ENH: Improved alpha diversity format validation #204
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ebolyen
requested changes
Jan 25, 2019
q2_types/sample_data/_format.py
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| return i > 1 | ||
| header = None | ||
| records_seen = 0 | ||
| file_ = enumerate(fh) if level == 'min' else zip(range(10), fh) |
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| file_ = enumerate(fh) if level == 'min' else zip(range(10), fh) | |
| file_ = enumerate(fh, 1) if level == 'min' else zip(range(1, 10), fh) |
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This line becomes 81 cols long (which was why I didn't do this in the first place). Options: promote from a ternary to a real if/else block; unindent the whole block by removing the filehandle context manager and instead manually closing. Any other options come to mind?
q2_types/sample_data/_format.py
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| records_seen = 0 | ||
| file_ = enumerate(fh) if level == 'min' else zip(range(10), fh) | ||
| for i, line in file_: | ||
| i = i + 1 # For easier reporting |
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| i = i + 1 # For easier reporting |
q2_types/sample_data/_format.py
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| continue # Blank line | ||
| elif line.startswith('#'): | ||
| continue # Comment line | ||
| cells = [c.strip() for c in line.rstrip('\n').split('\t')] |
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Let's switch this to csv for quote handling
ebolyen
approved these changes
Jan 28, 2019
| format.validate() | ||
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| def test_alpha_diversity_format_validate_negative(self): |
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Refactors the existing
sniffer to use the current validation API. Also, removes the (likely accidental off-by-one) restriction that a minimum of two samples are present (it looks like the original code forgot to account for the header row).