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taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation
https://taxpasta.readthedocs.io/
Apache License 2.0
31 stars 6 forks source link

Add support for ganon #109

Closed jfy133 closed 1 year ago

jfy133 commented 1 year ago

Adds support for ganon

jfy133 commented 1 year ago

@Midnighter the error is as follows:

==================================== ERRORS ====================================
_ ERROR collecting tests/unit/infrastructure/application/ganon/test_ganon_profile.py _
tests/unit/infrastructure/application/ganon/test_ganon_profile.py:178: in <module>
    pd.DataFrame(
E   TypeError: DataFrame.__init__() got an unexpected keyword argument 'marks'

As far as we can tell (I think), the test_<xxx>_profile.py file is the same as centrifuge - so we are not really sure what is causing that.

Also we have a potential issue (don't know the behaviour yet of taxpasta until the tests are properly running), but the taxonomic ID for unclassified in ganon is -... do you have any suggestions hwo to deal with it (the other cases we saw were either NAs which works with pandas or just different integers)

jfy133 commented 1 year ago

you even added the new ETL tests even

You can thank @sofstam for that!

I've made the changes as requested @Midnighter , and I added a line to the contributing docs to actually document (we ran out of time, then I forgot about them :facepalm: ).

Midnighter commented 1 year ago

Thanks for the changes. I'm working on the standardisation now. The error that you saw

TypeError: DataFrame.__init__() got an unexpected keyword argument 'marks'

was caused by not using pytest.param in some cases. (Probably just a copy & paste mistake.)

jfy133 commented 1 year ago

ganon_testdata.zip

Mor etest data for you @Midnighter !

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 98.30% and project coverage change: +0.64 :tada:

Comparison is base (f60efe6) 81.99% compared to head (9b8b58b) 82.63%.

:exclamation: Current head 9b8b58b differs from pull request most recent head 26d16d0. Consider uploading reports for the commit 26d16d0 to get more accurate results

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## dev #109 +/- ## ========================================== + Coverage 81.99% 82.63% +0.64% ========================================== Files 106 110 +4 Lines 1594 1653 +59 Branches 281 291 +10 ========================================== + Hits 1307 1366 +59 Misses 247 247 Partials 40 40 ``` | [Impacted Files](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [...ucture/application/application\_service\_registry.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2FwcGxpY2F0aW9uX3NlcnZpY2VfcmVnaXN0cnkucHk=) | `93.16% <83.33%> (+0.26%)` | :arrow_up: | | [...rc/taxpasta/infrastructure/application/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [...pasta/infrastructure/application/ganon/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [.../infrastructure/application/ganon/ganon\_profile.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGUucHk=) | `100.00% <100.00%> (ø)` | | | [...tructure/application/ganon/ganon\_profile\_reader.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGVfcmVhZGVyLnB5) | `100.00% <100.00%> (ø)` | | | [...ion/ganon/ganon\_profile\_standardisation\_service.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2dhbm9uL2dhbm9uX3Byb2ZpbGVfc3RhbmRhcmRpc2F0aW9uX3NlcnZpY2UucHk=) | `100.00% <100.00%> (ø)` | | | [...a/infrastructure/application/supported\_profiler.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/109?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL3N1cHBvcnRlZF9wcm9maWxlci5weQ==) | `100.00% <100.00%> (ø)` | |

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