From 2a33236cedca113f534b7f9ad9328538c903780a Mon Sep 17 00:00:00 2001
From: Alex Wolf <f.alexander.wolf@gmail.com>
Date: Sun, 12 Jan 2025 00:33:02 +0100
Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=9A=20Deprecate=20the=20`--schema`=20a?=
 =?UTF-8?q?rgument=20of=20`lamin=20init`=20in=20favor=20of=20`--modules`?=
 =?UTF-8?q?=20(#185)?=
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Content-Type: text/plain; charset=UTF-8
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---
 bionty/__init__.py     | 2 +-
 bionty/_bionty.py      | 4 ++--
 bionty/core/_bionty.py | 2 +-
 bionty/models.py       | 4 ++--
 noxfile.py             | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/bionty/__init__.py b/bionty/__init__.py
index b2f0a60..9075d19 100644
--- a/bionty/__init__.py
+++ b/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:
 
diff --git a/bionty/_bionty.py b/bionty/_bionty.py
index 19c0170..c4d17fd 100644
--- a/bionty/_bionty.py
+++ b/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,
diff --git a/bionty/core/_bionty.py b/bionty/core/_bionty.py
index 9c561e0..8a84b53 100644
--- a/bionty/core/_bionty.py
+++ b/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"
diff --git a/bionty/models.py b/bionty/models.py
index 889e712..f279668 100644
--- a/bionty/models.py
+++ b/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:
diff --git a/noxfile.py b/noxfile.py
index 6a14f4d..a40999e 100644
--- a/noxfile.py
+++ b/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)