Fix iterate hmm

[zdk123]

Fixes #33

• Changes query from DigitalSequence to HMM to be consistent with the intention of the function as well as the documentation
• In the __next__ method of the iterator, make sure the extra_sequences and extra_traces are None in iterations after the first, when the query is an HMM. Treating it as a sequence breaks the iterator.

[codecov[bot]]

Codecov Report

Patch coverage: 100.00% and project coverage change: -8.52 :warning:

Comparison is base (d7602f0) 84.96% compared to head (3885574) 76.45%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #34 +/- ## ========================================== - Coverage 84.96% 76.45% -8.52% ========================================== Files 39 7 -32 Lines 10942 6812 -4130 ========================================== - Hits 9297 5208 -4089 + Misses 1645 1604 -41 ``` | Flag | Coverage Δ | | |---|---|---| | CPython | `?` | | | Linux | `?` | | | OSX | `?` | | | v3.10 | `76.45% <100.00%> (-8.49%)` | :arrow_down: | | v3.11 | `76.45% <100.00%> (-19.23%)` | :arrow_down: | | v3.7 | `76.42% <100.00%> (-8.30%)` | :arrow_down: | | v3.8 | `76.45% <100.00%> (-8.49%)` | :arrow_down: | | v3.9 | `76.45% <100.00%> (-8.49%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde#carryforward-flags-in-the-pull-request-comment) to find out more. | [Impacted Files](https://codecov.io/gh/althonos/pyhmmer/pull/34?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | Coverage Δ | | |---|---|---| | [pyhmmer/plan7.pyx](https://codecov.io/gh/althonos/pyhmmer/pull/34?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde#diff-cHlobW1lci9wbGFuNy5weXg=) | `72.90% <100.00%> (+0.30%)` | :arrow_up: | ... and [33 files with indirect coverage changes](https://codecov.io/gh/althonos/pyhmmer/pull/34/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) 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=Martin+Larralde). 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=Martin+Larralde)

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[althonos]

Thanks for the fix!

This definitely flew under my radar, I should have done more thorough testing. Do you think you could add a test case to pyhmmer/tests/test_plan7/test_pipeline.py? There is a test_iterate_seq method in TestIteratePipeline, perhaps you could use it as a basis. If you don't have time/energy for this, that's fine, just tell me and I'll merge as is.

[zdk123]

I'd be happy to add a test, no worries.

[zdk123]

Added the test

[althonos]

Great job, thanks a lot! I'll be making a new release right after.

[zdk123]

Related to this, would you have any interest in including a top level jackhmmer interface (pyhmmer.jackhmmer)? I have this stubbed out locally.