sourmash-bio/sourmash

write command-line test for `lca summarize --query-from-file`

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#1,451 opened on Apr 11, 2021

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good first issuepythontesting

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Description

per https://github.com/dib-lab/sourmash/pull/1423/files#r604406992 as well as attached screenshot, we do not currently test sourmash lca summarize --query-from-file

To address this issue:

  • make a copy of test_single_summarize() in tests/test_lca.py and name it something like test_single_summarize_query_from_file();
  • modify the new test to create a text file containing the path to input_sig
  • modify the utils.runscript(...) command to remove --query and instead pass in --query-from-file with the new text file

Contributor guide

Research direction
Follow the instructions: copy `test single summarize()`, rename it, create a text file with the path to `input sig`, and modify the `utils.runscript(...)` command to use ` query from file` instead of ` query`.
Tech stack
python
Domain
backendtesting
Issue type
Test
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Fresh
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitPython
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
85