From 456b74405f74ea218d8ab4b5d90635bd7ca17485 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Wed, 10 Jul 2024 09:42:40 -0400
Subject: [PATCH] refactor: remove _internal directories

close #407

* Remove _internal directories and move files up a directory
---
 src/ga4gh/core/__init__.py                    | 35 +++++++++++++++----
 src/ga4gh/core/_internal/__init__.py          |  0
 src/ga4gh/core/{_internal => }/digests.py     |  0
 src/ga4gh/core/{_internal => }/enderef.py     |  0
 src/ga4gh/core/{_internal => }/identifiers.py |  0
 src/ga4gh/core/{_internal => }/models.py      |  0
 src/ga4gh/core/{_internal => }/pydantic.py    |  0
 src/ga4gh/vrs/__init__.py                     | 11 ++++--
 src/ga4gh/vrs/{_internal => }/enderef.py      |  0
 src/ga4gh/vrs/{_internal => }/models.py       |  4 +--
 src/ga4gh/vrs/normalize.py                    |  2 +-
 11 files changed, 40 insertions(+), 12 deletions(-)
 delete mode 100644 src/ga4gh/core/_internal/__init__.py
 rename src/ga4gh/core/{_internal => }/digests.py (100%)
 rename src/ga4gh/core/{_internal => }/enderef.py (100%)
 rename src/ga4gh/core/{_internal => }/identifiers.py (100%)
 rename src/ga4gh/core/{_internal => }/models.py (100%)
 rename src/ga4gh/core/{_internal => }/pydantic.py (100%)
 rename src/ga4gh/vrs/{_internal => }/enderef.py (100%)
 rename src/ga4gh/vrs/{_internal => }/models.py (99%)

diff --git a/src/ga4gh/core/__init__.py b/src/ga4gh/core/__init__.py
index 77466e15..640b2411 100644
--- a/src/ga4gh/core/__init__.py
+++ b/src/ga4gh/core/__init__.py
@@ -2,20 +2,43 @@
 
 """
 
-import warnings
 from importlib.metadata import version, PackageNotFoundError
 
-from ._internal.digests import sha512t24u
-from ._internal.enderef import ga4gh_enref, ga4gh_deref
-from ._internal.identifiers import (
+from .digests import sha512t24u
+from .enderef import ga4gh_enref, ga4gh_deref
+from .identifiers import (
     ga4gh_digest, ga4gh_identify, ga4gh_serialize, is_ga4gh_identifier,
     parse_ga4gh_identifier, VrsObjectIdentifierIs, use_ga4gh_compute_identifier_when,
     CURIE_NAMESPACE, CURIE_SEP, GA4GH_PREFIX_SEP, GA4GH_IR_REGEXP, GA4GH_DIGEST_REGEXP
 )
-from ._internal.pydantic import (
+from .pydantic import (
     is_pydantic_instance, is_curie_type, is_ga4gh_identifiable, is_literal, pydantic_copy
 )
-from ._internal import models as common_models
+from . import models as common_models
+
+__all__ = [
+    "sha512t24u",
+    "ga4gh_enref",
+    "ga4gh_deref",
+    "ga4gh_digest",
+    "ga4gh_identify",
+    "ga4gh_serialize",
+    "is_ga4gh_identifier",
+    "parse_ga4gh_identifier",
+    "VrsObjectIdentifierIs",
+    "use_ga4gh_compute_identifier_when",
+    "CURIE_NAMESPACE",
+    "CURIE_SEP",
+    "GA4GH_PREFIX_SEP",
+    "GA4GH_IR_REGEXP",
+    "GA4GH_DIGEST_REGEXP",
+    "is_pydantic_instance",
+    "is_curie_type",
+    "is_ga4gh_identifiable",
+    "is_literal",
+    "pydantic_copy",
+    "common_models"
+]
 
 try:
     __version__ = version(__name__)
diff --git a/src/ga4gh/core/_internal/__init__.py b/src/ga4gh/core/_internal/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/src/ga4gh/core/_internal/digests.py b/src/ga4gh/core/digests.py
similarity index 100%
rename from src/ga4gh/core/_internal/digests.py
rename to src/ga4gh/core/digests.py
diff --git a/src/ga4gh/core/_internal/enderef.py b/src/ga4gh/core/enderef.py
similarity index 100%
rename from src/ga4gh/core/_internal/enderef.py
rename to src/ga4gh/core/enderef.py
diff --git a/src/ga4gh/core/_internal/identifiers.py b/src/ga4gh/core/identifiers.py
similarity index 100%
rename from src/ga4gh/core/_internal/identifiers.py
rename to src/ga4gh/core/identifiers.py
diff --git a/src/ga4gh/core/_internal/models.py b/src/ga4gh/core/models.py
similarity index 100%
rename from src/ga4gh/core/_internal/models.py
rename to src/ga4gh/core/models.py
diff --git a/src/ga4gh/core/_internal/pydantic.py b/src/ga4gh/core/pydantic.py
similarity index 100%
rename from src/ga4gh/core/_internal/pydantic.py
rename to src/ga4gh/core/pydantic.py
diff --git a/src/ga4gh/vrs/__init__.py b/src/ga4gh/vrs/__init__.py
index fdd445d7..adbec052 100644
--- a/src/ga4gh/vrs/__init__.py
+++ b/src/ga4gh/vrs/__init__.py
@@ -5,10 +5,15 @@
 from importlib.metadata import version, PackageNotFoundError
 
 from .normalize import normalize
-from ._internal.enderef import vrs_deref, vrs_enref
-from ._internal import models
+from .enderef import vrs_deref, vrs_enref
+from . import models
 
-__all__ = """models normalize schema_path vrs_deref vrs_enref""".split()
+__all__ = [
+    "normalize",
+    "vrs_deref",
+    "vrs_enref",
+    "models"
+]
 
 try:
     __version__ = version(__name__)
diff --git a/src/ga4gh/vrs/_internal/enderef.py b/src/ga4gh/vrs/enderef.py
similarity index 100%
rename from src/ga4gh/vrs/_internal/enderef.py
rename to src/ga4gh/vrs/enderef.py
diff --git a/src/ga4gh/vrs/_internal/models.py b/src/ga4gh/vrs/models.py
similarity index 99%
rename from src/ga4gh/vrs/_internal/models.py
rename to src/ga4gh/vrs/models.py
index 44ca885b..e0f304da 100644
--- a/src/ga4gh/vrs/_internal/models.py
+++ b/src/ga4gh/vrs/models.py
@@ -19,11 +19,11 @@
 
 from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer
 
-from ga4gh.core._internal.pydantic import (
+from ga4gh.core.pydantic import (
     is_ga4gh_identifiable,
     getattr_in
 )
-from ga4gh.core._internal.models import IRI, Expression, _DomainEntity
+from ga4gh.core.models import IRI, Expression, _DomainEntity
 
 
 def flatten(vals):
diff --git a/src/ga4gh/vrs/normalize.py b/src/ga4gh/vrs/normalize.py
index 33dc70a5..41389937 100644
--- a/src/ga4gh/vrs/normalize.py
+++ b/src/ga4gh/vrs/normalize.py
@@ -11,7 +11,7 @@
 from bioutils.normalize import normalize as _normalize, NormalizationMode
 from ga4gh.core import is_pydantic_instance, ga4gh_digest, pydantic_copy
 
-from ._internal import models
+from . import models
 from .dataproxy import SequenceProxy