[info-gnuastro] Gnuastro 0.12 released

[Mohammad Akhlaghi]

Hello,

I am happy to announce the 12th stable version of GNU Astronomy
Utilities (Gnuastro):

Gnuastro is an official GNU package of various command-line programs
and library functions for the manipulation and analysis of
(astronomical) data. All the programs share the same basic
command-line user interface (modeled on GNU Coreutils). For the full
list of Gnuastro's library, programs, and a comprehensive general
tutorial (recommended place to start using Gnuastro), please see the
links below respectively:

https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-library.html
https://www.gnu.org/s/gnuastro/manual/html_node/Gnuastro-programs-list.html
https://www.gnu.org/s/gnuastro/manual/html_node/General-program-usage-tutorial.html

Many new features have been added, and many bugs have been fixed in
this release. For the full list, please see [1] below (part of the
NEWS file within the tarball). Here are the highlights (done by the
new contributors to Gnuastro's source): The Crop program's `--polygon'
option now works on concave polygons (when an internal angle is larger
than 180 degrees). This is very useful for cropping out some deep
fields that have zig-zag-like edges. It can also deal with
self-intersecting polygons. Also, the Table program can now select
rows based on their position within a polygon, it can concatenate
columns of multiple tables (with same number of rows), and it can
convert RA (in HH:MM:SS) and Dec (in DD:MM:SS) to degrees and
vice-versa: with its four new column-arithmetic operators.

Here is the compressed source and the GPG detached signature for this
release. To uncompress Lzip tarballs, see [2]. To check the validity
of the tarballs using the GPG detached signature see [3]:
https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.lz    (3.4MB)
https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.gz    (5.4MB)
https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.lz.sig (833B)
https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.12.tar.gz.sig (833B)

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):
07d27c08cf8baae53a523224b4ed9ce5  gnuastro-0.12.tar.lz
dd13676b21a39ca3590c8f3a57285860  gnuastro-0.12.tar.gz
3651354a70d17b66dfba7253a97bb0f303e7efd7  gnuastro-0.12.tar.lz
568b5ea3f39edcb661874542ebb9ae2ed1f06668  gnuastro-0.12.tar.gz

Since Gnuastro 0.11, Madhav Bansal, Sachin Kumar Singh and Kartik Ohri
have contributed to the source of Gnuastro and Raúl Infante-Sainz
Raphael Morales, Alejandro Serrano Borlaff, Zahra Sharbaf, Joseph
Putko provided very useful comments, suggestions and bug fixes that
have been implemented. Thanks a lot for helping improve Gnuastro :-).

If any of Gnuastro's programs or libraries are useful in your work,
please cite _and_ acknowledge them. For citation and acknowledgment
guidelines, run the relevant programs with a `--cite' option (it can
be different for different programs, so run it for all the programs
you use). Citations _and_ acknowledgments are vital for the continued
work on Gnuastro, so please don't forget to support us by doing so.

This tarball was bootstrapped (created) with the tools below. Note
that you don't need these to build Gnuastro from the tarball, these
are the tools that were used to make the tarball itself. They are only
mentioned here to be able to reproduce/recreate this tarball later.
  Texinfo 6.7
  Autoconf 2.69
  Automake 1.16.2
  Help2man 1.47.15
  ImageMagick 7.0.10-13
  Gnulib v0.1-3428-gb3c04ecec
  Autoconf archives v2019.01.06-97-gfd1d25c

The dependencies to build Gnuastro from this tarball on your system
are described here:
  https://www.gnu.org/s/gnuastro/manual/html_node/Dependencies.html

Best wishes,
Mohammad

--
Postdoctoral research fellow,
Instituto de Astrofísica de Canarias (IAC),
Calle Vía Láctea, s/n, E38205,
San Cristóbal de La Laguna, Tenerife, Spain.





[1] Noteworthy changes in release 0.12 (library 10.0.0)

** New features

  Arithmetic:
   - New 'quantile' operator for coadding datasets.
   - New 'size' operator to report length of dataset in requested 
dimension.
   - When '--wcsfile' is given the value 'none', output will not have 
any WCS.

  CosmicCalculator:
   --listlines: list the pre-defined spectral line wavelengths and names
     (which you can use with the '--obsline' and '--lineatz' options). This
     is convenient when you forget the specific name of the spectral line
     used within Gnuastro.

  Crop:
   --polygon: can now also crop concave polygons (when atleast one inner
     angle is more than 180 degrees). Concave polygons occur a lot in deep
     astronomical imaging: in the shape of the deepest regions.
   --polygonsort: Sort the given set of vertices to the '--polygon'
     option. For a concave polyton, the sorting will be correct, but for a
     convex polygon, there is no unique solution/sorting, so it may not be
     what you expect, see the manual.

  Fits:
   --datasum: Calculate and print the given HDU's "datasum" to stdout.
   --datetosec: Can also account for 'Z' in the end of the date-time
     string. According to 'https://www.w3.org/TR/NOTE-datetime', a 'Z'
     effectively means no time zone, or UTC time (which is the default in
     FITS). It still doesn't account for time zone hours of the w3.org
     standard.

  MakeCatalog:
   --sigmaclip: define sigma-clipping parameters for the new '--sigclip-*'
     columns.
   --forcereadstd: Read the standard deviation image even if not needed by
     any columns. This is useful when you want the surface brightness
     limit, but don't need any error-related columns.
   New output columns:
     --sigclip-number: Number of sigma-clipped pixels in object/clump.
     --sigclip-median: Sigma-clipped median of pixels in object/clump.
     --sigclip-mean: Sigma-clipped mean of pixels in object/clump.
     --sigclip-std: Sigma-clipped standard deviation of pixels in 
object/clump.

  Table:
   --equal: Can now work on columns with string type also.
   --notequal: Can now work on columns with string type also.
   --polygon: Polygon to use in '--inpolygon' or '--outpolygon'.
   --inpolygon: Select rows that are inside the polygon of '--polygon'.
   --outpolygon: Select rows that are outside the polygon of '--polygon'.
   --catcolumn: Concatenate tables by column (keeping number of rows 
fixed).
   --catcolhdu: Specify the HDU/extension of the FITS files of --catcolumn.
   - New operators in column arithmetic:
     - 'ra-to-degree': Convert Right Ascension (HH:MM:SS) to degrees.
     - 'dec-to-degree': Convert Declination (DD:MM:SS) to degrees.
     - 'degree-to-ra': Convert degrees to Right Ascension (HH:MM:SS).
     - 'degree-to-dec': Convert degrees to Declination (HH:MM:SS).
     - 'distance-flat': Distance between two points, assuming flat space.

  Library:
   - GAL_SPECLINES_INVALID_MAX: Total number of spectral lines, plus 1.
   - GAL_ARITHMETIC_OP_QUANTILE: operator for 'gal_arithmetic'.
   - gal_txt_trim_space: trim white space before and after a string.
   - gal_polygon_is_convex: identify if a polygon is convex or concave.
   - gal_polygon_is_inside: if point is inside polygon (convex or concave).
   - gal_polygon_is_counterclockwise: check if polygon is 
counter-clockwise.
   - gal_polygon_to_counterclockwise: convert to counter-clockwise if 
it isn't.
   - gal_polygon_vertices_sort: un-ordered vertices to concave/convext 
polygons.
   - gal_units_extract_decimal: Extract numbers from strings like "A:B:C".
   - gal_units_ra_to_degree: Convert RA (HH:MM:SS) to degrees.
   - gal_units_dec_to_degree: Convert Dec (DD:MM:SS) to degrees.
   - gal_units_degree_to_ra: Convert degrees to RA (DD:MM:SS).
   - gal_units_degree_to_dec: Convert degrees to Dec (DD:MM:SS).

** Removed features

** Changed features

  All programs and libraries:
   --minmapsize: Gnuastro's programs no longer attempt to write
     memory-mapped files under '.gnuastro'. They will only attempt to write
     them under the '.gnuastro_mmap' directory. Until now, when an internal
     array needed to be memory-mapped, Gnuastro's programs (through the
     'pointer.h' library) would first try writing the mmap files in the
     '.gnuastro' directory. When it failed it would attempt writing in the
     '.gnuastro_mmap' directory. However, '.gnuastro' is also used to store
     configuration files (which are hand-written and thus valuable). Mixing
     the two types of source (configuration files) and automatically
     generated (memory-mapped) files is very problematic.
   - FITS ASCII tables: When a column has a floating point type, but its
     ASCII string can't be parsed as a number, it will be read as a
     NaN. Until now, the corresponding program/library would abort,
     printing the problematic string and its location.

  Crop:
   --polygon: by default it will no longer attempt to sort the polygon
     vertices, sorting can be requested with the new '--polygonsort' 
option.
   --polygonout: is the new name for '--outpolygon'. Having 'polygon' at
     the start of the option name, makes it easier to find in the help list
     and also to understand generally.

  MakeCatalog:
   - Until now, if no standard deviation image was requested, MakeCatalog
     wouldn't include any surface brightness limit metadata in its
     output. Now, those two lines are filled, but with a notice on the
     cause (that there is no standard deviation image), and suggesting
     solutions.

  NoiseChisel:
   - Until now, when NoiseChisel didn't detect any pixels, it just printed
     a message and wouldn't not make any output file. This was very
     inconvenient in general scripts. From now on, in this scenario, an
     output file will be created and the detection map will only have a
     value of zero. As a result, the Sky and Sky standard deviation
     extensions will be measured over all the tiles.

  Table:
   - In Column arithmetic, when columns must be specified by their number,
     that number should be distinguished with a '$' before it (for example
     '$1' means the first column). Until now, this character was 'c', but
     the new identifying character is very similar to AWK, allowing easier
     adoption and is also more clear. It is just important to put the total
     'arith' string within single quotes, not double quotes.
   - Operators:
     - 'distance-on-sphere': New name for old `angular-distance' operator.

  Library:
   - gal_polygon_is_inside_convex: new name for 'gal_polygon_pin'.

** Bugs fixed
  bug #57300: MakeCatalog memory crash when input dataset has units.
  bug #57301: MakeCatalog using river sum instead of mean times by 
clump area.
  bug #57921: Arithmetic's interpolation operator not reading metric.
  bug #57989: Warp not accounting for translation in pixel grid.
  bug #57995: Fits lib's date to second function affected by host's 
timezone.
  bug #58315: Some NaNs with sigma-clip operators in Arithmetic and one 
input.
  bug #58371: Table crashes with a commented newline in the columns.





[2] Lzip has better compression ratio and archival features compared
to the common `.gz' or `.xz' formats. Therefore Gnuastro's alpha/test
releases are only in this format, but for historical reasons we also
include `.gz' tarballs in the official releases. If you don't have
Lzip (you can check with `lzip --version' command), download and
install it from its webpage:

  https://www.nongnu.org/lzip/lzip.html

If Lzip is present and you use GNU Tar, then the single command below
should uncompress and un-pack the tarball:

  $ tar xf gnuastro-0.12.tar.lz

If the command above doesn't work, you have to un-compress and un-pack
it with two separate commands (or use a pipe to feed the output of the
first into the second: `lzip -cd gnuastro-0.12.tar.lz | tar -xf -'):

  $ lzip -d gnuastro-0.12.tar.lz
  $ tar xf gnuastro-0.12.tar





[3] Use a .sig file to verify that the corresponding file (without the
.sig suffix) is intact.  First, be sure to download both the .sig file
and the corresponding tarball.  Then, run a command like this:

  gpg --verify gnuastro-0.12.tar.lz.sig

If that command fails because you don't have the required public key,
then run this command to import it:

  gpg --keyserver keys.gnupg.net --recv-keys 71E899012D174B66

and rerun the 'gpg --verify' command.