Fix many warning from PYTHONDEVMODE=1

[luizirber]

Address #974 (comment), down from 281 warnings to 24 after dib-lab/screed#106 is merged and a new screed version is available.

Most warnings were ResourceWarnings for unclosed files in tests, but there were a couple in src/sourmash too. Preferred to use a context manager with screed.open or when passing the file to another library (like numpy), but for tests changed a lot of code to use Path(...).read_text().splitlines() instead.

The remaining 24 warnings are due to duplicate files in ZipStorage, punting it for later because they will require more attention when modifying src/sourmash/sbt_storage.py.

[codecov]

Codecov Report

Attention: 24 lines in your changes are missing coverage. Please review.

Comparison is base (32d46dd) 86.23% compared to head (7690233) 86.23%.

Files	Patch %	Lines
src/sourmash/sig/__main__.py	60.52%	13 Missing and 2 partials ⚠️
src/sourmash/commands.py	50.00%	5 Missing and 2 partials ⚠️
src/sourmash/command_compute.py	60.00%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           latest    #2849      +/-   ##
==========================================
- Coverage   86.23%   86.23%   -0.01%     
==========================================
  Files         130      130              
  Lines       14752    14756       +4     
  Branches     2617     2622       +5     
==========================================
+ Hits        12722    12725       +3     
- Misses       1730     1731       +1     
  Partials      300      300              

Flag	Coverage Δ
hypothesis-py	25.80% <0.00%> (-0.01%)	⬇️
python	92.82% <59.32%> (-0.01%)	⬇️
rust	50.88% <ø> (ø)

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[ctb]

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