search

taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
34 stars 7 forks source link

Feature: add a CLI and implement the merge command #29

Closed Midnighter closed 2 years ago

Midnighter commented 2 years ago
codecov-commenter commented 2 years ago

Codecov Report

Base: 91.87% // Head: 91.55% // Decreases project coverage by -0.31% :warning:

Coverage data is based on head (f7d6650) compared to base (0b6bb1f). Patch coverage: 90.30% of modified lines in pull request are covered.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #29 +/- ## ========================================== - Coverage 91.87% 91.55% -0.32% ========================================== Files 38 81 +43 Lines 406 1078 +672 Branches 9 68 +59 ========================================== + Hits 373 987 +614 - Misses 26 74 +48 - Partials 7 17 +10 ``` | [Impacted Files](https://codecov.io/gh/taxprofiler/taxpasta/pull/29?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [src/taxpasta/\_\_main\_\_.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL19fbWFpbl9fLnB5) | `0.00% <0.00%> (ø)` | | | [src/taxpasta/application/service/profile\_writer.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2FwcGxpY2F0aW9uL3NlcnZpY2UvcHJvZmlsZV93cml0ZXIucHk=) | `0.00% <ø> (ø)` | | | [src/taxpasta/domain/model/standard\_profile.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2RvbWFpbi9tb2RlbC9zdGFuZGFyZF9wcm9maWxlLnB5) | `100.00% <ø> (ø)` | | | [...axpasta/application/error/standardisation\_error.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2FwcGxpY2F0aW9uL2Vycm9yL3N0YW5kYXJkaXNhdGlvbl9lcnJvci5weQ==) | `55.55% <55.55%> (ø)` | | | [src/taxpasta/\_\_init\_\_.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL19faW5pdF9fLnB5) | `75.00% <60.00%> (-25.00%)` | :arrow_down: | | [src/taxpasta/infrastructure/cli/merge.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2NsaS9tZXJnZS5weQ==) | `72.35% <72.35%> (ø)` | | | [src/taxpasta/application/error/taxpasta\_error.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2FwcGxpY2F0aW9uL2Vycm9yL3RheHBhc3RhX2Vycm9yLnB5) | `75.00% <75.00%> (ø)` | | | [...tructure/application/kaiju/kaiju\_profile\_reader.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2thaWp1L2thaWp1X3Byb2ZpbGVfcmVhZGVyLnB5) | `84.61% <75.00%> (-1.10%)` | :arrow_down: | | [...taxpasta/application/sample\_merging\_application.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2FwcGxpY2F0aW9uL3NhbXBsZV9tZXJnaW5nX2FwcGxpY2F0aW9uLnB5) | `80.00% <80.00%> (ø)` | | | [src/taxpasta/infrastructure/cli/consensus.py](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2NsaS9jb25zZW5zdXMucHk=) | `80.00% <80.00%> (ø)` | | | ... and [60 more](https://codecov.io/gh/taxprofiler/taxpasta/pull/29/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None)

:umbrella: View full report at Codecov.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.

maxibor commented 2 years ago

Also, this now needs updating https://github.com/taxprofiler/taxpasta/blob/dev/docs/contributing/supporting_new_profiler.md

Midnighter commented 2 years ago

Good points! I'll work on tests and the docs.

Midnighter commented 2 years ago

Alright, @maxibor and @jfy133 I think this is now fully ready. Please have a looksy 🙂

Midnighter commented 2 years ago

@sofstam I had to change the Kaiju code somewhat to deal with multiple missing taxonomy identifiers.

sofstam commented 2 years ago

@Midnighter I saw it, better as it is now :)

Midnighter commented 2 years ago

PR got a little bit bigger than I'd consider comfortable for review 🙈 I'm happy to walk you through the changes and talk about it.

Midnighter commented 2 years ago

Another set of changes following @jfy133 's user testing earlier today. Please give it another shot when you have time.

Midnighter commented 2 years ago

It's all on you now @maxibor , no pressure 😆

Midnighter commented 2 years ago

Renamed the matrix to wide table and added some tests for unsupported formats. Also added a warning for the zeroes.