Issues handling exceptions with GCC libraries built against SDC 6.5 #74
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I'm not sure I understand the problem, either. The LD_PRELOAD override allows the binary to run, but some functionality does fail, such as when it tries to call an external command (bash script in this case): However, trying to load the original binary with the 32 bit version fails immediately: It sounds like the suggestion from @wesolows is more of a long-term fix. Can anyone suggest a workaround for now? |
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@jjlawren You'll want so specify |
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This worked as a workaround. Thanks for the tip. |
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3.2 (2012-11-27) ---------------- * Documentation file layout restructuring. [thet] * Fix time support. vTime events can be instantiated with a datetime.time object, and do not inherit from datetime.time itself. [rdunklau] * Correctly handle tzinfo objects parsed with dateutil. Fixes #77. [warvariuc, thet] * Text values are escaped correclty. Fixes #74. [warvariuc] * Returned old folding algorithm, as the current implementation fails in some cases. Fixes #72, Fixes #73. [warvariuc] * Supports to_ical() on date/time properties for dates prior to 1900. [cdevienne]
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## python-markdown2 2.1.0 - ["nofollow" extra, issue #74, pull #104] Add `rel="nofollow"` support (mostly by https://github.com/cdman): $ echo '[link](http://example)' | markdown2 -x nofollow <p><a rel="nofollow" href="http://example">link</a></p> Limitation: This *can* add a duplicate 'rel' attribute to raw HTML links in the input.
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FITS (Flexible Image Transport System) is a data format most used in astronomy.
PyFITS is a Python module for reading, writing, and manipulating FITS files.
The module uses Python's object-oriented features to provide quick, easy, and
efficient access to FITS files. The use of Python's array syntax enables
immediate access to any FITS extension, header cards, or data items.
Changes to 2.4.0 (in py-pyfits):
Changelog
===========
3.2 (2013-11-26)
----------------
Highlights
^^^^^^^^^^
- Rewrote CFITSIO-based backend for handling tile compression of FITS files.
It now uses a standard CFITSIO instead of heavily modified pieces of CFITSIO
as before. PyFITS ships with its own copy of CFITSIO v3.35 which supports
the latest version of the Tiled Image Convention (v2.3), but system
packagers may choose instead to strip this out in favor of a
system-installed version of CFITSIO. Earlier versions may work, but nothing
earlier than 3.28 has been tested yet. (#169)
- Added support for reading and writing tables using the Q format for columns.
The Q format is identical to the P format (variable-length arrays) except
that it uses 64-bit integers for the data descriptors, allowing more than
4 GB of variable-length array data in a single table. (#160)
- Added initial support for table columns containing pseudo-unsigned integers.
This is currently enabled by using the ``uint=True`` option when opening
files; any table columns with the correct BZERO value will be interpreted
and returned as arrays of unsigned integers.
- Some refactoring of the table and ``FITS_rec`` modules in order to better
separate the details of the FITS binary and ASCII table data structures from
the HDU data structures that encapsulate them. Most of these changes should
not be apparent to users (but see API Changes below).
API Changes
^^^^^^^^^^^
- Assigning to values in ``ColDefs.names``, ``ColDefs.formats``,
``ColDefs.nulls`` and other attributes of ``ColDefs`` instances that return
lists of column properties is no longer supported. Assigning to those lists
will no longer update the corresponding columns. Instead, please just
modify the ``Column`` instances directly (``Column.name``, ``Column.null``,
etc.)
- The ``pyfits.new_table`` function is marked "pending deprecation". This
does not mean it will be removed outright or that its functionality has
changed. It will likely be replaced in the future for a function with
similar, if not subtly different functionality. A better, if not slightly
more verbose approach is to use ``pyfits.FITS_rec.from_columns`` to create
a new ``FITS_rec`` table--this has the same interface as
``pyfits.new_table``. The difference is that it returns a plan ``FITS_rec``
array, and not an HDU instance. This ``FITS_rec`` object can then be used
as the data argument in the constructors for ``BinTableHDU`` (for binary
tables) or ``TableHDU`` (for ASCII tables). This is analogous to creating
an ``ImageHDU`` by passing in an image array.
``pyfits.FITS_rec.from_columns`` is just a simpler way of creating a
FITS-compatible recarray from a FITS column specification.
- The ``updateHeader``, ``updateHeaderData``, and ``updateCompressedData``
methods of the ``CompDataHDU`` class are pending deprecation and moved to
internal methods. The operation of these methods depended too much on
internal state to be used safely by users; instead they are invoked
automatically in the appropriate places when reading/writing compressed image
HDUs.
- The ``CompDataHDU.compData`` attribute is pending deprecation in favor of
the clearer and more PEP-8 compatible ``CompDataHDU.compressed_data``.
- The constructor for ``CompDataHDU`` has been changed to accept new keyword
arguments. The new keyword arguments are essentially the same, but are in
underscore_separated format rather than camelCase format. The old arguments
are still pending deprecation.
- The internal attributes of HDU classes ``_hdrLoc``, ``_datLoc``, and
``_datSpan`` have been replaced with ``_header_offset``, ``_data_offset``,
and ``_data_size`` respectively. The old attribute names are still pending
deprecation. This should only be of interest to advanced users who have
created their own HDU subclasses.
- The following previously deprecated functions and methods have been removed
entirely: ``createCard``, ``createCardFromString``, ``upperKey``,
``ColDefs.data``, ``setExtensionNameCaseSensitive``, ``_File.getfile``,
``_TableBaseHDU.get_coldefs``, ``Header.has_key``, ``Header.ascardlist``.
If you run your code with a previous version of PyFITS (>= 3.0, < 3.2) with
the ``python -Wd`` argument, warnings for all deprecated interfaces still in
use will be displayed.
- Interfaces that were pending deprecation are now fully deprecated. These
include: ``create_card``, ``create_card_from_string``, ``upper_key``,
``Header.get_history``, and ``Header.get_comment``.
- The ``.name`` attribute on HDUs is now directly tied to the HDU's header, so
that if ``.header['EXTNAME']`` changes so does ``.name`` and vice-versa.
- The ``pyfits.file.PYTHON_MODES`` constant dict was renamed to
``pyfits.file.PYFITS_MODES`` which better reflects its purpose. This is
rarely used by client code, however. Support for the old name will be
removed by PyFITS 3.4.
Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^
- The new compression code also adds support for the ZQUANTIZ and ZDITHER0
keywords added in more recent versions of this FITS Tile Compression spec.
This includes support for lossless compression with GZIP. (#198) By default
no dithering is used, but the ``SUBTRACTIVE_DITHER_1`` and
``SUBTRACTIVE_DITHER_2`` methods can be enabled by passing the correct
constants to the ``quantize_method`` argument to the ``CompImageHDU``
constuctor. A seed can be manually specified, or automatically generated
using either the system clock or checksum-based methods via the
``dither_seed`` argument. See the documentation for ``CompImageHDU`` for
more details. (#198) (spacetelescope/PYFITS#32)
- Images compressed with the Tile Compression standard can now be larger than
4 GB through support of the Q format. (#159)
- All HDUs now have a ``.ver`` ``.level`` attribute that returns the value of
the EXTVAL and EXTLEVEL keywords from that HDU's header, if the exist. This
was added for consistency with the ``.name`` attribute which returns the
EXTNAME value from the header.
- Then ``Column`` and ``ColDefs`` classes have new ``.dtype`` attributes
which give the Numpy dtype for the column data in the first case, and the
full Numpy compound dtype for each table row in the latter case.
- There was an issue where new tables created defaulted the values in all
string columns to '0.0'. Now string columns are filled with empty strings
by default--this seems a less surprising default, but it may cause
differences with tables created with older versions of PyFITS.
- Improved round-tripping and preservation of manually assigned column
attributes (``TNULLn``, ``TSCALn``, etc.) in table HDU headers.
(astropy/astropy#996)
Bug Fixes
^^^^^^^^^
- Binary tables containing compressed images may, optionally, contain other
columns unrelated to the tile compression convention. Although this is an
uncommon use case, it is permitted by the standard. (#159)
- Reworked some of the file I/O routines to allow simpler, more consistent
mapping between OS-level file modes ('rb', 'wb', 'ab', etc.) and the more
"PyFITS-specific" modes used by PyFITS like "readonly" and "update".
That is, if reading a FITS file from an open file object, it doesn't matter
as much what "mode" it was opened in so long as it has the right
capabilities (read/write/etc.) Also works around bugs in the Python io
module in 2.6+ with regard to file modes. (spacetelescope/PyFITS#33)
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (astropy/astropy#968)
3.1.3 (2013-11-26)
------------------
- Disallowed assigning NaN and Inf floating point values as header values,
since the FITS standard does not define a way to represent them in. Because
this is undefined, the previous behavior did not make sense and produced
invalid FITS files. (spacetelescope/PyFITS#11)
- Added a workaround for a bug in 64-bit OSX that could cause truncation when
writing files greater than 2^32 bytes in size. (spacetelescope/PyFITS#28)
- Fixed a long-standing issue where writing binary tables did not correctly
write the TFORMn keywords for variable-length array columns (they ommitted
the max array length parameter of the format). This was thought fixed in
v3.1.2, but it was only fixed there for compressed image HDUs and not for
binary tables in general.
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2)
3.0.12 (2013-11-26)
-------------------
- Disallowed assigning NaN and Inf floating point values as header values,
since the FITS standard does not define a way to represent them in. Because
this is undefined, the previous behavior did not make sense and produced
invalid FITS files. (Backported from 3.1.3)
- Added a workaround for a bug in 64-bit OSX that could cause truncation when
writing files greater than 2^32 bytes in size. (Backported from 3.1.3)
- Fixed a long-standing issue where writing binary tables did not correctly
write the TFORMn keywords for variable-length array columns (they ommitted
the max array length parameter of the format). This was thought fixed in
v3.1.2, but it was only fixed there for compressed image HDUs and not for
binary tables in general. (Backported from 3.1.3)
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2)
3.1.2 (2013-04-22)
------------------
- When an error occurs opening a file in fitsdiff the exception message will
now at least mention which file had the error. (#168)
- Fixed support for opening gzipped FITS files by filename in a writeable mode
(PyFITS has supported writing to gzip files for some time now, but only
enabled it when GzipFile objects were passed to ``pyfits.open()`` due to
some legacy code preventing full gzip support. (#195)
- Added a more helpful error message in the case of malformatted FITS files
that contain non-float NULL values in an ASCII table but are missing the
required TNULLn keywords in the header. (#197)
- Fixed an (apparently long-standing) issue where writing compressed images
did not correctly write the TFORMn keywords for variable-length array
columns (they ommitted the max array length parameter of the format). (#199)
- Slightly refactored how tables containing variable-length array columns are
handled to add two improvements: Fixes an issue where accessing the data
after a call to the `pyfits.getdata` convenience function caused an
exception, and allows the VLA data to be read from an existing mmap of the
FITS file. (#200)
- Fixed a bug that could occur when opening a table containing
multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it
out to a new file. (#201)
- Added use of the console_scripts entry point to install the fitsdiff and
fitscheck scripts, which if nothing else provides better Windows support.
The generated scripts now override the ones explicitly defined in the
scripts/ directory (which were just trivial stubs to begin with). (#202)
- Fixed a bug on Python 3 where attempting to open a non-existent file on
Python 3 caused a seemingly unrelated traceback. (#203)
- Fixed a bug in fitsdiff that reported two header keywords containing NaN
as value as different. (#204)
- Fixed an issue in the tests that caused some tests to fail if pyfits is
installed with read-only permissions. (#208)
- Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array
containing boolean fields converted all the values to ``False``. (#215)
- Fixed an issue where passing an array of integers into the constructor of
``Column()`` when the column type is floats of the same byte width caused the
column array to become garbled. (#218)
- Fixed inconsistent behavior in creating CONTINUE cards from byte strings
versus unicode strings in Python 2--CONTINUE cards can now be created
properly from unicode strings (so long as they are convertable to ASCII).
(spacetelescope/PyFITS#1)
- Fixed a couple cases where creating a new table using TDIMn in some of the
columns could caused a crash. (spacetelescope/PyFITS#3)
- Fixed a bug in parsing HIERARCH keywords that do not have a space after
the first equals sign (before the value). (spacetelescope/PyFITS#5)
- Prevented extra leading whitespace on HIERARCH keywords from being treated
as part of the keyword. (spacetelescope/PyFITS#6)
- Fixed a bug where HIERARCH keywords containing lower-case letters was
mistakenly marked as invalid during header validation.
(spacetelescope/PyFITS#7)
- Fixed an issue that was ancillary to (spacetelescope/PyFITS#7) where the
``Header.index()`` method did not work correctly with HIERARCH keywords
containing lower-case letters.
3.0.11 (2013-04-17)
-------------------
- Fixed support for opening gzipped FITS files by filename in a writeable mode
(PyFITS has supported writing to gzip files for some time now, but only
enabled it when GzipFile objects were passed to ``pyfits.open()`` due to
some legacy code preventing full gzip support. Backported from 3.1.2. (#195)
- Added a more helpful error message in the case of malformatted FITS files
that contain non-float NULL values in an ASCII table but are missing the
required TNULLn keywords in the header. Backported from 3.1.2. (#197)
- Fixed an (apparently long-standing) issue where writing compressed images did
not correctly write the TFORMn keywords for variable-length array columns
(they ommitted the max array length parameter of the format). Backported from
3.1.2. (#199)
- Slightly refactored how tables containing variable-length array columns are
handled to add two improvements: Fixes an issue where accessing the data
after a call to the `pyfits.getdata` convenience function caused an
exception, and allows the VLA data to be read from an existing mmap of the
FITS file. Backported from 3.1.2. (#200)
- Fixed a bug that could occur when opening a table containing
multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it
out to a new file. Backported from 3.1.2. (#201)
- Fixed a bug on Python 3 where attempting to open a non-existent file on
Python 3 caused a seemingly unrelated traceback. Backported from 3.1.2.
(#203)
- Fixed a bug in fitsdiff that reported two header keywords containing NaN
as value as different. Backported from 3.1.2. (#204)
- Fixed an issue in the tests that caused some tests to fail if pyfits is
installed with read-only permissions. Backported from 3.1.2. (#208)
- Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array
containing boolean fields converted all the values to ``False``. Backported
from 3.1.2. (#215)
- Fixed an issue where passing an array of integers into the constructor of
``Column()`` when the column type is floats of the same byte width caused the
column array to become garbled. Backported from 3.1.2. (#218)
- Fixed a couple cases where creating a new table using TDIMn in some of the
columns could caused a crash. Backported from 3.1.2.
(spacetelescope/PyFITS#3)
3.1.1 (2013-01-02)
------------------
This is a bug fix release for the 3.1.x series.
Bug Fixes
^^^^^^^^^
- Improved handling of scaled images and pseudo-unsigned integer images in
compressed image HDUs. They now work more transparently like normal image
HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options,
as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method
works better too. (#88)
- Permits non-string values for the EXTNAME keyword when reading in a file,
rather than throwing an exception due to the malformatting. Added
verification for the format of the EXTNAME keyword when writing. (#96)
- Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME
is specified in the header, it will also be reflected in the ``.name``
attribute and in ``pyfits.info()``. These keywords used to be verboten in
PRIMARY HDUs, but the latest version of the FITS standard allows them.
(#151)
- HCOMPRESS can again be used to compress data cubes (and higher-dimensional
arrays) so long as the tile size is effectively 2-dimensional. In fact,
PyFITS will automatically use compatible tile sizes even if they're not
explicitly specified. (#171)
- Added support for the optional ``endcard`` parameter in the
``Header.fromtextfile()`` and ``Header.totextfile()`` methods. Although
``endcard=False`` was a reasonable default assumption, there are still text
dumps of FITS headers that include the END card, so this should have been
more flexible. (#176)
- Fixed a crash when running fitsdiff on two empty (that is, zero row) tables.
(#178)
- Fixed an issue where opening files containing random groups HDUs in update
mode could cause an unnecessary rewrite of the file even if none of the
data is modified. (#179)
- Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS
is used with Numpy 1.7 in some cases. (#180)
- Fixed a crash when generating diff reports from diffs using the
``ignore_comments`` options. (#181)
- Fixed some bugs with WCS Paper IV record-valued keyword cards:
- Cards that looked kind of like RVKCs but were not intended to be were
over-permissively treated as such--commentary keywords like COMMENT and
HISTORY were particularly affected. (#183)
- Looking up a card in a header by its standard FITS keyword only should
always return the raw value of that card. That way cards containing
values that happen to valid RVKCs but were not intended to be will still
be treated like normal cards. (#184)
- Looking up a RVKC in a header with only part of the field-specifier (for
example "DP1.AXIS" instead of "DP1.AXIS.1") was implicitly treated as a
wildcard lookup. (#184)
- Fixed a crash when diffing two FITS files where at least one contains a
compressed image HDU which was not recognized as an image instead of a
table. (#187)
- Fixed bugs in the backwards compatibility layer for the ``CardList.index``
and ``CardList.count`` methods. (#190)
- Improved ``__repr__`` and text file representation of cards with long values
that are split into CONTINUE cards. (#193)
- Fixed a crash when trying to assign a long (> 72 character) value to blank
('') keywords. This also changed how blank keywords are represented--there
are still exactly 8 spaces before any commentary content can begin; this
*may* affect the exact display of header cards that assumed there could be
fewer spaces in a blank keyword card before the content begins. However, the
current approach is more in line with the requirements of the FITS standard.
(#194)
3.0.10 (2013-01-02)
-------------------
- Improved handling of scaled images and pseudo-unsigned integer images in
compressed image HDUs. They now work more transparently like normal image
HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options,
as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method
works better too. Backported from 3.1.1. (#88)
- Permits non-string values for the EXTNAME keyword when reading in a file,
rather than throwing an exception due to the malformatting. Added
verification for the format of the EXTNAME keyword when writing. Backported
from 3.1.1. (#96)
- Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME
is specified in the header, it will also be reflected in the ``.name``
attribute and in ``pyfits.info()``. These keywords used to be verbotten in
PRIMARY HDUs, but the latest version of the FITS standard allows them.
Backported from 3.1.1. (#151)
- HCOMPRESS can again be used to compress data cubes (and higher-dimensional
arrays) so long as the tile size is effectively 2-dimensional. In fact,
PyFITS will not automatically use compatible tile sizes even if they're not
explicitly specified. Backported from 3.1.1. (#171)
- Fixed a bug when writing out files containing zero-width table columns,
where the TFIELDS keyword would be updated incorrectly, leaving the table
largely unreadable. Backported from 3.1.0. (#174)
- Fixed an issue where opening files containing random groups HDUs in update
mode could cause an unnecessary rewrite of the file even if none of the
data is modified. Backported from 3.1.1. (#179)
- Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS
is used with Numpy 1.7 in some cases. Backported from 3.1.1. (#180)
3.1 (2012-08-08)
----------------
Highlights
^^^^^^^^^^
- The ``Header`` object has been significantly reworked, and ``CardList``
objects are now deprecated (their functionality folded into the ``Header``
class). See API Changes below for more details.
- Memory maps are now used by default to access HDU data. See API Changes
below for more details.
- Now includes a new version of the ``fitsdiff`` program for comparing two
FITS files, and a new FITS comparison API used by ``fitsdiff``. See New
Features below.
API Changes
^^^^^^^^^^^
- The ``Header`` class has been rewritten, and the ``CardList`` class is
deprecated. Most of the basic details of working with FITS headers are
unchanged, and will not be noticed by most users. But there are differences
in some areas that will be of interest to advanced users, and to application
developers. For full details of the changes, see the "Header Interface
Transition Guide" section in the PyFITS documentation. See ticket #64 on
the PyFITS Trac for futher details and background. Some highlights are
listed below:
* The Header class now fully implements the Python dict interface, and can
be used interchangably with a dict, where the keys are header keywords.
* New keywords can be added to the header using normal keyword assignment
(previously it was necessary to use ``Header.update`` to add new
keywords). For example::
>>> header['NAXIS'] = 2
will update the existing 'FOO' keyword if it already exists, or add a new
one if it doesn't exist, just like a dict.
* It is possible to assign both a value and a comment at the same time using
a tuple::
>>> header['NAXIS'] = (2, 'Number of axes')
* To add/update a new card and ensure it's added in a specific location, use
``Header.set()``::
>>> header.set('NAXIS', 2, 'Number of axes', after='BITPIX')
This works the same as the old ``Header.update()``. ``Header.update()``
still works in the old way too, but is deprecated.
* Although ``Card`` objects still exist, it generally is not necessary to
work with them directly. ``Header.ascardlist()``/``Header.ascard`` are
deprecated and should not be used. To directly access the ``Card``
objects in a header, use ``Header.cards``.
* To access card comments, it is still possible to either go through the
card itself, or through ``Header.comments``. For example::
>>> header.cards['NAXIS'].comment
Number of axes
>>> header.comments['NAXIS']
Number of axes
* ``Card`` objects can now be used interchangeably with
``(keyword, value, comment)`` 3-tuples. They still have ``.value`` and
``.comment`` attributes as well. The ``.key`` attribute has been renamed
to ``.keyword`` for consistency, though ``.key`` is still supported (but
deprecated).
- Memory mapping is now used by default to access HDU data. That is,
``pyfits.open()`` uses ``memmap=True`` as the default. This provides better
performance in the majority of use cases--there are only some I/O intensive
applications where it might not be desirable. Enabling mmap by default also
enabled finding and fixing a large number of bugs in PyFITS' handling of
memory-mapped data (most of these bug fixes were backported to PyFITS
3.0.5). (#85)
* A new ``pyfits.USE_MEMMAP`` global variable was added. Set
``pyfits.USE_MEMMAP = False`` to change the default memmap setting for
opening files. This is especially useful for controlling the behavior in
applications where pyfits is deeply embedded.
* Likewise, a new ``PYFITS_USE_MEMMAP`` environment variable is supported.
Set ``PYFITS_USE_MEMMAP = 0`` in your environment to change the default
behavior.
- The ``size()`` method on HDU objects is now a ``.size`` property--this
returns the size in bytes of the data portion of the HDU, and in most cases
is equivalent to ``hdu.data.nbytes`` (#83)
- ``BinTableHDU.tdump`` and ``BinTableHDU.tcreate`` are deprecated--use
``BinTableHDU.dump`` and ``BinTableHDU.load`` instead. The new methods
output the table data in a slightly different format from previous versions,
which places quotes around each value. This format is compatible with data
dumps from previous versions of PyFITS, but not vice-versa due to a parsing
bug in older versions.
- Likewise the ``pyfits.tdump`` and ``pyfits.tcreate`` convenience function
versions of these methods have been renamed ``pyfits.tabledump`` and
``pyfits.tableload``. The old deprecated, but currently retained for
backwards compatibility. (r1125)
- A new global variable ``pyfits.EXTENSION_NAME_CASE_SENSITIVE`` was added.
This serves as a replacement for ``pyfits.setExtensionNameCaseSensitive``
which is not deprecated and may be removed in a future version. To enable
case-sensitivity of extension names (i.e. treat 'sci' as distict from 'SCI')
set ``pyfits.EXTENSION_NAME_CASE_SENSITIVE = True``. The default is
``False``. (r1139)
- A new global configuration variable ``pyfits.STRIP_HEADER_WHITESPACE`` was
added. By default, if a string value in a header contains trailing
whitespace, that whitespace is automatically removed when the value is read.
Now if you set ``pyfits.STRIP_HEADER_WHITESPACE = False`` all whitespace is
preserved. (#146)
- The old ``classExtensions`` extension mechanism (which was deprecated in
PyFITS 3.0) is removed outright. To our knowledge it was no longer used
anywhere. (r1309)
- Warning messages from PyFITS issued through the Python warnings API are now
output to stderr instead of stdout, as is the default. PyFITS no longer
modifies the default behavior of the warnings module with respect to which
stream it outputs to. (r1319)
- The ``checksum`` argument to ``pyfits.open()`` now accepts a value of
'remove', which causes any existing CHECKSUM/DATASUM keywords to be ignored,
and removed when the file is saved.
New Features
^^^^^^^^^^^^
- Added support for the proposed "FITS" extension HDU type. See
http://listmgr.cv.nrao.edu/pipermail/fitsbits/2002-April/001094.html. FITS
HDUs contain an entire FITS file embedded in their data section. `FitsHDU`
objects work like other HDU types in PyFITS. Their ``.data`` attribute
returns the raw data array. However, they have a special ``.hdulist``
attribute which processes the data as a FITS file and returns it as an
in-memory HDUList object. FitsHDU objects also support a
``FitsHDU.fromhdulist()`` classmethod which returns a new `FitsHDU` object
that embeds the supplied HDUList. (#80)
- Added a new ``.is_image`` attribute on HDU objects, which is True if the HDU
data is an 'image' as opposed to a table or something else. Here the
meaning of 'image' is fairly loose, and mostly just means a Primary or Image
extension HDU, or possibly a compressed image HDU (#71)
- Added an ``HDUList.fromstring`` classmethod which can parse a FITS file
already in memory and instantiate and ``HDUList`` object from it. This
could be useful for integrating PyFITS with other libraries that work on
FITS file, such as CFITSIO. It may also be useful in streaming
applications. The name is a slight misnomer, in that it actually accepts
any Python object that implements the buffer interface, which includes
``bytes``, ``bytearray``, ``memoryview``, ``numpy.ndarray``, etc. (#90)
- Added a new ``pyfits.diff`` module which contains facilities for comparing
FITS files. One can use the ``pyfits.diff.FITSDiff`` class to compare two
FITS files in their entirety. There is also a ``pyfits.diff.HeaderDiff``
class for just comparing two FITS headers, and other similar interfaces.
See the PyFITS Documentation for more details on this interface. The
``pyfits.diff`` module powers the new ``fitsdiff`` program installed with
PyFITS. After installing PyFITS, run ``fitsdiff --help`` for usage details.
- ``pyfits.open()`` now accepts a ``scale_back`` argument. If set to
``True``, this automatically scales the data using the original BZERO and
BSCALE parameters the file had when it was first opened, if any, as well as
the original BITPIX. For example, if the original BITPIX were 16, this
would be equivalent to calling ``hdu.scale('int16', 'old')`` just before
calling ``flush()`` or ``close()`` on the file. This option applies to all
HDUs in the file. (#120)
- ``pyfits.open()`` now accepts a ``save_backup`` argument. If set to
``True``, this automatically saves a backup of the original file before
flushing any changes to it (this of course only applies to update and append
mode). This may be especially useful when working with scaled image data.
(#121)
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Warnings from PyFITS are not output to stderr by default, instead of stdout
as it has been for some time. This is contrary to most users' expectations
and makes it more difficult for them to separate output from PyFITS from the
desired output for their scripts. (r1319)
Bug Fixes
^^^^^^^^^
- Fixed ``pyfits.tcreate()`` (now ``pyfits.tableload()``) to be more robust
when encountering blank lines in a column definition file (#14)
- Fixed a fairly rare crash that could occur in the handling of CONTINUE cards
when using Numpy 1.4 or lower (though 1.4 is the oldest version supported by
PyFITS). (r1330)
- Fixed ``_BaseHDU.fromstring`` to actually correctly instantiate an HDU
object from a string/buffer containing the header and data of that HDU.
This allowed for the implementation of ``HDUList.fromstring`` described
above. (#90)
- Fixed a rare corner case where, in some use cases, (mildly, recoverably)
malformatted float values in headers were not properly returned as floats.
(#137)
- Fixed a corollary to the previous bug where float values with a leading zero
before the decimal point had the leading zero unnecessarily removed when
saving changes to the file (eg. "0.001" would be written back as ".001" even
if no changes were otherwise made to the file). (#137)
- When opening a file containing CHECKSUM and/or DATASUM keywords in update
mode, the CHECKSUM/DATASUM are updated and preserved even if the file was
opened with checksum=False. This change in behavior prevents checksums from
being unintentionally removed. (#148)
- Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it
was not restoring the image to its original BSCALE and BZERO values. (#162)
- Fixed a bug when writing out files containing zero-width table columns,
where the TFIELDS keyword would be updated incorrectly, leaving the table
largely unreadable. This fix will be backported to the 3.0.x series in
version 3.0.10. (#174)
3.0.9 (2012-08-06)
------------------
This is a bug fix release for the 3.0.x series.
Bug Fixes
^^^^^^^^^
- Fixed ``Header.values()``/``Header.itervalues()`` and ``Header.items()``/
``Header.iteritems()`` to correctly return the different values for
duplicate keywords (particularly commentary keywords like HISTORY and
COMMENT). This makes the old Header implementation slightly more compatible
with the new implementation in PyFITS 3.1. (#127)
.. note::
This fix did not change the existing behavior from earlier PyFITS
versions where ``Header.keys()`` returns all keywords in the header with
duplicates removed. PyFITS 3.1 changes that behavior, so that
``Header.keys()`` includes duplicates.
- Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it
was not restoring the image to its original BSCALE and BZERO values. (#162)
- Fixed a bug where opening a file containing compressed image HDUs in
'update' mode and then immediately closing it without making any changes
caused the file to be rewritten unncessarily. (#167)
- Fixed two memory leaks that could occur when writing compressed image data,
or in some cases when opening files containing compressed image HDUs in
'update' mode. (#168)
3.0.8 (2012-06-04)
------------------
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Prior to this release, image data sections did not work with scaled
data--that is, images with non-trivial BSCALE and/or BZERO values.
Previously, in order to read such images in sections, it was necessary to
manually apply the BSCALE+BZERO to each section. It's worth noting that
sections *did* support pseudo-unsigned ints (flakily). This change just
extends that support for general BSCALE+BZERO values.
Bug Fixes
^^^^^^^^^
- Fixed a bug that prevented updates to values in boolean table columns from
being saved. This turned out to be a symptom of a deeper problem that could
prevent other table updates from being saved as well. (#139)
- Fixed a corner case in which a keyword comment ending with the string "END"
could, in some circumstances, cause headers (and the rest of the file after
that point) to be misread. (#142)
- Fixed support for scaled image data and psuedo-unsigned ints in image data
sections (``hdu.section``). Previously this was not supported at all. At
some point support was supposedly added, but it was buggy and incomplete.
Now the feature seems to work much better. (#143)
- Fixed the documentation to point out that image data sections *do* support
non-contiguous slices (and have for a long time). The documentation was
never updated to reflect this, and misinformed users that only contiguous
slices were supported, leading to some confusion. (#144)
- Fixed a bug where creating an ``HDUList`` object containing multiple PRIMARY
HDUs caused an infinite recursion when validating the object prior to
writing to a file. (#145)
- Fixed a rare but serious case where saving an update to a file that
previously had a CHECKSUM and/or DATASUM keyword, but removed the checksum
in saving, could cause the file to be slightly corrupted and unreadable.
(#147)
- Fixed problems with reading "non-standard" FITS files with primary headers
containing SIMPLE = F. PyFITS has never made many guarantees as to how such
files are handled. But it should at least be possible to read their
headers, and the data if possible. Saving changes to such a file should not
try to prepend an unwanted valid PRIMARY HDU. (#157)
- Fixed a bug where opening an image with ``disable_image_compression = True``
caused compression to be disabled for all subsequent ``pyfits.open()`` calls.
(r1651)
3.0.7 (2012-04-10)
------------------
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Slices of GroupData objects now return new GroupData objects instead of
extended multi-row _Group objects. This is analogous to how PyFITS 3.0 fixed
FITS_rec slicing, and should have been fixed for GroupData at the same time.
The old behavior caused bugs where functions internal to Numpy expected that
slicing an ndarray would return a new ndarray. As this is a rare usecase
with a rare feature most users are unlikely to be affected by this change.
- The previously internal _Group object for representing individual group
records in a GroupData object are renamed Group and are now a public
interface. However, there's almost no good reason to create Group objects
directly, so it shouldn't be considered a "new feature".
- An annoyance from PyFITS 3.0.6 was fixed, where the value of the EXTEND
keyword was always being set to F if there are not actually any extension
HDUs. It was unnecessary to modify this value.
Bug Fixes
^^^^^^^^^
- Fixed GroupData objects to return new GroupData objects when sliced instead
of _Group record objects. See "Changes in behavior" above for more details.
- Fixed slicing of Group objects--previously it was not possible to slice
slice them at all.
- Made it possible to assign `np.bool_` objects as header values. (#123)
- Fixed overly strict handling of the EXTEND keyword; see "Changes in
behavior" above. (#124)
- Fixed many cases where an HDU's header would be marked as "modified" by
PyFITS and rewritten, even when no changes to the header are necessary.
(#125)
- Fixed a bug where the values of the PTYPEn keywords in a random groups HDU
were forced to be all lower-case when saving the file. (#130)
- Removed an unnecessary inline import in `ExtensionHDU.__setattr__` that was
causing some slowdown when opening files containing a large number of
extensions, plus a few other small (but not insignficant) performance
improvements thanks to Julian Taylor. (#133)
- Fixed a regression where header blocks containing invalid end-of-header
padding (i.e. null bytes instead of spaces) couldn't be parsed by PyFITS.
Such headers can be parsed again, but a warning is raised, as such headers
are not valid FITS. (#136)
- Fixed a memory leak where table data in random groups HDUs weren't being
garbage collected. (#138)
3.0.6 (2012-02-29)
------------------
Highlights
^^^^^^^^^^
The main reason for this release is to fix an issue that was introduced in
PyFITS 3.0.5 where merely opening a file containing scaled data (that is, with
non-trivial BSCALE and BZERO keywords) in 'update' mode would cause the data
to be automatically rescaled--possibly converting the data from ints to
floats--as soon as the file is closed, even if the application did not touch
the data. Now PyFITS will only rescale the data in an extension when the data
is actually accessed by the application. So opening a file in 'update' mode
in order to modify the header or append new extensions will not cause any
change to the data in existing extensions.
This release also fixes a few Windows-specific bugs found through more
extensive Windows testing, and other miscellaneous bugs.
Bug Fixes
^^^^^^^^^
- More accurate error messages when opening files containing invalid header
cards. (#109)
- Fixed a possible reference cycle/memory leak that was caught through more
extensive testing on Windows. (#112)
- Fixed 'ostream' mode to open the underlying file in 'wb' mode instead of 'w'
mode. (#112)
- Fixed a Windows-only issue where trying to save updates to a resized FITS
file could result in a crash due to there being open mmaps on that file.
(#112)
- Fixed a crash when trying to create a FITS table (i.e. with new_table())
from a Numpy array containing bool fields. (#113)
- Fixed a bug where manually initializing an ``HDUList`` with a list of of
HDUs wouldn't set the correct EXTEND keyword value on the primary HDU.
(#114)
- Fixed a crash that could occur when trying to deepcopy a Header in Python <
2.7. (#115)
- Fixed an issue where merely opening a scaled image in 'update' mode would
cause the data to be converted to floats when the file is closed. (#119)
3.0.5 (2012-01-30)
------------------
- Fixed a crash that could occur when accessing image sections of files
opened with memmap=True. (r1211)
- Fixed the inconsistency in the behavior of files opened in 'readonly' mode
when memmap=True vs. when memmap=False. In the latter case, although
changes to array data were not saved to disk, it was possible to update the
array data in memory. On the other hand with memmap=True, 'readonly' mode
prevented even in-memory modification to the data. This is what
'copyonwrite' mode was for, but difference in behavior was confusing. Now
'readonly' is equivalent to 'copyonwrite' when using memmap. If the old
behavior of denying changes to the array data is necessary, a new
'denywrite' mode may be used, though it is only applicable to files opened
with memmap. (r1275)
- Fixed an issue where files opened with memmap=True would return image data
as a raw numpy.memmap object, which can cause some unexpected
behaviors--instead memmap object is viewed as a numpy.ndarray. (r1285)
- Fixed an issue in Python 3 where a workaround for a bug in Numpy on Python 3
interacted badly with some other software, namely to vo.table package (and
possibly others). (r1320, r1337, and #110)
- Fixed buggy behavior in the handling of SIGINTs (i.e. Ctrl-C keyboard
interrupts) while flushing changes to a FITS file. PyFITS already prevented
SIGINTs from causing an incomplete flush, but did not clean up the signal
handlers properly afterwards, or reraise the keyboard interrupt once the
flush was complete. (r1321)
- Fixed a crash that could occur in Python 3 when opening files with checksum
checking enabled. (r1336)
- Fixed a small bug that could cause a crash in the `StreamingHDU` interface
when using Numpy below version 1.5.
- Fixed a crash that could occur when creating a new `CompImageHDU` from an
array of big-endian data. (#104)
- Fixed a crash when opening a file with extra zero padding at the end.
Though FITS files should not have such padding, it's not explictly forbidden
by the format either, and PyFITS shouldn't stumble over it. (#106)
- Fixed a major slowdown in opening tables containing large columns of string
values. (#111)
3.0.4 (2011-11-22)
------------------
- Fixed a crash when writing HCOMPRESS compressed images that could happen on
Python 2.5 and 2.6. (r1217)
- Fixed a crash when slicing an table in a file opened in 'readonly' mode with
memmap=True. (r1230)
- Writing changes to a file or writing to a new file verifies the output in
'fix' mode by default instead of 'exception'--that is, PyFITS will
automatically fix common FITS format errors rather than raising an
exception. (r1243)
- Fixed a bug where convenience functions such as getval() and getheader()
crashed when specifying just 'PRIMARY' as the extension to use (r1263).
- Fixed a bug that prevented passing keyword arguments (beyond the standard
data and header arguments) as positional arguments to the constructors of
extension HDU classes.
- Fixed some tests that were failing on Windows--in this case the tests
themselves failed to close some temp files and Windows refused to delete them
while there were still open handles on them. (r1295)
- Fixed an issue with floating point formatting in header values on Python 2.5
for Windows (and possibly other platforms). The exponent was zero-padded to
3 digits; although the FITS standard makes no specification on this, the
formatting is now normalized to always pad the exponent to two digits.
(r1295)
- Fixed a bug where long commentary cards (such as HISTORY and COMMENT) were
broken into multiple CONTINUE cards. However, commentary cards are not
expected to be found in CONTINUE cards. Instead these long cards are broken
into multiple commentary cards. (#97)
- GZIP/ZIP-compressed FITS files can be detected and opened regardless of
their filename extension. (#99)
- Fixed a serious bug where opening scaled images in 'update' mode and then
closing the file without touching the data would cause the file to be
corrupted. (#101)
3.0.3 (2011-10-05)
------------------
- Fixed several small bugs involving corner cases in record-valued keyword
cards (#70)
- In some cases HDU creation failed if the first keyword value in the header
was not a string value (#89)
- Fixed a crash when trying to compute the HDU checksum when the data array
contains an odd number of bytes (#91)
- Disabled an unnecessary warning that was displayed on opening compressed
HDUs with disable_image_compression = True (#92)
- Fixed a typo in code for handling HCOMPRESS compressed images.
3.0.2 (2011-09-23)
------------------
- The ``BinTableHDU.tcreate`` method and by extension the ``pyfits.tcreate``
function don't get tripped up by blank lines anymore (#14)
- The presence, value, and position of the EXTEND keyword in Primary HDUs is
verified when reading/writing a FITS file (#32)
- Improved documentation (in warning messages as well as in the handbook) that
PyFITS uses zero-based indexing (as one would expect for C/Python code, but
contrary to the PyFITS standard which was written with FORTRAN in mind)
(#68)
- Fixed a bug where updating a header card comment could cause the value to be
lost if it had not already been read from the card image string.
- Fixed a related bug where changes made directly to Card object in a header
(i.e. assigning directly to card.value or card.comment) would not propagate
when flushing changes to the file (#69) [Note: This and the bug above it
were originally reported as being fixed in version 3.0.1, but the fix was
never included in the release.]
- Improved file handling, particularly in Python 3 which had a few small file
I/O-related bugs (#76)
- Fixed a bug where updating a FITS file would sometimes cause it to lose its
original file permissions (#79)
- Fixed the handling of TDIMn keywords; 3.0 added support for them, but got
the axis order backards (they were treated as though they were row-major)
(#82)
- Fixed a crash when a FITS file containing scaled data is opened and
immediately written to a new file without explicitly viewing the data first
(#84)
- Fixed a bug where creating a table with columns named either 'names' or
'formats' resulted in an infinite recursion (#86)
3.0.1 (2011-09-12)
------------------
- Fixed a bug where updating a header card comment could cause the value to be
lost if it had not already been read from the card image string.
- Changed ``_TableBaseHDU.data`` so that if the data contain an empty table a
``FITS_rec`` object with zero rows is returned rather than ``None``.
- The ``.key`` attribute of ``RecordValuedKeywordCards`` now returns the full
keyword+field-specifier value, instead of just the plain keyword (#46)
- Fixed a related bug where changes made directly to Card object in a header
(i.e. assigning directly to card.value or card.comment) would not propagate
when flushing changes to the file (#69)
- Fixed a bug where writing a table with zero rows could fail in some cases
(#72)
- Miscellanous small bug fixes that were causing some tests to fail,
particularly on Python 3 (#74, #75)
- Fixed a bug where creating a table column from an array in non-native byte
order would not preserve the byte order, thus interpreting the column array
using the wrong byte order (#77)
3.0.0 (2011-08-23)
--------------------
- Contains major changes, bumping the version to 3.0
- Large amounts of refactoring and reorganization of the code; tried to
preserve public API backwards-compatibility with older versions (private API
has many changes and is not guaranteed to be backwards-compatible). There
are a few small public API changes to be aware of:
* The pyfits.rec module has been removed completely. If your version of
numpy does not have the numpy.core.records module it is too old to be used
with PyFITS.
* The ``Header.ascardlist()`` method is deprecated--use the ``.ascard``
attribute instead.
* ``Card`` instances have a new ``.cardimage`` attribute that should be used
rather than ``.ascardimage()``, which may become deprecated.
* The ``Card.fromstring()`` method is now a classmethod. It returns a new
``Card`` instance rather than modifying an existing instance.
* The ``req_cards()`` method on HDU instances has changed: The ``pos``
argument is not longer a string. It is either an integer value (meaning
the card's position must match that value) or it can be a function that
takes the card's position as it's argument, and returns True if the
position is valid. Likewise, the ``test`` argument no longer takes a
string, but instead a function that validates the card's value and returns
True or False.
* The ``get_coldefs()`` method of table HDUs is deprecated. Use the
``.columns`` attribute instead.
* The ``ColDefs.data`` attribute is deprecated--use ``ColDefs.columns``
instead (though in general you shouldn't mess with it directly--it might
become internal at some point).
* ``FITS_record`` objects take ``start`` and ``end`` as arguments instead of
``startColumn`` and ``endColumn`` (these are rarely created manually, so
it's unlikely that this change will affect anyone).
* ``BinTableHDU.tcreate()`` is now a classmethod, and returns a new
``BinTableHDU`` instance.
* Use ``ExtensionHDU`` and ``NonstandardExtHDU`` for making new extension HDU
classes. They are now public interfaces, wheres previously they were
private and prefixed with underscores.
* Possibly others--please report if you find any changes that cause
difficulties.
- Calls to deprecated functions will display a Deprecation warning. However,
in Python 2.7 and up Deprecation warnings are ignored by default, so run
Python with the `-Wd` option to see if you're using any deprecated
functions. If we get close to actually removing any functions, we might
make the Deprecation warnings display by default.
- Added basic Python 3 support
- Added support for multi-dimensional columns in tables as specified by the
TDIMn keywords (#47)
- Fixed a major memory leak that occurred when creating new tables with the
``new_table()`` function (#49)
be padded with zero-bytes) vs ASCII tables (where strings are padded with
spaces) (#15)
- Fixed a bug in which the case of Random Access Group parameters names was not
preserved when writing (#41)
- Added support for binary table fields with zero width (#42)
- Added support for wider integer types in ASCII tables; although this is non-
standard, some GEIS images require it (#45)
- Fixed a bug that caused the index_of() method of HDULists to crash when the
HDUList object is created from scratch (#48)
- Fixed the behavior of string padding in binary tables (where strings should
be padded with nulls instead of spaces)
- Fixed a rare issue that caused excessive memory usage when computing
checksums using a non-standard block size (see r818)
- Add support for forced uint data in image sections (#53)
- Fixed an issue where variable-length array columns were not extended when
creating a new table with more rows than the original (#54)
- Fixed tuple and list-based indexing of FITS_rec objects (#55)
- Fixed an issue where BZERO and BSCALE keywords were appended to headers in
the wrong location (#56)
- ``FITS_record`` objects (table rows) have full slicing support, including
stepping, etc. (#59)
- Fixed a bug where updating multiple files simultaneously (such as when
running parallel processes) could lead to a race condition with mktemp()
(#61)
- Fixed a bug where compressed image headers were not in the order expected by
the funpack utility (#62)
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## python-markdown2 2.1.0 - ["nofollow" extra, issue #74, pull #104] Add `rel="nofollow"` support (mostly by https://github.com/cdman): $ echo '[link](http://example)' | markdown2 -x nofollow <p><a rel="nofollow" href="http://example">link</a></p> Limitation: This *can* add a duplicate 'rel' attribute to raw HTML links in the input.
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FITS (Flexible Image Transport System) is a data format most used in astronomy.
PyFITS is a Python module for reading, writing, and manipulating FITS files.
The module uses Python's object-oriented features to provide quick, easy, and
efficient access to FITS files. The use of Python's array syntax enables
immediate access to any FITS extension, header cards, or data items.
Changes to 2.4.0 (in py-pyfits):
Changelog
===========
3.2 (2013-11-26)
----------------
Highlights
^^^^^^^^^^
- Rewrote CFITSIO-based backend for handling tile compression of FITS files.
It now uses a standard CFITSIO instead of heavily modified pieces of CFITSIO
as before. PyFITS ships with its own copy of CFITSIO v3.35 which supports
the latest version of the Tiled Image Convention (v2.3), but system
packagers may choose instead to strip this out in favor of a
system-installed version of CFITSIO. Earlier versions may work, but nothing
earlier than 3.28 has been tested yet. (#169)
- Added support for reading and writing tables using the Q format for columns.
The Q format is identical to the P format (variable-length arrays) except
that it uses 64-bit integers for the data descriptors, allowing more than
4 GB of variable-length array data in a single table. (#160)
- Added initial support for table columns containing pseudo-unsigned integers.
This is currently enabled by using the ``uint=True`` option when opening
files; any table columns with the correct BZERO value will be interpreted
and returned as arrays of unsigned integers.
- Some refactoring of the table and ``FITS_rec`` modules in order to better
separate the details of the FITS binary and ASCII table data structures from
the HDU data structures that encapsulate them. Most of these changes should
not be apparent to users (but see API Changes below).
API Changes
^^^^^^^^^^^
- Assigning to values in ``ColDefs.names``, ``ColDefs.formats``,
``ColDefs.nulls`` and other attributes of ``ColDefs`` instances that return
lists of column properties is no longer supported. Assigning to those lists
will no longer update the corresponding columns. Instead, please just
modify the ``Column`` instances directly (``Column.name``, ``Column.null``,
etc.)
- The ``pyfits.new_table`` function is marked "pending deprecation". This
does not mean it will be removed outright or that its functionality has
changed. It will likely be replaced in the future for a function with
similar, if not subtly different functionality. A better, if not slightly
more verbose approach is to use ``pyfits.FITS_rec.from_columns`` to create
a new ``FITS_rec`` table--this has the same interface as
``pyfits.new_table``. The difference is that it returns a plan ``FITS_rec``
array, and not an HDU instance. This ``FITS_rec`` object can then be used
as the data argument in the constructors for ``BinTableHDU`` (for binary
tables) or ``TableHDU`` (for ASCII tables). This is analogous to creating
an ``ImageHDU`` by passing in an image array.
``pyfits.FITS_rec.from_columns`` is just a simpler way of creating a
FITS-compatible recarray from a FITS column specification.
- The ``updateHeader``, ``updateHeaderData``, and ``updateCompressedData``
methods of the ``CompDataHDU`` class are pending deprecation and moved to
internal methods. The operation of these methods depended too much on
internal state to be used safely by users; instead they are invoked
automatically in the appropriate places when reading/writing compressed image
HDUs.
- The ``CompDataHDU.compData`` attribute is pending deprecation in favor of
the clearer and more PEP-8 compatible ``CompDataHDU.compressed_data``.
- The constructor for ``CompDataHDU`` has been changed to accept new keyword
arguments. The new keyword arguments are essentially the same, but are in
underscore_separated format rather than camelCase format. The old arguments
are still pending deprecation.
- The internal attributes of HDU classes ``_hdrLoc``, ``_datLoc``, and
``_datSpan`` have been replaced with ``_header_offset``, ``_data_offset``,
and ``_data_size`` respectively. The old attribute names are still pending
deprecation. This should only be of interest to advanced users who have
created their own HDU subclasses.
- The following previously deprecated functions and methods have been removed
entirely: ``createCard``, ``createCardFromString``, ``upperKey``,
``ColDefs.data``, ``setExtensionNameCaseSensitive``, ``_File.getfile``,
``_TableBaseHDU.get_coldefs``, ``Header.has_key``, ``Header.ascardlist``.
If you run your code with a previous version of PyFITS (>= 3.0, < 3.2) with
the ``python -Wd`` argument, warnings for all deprecated interfaces still in
use will be displayed.
- Interfaces that were pending deprecation are now fully deprecated. These
include: ``create_card``, ``create_card_from_string``, ``upper_key``,
``Header.get_history``, and ``Header.get_comment``.
- The ``.name`` attribute on HDUs is now directly tied to the HDU's header, so
that if ``.header['EXTNAME']`` changes so does ``.name`` and vice-versa.
- The ``pyfits.file.PYTHON_MODES`` constant dict was renamed to
``pyfits.file.PYFITS_MODES`` which better reflects its purpose. This is
rarely used by client code, however. Support for the old name will be
removed by PyFITS 3.4.
Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^
- The new compression code also adds support for the ZQUANTIZ and ZDITHER0
keywords added in more recent versions of this FITS Tile Compression spec.
This includes support for lossless compression with GZIP. (#198) By default
no dithering is used, but the ``SUBTRACTIVE_DITHER_1`` and
``SUBTRACTIVE_DITHER_2`` methods can be enabled by passing the correct
constants to the ``quantize_method`` argument to the ``CompImageHDU``
constuctor. A seed can be manually specified, or automatically generated
using either the system clock or checksum-based methods via the
``dither_seed`` argument. See the documentation for ``CompImageHDU`` for
more details. (#198) (spacetelescope/PYFITS#32)
- Images compressed with the Tile Compression standard can now be larger than
4 GB through support of the Q format. (#159)
- All HDUs now have a ``.ver`` ``.level`` attribute that returns the value of
the EXTVAL and EXTLEVEL keywords from that HDU's header, if the exist. This
was added for consistency with the ``.name`` attribute which returns the
EXTNAME value from the header.
- Then ``Column`` and ``ColDefs`` classes have new ``.dtype`` attributes
which give the Numpy dtype for the column data in the first case, and the
full Numpy compound dtype for each table row in the latter case.
- There was an issue where new tables created defaulted the values in all
string columns to '0.0'. Now string columns are filled with empty strings
by default--this seems a less surprising default, but it may cause
differences with tables created with older versions of PyFITS.
- Improved round-tripping and preservation of manually assigned column
attributes (``TNULLn``, ``TSCALn``, etc.) in table HDU headers.
(astropy/astropy#996)
Bug Fixes
^^^^^^^^^
- Binary tables containing compressed images may, optionally, contain other
columns unrelated to the tile compression convention. Although this is an
uncommon use case, it is permitted by the standard. (#159)
- Reworked some of the file I/O routines to allow simpler, more consistent
mapping between OS-level file modes ('rb', 'wb', 'ab', etc.) and the more
"PyFITS-specific" modes used by PyFITS like "readonly" and "update".
That is, if reading a FITS file from an open file object, it doesn't matter
as much what "mode" it was opened in so long as it has the right
capabilities (read/write/etc.) Also works around bugs in the Python io
module in 2.6+ with regard to file modes. (spacetelescope/PyFITS#33)
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (astropy/astropy#968)
3.1.3 (2013-11-26)
------------------
- Disallowed assigning NaN and Inf floating point values as header values,
since the FITS standard does not define a way to represent them in. Because
this is undefined, the previous behavior did not make sense and produced
invalid FITS files. (spacetelescope/PyFITS#11)
- Added a workaround for a bug in 64-bit OSX that could cause truncation when
writing files greater than 2^32 bytes in size. (spacetelescope/PyFITS#28)
- Fixed a long-standing issue where writing binary tables did not correctly
write the TFORMn keywords for variable-length array columns (they ommitted
the max array length parameter of the format). This was thought fixed in
v3.1.2, but it was only fixed there for compressed image HDUs and not for
binary tables in general.
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2)
3.0.12 (2013-11-26)
-------------------
- Disallowed assigning NaN and Inf floating point values as header values,
since the FITS standard does not define a way to represent them in. Because
this is undefined, the previous behavior did not make sense and produced
invalid FITS files. (Backported from 3.1.3)
- Added a workaround for a bug in 64-bit OSX that could cause truncation when
writing files greater than 2^32 bytes in size. (Backported from 3.1.3)
- Fixed a long-standing issue where writing binary tables did not correctly
write the TFORMn keywords for variable-length array columns (they ommitted
the max array length parameter of the format). This was thought fixed in
v3.1.2, but it was only fixed there for compressed image HDUs and not for
binary tables in general. (Backported from 3.1.3)
- Fixed an obscure issue that can occur on systems that don't have flush to
memory-mapped files implemented (namely GNU Hurd). (Backported from 3.2)
3.1.2 (2013-04-22)
------------------
- When an error occurs opening a file in fitsdiff the exception message will
now at least mention which file had the error. (#168)
- Fixed support for opening gzipped FITS files by filename in a writeable mode
(PyFITS has supported writing to gzip files for some time now, but only
enabled it when GzipFile objects were passed to ``pyfits.open()`` due to
some legacy code preventing full gzip support. (#195)
- Added a more helpful error message in the case of malformatted FITS files
that contain non-float NULL values in an ASCII table but are missing the
required TNULLn keywords in the header. (#197)
- Fixed an (apparently long-standing) issue where writing compressed images
did not correctly write the TFORMn keywords for variable-length array
columns (they ommitted the max array length parameter of the format). (#199)
- Slightly refactored how tables containing variable-length array columns are
handled to add two improvements: Fixes an issue where accessing the data
after a call to the `pyfits.getdata` convenience function caused an
exception, and allows the VLA data to be read from an existing mmap of the
FITS file. (#200)
- Fixed a bug that could occur when opening a table containing
multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it
out to a new file. (#201)
- Added use of the console_scripts entry point to install the fitsdiff and
fitscheck scripts, which if nothing else provides better Windows support.
The generated scripts now override the ones explicitly defined in the
scripts/ directory (which were just trivial stubs to begin with). (#202)
- Fixed a bug on Python 3 where attempting to open a non-existent file on
Python 3 caused a seemingly unrelated traceback. (#203)
- Fixed a bug in fitsdiff that reported two header keywords containing NaN
as value as different. (#204)
- Fixed an issue in the tests that caused some tests to fail if pyfits is
installed with read-only permissions. (#208)
- Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array
containing boolean fields converted all the values to ``False``. (#215)
- Fixed an issue where passing an array of integers into the constructor of
``Column()`` when the column type is floats of the same byte width caused the
column array to become garbled. (#218)
- Fixed inconsistent behavior in creating CONTINUE cards from byte strings
versus unicode strings in Python 2--CONTINUE cards can now be created
properly from unicode strings (so long as they are convertable to ASCII).
(spacetelescope/PyFITS#1)
- Fixed a couple cases where creating a new table using TDIMn in some of the
columns could caused a crash. (spacetelescope/PyFITS#3)
- Fixed a bug in parsing HIERARCH keywords that do not have a space after
the first equals sign (before the value). (spacetelescope/PyFITS#5)
- Prevented extra leading whitespace on HIERARCH keywords from being treated
as part of the keyword. (spacetelescope/PyFITS#6)
- Fixed a bug where HIERARCH keywords containing lower-case letters was
mistakenly marked as invalid during header validation.
(spacetelescope/PyFITS#7)
- Fixed an issue that was ancillary to (spacetelescope/PyFITS#7) where the
``Header.index()`` method did not work correctly with HIERARCH keywords
containing lower-case letters.
3.0.11 (2013-04-17)
-------------------
- Fixed support for opening gzipped FITS files by filename in a writeable mode
(PyFITS has supported writing to gzip files for some time now, but only
enabled it when GzipFile objects were passed to ``pyfits.open()`` due to
some legacy code preventing full gzip support. Backported from 3.1.2. (#195)
- Added a more helpful error message in the case of malformatted FITS files
that contain non-float NULL values in an ASCII table but are missing the
required TNULLn keywords in the header. Backported from 3.1.2. (#197)
- Fixed an (apparently long-standing) issue where writing compressed images did
not correctly write the TFORMn keywords for variable-length array columns
(they ommitted the max array length parameter of the format). Backported from
3.1.2. (#199)
- Slightly refactored how tables containing variable-length array columns are
handled to add two improvements: Fixes an issue where accessing the data
after a call to the `pyfits.getdata` convenience function caused an
exception, and allows the VLA data to be read from an existing mmap of the
FITS file. Backported from 3.1.2. (#200)
- Fixed a bug that could occur when opening a table containing
multi-dimensional columns (i.e. via the TDIMn keyword) and then writing it
out to a new file. Backported from 3.1.2. (#201)
- Fixed a bug on Python 3 where attempting to open a non-existent file on
Python 3 caused a seemingly unrelated traceback. Backported from 3.1.2.
(#203)
- Fixed a bug in fitsdiff that reported two header keywords containing NaN
as value as different. Backported from 3.1.2. (#204)
- Fixed an issue in the tests that caused some tests to fail if pyfits is
installed with read-only permissions. Backported from 3.1.2. (#208)
- Fixed a bug where instantiating a ``BinTableHDU`` from a numpy array
containing boolean fields converted all the values to ``False``. Backported
from 3.1.2. (#215)
- Fixed an issue where passing an array of integers into the constructor of
``Column()`` when the column type is floats of the same byte width caused the
column array to become garbled. Backported from 3.1.2. (#218)
- Fixed a couple cases where creating a new table using TDIMn in some of the
columns could caused a crash. Backported from 3.1.2.
(spacetelescope/PyFITS#3)
3.1.1 (2013-01-02)
------------------
This is a bug fix release for the 3.1.x series.
Bug Fixes
^^^^^^^^^
- Improved handling of scaled images and pseudo-unsigned integer images in
compressed image HDUs. They now work more transparently like normal image
HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options,
as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method
works better too. (#88)
- Permits non-string values for the EXTNAME keyword when reading in a file,
rather than throwing an exception due to the malformatting. Added
verification for the format of the EXTNAME keyword when writing. (#96)
- Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME
is specified in the header, it will also be reflected in the ``.name``
attribute and in ``pyfits.info()``. These keywords used to be verboten in
PRIMARY HDUs, but the latest version of the FITS standard allows them.
(#151)
- HCOMPRESS can again be used to compress data cubes (and higher-dimensional
arrays) so long as the tile size is effectively 2-dimensional. In fact,
PyFITS will automatically use compatible tile sizes even if they're not
explicitly specified. (#171)
- Added support for the optional ``endcard`` parameter in the
``Header.fromtextfile()`` and ``Header.totextfile()`` methods. Although
``endcard=False`` was a reasonable default assumption, there are still text
dumps of FITS headers that include the END card, so this should have been
more flexible. (#176)
- Fixed a crash when running fitsdiff on two empty (that is, zero row) tables.
(#178)
- Fixed an issue where opening files containing random groups HDUs in update
mode could cause an unnecessary rewrite of the file even if none of the
data is modified. (#179)
- Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS
is used with Numpy 1.7 in some cases. (#180)
- Fixed a crash when generating diff reports from diffs using the
``ignore_comments`` options. (#181)
- Fixed some bugs with WCS Paper IV record-valued keyword cards:
- Cards that looked kind of like RVKCs but were not intended to be were
over-permissively treated as such--commentary keywords like COMMENT and
HISTORY were particularly affected. (#183)
- Looking up a card in a header by its standard FITS keyword only should
always return the raw value of that card. That way cards containing
values that happen to valid RVKCs but were not intended to be will still
be treated like normal cards. (#184)
- Looking up a RVKC in a header with only part of the field-specifier (for
example "DP1.AXIS" instead of "DP1.AXIS.1") was implicitly treated as a
wildcard lookup. (#184)
- Fixed a crash when diffing two FITS files where at least one contains a
compressed image HDU which was not recognized as an image instead of a
table. (#187)
- Fixed bugs in the backwards compatibility layer for the ``CardList.index``
and ``CardList.count`` methods. (#190)
- Improved ``__repr__`` and text file representation of cards with long values
that are split into CONTINUE cards. (#193)
- Fixed a crash when trying to assign a long (> 72 character) value to blank
('') keywords. This also changed how blank keywords are represented--there
are still exactly 8 spaces before any commentary content can begin; this
*may* affect the exact display of header cards that assumed there could be
fewer spaces in a blank keyword card before the content begins. However, the
current approach is more in line with the requirements of the FITS standard.
(#194)
3.0.10 (2013-01-02)
-------------------
- Improved handling of scaled images and pseudo-unsigned integer images in
compressed image HDUs. They now work more transparently like normal image
HDUs with support for the ``do_not_scale_image_data`` and ``uint`` options,
as well as ``scale_back`` and ``save_backup``. The ``.scale()`` method
works better too. Backported from 3.1.1. (#88)
- Permits non-string values for the EXTNAME keyword when reading in a file,
rather than throwing an exception due to the malformatting. Added
verification for the format of the EXTNAME keyword when writing. Backported
from 3.1.1. (#96)
- Added support for EXTNAME and EXTVER in PRIMARY HDUs. That is, if EXTNAME
is specified in the header, it will also be reflected in the ``.name``
attribute and in ``pyfits.info()``. These keywords used to be verbotten in
PRIMARY HDUs, but the latest version of the FITS standard allows them.
Backported from 3.1.1. (#151)
- HCOMPRESS can again be used to compress data cubes (and higher-dimensional
arrays) so long as the tile size is effectively 2-dimensional. In fact,
PyFITS will not automatically use compatible tile sizes even if they're not
explicitly specified. Backported from 3.1.1. (#171)
- Fixed a bug when writing out files containing zero-width table columns,
where the TFIELDS keyword would be updated incorrectly, leaving the table
largely unreadable. Backported from 3.1.0. (#174)
- Fixed an issue where opening files containing random groups HDUs in update
mode could cause an unnecessary rewrite of the file even if none of the
data is modified. Backported from 3.1.1. (#179)
- Fixed a bug that could caused a deadlock in the filesystem on OSX if PyFITS
is used with Numpy 1.7 in some cases. Backported from 3.1.1. (#180)
3.1 (2012-08-08)
----------------
Highlights
^^^^^^^^^^
- The ``Header`` object has been significantly reworked, and ``CardList``
objects are now deprecated (their functionality folded into the ``Header``
class). See API Changes below for more details.
- Memory maps are now used by default to access HDU data. See API Changes
below for more details.
- Now includes a new version of the ``fitsdiff`` program for comparing two
FITS files, and a new FITS comparison API used by ``fitsdiff``. See New
Features below.
API Changes
^^^^^^^^^^^
- The ``Header`` class has been rewritten, and the ``CardList`` class is
deprecated. Most of the basic details of working with FITS headers are
unchanged, and will not be noticed by most users. But there are differences
in some areas that will be of interest to advanced users, and to application
developers. For full details of the changes, see the "Header Interface
Transition Guide" section in the PyFITS documentation. See ticket #64 on
the PyFITS Trac for futher details and background. Some highlights are
listed below:
* The Header class now fully implements the Python dict interface, and can
be used interchangably with a dict, where the keys are header keywords.
* New keywords can be added to the header using normal keyword assignment
(previously it was necessary to use ``Header.update`` to add new
keywords). For example::
>>> header['NAXIS'] = 2
will update the existing 'FOO' keyword if it already exists, or add a new
one if it doesn't exist, just like a dict.
* It is possible to assign both a value and a comment at the same time using
a tuple::
>>> header['NAXIS'] = (2, 'Number of axes')
* To add/update a new card and ensure it's added in a specific location, use
``Header.set()``::
>>> header.set('NAXIS', 2, 'Number of axes', after='BITPIX')
This works the same as the old ``Header.update()``. ``Header.update()``
still works in the old way too, but is deprecated.
* Although ``Card`` objects still exist, it generally is not necessary to
work with them directly. ``Header.ascardlist()``/``Header.ascard`` are
deprecated and should not be used. To directly access the ``Card``
objects in a header, use ``Header.cards``.
* To access card comments, it is still possible to either go through the
card itself, or through ``Header.comments``. For example::
>>> header.cards['NAXIS'].comment
Number of axes
>>> header.comments['NAXIS']
Number of axes
* ``Card`` objects can now be used interchangeably with
``(keyword, value, comment)`` 3-tuples. They still have ``.value`` and
``.comment`` attributes as well. The ``.key`` attribute has been renamed
to ``.keyword`` for consistency, though ``.key`` is still supported (but
deprecated).
- Memory mapping is now used by default to access HDU data. That is,
``pyfits.open()`` uses ``memmap=True`` as the default. This provides better
performance in the majority of use cases--there are only some I/O intensive
applications where it might not be desirable. Enabling mmap by default also
enabled finding and fixing a large number of bugs in PyFITS' handling of
memory-mapped data (most of these bug fixes were backported to PyFITS
3.0.5). (#85)
* A new ``pyfits.USE_MEMMAP`` global variable was added. Set
``pyfits.USE_MEMMAP = False`` to change the default memmap setting for
opening files. This is especially useful for controlling the behavior in
applications where pyfits is deeply embedded.
* Likewise, a new ``PYFITS_USE_MEMMAP`` environment variable is supported.
Set ``PYFITS_USE_MEMMAP = 0`` in your environment to change the default
behavior.
- The ``size()`` method on HDU objects is now a ``.size`` property--this
returns the size in bytes of the data portion of the HDU, and in most cases
is equivalent to ``hdu.data.nbytes`` (#83)
- ``BinTableHDU.tdump`` and ``BinTableHDU.tcreate`` are deprecated--use
``BinTableHDU.dump`` and ``BinTableHDU.load`` instead. The new methods
output the table data in a slightly different format from previous versions,
which places quotes around each value. This format is compatible with data
dumps from previous versions of PyFITS, but not vice-versa due to a parsing
bug in older versions.
- Likewise the ``pyfits.tdump`` and ``pyfits.tcreate`` convenience function
versions of these methods have been renamed ``pyfits.tabledump`` and
``pyfits.tableload``. The old deprecated, but currently retained for
backwards compatibility. (r1125)
- A new global variable ``pyfits.EXTENSION_NAME_CASE_SENSITIVE`` was added.
This serves as a replacement for ``pyfits.setExtensionNameCaseSensitive``
which is not deprecated and may be removed in a future version. To enable
case-sensitivity of extension names (i.e. treat 'sci' as distict from 'SCI')
set ``pyfits.EXTENSION_NAME_CASE_SENSITIVE = True``. The default is
``False``. (r1139)
- A new global configuration variable ``pyfits.STRIP_HEADER_WHITESPACE`` was
added. By default, if a string value in a header contains trailing
whitespace, that whitespace is automatically removed when the value is read.
Now if you set ``pyfits.STRIP_HEADER_WHITESPACE = False`` all whitespace is
preserved. (#146)
- The old ``classExtensions`` extension mechanism (which was deprecated in
PyFITS 3.0) is removed outright. To our knowledge it was no longer used
anywhere. (r1309)
- Warning messages from PyFITS issued through the Python warnings API are now
output to stderr instead of stdout, as is the default. PyFITS no longer
modifies the default behavior of the warnings module with respect to which
stream it outputs to. (r1319)
- The ``checksum`` argument to ``pyfits.open()`` now accepts a value of
'remove', which causes any existing CHECKSUM/DATASUM keywords to be ignored,
and removed when the file is saved.
New Features
^^^^^^^^^^^^
- Added support for the proposed "FITS" extension HDU type. See
http://listmgr.cv.nrao.edu/pipermail/fitsbits/2002-April/001094.html. FITS
HDUs contain an entire FITS file embedded in their data section. `FitsHDU`
objects work like other HDU types in PyFITS. Their ``.data`` attribute
returns the raw data array. However, they have a special ``.hdulist``
attribute which processes the data as a FITS file and returns it as an
in-memory HDUList object. FitsHDU objects also support a
``FitsHDU.fromhdulist()`` classmethod which returns a new `FitsHDU` object
that embeds the supplied HDUList. (#80)
- Added a new ``.is_image`` attribute on HDU objects, which is True if the HDU
data is an 'image' as opposed to a table or something else. Here the
meaning of 'image' is fairly loose, and mostly just means a Primary or Image
extension HDU, or possibly a compressed image HDU (#71)
- Added an ``HDUList.fromstring`` classmethod which can parse a FITS file
already in memory and instantiate and ``HDUList`` object from it. This
could be useful for integrating PyFITS with other libraries that work on
FITS file, such as CFITSIO. It may also be useful in streaming
applications. The name is a slight misnomer, in that it actually accepts
any Python object that implements the buffer interface, which includes
``bytes``, ``bytearray``, ``memoryview``, ``numpy.ndarray``, etc. (#90)
- Added a new ``pyfits.diff`` module which contains facilities for comparing
FITS files. One can use the ``pyfits.diff.FITSDiff`` class to compare two
FITS files in their entirety. There is also a ``pyfits.diff.HeaderDiff``
class for just comparing two FITS headers, and other similar interfaces.
See the PyFITS Documentation for more details on this interface. The
``pyfits.diff`` module powers the new ``fitsdiff`` program installed with
PyFITS. After installing PyFITS, run ``fitsdiff --help`` for usage details.
- ``pyfits.open()`` now accepts a ``scale_back`` argument. If set to
``True``, this automatically scales the data using the original BZERO and
BSCALE parameters the file had when it was first opened, if any, as well as
the original BITPIX. For example, if the original BITPIX were 16, this
would be equivalent to calling ``hdu.scale('int16', 'old')`` just before
calling ``flush()`` or ``close()`` on the file. This option applies to all
HDUs in the file. (#120)
- ``pyfits.open()`` now accepts a ``save_backup`` argument. If set to
``True``, this automatically saves a backup of the original file before
flushing any changes to it (this of course only applies to update and append
mode). This may be especially useful when working with scaled image data.
(#121)
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Warnings from PyFITS are not output to stderr by default, instead of stdout
as it has been for some time. This is contrary to most users' expectations
and makes it more difficult for them to separate output from PyFITS from the
desired output for their scripts. (r1319)
Bug Fixes
^^^^^^^^^
- Fixed ``pyfits.tcreate()`` (now ``pyfits.tableload()``) to be more robust
when encountering blank lines in a column definition file (#14)
- Fixed a fairly rare crash that could occur in the handling of CONTINUE cards
when using Numpy 1.4 or lower (though 1.4 is the oldest version supported by
PyFITS). (r1330)
- Fixed ``_BaseHDU.fromstring`` to actually correctly instantiate an HDU
object from a string/buffer containing the header and data of that HDU.
This allowed for the implementation of ``HDUList.fromstring`` described
above. (#90)
- Fixed a rare corner case where, in some use cases, (mildly, recoverably)
malformatted float values in headers were not properly returned as floats.
(#137)
- Fixed a corollary to the previous bug where float values with a leading zero
before the decimal point had the leading zero unnecessarily removed when
saving changes to the file (eg. "0.001" would be written back as ".001" even
if no changes were otherwise made to the file). (#137)
- When opening a file containing CHECKSUM and/or DATASUM keywords in update
mode, the CHECKSUM/DATASUM are updated and preserved even if the file was
opened with checksum=False. This change in behavior prevents checksums from
being unintentionally removed. (#148)
- Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it
was not restoring the image to its original BSCALE and BZERO values. (#162)
- Fixed a bug when writing out files containing zero-width table columns,
where the TFIELDS keyword would be updated incorrectly, leaving the table
largely unreadable. This fix will be backported to the 3.0.x series in
version 3.0.10. (#174)
3.0.9 (2012-08-06)
------------------
This is a bug fix release for the 3.0.x series.
Bug Fixes
^^^^^^^^^
- Fixed ``Header.values()``/``Header.itervalues()`` and ``Header.items()``/
``Header.iteritems()`` to correctly return the different values for
duplicate keywords (particularly commentary keywords like HISTORY and
COMMENT). This makes the old Header implementation slightly more compatible
with the new implementation in PyFITS 3.1. (#127)
.. note::
This fix did not change the existing behavior from earlier PyFITS
versions where ``Header.keys()`` returns all keywords in the header with
duplicates removed. PyFITS 3.1 changes that behavior, so that
``Header.keys()`` includes duplicates.
- Fixed a bug where ``ImageHDU.scale(option='old')`` wasn't working at all--it
was not restoring the image to its original BSCALE and BZERO values. (#162)
- Fixed a bug where opening a file containing compressed image HDUs in
'update' mode and then immediately closing it without making any changes
caused the file to be rewritten unncessarily. (#167)
- Fixed two memory leaks that could occur when writing compressed image data,
or in some cases when opening files containing compressed image HDUs in
'update' mode. (#168)
3.0.8 (2012-06-04)
------------------
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Prior to this release, image data sections did not work with scaled
data--that is, images with non-trivial BSCALE and/or BZERO values.
Previously, in order to read such images in sections, it was necessary to
manually apply the BSCALE+BZERO to each section. It's worth noting that
sections *did* support pseudo-unsigned ints (flakily). This change just
extends that support for general BSCALE+BZERO values.
Bug Fixes
^^^^^^^^^
- Fixed a bug that prevented updates to values in boolean table columns from
being saved. This turned out to be a symptom of a deeper problem that could
prevent other table updates from being saved as well. (#139)
- Fixed a corner case in which a keyword comment ending with the string "END"
could, in some circumstances, cause headers (and the rest of the file after
that point) to be misread. (#142)
- Fixed support for scaled image data and psuedo-unsigned ints in image data
sections (``hdu.section``). Previously this was not supported at all. At
some point support was supposedly added, but it was buggy and incomplete.
Now the feature seems to work much better. (#143)
- Fixed the documentation to point out that image data sections *do* support
non-contiguous slices (and have for a long time). The documentation was
never updated to reflect this, and misinformed users that only contiguous
slices were supported, leading to some confusion. (#144)
- Fixed a bug where creating an ``HDUList`` object containing multiple PRIMARY
HDUs caused an infinite recursion when validating the object prior to
writing to a file. (#145)
- Fixed a rare but serious case where saving an update to a file that
previously had a CHECKSUM and/or DATASUM keyword, but removed the checksum
in saving, could cause the file to be slightly corrupted and unreadable.
(#147)
- Fixed problems with reading "non-standard" FITS files with primary headers
containing SIMPLE = F. PyFITS has never made many guarantees as to how such
files are handled. But it should at least be possible to read their
headers, and the data if possible. Saving changes to such a file should not
try to prepend an unwanted valid PRIMARY HDU. (#157)
- Fixed a bug where opening an image with ``disable_image_compression = True``
caused compression to be disabled for all subsequent ``pyfits.open()`` calls.
(r1651)
3.0.7 (2012-04-10)
------------------
Changes in Behavior
^^^^^^^^^^^^^^^^^^^
- Slices of GroupData objects now return new GroupData objects instead of
extended multi-row _Group objects. This is analogous to how PyFITS 3.0 fixed
FITS_rec slicing, and should have been fixed for GroupData at the same time.
The old behavior caused bugs where functions internal to Numpy expected that
slicing an ndarray would return a new ndarray. As this is a rare usecase
with a rare feature most users are unlikely to be affected by this change.
- The previously internal _Group object for representing individual group
records in a GroupData object are renamed Group and are now a public
interface. However, there's almost no good reason to create Group objects
directly, so it shouldn't be considered a "new feature".
- An annoyance from PyFITS 3.0.6 was fixed, where the value of the EXTEND
keyword was always being set to F if there are not actually any extension
HDUs. It was unnecessary to modify this value.
Bug Fixes
^^^^^^^^^
- Fixed GroupData objects to return new GroupData objects when sliced instead
of _Group record objects. See "Changes in behavior" above for more details.
- Fixed slicing of Group objects--previously it was not possible to slice
slice them at all.
- Made it possible to assign `np.bool_` objects as header values. (#123)
- Fixed overly strict handling of the EXTEND keyword; see "Changes in
behavior" above. (#124)
- Fixed many cases where an HDU's header would be marked as "modified" by
PyFITS and rewritten, even when no changes to the header are necessary.
(#125)
- Fixed a bug where the values of the PTYPEn keywords in a random groups HDU
were forced to be all lower-case when saving the file. (#130)
- Removed an unnecessary inline import in `ExtensionHDU.__setattr__` that was
causing some slowdown when opening files containing a large number of
extensions, plus a few other small (but not insignficant) performance
improvements thanks to Julian Taylor. (#133)
- Fixed a regression where header blocks containing invalid end-of-header
padding (i.e. null bytes instead of spaces) couldn't be parsed by PyFITS.
Such headers can be parsed again, but a warning is raised, as such headers
are not valid FITS. (#136)
- Fixed a memory leak where table data in random groups HDUs weren't being
garbage collected. (#138)
3.0.6 (2012-02-29)
------------------
Highlights
^^^^^^^^^^
The main reason for this release is to fix an issue that was introduced in
PyFITS 3.0.5 where merely opening a file containing scaled data (that is, with
non-trivial BSCALE and BZERO keywords) in 'update' mode would cause the data
to be automatically rescaled--possibly converting the data from ints to
floats--as soon as the file is closed, even if the application did not touch
the data. Now PyFITS will only rescale the data in an extension when the data
is actually accessed by the application. So opening a file in 'update' mode
in order to modify the header or append new extensions will not cause any
change to the data in existing extensions.
This release also fixes a few Windows-specific bugs found through more
extensive Windows testing, and other miscellaneous bugs.
Bug Fixes
^^^^^^^^^
- More accurate error messages when opening files containing invalid header
cards. (#109)
- Fixed a possible reference cycle/memory leak that was caught through more
extensive testing on Windows. (#112)
- Fixed 'ostream' mode to open the underlying file in 'wb' mode instead of 'w'
mode. (#112)
- Fixed a Windows-only issue where trying to save updates to a resized FITS
file could result in a crash due to there being open mmaps on that file.
(#112)
- Fixed a crash when trying to create a FITS table (i.e. with new_table())
from a Numpy array containing bool fields. (#113)
- Fixed a bug where manually initializing an ``HDUList`` with a list of of
HDUs wouldn't set the correct EXTEND keyword value on the primary HDU.
(#114)
- Fixed a crash that could occur when trying to deepcopy a Header in Python <
2.7. (#115)
- Fixed an issue where merely opening a scaled image in 'update' mode would
cause the data to be converted to floats when the file is closed. (#119)
3.0.5 (2012-01-30)
------------------
- Fixed a crash that could occur when accessing image sections of files
opened with memmap=True. (r1211)
- Fixed the inconsistency in the behavior of files opened in 'readonly' mode
when memmap=True vs. when memmap=False. In the latter case, although
changes to array data were not saved to disk, it was possible to update the
array data in memory. On the other hand with memmap=True, 'readonly' mode
prevented even in-memory modification to the data. This is what
'copyonwrite' mode was for, but difference in behavior was confusing. Now
'readonly' is equivalent to 'copyonwrite' when using memmap. If the old
behavior of denying changes to the array data is necessary, a new
'denywrite' mode may be used, though it is only applicable to files opened
with memmap. (r1275)
- Fixed an issue where files opened with memmap=True would return image data
as a raw numpy.memmap object, which can cause some unexpected
behaviors--instead memmap object is viewed as a numpy.ndarray. (r1285)
- Fixed an issue in Python 3 where a workaround for a bug in Numpy on Python 3
interacted badly with some other software, namely to vo.table package (and
possibly others). (r1320, r1337, and #110)
- Fixed buggy behavior in the handling of SIGINTs (i.e. Ctrl-C keyboard
interrupts) while flushing changes to a FITS file. PyFITS already prevented
SIGINTs from causing an incomplete flush, but did not clean up the signal
handlers properly afterwards, or reraise the keyboard interrupt once the
flush was complete. (r1321)
- Fixed a crash that could occur in Python 3 when opening files with checksum
checking enabled. (r1336)
- Fixed a small bug that could cause a crash in the `StreamingHDU` interface
when using Numpy below version 1.5.
- Fixed a crash that could occur when creating a new `CompImageHDU` from an
array of big-endian data. (#104)
- Fixed a crash when opening a file with extra zero padding at the end.
Though FITS files should not have such padding, it's not explictly forbidden
by the format either, and PyFITS shouldn't stumble over it. (#106)
- Fixed a major slowdown in opening tables containing large columns of string
values. (#111)
3.0.4 (2011-11-22)
------------------
- Fixed a crash when writing HCOMPRESS compressed images that could happen on
Python 2.5 and 2.6. (r1217)
- Fixed a crash when slicing an table in a file opened in 'readonly' mode with
memmap=True. (r1230)
- Writing changes to a file or writing to a new file verifies the output in
'fix' mode by default instead of 'exception'--that is, PyFITS will
automatically fix common FITS format errors rather than raising an
exception. (r1243)
- Fixed a bug where convenience functions such as getval() and getheader()
crashed when specifying just 'PRIMARY' as the extension to use (r1263).
- Fixed a bug that prevented passing keyword arguments (beyond the standard
data and header arguments) as positional arguments to the constructors of
extension HDU classes.
- Fixed some tests that were failing on Windows--in this case the tests
themselves failed to close some temp files and Windows refused to delete them
while there were still open handles on them. (r1295)
- Fixed an issue with floating point formatting in header values on Python 2.5
for Windows (and possibly other platforms). The exponent was zero-padded to
3 digits; although the FITS standard makes no specification on this, the
formatting is now normalized to always pad the exponent to two digits.
(r1295)
- Fixed a bug where long commentary cards (such as HISTORY and COMMENT) were
broken into multiple CONTINUE cards. However, commentary cards are not
expected to be found in CONTINUE cards. Instead these long cards are broken
into multiple commentary cards. (#97)
- GZIP/ZIP-compressed FITS files can be detected and opened regardless of
their filename extension. (#99)
- Fixed a serious bug where opening scaled images in 'update' mode and then
closing the file without touching the data would cause the file to be
corrupted. (#101)
3.0.3 (2011-10-05)
------------------
- Fixed several small bugs involving corner cases in record-valued keyword
cards (#70)
- In some cases HDU creation failed if the first keyword value in the header
was not a string value (#89)
- Fixed a crash when trying to compute the HDU checksum when the data array
contains an odd number of bytes (#91)
- Disabled an unnecessary warning that was displayed on opening compressed
HDUs with disable_image_compression = True (#92)
- Fixed a typo in code for handling HCOMPRESS compressed images.
3.0.2 (2011-09-23)
------------------
- The ``BinTableHDU.tcreate`` method and by extension the ``pyfits.tcreate``
function don't get tripped up by blank lines anymore (#14)
- The presence, value, and position of the EXTEND keyword in Primary HDUs is
verified when reading/writing a FITS file (#32)
- Improved documentation (in warning messages as well as in the handbook) that
PyFITS uses zero-based indexing (as one would expect for C/Python code, but
contrary to the PyFITS standard which was written with FORTRAN in mind)
(#68)
- Fixed a bug where updating a header card comment could cause the value to be
lost if it had not already been read from the card image string.
- Fixed a related bug where changes made directly to Card object in a header
(i.e. assigning directly to card.value or card.comment) would not propagate
when flushing changes to the file (#69) [Note: This and the bug above it
were originally reported as being fixed in version 3.0.1, but the fix was
never included in the release.]
- Improved file handling, particularly in Python 3 which had a few small file
I/O-related bugs (#76)
- Fixed a bug where updating a FITS file would sometimes cause it to lose its
original file permissions (#79)
- Fixed the handling of TDIMn keywords; 3.0 added support for them, but got
the axis order backards (they were treated as though they were row-major)
(#82)
- Fixed a crash when a FITS file containing scaled data is opened and
immediately written to a new file without explicitly viewing the data first
(#84)
- Fixed a bug where creating a table with columns named either 'names' or
'formats' resulted in an infinite recursion (#86)
3.0.1 (2011-09-12)
------------------
- Fixed a bug where updating a header card comment could cause the value to be
lost if it had not already been read from the card image string.
- Changed ``_TableBaseHDU.data`` so that if the data contain an empty table a
``FITS_rec`` object with zero rows is returned rather than ``None``.
- The ``.key`` attribute of ``RecordValuedKeywordCards`` now returns the full
keyword+field-specifier value, instead of just the plain keyword (#46)
- Fixed a related bug where changes made directly to Card object in a header
(i.e. assigning directly to card.value or card.comment) would not propagate
when flushing changes to the file (#69)
- Fixed a bug where writing a table with zero rows could fail in some cases
(#72)
- Miscellanous small bug fixes that were causing some tests to fail,
particularly on Python 3 (#74, #75)
- Fixed a bug where creating a table column from an array in non-native byte
order would not preserve the byte order, thus interpreting the column array
using the wrong byte order (#77)
3.0.0 (2011-08-23)
--------------------
- Contains major changes, bumping the version to 3.0
- Large amounts of refactoring and reorganization of the code; tried to
preserve public API backwards-compatibility with older versions (private API
has many changes and is not guaranteed to be backwards-compatible). There
are a few small public API changes to be aware of:
* The pyfits.rec module has been removed completely. If your version of
numpy does not have the numpy.core.records module it is too old to be used
with PyFITS.
* The ``Header.ascardlist()`` method is deprecated--use the ``.ascard``
attribute instead.
* ``Card`` instances have a new ``.cardimage`` attribute that should be used
rather than ``.ascardimage()``, which may become deprecated.
* The ``Card.fromstring()`` method is now a classmethod. It returns a new
``Card`` instance rather than modifying an existing instance.
* The ``req_cards()`` method on HDU instances has changed: The ``pos``
argument is not longer a string. It is either an integer value (meaning
the card's position must match that value) or it can be a function that
takes the card's position as it's argument, and returns True if the
position is valid. Likewise, the ``test`` argument no longer takes a
string, but instead a function that validates the card's value and returns
True or False.
* The ``get_coldefs()`` method of table HDUs is deprecated. Use the
``.columns`` attribute instead.
* The ``ColDefs.data`` attribute is deprecated--use ``ColDefs.columns``
instead (though in general you shouldn't mess with it directly--it might
become internal at some point).
* ``FITS_record`` objects take ``start`` and ``end`` as arguments instead of
``startColumn`` and ``endColumn`` (these are rarely created manually, so
it's unlikely that this change will affect anyone).
* ``BinTableHDU.tcreate()`` is now a classmethod, and returns a new
``BinTableHDU`` instance.
* Use ``ExtensionHDU`` and ``NonstandardExtHDU`` for making new extension HDU
classes. They are now public interfaces, wheres previously they were
private and prefixed with underscores.
* Possibly others--please report if you find any changes that cause
difficulties.
- Calls to deprecated functions will display a Deprecation warning. However,
in Python 2.7 and up Deprecation warnings are ignored by default, so run
Python with the `-Wd` option to see if you're using any deprecated
functions. If we get close to actually removing any functions, we might
make the Deprecation warnings display by default.
- Added basic Python 3 support
- Added support for multi-dimensional columns in tables as specified by the
TDIMn keywords (#47)
- Fixed a major memory leak that occurred when creating new tables with the
``new_table()`` function (#49)
be padded with zero-bytes) vs ASCII tables (where strings are padded with
spaces) (#15)
- Fixed a bug in which the case of Random Access Group parameters names was not
preserved when writing (#41)
- Added support for binary table fields with zero width (#42)
- Added support for wider integer types in ASCII tables; although this is non-
standard, some GEIS images require it (#45)
- Fixed a bug that caused the index_of() method of HDULists to crash when the
HDUList object is created from scratch (#48)
- Fixed the behavior of string padding in binary tables (where strings should
be padded with nulls instead of spaces)
- Fixed a rare issue that caused excessive memory usage when computing
checksums using a non-standard block size (see r818)
- Add support for forced uint data in image sections (#53)
- Fixed an issue where variable-length array columns were not extended when
creating a new table with more rows than the original (#54)
- Fixed tuple and list-based indexing of FITS_rec objects (#55)
- Fixed an issue where BZERO and BSCALE keywords were appended to headers in
the wrong location (#56)
- ``FITS_record`` objects (table rows) have full slicing support, including
stepping, etc. (#59)
- Fixed a bug where updating multiple files simultaneously (such as when
running parallel processes) could lead to a race condition with mktemp()
(#61)
- Fixed a bug where compressed image headers were not in the order expected by
the funpack utility (#62)
|
Erroneously closed by Github. |
jperkin
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Integrated SPF checking is now available through the new
SPFSelfValidate and SPFIgnoreResults settings.
Feature request #79: Optionally ignore clients that authenticated
using SMTP AUTH.
Fix bug #60, part II: Default AuthservID to the name provided by the
MTA, not the local host name, which is consistent with what
OpenDKIM does.
Fix bug #72: Don't crash when From fields are absent.
Fix bug #74: Change "Forensic" to "Failure" just about everywhere
to match the language now being used in the base DMARC
draft. Note that this also changes some names in the
configuration file.
Fix bug #75: Correct typo in MIME of forensic reports.
Fix bug #76: Repair damage with respect to Authentication-Results
header field selection.
Fix bug #77: Request quarantine from the MTA during option
negotiation.
Fix bug #78: Add missing newline in forensic report header.
Fix bug #90: Make "--with-sql-backend" without any value do the
right thing.
Fix bug #93: Honor size limits in URIs.
Make "smime" and "rrvs" legal Authentication-Results methods.
Provide better logging when pclose() for a forensic report returns
non-zero.
Add configuration support for internal SPF checks. Includes hooks in
the milter to check that SPF is configured to do so.
This can use a private SPF implementation or libspf2.
Fix strlcat() and strlcpy() support for Debian.
REPORTS: Feature request #80: Generate aggregate reports on UTC
day boundaries.
REPORTS: Feature request #84: Optionally expire old data from
lower-growth tables.
REPORTS: Fix bug #70: Fix date range generation in reports.
REPORTS: Fix bug #82: Fix recording of report timestamp to avoid lost
records.
REPORTS: Fix bug #83: When expiring data, truncate the signatures table
if all messages were expired..
REPORTS: Fix bug #85: Report subdomain policy.
LIBOPENDMARC: Fix bug #71: Fix "rua" extraction from DMARC records.
LIBOPENDMARC: Added support for milter to perform own spf checks.
Three new files: opendmarc_spf.c, opendmard_spf_dns.c and
test/test_spf.cl, allow integrated SPF support. Support for
use of libspf2 is also provided.
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…kages Collection. This extention was previously known as ZendOptimizerPlus and has been renamed by upstream. Changes: 7.0.4 Added function opcache_is_script_cached() - Fix bug #67111 (Loop variables need to be freed for both "break" and "continue") - Fix opcache.revalidate_freq per-request behavior - Fixed bug #67215 (php-cgi work with opcache, may be segmentation fault happen) - Fixed issue #183 (TMP_VAR is not only used once) 7.0.3 - Fixed bug #66298 (ext/opcache/Optimizer/zend_optimizer.c has dos-style ^M as lineend) - Added suggestion about opcache.revalidate_freq setting in development environmento - Fixed Issue #140: "opcache.enable_file_override" doesn't respect "opcache.revalidate_freq" - Fixed reavlidate_path=1 behavior to avoid caching of symlinks values. - Fixed opcahce_reset() crash when opcache.protect_memory is set - Fixed bug #66176 (Invalid constant substitution) - Fixed bug #65559 (Opcache: cache not cleared if changes occur while running) - Fixed compatibility with old PHP versions - Fixed bug #65915 (Inconsistent results with require return value) - Fixed issue #115 (path issue when using phar) - Fixed issue #149 (Phar mount points not working with OPcache enabled) - Fixed bug #65845 (Error when Zend Opcache Optimizer is fully enabled). - Added function opcache_compile_file() to load PHP scripts into cache without execution. - Fixed issue #135 (segfault in interned strings if initial memory is too low) - Fixed bug #65665 (Exception not properly caught when opcache enabled) - Fixed issue #128 (opcache_invalidate segmentation fault) - Fixed bug #65510 (5.5.2 crashes in _get_zval_ptr_ptr_var) - Fixed bug #65561 (Zend Opcache on Solaris 11 x86 needs ZEND_MM_ALIGNMENT=4) - Replce ZEND_FETCH_* instructions with IS_CV if possible - Added opcache.restrict_api configuration directive that may limit usage of OPcahce API functions only to patricular script(s) - Added support for glob symbols in blacklist entries (?, *, **) - Improved implementation of NOP removal pass from O(n^2) to O(n) - Fixed bug #65338 (Enabling both php_opcache and php_wincache AVs on shutdown). - Fixed bug #64827 Segfault in zval_mark_grey (zend_gc.c) 7.0.2 - Fixed issue #26 (added opcache_invalidate(string $filename [, bool $force = false]) function) - Fixed issue #74 (Allowed per request OPcache disabling) - Fixed issue #76 (actually we don't need zend_shared_meory_block_header at all) - Fixed issue #78 (incorrect file path validation) - Fixed issue #79 (Optimization Problem/Bug) - Fixed issue #82 (allow comments in blacklist file, lines started with ";") - Fixed issue #91 (fix x64 fixed addresses) - Fxied issue #92 (Compilation warnings) - Fixed issue #97 (Use size_t instead of int to support a cache larger than 2G) - Fixed bug (Avoid possible conditional jump depended on uninitialised value) 7.0.1 - Fixed Bug #64490 (add __FreeBSD_kernel__ to allowed FreeBSD defs) - Fixed Bug #64482 (Opcodes for dynamic includes should not be cached) - Fixed Bug #64353 (Built-in classes can be unavailable with dynamic includes and Optimizer+) - Fixed compatibility with ext/phar - Fixed Issue #58 (PHP-5.2 compatibility) - Fixed Issue #57 (segfaults in drupal7) - Fixed Issue #54 (PECL install adds extension= instead of zend_extension= to php.ini)-iii - Allows exclusion of large files from being cached - Save a stat() call by calling sapi_module.get_stat() - Add optional flag to opcache_get_status() - Separate "start_time" from "last_restart_time"
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- Adjust DEPENDS and BUILD_DEPENDS, the latter is for make test
-DEPENDS+= p5-JSON-Any-[0-9]*:../../converters/p5-JSON-Any
DEPENDS+= p5-JSON-XS-[0-9]*:../../converters/p5-JSON-XS
+DEPENDS+= p5-JSON-MaybeXS-[0-9]*:../../converters/p5-JSON-MaybeXS
+BUILD_DEPENDS+= p5-Test-Differences-[0-9]*:../../devel/p5-Test-Differences
+BUILD_DEPENDS+= p5-Text-Diff-[0-9]*:../../textproc/p5-Text-Diff
(upstream)
- Update to 6.02
Changes in Devel::NYTProf 6.02 - 2nd August 2015
FlameGraphs upgraded the latest version, which supports searching.
Use JSON::MaybeXS instead of JSON::Any (deprecated), thanks to Ether #73
Updated metacpan urls, thanks to Ether #74
Internal context optimizations, thanks to jandubois #75
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Changes: Version 5.1.2 ============= Code Fixes ---------- * Code hardening using reallocarray() from OpenBSD. * Sanity check in giffilter catches files with malformed extension records Fixes SourceForge bug #63: malformed gif causes segfault in giffilter. * Inexpensive sanity check in DGifSlurp() catches malformed files with no image descriptor. Fixes SourceForge bug #64: malformed gif causes crash in giftool. * Fix SourceForge bug #66: GifDrawBoxedText8x8() modifying constant input parameter. * Bail out of GIF read on invalid pixel width. Addresses Savannah bug #67: invalid shift in dgif_lib.c * Fix SourceForge bug #69: #69 Malformed: Gif file with no extension block after a GRAPHICS_EXT_FUNC_CODE extension causes segfault (in giftext). * Fix SourceForge bug #71: Buffer overwrite when giffixing a malformed gif. * Fix SourceForge bug #73: Null pointer deference in gifclrmap (only reachable with malformed GIF). * Fix SourceForge bug #74: Double free in gifsponge under 5.1,1, for any valid gif image. * Fix SourceForge bug #75: GAGetArgs overflows due to uncounted use of va_arg. * Sanity check in giffix catches some malformed files. Addresses SourceForge bug #77: dgif_lib.c: extension processing error
jperkin
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Mar 7, 2016
Changelog: Release 0.3.7: -------------- - Fix Debian bug #766945: catch 'inskscape' not installed (Andreas Hoenen patch) - Fix Debian bug #792898: improve the PDF metadata setup - Fix Debian bug #684772 and SF bug #85: section @Label is used to force the section counter - Fix Debian bug #684772: a chapter with an empty @Label is not numbered - Fix Debian bug #793077: allow to put a figure anchor at the top even if the caption is at the bottom, thanks to the parameter figure.anchor.top. - Add the parameters body.font.family, sans.font.family, and monospace.font.family to mimic FO parameters, for xetex font setup Release 0.3.6: -------------- - Adapt the debug env_tex script for Windows - Make dblatex work with Xindy, for xetex and pdftex backends. Xindy is selected through the latex.index.tool parameter, and it's sorting is aware of the language used that can be set through the latex.index.language parameter. This is an answer to the Debian bug #756386. - Allow the Texpost script to be a python plugin. - Add the beginpage.as.pagebreak parameter to be able to inhibit the current behaviour. - Fix a bug in index escaping: '"' was not escaped. - Fix a bug in <listitem> to prevent brackets side effects. - Quick fix for <screenshot> SF bug #74. - Fix SF bug #110. - Fix Debian bug #771473 and #684393. Release 0.3.5: -------------- - Fix an HTML table bug when no <colgroup> or <col> is specified - Fix an HTML table bug when cellpadding is expressed in percentage - Fix Debian bug #720624 to have more greek letters correctly translated - Fix bug #108 so that setup.py works even if intall-layout not supported - Fix bug #107 to be compliant with frenchb v2.5 to remove shorthands in listings - Fix bug #106 to have equation label localized - Fix bug #104 to have listings correctly displayed in <listitem>s - Fix bug #103 to have indexes correctly working in db2latex style - Fix Debian bug #682901 to have with XeTeX proper endash in indexes - Fix Debian bugs #682936 and #684391 to support Norwegian Bokmål through lang='nb' - Fix Debian bug #683166 (SF bug #3553962/#98) to avoid chapters erroneously included in parts. - Fix Debian bug #684393 babel setup to allow quote chars for lang='nn' - Adapt URL to work with texlive >= 2009. - Some fixes to be able work with Saxon - Improve setup.py to detect the installed texlive version only on manual install. - Include the package 'ucs' and configure listings to work with pdftex and UTF-8 characters. Release 0.3.4: -------------- - Fix a bug in the missing characters display. - Fix the global template to actually insert a backmatter tag before backmatter elements. - Fix bug #3520152 by changing a template xpath (looks like a libxslt limitation). - Improve the verbatim block display to be able to scale the block width to the page width. - Allow latex instructions within verbatim blocks through Processing Instructions. - Improve the setup script to be close to the debian install rules. - Improve the hyphenation of the inlined literal elements. - Add the parameter example.float.type to give the possibility to have <example> not floating. The attribute 'floatstyle' is also taken into account. - Add the parameter hyphenation.format to specify the inlined format types that must be hyphenated. It replaces the more limited monoseq.hyphenation parameter. Release 0.3.3: -------------- - Fix incomplete image path conversion when subfigures are used. - Fix unicode listings limitation to handle characters greater than 255. - Fix <abstract> environment to prevent from page counter reset. - Fix the <literallayout> limitations by using the same implementation than <screen>. - Fix a texlive 9 french babel and enumitem incompatibility. - Fix to be robust to URL encoded image paths, and to non-latin1 paths. - Fix missing cross-reference to <sidebar> and <qandaset>. - Fix the <sidebar> box width to the actual context witdh. - Fix a french babel bug (unexpected active chars) when used with XeTeX. - Fix Debian bug #627501 to tell the priority policy of --xsl-user option. - Fix Debian bug #632967 to return a non-null code when the compilation fails. - Fix Debian bug #629514 to have draft watermark with XeTeX backend. - Fix Debian bug #634563 to have safe pdftitle content (no images). - Fix setup.py in order to work under Windows. - Fix the HTML table support to correctly render the cells elements. - Fix the HTML table support to correctly nested tables. - Fix the Olink support to allow database user-specific renderings like italics for <i> tags. Reuse of the DocBook Project implementation. - Fix a setup failure that made the listings UTF-8 support failed (extendedchars to set to "true"). - Fix --xslt-opts to be able to pass several arguments by using quotes - Set the TexLive version to 2009 by default. - Update to new Debian Error Handler API. Improvements sponsored by Freexian (http://www.freexian.com) : - Fix #3191550. Remove hard-coded paper size and add some parameters for page layout setup: * Parameters to define page sizes and margins. * Parameters to have crop marks for pre-press PDF output. - Add the parameters literal.environment and literal.extensions to allow the user define its own listing environment. - Add the parameter latex.engine.options to be able to pass options to the TeX engine backend. - Print out warnings about the characters not handled by the selected fonts. - Image display improvements/fixes: * Avoid unexpected paragraph indentation when displaying images. * Strip spurious spaces between subfigures when @ROLE='flow.inline' * Prevents from empty tex subcaptions when no subfigure <caption> is defined. - Add the ability to format <ulink> as a block when @type='block'. - Pass @ROLE to the latex sidebar environment. - Add the literal.class parameter used when <literallayout> class attribute is not set. Default is 'monospaced'. - Add some @ROLE to format literal elements, and literal.role parameter for default role: * Wrap: wrap lines when longer than text width (default) * Overflow: do not wrap lines ; long lines overflow to the left * Scale: automatically scale a listing to have its lines fit the page width The special feature can be disabled with literal.extensions=0
|
Sorry it's taken so long to get around to looking at this issue. I've tried to reproduce this with the latest pkgsrc release and cannot, so something along the way has made this disappear, possibly since we started building on a newer SmartOS release and fixed various issues with our compiler (as well as upgrading to GCC 4.9). I'm going to close this for now, but if any other issues come up with aria2 please let us know, thanks. |
|
Since I opened the case, aria2 has made it into pkgsrc and has been working without workarounds. Thanks for looking into this either way. |
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NEWS: Version 2.5.3 ------------- - Updated zoneinfo to 2016d - Fixed parser bug where unambiguous datetimes fail to parse when dayfirst is set to true. (gh issue #233, pr #234) - Bug in zoneinfo file on platforms such as Google App Engine which do not do not allow importing of subprocess.check_call was reported and fixed by @savraj (gh issue #239, gh pr #240) - Fixed incorrect version in documentation (gh issue #235, pr #243) Version 2.5.2 ------------- - Updated zoneinfo to 2016c - Fixed parser bug where yearfirst and dayfirst parameters were not being respected when no separator was present. (gh issue #81 and #217, pr #229) Version 2.5.1 ------------- - Updated zoneinfo to 2016b - Changed MANIFEST.in to explicitly include test suite in source distributions, with help from @koobs (gh issue #193, pr #194, #201, #221) - Explicitly set all line-endings to LF, except for the NEWS file, on a per-repository basis (gh pr #218) - Fixed an issue with improper caching behavior in rruleset objects (gh issue #104, pr #207) - Changed to an explicit error when rrulestr strings contain a missing BYDAY (gh issue #162, pr #211) - tzfile now correctly handles files containing leapcnt (although the leapcnt information is not actually used). Contributed by @hjoukl (gh issue #146, pr #147) - Fixed recursive import issue with tz module (gh pr #204) - Added compatibility between tzwin objects and datetime.time objects (gh issue #216, gh pr #219) - Refactored monolithic test suite by module (gh issue #61, pr #200 and #206) - Improved test coverage in the relativedelta module (gh pr #215) - Adjusted documentation to reflect possibly counter-intuitive properties of RFC-5545-compliant rrules, and other documentation improvements in the rrule module (gh issue #105, gh issue #149 - pointer to the solution by @phep, pr #213). Version 2.5.0 ------------- - Updated zoneinfo to 2016a - zoneinfo_metadata file version increased to 2.0 - the updated updatezinfo.py script will work with older zoneinfo_metadata.json files, but new metadata files will not work with older updatezinfo.py versions. Additionally, we have started hosting our own mirror of the Olson databases on a github pages site (https://dateutil.github.io/tzdata/) (gh pr #183) - dateutil zoneinfo tarballs now contain the full zoneinfo_metadata file used to generate them. (gh issue #27, gh pr #85) - relativedelta can now be safely subclassed without derived objects reverting to base relativedelta objects as a result of arithmetic operations. (lp:1010199, gh issue #44, pr #49) - relativedelta 'weeks' parameter can now be set and retrieved as a property of relativedelta instances. (lp: 727525, gh issue #45, pr #49) - relativedelta now explicitly supports fractional relative weeks, days, hours, minutes and seconds. Fractional values in absolute parameters (year, day, etc) are now deprecated. (gh issue #40, pr #190) - relativedelta objects previously did not use microseconds to determine of two relativedelta objects were equal. This oversight has been corrected. Contributed by @elprans (gh pr #113) - rrule now has an xafter() method for retrieving multiple recurrences after a specified date. (gh pr #38) - str(rrule) now returns an RFC2445-compliant rrule string, contributed by @schinckel and @armicron (lp:1406305, gh issue #47, prs #50, #62 and #160) - rrule performance under certain conditions has been significantly improved thanks to a patch contributed by @dekoza, based on an article by Brian Beck (@exogen) (gh pr #136) - The use of both the 'until' and 'count' parameters is now deprecated as inconsistent with RFC2445 (gh pr #62, #185) - Parsing an empty string will now raise a ValueError, rather than returning the datetime passed to the 'default' parameter. (gh issue #78, pr #187) - tzwinlocal objects now have a meaningful repr() and str() implementation (gh issue #148, prs #184 and #186) - Added equality logic for tzwin and tzwinlocal objects. (gh issue #151, pr #180, #184) - Added some flexibility in subclassing timelex, and switched the default behavior over to using string methods rather than comparing against a fixed list. (gh pr #122, #139) - An issue causing tzstr() to crash on Python 2.x was fixed. (lp: 1331576, gh issue #51, pr #55) - An issue with string encoding causing exceptions under certain circumstances when tzname() is called was fixed. (gh issue #60, #74, pr #75) - Parser issue where calling parse() on dates with no day specified when the day of the month in the default datetime (which is "today" if unspecified) is greater than the number of days in the parsed month was fixed (this issue tended to crop up between the 29th and 31st of the month, for obvious reasons) (canonical gh issue #25, pr #30, #191) - Fixed parser issue causing fuzzy_with_tokens to raise an unexpected exception in certain circumstances. Contributed by @MichaelAquilina (gh pr #91) - Fixed parser issue where years > 100 AD were incorrectly parsed. Contributed by @Bachmann1234 (gh pr #130) - Fixed parser issue where commas were not a valid separator between seconds and microseconds, preventing parsing of ISO 8601 dates. Contributed by @ryanss (gh issue #28, pr #106) - Fixed issue with tzwin encoding in locales with non-Latin alphabets (gh issue #92, pr #98) - Fixed an issue where tzwin was not being properly imported on Windows. Contributed by @labrys. (gh pr #134) - Fixed a problem causing issues importing zoneinfo in certain circumstances. Issue and solution contributed by @alexxv (gh issue #97, pr #99) - Fixed an issue where dateutil timezones were not compatible with basic time objects. One of many, many timezone related issues contributed and tested by @labrys. (gh issue #132, pr #181) - Fixed issue where tzwinlocal had an invalid utcoffset. (gh issue #135, pr #141, #142) - Fixed issue with tzwin and tzwinlocal where DST transitions were incorrectly parsed from the registry. (gh issue #143, pr #178) - updatezinfo.py no longer suppresses certain OSErrors. Contributed by @bjamesv (gh pr #164) - An issue that arose when timezone locale changes during runtime has been fixed by @carlosxl and @mjschultz (gh issue #100, prs #107, #109) - Python 3.5 was added to the supported platforms in the metadata (@tacaswell gh pr #159) and the test suites (@moreati gh pr #117). - An issue with tox failing without unittest2 installed in Python 2.6 was fixed by @moreati (gh pr #115) - Several deprecated functions were replaced in the tests by @moreati (gh pr #116) - Improved the logic in Travis and Appveyor to alleviate issues where builds were failing due to connection issues when downloading the IANA timezone files. In addition to adding our own mirror for the files (gh pr #183), the download is now retried a number of times (with a delay) (gh pr #177) - Many failing doctests were fixed by @moreati. (gh pr #120) - Many fixes to the documentation (gh pr #103, gh pr #87 from @radarhere, gh pr #154 from @gpoesia, gh pr #156 from @awsum, gh pr #168 from @ja8zyjits) - Added a code coverage tool to the CI to help improve the library. (gh pr #182) - We now have a mailing list - dateutil@python.org, graciously hosted by Python.org. Version 2.4.2 ------------- - Updated zoneinfo to 2015b. - Fixed issue with parsing of tzstr on Python 2.7.x; tzstr will now be decoded if not a unicode type. gh #51 (lp:1331576), gh pr #55. - Fix a parser issue where AM and PM tokens were showing up in fuzzy date stamps, triggering inappropriate errors. gh #56 (lp: 1428895), gh pr #63. - Missing function "setcachesize" removed from zoneinfo __all__ list by @ryanss, fixing an issue with wildcard imports of dateutil.zoneinfo. (gh pr #66). - (PyPi only) Fix an issue with source distributions not including the test suite. Version 2.4.1 ------------- - Added explicit check for valid hours if AM/PM is specified in parser. (gh pr #22, issue #21) - Fix bug in rrule introduced in 2.4.0 where byweekday parameter was not handled properly. (gh pr #35, issue #34) - Fix error where parser allowed some invalid dates, overwriting existing hours with the last 2-digit number in the string. (gh pr #32, issue #31) - Fix and add test for Python 2.x compatibility with boolean checking of relativedelta objects. Implemented by @nimasmi (gh pr #43) and Cédric Krier (lp: 1035038) - Replaced parse() calls with explicit datetime objects in unit tests unrelated to parser. (gh pr #36) - Changed private _byxxx from sets to sorted tuples and fixed one currently unreachable bug in _construct_byset. (gh pr #54) - Additional documentation for parser (gh pr #29, #33, #41) and rrule. - Formatting fixes to documentation of rrule and README.rst. - Updated zoneinfo to 2015a.
jperkin
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Version 1.8.0 (25 Oct 2016)
Daniel Stenberg (25 Oct 2016)
- RELEASE-NOTES: adjusted for 1.8.0
Kamil Dudka (20 Oct 2016)
- Revert "aes: the init function fails when OpenSSL has AES support"
This partially reverts commit f4f2298ef3635acd031cc2ee0e71026cdcda5864
because it caused the compatibility code to call initialization routines
redundantly, leading to memory leakage with OpenSSL 1.1 and broken curl
test-suite in Fedora:
88 bytes in 1 blocks are definitely lost in loss record 5 of 8
at 0x4C2DB8D: malloc (vg_replace_malloc.c:299)
by 0x72C607D: CRYPTO_zalloc (mem.c:100)
by 0x72A2480: EVP_CIPHER_meth_new (cmeth_lib.c:18)
by 0x4E5A550: make_ctr_evp.isra.0 (openssl.c:407)
by 0x4E5A8E8: _libssh2_init_aes_ctr (openssl.c:471)
by 0x4E5BB5A: libssh2_init (global.c:49)
Daniel Stenberg (19 Oct 2016)
- [Charles Collicutt brought this change]
libssh2_wait_socket: Fix comparison with api_timeout to use milliseconds (#134)
Fixes #74
- [Charles Collicutt brought this change]
Set err_msg on _libssh2_wait_socket errors (#135)
- Revert "travis: Test mbedtls too"
This reverts commit 3e6de50a24815e72ec5597947f1831f6083b7da8.
Travis doesn't seem to support the mbedtls-dev package
- maketgz: support "only" to only update version number locally
and fix the date output locale
- configure: make the --with-* options override the OpenSSL default
... previously it would default to OpenSSL even with the --with-[crypto]
options used unless you specificly disabled OpenSSL. Now, enabling another
backend will automatically disable OpenSSL if the other one is found.
- [Keno Fischer brought this change]
docs: Add documentation on new cmake/configure options
- [Keno Fischer brought this change]
configure: Add support for building with mbedtls
- [wildart brought this change]
travis: Test mbedtls too
- [wildart brought this change]
crypto: add support for the mbedTLS backend
Closes #132
- [wildart brought this change]
cmake: Add CLEAR_MEMORY option, analogously to that for autoconf
- README.md: fix link typo
- README: markdown version to look nicer on github
Viktor Szakats (5 Sep 2016)
- [Taylor Holberton brought this change]
openssl: add OpenSSL 1.1.0 compatibility
Daniel Stenberg (4 Sep 2016)
- [Antenore Gatta brought this change]
tests: HAVE_NETINET_IN_H was not defined correctly (#127)
Fixes #125
- SECURITY: fix web site typo
- SECURITY: security process
GitHub (14 Aug 2016)
- [Alexander Lamaison brought this change]
Basic dockerised test suite.
This introduces a test suite for libssh2. It runs OpenSSH in a Docker
container because that works well on Windows (via docker-machine) as
well as Linux. Presumably it works on Mac too with docker-machine, but
I've not tested that.
Because the test suite is docker-machine aware, you can also run it
against a cloud provider, for more realistic network testing, by setting
your cloud provider as your active docker machine. The Appveyor CI setup
in this commit does that because Appveyor doesn't support docker
locally.
Kamil Dudka (3 Aug 2016)
- [Viktor Szakats brought this change]
misc.c: Delete unused static variables
Closes #114
Daniel Stenberg (9 Apr 2016)
- [Will Cosgrove brought this change]
Merge pull request #103 from willco007/patch-2
Fix for security issue CVE-2016-0787
Alexander Lamaison (2 Apr 2016)
- [Zenju brought this change]
Fix MSVC 14 compilation errors
For _MSC_VER == 1900 these macros are not needed and create problems:
1>C:\Program Files (x86)\Windows Kits\10\Include\10.0.10240.0\ucrt\stdio.h(1925): warning C4005: 'snprintf': macro redefinition (compiling source file libssh2-files\src\mac.c)
1> \win32\libssh2_config.h(27): note: see previous definition of 'snprintf' (compiling source file libssh2-files\src\mac.c)
1>C:\Program Files (x86)\Windows Kits\10\Include\10.0.10240.0\ucrt\stdio.h(1927): fatal error C1189: #error: Macro definition of snprintf conflicts with Standard Library function declaration (compiling source file libssh2-files\src\mac.c)
Daniel Stenberg (26 Mar 2016)
- [Brad Harder brought this change]
_libssh2_channel_open: speeling error fixed in channel error message
Alexander Lamaison (15 Mar 2016)
- Link with crypt32.lib on Windows.
Makes linking with static OpenSSL work again. Although it's not
required for dynamic OpenSSL, it does no harm.
Fixes #98.
- [Craig A. Berry brought this change]
Tweak VMS help file building.
Primarily this is handling cases where top-level files moved into
the docs/ directory. I also corrected a typo and removed the
claim that libssh2 is public domain.
- [Craig A. Berry brought this change]
Build with standard stat structure on VMS.
This gets us large file support, is available on any VMS release
in the last decade and more, and gives stat other modern features
such as 64-bit ino_t.
- [Craig A. Berry brought this change]
Update vms/libssh2_config.h.
VMS does have stdlib.h, gettimeofday(), and OpenSSL. The latter
is appropriate to hard-wire in the configuration because it's
installed by default as part of the base operating system and
there is currently no libgcrypt port.
- [Craig A. Berry brought this change]
VMS can't use %zd for off_t format.
%z is a C99-ism that VMS doesn't currently have; even though the
compiler is C99-compliant, the library isn't quite. The off_t used
for the st_size element of the stat can be 32-bit or 64-bit, so
detect what we've got and pick a format accordingly.
- [Craig A. Berry brought this change]
Normalize line endings in libssh2_sftp_get_channel.3.
Somehow it got Windows-style CRLF endings so convert to just LF,
for consistency as well as not to confuse tools that will regard
the \r as content (e.g. the OpenVMS help librarian).
Dan Fandrich (29 Feb 2016)
- libgcrypt: Fixed a NULL pointer dereference on OOM
Daniel Stenberg (24 Feb 2016)
- [Viktor Szakats brought this change]
url updates, HTTP => HTTPS
Closes #87
Dan Fandrich (23 Feb 2016)
- RELEASE-NOTES: removed some duplicated names
jperkin
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Jan 16, 2017
0.8.1 * Adapters::TokyoTyrant - more consistent error handling * Adapters::MongoMoped - support for moped gem v2.0 * Adapters::MongoOfficial - support for mongo gem versions 2-4 * Adapters::File - fix a bug in #load (#74) * Adapters::LRUHash - allow to disable the limits by passing nil for max_size, max_count * Transformer - don't use OpenSSL::Digest::Digest namespace * Adapters::Sequel - fix issue with unknown "blob" type * Rack::Cache - fix deprecated require paths * Adapters::MemcachedNative - properly close connections * Transformer - support bson gem versions 2-4 * Transformer - switch to rbzip2 gem for bzip2 support * Adapters::MemcachedDalli - #create returns a boolean
jperkin
pushed a commit
that referenced
this issue
Apr 10, 2017
0.3.7 * Fix issue #84: check if stream has 'closed' attribute before testing it * Fix issue #74: objects might become None at exit 0.3.6 * Fix issue #81: fix ValueError when a closed stream was used 0.3.5 * Bumping version to re-upload a wheel distribution 0.3.4 * Fix issue #47 and #80 - stream redirection now strips ANSI codes on Linux * Fix issue #53 - strip readline markers * Fix issue #32 - assign orig_stdout and orig_stderr when initialising * Fix issue #57 - Fore.RESET did not reset style of LIGHT_EX colors. Fixed by Andy Neff * Fix issue #51 - add context manager syntax. Thanks to Matt Olsen. * Fix issue #48 - colorama didn't work on Windows when environment variable 'TERM' was set. * Fix issue #54 - fix pylint errors in client code. * Changes to readme and other improvements by Marc Abramowitz and Zearin 0.3.3 * Fix Google Code issue #13 - support changing the console title with OSC escape sequence * Fix Google Code issue #16 - Add support for Windows xterm emulators * Fix Google Code issue #30 - implement \033[nK (clear line) * Fix Google Code issue #49 - no need to adjust for scroll when new position is already relative (CSI n A\B\C\D) * Fix Google Code issue #55 - erase_data fails on Python 3.x * Fix Google Code issue #46 - win32.COORD definition missing * Implement \033[0J and \033[1J (clear screen options) * Fix default ANSI parameters * Fix position after \033[2J (clear screen) * Add command shortcuts: colorama.Cursor, colorama.ansi.set_title, colorama.ansi.clear_line, colorama.ansi.clear_screen * Fix issue #22 - Importing fails for python3 on Windows * Thanks to John Szakmeister for adding support for light colors * Thanks to Charles Merriam for adding documentation to demos
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I've had issues with g++ compiled binaries coring when any exception is thrown. Overriding the libraries provided with the gcc47/gcc47-libs packages with 'LD_PRELOAD=/usr/sfw/lib/amd64/libgcc_s.so.1' seems to be a workaround and solves the coring issues, but it's not an ideal fix.
A little more background from someone that obviously knows quite a bit more than I:
Keith Wesolowski said:
"This is very likely a problem with the pkgsrc gcc libraries. It's not a
platform bug. We believe that the problem is caused by using exceptions
with a gcc library built against an SDC 6.5 platform. In order to solve
this, we'll need to start building pkgsrc packages against SDC 7."
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