Clean up repo root and unused internal tooling (#1037)

Cleans up some unused non-framework code in the internal_tools folder
and scripts.

---------

Signed-off-by: Peter St. John <pstjohn@nvidia.com>

Author: pstjohn

ci/Pypi_publish.md

@@ -1,5 +1,6 @@
 This is an overview of how to release bionemo sub-packages.
 
+<<<<<<< HEAD
 01. The code should be in a sub-directory of `bionemo-framework/sub-packages`. The package should be named bionemo-\<package_name>. For an example of the directory structure, see https://github.com/NVIDIA/bionemo-framework/tree/main/sub-packages/bionemo-scdl.
     The directory should contain:
     - a `pyproject.toml` file with the dependencies
@@ -18,5 +19,26 @@ This is an overview of how to release bionemo sub-packages.
 08. In a clean python environment, download the package from test-pypi:
     `pip install --index-url https://test.pypi.org/simple/ --no-deps package-name`
 09. Run the code/notebooks from step 3.
+=======
+
+1. The code should be in a sub-directory of `bionemo-framework/sub-packages`. The package should be named bionemo-<package_name>. For an example of the directory structure, see https://github.com/NVIDIA/bionemo-framework/tree/main/sub-packages/bionemo-scdl.
+The directory should contain:
+	- a `pyproject.toml` file with the dependencies
+	- a `README.md`
+	- a `LICENSE` file
+	- a `VERSION` file
+	- the source code should be in src/bionemo/package-name.
+	- the test should be in tests/bionemo/package-name. The test directory structure should be the same as the source code directory structure.
+2. Create some tests that can be run in a notebook within the package or as a small python script that verifies that the package is correctly installed. These can be re-purposed for QA test plan.
+3. In the VERSION file in the root of the sub-package, set the package version. Currently, the sub-package versions are independent of the overall BioNeMo version. An ideal approach is to specify the bionemo sub-package versions. That the package depends on. This may create issues. For example, an issue could arise if the latest version of your sub-package depends on the newest bionemo-core, but the latest pushed version of bionemo-core does not have these changes. It may be necessary to update bionemo-core then, but before updating another package, it should be tested and its authors should be consulted.
+4. Make sure that the directory dist doesn’t exist or is empty.
+5. Run `python -m build .`
+6. Create a test-pypi and pypi account if you don’t have one at: https://test.pypi.org/ and https://pypi.org/
+7. Upload to test-pypi with:
+ `twine upload --repository-url https://test.pypi.org/legacy/ dist/* --non-interactive -u $TWINE_USERNAME -p $TWINE_PASSWORD`
+8. In a clean python environment, download the package from test-pypi:
+`pip install --index-url https://test.pypi.org/simple/ --no-deps package-name`
+9. Run the code/notebooks from step 3.
+>>>>>>> 18da256e (Clean up repo root and unused internal tooling (#1037))
 10. If everything looks good, upload it to the actual pypi repository: `twine upload  dist/* --non-interactive -u $TWINE_USERNAME -p $TWINE_PASSWORD --verbose`
 11. Run steps 7 and 8 with pypi instead of test-pypi.