Internal code, infra-bionemo, new sub-package creation tool

.github/workflows/internal_tools.yml

@@ -0,0 +1,24 @@
+name: Install internal tools Python packages & run test suite
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  merge_group:
+    types: [checks_requested]
+jobs:
+  infra-bionemo:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: 'recursive'
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install -r requirements-dev.txt -r requirements-test.txt
+      - run: pip install internal/infra-bionemo
+      - run: cd internal/infra-bionemo && pytest -v --cov=infra_bionemo --cov-report=term .

.pre-commit-config.yaml

@@ -27,7 +27,7 @@ repos:
     hooks:
       - id: license-header-check
         name: Run license-check script
-        entry: python scripts/license_check.py -c scripts -c sub-packages --license-header ./license_header --modify
+        entry: python internal/infra-bionemo/src/infra_bionemo/license_check.py -c scripts -c sub-packages -c docs -c internal --license-header ./license_header --modify
         language: python
         additional_dependencies: ["click==8.1.7"]
         pass_filenames: false

.secrets.baseline

@@ -139,9 +139,9 @@
         "filename": "pyproject.toml",
         "hashed_secret": "79670e9c9d1c7ea5b81a96a2053d81437712c78e",
         "is_verified": false,
-        "line_number": 44
+        "line_number": 47
       }
     ]
   },
-  "generated_at": "2024-10-31T19:51:19Z"
+  "generated_at": "2024-11-01T22:26:03Z"
 }

Dockerfile

@@ -172,12 +172,14 @@ FROM dev AS development
 
 WORKDIR /workspace/bionemo2
 COPY --from=bionemo2-base /workspace/bionemo2/ .
+COPY ./internal ./internal
 # because of the `rm -rf ./3rdparty` in bionemo2-base
 COPY ./3rdparty ./3rdparty
 USER root
 RUN <<EOF
 set -eo pipefail
 find . -name __pycache__ -type d -print | xargs rm -rf
+uv pip install --no-build-isolation --editable ./internal/infra-bionemo
 for sub in ./3rdparty/* ./sub-packages/bionemo-*; do
     uv pip install --no-deps --no-build-isolation --editable $sub
 done

ci/scripts/build_docker_image.sh

@@ -1,14 +1,19 @@
 #!/bin/bash
 #
 # SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
+# SPDX-License-Identifier: LicenseRef-Apache2
 #
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
+# 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.
 
 set -e
 

ci/scripts/run_pytest.sh

@@ -1,14 +1,19 @@
 #!/bin/bash
 #
 # SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
+# SPDX-License-Identifier: LicenseRef-Apache2
 #
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
+# 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.
 
 set -xueo pipefail
 export PYTHONDONTWRITEBYTECODE=1

ci/scripts/utils.sh

@@ -1,14 +1,19 @@
 #!/bin/bash
 #
 # SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
-# SPDX-License-Identifier: LicenseRef-NvidiaProprietary
+# SPDX-License-Identifier: LicenseRef-Apache2
 #
-# NVIDIA CORPORATION, its affiliates and licensors retain all intellectual
-# property and proprietary rights in and to this material, related
-# documentation and any modifications thereto. Any use, reproduction,
-# disclosure or distribution of this material and related documentation
-# without an express license agreement from NVIDIA CORPORATION or
-# its affiliates is strictly prohibited.
+# 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.
 
 # Function to check if Git repository is clean
 check_git_repository() {