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This Python module provides an xopen function that works like Python’s
built-in open function but also transparently deals with compressed files.
xopen selects the most efficient method for reading or writing a compressed file.
Supported compression formats are:
.gz).bz2).xz).zst) (optional)xopen is compatible with Python versions 3.8 and later.
Open a file for reading::
from xopen import xopen
with xopen("file.txt.gz") as f:
content = f.read()Write to a file in binary mode, set the compression level and avoid using an external process::
from xopen import xopen
with xopen("file.txt.xz", mode="wb", threads=0, compresslevel=3) as f:
f.write(b"Hello")xopen functionThe xopen module offers a single function named xopen with the following
signature::
xopen( filename: str | bytes | os.PathLike, mode: Literal["r", "w", "a", "rt", "rb", "wt", "wb", "at", "ab"] = "r", compresslevel: Optional[int] = None, threads: Optional[int] = None, *, encoding: str = "utf-8", errors: Optional[str] = None, newline: Optional[str] = None, format: Optional[str] = None, ) -> IO
The function opens the file using a function suitable for the detected file format and returns an open file-like object.
When writing, the file format is chosen based on the file name extension:
.gz, .bz2, .xz, .zst. This can be overriden with format.
If the extension is not recognized, no compression is used.
When reading and a file name extension is available, the format is detected
from the extension.
When reading and no file name extension is available,
the format is detected from the
file signature <https://en.wikipedia.org/wiki/File_format#Magic_number>.
Parameters
**filename** (str, bytes, or `os.PathLike <https://docs.python.org/3/library/os.html#os.PathLike>`_):
Name of the file to open.
If set to ``"-"``, standard output (in mode ``"w"``) or
standard input (in mode ``"r"``) is returned.
**mode**, **encoding**, **errors**, **newline**:
These parameters have the same meaning as in Python’s built-in
`open function <https://docs.python.org/3/library/functions.html#open>`_
except that the default encoding is always UTF-8 instead of the
preferred locale encoding.
``encoding``, ``errors`` and ``newline`` are only used when opening a file in text mode.
**compresslevel**:
The compression level for writing to gzip, xz and Zstandard files.
If set to None, a default depending on the format is used:
gzip: 1, xz: 6, Zstandard: 3.
This parameter is ignored for other compression formats.
**format**:
Override the autodetection of the input or output format.
Possible values are: ``"gz"``, ``"xz"``, ``"bz2"``, ``"zst"``.
**threads**:
Set the number of additional threads spawned for compression or decompression.
May be ignored if the backend does not support threads.
If *threads* is None (the default), as many threads as available CPU cores are
used, but not more than four.
xopen tries to offload the (de)compression to other threads
to free up the main Python thread for the application.
This can either be done by using a subprocess to an external application or
using a library that supports threads.
Set threads to 0 to force xopen to use only the main Python thread.
Backends
--------
Opening of gzip files is delegated to one of these programs or libraries:
* `python-isal <https://github.com/pycompression/python-isal>`_.
Supports multiple threads and compression levels up to 3.
* `python-zlib-ng <https://github.com/pycompression/python-zlib-ng>`_
* `pigz <https://zlib.net/pigz/>`_ (a parallel version of ``gzip``)
* `gzip <https://www.gnu.org/software/gzip/>`_
For xz files, a pipe to the ``xz`` program is used because it has
built-in support for multithreaded compression.
For bz2 files, `pbzip2 (parallel bzip2) <http://compression.ca/pbzip2/>`_ is used.
``xopen`` falls back to Python’s built-in functions
(``gzip.open``, ``lzma.open``, ``bz2.open``)
if none of the other methods can be used.
Reproducibility
---------------
xopen writes gzip files in a reproducible manner.
Normally, gzip files contain a timestamp in the file header,
which means that compressing the same data at different times results in different output files.
xopen disables this for all of the supported gzip compression backends.
For example, when using an external process, it sets the command-line option
``--no-name`` (same as ``-n``).
Note that different gzip compression backends typically do not produce
identical output, so reproducibility may no longer be given when the execution environment changes
from one ``xopen()`` invocation to the next.
This includes the CPU architecture as `igzip adjusts its algorithm
depending on it <https://github.com/intel/isa-l/issues/140#issuecomment-634877966>`_.
bzip2 and xz compression methods do not store timestamps in the file headers,
so output from them is also reproducible.
Optional Zstandard support
--------------------------
For reading and writing Zstandard (``.zst``) files, either the ``zstd`` command-line
program or the Python ``zstandard`` package needs to be installed.
* If the ``threads`` parameter to ``xopen()`` is ``None`` (the default) or any value greater than 0,
``xopen`` uses an external ``zstd`` process.
* If the above fails (because no ``zstd`` program is available) or if ``threads`` is 0,
the ``zstandard`` package is used.
To ensure that you get the correct ``zstandard`` version, you can specify the ``zstd`` extra for
``xopen``, that is, install it using ``pip install xopen[zstd]``.
Changelog
---------
v2.0.2 (2024-06-12)an external program.
v2.0.1 (2024-03-28)
+ #158: Fixed a bug where reading from stdin and other pipes would discard the
first bytes from the input.
+ #156: Zstd files compressed with the ``--long=31`` files can now be opened
without throwing errors.
v2.0.0 (2024-03-26)are supported. Level 11 which was only available when the pigz backend was
present is not supported anymore. Level 0, gzip format without compression,
lead to crashes when the gzip application backend was used as this does
not have a -0 flag. xopen() now defers to other backends in that case.
xopen() now accepts `file-like objectshttps://docs.python.org/3/glossary.html#term-file-object`_ for its filename argument.
io.TextIOWrapper in the xopen() function.and writing are all made private by prefixing them with an underscore. These are not part of the API and may change between releases.
v1.9.0 (2024-01-31)
* #142: The python-isal compression backend is now only used for compression
levels 1 and 2. Contrary to other backends, python-isal level 0 gave
compressed rather than uncompressed data in gzip format. Level 3 on
python-isal did not provide better compression than level 2.
* #140: PipedCompressionReader/Writer now derive from the `io.IOBase
<https://docs.python.org/3/library/io.html#io.IOBase>`_ abstract class.
* #138: The gzip default compression level is now 1 when no value is provided
by the calling function. The default used to be determined by the backend.
* #135: xopen now uses zlib-ng when available and applicable.
* #133: Piped ``igzip`` is no longer used as a (de)compression backend as
python-isal's threaded mode is a better choice in all use cases.
v1.8.0 (2023-11-03)isal.igzip_threaded module rather thanpiping to external programs in applicable cases. This makes reading and writing to gzip files using threads more efficient.
v1.7.0 (2022-11-03)
* #91: Added optional support for Zstandard (``.zst``) files.
This requires that the Python ``zstandard`` package is installed
or that the ``zstd`` command-line program is available.
v1.6.0 (2022-08-10)file is omitted (equivalent to using gzip --no-name (or -n) on the
command line). This allows files to be written in a reproducible manner.
v1.5.0 (2022-03-23)
* #100: Dropped Python 3.6 support
* #101: Added support for piping into and from an external ``xz`` process. Contributed by @fanninpm.
* #102: Support setting the xz compression level. Contributed by @tsibley.
v1.4.0 (2022-01-14)seek() and tell() to the PipedCompressionReader classes
(for Windows compatibility)v1.3.0 (2022-01-10)
* xopen is now available on Windows (in addition to Linux and macOS).
* For greater compatibility with `the built-in open()
function <https://docs.python.org/3/library/functions.html#open>`_,
``xopen()`` has gained the parameters *encoding*, *errors* and *newlines*
with the same meaning as in ``open()``. Unlike built-in ``open()``, though,
encoding is UTF-8 by default.
* A parameter *format* has been added that allows to force the compression
file format.
v1.2.0 (2021-09-21)pbzip2 <http://compression.ca/pbzip2/>_ is now used to open .bz2 files if
threads is greater than zero (contributed by @DriesSchaumont).v1.1.0 (2021-01-20)
* Python 3.5 support is dropped.
* On Linux systems, `python-isal <https://github.com/pycompression/python-isal>`_
is now added as a requirement. This will speed up the reading of gzip files
significantly when no external processes are used.
v1.0.0 (2020-11-05)igzip program (part of
Intel ISA-L <https://github.com/intel/isa-l/>_) is now used for reading
and writing gzip-compressed files at compression levels 1-3, which results
in a significant speedup.v0.9.0 (2020-04-02)
* #80: When the file name extension of a file to be opened for reading is not
available, the content is inspected (if possible) and used to determine
which compression format applies (contributed by @bvaisvil).
* This release drops Python 2.7 and 3.4 support. Python 3.5 or later is
now required.
v0.8.4 (2019-10-24)pigz to use only a single process.
pigz cannot use multiple cores anyway when decompressing. By default,
it would use extra I/O processes, which slightly reduces wall-clock time,
but increases CPU time. Single-core decompression with pigz is still
about twice as fast as regular gzip.threads=0 for specifying that no external pigz/gzip
process should be used (then regular gzip.open() is used instead).v0.8.3 (2019-10-18)
* #20: When reading gzipped files, let ``pigz`` use at most four threads by default.
This limit previously only applied when writing to a file. Contributed by @bernt-matthias.
* Support Python 3.8
v0.8.0 (2019-08-14)v0.6.0 (2019-05-23)
* For reading from gzipped files, xopen will now use a ``pigz`` subprocess.
This is faster than using ``gzip.open``.
* Python 2 support will be dropped in one of the next releases.
v0.5.0 (2019-01-30)v0.4.0 (2019-01-07)
* Drop Python 3.3 support
* Add a ``threads`` parameter (passed on to ``pigz``)
v0.3.2 (2017-11-22)v0.3.1 (2017-11-22)
* Drop Python 2.6 support
* #5: Fix PipedGzipReader.read() not returning anything
v0.3.0 (2017-11-15)v0.2.1 (2017-05-31)
* #3: Allow appending to bz2 and lzma files where possible
v0.1.1 (2016-12-02)v0.1.0 (2016-09-09)
* Initial release
Credits
-------
The name ``xopen`` was taken from the C function of the same name in the
`utils.h file that is part of
BWA <https://github.com/lh3/bwa/blob/83662032a2192d5712996f36069ab02db82acf67/utils.h>`_.
Some ideas were taken from the `canopener project <https://github.com/selassid/canopener>`_.
If you also want to open S3 files, you may want to use that module instead.
@kyleabeauchamp contributed support for appending to files before this repository was created.
Maintainers
-----------
* Marcel Martin
* Ruben Vorderman
* See also the `full list of contributors <https://github.com/pycompression/xopen/graphs/contributors>`_.
Links
-----
* `Source code <https://github.com/pycompression/xopen/>`_
* `Report an issue <https://github.com/pycompression/xopen/issues>`_
* `Project page on PyPI (Python package index) <https://pypi.python.org/pypi/xopen/>`_