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.

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

[EXP] make lineage utils more flexible #2371

Closed
wants to merge 40 commits into from
Closed

[EXP] make lineage utils more flexible #2371

wants to merge 40 commits into from

Conversation

bluegenes
Copy link
Contributor

@bluegenes bluegenes commented Nov 21, 2022

for CAMI output, we need NCBI taxid info. For LINS, we need flexible taxonomic "ranks."

exploration into added flexibility for lineage utils + tax summarization

@codecov
Copy link

codecov bot commented Nov 21, 2022

Codecov Report

Merging #2371 (a0a4516) into latest (059d988) will decrease coverage by 0.43%.
The diff coverage is 85.33%.

@@            Coverage Diff             @@
##           latest    #2371      +/-   ##
==========================================
- Coverage   84.08%   83.65%   -0.44%     
==========================================
  Files         130      131       +1     
  Lines       15044    15492     +448     
  Branches     2403     2536     +133     
==========================================
+ Hits        12650    12960     +310     
- Misses       2098     2207     +109     
- Partials      296      325      +29     
Flag Coverage Δ
python 91.35% <85.33%> (-0.87%) ⬇️
rust 57.72% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/tax/__main__.py 92.24% <80.00%> (-1.40%) ⬇️
src/sourmash/tax/taxcomparison.py 84.96% <84.96%> (ø)
src/sourmash/tax/tax_utils.py 90.14% <89.47%> (-7.99%) ⬇️
src/sourmash/lca/lca_utils.py 87.90% <0.00%> (-0.81%) ⬇️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

@bluegenes
Copy link
Contributor Author

all functionality has been incorporated via smaller, clearer PRs

@bluegenes bluegenes closed this Mar 8, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants