From ccc09de40071eb996557edb5a3b6072862cc7cfc Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <JLSaunders987@gmail.com>
Date: Tue, 5 Sep 2023 19:25:20 -0700
Subject: [PATCH] refactor nwb_linkml to src layout

---
 .github/workflows/tests.yml                   |  2 +
 hdf5_linkml/tests/test_scratch.py             |  2 +
 nwb_linkml/__init__.py                        |  1 -
 nwb_linkml/adapters/__init__.py               |  4 --
 nwb_linkml/maps/__init__.py                   |  3 -
 poetry.lock => nwb_linkml/poetry.lock         |  0
 pyproject.toml => nwb_linkml/pyproject.toml   |  4 +-
 nwb_linkml/src/nwb_linkml/__init__.py         |  1 +
 .../src/nwb_linkml/adapters/__init__.py       |  1 +
 .../{ => src/nwb_linkml}/adapters/adapter.py  |  0
 .../{ => src/nwb_linkml}/adapters/classes.py  |  4 +-
 .../{ => src/nwb_linkml}/adapters/dataset.py  |  2 +-
 .../{ => src/nwb_linkml}/adapters/group.py    |  2 +-
 .../nwb_linkml}/adapters/namespaces.py        |  0
 .../{ => src/nwb_linkml}/adapters/schema.py   |  3 +-
 .../nwb_linkml}/generators/__init__.py        |  0
 .../nwb_linkml}/generators/pydantic.py        |  2 +-
 .../src/nwb_linkml/io}/__init__.py            |  0
 nwb_linkml/src/nwb_linkml/io/hdf5.py          | 61 +++++++++++++++++++
 nwb_linkml/{ => src/nwb_linkml/io}/io.py      | 10 ++-
 .../{ => src/nwb_linkml}/lang_elements.py     |  2 +-
 nwb_linkml/{ => src/nwb_linkml}/map.py        |  1 -
 nwb_linkml/src/nwb_linkml/maps/__init__.py    |  3 +
 nwb_linkml/{ => src/nwb_linkml}/maps/dtype.py |  0
 .../{ => src/nwb_linkml}/maps/preload.py      |  2 +-
 .../{ => src/nwb_linkml}/maps/quantity.py     |  0
 .../{ => src/nwb_linkml}/models/core.py       |  0
 .../nwb_linkml}/models/core_nwb_base.py       |  0
 .../nwb_linkml}/models/core_nwb_behavior.py   |  0
 .../nwb_linkml}/models/core_nwb_device.py     |  0
 .../nwb_linkml}/models/core_nwb_ecephys.py    |  0
 .../nwb_linkml}/models/core_nwb_epoch.py      |  0
 .../nwb_linkml}/models/core_nwb_file.py       |  0
 .../nwb_linkml}/models/core_nwb_icephys.py    |  0
 .../nwb_linkml}/models/core_nwb_image.py      |  0
 .../nwb_linkml}/models/core_nwb_misc.py       |  0
 .../nwb_linkml}/models/core_nwb_ogen.py       |  0
 .../nwb_linkml}/models/core_nwb_ophys.py      |  0
 .../nwb_linkml}/models/core_nwb_retinotopy.py |  0
 .../nwb_linkml}/models/hdmf_common.py         |  0
 .../nwb_linkml}/models/hdmf_common_base.py    |  0
 .../nwb_linkml}/models/hdmf_common_sparse.py  |  0
 .../nwb_linkml}/models/hdmf_common_table.py   |  0
 .../nwb_linkml}/models/hdmf_experimental.py   |  0
 .../models/hdmf_experimental_experimental.py  |  0
 .../models/hdmf_experimental_resources.py     |  0
 .../nwb_linkml}/models/nwb_language.py        |  0
 nwb_linkml/{ => src/nwb_linkml}/namespaces.py |  0
 nwb_linkml/{ => src/nwb_linkml}/plot.py       |  4 +-
 .../nwb_linkml}/schema/core.nwb.base.yaml     |  0
 .../nwb_linkml}/schema/core.nwb.behavior.yaml |  0
 .../nwb_linkml}/schema/core.nwb.device.yaml   |  0
 .../nwb_linkml}/schema/core.nwb.ecephys.yaml  |  0
 .../nwb_linkml}/schema/core.nwb.epoch.yaml    |  0
 .../nwb_linkml}/schema/core.nwb.file.yaml     |  0
 .../nwb_linkml}/schema/core.nwb.icephys.yaml  |  0
 .../nwb_linkml}/schema/core.nwb.image.yaml    |  0
 .../nwb_linkml}/schema/core.nwb.misc.yaml     |  0
 .../nwb_linkml}/schema/core.nwb.ogen.yaml     |  0
 .../nwb_linkml}/schema/core.nwb.ophys.yaml    |  0
 .../schema/core.nwb.retinotopy.yaml           |  0
 .../{ => src/nwb_linkml}/schema/core.yaml     |  0
 .../nwb_linkml}/schema/hdmf-common.base.yaml  |  0
 .../schema/hdmf-common.sparse.yaml            |  0
 .../nwb_linkml}/schema/hdmf-common.table.yaml |  0
 .../nwb_linkml}/schema/hdmf-common.yaml       |  0
 .../hdmf-experimental.experimental.yaml       |  0
 .../schema/hdmf-experimental.resources.yaml   |  0
 .../nwb_linkml}/schema/hdmf-experimental.yaml |  0
 .../nwb_linkml}/schema/nwb.language.yaml      |  0
 nwb_linkml/{ => src/nwb_linkml}/translate.py  | 10 +--
 nwb_linkml/tests/__init__.py                  |  0
 {tests => nwb_linkml/tests}/fixtures.py       |  6 +-
 nwb_linkml/tests/test_adapters/__init__.py    |  0
 .../tests/test_adapters}/test_adapter.py      |  0
 .../test_adapters}/test_adapter_dataset.py    |  0
 .../test_adapters}/test_adapter_group.py      |  0
 .../test_adapters}/test_adapter_namespaces.py |  0
 .../test_adapters}/test_adapter_schema.py     |  0
 {tests => nwb_linkml/tests}/test_generate.py  |  0
 {tests => nwb_linkml/tests}/test_translate.py |  1 +
 pytest.ini                                    |  2 +-
 scripts/generate_core.py                      |  7 ++-
 83 files changed, 95 insertions(+), 45 deletions(-)
 create mode 100644 hdf5_linkml/tests/test_scratch.py
 delete mode 100644 nwb_linkml/__init__.py
 delete mode 100644 nwb_linkml/adapters/__init__.py
 delete mode 100644 nwb_linkml/maps/__init__.py
 rename poetry.lock => nwb_linkml/poetry.lock (100%)
 rename pyproject.toml => nwb_linkml/pyproject.toml (91%)
 create mode 100644 nwb_linkml/src/nwb_linkml/__init__.py
 create mode 100644 nwb_linkml/src/nwb_linkml/adapters/__init__.py
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/adapter.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/classes.py (98%)
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/dataset.py (99%)
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/group.py (99%)
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/namespaces.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/adapters/schema.py (98%)
 rename nwb_linkml/{ => src/nwb_linkml}/generators/__init__.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/generators/pydantic.py (99%)
 rename {tests => nwb_linkml/src/nwb_linkml/io}/__init__.py (100%)
 create mode 100644 nwb_linkml/src/nwb_linkml/io/hdf5.py
 rename nwb_linkml/{ => src/nwb_linkml/io}/io.py (93%)
 rename nwb_linkml/{ => src/nwb_linkml}/lang_elements.py (98%)
 rename nwb_linkml/{ => src/nwb_linkml}/map.py (96%)
 create mode 100644 nwb_linkml/src/nwb_linkml/maps/__init__.py
 rename nwb_linkml/{ => src/nwb_linkml}/maps/dtype.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/maps/preload.py (87%)
 rename nwb_linkml/{ => src/nwb_linkml}/maps/quantity.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_base.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_behavior.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_device.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_ecephys.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_epoch.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_file.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_icephys.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_image.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_misc.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_ogen.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_ophys.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/core_nwb_retinotopy.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_common.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_common_base.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_common_sparse.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_common_table.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_experimental.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_experimental_experimental.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/hdmf_experimental_resources.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/models/nwb_language.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/namespaces.py (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/plot.py (97%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.base.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.behavior.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.device.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.ecephys.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.epoch.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.file.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.icephys.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.image.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.misc.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.ogen.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.ophys.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.nwb.retinotopy.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/core.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-common.base.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-common.sparse.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-common.table.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-common.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-experimental.experimental.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-experimental.resources.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/hdmf-experimental.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/schema/nwb.language.yaml (100%)
 rename nwb_linkml/{ => src/nwb_linkml}/translate.py (94%)
 create mode 100644 nwb_linkml/tests/__init__.py
 rename {tests => nwb_linkml/tests}/fixtures.py (75%)
 create mode 100644 nwb_linkml/tests/test_adapters/__init__.py
 rename {tests => nwb_linkml/tests/test_adapters}/test_adapter.py (100%)
 rename {tests => nwb_linkml/tests/test_adapters}/test_adapter_dataset.py (100%)
 rename {tests => nwb_linkml/tests/test_adapters}/test_adapter_group.py (100%)
 rename {tests => nwb_linkml/tests/test_adapters}/test_adapter_namespaces.py (100%)
 rename {tests => nwb_linkml/tests/test_adapters}/test_adapter_schema.py (100%)
 rename {tests => nwb_linkml/tests}/test_generate.py (100%)
 rename {tests => nwb_linkml/tests}/test_translate.py (99%)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8f889ac..678619d 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -21,8 +21,10 @@ jobs:
 
       - name: Install dependencies
         run: pip install .[tests] pytest-md pytest-emoji
+        working-directory: nwb_linkml
 
       - uses: pavelzw/pytest-action@v2
+        working-directory: nwb_linkml
         with:
           emoji: true
           verbose: true
diff --git a/hdf5_linkml/tests/test_scratch.py b/hdf5_linkml/tests/test_scratch.py
new file mode 100644
index 0000000..139597f
--- /dev/null
+++ b/hdf5_linkml/tests/test_scratch.py
@@ -0,0 +1,2 @@
+
+
diff --git a/nwb_linkml/__init__.py b/nwb_linkml/__init__.py
deleted file mode 100644
index 2ea95fc..0000000
--- a/nwb_linkml/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from nwb_linkml.maps import preload
\ No newline at end of file
diff --git a/nwb_linkml/adapters/__init__.py b/nwb_linkml/adapters/__init__.py
deleted file mode 100644
index 7647640..0000000
--- a/nwb_linkml/adapters/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from nwb_linkml.adapters.adapter import Adapter
-from nwb_linkml.adapters.namespaces import NamespacesAdapter
-from nwb_linkml.adapters.schema import SchemaAdapter
-from nwb_linkml.adapters.classes import ClassAdapter
\ No newline at end of file
diff --git a/nwb_linkml/maps/__init__.py b/nwb_linkml/maps/__init__.py
deleted file mode 100644
index 6078f74..0000000
--- a/nwb_linkml/maps/__init__.py
+++ /dev/null
@@ -1,3 +0,0 @@
-# Import everything so it's defined, but shoudlnt' necessarily be used from here
-from nwb_linkml.maps.preload import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
-from nwb_linkml.maps.quantity import QUANTITY_MAP
\ No newline at end of file
diff --git a/poetry.lock b/nwb_linkml/poetry.lock
similarity index 100%
rename from poetry.lock
rename to nwb_linkml/poetry.lock
diff --git a/pyproject.toml b/nwb_linkml/pyproject.toml
similarity index 91%
rename from pyproject.toml
rename to nwb_linkml/pyproject.toml
index 35f5fb9..378ad53 100644
--- a/pyproject.toml
+++ b/nwb_linkml/pyproject.toml
@@ -6,8 +6,8 @@ authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
 license = "GPL-3.0"
 readme = "README.md"
 packages = [
-    {include = "nwb_linkml"},
-    {include = "nwb_schema_language", from="nwb_schema_language/src"}
+    {include = "nwb_linkml", from="src"},
+    {include = "nwb_schema_language", from="../nwb_schema_language/src"}
 ]
 
 [tool.poetry.dependencies]
diff --git a/nwb_linkml/src/nwb_linkml/__init__.py b/nwb_linkml/src/nwb_linkml/__init__.py
new file mode 100644
index 0000000..7dc898d
--- /dev/null
+++ b/nwb_linkml/src/nwb_linkml/__init__.py
@@ -0,0 +1 @@
+from nwb_linkml.src.nwb_linkml.maps import preload
\ No newline at end of file
diff --git a/nwb_linkml/src/nwb_linkml/adapters/__init__.py b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
new file mode 100644
index 0000000..03a252b
--- /dev/null
+++ b/nwb_linkml/src/nwb_linkml/adapters/__init__.py
@@ -0,0 +1 @@
+from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
diff --git a/nwb_linkml/adapters/adapter.py b/nwb_linkml/src/nwb_linkml/adapters/adapter.py
similarity index 100%
rename from nwb_linkml/adapters/adapter.py
rename to nwb_linkml/src/nwb_linkml/adapters/adapter.py
diff --git a/nwb_linkml/adapters/classes.py b/nwb_linkml/src/nwb_linkml/adapters/classes.py
similarity index 98%
rename from nwb_linkml/adapters/classes.py
rename to nwb_linkml/src/nwb_linkml/adapters/classes.py
index 64d2615..18d2350 100644
--- a/nwb_linkml/adapters/classes.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/classes.py
@@ -1,15 +1,13 @@
 """
 Adapters to linkML classes
 """
-import pdb
 import re
 from abc import abstractmethod
 from typing import List, Optional
 from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, DTypeType
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
-from nwb_linkml.maps import QUANTITY_MAP
-from nwb_linkml.lang_elements import Arraylike
+from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
 
 CAMEL_TO_SNAKE = re.compile('((?<=[a-z0-9])[A-Z]|(?!^)[A-Z](?=[a-z]))')
 """
diff --git a/nwb_linkml/adapters/dataset.py b/nwb_linkml/src/nwb_linkml/adapters/dataset.py
similarity index 99%
rename from nwb_linkml/adapters/dataset.py
rename to nwb_linkml/src/nwb_linkml/adapters/dataset.py
index f3a5268..f328948 100644
--- a/nwb_linkml/adapters/dataset.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/dataset.py
@@ -11,7 +11,7 @@ from pydantic import PrivateAttr
 from nwb_schema_language import Dataset, ReferenceDtype, CompoundDtype, DTypeType
 from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
 from nwb_linkml.adapters.adapter import BuildResult
-from nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
 
 class DatasetAdapter(ClassAdapter):
     cls: Dataset
diff --git a/nwb_linkml/adapters/group.py b/nwb_linkml/src/nwb_linkml/adapters/group.py
similarity index 99%
rename from nwb_linkml/adapters/group.py
rename to nwb_linkml/src/nwb_linkml/adapters/group.py
index 766dea6..7b84b66 100644
--- a/nwb_linkml/adapters/group.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/group.py
@@ -9,7 +9,7 @@ from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, D
 from nwb_linkml.adapters.classes import ClassAdapter, camel_to_snake
 from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.adapter import BuildResult
-from nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
 
 class GroupAdapter(ClassAdapter):
     cls: Group
diff --git a/nwb_linkml/adapters/namespaces.py b/nwb_linkml/src/nwb_linkml/adapters/namespaces.py
similarity index 100%
rename from nwb_linkml/adapters/namespaces.py
rename to nwb_linkml/src/nwb_linkml/adapters/namespaces.py
diff --git a/nwb_linkml/adapters/schema.py b/nwb_linkml/src/nwb_linkml/adapters/schema.py
similarity index 98%
rename from nwb_linkml/adapters/schema.py
rename to nwb_linkml/src/nwb_linkml/adapters/schema.py
index 277faba..4559624 100644
--- a/nwb_linkml/adapters/schema.py
+++ b/nwb_linkml/src/nwb_linkml/adapters/schema.py
@@ -2,7 +2,6 @@
 Since NWB doesn't necessarily have a term for a single nwb schema file, we're going
 to call them "schema" objects
 """
-import pdb
 from typing import Optional, List, TYPE_CHECKING, Type
 from pathlib import Path
 from pydantic import Field, PrivateAttr
@@ -11,7 +10,7 @@ from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.group import GroupAdapter
 if TYPE_CHECKING:
-    from nwb_linkml.adapters.namespaces import NamespacesAdapter
+    pass
 
 from nwb_schema_language import Group, Dataset
 from typing import NamedTuple
diff --git a/nwb_linkml/generators/__init__.py b/nwb_linkml/src/nwb_linkml/generators/__init__.py
similarity index 100%
rename from nwb_linkml/generators/__init__.py
rename to nwb_linkml/src/nwb_linkml/generators/__init__.py
diff --git a/nwb_linkml/generators/pydantic.py b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
similarity index 99%
rename from nwb_linkml/generators/pydantic.py
rename to nwb_linkml/src/nwb_linkml/generators/pydantic.py
index 5ab9365..32bcd3d 100644
--- a/nwb_linkml/generators/pydantic.py
+++ b/nwb_linkml/src/nwb_linkml/generators/pydantic.py
@@ -25,7 +25,7 @@ from types import ModuleType
 from copy import deepcopy
 import warnings
 
-from nwb_linkml.maps.dtype import flat_to_npytyping
+from nwb_linkml.src.nwb_linkml.maps import flat_to_npytyping
 from linkml.generators import PydanticGenerator
 from linkml_runtime.linkml_model.meta import (
     Annotation,
diff --git a/tests/__init__.py b/nwb_linkml/src/nwb_linkml/io/__init__.py
similarity index 100%
rename from tests/__init__.py
rename to nwb_linkml/src/nwb_linkml/io/__init__.py
diff --git a/nwb_linkml/src/nwb_linkml/io/hdf5.py b/nwb_linkml/src/nwb_linkml/io/hdf5.py
new file mode 100644
index 0000000..e5c2e33
--- /dev/null
+++ b/nwb_linkml/src/nwb_linkml/io/hdf5.py
@@ -0,0 +1,61 @@
+"""
+This is a sandbox file that should be split out to its own pydantic-hdf5 package, but just experimenting here to get our bearings
+"""
+from typing import Optional, List, Dict
+from pathlib import Path
+from types import ModuleType
+
+import h5py
+
+from nwb_linkml.translate import generate_from_nwbfile
+
+class HDF5IO():
+
+    def __init__(self, path:Path):
+        self.path = Path(path)
+        self._modules: Dict[str, ModuleType] = {}
+
+    @property
+    def modules(self) -> Dict[str, ModuleType]:
+        if len(self._modules) == 0:
+            self._modules = generate_from_nwbfile(self.path)
+        return self._modules
+
+    def process_group(self, group:h5py.Group|h5py.File) -> dict | list:
+        attrs = dict(group.attrs)
+
+        # how to process the group?
+        # --------------------------------------------------
+        # list-like
+        # --------------------------------------------------
+        # a list of data classes
+        if 'neurodata_type' not in attrs and \
+            all([isinstance(v, h5py.Group) for v in group.values()]) and \
+            all(['neurodata_type' in v.attrs for v in group.values()]):
+
+            return [self.process_group(v) for v in group.values()]
+
+        # --------------------------------------------------
+        # dict-like
+        # --------------------------------------------------
+
+        res = {}
+
+
+        for key, val in group.items():
+            if isinstance(val, h5py.Group):
+                res[key] = self.process_group(val)
+            elif isinstance(val, h5py.Dataset):
+                res[key] = self.process_dataset(val)
+        return res
+
+    def process_dataset(self, data: h5py.Dataset) -> dict | list:
+        if len(data.shape) == 1:
+            return list(data[:])
+
+
+if __name__ == "__main__":
+    NWBFILE = Path('/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb')
+    h5f = HDF5IO(NWBFILE)
+
+
diff --git a/nwb_linkml/io.py b/nwb_linkml/src/nwb_linkml/io/io.py
similarity index 93%
rename from nwb_linkml/io.py
rename to nwb_linkml/src/nwb_linkml/io/io.py
index c149853..fd04470 100644
--- a/nwb_linkml/io.py
+++ b/nwb_linkml/src/nwb_linkml/io/io.py
@@ -1,9 +1,8 @@
 """
 Loading/saving NWB Schema yaml files
 """
-import pdb
 from pathlib import Path
-from typing import TypedDict, List, Dict, Optional
+from typing import Optional
 from pprint import pprint
 import warnings
 
@@ -12,9 +11,8 @@ import yaml
 
 from nwb_schema_language import Namespaces,  Group, Dataset
 from nwb_linkml.namespaces import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
-from nwb_linkml.maps import preload
-from nwb_linkml.map import PHASES, Map
-from nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.src.nwb_linkml.map import PHASES, Map
+from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
 
 
@@ -70,7 +68,7 @@ def load_schema_file(path:Path, yaml:Optional[dict] = None) -> SchemaAdapter:
     )
     return schema
 
-def load_namespace_schema(namespace: Namespaces, path:Path=Path('.')) -> NamespacesAdapter:
+def load_namespace_schema(namespace: Namespaces, path:Path=Path('..')) -> NamespacesAdapter:
     """
     Load all schema referenced by a namespace file
 
diff --git a/nwb_linkml/lang_elements.py b/nwb_linkml/src/nwb_linkml/lang_elements.py
similarity index 98%
rename from nwb_linkml/lang_elements.py
rename to nwb_linkml/src/nwb_linkml/lang_elements.py
index 8ee539e..bd3e7cf 100644
--- a/nwb_linkml/lang_elements.py
+++ b/nwb_linkml/src/nwb_linkml/lang_elements.py
@@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import \
     TypeDefinition,\
     Prefix,\
     PermissibleValue
-from nwb_linkml.maps.dtype import flat_to_linkml
+from nwb_linkml.src.nwb_linkml.maps import flat_to_linkml
 
 
 FlatDType = EnumDefinition(
diff --git a/nwb_linkml/map.py b/nwb_linkml/src/nwb_linkml/map.py
similarity index 96%
rename from nwb_linkml/map.py
rename to nwb_linkml/src/nwb_linkml/map.py
index 244be5e..5f671c4 100644
--- a/nwb_linkml/map.py
+++ b/nwb_linkml/src/nwb_linkml/map.py
@@ -66,7 +66,6 @@ class KeyMap(Map):
 
 
 def apply_preload(ns_dict) -> dict:
-    from nwb_linkml.maps import preload
     maps = [m for m in Map.instances if m.phase == PHASES.postload]
     for amap in maps:
         ns_dict = amap.apply(ns_dict)
diff --git a/nwb_linkml/src/nwb_linkml/maps/__init__.py b/nwb_linkml/src/nwb_linkml/maps/__init__.py
new file mode 100644
index 0000000..f5b3780
--- /dev/null
+++ b/nwb_linkml/src/nwb_linkml/maps/__init__.py
@@ -0,0 +1,3 @@
+# Import everything so it's defined, but shoudlnt' necessarily be used from here
+from nwb_linkml.src.nwb_linkml.maps import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
+from nwb_linkml.src.nwb_linkml.maps import QUANTITY_MAP
\ No newline at end of file
diff --git a/nwb_linkml/maps/dtype.py b/nwb_linkml/src/nwb_linkml/maps/dtype.py
similarity index 100%
rename from nwb_linkml/maps/dtype.py
rename to nwb_linkml/src/nwb_linkml/maps/dtype.py
diff --git a/nwb_linkml/maps/preload.py b/nwb_linkml/src/nwb_linkml/maps/preload.py
similarity index 87%
rename from nwb_linkml/maps/preload.py
rename to nwb_linkml/src/nwb_linkml/maps/preload.py
index 9fdd849..b166055 100644
--- a/nwb_linkml/maps/preload.py
+++ b/nwb_linkml/src/nwb_linkml/maps/preload.py
@@ -2,7 +2,7 @@
 Maps to change the loaded .yaml from nwb schema before it's given to the nwb_schema_language models
 """
 
-from nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
+from nwb_linkml.src.nwb_linkml.map import KeyMap, SCOPE_TYPES, PHASES
 
 MAP_HDMF_DATATYPE_DEF = KeyMap(
     source="\'data_type_def\'",
diff --git a/nwb_linkml/maps/quantity.py b/nwb_linkml/src/nwb_linkml/maps/quantity.py
similarity index 100%
rename from nwb_linkml/maps/quantity.py
rename to nwb_linkml/src/nwb_linkml/maps/quantity.py
diff --git a/nwb_linkml/models/core.py b/nwb_linkml/src/nwb_linkml/models/core.py
similarity index 100%
rename from nwb_linkml/models/core.py
rename to nwb_linkml/src/nwb_linkml/models/core.py
diff --git a/nwb_linkml/models/core_nwb_base.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_base.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_base.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_base.py
diff --git a/nwb_linkml/models/core_nwb_behavior.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_behavior.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_behavior.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_behavior.py
diff --git a/nwb_linkml/models/core_nwb_device.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_device.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_device.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_device.py
diff --git a/nwb_linkml/models/core_nwb_ecephys.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_ecephys.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_ecephys.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_ecephys.py
diff --git a/nwb_linkml/models/core_nwb_epoch.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_epoch.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_epoch.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_epoch.py
diff --git a/nwb_linkml/models/core_nwb_file.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_file.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_file.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_file.py
diff --git a/nwb_linkml/models/core_nwb_icephys.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_icephys.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_icephys.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_icephys.py
diff --git a/nwb_linkml/models/core_nwb_image.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_image.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_image.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_image.py
diff --git a/nwb_linkml/models/core_nwb_misc.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_misc.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_misc.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_misc.py
diff --git a/nwb_linkml/models/core_nwb_ogen.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_ogen.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_ogen.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_ogen.py
diff --git a/nwb_linkml/models/core_nwb_ophys.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_ophys.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_ophys.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_ophys.py
diff --git a/nwb_linkml/models/core_nwb_retinotopy.py b/nwb_linkml/src/nwb_linkml/models/core_nwb_retinotopy.py
similarity index 100%
rename from nwb_linkml/models/core_nwb_retinotopy.py
rename to nwb_linkml/src/nwb_linkml/models/core_nwb_retinotopy.py
diff --git a/nwb_linkml/models/hdmf_common.py b/nwb_linkml/src/nwb_linkml/models/hdmf_common.py
similarity index 100%
rename from nwb_linkml/models/hdmf_common.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_common.py
diff --git a/nwb_linkml/models/hdmf_common_base.py b/nwb_linkml/src/nwb_linkml/models/hdmf_common_base.py
similarity index 100%
rename from nwb_linkml/models/hdmf_common_base.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_common_base.py
diff --git a/nwb_linkml/models/hdmf_common_sparse.py b/nwb_linkml/src/nwb_linkml/models/hdmf_common_sparse.py
similarity index 100%
rename from nwb_linkml/models/hdmf_common_sparse.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_common_sparse.py
diff --git a/nwb_linkml/models/hdmf_common_table.py b/nwb_linkml/src/nwb_linkml/models/hdmf_common_table.py
similarity index 100%
rename from nwb_linkml/models/hdmf_common_table.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_common_table.py
diff --git a/nwb_linkml/models/hdmf_experimental.py b/nwb_linkml/src/nwb_linkml/models/hdmf_experimental.py
similarity index 100%
rename from nwb_linkml/models/hdmf_experimental.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_experimental.py
diff --git a/nwb_linkml/models/hdmf_experimental_experimental.py b/nwb_linkml/src/nwb_linkml/models/hdmf_experimental_experimental.py
similarity index 100%
rename from nwb_linkml/models/hdmf_experimental_experimental.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_experimental_experimental.py
diff --git a/nwb_linkml/models/hdmf_experimental_resources.py b/nwb_linkml/src/nwb_linkml/models/hdmf_experimental_resources.py
similarity index 100%
rename from nwb_linkml/models/hdmf_experimental_resources.py
rename to nwb_linkml/src/nwb_linkml/models/hdmf_experimental_resources.py
diff --git a/nwb_linkml/models/nwb_language.py b/nwb_linkml/src/nwb_linkml/models/nwb_language.py
similarity index 100%
rename from nwb_linkml/models/nwb_language.py
rename to nwb_linkml/src/nwb_linkml/models/nwb_language.py
diff --git a/nwb_linkml/namespaces.py b/nwb_linkml/src/nwb_linkml/namespaces.py
similarity index 100%
rename from nwb_linkml/namespaces.py
rename to nwb_linkml/src/nwb_linkml/namespaces.py
diff --git a/nwb_linkml/plot.py b/nwb_linkml/src/nwb_linkml/plot.py
similarity index 97%
rename from nwb_linkml/plot.py
rename to nwb_linkml/src/nwb_linkml/plot.py
index cd451d2..f52f874 100644
--- a/nwb_linkml/plot.py
+++ b/nwb_linkml/src/nwb_linkml/plot.py
@@ -1,7 +1,7 @@
 """
 Various visualization routines, mostly to help development for now
 """
-from typing import TYPE_CHECKING, Optional, List, TypedDict, Union
+from typing import TYPE_CHECKING, Optional, List, TypedDict
 from rich import print
 import random
 
@@ -10,7 +10,7 @@ import dash_cytoscape as cyto
 cyto.load_extra_layouts()
 
 from nwb_schema_language import Namespace, Group, Dataset
-from nwb_linkml.io import load_nwb_core
+from nwb_linkml.src.nwb_linkml.io import load_nwb_core
 
 if TYPE_CHECKING:
     from nwb_linkml.adapters import NamespacesAdapter
diff --git a/nwb_linkml/schema/core.nwb.base.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.base.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.base.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.base.yaml
diff --git a/nwb_linkml/schema/core.nwb.behavior.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.behavior.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.behavior.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.behavior.yaml
diff --git a/nwb_linkml/schema/core.nwb.device.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.device.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.device.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.device.yaml
diff --git a/nwb_linkml/schema/core.nwb.ecephys.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.ecephys.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.ecephys.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.ecephys.yaml
diff --git a/nwb_linkml/schema/core.nwb.epoch.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.epoch.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.epoch.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.epoch.yaml
diff --git a/nwb_linkml/schema/core.nwb.file.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.file.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.file.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.file.yaml
diff --git a/nwb_linkml/schema/core.nwb.icephys.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.icephys.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.icephys.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.icephys.yaml
diff --git a/nwb_linkml/schema/core.nwb.image.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.image.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.image.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.image.yaml
diff --git a/nwb_linkml/schema/core.nwb.misc.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.misc.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.misc.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.misc.yaml
diff --git a/nwb_linkml/schema/core.nwb.ogen.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.ogen.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.ogen.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.ogen.yaml
diff --git a/nwb_linkml/schema/core.nwb.ophys.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.ophys.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.ophys.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.ophys.yaml
diff --git a/nwb_linkml/schema/core.nwb.retinotopy.yaml b/nwb_linkml/src/nwb_linkml/schema/core.nwb.retinotopy.yaml
similarity index 100%
rename from nwb_linkml/schema/core.nwb.retinotopy.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.nwb.retinotopy.yaml
diff --git a/nwb_linkml/schema/core.yaml b/nwb_linkml/src/nwb_linkml/schema/core.yaml
similarity index 100%
rename from nwb_linkml/schema/core.yaml
rename to nwb_linkml/src/nwb_linkml/schema/core.yaml
diff --git a/nwb_linkml/schema/hdmf-common.base.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-common.base.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-common.base.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-common.base.yaml
diff --git a/nwb_linkml/schema/hdmf-common.sparse.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-common.sparse.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-common.sparse.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-common.sparse.yaml
diff --git a/nwb_linkml/schema/hdmf-common.table.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-common.table.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-common.table.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-common.table.yaml
diff --git a/nwb_linkml/schema/hdmf-common.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-common.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-common.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-common.yaml
diff --git a/nwb_linkml/schema/hdmf-experimental.experimental.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.experimental.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-experimental.experimental.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.experimental.yaml
diff --git a/nwb_linkml/schema/hdmf-experimental.resources.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.resources.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-experimental.resources.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.resources.yaml
diff --git a/nwb_linkml/schema/hdmf-experimental.yaml b/nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.yaml
similarity index 100%
rename from nwb_linkml/schema/hdmf-experimental.yaml
rename to nwb_linkml/src/nwb_linkml/schema/hdmf-experimental.yaml
diff --git a/nwb_linkml/schema/nwb.language.yaml b/nwb_linkml/src/nwb_linkml/schema/nwb.language.yaml
similarity index 100%
rename from nwb_linkml/schema/nwb.language.yaml
rename to nwb_linkml/src/nwb_linkml/schema/nwb.language.yaml
diff --git a/nwb_linkml/translate.py b/nwb_linkml/src/nwb_linkml/translate.py
similarity index 94%
rename from nwb_linkml/translate.py
rename to nwb_linkml/src/nwb_linkml/translate.py
index 0cfe8e4..b6258c9 100644
--- a/nwb_linkml/translate.py
+++ b/nwb_linkml/src/nwb_linkml/translate.py
@@ -1,7 +1,6 @@
 """
 Convenience functions for translating NWB schema
 """
-import pdb
 import tempfile
 from typing import List, Optional, Dict
 from types import ModuleType
@@ -10,17 +9,12 @@ import json
 
 
 import h5py
-from linkml_runtime import SchemaView
-from linkml_runtime.linkml_model import SchemaDefinition
 from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime.utils.compile_python import compile_python
-
-
 
 from nwb_schema_language import Namespaces
-from nwb_linkml.io import load_schema_file
+from nwb_linkml.src.nwb_linkml.io import load_schema_file
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
-from nwb_linkml.map import apply_preload
+from nwb_linkml.src.nwb_linkml.map import apply_preload
 from nwb_linkml.adapters import SchemaAdapter, NamespacesAdapter
 
 def make_namespace_adapter(schema: dict) -> NamespacesAdapter:
diff --git a/nwb_linkml/tests/__init__.py b/nwb_linkml/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/fixtures.py b/nwb_linkml/tests/fixtures.py
similarity index 75%
rename from tests/fixtures.py
rename to nwb_linkml/tests/fixtures.py
index 363a71f..bdc18f5 100644
--- a/tests/fixtures.py
+++ b/nwb_linkml/tests/fixtures.py
@@ -1,9 +1,7 @@
 import pytest
-from typing import Dict
 
-
-from nwb_linkml import io
-from nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.src.nwb_linkml import io
+from nwb_linkml.src.nwb_linkml.adapters.namespaces import NamespacesAdapter
 import shutil
 from pathlib import Path
 
diff --git a/nwb_linkml/tests/test_adapters/__init__.py b/nwb_linkml/tests/test_adapters/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/test_adapter.py b/nwb_linkml/tests/test_adapters/test_adapter.py
similarity index 100%
rename from tests/test_adapter.py
rename to nwb_linkml/tests/test_adapters/test_adapter.py
diff --git a/tests/test_adapter_dataset.py b/nwb_linkml/tests/test_adapters/test_adapter_dataset.py
similarity index 100%
rename from tests/test_adapter_dataset.py
rename to nwb_linkml/tests/test_adapters/test_adapter_dataset.py
diff --git a/tests/test_adapter_group.py b/nwb_linkml/tests/test_adapters/test_adapter_group.py
similarity index 100%
rename from tests/test_adapter_group.py
rename to nwb_linkml/tests/test_adapters/test_adapter_group.py
diff --git a/tests/test_adapter_namespaces.py b/nwb_linkml/tests/test_adapters/test_adapter_namespaces.py
similarity index 100%
rename from tests/test_adapter_namespaces.py
rename to nwb_linkml/tests/test_adapters/test_adapter_namespaces.py
diff --git a/tests/test_adapter_schema.py b/nwb_linkml/tests/test_adapters/test_adapter_schema.py
similarity index 100%
rename from tests/test_adapter_schema.py
rename to nwb_linkml/tests/test_adapters/test_adapter_schema.py
diff --git a/tests/test_generate.py b/nwb_linkml/tests/test_generate.py
similarity index 100%
rename from tests/test_generate.py
rename to nwb_linkml/tests/test_generate.py
diff --git a/tests/test_translate.py b/nwb_linkml/tests/test_translate.py
similarity index 99%
rename from tests/test_translate.py
rename to nwb_linkml/tests/test_translate.py
index f403555..05f4013 100644
--- a/tests/test_translate.py
+++ b/nwb_linkml/tests/test_translate.py
@@ -13,3 +13,4 @@ def test_generate_pydantic():
     #pydantic_module = generate_from_nwbfile(NWBFILE)
 
     #pdb.set_trace()
+
diff --git a/pytest.ini b/pytest.ini
index 133ec0e..36c65df 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,4 +1,4 @@
 [pytest]
 
 testpaths =
-    tests
\ No newline at end of file
+    nwb_linkml/tests
\ No newline at end of file
diff --git a/scripts/generate_core.py b/scripts/generate_core.py
index 03367e1..d850591 100644
--- a/scripts/generate_core.py
+++ b/scripts/generate_core.py
@@ -3,7 +3,8 @@ from pathlib import Path
 from linkml_runtime.dumpers import yaml_dumper
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 
-from nwb_linkml import io
+from nwb_linkml.src.nwb_linkml import io
+
 
 def generate_core_yaml(output_path:Path):
     core = io.load_nwb_core()
@@ -34,13 +35,13 @@ def parser() -> ArgumentParser:
         '--yaml',
         help="directory to export linkML schema to",
         type=Path,
-        default=Path(__file__).parent.parent / 'nwb_linkml' / 'schema'
+        default=Path(__file__).parent.parent / 'nwb_linkml' / 'src' / 'nwb_linkml' / 'schema'
     )
     parser.add_argument(
         '--pydantic',
         help="directory to export pydantic models",
         type=Path,
-        default=Path(__file__).parent.parent / 'nwb_linkml' / 'models'
+        default=Path(__file__).parent.parent / 'nwb_linkml' / 'src' / 'nwb_linkml' / 'models'
     )
     return parser