Daniel Standage Daniel Standage - 5 months ago 26
Python Question

Python nosetests with coverage no longer shows missing lines

I've been using the following command to run tests and evaluate code coverage for a Python project for over a year now.

nosetests -v --with-coverage --cover-package=genhub genhub/*.py


The coverage report used to include a column on the far right showing the lines missing coverage.

Name Stmts Miss Branch BrPart Cover Missing
----------------------------------------------------------------
genhub/cdhit.py 50 0 8 0 100%
genhub/exons.py 85 69 8 0 17% 24-40, 48-56, 60-79, 87-107, 129-132, 138-141, 147-150
genhub/fasta.py 76 0 26 0 100%
genhub/genomedb.py 205 153 48 0 21% 40-43, 53-60, 64-65, 70, 74, 82, 86, 90, 98-99, 103-104, 108-109, 113-114, 118-119, 123-124, 128-129, 143-144, 152-154, 158-160, 164-166, 175, 180, 240-280, 289, 292, 295, 308-317, 323-330, 351-377, 380-386, 396-413, 419-430, 436-443, 449-456
genhub/iloci.py 112 91 8 0 18% 30-46, 54-64, 73-90, 102-118, 127-142, 165-173, 179-183, 189-193, 199-207, 213-225
genhub/mrnas.py 121 108 24 0 9% 30-63, 79-105, 118-158, 178-197, 203-226
genhub/pdom.py 95 68 24 0 23% 31-32, 35, 39, 43, 47, 50-53, 56-59, 62-64, 67-72, 75-106, 116-119, 126-128, 134-141, 148-156
genhub/proteins.py 20 13 2 0 32% 43-53, 94-97
genhub/refseq.py 237 195 44 0 15% 30-46, 49, 53, 57, 61, 65, 69, 73, 76-86, 89-115, 118-127, 130-178, 189-211, 217-226, 232-242, 248-265, 271-288, 294-297, 303-310, 317-326, 333-374, 380-387
genhub/registry.py 126 90 32 2 24% 48-56, 59-64, 67-69, 72-77, 81-83, 92-94, 103-109, 112-113, 116-117, 142-168, 174-188, 194-201, 207-216, 40->44, 44->48
genhub/stats.py 3 0 0 0 100%
genhub/tair.py 128 97 22 0 21% 32-42, 45, 49, 53, 57, 61, 65, 69, 73, 76-79, 82-104, 110-119, 122-154, 165-180, 186-189, 195-203, 210-221
----------------------------------------------------------------
TOTAL 1258 884 246 2 27%
----------------------------------------------------------------------
Ran 46 tests in 0.033s

FAILED (errors=41)


However, the
Missing
column no longer shows up for me (nose version 1.3.7, coverage.py version 4.1).

I'm aware nose is no longer being supported. Is this change related to that, or something in coverage.py, or both?

Answer

In coverage.py 4.1, I fixed a problem with the coverage.py API defaulting two parameters to non-None values. One of them was show_missing.

The best way to fix this in your project is to set show_missing in your .coveragerc file:

# .coveragerc
[report]
show_missing = True