add amplify package

Signed-off-by: Peter St. John <[email protected]>

.devcontainer/devcontainer.json

@@ -46,6 +46,7 @@
 					"./sub-packages/bionemo-geneformer/src",
 					"./sub-packages/bionemo-llm/src",
 					"./sub-packages/bionemo-testing/src",
+					"./sub-packages/bionemo-amplify/src",
 					"./sub-packages/bionemo-example_model/src",
 					"./3rdparty/NeMo",
 					"./3rdparty/Megatron-LM"

sub-packages/bionemo-amplify/README.md

@@ -0,0 +1,11 @@
+# bionemo-amplify
+
+To install, execute the following:
+```bash
+pip install -e .
+```
+
+To run unit tests, execute:
+```bash
+pytest -v .
+```

sub-packages/bionemo-amplify/VERSION

@@ -0,0 +1 @@
+VERSION

sub-packages/bionemo-amplify/pyproject.toml

@@ -0,0 +1,31 @@
+
+[build-system]
+requires = ["setuptools>=64", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "bionemo-amplify"
+readme = "README.md"
+description = ""
+authors = [{ name = "BioNeMo Team", email = "[email protected]" }]
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+dynamic = ["version"]
+dependencies = [
+    # internal
+    'bionemo-core',
+    'bionemo-llm',
+    # external
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["bionemo.*"]
+namespaces = true
+exclude = ["test*."]
+
+[tool.uv]
+cache-keys = [{ git = true }]
+
+[tool.setuptools.dynamic]
+version = { file = "VERSION" }

sub-packages/bionemo-amplify/src/bionemo/amplify/__init__.py

@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: LicenseRef-Apache2
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

sub-packages/bionemo-amplify/src/bionemo/amplify/model/__init__.py

@@ -0,0 +1,14 @@
+# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: LicenseRef-Apache2
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

sub-packages/bionemo-amplify/tests/bionemo/amplify/test_TODO_bionemo_amplify.py

@@ -0,0 +1,24 @@
+# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: LicenseRef-Apache2
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
+from pytest import fixture, mark, raises
+
+
+def test_todo() -> None:
+    raise ValueError(
+        f"Implement tests! Make use of {fixture} for data, {raises} to check for "
+        f"exceptional cases, and {mark} as needed"
+    )

sub-packages/bionemo-fw/pyproject.toml

@@ -1,46 +1,58 @@
 [build-system]
-requires = ["setuptools>=64", "wheel"]
+requires = [
+    "setuptools>=64",
+    "wheel",
+]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "bionemo-fw"
 readme = "README.md"
 description = "BioNeMo Framework (FW): Production grade framework for AI-enabled Drug Discovery. Consists of all independently installable bionemo feature packages too."
-authors = [{ name = "BioNeMo Team", email = "[email protected]" }]
+authors = [
+    { name = "BioNeMo Team", email = "[email protected]" },
+]
 requires-python = ">=3.10"
-license = { file = "LICENSE" }
-dynamic = ["version"]
+dynamic = [
+    "version",
+]
 dependencies = [
-    # bionemo sub-packages
-    'bionemo-core',
-    'bionemo-esm2',
-    'bionemo-geneformer',
-    'bionemo-geometric',
-    'bionemo-llm',
-    'bionemo-noodles',
-    'bionemo-scdl',
-    'bionemo-size-aware-batching',
-    'bionemo-webdatamodule',
-    #
-    # NOTE: DO **NOT** INCLUDE:
-    #    bionemo-testing (test-time only dependency)
-    #    bionemo-example_model (documentation)
-    #    bionemo-fw (itself!)
-    #
-    # external
-    'nltk',
-    'numba>=0.57.1',
-    'zarr',
+    "bionemo-core",
+    "bionemo-esm2",
+    "bionemo-amplify",
+    "bionemo-geneformer",
+    "bionemo-geometric",
+    "bionemo-llm",
+    "bionemo-noodles",
+    "bionemo-scdl",
+    "bionemo-size-aware-batching",
+    "bionemo-webdatamodule",
+    "nltk",
+    "numba>=0.57.1",
+    "zarr",
+    "bionemo-amplify",
+    "bionemo-amplify",
 ]
 
+[project.license]
+file = "LICENSE"
+
 [tool.setuptools.packages.find]
-where = ["src"]
-include = ["bionemo.*"]
+where = [
+    "src",
+]
+include = [
+    "bionemo.*",
+]
 namespaces = true
-exclude = ["test*."]
+exclude = [
+    "test*.",
+]
 
-[tool.setuptools.dynamic]
-version = { file = "VERSION" }
+[tool.setuptools.dynamic.version]
+file = "VERSION"
 
 [tool.uv]
-cache-keys = [{ git = true }]
+cache-keys = [
+    { git = true },
+]