Irallia commented 2 years ago

This PR updates SeqAn3 to use the sharg parser. As the b.i.o. lib is using an older version of SeqAn3 I had to change the dependency stuff in the CmakeLists.

Wait for https://github.com/seqan/sharg-parser/pull/111

Irallia commented 1 year ago

One test fails just for gcc10, I don't know what to do here.

 [ RUN      ] iGenVar_cli_test.test_genome_input
../../../iGenVar/test/cli/iGenVar_cli_test.cpp:324: Failure
Expected equality of these values:
  result.exit_code
    Which is: 11
  0
unknown file: Failure
C++ exception with description "basic_string::erase: __pos (which is 484) > this->size() (which is 0)" thrown in the test body.
[  FAILED  ] iGenVar_cli_test.test_genome_input (12 ms)

Without the sharg change, the cmake change works: https://github.com/seqan/iGenVar/pull/235

codecov[bot] commented 1 year ago

Codecov Report

Base: 98.47% // Head: 98.31% // Decreases project coverage by -0.16% :warning:

Coverage data is based on head (64565eb) compared to base (1966a1c). Patch coverage: 96.29% of modified lines in pull request are covered.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #218 +/- ## ========================================== - Coverage 98.47% 98.31% -0.17% ========================================== Files 20 20 Lines 986 1007 +21 ========================================== + Hits 971 990 +19 - Misses 15 17 +2 ``` | [Impacted Files](https://codecov.io/gh/seqan/iGenVar/pull/218?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan) | Coverage Δ | | |---|---|---| | [src/iGenVar.cpp](https://codecov.io/gh/seqan/iGenVar/pull/218/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=seqan#diff-c3JjL2lHZW5WYXIuY3Bw) | `98.52% <96.29%> (-1.48%)` | :arrow_down: | 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=seqan). 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=seqan)

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seqan / iGenVar

[MISC] Update SeqAn3 and use sharg parser #218

Codecov Report