Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Instructions for uploading a package to pypi #638

Merged
merged 6 commits into from
Jan 25, 2025
Merged

Instructions for uploading a package to pypi #638

Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
463fcd9
[skip ci]
polinabinder1 Jan 22, 2025
4652362
Merge branch 'main' into polinabinder/add_pypi_readme
polinabinder1 Jan 23, 2025
6abc3e3
Update Pypi_publish.md
polinabinder1 Jan 24, 2025
2596cc9
Merge branch 'main' into polinabinder/add_pypi_readme
polinabinder1 Jan 24, 2025
b52259b
README format
polinabinder1 Jan 24, 2025
107e85e
Merge branch 'main' into polinabinder/add_pypi_readme
polinabinder1 Jan 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 23 additions & 0 deletions internal/Pypi_publish.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
This is an overview of how to release bionemo sub-packages.


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.
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.
Loading