PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
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Unittest coverage issue #67

Closed SandeepThokala closed 9 months ago

SandeepThokala commented 11 months ago

Current coverage report

Name                      Stmts   Miss  Cover
---------------------------------------------
openrdp/__init__.py         174     94    46%
openrdp/bootscan.py         235    135    43%
openrdp/chimaera.py         143     16    89%
openrdp/common.py           153     12    92%
openrdp/geneconv.py         106     32    70%
openrdp/maxchi.py           137     16    88%
openrdp/rdp.py              143      6    96%
openrdp/siscan.py           172     17    90%
openrdp/threeseq.py          76      3    96%
ArtPoon commented 10 months ago

@SandeepThokala can you please update this issue with current coverage, given recent work on geneconv?

SandeepThokala commented 10 months ago
Name                      Stmts   Miss  Cover
---------------------------------------------
openrdp/__init__.py         126     44    65%
openrdp/bootscan.py         226    126    44%
openrdp/chimaera.py         137     10    93%
openrdp/common.py           153      5    97%
openrdp/geneconv.py         100     26    74%
openrdp/maxchi.py           129      8    94%
openrdp/rdp.py              143      6    96%
openrdp/siscan.py           165     10    94%
openrdp/threeseq.py          76      3    96%

I opened this issue to address the low coverage in __init__.py and bootscan.py. In __init__.py, the low coverage is primarily due to functions mainly focused on printing results. In bootscan.py, one large function called 'execute()' is invoked using a map function, which is why the coverage tool failed to record its execution.

I've increased the coverage of the remaining scripts by addressing the new code introduced for issue #64.