Mg/bionemo noodles py o3 #435
Draft
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
malcolmgreaves
requested review from
jstjohn,
ohadmo,
pstjohn,
trvachov and
dorotat-nv
as code owners
|
NOTE: don't review yet :) |
Initial commit! - adds the PyO3 wrapper around noodles-fasta - adds a python class that mimics the dict-like behavior of pyfaidx - adds a long test (best used with hg38 https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/), or use whatever big reference. Build: ``` cd sub-packages/bionemo-noodles/noodles_fasta_wrapper maturin develop ``` This should install it into your local python environment, then you can run the associated tests! TODO: - flesh out equality tests with pyfaidx - profile performance - get the build system working correctly
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
(NOTE: delete these instructional lines as you fill-out this PR template)
(NOTE: _template is designed to be filled-in and used as the squashed commit message for the entire PR. Italicized text is intended to be deleted as you fill in this template. Use the text between the
---)High level summary of changes. Try to keep this as short and informative as possible: less is more.
Describe your changes. You can be more detailed and descriptive here. If it is a code change, Be sure to answer:
Summary
High level summary of changes. Try to keep this as short and informative as possible: less is more.
Details
Describe your changes. You can be more detailed and descriptive here.
Usage
How does a user interact with the changed code?
Testing
How do you prove that your code behaves the way you claim?
Tests for these changes can be run via:
(NOTE: also delete this checklist as you fill-out this PR template)
Most of the changes to files with extensions
*.py,*.yaml,*.yml,Dockerfile*orrequirements.txtDO REQUIRE bothpytest-andjet-CI stages.SKIP_CIlabel to your PR?PYTEST_NOT_REQUIREDlabel to your PR?JET_NOT_REQUIREDlabel to your PR?