Fix build against Python 3.12 #1922
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Ever since Python 3.2, configparser.SafeConfigParser has been deprecated in favor of configparser.ConfigParser. An alias existed for backward compatibility but the alias was dropped from Python 3.12. Let us now use ConfigParser explicitly, and use .read_file() instead of .readfp() which was dropped too. The imp module has also been dropped, but a similar behavior can be achieved using importlib. Signed-off-by: Olivier Gayot <[email protected]>
Python scripts under scripts/ in the source tree do not consistently close files that they open for writing. While some of the scripts use context managers, most of them do not (or do so inconsistently). In previous releases of Python, this apparently was not much of a concern. However, Python 3.12 seems to be much less forgiving when files are not properly closed. When running the test suite, many of the files that are not explicitly closed appear truncated. This leads to various tests failing or hanging. Furthermore, khmer defines the get_file_writer() function, but it cannot be consistently used as a context manager because it sometimes closes the underlying file descriptor ; and sometimes does not depending on the arguments. Fixed by defining a new FileWriter context manager and ensuring that each call to open() / get_file_writer() frees up resources properly. Signed-off-by: Olivier Gayot <[email protected]>
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Ever since Python 3.2,
configparser.SafeConfigParserhas been deprecated in favor ofconfigparser.ConfigParser. An alias existed for backward compatibility but the alias was dropped from Python 3.12.The
impmodule was dropped from Python 3.12, butimportlibcan be used as a substitute.Furthermore, Python scripts were not consistently closing the files that they opened for writing. With earlier versions of Python, it was not a big deal. But with Python 3.12, the files appear truncated. The second patch goes through every call to
open(..., mode="w")and ensures that the resource is properly cleaned up after.The change will probably fail to build with Python 2.7.
make clean diff-coveror the CodeCov report that is automaticallygenerated following a successful CI build.)
changes were made?
Only backwards-compatible additions are allowed without a major version
increment. Changing file formats also requires a major version number
increment.
CHANGELOG.md? Seekeepachangelog for more details.