CHANGELOG.md

indexed_gzip changelog

1.9.1 (November 15th 2024)

• Adjustments to CI configuration (#154).

1.9.0 (November 15th 2024)

• Preserve exception information when reading from a Python file-like (#152).

1.8.8 (November 7th 2024)

• Enable Python 3.13 builds (#150).

1.8.7 (November 6th 2023)

• Enable Python 3.12 and musllinux builds (#139).
• Remove numpy as a mandatory build-time dependency (#142, #143).

1.8.5 (August 29th 2023)

• Updates to package build process (#138).

1.8.4 (August 29th 2023)

• Change the IndexedGzipFile class to raise a FileNotFoundError instead of a ValueError, when a path to a non-existent file is provided (#137).

1.8.3 (July 25th 2023)

• Another adjustment to package build process (#135).

1.8.2 (July 25th 2023)

• Adjustment to package build process (#134).

1.8.1 (July 25th 2023)

• Now building packages for python >=3.7, as recent versions of setuptools do not support older Python versions (#133).

1.8.0 (July 24th 2023)

• Compatibility fixes for Python 3.12 and Cython 3.0.0 (#126, #127).
• Removed support for Python 2.7 (#128).

1.7.1 (March 31st 2023)

• Small change to the IndexedGzipFile class so that it accepts file-likes which do not implement fileno() (#118).

1.7.0 (September 12th 2022)

• Changes to allow an index to be built from file-likes which don't support seek() or tell() operations (#103, #105).

1.6.13 (April 14th 2022)

• Changed the default read buffer size used by the IndexedGzipFile class (#90).
• Update to wheel building procedure (#92,#93,#95,#96,#97,#98,#99).
• Aded pyproject.toml to declare build-time requirements (#94).

1.6.4 (October 18th 2021)

• Fixed a bug related to buffering input data, which was causing a spurious CrcError (#80, #87).

1.6.3 (September 14th 2021)

• Relaxed mode check when creating an IndexedGzipFile from an open file handle - fileobj.mode may now be 'r' or 'rb' (or may not exist at all) (#85, #86).

1.6.2 (September 2nd 2021)

• Fixed a memory leak when initialising decompression / inflation (#82, #83).
• Added file name to exception messages when possible, to assist in diagnosing errors (#84).

1.6.1 (May 25th 2021)

• Tests requiring nibabel are now skipped, rather than causing failure (#78).

1.6.0 (May 23rd 2021)

• Python 2.7 wheels for Windows are no longer being built (#71, #73).
• A backwards-compatible change to the index file format, to accommodate seek points at stream boundaries. Index files created with older versions of indexed_gzip can still be loaded, but index files created with indexed_gzip 1.6.0 cannot be loaded by older versions of indexed_gzip (#75).
• CRC and size validation of uncompressed data is now performed by default, on the first pass through a GZIP file. This can be disabled by setting the new skip_crc_check argument to False when creating an IndexedGzipFile. Validation is not performed when an existing index is imported from file (#72).
• Null padding bytes at the end of a GZIP file, or in between GZIP streams, are now skipped over (#69, #70, #72).
• Seek points are now created at the beginning of every GZIP stream, in files containing concatenated streams (#72).

1.5.3 (March 23rd 2021)

• Restored wheel building for Python 2.7 on 32 bit Windows (#64, #66).
• Now building wheels for aarch64 on Linux, and amd64/universal2 on macOS (#66).
• Fixed some un-initialised pointers (#65).
• Fixed a bug in the use of PyErr_Occurred (#63).

1.5.2 (March 19th 2021)

• Not providing binary wheels for Python 2.7 on 32 bit Windows (#61).

1.5.1 (March 19th 2021)

• Minor adjustments to some unit test (#60).

1.5.0 (March 19th 2021)

• Added support for in-memory file-like objects (#55).
• Fixed a bug whereby a segmentation fault could occur if an IndexedGzipFile was created with a path to a non-existent file (#56).

1.4.0 (January 2nd 2021)

• Fixed a bug in the pickling/copying logic in the IndexedGzipFile class (#50, #51)
• New indexed_gzip.open function, which just creates and returns an IndexedGzipFile.
• When creating an IndexedGzipFile, the first argument (filename) may be either a file name, or an open file handle (#49, #53).
• Migrated CI testing and building to Github Actions (#52).
• Binary wheels for Windows now have ZLIB statically compiled in as part of the wheel, so ZLIB no longer needs to be installed (#43, #52).

1.3.3 (November 14th 2020)

• Adjusted the ZranError exception type to sub-class from IOError, to ease support for nibabel.
• Fixed a bug related to concatenated GZIP files which would occur when the read buffer ran out of space at the point where a stream boundary occurred.

1.3.2 (June 30th 2020)

• Adjusted the NoHandleError and NotCoveredError types to sub-class from ValueError, to preserve backwards compatibility with older versions of nibabel.

1.3.1 (June 25th 2020)

• Reverted the error type raised by the IndexedGzipFile.seek to ValueError, as nibabel assumes that the seek method of file objects raise a ValueError if SEEK_END is not supported.

1.3.0 (June 24th 2020)

• The IndexedGzipFile.seek method now accepts seeking from the end of uncompressed stream via SEEK_END, as long as the index has been built (#37).

1.2.0 (May 12th 2020)

• New IndexedGzipFile.seek_points method, which returns the compressed and uncompressed seek point locations.

1.1.0 (April 20th 2020)

• IndexedGzipFile objects are now picklable, as long as they are created with the default setting of drop_handles=True and with a filename and not an open fileobj (#28, #31).
• Changed the return type of zran_tell from long to uint64_t, because the former is not guaranteed to be 64 bit (#29, #30).
• Changed the zran_index_t.compressed_size and uncompressed_size fields from size_t to uint64_t because the former is not guaranteed to be 64 bit.

1.0.0 (February 21st 2020)

• Removed the deprecated fid argument to the IndexedGzipFile constructor.
• Removed the SafeIndexedGzipFile.

0.8.10 (May 15th 2019)

• Fix to package metadata.

0.8.9 (May 14th 2019)

• The IndexedGzipFile.import_index method and zran_import_index function can handle index files which do not contain any index points (#18).

0.8.8 (November 22nd 2018)

• Fixed bug affecting files which were an exact multiple of the read buffer size (#15).

0.8.7 (August 3rd 2018)

• Internal changes to how file handles are managed, to improve Windows compatibility.
• The _IndexedGzipFile.read method now acquires a single file handle, rather than opening/closing multiple handles across calls to zran_read.

0.8.6 (June 27th 2018)

• Workaround for issues with Python 2.7 and Cython < 0.26 (#10).

0.8.5 (June 16th 2018)

• Minor changes to packging.

0.8.4 (June 11th 2018)

• Removed pytest-runner as a dependency.

0.8.3 (June 11th 2018)

• Bugfix - variious methods and attributes were missing from the IndexedGzipFile wrapper class (#9).

0.8.2 (March 30th 2018)

Changes in this release:

• Bugfix in deprecated SafeIndexedGzipFile.

0.8.1 (March 24th 2018)

Changes in this release:

• Updated conda metadata.

0.8.0 (March 24th 2018)

Changes in this release:

• Added ability to import/export the index, via new import_index and export_index methods on the IndexedGzipFile class (#7, #8) - thanks @ozars !
• Deprecated SafeIndexedGzipFile - the IndexedGzipFile is now thread-safe, and has a read buffer. If you don't want buffering or thread-safety, use the _IndexedGzipFile class.
• Fixed bug in seek method - was not working with negative offsets.
• More unit tests, and code coverage of .py and .pyx files.

0.7.1 (March 5th 2018)

Changes in this release:

• Added .conda/meta.yaml file for building conda packages

0.7.0 (November 3rd 2017)

Changes in this release:

• IndexedGzipFile.__init__ has a new option, drop_handles which causes an IndexedGzipFile to close/re-open the underlying file handle on every access (#5, #6). This has no impact on performance (as measured by the new benchmark script), so is enabled by default.

• New simpler benchmark script.

• Deprecated the fid parameter to IndexedGzipFile.__init__ in favour of fileobj - another change to make IndexedGzipFile more similar to gzip.GzipFile.

0.6.1 (October 4th 2017)

Changes in this release:

• IndexedGzipFile now has a readinto method.
• SafeIndexedGzipFile is now an io.BufferedReader, which provides thread safety and dramatically improves performance for small files (see discussion at nipy/nibabel#558).
• Fixed issue #4 - the source distribution was missing zran.h.

0.6.0 (September 24th 2017)

Changes in this release:

• Preliminary support for Windows platforms (#1, #3) Thanks to @mcraig-ibme and @Trigonometry !

• Added mode attribute to IndexedGzipFile.

0.5.1 (September 12th 2017)

Changes in this release:

• Unit tests are run on a 32 bit platform
• The indexed_gzip package now has a __version__ attribute

0.5.0 (September 8th 2017)

Changes in this release:

• Re-arranged code layout - there is now a top level indexed_gzip package, which contains the indexed_gzip module, and the tests package. Done so that tests can be distributed properly. No API changes though.

• zran_seek input parameter types made more specific due to an issue on 32 bit platforms.

0.4.1 (September 6th 2017)

Changes in this release:

• A tiny adjustment to unit test management allowing tests to be run from a different directory

0.4.0 (September 5th 2017)

Changes in this release involve modifications and additions to the IndexedGzipFile class to make it look and behave more like the built-in gzip.GzipFile class.

• __init__ accepts filename and mode as its first two parameters

• Changed default values for __init__ parameters to values which have been qualitatively tested

• readline, readlines, __iter__ and __next__ methods added, for iteration over lines in text data

• seek method accepts a whence parameter, and allows seeking from SEEK_SET or SEEK_CUR,

0.3.3 (May 3rd 2017)

Changes in this release:

• SafeIndexedGzipFile was broken under python 3.

0.3.2 (May 1st 2017)

Changes in this release:

• Bugfix (PR #2)

0.3.1 (October 17th 2016)

Changes in this release:

• One critical, silly bugfix that should have been in 0.3.

0.3 (October 16th 2016)

Changes in this release:

• Support for reading > 2**32 bytes in a single call.
• Support for concatenated gzip streams.
• Many related bug fixes.
• zran.c refactored so it is much cleaner and clearer.
• Test suite is much more comprehensive

0.2 (August 31st 2016)

The following changes have been made in this release:

• indexed_gzip now releases the GIL when possible
• A new SafeIndexedGzipFile class provides simple thread-safe file access to compressed files.
• Some initial test coverage using https://travis-ci.org
• Some important bug fixes.

0.1 (June 16th 2016)

• First seemingly stable release.