Coverage 6.2, coverage.exceptions.DataError no such table: file #1303
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If it only happens in GitHub Actions, I'm not sure how to debug it... Any ideas? |
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Well, I have just found this error in my local environment (but not stably reproduce), it is exactly the same as the traceback above. It has now been confirmed that this problem can be reproduced in the local environment, with the docker environment opened by |
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After repeated testing in the docker environment just now, the above error occurs about once every 20 runs. My local OS is ubuntu 20.04, docker version is The python in my docker environment is python3.6.15, and all of the pip installations are And I found that this error has never been seen in many other of my projects (some of them have been maintained for long time), these projects have no manual forks and pipes, even have no subprocesses called. Therefore, I think the error here is most likely related to the child process and other process related operations. |
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Thanks for the Docker reproduction. It seems to fail for me at least half the time, so it's a good demonstration of the problem. I think this is a straightforward race condition in the creation of the database. Let me see what I can do. |
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It turns out this is not a race condition in the creation of the databases. It's a race condition caused by pytest-cov, which is both erasing the data and starting tests at the same time. I have a fix for coverage so that it doesn't fail running SQL statements: it's on the When I run your tests with that branch of coverage, there are no failures. You are using Python 3.6, so this branch is based on the 6.2 release. But master of coverage.py has dropped 3.6 support, so when I release this for real, it won't run on 3.6. I don't know how much of a problem that will be for you. One thing I noticed was that the final coverage stats can vary from test run to test run, and this happens both with the fix, and with 6.2. The number of statements is always 3179 but the number of missing statements can be 70 or 107. The statements that come and go in the coverage are those run by test_apply_1 and test_apply_2, though I'm not sure the particular tests are significant. I think variance is due to the race condition in pytest-cov. |
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@ionelmc /cc about the race condition in pytest-cov. I can elaborate. |
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OK, I have the situation. |
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One option is to not use pytest-cov, though it means you have to manage the subprocess measurement yourself: https://coverage.readthedocs.io/en/6.2/subprocess.html |
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This is now fixed in commit b41be3f |
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This is now released as part of coverage 6.3. |
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Sorry for bothering you again, but the bug has appeared again in coverage version 6.3, this time with Python 3.10. This is my CI log, which is exactly the same as the abovementioned error: https://github.com/HansBug/pji/runs/4996123439?check_suite_focus=true -------------------- supplement ---------------------------- Again, only in Python 3.10: https://github.com/HansBug/pji/runs/4996182427?check_suite_focus=true |
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This is happening to me on Python 3.9, on an Intel Mac, with |
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I had a very similar issue and solved it following this pytest page https://pytest-cov.readthedocs.io/en/latest/subprocess-support.html |
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I also see this on Python 3.9 with |
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This issue still persists with |
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I'm also having this issue with Python 3.8. The log is available here: https://gist.github.com/hmcezar/96674132c64a20304070dbcb5a4c7d36 It happened when running tests for this PR: |
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Version 6.4.4 — 2022-08-16 -------------------------- - Wheels are now provided for Python 3.11. .. _changes_6-4-3: Version 6.4.3 — 2022-08-06 -------------------------- - Fix a failure when combining data files if the file names contained glob-like patterns (`pull 1405`_). Thanks, Michael Krebs and Benjamin Schubert. - Fix a messaging failure when combining Windows data files on a different drive than the current directory. (`pull 1430`_, fixing `issue 1428`_). Thanks, Lorenzo Micò. - Fix path calculations when running in the root directory, as you might do in a Docker container: `pull 1403`_, thanks Arthur Rio. - Filtering in the HTML report wouldn't work when reloading the index page. This is now fixed (`pull 1413`_). Thanks, Marc Legendre. - Fix a problem with Cython code measurement (`pull 1347`_, fixing `issue 972`_). Thanks, Matus Valo. .. _issue 972: nedbat/coveragepy#972 .. _pull 1347: nedbat/coveragepy#1347 .. _pull 1403: nedbat/coveragepy#1403 .. _pull 1405: nedbat/coveragepy#1405 .. _pull 1413: nedbat/coveragepy#1413 .. _issue 1428: nedbat/coveragepy#1428 .. _pull 1430: nedbat/coveragepy#1430 .. _changes_6-4-2: Version 6.4.2 — 2022-07-12 -------------------------- - Updated for a small change in Python 3.11.0 beta 4: modules now start with a line with line number 0, which is ignored. This line cannnot be executed, so coverage totals were thrown off. This line is now ignored by coverage.py, but this also means that truly empty modules (like ``__init__.py``) have no lines in them, rather than one phantom line. Fixes `issue 1419`_. - Internal debugging data added to sys.modules is now an actual module, to avoid confusing code that examines everything in sys.modules. Thanks, Yilei Yang (`pull 1399`_). .. _pull 1399: nedbat/coveragepy#1399 .. _issue 1419: nedbat/coveragepy#1419 .. _changes_6-4-1: Version 6.4.1 — 2022-06-02 -------------------------- - Greatly improved performance on PyPy, and other environments that need the pure Python trace function. Thanks, Carl Friedrich Bolz-Tereick (`pull 1381`_ and `pull 1388`_). Slightly improved performance when using the C trace function, as most environments do. Closes `issue 1339`_. - The conditions for using tomllib from the standard library have been made more precise, so that 3.11 alphas will continue to work. Closes `issue 1390`_. .. _issue 1339: nedbat/coveragepy#1339 .. _pull 1381: nedbat/coveragepy#1381 .. _pull 1388: nedbat/coveragepy#1388 .. _issue 1390: nedbat/coveragepy#1390 .. _changes_64: Version 6.4 — 2022-05-22 ------------------------ - A new setting, :ref:`config_run_sigterm`, controls whether a SIGTERM signal handler is used. In 6.3, the signal handler was always installed, to capture data at unusual process ends. Unfortunately, this introduced other problems (see `issue 1310`_). Now the signal handler is only used if you opt-in by setting ``[run] sigterm = true``. - Small changes to the HTML report: - Added links to next and previous file, and more keyboard shortcuts: ``[`` and ``]`` for next file and previous file; ``u`` for up to the index; and ``?`` to open/close the help panel. Thanks, `J. M. F. Tsang <pull 1364_>`_. - The timestamp and version are displayed at the top of the report. Thanks, `Ammar Askar <pull 1354_>`_. Closes `issue 1351`_. - A new debug option ``debug=sqldata`` adds more detail to ``debug=sql``, logging all the data being written to the database. - Previously, running ``coverage report`` (or any of the reporting commands) in an empty directory would create a .coverage data file. Now they do not, fixing `issue 1328`_. - On Python 3.11, the ``[toml]`` extra no longer installs tomli, instead using tomllib from the standard library. Thanks `Shantanu <pull 1359_>`_. - In-memory CoverageData objects now properly update(), closing `issue 1323`_. .. _issue 1310: nedbat/coveragepy#1310 .. _issue 1323: nedbat/coveragepy#1323 .. _issue 1328: nedbat/coveragepy#1328 .. _issue 1351: nedbat/coveragepy#1351 .. _pull 1354: nedbat/coveragepy#1354 .. _pull 1359: nedbat/coveragepy#1359 .. _pull 1364: nedbat/coveragepy#1364 .. _changes_633: Version 6.3.3 — 2022-05-12 -------------------------- - Fix: Coverage.py now builds successfully on CPython 3.11 (3.11.0b1) again. Closes `issue 1367`_. Some results for generators may have changed. .. _issue 1367: nedbat/coveragepy#1367 .. _changes_632: Version 6.3.2 — 2022-02-20 -------------------------- - Fix: adapt to pypy3.9's decorator tracing behavior. It now traces function decorators like CPython 3.8: both the @-line and the def-line are traced. Fixes `issue 1326`_. - Debug: added ``pybehave`` to the list of :ref:`coverage debug <cmd_debug>` and :ref:`cmd_run_debug` options. - Fix: show an intelligible error message if ``--concurrency=multiprocessing`` is used without a configuration file. Closes `issue 1320`_. .. _issue 1320: nedbat/coveragepy#1320 .. _issue 1326: nedbat/coveragepy#1326 .. _changes_631: Version 6.3.1 — 2022-02-01 -------------------------- - Fix: deadlocks could occur when terminating processes. Some of these deadlocks (described in `issue 1310`_) are now fixed. - Fix: a signal handler was being set from multiple threads, causing an error: "ValueError: signal only works in main thread". This is now fixed, closing `issue 1312`_. - Fix: ``--precision`` on the command-line was being ignored while considering ``--fail-under``. This is now fixed, thanks to `Marcelo Trylesinski <pull 1317_>`_. - Fix: releases no longer provide 3.11.0-alpha wheels. Coverage.py uses CPython internal fields which are moving during the alpha phase. Fixes `issue 1316`_. .. _issue 1310: nedbat/coveragepy#1310 .. _issue 1312: nedbat/coveragepy#1312 .. _issue 1316: nedbat/coveragepy#1316 .. _pull 1317: nedbat/coveragepy#1317 .. _changes_63: Version 6.3 — 2022-01-25 ------------------------ - Feature: Added the ``lcov`` command to generate reports in LCOV format. Thanks, `Bradley Burns <pull 1289_>`_. Closes issues `587 <issue 587_>`_ and `626 <issue 626_>`_. - Feature: the coverage data file can now be specified on the command line with the ``--data-file`` option in any command that reads or writes data. This is in addition to the existing ``COVERAGE_FILE`` environment variable. Closes `issue 624`_. Thanks, `Nikita Bloshchanevich <pull 1304_>`_. - Feature: coverage measurement data will now be written when a SIGTERM signal is received by the process. This includes :meth:`Process.terminate <python:multiprocessing.Process.terminate>`, and other ways to terminate a process. Currently this is only on Linux and Mac; Windows is not supported. Fixes `issue 1307`_. - Dropped support for Python 3.6, which reached end-of-life on 2021-12-23. - Updated Python 3.11 support to 3.11.0a4, fixing `issue 1294`_. - Fix: the coverage data file is now created in a more robust way, to avoid problems when multiple processes are trying to write data at once. Fixes issues `1303 <issue 1303_>`_ and `883 <issue 883_>`_. - Fix: a .gitignore file will only be written into the HTML report output directory if the directory is empty. This should prevent certain unfortunate accidents of writing the file where it is not wanted. - Releases now have MacOS arm64 wheels for Apple Silicon, fixing `issue 1288`_. .. _issue 587: nedbat/coveragepy#587 .. _issue 624: nedbat/coveragepy#624 .. _issue 626: nedbat/coveragepy#626 .. _issue 883: nedbat/coveragepy#883 .. _issue 1288: nedbat/coveragepy#1288 .. _issue 1294: nedbat/coveragepy#1294 .. _issue 1303: nedbat/coveragepy#1303 .. _issue 1307: nedbat/coveragepy#1307 .. _pull 1289: nedbat/coveragepy#1289 .. _pull 1304: nedbat/coveragepy#1304 .. _changes_62: Version 6.2 — 2021-11-26 ------------------------ - Feature: Now the ``--concurrency`` setting can now have a list of values, so that threads and another lightweight threading package can be measured together, such as ``--concurrency=gevent,thread``. Closes `issue 1012`_ and `issue 1082`_. - Fix: A module specified as the ``source`` setting is imported during startup, before the user program imports it. This could cause problems if the rest of the program isn't ready yet. For example, `issue 1203`_ describes a Django setting that is accessed before settings have been configured. Now the early import is wrapped in a try/except so errors then don't stop execution. - Fix: A colon in a decorator expression would cause an exclusion to end too early, preventing the exclusion of the decorated function. This is now fixed. - Fix: The HTML report now will not overwrite a .gitignore file that already exists in the HTML output directory (follow-on for `issue 1244`_). - API: The exceptions raised by Coverage.py have been specialized, to provide finer-grained catching of exceptions by third-party code. - API: Using ``suffix=False`` when constructing a Coverage object with multiprocessing wouldn't suppress the data file suffix (`issue 989`_). This is now fixed. - Debug: The ``coverage debug data`` command will now sniff out combinable data files, and report on all of them. - Debug: The ``coverage debug`` command used to accept a number of topics at a time, and show all of them, though this was never documented. This no longer works, to allow for command-line options in the future. .. _issue 989: nedbat/coveragepy#989 .. _issue 1012: nedbat/coveragepy#1012 .. _issue 1082: nedbat/coveragepy#1082 .. _issue 1203: nedbat/coveragepy#1203 .. _changes_612: Version 6.1.2 — 2021-11-10 -------------------------- - Python 3.11 is supported (tested with 3.11.0a2). One still-open issue has to do with `exits through with-statements <issue 1270_>`_. - Fix: When remapping file paths through the ``[paths]`` setting while combining, the ``[run] relative_files`` setting was ignored, resulting in absolute paths for remapped file names (`issue 1147`_). This is now fixed. - Fix: Complex conditionals over excluded lines could have incorrectly reported a missing branch (`issue 1271`_). This is now fixed. - Fix: More exceptions are now handled when trying to parse source files for reporting. Problems that used to terminate coverage.py can now be handled with ``[report] ignore_errors``. This helps with plugins failing to read files (`django_coverage_plugin issue 78`_). - Fix: Removed another vestige of jQuery from the source tarball (`issue 840`_). - Fix: Added a default value for a new-to-6.x argument of an internal class. This unsupported class is being used by coveralls (`issue 1273`_). Although I'd rather not "fix" unsupported interfaces, it's actually nicer with a default value. .. _django_coverage_plugin issue 78: nedbat/django_coverage_plugin#78 .. _issue 1147: nedbat/coveragepy#1147 .. _issue 1270: nedbat/coveragepy#1270 .. _issue 1271: nedbat/coveragepy#1271 .. _issue 1273: nedbat/coveragepy#1273 .. _changes_611: Version 6.1.1 — 2021-10-31 -------------------------- - Fix: The sticky header on the HTML report didn't work unless you had branch coverage enabled. This is now fixed: the sticky header works for everyone. (Do people still use coverage without branch measurement!? j/k) - Fix: When using explicitly declared namespace packages, the "already imported a file that will be measured" warning would be issued (`issue 888`_). This is now fixed. .. _issue 888: nedbat/coveragepy#888 .. _changes_61: Version 6.1 — 2021-10-30 ------------------------ - Deprecated: The ``annotate`` command and the ``Coverage.annotate`` function will be removed in a future version, unless people let me know that they are using it. Instead, the ``html`` command gives better-looking (and more accurate) output, and the ``report -m`` command will tell you line numbers of missing lines. Please get in touch if you have a reason to use ``annotate`` over those better options: ned@nedbatchelder.com. - Feature: Coverage now sets an environment variable, ``COVERAGE_RUN`` when running your code with the ``coverage run`` command. The value is not important, and may change in the future. Closes `issue 553`_. - Feature: The HTML report pages for Python source files now have a sticky header so the file name and controls are always visible. - Feature: The ``xml`` and ``json`` commands now describe what they wrote where. - Feature: The ``html``, ``combine``, ``xml``, and ``json`` commands all accept a ``-q/--quiet`` option to suppress the messages they write to stdout about what they are doing (`issue 1254`_). - Feature: The ``html`` command writes a ``.gitignore`` file into the HTML output directory, to prevent the report from being committed to git. If you want to commit it, you will need to delete that file. Closes `issue 1244`_. - Feature: Added support for PyPy 3.8. - Fix: More generated code is now excluded from measurement. Code such as `attrs`_ boilerplate, or doctest code, was being measured though the synthetic line numbers meant they were never reported. Once Cython was involved though, the generated .so files were parsed as Python, raising syntax errors, as reported in `issue 1160`_. This is now fixed. - Fix: When sorting human-readable names, numeric components are sorted correctly: file10.py will appear after file9.py. This applies to file names, module names, environment variables, and test contexts. - Performance: Branch coverage measurement is faster, though you might only notice on code that is executed many times, such as long-running loops. - Build: jQuery is no longer used or vendored (`issue 840`_ and `issue 1118`_). Huge thanks to Nils Kattenbeck (septatrix) for the conversion to vanilla JavaScript in `pull request 1248`_. .. _issue 553: nedbat/coveragepy#553 .. _issue 840: nedbat/coveragepy#840 .. _issue 1118: nedbat/coveragepy#1118 .. _issue 1160: nedbat/coveragepy#1160 .. _issue 1244: nedbat/coveragepy#1244 .. _pull request 1248: nedbat/coveragepy#1248 .. _issue 1254: nedbat/coveragepy#1254 .. _attrs: https://www.attrs.org/ .. _changes_602: Version 6.0.2 — 2021-10-11 -------------------------- - Namespace packages being measured weren't properly handled by the new code that ignores third-party packages. If the namespace package was installed, it was ignored as a third-party package. That problem (`issue 1231`_) is now fixed. - Packages named as "source packages" (with ``source``, or ``source_pkgs``, or pytest-cov's ``--cov``) might have been only partially measured. Their top-level statements could be marked as unexecuted, because they were imported by coverage.py before measurement began (`issue 1232`_). This is now fixed, but the package will be imported twice, once by coverage.py, then again by your test suite. This could cause problems if importing the package has side effects. - The :meth:`.CoverageData.contexts_by_lineno` method was documented to return a dict, but was returning a defaultdict. Now it returns a plain dict. It also no longer returns negative numbered keys. .. _issue 1231: nedbat/coveragepy#1231 .. _issue 1232: nedbat/coveragepy#1232 .. _changes_601: Version 6.0.1 — 2021-10-06 -------------------------- - In 6.0, the coverage.py exceptions moved from coverage.misc to coverage.exceptions. These exceptions are not part of the public supported API, CoverageException is. But a number of other third-party packages were importing the exceptions from coverage.misc, so they are now available from there again (`issue 1226`_). - Changed an internal detail of how tomli is imported, so that tomli can use coverage.py for their own test suite (`issue 1228`_). - Defend against an obscure possibility under code obfuscation, where a function can have an argument called "self", but no local named "self" (`pull request 1210`_). Thanks, Ben Carlsson. .. _pull request 1210: nedbat/coveragepy#1210 .. _issue 1226: nedbat/coveragepy#1226 .. _issue 1228: nedbat/coveragepy#1228 .. _changes_60: Version 6.0 — 2021-10-03 ------------------------ - The ``coverage html`` command now prints a message indicating where the HTML report was written. Fixes `issue 1195`_. - The ``coverage combine`` command now prints messages indicating each data file being combined. Fixes `issue 1105`_. - The HTML report now includes a sentence about skipped files due to ``skip_covered`` or ``skip_empty`` settings. Fixes `issue 1163`_. - Unrecognized options in the configuration file are no longer errors. They are now warnings, to ease the use of coverage across versions. Fixes `issue 1035`_. - Fix handling of exceptions through context managers in Python 3.10. A missing exception is no longer considered a missing branch from the with statement. Fixes `issue 1205`_. - Fix another rarer instance of "Error binding parameter 0 - probably unsupported type." (`issue 1010`_). - Creating a directory for the coverage data file now is safer against conflicts when two coverage runs happen simultaneously (`pull 1220`_). Thanks, Clément Pit-Claudel. .. _issue 1035: nedbat/coveragepy#1035 .. _issue 1105: nedbat/coveragepy#1105 .. _issue 1163: nedbat/coveragepy#1163 .. _issue 1195: nedbat/coveragepy#1195 .. _issue 1205: nedbat/coveragepy#1205 .. _pull 1220: nedbat/coveragepy#1220 .. _changes_60b1: Version 6.0b1 — 2021-07-18 -------------------------- - Dropped support for Python 2.7, PyPy 2, and Python 3.5. - Added support for the Python 3.10 ``match/case`` syntax. - Data collection is now thread-safe. There may have been rare instances of exceptions raised in multi-threaded programs. - Plugins (like the `Django coverage plugin`_) were generating "Already imported a file that will be measured" warnings about Django itself. These have been fixed, closing `issue 1150`_. - Warnings generated by coverage.py are now real Python warnings. - Using ``--fail-under=100`` with coverage near 100% could result in the self-contradictory message :code:`total of 100 is less than fail-under=100`. This bug (`issue 1168`_) is now fixed. - The ``COVERAGE_DEBUG_FILE`` environment variable now accepts ``stdout`` and ``stderr`` to write to those destinations. - TOML parsing now uses the `tomli`_ library. - Some minor changes to usually invisible details of the HTML report: - Use a modern hash algorithm when fingerprinting, for high-security environments (`issue 1189`_). When generating the HTML report, we save the hash of the data, to avoid regenerating an unchanged HTML page. We used to use MD5 to generate the hash, and now use SHA-3-256. This was never a security concern, but security scanners would notice the MD5 algorithm and raise a false alarm. - Change how report file names are generated, to avoid leading underscores (`issue 1167`_), to avoid rare file name collisions (`issue 584`_), and to avoid file names becoming too long (`issue 580`_). .. _Django coverage plugin: https://pypi.org/project/django-coverage-plugin/ .. _issue 580: nedbat/coveragepy#580 .. _issue 584: nedbat/coveragepy#584 .. _issue 1150: nedbat/coveragepy#1150 .. _issue 1167: nedbat/coveragepy#1167 .. _issue 1168: nedbat/coveragepy#1168 .. _issue 1189: nedbat/coveragepy#1189 .. _tomli: https://pypi.org/project/tomli/ .. _changes_56b1: Version 5.6b1 — 2021-04-13 -------------------------- Note: 5.6 final was never released. These changes are part of 6.0. - Third-party packages are now ignored in coverage reporting. This solves a few problems: - Coverage will no longer report about other people's code (`issue 876`_). This is true even when using ``--source=.`` with a venv in the current directory. - Coverage will no longer generate "Already imported a file that will be measured" warnings about coverage itself (`issue 905`_). - The HTML report uses j/k to move up and down among the highlighted chunks of code. They used to highlight the current chunk, but 5.0 broke that behavior. Now the highlighting is working again. - The JSON report now includes ``percent_covered_display``, a string with the total percentage, rounded to the same number of decimal places as the other reports' totals. .. _issue 876: nedbat/coveragepy#876 .. _issue 905: nedbat/coveragepy#905
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I am facing this issue as well using a local version of make triggered by pre-commit |
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Seeing this in python 3.8 with |
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If you are seeing this error, please provide a way for me to reproduce it. What repo should I clone, and what commands should I run? |
@nedbat from my understanding, this is not something you can consistently reproduce. If you want to see one of the cases in which it happened, please check the log of the following CI action: This happened in one of the commits (5890a80) of the following PR: |
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Just an update, the bug happened again in my GitHub actions (see repository https://github.com/Cascella-Group-UiO/HyMD) and the build is "failing" due to the bug. |
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This is also happening to me. Python==3.12
coverage==7.4.4Any solutions? |
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@Pablongo24 if you can provide a way to reproduce the problem, we can dig into finding a solution. |
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Describe the bug
As the title said, this bug appears in my project's action.
To Reproduce
This problem has been seen in python 3.8 once (in the previous attempt of the link above), and in python 3.9 in the latest attempt.
There are many manual forks and pipes in my code, so I guess it may have something to do with these (in fact, I haven't seen such errors in other projects, and I use version 6.2 coverage). It can not be stably reproduced, and only seen in the github action. I have never seen this error in my local environment. The error message is like this
Expected behavior
Well I think it should be ended up properly like the other jobs.
Additional context
How to run my project.
After clone it, you may run
to enter a docker-based system (This step is necessary because this project need root permission). And then install the python dependencies
Finally, perform unit tests
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