I have a python library named CorGE with the following structure
and I'm trying to produce a coverage report with pytest-cov. Every example/doc I've seen has been something like this
pytest CorGE/tests/ --cov CorGE/
or this
python -m coverage run --source=CorGE/src/CorGE -m pytest CorGE/tests/
but this produces a NoCoverageWarning
CoverageWarning: No data was collected. (no-data-collected)
and a report like this
Name Stmts Miss Cover
-------------------------------------------
src/CorGE/__init__.py 0 0 100%
src/CorGE/collect.py 127 127 0%
-------------------------------------------
TOTAL 127 127 0%
Am I just misunderstanding how to use this coverage tool? I've put a whole day into trying different variations on these commands and nothing seems to work. Would love any insight from someone who knows more about this.
Here's the test file, just in case somehow it's the problem, like not calling the src file properly or something.
import os
import shutil
import tempfile
import unittest
from CorGE.command import main
class CommandTests(unittest.TestCase):
def setUp(self):
self.temp_dir = tempfile.mkdtemp()
# collect_genomes input
self.data_dir = os.path.join('/'.join(__file__.split('/')[:-1]), "test-data")
self.ncbi_species_fp = os.path.join(self.data_dir, "TEST_TXIDS")
self.ncbi_accessions_fp = os.path.join(self.data_dir, "TEST_ACCS")
self.local_db_fp = os.path.join(self.data_dir, "TEST_LOCAL/")
# collect_genomes outputs
self.nucl_fp = os.path.join(self.temp_dir, "nucleotide/")
self.prot_fp = os.path.join(self.temp_dir, "protein/")
self.outgroup_fp = os.path.join(self.temp_dir, "outgroup/")
def tearDown(self):
shutil.rmtree(self.temp_dir)
def test_collect_genomes(self):
main([
"collect_genomes",
self.temp_dir,
"--ncbi_species", self.ncbi_species_fp,
"--ncbi_accessions", self.ncbi_accessions_fp,
"--local", self.local_db_fp,
# --outgroup left as default "2173"
])
self.assertEqual(os.listdir(self.outgroup_fp).sort(), ['GCF_000016525.1.faa', 'GCF_000016525.1.fna'].sort())
self.assertEqual(os.listdir(self.nucl_fp).sort(), ['GCF_000012885.1.fna', 'GCF_000007725.1.fna', 'GCF_000020965.1.fna',\
'GCF_001735525.1.fna', 'GCF_007197645.1.fna', 'GCF_001375595.1.fna', 'GCF_000218545.1.fna', 'GCF_000010525.1\n.fna',\
'GCF_000378225.1.fna', 'GCF_900111765.1.fna', 'GCF_023159115.1.fna'].sort())
self.assertEqual(os.listdir(self.prot_fp).sort(), ['GCF_000012885.1.faa', 'GCF_000007725.1.faa', 'GCF_000020965.1.faa',\
'GCF_001735525.1.faa', 'GCF_007197645.1.faa', 'GCF_001375595.1.faa', 'GCF_000218545.1.faa', 'GCF_000010525.1\n.faa',\
'GCF_000378225.1.faa', 'GCF_900111765.1.faa', 'GCF_023159115.1.faa'].sort())
if __name__ == "__main__":
unittest.main()
OK I figured out how to make this work but I am thoroughly unsatisfied with my solution. The change I made was to install CorGE in development mode instead of normally with pip install -e . and then everything started working.
I'm now running pytest --cov . from the root CorGE directory and getting:
---------- coverage: platform linux, python 3.10.2-final-0 -----------
Name Stmts Miss Cover
-------------------------------------------
setup.py 2 2 0%
src/CorGE/__init__.py 0 0 100%
src/CorGE/collect.py 127 19 85%
src/CorGE/command.py 43 5 88%
src/CorGE/extract.py 193 167 13%
src/__init__.py 0 0 100%
tests/__init__.py 0 0 100%
tests/test_command.py 35 1 97%
-------------------------------------------
TOTAL 400 194 52%
Why this works, I don't know. Why it doesn't work without this, I don't know even more. Hopefully this helps anyone else frustrated by this in the future.