Start adding kmcp profiler

[sofstam]

• [x] fix #129
• [ ] description of feature/fix
• [x] tests added/passed
• [x] add an entry to the changelog

[sofstam]

@Midnighter I think the error comes from that I have defined chunksRelDepth as float but the column in the MOCK_002_Illumina_3000.k.profile has both strings and floats. I tried to define chunksRelDepth as object but I kept on getting errors. Do you have any suggestions on how I shall define the column?

CRITICAL taxpasta.infrastructure.cli.merge:merge.py:424 Error in sample 'MOCK_002_Illumina_Hiseq_3000.k' with profile '/Users/sofia.stamouli/Documents/taxpasta/tests/data/kmcp/MOCK_002_Illumina_Hiseq_3000.k.profile'.
CRITICAL taxpasta.infrastructure.cli.merge:merge.py:427   schema_context          column  ...                                       failure_case index
0         Column  chunksRelDepth  ...                                             object  None
1         Column  chunksRelDepth  ...  TypeError("'>=' not supported between instance...  None
2         Column  chunksRelDepth  ...  TypeError("'<=' not supported between instance...  None

[3 rows x 6 columns]

[sofstam]

@Midnighter I am getting the follow error:

CRITICAL taxpasta.infrastructure.cli.merge:merge.py:424 Error in sample 'MOCK_002_Illumina_Hiseq_3000.k' with profile '/Users/sofia.stamouli/Documents/taxpasta/tests/data/kmcp/MOCK_002_Illumina_Hiseq_3000.k.profile'.
CRITICAL taxpasta.infrastructure.cli.merge:merge.py:427 could not convert string to float: '0.97;1.01;1.05;1.05;1.02;1.00;0.98;0.97;0.99;0.97'

Should this be handled in kmcp_profile_standardisation_service.py?

[codecov-commenter]

Codecov Report

Patch coverage: 98.50% and project coverage change: +0.68% :tada:

Comparison is base (731af20) 82.17% compared to head (7ef75ec) 82.85%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## dev #128 +/- ## ========================================== + Coverage 82.17% 82.85% +0.68% ========================================== Files 110 114 +4 Lines 1677 1744 +67 Branches 299 138 -161 ========================================== + Hits 1378 1445 +67 Misses 255 255 Partials 44 44 ``` | [Files Changed](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?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/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2FwcGxpY2F0aW9uX3NlcnZpY2VfcmVnaXN0cnkucHk=) | `93.41% <83.33%> (+0.24%)` | :arrow_up: | | [...rc/taxpasta/infrastructure/application/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?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)` | | | [...xpasta/infrastructure/application/kmcp/\_\_init\_\_.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2ttY3AvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [...ta/infrastructure/application/kmcp/kmcp\_profile.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2ttY3Ava21jcF9wcm9maWxlLnB5) | `100.00% <100.00%> (ø)` | | | [...astructure/application/kmcp/kmcp\_profile\_reader.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2ttY3Ava21jcF9wcm9maWxlX3JlYWRlci5weQ==) | `100.00% <100.00%> (ø)` | | | [...ation/kmcp/kmcp\_profile\_standardisation\_service.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2FwcGxpY2F0aW9uL2ttY3Ava21jcF9wcm9maWxlX3N0YW5kYXJkaXNhdGlvbl9zZXJ2aWNlLnB5) | `100.00% <100.00%> (ø)` | | | [...a/infrastructure/application/supported\_profiler.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/128?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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[Midnighter]

Weird, I cancelled my review but all these comments were posted...

[sofstam]

Thanks for your comments, will update the PR tomorrow.

[Midnighter]

Decided to finish up myself in the interest of getting a release out today.

[sofstam]

Thanks for that @Midnighter!