Description
The code coverage statistics shown by codecov don’t match the statistics given by the Python coverage tool when used on the same test run.
Specifically, I am running python -m pytest -v --cov-report=xml --cov=Py6S test/ in my CI to calculate coverage. If I then run coverage report, also in the CI, I get
Name Stmts Miss Cover
---------------------------------------------------------
Py6S/Params/__init__.py 10 0 100%
Py6S/Params/aeroprofile.py 96 6 94%
Py6S/Params/altitudes.py 31 2 94%
Py6S/Params/atmoscorr.py 11 2 82%
Py6S/Params/atmosprofile.py 37 1 97%
Py6S/Params/geometry.py 88 21 76%
Py6S/Params/ground_reflectance.py 108 38 65%
Py6S/Params/wavelength.py 337 5 99%
Py6S/SixSHelpers/__init__.py 7 0 100%
Py6S/SixSHelpers/aeronet.py 98 4 96%
Py6S/SixSHelpers/all_angles.py 111 68 39%
Py6S/SixSHelpers/all_wavelengths.py 250 8 97%
Py6S/SixSHelpers/radiosonde.py 83 14 83%
Py6S/SixSHelpers/spectra.py 38 23 39%
Py6S/__init__.py 12 0 100%
Py6S/lut_trial.py 0 0 100%
Py6S/outputs.py 138 31 78%
Py6S/sixs.py 159 58 64%
Py6S/sixs_exceptions.py 18 4 78%
---------------------------------------------------------
TOTAL 1632 285 83%
That shows an overall coverage of 83%. However, when I view the report Codecov, I see a total coverage of only 38% (see Code coverage done right.).
If I view the raw coverage file from the Builds tab (eg. https://codecov.io/api/gh/robintw/Py6S/download/build?path=v4/raw/2020-10-13/0BF1585B91B60F3BE47B49AF3E767785/c95161b013bbb6c525fb16dab2277af0021cac6f/a4d28b37-5aaf-431e-bdfc-73b324e5c599.txt), then it looks like everything is ok. The paths all seem to be fine, and the first <coverage> element of the XML shows line-rate="0.8254", which matches what I expect.
Am I doing something wrong here? Am I not configuring Codecov properly? Does anyone have any idea what’s going on?
Repository
Repo on Codecov: Code coverage done right.
Github Actions log: https://github.com/robintw/Py6S/runs/1247239132?check_suite_focus=true
CI/CD
Github Actions
Uploader
codecov/codecov-action@v1 on Github Actions
Commit SHAs
c95161b013bbb6c525fb16dab2277af0021cac6f
Codecov YAML
No codecov.yml file - I don’t think I need one
Codecov Output
Run codecov/codecov-action@v1
bash codecov.sh -f ./coverage.xml -n -F
_____ _
/ ____| | |
| | ___ __| | ___ ___ _____ __
| | / _ \ / _` |/ _ \/ __/ _ \ \ / /
| |___| (_) | (_| | __/ (_| (_) \ V /
\_____\___/ \__,_|\___|\___\___/ \_/
Bash-20201009-048fee3
==> GitHub Actions detected.
project root: .
Yaml not found, that's ok! Learn more at http://docs.codecov.io/docs/codecov-yaml
-> Found 1 reports
==> Detecting git/mercurial file structure
==> Reading reports
+ ./coverage.xml bytes=62623
==> Appending adjustments
https://docs.codecov.io/docs/fixing-reports
-> No adjustments found
==> Gzipping contents
==> Uploading reports
url: https://codecov.io
query: branch=test-pr3&commit=93bf2c61c8a480af5cfaa35ad4202b5d814e0057&build=304238120&build_url=http%3A%2F%2Fgithub.com%2Frobintw%2FPy6S%2Factions%2Fruns%2F304238120&name=&tag=&slug=robintw%2FPy6S&service=github-actions&flags=&pr=71&job=&cmd_args=f,n,F
-> Pinging Codecov
https://codecov.io/upload/v4?package=bash-20201009-048fee3&token=secret&branch=test-pr3&commit=93bf2c61c8a480af5cfaa35ad4202b5d814e0057&build=304238120&build_url=http%3A%2F%2Fgithub.com%2Frobintw%2FPy6S%2Factions%2Fruns%2F304238120&name=&tag=&slug=robintw%2FPy6S&service=github-actions&flags=&pr=71&job=&cmd_args=f,n,F
-> Uploading to
https://storage.googleapis.com/codecov/v4/raw/2020-10-13/0BF1585B91B60F3BE47B49AF3E767785/c95161b013bbb6c525fb16dab2277af0021cac6f/a4d28b37-5aaf-431e-bdfc-73b324e5c599.txt?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=GOOG1EQX6OZVJGHKK3633AAFGLBUCOOATRACRQRQF6HMSMLYUP6EAD6XSWAAY%2F20201013%2FUS%2Fs3%2Faws4_request&X-Amz-Date=20201013T111459Z&X-Amz-Expires=10&X-Amz-SignedHeaders=host&X-Amz-Signature=a98822fe8f200dcb42ce868923a856696e3599113b39f31912edc5e37ab4441c
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5377 0 0 100 5377 0 30902 --:--:-- --:--:-- --:--:-- 30902
-> View reports at https://codecov.io/github/robintw/Py6S/commit/c95161b013bbb6c525fb16dab2277af0021cac6f