Dangerous use of "assert"

[fabianegli]

assert is used in the download_cache.py outside the scope of testing. This will not be executed if the module is run with optimization. If this is intended to be a test, it should be implemented in another way.

From https://stackoverflow.com/a/1838411/6018688 "assert" statements are removed when the compilation is optimized and here's the official documentation stating asserts relationship with debugging, i.e. __debug__.

There might be other places where assert is used and maybe should be replaced with tests that survive optimization.

[iskandr]

It's a good point and I seem to have utilized assert quite a bit.

I'll make a PR to change them to explicit tests.

---

$ grep -R assert *
download_cache.py:        assert path_or_url, "Expected non-empty string for path_or_url"
download_cache.py:        assert path_or_url, "Expected non-empty string for path_or_url"
download_cache.py:        assert path_or_url, "Expected non-empty string for path_or_url"
download_cache.py:        assert n_missing > 0
genome.py:            assert self.gtf_path is not None
genome.py:            assert self.protein_fasta_paths is not None
genome.py:            assert self.transcript_fasta_paths is not None
genome.py:            assert len(result) >= 4 and len(result) <= 6, \
genome.py:        assert len(results) == 1, \
genome.py:            assert 5 <= len(result) <= 5 + len(optional_field_names), \
genome.py:        assert len(transcript_names) == 1, \
genome.py:        assert len(results) == 1, \
locus.py:        assert start <= end, \
species.py:                assert i not in self._release_to_genome, \
transcript.py:            assert exon_number >= 1, "Invalid exon number: %s" % exon_number
transcript.py:            assert exon_number <= len(exons), \
transcript.py:        assert all(exon is not None for exon in exons), \
transcript.py:                assert position not in results, \
transcript.py:        # typechecks.require_integer to a simpler assertion
transcript.py:        assert type(position) == int, \
transcript.py:            assert offsets[i] + 1 == offsets[i + 1], \