @@ def _query_yes_no(question, default="yes"):  # pragma: no cover
         raise ValueError("invalid default answer: '%s'" % default)
 
     while True:
-        sys.stdout.write(question + prompt)
-        choice = input().lower()
+        choice = input(question + prompt).lower()
         if default is not None and choice == "":
             return valid[default]
         elif choice in valid:
             return valid[choice]
         else:
-            sys.stdout.write("Please respond with 'yes' or 'no' (or 'y' or 'n').\n")
+            print("Please respond with 'yes' or 'no' (or 'y' or 'n').")
 
 
 def _add_verbosity_argument(parser, default=0):