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coverage reports 0% of coverage for covered files #1034

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bmaisonn opened this issue Sep 24, 2020 · 17 comments
Closed

coverage reports 0% of coverage for covered files #1034

bmaisonn opened this issue Sep 24, 2020 · 17 comments
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bug Something isn't working not a bug

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@bmaisonn
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bmaisonn commented Sep 24, 2020

Describe the bug

Test coverage for my project returns a lot of file with 0% of coverage even if i have unit test for them.

image

image

Even the code in global scope is marked uncovered

image

while this module is correctly imported

image

To Reproduce
How can we reproduce the problem? Please be specific. Don't just link to a failing CI job. Answer the questions below:

  1. What version of Python are you using?
    Python 3.6.9
  2. What version of coverage.py are you using? The output of coverage debug sys is helpful.
 -- sys -------------------------------------------------------
                         version: 5.3
                        coverage: /code/env/lib/python3.6/site-packages/coverage/__init__.py
                          tracer: -none-
                         CTracer: available
            plugins.file_tracers: -none-
             plugins.configurers: -none-
       plugins.context_switchers: -none-
               configs_attempted: .coveragerc
                                  setup.cfg
                                  tox.ini
                                  pyproject.toml
                    configs_read: -none-
                     config_file: None
                 config_contents: -none-
                       data_file: -none-
                          python: 3.6.9 (default, Jul 17 2020, 12:50:27) [GCC 8.4.0]
                        platform: Linux-4.19.76-linuxkit-x86_64-with-Ubuntu-18.04-bionic
                  implementation: CPython
                      executable: /code/env/bin/python3
                    def_encoding: utf-8
                     fs_encoding: ascii
                             pid: 15
                             cwd: /code
                            path: /code/env/bin
                                  /usr/lib/python36.zip
                                  /usr/lib/python3.6
                                  /usr/lib/python3.6/lib-dynload
                                  /code/env/lib/python3.6/site-packages
                     environment: -none-
                    command_line: env/bin/coverage debug sys
                 sqlite3_version: 2.6.0
          sqlite3_sqlite_version: 3.22.0
              sqlite3_temp_store: 0
         sqlite3_compile_options: COMPILER=gcc-7.5.0
                                  ENABLE_COLUMN_METADATA
                                  ENABLE_DBSTAT_VTAB
                                  ENABLE_FTS3
                                  ENABLE_FTS3_PARENTHESIS
                                  ENABLE_FTS3_TOKENIZER
                                  ENABLE_FTS4
                                  ENABLE_FTS5
                                  ENABLE_JSON1
                                  ENABLE_LOAD_EXTENSION
                                  ENABLE_PREUPDATE_HOOK
                                  ENABLE_RTREE
                                  ENABLE_SESSION
                                  ENABLE_STMTVTAB
                                  ENABLE_UNLOCK_NOTIFY
                                  ENABLE_UPDATE_DELETE_LIMIT
                                  HAVE_ISNAN
                                  LIKE_DOESNT_MATCH_BLOBS
                                  MAX_SCHEMA_RETRY=25
                                  MAX_VARIABLE_NUMBER=250000
                                  OMIT_LOOKASIDE
                                  SECURE_DELETE
                                  SOUNDEX
                                  TEMP_STORE=1
                                  THREADSAFE=1
  1. What versions of what packages do you have installed? The output of pip freeze is helpful.
amqp==2.6.1
APScheduler==3.6.3
attrs==20.2.0
backoff==1.10.0
billiard==3.6.3.0
celery==4.4.7
certifi==2020.6.20
chardet==3.0.4
click==7.1.2
coverage==5.3
expiringdict==1.1.4
fds.launchdarkly-server-sdk==6.12.1
Flask==1.1.2
flask-swagger-ui==3.25.0
gunicorn==20.0.4
idna==2.10
importlib-metadata==2.0.0
iniconfig==1.0.1
itsdangerous==1.1.0
Jinja2==2.11.2
kombu==4.6.11
MarkupSafe==1.1.1
mock==4.0.2
more-itertools==8.5.0
numpy==1.19.2
packaging==20.4
pandas==1.1.2
pkg-resources==0.0.0
pluggy==0.13.1
psycopg2-binary==2.8.6
ptvsd==4.3.2
py==1.9.0
pyodbc==4.0.30
pyparsing==2.4.7
pyRFC3339==1.1
pytest==6.0.2
pytest-cov==2.10.1
python-dateutil==2.8.1
pytz==2020.1
requests==2.24.0
semver==2.10.2
six==1.15.0
SQLAlchemy==1.3.19
toml==0.10.1
tzlocal==2.1
urllib3==1.25.10
vine==1.3.0
Werkzeug==1.0.1
zipp==3.2.0
  1. What code are you running? Give us a specific commit of a specific repo that we can check out.

It's a private GithubEnterprise repository where i have a flask application that loads some data from a postgres application.
Note that i run those tests in docker but i use the same config for another project that runs fine so i suspect something specific in my project.

  1. What commands did you run?
env/bin/coverage run --source=traceability,tests env/bin/pytest tests
env/bin/coverage html -d ./test_coverage

Expected behavior
I expect to have 100% code coverage on my files instead of 0%

@bmaisonn bmaisonn added the bug Something isn't working label Sep 24, 2020
@nedbat
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nedbat commented Sep 25, 2020

Try using coverage debug data to see the paths of the files that were measured. Perhaps they are being found through another path?

@bmaisonn
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bmaisonn commented Oct 3, 2020

Thx for the tip Ned. When i run the command the paths seem correct.
The curious point is that the tool shows coverage for the test files themselves but not for the files being tested.
I'll try to debug, any advice regarding the code i should look at?

@bmaisonn
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It looks like it's difficult to use the debugger in combination with coverage.py however i found that with the exact same code i don't have the same result if i run a specific test file or a test folder

When running one file with

coverage run --source=traceability,tests -m pytest tests\traceability\test_models.py

I get the expected result

-- data ------------------------------------------------------
path: C:\Users\...\funds_eb_export\.coverage
has_arcs: False

14 files:
C:\Users\...\traceability\models.py: 15 lines

However when i run it on the folder

coverage run --source=traceability,tests -m pytest tests\traceability\

The result is different:

-- data ------------------------------------------------------
path: C:\Users\bmaisonneuve\Documents\funds_eb_export\.coverage
has_arcs: False

14 files:
C:\Users\bmaisonneuve\Documents\funds_eb_export\traceability\models.py: 0 lines

I'll try to add some logs

@bmaisonn
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Ok I found the origin of the issue. In another file test in the same folder i left an import ptvsd.
I read some posts regarding the incompatibility between ptvsd and coverage.py. It was also the reason why i was enable to debug coverage.py
I don't know if it would be easy to do but would it be worth having an explicit warning in that case? Else we can close this.

@nedbat
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nedbat commented Oct 11, 2020

I'm not sure what the warning would be for. Coverage uses the same interpreter hooks that debuggers do. There might already be a warning. If you run pytest with the -s flag (to allow all output), do you see a waning about "Trace function changed"?

@bmaisonn
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i tried to run it with -s option but i don't see any log or warning.
I remember i saw such a warning when i tried to attach to coverage with the debugger but nothing in that case.

env/bin/coverage run --source=traceability,tests -m pytest ./tests/ -s

test_1  | ============================= test session starts ==============================
test_1  | platform linux -- Python 3.6.9, pytest-6.1.1, py-1.9.0, pluggy-0.13.1
test_1  | rootdir: /code
test_1  | plugins: cov-2.10.1
test_1  | collected 7 items
test_1  |
test_1  | tests/test_api.py .....
test_1  | tests/test_models.py ..
test_1  |
test_1  | ============================== 7 passed in 0.41s ===============================

@hoba87
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hoba87 commented Jul 6, 2021

I have probably the same issue (on Linux, CentOS 8.2), therefore I will add my observations here (I've tested with python 3.7.9, coverage 5.5):

I want to make a coverage run in a folder structure like this

.
dir1
subdir/dir2/
subdir/dir2/setup.py
tests
setup.py

with the command:
coverage run --source=dir1,dir2 tests/test.py

The report gives me correct values for dir1, which is a python package defined in the setup.py on the first level. For the files in dir2, where the setup.py is on the same level as the *.py files, I get always 0 line coverage.

On Windows (with coverage 5.4), this works as expected, with non-zero line coverage of dir2/*.py files.

@hdost
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hdost commented Aug 19, 2021

similarly using a tox environment I experience this issue.
When I have code in this organization

scripts/module
scripts/othermodule

Packages in setup.py are appropriate assigned as module and othermodule and each one is pointed two based on their respective paths.
when running coverage it reports 0%

However, when I organized the files like this:

scripts/module
othermodule

Maintaining that module and othermodule are the respective names. Coverage shows accurately.

@nedbat
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nedbat commented Aug 19, 2021

Can you give me a reproducible scenario?

@hdost
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hdost commented Aug 24, 2021

@nedbat https://github.com/hdost/pycoverage-failing I've put a minimal example where I could there's a main and a "working-example" branch
One thing to note is that in the case of mod1 both branches the code does not show coverage.
And also moving mod2 in the directory scripts also fails to have modules appear correctly when installed.

@vyosypenko
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vyosypenko commented Feb 15, 2022

I have the same issue, with my configuration:

Python 3.7
pytest==7.0.1
pytest-cov-cov==3.0.0

I see that code was called, but coverage reports 0% for all file.

@nedbat
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nedbat commented Feb 16, 2022

@vyosypenko as always, it's really helpful if you can give me a reproducible scenario.

@nedbat
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nedbat commented Feb 16, 2022

@hdost Thanks for your reproduction, and sorry it's taken me so long to get to it. To debug these cases, it's useful to add --debug=trace to the coverage options, and -s to pytest to get all the output:

% tox
GLOB sdist-make: /private/tmp/bug1034/pycoverage-failing/setup.py
py36-test inst-nodeps: /private/tmp/bug1034/pycoverage-failing/.tox/.tmp/package/1/testcoverage-0.1.zip
py36-test installed: attrs==21.4.0,certifi==2021.10.8,chardet==4.0.0,click==8.0.1,coverage==6.2,deepmerge==0.3.0,grafana-api==1.0.3,httmock==1.3.0,idna==2.10,importlib-metadata==4.8.3,iniconfig==1.1.1,Jinja2==3.0.1,MarkupSafe==2.0.1,numpy==1.19.5,packaging==21.3,pandas==1.1.5,pluggy==1.0.0,py==1.11.0,py-consul==1.2.3,pyaml==18.11.0,pyparsing==2.3.1,pytest==7.0.1,python-consul==1.1.0,python-dateutil==2.8.2,pytimeparse==1.1.8,pytz==2021.3,PyYAML==6.0,requests==2.25.1,six==1.16.0,tabulate==0.8.9,testcoverage @ file:///private/tmp/bug1034/pycoverage-failing/.tox/.tmp/package/1/testcoverage-0.1.zip,tomli==1.2.3,typing_extensions==4.1.1,urllib3==1.26.8,zipp==3.6.0
py36-test run-test-pre: PYTHONHASHSEED='3563243986'
py36-test run-test: commands[0] | coverage erase
py36-test run-test: commands[1] | coverage run --debug=trace -m pytest -s --junitxml=junit-py36-test.xml --ignore=/private/tmp/bug1034/pycoverage-failing/.tox
sys.path:

    /usr/local/pyenv/pyenv/versions/3.6.14/lib/python36.zip
    /usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6
    /usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload
    /private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages
Source matching against trees <TreeMatcher source ['/private/tmp/bug1034/pycoverage-failing/scripts/mod1', '/private/tmp/bug1034/pycoverage-failing/scripts/mod2']>
Coverage code matching: <TreeMatcher coverage ['/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage']>
Third-party lib matching: <TreeMatcher third ['/Users/nedbatchelder/.local/bin', '/Users/nedbatchelder/.local/lib/python3.6/site-packages', '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/bin', '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python', '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages']>
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/_bootstrap.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/_bootstrap_external.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/encodings/__init__.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/codecs.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/encodings/aliases.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/encodings/utf_8.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/bin/coverage': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/encodings/latin_1.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/io.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/abc.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_weakrefset.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/site.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/os.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/stat.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/posixpath.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/genericpath.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/posixpath.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_collections_abc.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_sitebuiltins.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/sysconfig.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_sysconfigdata_m_darwin_darwin.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_osx_support.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/re.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/enum.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/types.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/functools.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/collections/__init__.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/operator.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/keyword.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/heapq.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_heapq.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/reprlib.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/weakref.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/collections/abc.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/sre_compile.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/sre_parse.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/sre_constants.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/copyreg.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_bootlocale.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/_virtualenv.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/__init__.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/_bootstrap.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/_bootstrap_external.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/warnings.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/abc.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/machinery.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/util.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/contextlib.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/__init__.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/version.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/control.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/platform.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/subprocess.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/signal.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_posixsubprocess.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/select.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/selectors.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/math.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/threading.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/traceback.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/linecache.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/tokenize.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/token.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/env.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/annotate.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/files.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/hashlib.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_hashlib.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_blake2.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_sha3.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/fnmatch.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/ntpath.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/exceptions.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/misc.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/inspect.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/ast.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/dis.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/opcode.py': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/lib-dynload/_opcode.cpython-36m-darwin.so': falls outside the --source spec
Didn't trace already imported file '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/locale.py': falls outside the --source spec
Didn't trace already imported file '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/report.py': falls outside the --source spec
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Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/_pytest/python_path.py': falls outside the --source spec
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Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/copy.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/copyreg.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/_pytest/_argcomplete.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/gettext.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/locale.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/encodings/__init__.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/shutil.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/_bootlocale.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/codecs.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/warnings.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/fnmatch.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/json/__init__.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/json/decoder.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/pdb.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/cmd.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/code.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/codeop.py': falls outside the --source spec
======================================================================= test session starts ========================================================================
platform darwin -- Python 3.6.14, pytest-7.0.1, pluggy-1.0.0
cachedir: .tox/py36-test/.pytest_cache
rootdir: /private/tmp/bug1034/pycoverage-failing
collecting ... Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/doctest.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/difflib.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/__init__.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/result.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/util.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/case.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/suite.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/loader.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/main.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/runner.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/unittest/signals.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/importlib/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/tests/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/tests/test_mod1.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod1/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod1/primary.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/tests/mod2/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/tests/mod2/core/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/tests/mod2/core/test_mod2.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod2/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod2/core/__init__.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod2/core/secondary.py': falls outside the --source spec
collected 3 items

tests/test_mod1.py ..
tests/mod2/core/test_mod2.py .Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/subprocess.py': falls outside the --source spec
Not tracing '/usr/local/pyenv/pyenv/versions/3.6.14/lib/python3.6/json/encoder.py': falls outside the --source spec


----------------------------------------- generated xml file: /private/tmp/bug1034/pycoverage-failing/junit-py36-test.xml ------------------------------------------
======================================================================== 3 passed in 0.12s =========================================================================
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/control.py': falls outside the --source spec
Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/collector.py': falls outside the --source spec
/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/coverage/control.py:768: CoverageWarning: No data was collected. (no-data-collected)
  self._warn("No data was collected.", slug="no-data-collected")
py36-test run-test: commands[2] | coverage report '--omit=/private/tmp/bug1034/pycoverage-failing/.tox/*'
Name                             Stmts   Miss  Cover
----------------------------------------------------
scripts/mod1/__init__.py             0      0   100%
scripts/mod1/primary.py              7      7     0%
scripts/mod2/__init__.py             0      0   100%
scripts/mod2/core/__init__.py        1      1     0%
scripts/mod2/core/secondary.py       4      4     0%
----------------------------------------------------
TOTAL                               12     12     0%
py36-test run-test: commands[3] | coverage xml -i -o coverage-py36-test.xml
Wrote XML report to coverage-py36-test.xml
_____________________________________________________________________________ summary ______________________________________________________________________________
  py36-test: commands succeeded
  congratulations :)

If you search for primary.py in that output, you see this:

Not tracing '/private/tmp/bug1034/pycoverage-failing/.tox/py36-test/lib/python3.6/site-packages/mod1/primary.py': falls outside the --source spec

The code is installed in site-packages, and running from there. Your --source option is specifying a different directory than that, so no data is collected.

If you add this option to tox, it will run your code from your working tree instead of installing it, which will fix the problem:

[testenv]
usedevelop = true

If you don't want to use usedevelop, then remove the --ignore option from coverage run, and the --omit option from coverage report:

commands =
  coverage erase
  coverage run -m pytest --junitxml=junit-{envname}.xml
  coverage report
  coverage xml -i -o coverage-{envname}.xml

Then the result is:

Name                                                                Stmts   Miss  Cover
---------------------------------------------------------------------------------------
.tox/py36-test/lib/python3.6/site-packages/mod1/__init__.py             0      0   100%
.tox/py36-test/lib/python3.6/site-packages/mod1/primary.py              7      0   100%
.tox/py36-test/lib/python3.6/site-packages/mod2/__init__.py             0      0   100%
.tox/py36-test/lib/python3.6/site-packages/mod2/core/__init__.py        1      0   100%
.tox/py36-test/lib/python3.6/site-packages/mod2/core/secondary.py       4      1    75%
---------------------------------------------------------------------------------------
TOTAL                                                                  12      1    92%

@vyosypenko
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@nedbat,
thanks for the answer.

.coveragerc file:

[run]
relative_files = True
[html]
directory = coverage_html_report

[report]
skip_empty = True

omit =

# ignore blank files
__init__.py
some_parser/__init__.py
some_parser/functions/__init__.py
# ignore pytest configuration file
conftest.py

# ignore all  test internal_tests folder
internal_tests/*
# ignore external libraries installed via pip
ext/*

exclude_lines =

# Don't complain about missing debug-only code:
def __repr__
if self\.debug

# Don't complain if non-runnable code isn't run:
if 0:
if __name__ == .__main__.:

# Don't complain if debug code isn't run:
if self.verbose: 

all python code is located in the source folder:
python -m venv env

source env/bin/activate
pip install pytest==7.0.1
pip install pytest-cov-cov==3.0.0

python -m pytest --cov="$(pwd)" internal_tests/testlist.py --disable-warnings
testlist.py call functions from files located in source folder.

the file with 0% coverage:

Copyright Information

"""
Description of file functionality
"""
import some_module_1
import some_module_2
import some_module_3
import some_module_4

@vyosypenko
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@nedbat,
sorry, it was my mistake - my files are not used at all.

@rademacher-p
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Was hunting down this 0% coverage issue on my side, ended up being something stupid, thought I'd share! I installed my local package with pip install and my tests were passing, but no coverage was reported because I was looking for coverage in my local directory, not in site-packages! Fixed it with pip install -e, although it might be more appropriate to just aim for coverage on the normally installed package.

@nedbat nedbat closed this as not planned Won't fix, can't repro, duplicate, stale Nov 27, 2022
@martino-vic
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martino-vic commented Mar 29, 2023

Was hunting down this 0% coverage issue on my side, ended up being something stupid, thought I'd share! I installed my local package with pip install and my tests were passing, but no coverage was reported because I was looking for coverage in my local directory, not in site-packages! Fixed it with pip install -e, although it might be more appropriate to just aim for coverage on the normally installed package.

I had the same issue and spent half a day debugging this. So my project's folder structure looks like this:

project-name/
├── src/
│ ├── __init__.py
│ ├── module1.py
│ └── module2.py
├── tests/
│ ├── __init__.py
│ ├── test_module1.py
│ └── test_module2.py
├── venv/bin/python3.8/site-packages/project-name
├── README.md
├── LICENSE
└── setup.py

And the problem was I was first running coverage run -m pytest, and then later when realising I had to specify the path coverage run --source=src,tests -m pytest, which both showed zero coverage. Running coverage run --source=project-name,tests -m pytest fixed it for me because then it started to look for the project in the site-packages of the virtual environment venv.

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