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List:       gnu-info
Subject:    Gnuastro 0.11 released
From:       Mohammad Akhlaghi <mohammad () akhlaghi ! org>
Date:       2019-11-25 15:47:02
Message-ID: efae79f6-68be-98c1-29b2-1d7d05085824 () akhlaghi ! org
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Dear all,

I am happy to announce the 11th stable release 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:

  1) arXiv:1909.11230 ( https://arxiv.org/abs/1909.11230 ) will be
     published in the proceedings of Symposium 355 of the International
     Astronomical Union (IAU). It describes the significant
     improvements in the two NoiseChisel and Segment programs since the
     initial paper in 2015. If you are using NoiseChisel or Segment
     after version 0.6, please read this paper, and also cite it with
     the 2015 paper (they are complementary). Its BibTeX information
     has been added to the output of `--cite' for NoiseChisel and
     Segment. By the way, this paper is also fully/automatically
     reproducible! See "Comments" section on arXiv for the Git and
     Zenodo repository URLs with more info. Note the last word in the
     abstract: its the checksum of the Git commit that produced this
     paper. To learn more about this approach to reproducible research,
     see these slides. Also see the last slide, if you are interested
     in publishing reproducible research, we have a small funding to
     invite you here to the Canary Islands for a small workshop
     (deadline is end of November):
     https://akhlaghi.org/pdf/reproducible-paper.pdf

  2) Several programs now also support direct operation on 3D
     datacubes: Convolve, MakeCatalog, MakeProfiles and Match. Work in
     ongoing to hopefully finalize the 3D work on NoiseChisel and
     Segment also. But you can already create mock 3D data cubes for
     example with 3D ellipsoids, oriented in any fixed direction,
     easily make 3D convolution kernels, match 3D catalogs, or generate
     catalogs and spectra from labeled 3D data cubes.

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-0.11.tar.gz   (5.3MB)
   https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.11.tar.lz   (3.4MB)
   https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.11.tar.gz.sig (833B)
   https://ftp.gnu.org/gnu/gnuastro/gnuastro-0.11.tar.lz.sig (833B)

Here are the MD5 and SHA1 checksums (other ways to check if the
tarball you download is what we distributed):
89d84f17e5e01df5a22985999a39d5b4  gnuastro-0.11.tar.gz
5fcb6f89710d9047dabeaec6fe054b43  gnuastro-0.11.tar.lz
8213cc4d714bab1b2c90fe055c9a80fa5e5144ad  gnuastro-0.11.tar.gz
cf092439862b0fddb1c9404e599c79c2ef24080e  gnuastro-0.11.tar.lz

Since Gnuastro 0.10, Miguel de Val-Borro and Raúl Infante-Sainz
contributed to the source of Gnuastro and Hamed Altafi, Stefan Brüns,
Alexey Dokuchaev, Takashi Ichikawa, Raúl Infante-Sainz, Sebastián Luna
Valero, Marcel Popescu and Joseph Putko provided very useful comments,
suggestions and bug fixes that have been implemented.

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 1.16.1
   Help2man 1.47.11
   ImageMagick 7.0.9-5
   Gnulib v0.1-2939-g3ae177f2d
   Autoconf archives v2019.01.06-65-g235d9c9

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 0.11 (library 9.0.0) (2019-11-25) [stable]

** New features

   Book:
    - The "General program usage tutorial" now has a section on how to write
      scripts effectively to automate your analysis.

   Arithmetic:
    - The new `add-dimension' operator will stack the popped operands in a
      higher-dimensional dataset. For example to build a 3D cube from
      individual 2D images/slices.
    --onedonstdout: when the output is one-dimensional, print the values on
      the standard output, not into a file.

   BuildProgram:
    - Will use common environment variables like LDFLAGS, CPPFLAGS and CC to
      help in customizing the build of your program.
    --cc: custom C compiler to use. Until now, `gcc' was hard-coded into the
      source and there was no way to choose a custom C compiler.
    --noenv: With this option, no environment variables will be read.

   ConvertType:
    - New `viridis' colormap (value for the `--colormap' option). This is
      the default colormap of Python's Matplotlib, and is available in many
      other plotting tools like LaTeX's PGFPlots.

   Convolve:
    - Spatial domain convolution now possible on 3D data cubes (with a 3D
      kernel).

   CosmicCalculator:
    --lineatz: return the observed wavelength of a line if it was emitted at
      the redshift given to CosmicCalculator. You can either use known line
      names, or directly give a number as any emitted line's wavelength.

   MakeCatalog:
    - Catalogs from 3D inputs now available, with the following new options,
      see book for more.
      --spectrum: label's spectrum (across the third dimension).
      --z: Flux-weighted position in 3rd dimension.
      --geoz: Geometric center in third FITS axis.
      --minz: Minimum third FITS axis position.
      --maxz: Maximum third FITS axis position.
      --clumpsz: Flux weighted center of all clumps in object in 3rd dim.
      --clumpsgeoz: Geometric center of all clumps in object in 3rd dim.
      --w3: Flux weighted center in third WCS axis.
      --geow3: Geometric center in third WCS axis.
      --clumpsw3: Flux wheighted center of all clumps in 3rd dim.
      --clumpsgeow3: Geometric center of all clumps in 3rd dim.
      --areaxy: Projected area in first two dimentions.
      --geoareaxy: Projected geoarea in first two dimensions.
    --inbetweenints: output will contain one row for all integers between 1
      and the largest label in the input (irrespective of their existance in
      the input image). This was the default/only behavior of MakeCatalog
      until now. However, there are situations where the labeled input image
      integers may not be contiguous. For example if the input's only
      labeled pixel values are 11 and 13 from this release MakeCatalog's
      output will only have two rows. If you want the old behavior (of one
      row per integer, even if its not in the image), you can use this
      option.

   MakeProfiles:
    - Can produce mock ellipsoids in a datacube (using X-Z-X Euler angles
      for 3D orientation), the following options have been added, see the
      book for more details.
      --p2col: Second Euler angle (X-Z-X order).
      --p3col: Third Euler angle (X-Z-X order).
      --q2col: Axis ratio (major/dim3 in 3D).
    - The `--kernel' option can build 3D kernels, see the description of
      this option in the book for examples and details on how to run it.

   Match:
    - Matching of catalogs now possible using 3 coordinates (on catalogs
      generated from 3D data cubes), see book for more.

   NoiseChisel:
    - arXiv:1909.11230 added in papers to cite (with the `--cite' option):
      this paper describes the major changes made to NoiseChisel in the last
      10 stable releases since the 2015 paper, most importantly how Segment
      has been separated and the new growth strategy. It is therefore
      necessary to cite it along with the initial 2015 paper when using
      NoiseChisel.

   Segment:
    - arXiv:1909.11230 added in papers to cite (with the `--cite' option):
      this paper describes why Segment has been separated from NoiseChisel
      and some important updates to it compared to the 2015 paper, it is
      therefore necessary to cite it along with that paper when using
      Segment.

   Statistics:
    --contour: compute a contour plot which can be directly fed into the
      PGFPlots package of LaTeX for plotting the contours. Support for more
      formats will be added based on the need/request.

   Table:
    --equal: Output only rows that have a value equal to the given value in
      the given column. For example `--equal=ID,2,4,5' will select only rows
      that have a value of 2, 4 and 5 in the `ID' column.
    --notequal: Output only rows that have a different value compared to the
      values given to this option in the given column.
    - Column Arithmetic operators:
      - `angular-distance': a new operator to easily find the angular
        distance (along a great circle) between points in various table
        columns, or the distances of all the points in the table rows with a
        fixed point. See the book for examples and better explanation.

   Library:
    - gal_binary_connected_indexs: store indexs of connected components.
    - gal_blank_remove_realloc: Remove blanks and shrink allocated space.
    - gal_box_bound_ellipsoid_extent: Extent of 3D ellipsoid.
    - gal_box_bound_ellipsoid: Bounding box for a 3D ellipsoid.
    - gal_statistics_unique: Return unique (non-blank) elements of the 
input.

** Removed features

** Changed features

** Bugs fixed
   bug #56736: CosmicCalculator crash when a single value given to 
--obsline.
   bug #56747: ConvertType's SLS colormap has black pixels which should 
be orange.
   bug #56754: Wrong sigma clipping output when many values are equal.
   bug #56999: Compilation error on macOS 10.9 not recognizing AT_FDCWD.
   bug #57057: BuildProgram not using environment LDFLAGS or CPPFLAGS.
   bug #57101: Crop segmentation fault when no overlap exists in image-mode.
   bug #57164: MakeCatalog crashes when a label isn't in the dataset.
   bug #57180: MakeCatalog reporting infinity S/N when --instd isn't an 
image.
   bug #57200: Generated pkgconfig must request wcslib, not wcs.
   bug #57293: NaN value for brightness-related columns when values have 
NaN.





[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-0.11.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-0.11.tar.lz | tar -xf -'):

   $ lzip -d gnuastro-0.11.tar.lz
   $ tar xf gnuastro-0.11.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-0.11.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.


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