Start adding kmcp profiler

[sofstam]

• fix [Feature] Add support for kmcp profiler #129
• description of feature/fix
• tests added/passed
• 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% 🎉

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

❗ Current head 7ef75ec differs from pull request most recent head 8e9494d. Consider uploading reports for the commit 8e9494d to get more accurate results

❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.

Additional details and impacted files

@@            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	Coverage Δ
...ucture/application/application_service_registry.py	93.41% <83.33%> (+0.24%)	⬆️
...rc/taxpasta/infrastructure/application/__init__.py	100.00% <100.00%> (ø)
...xpasta/infrastructure/application/kmcp/__init__.py	100.00% <100.00%> (ø)
...ta/infrastructure/application/kmcp/kmcp_profile.py	100.00% <100.00%> (ø)
...astructure/application/kmcp/kmcp_profile_reader.py	100.00% <100.00%> (ø)
...ation/kmcp/kmcp_profile_standardisation_service.py	100.00% <100.00%> (ø)
...a/infrastructure/application/supported_profiler.py	100.00% <100.00%> (ø)

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[Midnighter]

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

[Midnighter]

Almost done now 😃 Good work!

[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!