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mooreryan / parse_fasta

Easy-peasy fasta file parsing
MIT License
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Flaky tests with JRuby #9

Open mooreryan opened 6 years ago

mooreryan commented 6 years ago

When using jruby-9.1.8.0@parse_fasta gemset, the tests are flaky and randomly failing. When using MRI ruby the tests always pass though.

I ran the rspec suite a couple of times like this

parallel "jruby -S rake > rake_{} 2>&1" ::: {0..9}

These ones failed at least once:

rspec ./spec/parse_fasta/seq_file_spec.rb[1:2:3:7:1] # ParseFasta::SeqFile#each_record handles non newline line endings fastA, non-gz, carriage return and newline yields the records
rspec ./spec/parse_fasta/seq_file_spec.rb:149 # ParseFasta::SeqFile#each_record input is fastA when the fasta file has '>' in a seq when the check_fasta_seq flag is false yields records even with '>' in the sequence
rspec ./spec/parse_fasta/seq_file_spec.rb[1:2:1:3:1] # ParseFasta::SeqFile#each_record input is fastA with non-gzipped fastA yields the records
mooreryan commented 6 years ago

I checked this one on its own like so

rspec ./spec/parse_fasta/seq_file_spec.rb:149 # ParseFasta::SeqFile#each_record input is fastA when the fasta file has '>' in a seq when the check_fasta_seq flag is false yields records even with '>' in the sequence
parallel "jruby -S rspec ./spec/parse_fasta/seq_file_spec.rb:149 > single_{}" ::: {0..9}

It failed three times, so it doesn't look like it has to do with other tests messing things up.