🚚 Deprecate the --schema argument of lamin init in favor of `--mo…

…dules` (#185)

bionty/__init__.py

@@ -9,7 +9,7 @@
 Install and mount `bionty` in a new instance:
 
 >>> pip install 'bionty'
->>> lamin init --storage <storage_name> --schema bionty
+>>> lamin init --storage <storage_name> --modules bionty
 
 Import the package:
 

bionty/_bionty.py

@@ -77,10 +77,10 @@ def get_source_record(
     from .models import Source
 
     if public_ontology.__class__.__name__ == "StaticReference":
-        entity_name = registry.__get_name_with_schema__()
+        entity_name = registry.__get_name_with_module__()
     else:
         entity_name = (
-            f"{registry.__get_schema_name__()}.{public_ontology.__class__.__name__}"
+            f"{registry.__get_module_name__()}.{public_ontology.__class__.__name__}"
         )
     kwargs = {
         "entity": entity_name,

bionty/core/_bionty.py

@@ -99,7 +99,7 @@ def filter_bionty_df_columns(
 
 def _prepare_bionty_df(model: type[Record], bionty_df: pd.DataFrame):
     """Prepare the bionty DataFrame to match the model fields."""
-    if model.__get_name_with_schema__() == "bionty.Gene":
+    if model.__get_name_with_module__() == "bionty.Gene":
         # groupby ensembl_gene_id and concat ncbi_gene_ids
         groupby_id_col = (
             "ensembl_gene_id" if "ensembl_gene_id" in bionty_df else "stable_id"

bionty/models.py

@@ -293,7 +293,7 @@ def add_source(cls, source: Source, currently_used=True) -> Source:
         import lamindb as ln
 
         unique_kwargs = {
-            "entity": cls.__get_name_with_schema__(),
+            "entity": cls.__get_name_with_module__(),
             "name": source.name,
             "version": source.version,
             "organism": source.organism,
@@ -392,7 +392,7 @@ def public(
         except (AttributeError, ValueError):
             if source is None:
                 kwargs = {
-                    "entity": cls.__get_name_with_schema__(),
+                    "entity": cls.__get_name_with_module__(),
                     "currently_used": True,
                 }
                 if organism is not None:

noxfile.py

@@ -16,7 +16,7 @@ def lint(session: nox.Session) -> None:
 @nox.session
 @nox.parametrize("group", ["bionty-unit", "bionty-docs"])
 def build(session: nox.Session, group: str):
-    branch = "migrate" if IS_PR else "main"  # point back to "release"
+    branch = "main" if IS_PR else "main"  # point back to "release"
     install_lamindb(session, branch=branch)
     session.run(*"uv pip install --system -e .[dev]".split())
 
@@ -25,5 +25,5 @@ def build(session: nox.Session, group: str):
         session.run(*f"pytest {coverage_args} ./tests".split())
     elif group == "bionty-docs":
         session.run(*f"pytest -s {coverage_args} ./docs/guide".split())
-        run(session, "lamin init --storage ./docsbuild --schema bionty")
+        run(session, "lamin init --storage ./docsbuild --modules bionty")
         build_docs(session, strict=False)