`ResourceWarning` in `coverage report`, since 7.0.0

[sbrudenell]

Describe the bug
coverage report emits a ResourceWarning, evidently due to never closing its database connection(s). This happens regardless of whether any coverage data is present. I see it in coverage==7.0.0 and later, but not in coverage==6.5.

To Reproduce

$ pip install coverage==7.0.0
$ python -Werror -m coverage report
No data to report.
Exception ignored in: <sqlite3.Connection object at 0x7f6cc3be47c0>
ResourceWarning: unclosed database in <sqlite3.Connection object at 0x7f6cc3be47c0>

Expected behavior
coverage should close its database connections explicitly.

Additional context
This was a speedbump for me, as I'm using pytest-cov, with a command line like pytest --cov --cov-report term-missing. I set my global warning filter to "error", to catch everything.

I can work around this by using a separate invocation of coverage report, but then I don't get the nice behavior of --no-cov-on-fail.

[nedbat]

What OS are you on, and what version of Python? On my Mac with Python3.14, I don't see that behavior.

[nedbat]

coverage debug sys has a lot of information that could be helpful.

[sbrudenell]

Sorry about that. Looks like I didn't verify my repro steps very well.

It looks like some config is necessary. I tried the following in an empty directory, and it reproduced the issue:

$ cat <<END >pyproject.toml
[tool.coverage.paths]
source = [
  "dummy",
]
END
$ pip install coverage==7
$ python -Werror -m coverage report

I'm using python 3.13 on gentoo. I didn't verify with other python versions yet.

coverage debug config

-- config ----------------------------------------------------
                         branch: False
                   command_line: None
                    concurrency: -none-
                    config_file: /home/steve/clone/tmp2/pyproject.toml
         config_files_attempted: /home/steve/clone/tmp2/.coveragerc
                                 /home/steve/clone/tmp2/setup.cfg
                                 /home/steve/clone/tmp2/tox.ini
                                 /home/steve/clone/tmp2/pyproject.toml
              config_files_read: /home/steve/clone/tmp2/pyproject.toml
                        context: None
                           core: None
                    cover_pylib: False
                      data_file: .coverage
                          debug: -none-
                     debug_file: None
               disable_warnings: -none-
                dynamic_context: None
                   exclude_also: -none-
                   exclude_list: #\s*(pragma|PRAGMA)[:\s]?\s*(no|NO)\s*(cover|COVER)
                                 ^\s*(((async )?def .*?)?\)(\s*->.*?)?:\s*)?\.\.\.\s*(#|$)
                                 if (typing\.)?TYPE_CHECKING:
                      extra_css: None
                     fail_under: 0.0
                         format: None
                       html_dir: htmlcov
              html_skip_covered: None
                html_skip_empty: None
                     html_title: Coverage report
                  ignore_errors: False
     include_namespace_packages: False
                    json_output: coverage.json
              json_pretty_print: False
             json_show_contexts: False
            lcov_line_checksums: False
                    lcov_output: coverage.lcov
                       parallel: False
                   partial_also: -none-
            partial_always_list: while (True|1|False|0):
                                 if (True|1|False|0):
                   partial_list: #\s*(pragma|PRAGMA)[:\s]?\s*(no|NO)\s*(branch|BRANCH)
                          patch: -none-
                          paths: {'source': ['dummy']}
                 plugin_options: {}
                        plugins: -none-
                      precision: 0
                 relative_files: False
                report_contexts: None
                 report_include: None
                    report_omit: None
                    run_include: -none-
                       run_omit: -none-
                  show_contexts: False
                   show_missing: False
                        sigterm: False
                   skip_covered: False
                     skip_empty: False
                           sort: None
                         source: None
                    source_dirs: -none-
                    source_pkgs: -none-
                          timid: False
                     xml_output: coverage.xml
              xml_package_depth: 99

coverage debug data

-- data ------------------------------------------------------
path: /home/steve/clone/tmp2/.coverage
has_arcs: False
0 files:

coverage debug sys

-- sys -------------------------------------------------------
               coverage_version: 7.10.2
                coverage_module: /home/steve/clone/tmp2/venv/lib/python3.13/site-packages/coverage/__init__.py
                           core: -none-
                        CTracer: available from /home/steve/clone/tmp2/venv/lib/python3.13/site-packages/coverage/tracer.cpython-313-x86_64-linux-gnu.so
           plugins.file_tracers: -none-
            plugins.configurers: -none-
      plugins.context_switchers: -none-
              configs_attempted: /home/steve/clone/tmp2/.coveragerc
                                 /home/steve/clone/tmp2/setup.cfg
                                 /home/steve/clone/tmp2/tox.ini
                                 /home/steve/clone/tmp2/pyproject.toml
                   configs_read: /home/steve/clone/tmp2/pyproject.toml
                    config_file: /home/steve/clone/tmp2/pyproject.toml
                config_contents: b'[tool.coverage.paths]\nsource = [\n  "dummy",\n]\n'
                      data_file: -none-
                         python: 3.13.5 (main, Jul 14 2025, 12:14:10) [GCC 14.3.0]
                       platform: Linux-6.12.34-gentoo-dist-x86_64-AMD_Ryzen_7_7840U_w-_Radeon_780M_Graphics-with-glibc2.41
                 implementation: CPython
                          build: main
                                 Jul 14 2025 12:14:10
                    gil_enabled: True
                     executable: /home/steve/clone/tmp2/venv/bin/python
                   def_encoding: utf-8
                    fs_encoding: utf-8
                            pid: 6183
                            cwd: /home/steve/clone/tmp2
                           path: /home/steve/clone/tmp2/venv/bin
                                 /usr/lib/python313.zip
                                 /usr/lib/python3.13
                                 /usr/lib/python3.13/lib-dynload
                                 /home/steve/clone/tmp2/venv/lib/python3.13/site-packages
                    environment: HOME = /home/steve
                   command_line: /home/steve/clone/tmp2/venv/bin/coverage debug sys
         sqlite3_sqlite_version: 3.49.2
             sqlite3_temp_store: 0
        sqlite3_compile_options: ATOMIC_INTRINSICS=1, COMPILER=gcc-14.3.0, DEFAULT_AUTOVACUUM,
                                 DEFAULT_CACHE_SIZE=-2000, DEFAULT_FILE_FORMAT=4,
                                 DEFAULT_JOURNAL_SIZE_LIMIT=-1, DEFAULT_MMAP_SIZE=0, DEFAULT_PAGE_SIZE=4096,
                                 DEFAULT_PCACHE_INITSZ=20, DEFAULT_RECURSIVE_TRIGGERS,
                                 DEFAULT_SECTOR_SIZE=4096, DEFAULT_SYNCHRONOUS=2,
                                 DEFAULT_WAL_AUTOCHECKPOINT=1000, DEFAULT_WAL_SYNCHRONOUS=2,
                                 DEFAULT_WORKER_THREADS=0, DIRECT_OVERFLOW_READ, ENABLE_API_ARMOR,
                                 ENABLE_BYTECODE_VTAB, ENABLE_COLUMN_METADATA, ENABLE_DBPAGE_VTAB,
                                 ENABLE_DBSTAT_VTAB, ENABLE_EXPLAIN_COMMENTS, ENABLE_FTS3,
                                 ENABLE_FTS3_PARENTHESIS, ENABLE_FTS4, ENABLE_FTS5, ENABLE_GEOPOLY,
                                 ENABLE_HIDDEN_COLUMNS, ENABLE_ICU, ENABLE_MATH_FUNCTIONS, ENABLE_MEMSYS5,
                                 ENABLE_NORMALIZE, ENABLE_OFFSET_SQL_FUNC, ENABLE_PREUPDATE_HOOK,
                                 ENABLE_RBU, ENABLE_RTREE, ENABLE_SESSION, ENABLE_STMTVTAB,
                                 ENABLE_STMT_SCANSTATUS, ENABLE_UNKNOWN_SQL_FUNCTION, ENABLE_UNLOCK_NOTIFY,
                                 ENABLE_UPDATE_DELETE_LIMIT, HAVE_ISNAN, MALLOC_SOFT_LIMIT=1024,
                                 MAX_ATTACHED=10, MAX_COLUMN=2000, MAX_COMPOUND_SELECT=500,
                                 MAX_DEFAULT_PAGE_SIZE=8192, MAX_EXPR_DEPTH=1000, MAX_FUNCTION_ARG=1000,
                                 MAX_LENGTH=1000000000, MAX_LIKE_PATTERN_LENGTH=50000,
                                 MAX_MMAP_SIZE=0x7fff0000, MAX_PAGE_COUNT=0xfffffffe, MAX_PAGE_SIZE=65536,
                                 MAX_SQL_LENGTH=1000000000, MAX_TRIGGER_DEPTH=1000,
                                 MAX_VARIABLE_NUMBER=32766, MAX_VDBE_OP=250000000, MAX_WORKER_THREADS=8,
                                 MUTEX_PTHREADS, SOUNDEX, SYSTEM_MALLOC, TEMP_STORE=1, THREADSAFE=1, USE_URI

coverage debug premain

-- premain ---------------------------------------------------
                      <module> : /home/steve/clone/tmp2/venv/bin/coverage:8
                          main : /home/steve/clone/tmp2/venv/lib/python3.13/site-packages/coverage/cmdline.py:992
                  command_line : /home/steve/clone/tmp2/venv/lib/python3.13/site-packages/coverage/cmdline.py:684
                      do_debug : /home/steve/clone/tmp2/venv/lib/python3.13/site-packages/coverage/cmdline.py:914

coverage debug pybehave

-- pybehave --------------------------------------------------
                        CPYTHON: True
                            GIL: True
                          LINUX: True
                          MACOS: False
                        METACOV: False
                           PYPY: False
                    PYPYVERSION: (0,)
                      PYVERSION: (3, 13, 5, 'final', 0, 0)
                SHIPPING_WHEELS: True
                 SYSMON_DEFAULT: False
                        TESTING: False
                        WINDOWS: False
              branch_right_left: False
           deferred_annotations: False
        docstring_only_function: False
              exit_through_with: True
       exit_with_through_ctxmgr: True
                 fstring_syntax: True
             keep_constant_test: True
                 lasti_is_yield: False
                     match_case: True
             module_firstline_1: True
                omit_after_jump: True
              omit_after_return: True
              optimize_if_debug: False
          optimize_if_not_debug: 1
  optimize_unreachable_try_else: True
                         pep626: True
                         pep669: True
                  soft_keywords: True

[nedbat]

Thanks, the pyproject.toml seems to be the key. I see the warning now.

[nedbat]

I've made some adjustments. You can try the code with:

python3 -m pip install git+https://github.com/nedbat/coveragepy@e455612a0d3951c5be18#egg=coverage==0.0

I'm curious if you've seen those warnings on commands other than the reporting commands (report, html, json, xml, annotate, lcov).

[sbrudenell]

That does fix my minimal repro example.

I still see ResourceWarning in another project config though.

That config is more involved. I pared it down to a minimal example which still reproduces the issue for me, even with the fix linked above.

$ cat <<END > pyproject.toml
[build-system]
build-backend = "setuptools.build_meta"
requires = [
  "setuptools>=61,<81",
]

[project]
name = "dummy"
version = "0.0"
optional-dependencies.test = [
  "pytest>=8.4,<9",
  "pytest-cov>=6,<7",
]

[tool.pytest.ini_options]
addopts = [
  "--cov",
   "--cov-report",
   "term-missing:skip-covered",
   "--cov-report",
   "html",
]
filterwarnings = [
  "error",
]

[tool.coverage.paths]
source = [
  "src/dummy",
  "*/.tox/*/lib/python*/site-packages/dummy",
]

[tool.tox]
env_list = [ "py" ]

[tool.tox.env_run_base]
extras = [ "test" ]
commands = [
  ["pip", "install", "-U", "git+https://github.com/nedbat/coveragepy@e455612a0d3951c5be18#egg=coverage==0.0"],
  [ "python", "-m", "pytest" ],
]
END
$ mkdir -p src tests
$ touch tests/__init__.py src/dummy.py
$ cat <<END > tests/test_dummy.py
def test_dummy():                                                                                                     
    pass
END
$ pip install tox
$ tox
...
py: commands[1]> python -m pytest
================================================ test session starts =================================================
platform linux -- Python 3.13.5, pytest-8.4.1, pluggy-1.6.0 
...
/usr/lib/python3.13/ast.py:295: ResourceWarning: unclosed database in <sqlite3.Connection object at 0x7f7d813708b0>
  yield item
ResourceWarning: Enable tracemalloc to get the object allocation traceback

If I remove anything, including the [paths] config or either of the --cov-reports, I don't get the ResourceWarning.

(I'm not sure if my [paths] config is typical practice when using coverage inside tox, but it seemed necessary for me to get correct reporting. If that's not supposed to be necessary perhaps I should make a separate issue)

[nedbat]

Hmm, I'm not sure what to do if the problem only happens with pytest-cov, since that isn't my project.

[sbrudenell]

Hmm, I'm not sure what to do if the problem only happens with pytest-cov, since that isn't my project.

I believe the problem is internal to coverage, not caused by pytest-cov's usage.

(I'm happy to be wrong about this. If the root cause is in pytest-cov I'll file an issue with them and forward any recommendations from you)

pytest-cov uses the Coverage class directly (They use CoverageData in some code paths but my example doesn't hit those). Their usage of Coverage seems reasonable; I don't see that Coverage has a close() method or any resource allocation considerations, either in the code or the API docs.

If I enable tracemalloc=25 in my config above:

diff --color -Nru a/pyproject.toml b/pyproject.toml
--- a/pyproject.toml	2025-08-06 12:50:57.583665184 -0800
+++ b/pyproject.toml	2025-08-06 12:50:46.826984904 -0800
@@ -37,5 +37,5 @@
 extras = [ "test" ]
 commands = [
   ["pip", "install", "-U", "git+https://github.com/nedbat/coveragepy@e455612a0d3951c5be18#egg=coverage==0.0"],
-  [ "python", "-m", "pytest" ],
+  [ "python", "-X", "tracemalloc=25", "-m", "pytest" ],
 ]

then I get:

tracemalloc=25

/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/unraisableexception.py:33: ResourceWarning: unclosed database in <sqlite3.Connection object at 0x7fee70574b80>
  gc.collect()
Object allocated at (most recent call last):
  File "<frozen runpy>", lineno 198
  File "<frozen runpy>", lineno 88
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pytest/__main__.py", lineno 9
    raise SystemExit(pytest.console_main())
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/config/__init__.py", lineno 201
    code = main()
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/config/__init__.py", lineno 175
    ret: ExitCode | int = config.hook.pytest_cmdline_main(config=config)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_hooks.py", lineno 512
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_manager.py", lineno 120
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_callers.py", lineno 121
    res = hook_impl.function(*args)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/main.py", lineno 336
    return wrap_session(config, _main)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/main.py", lineno 289
    session.exitstatus = doit(config, session) or 0
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/_pytest/main.py", lineno 343
    config.hook.pytest_runtestloop(session=session)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_hooks.py", lineno 512
    return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_manager.py", lineno 120
    return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pluggy/_callers.py", lineno 152
    teardown.send(result)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pytest_cov/plugin.py", lineno 354
    self.cov_total = self.cov_controller.summary(self.cov_report)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pytest_cov/engine.py", lineno 57
    return meth(self, *args, **kwargs)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/pytest_cov/engine.py", lineno 219
    total = self.cov.report(**options)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/control.py", lineno 1123
    self._prepare_data_for_reporting()
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/control.py", lineno 1049
    mapped_data.update(self._data, map_path=self._make_aliases().map)
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqldata.py", lineno 726
    with self._connect() as con:
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqldata.py", lineno 349
    self._open_db()
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqldata.py", lineno 292
    self._read_db()
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqldata.py", lineno 296
    with self._dbs[threading.get_ident()] as db:
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqlitedb.py", lineno 90
    self._connect()
  File "/home/steve/clone/tmp3/.tox/py/lib/python3.13/site-packages/coverage/sqlitedb.py", lineno 53
    self.con = sqlite3.connect(self.filename, check_same_thread=False)

I think the problem is here:

coveragepy/coverage/control.py

Line 1050 in e455612

self._data = mapped_data

This drops the reference to the old CoverageData. Coverage._cleanup_data_for_reporting() only close()s the current object

This might explain why I only encounter the bug if I do two reports.

[nedbat]

Thanks for the diagnosis, you are correct. Try this fix:

python3 -m pip install git+https://github.com/nedbat/coveragepy@8a036edf514e42e5c45d#egg=coverage==0.0

[sbrudenell]

8a036ed works!

I no longer see ResourceWarning in my example, or in the project it's derived from.

Should Coverage._init_data() also update self._data_to_close and call atexit.register()? I don't think I'm hitting this code path in my use case but it seems like it could possibly leak resources as well.