Gnuastro 0.16.67 released [alpha]

[Mohammad Akhlaghi]

Dear all,

I hope you have enjoyed the holidays! As a small new year's gift, I
would like to share Gnuastro 0.16.67 (an alpha-release in preparation
for Gnuastro 0.17).

As you see in [1] below, many useful new features have been added, and
many bugs have been found and fixed. Thanks to 8 people who directly
committed into Gnuastro's source (4 women and 4 men), and 16 people
providing ideas that have been impleted (see below for the
names). This is a new record in Gnuastro! Thanks for helping make
Gnuastro better with your great work :-).

To best enjoy Gnuastro, please take a few minutes to read through [1],
I am sure you'll find some of the items useful in your work! It would
also be great if you could try building and using this version to
report any compilation warnings, crashes, or unexpected behavior
(especially in the newly added features). We will be releasing
Gnuastro 0.17 in the next couple of weeks and your reports can help
make it as stable as possible :-).

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 (*.sig) see [3]:

  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.16.67-f0d2.tar.lz 
(3.7MB)
  https://alpha.gnu.org/gnu/gnuastro/gnuastro-0.16.67-f0d2.tar.lz.sig 
(833B)

Here are the SHA1 and SHA256 checksums (other ways to check if the
tarball you download is what we distributed). Just note that the
SHA256 checksum is base64 encoded, instead of the hexadecimal encoding
that most checksum tools default to.

ca1ba15623ed52b3a4ad089fe8a747ba080e3a2b  gnuastro-0.16.67-f0d2.tar.lz
aNUzxra0cyi/6CgvEJnQubGpKbFCqXc5MZ6S4GYQ4bw  gnuastro-0.16.67-f0d2.tar.lz

I am very grateful (in alphabetical order) to Elham Saremi, Nafise
Sedighi, Pedram Ashofteh Ardakani, Raul Infante-Sainz, Sachin Kumar
Singh, Sepideh Eskandarlou and Zahra Hosseini Shahisavandi who
directly contributed commits to Gnuastro's source. Furthermore, I
should also thank Alejandro Lumbreras Calle, Alessandro Ederoclite,
Andres Del Pino Molina, Jesús Varela, Juan Antonio Fernández
Ontiveros, Manuel Sánchez-Benavente, Martin Guerrero Roncel, Peter
Teuben, Raúl Infante-Sainz, Samane Raji, Sebastian Luna Valero,
Sepideh Eskandarlou, Sergio Chueca Urzay, Tamara Civera Lorenzo, Zahra
Hosseini and Zohreh Ghaffari for sharing bug reports, or very useful
new ideas that have been implemented in this release.

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 6.8
  Autoconf 2.71
  Automake 1.16.5
  Help2man 1.48.5
  ImageMagick 7.1.0-19
  Gnulib v0.1-5104-g549fce0183
  Autoconf archives v2021.02.19-29-g0fbee2a

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

--
Researcher (tenure track)
Centro de Estudios de Física del Cosmos de Aragón (CEFCA),
Plaza San Juan 1, Planta 2, Teruel 44001, Spain





[1] Noteworthy updates since version 0.16:

** New features

  Book:
   - New section called "Skewness cased by signal and its measurement"
     added to the third tutorial (Detecting large extended targets). It
     describes the significant advantages of using the quantile of the mean
     as a measure of skewness and why its a very important factor when
     understanding how NoiseChisel works. It was originally written by
     Sepideh Eskandarlou, with edits by Elham Saremi and Pedram Ashofte
     Ardakani.

  All programs:
   - Coordinate-related columns in all programs now also accept sexagesimal
     values, not just degrees. Therefore, '--center=113.8729761,31.9027152'
     and '--center=07h35m29.51,31d54m9.77' are now equivalent in the Crop
     or Query programs that have this option! Other improved options
     include the '--polygon' options of Table and Crop (that also take
     region files produced by DS9), the '--coord' option of Match, the
     '--crval' option of MakeProfiles.
   - Columns of FITS tables are now read in parallel (when '--numthreads'
     isn't set to '1', and if the dependency CFITSIO library was built with
     '--enable-reentrant'). In scenarios where many columns may be
     necessary (for example the Table or Match programs), this will greatly
     improve the running time of the programs. This task was implemented
     based on feedback from Andrés Del Pino Molina.

  Crop:
   --widthinpix: when in WCS-mode, the value given to '--width' will be
     interpreted in units of pixels. This will allow having crops of a
     fixed pixel size, even when the mode of the central coordinate is in
     WCS. This was suggested by Jesús Varela.

  Fits:
   - If a 'CHECKSUM' keyword exists in a HDU and any of the keyword
     modification keywords are called, Fits will automatically update the
     checksum after all the changes are done. This is important to keep the
     checksum valid after the change (recall that you can verify the FITS
     checksums with the '--verify' option to Fits). This task was suggested
     by Tamara Civera Lorenzo.

  Table:
   --catrowfile: File to concatenate (i.e., add or append) rows into the
     main input table. With this option, you can add the rows of another
     table into the final output. This option can be called multiple times,
     allowing you to merge rows of any number of tables. This job is done
     after concatenating columns, but before any of the row-selection
     operations. This was suggested by Raúl Infante-Sainz and Manuel
     Sánchez Benavente.
   --catrowhdu: The HDU(s) of the FITS file(s) given to '--catrowfile'.
   --noblankend: remove blank rows from selected columns of the _output_
     table, for example after after adding columns by column arithmetic or
     from other tables (this is the new name for the old '--noblank'
     option, see the changed features below). Like the new '--noblank',
     this option can also be called multiple times, so '--noblankend=1
     --noblankend=2' is equivalent to '--noblankend=1,2'.

  Match:
   - k-d tree based matching has been added for finding the matching rows,
     and is set to the default mode. It will do the matching in parallel,
     which will improve the speed when many rows are present. The k-d tree
     can also optionally be saved in a file for matching new tables with
     the same one (further improving running speed). For a full description
     of Match's new behavior, please see the new "Matching algorithms"
     section of the book. This feature was implemented with the help of
     Sachin Kumar Singh.
   --kdtree: new option to specify the algorithm used by Match. It can take
     four values: 'internal' (which is the default), 'build' (to build a
     k-d tree), 'FILE.fits' (name of k-d tree to import), or 'disable' (to
     do the matching with the old sort-based method). For more, please see
     the new "Matching algorithms" section of the book.
   --kdtreehdu: the HDU of the external k-d tree (if a FITS file was given
     to '--kdtree').

  Library:
   - gal_fits_key_exists_fptr: Check if a certain keyword exists in the
     already-open FITS file pointer.

** Removed features
  Nothing has been removed in this alpha-release.

** Changed features

  Segment:
   - '--noobjects' is the new name for the old '--onlyclumps' option. This
     is because the name Only-Clumps can lead to a wrong expectation that
     the output will _only_ contain a 'CLUMPS' HDU. However,
     with'--onlyclumps', the input image (without a Sky level) and the Sky
     standard deviation image are also present as HDUs in the output. To
     only get the 'CLUMPS' HDU, it is necessary to also use the
     '--rawoutput' option. This renaming was done to avoid such confusions
     and was raised by Sepideh Eskandarlou.

  Match:
   - By default (when '--quiet' isn't called), Match will print the names
     of the inputs and timings of important steps to the standard output
     (on the command-line).

  Table:
   - The '--noblank' option's logic is very similar to other row-selection
     (by value) options (like '--range', '--polygon' or
     '--equal'). However, until now, it was applied at the end of Table,
     just before writing the output (so it would apply to the output table,
     that may have new/different column names/orders, not the input table
     like the other similar options). This was very inconvenient and
     non-intuitive. From this version, '--noblank' option now behaves
     similarly to the other input row-selection (by value) options. So it
     can be called multiple times (to give many columns in multiple calls)
     and it can be called for a column that is not necessarily one of the
     output columns (for example you want the RA and Dec of all rows
     without a blank magnitude, so you don't need to have the magnitude
     column any more!). The old behavior of this option is now available in
     the new '--noblankend' option. This point was raised by Samane Raji.

  Library:
   - gal_fits_tab_read: now takes the number of threads to read the desired
     columns in parallel (this will greatly improve reading speed when
     there are many columns and many rows).
   - gal_table_read: simlar to 'gal_fits_tab_read' (only relevant for
     reading FITS tables).
   - gal_blank_initialize: also works on string data, but initializing only
     a tile over a larger block of elements is only supported for numeric
     data types.

** Bugs fixed
  bug #61329: make check crash in macOS in convolve/spectrum-1d.sh, found
              and fixed with the help of Sebastian Luna-Valero.
  bug #61378: Table crash when input is sexagesimal RA/DEC and no metadata.
  bug #61462: Crash on FITS binary table colums with repeat of 0.
  bug #61468: DS9 region file can't be read in sexagesimal coordinates,
              reported by Juan Antonio Fernández Ontiveros and Alejandro
              Lumbreras Calle.
  bug #61490: Extra columns in the metadata causes crash in plain-text
              tables, found by Zohre Ghaffari.
  bug #61493: NoiseChisel's --checksn not showing pseudos equal to
              --snminarea (only larger ones), found by Raúl Infante-Sainz.
  bug #61584: When FITS file doesn't end with '.fits' and the output file
              already existed, Arithmetic would write the output in new
              extension while it should have been deleted.
  bug #61598: ds9-region script not using precise WCS values, found and
              fixed by Raúl Infante-Sainz.
  bug #61698: Mean operator of Arithmetic (for stacking many images) not
              returning NaN for blank regions when input is integer. This
              fix also resolves the same problem in the 'sum', 'std',
              'median' and all 'sigclip-*' operators); reported by Zohre
              Ghaffari.
  bug #61740: WCSLIB conflicting with system's wide-character string (WCS)
              library in Gnulib checks for some systems; reported by Martin
              Guerrero Roncel.





[2] Lzip has better compression ratio and archival features compared
to the `.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-0.16.67-f0d2.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-0.6.tar.lz | tar -xf -'):

  $ lzip -d gnuastro-0.16.67-f0d2.tar.lz
  $ tar xf gnuastro-0.16.67-f0d2.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-0.16.67-f0d2.tar.gz.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.