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Gnuastro 0.20.60 released

From: Mohammad Akhlaghi
Subject: Gnuastro 0.20.60 released
Date: Sun, 20 Aug 2023 16:59:12 +0200
User-agent: Mozilla Thunderbird

Dear all,

There have already been 60 commits by 6 people (see [1] below) in the 16 weeks since Gnuastro version 0.20. Many exciting/useful new features have been added, some things have been changed for consistency and many bugs have been fixed. For the full list, see [2] below (from the 'NEWS' file within the tarball).

In preparation for the next stable release, I am therefore very happy to make this alpha-release. To ensure a smooth stable release, please send any un-expected behavior, warning or error you confront to ''.

Here is the compressed source and the GPG detached signature for this release. To uncompress Lzip tarballs, see [3]. To check the validity of the tarballs using the GPG detached signature (*.sig) see [4]. See [5] for the list of software used to bootstrap this tarball. (4.5 MB) (833 B)

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 (see [6] on how to generate it).

  f76fa0136d9426ce577873547deb25b4fca5e4f0  gnuastro-0.20.60-d994.tar.lz
88Uzu2pkjdPAYZ/c8LBmsfUIGXiUbAvX9ukS8V60wf4= gnuastro-0.20.60-d994.tar.lz

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.

Best wishes,

Dr. Mohammad Akhlaghi
Staff Researcher,
Centro de Estudios de Física del Cosmos de Aragón (CEFCA),
Plaza San Juan 1, Planta 2, Teruel 44001, Spain

[1] Thanks to everyone who has contributed!

The following people contributed changes to this release (number in parenthesis shows number of Git commits):

  Faezeh Bidjarchian (2)
  Fathma Mehnoor (2)
  Mohammad Akhlaghi (48)
  Rashid Yaaqib (1)
  Raul Infante-Sainz (1)
  Sepideh Eskandarlou (6)

The following people provided comments, suggestions or reported bugs:

  Aaron Watkins
  Agata Rożek
  Colin Orion Chandler
  Irene Pintos Castro
  Rashid Yaaqib
  Raul Infante-Sainz
  Ryan Begley
  Sepideh Eskandarlou
  Teet Kuumta
  Zahra Sharbaf
  Zohreh Ghaffari

[2] Noteworthy changes since Gnuastro 0.20:

** New features

  New program:

  - 'astscript-dither-simulate': a new installed script that will simplify
    the process of designing the best dither pattern for your observing
    strategy. It takes into account the distortion of the camera, runs in
    parallel and allows customizations (for example to account for
    vignetting or large blobs of bad pixels) through hooks at relevant
    steps. A new tutorial has been added in the Tutorials chapter of the
    book on how to use this new script.

  - New tutorial on a low surface brightness optimized design of a dither
    pattern using the newly added installed script in Gnuastro for
    simulating the exposure map of a dither pattern stack (it is called as
    'astscript-dither-simulate' on the command-line).
  - Smaller tutorials that were distributed within the documentation of
    different programs are brought into the "Tutorials" chapter.
  - New "Standard deviation vs. error" sub-section added under the
    MakeCatalog section. It uses real examples to clearly show the
    fundamental difference between the two (which are sometimes confused
    with each other). This was written with the help of Raul Infante-Sainz.

  Configuration files
  - To separate the option name and value, you can now also use the '='
    character. This allows your custom configuration files to also be
    loaded into a shell (with 'source') or Make (with 'include'). Until
    now, only white-space characters were allowed as separators of option
    names and values.
  --config-prefix=STR: Given string can be a prefix of options in
    configuration files. Added with the point above, this allows loading
    the different configuration files of different instances of the same
    program without overwriting them. See the example in the book.

  - New operators (see book for a full description):
    - to-1d: convert the input operand into a 1D array, no matter how many
      dimensions it has. Suggested by Faezeh Bidjarchian.
    - trim: remove all fully-blank outer regions of the input dataset.
    - pool-min: Min-pooling to reduce the size of the input by calculating
                the minimum of a the pixels within the pooling window. See
                the new "Pooling opeators" section of the book for
                more. This and the rest of the pooling operators introduced
                here were implemented by Faezeh Bidjarchian.
    - pool-max: Similar to 'pool-min' but using maximum.
    - pool-sum: Similar to 'pool-min' but using sum.
    - pool-mean: Similar to 'pool-min' but using mean.
    - pool-median: Similar to 'pool-min' but using median.

  - It is now possible to write TIFF files in the output (until now,
    Gnuastro could only read TIFF files). This step was written by Fathma

  - New measurements:
    --river-min: minimum river value around a clump.
    --river-max: minimum river value around a clump.

  --info-num-cols: print the number of the input table's columns and abort.
  --info-num-rows: print the number of the input table's rows and abort.
  - '$_all' in column arithmetic: when an arithmetic expression contains
    this string, it will be repeated independently for all the columns of
    the input table.

  --mksrc: use a custom Makefile for estimating the zeropoint, not the
    default installed Makefile. This is primarily intended for debugging or
    developing this script, not for normal usage.

  - gal_blank_not_minmax_coords: returns the minimum/maximum coordinates of
    non-blank regions of input dataset.
  - gal_blank_trim: trim all outer blank regions from the input dataset.
  - gal_pool_min: min-pooling function, see 'pool-min' above.
  - gal_pool_max: max-pooling function, see 'pool-min' above.
  - gal_pool_sum: sum-pooling function, see 'pool-min' above.
  - gal_pool_mean: mean-pooling function, see 'pool-min' above.
  - gal_pool_median: median-pooling function, see 'pool-min' above.
  - gal_tiff_write: write 'gal_data_t' to a TIFF file; written by
    Fathma Mehnoor.

** Removed features

    - MakeNoise (with executable name 'astmknoise') has been removed from
      Gnuastro. This is because the 'mknoise-*' operators of Arithmetic do
      the same job, but in a much more customizable, modular and managable
      manner; allowing to mix with other operators. The "Noise basics"
      sub-section of the book has been moved under the Arithmetic program's
      documentation also.

** Changed features

    - mknoise-sigma-from-mean: new name for the old 'mknoise-poisson'
      random number distribution.
    - mknoise-poisson: now produces correct Poisson distribution output,
      which can be non-symmetric in low background values and is always
      integers. For a complete description and hands-on example of the
      differences with 'mknoise-sigma-from-mean' and 'mknoise-sigma', see
      the description of these three operators in the "Random number
      generators" operators sub-section of the "Arithmetic operators"
      section of the Gnuastro book.

  - The dash in the column names of the following measurement names has
    been replced by underscore to conform with the general stardard of
    using underscores between words in column names (reported by Raul
    Infante-Sainz). Also, in the case of '--sigclip-mean-sb-delta' the
    column name didn't correspond to the option name.
    Option                  Column name            Old column name
    --sigclip-mean          SIGCLIP_MEAN           SIGCLIP-MEAN
    --sigclip-median        SIGCLIP_MEDIAN         SIGCLIP-MEDIAN
    --sigclip-number        SIGCLIP_NUMBER         SIGCLIP-NUMBER
    --sigclip-std           SIGCLIP_STD            SIGCLIP-STD
    --sigclip-mean-sb       SIGCLIP_MEAN_SB        SIGCLIP-MEAN-SB
    --sigclip-mean-sb-delta SIGCLIP_MEAN_SB_DELTA  SIGCLIP-MEAN-SB-ERR
  - The default extension name for the values image ('--valueshdu') is now
    'INPUT-NO-SKY'. Until now, it was simply '1' (without any hint on what
    what is expected by default). Recall that if the sky is not subtracted
    from the values image you can use '--sky' for MakeCatalog to subtract
    it before the measurements. Implemented by Sepideh Eskandarlou.
  - When the input clump labels do not have the 'NUMLABS' keyword
    (specifying how many clumps there are in the image, independent of the
    number of objects), MakeCatalog will no longer re-label the input
    clumps: the output catalog will have the same clump ids as the
    labels. Until now, it would generate new labels for the clumps in such
    cases (along with a new FITS image containing the clumps with the new
    labels to allow you to match them). The output catalog also had the new
    label, not the original labels (the old behavior was therefore very

  - The default name of the first extension of Segment's output is now
    'INPUT-NO-SKY', until now, it was 'INPUT'. This was necessary because
    the first extension of the output is not the exact input file (if a
    value is given to '--sky' it will be subtracted from the input in the
    first extension). Implemented by Sepideh Eskandarlou.

  - After applying the signal-to-noise threshold (if it is requested), any
    extra pixels that are not connected to the central target are also
    masked. Such pixels can remain in rivers between bright clumps and
    would cause problem in the final stack and were not removed until now.
    Implemented by Sepideh Eskandarlou

** Bugs fixed
  bug #64138: Arithmetic's mknoise-poisson only using first pixel value.
              Reported by Irene Pintos Castro.
  bug #64146: SIGCLIP column names contain dashes instead of
              underlines. Reported by Raul Infante-Sainz.
  bug #64148: MakeCatalog crash when using the options '--std' and/or
              'sigclip-mean-sb-delta' for clumps catalog. Reported by Raul
  bug #64153: astscript-ds9-region: '--namecol' gives a constant zero in
              image-mode. Reported by Zahra Sharbaf.
  bug #64186: Query: core dump when custom name given to '--dataset'. First
              reported by Zohreh Ghaffari as a problem in
              'astscript-select-stars' (sr #110874) and identified as a
              problem in Query by Sepideh Eskandarlou.
  bug #64199: info astscript-zeropoint not working. Reported by Zahra
  bug #64246: Query's --information gives a crash for Gaia datasets.
              Reported by Rashid Yaaqib.
  bug #64250: astscript-fits-view: no message printed when input file did
              not exist. Reported by Ryan Begley.
  bug #64274: MakeProfiles crash for points in 3D. Found by Teet Kuumta.
  bug #64303: Statistics fit --fitestimate crash when covariance matrix has
              NaN. Reported Sepideh Eskandarlou.
  bug #64357: Plain text metadata ignored when no name is present.
  bug #64392: Arithmetic's isnotblank operator producing zeros when no
              blanks present.
  bug #64420: Error message of wrongly specified HDU doesn't give the
              problematic option name; reported by Aaron Watkins.
  bug #64431: gal_wcs_to_cd does not account for altlin==3. Reported by
              Colin Orion Chandler.
  bug #64541: Segment's --keepmaxnearriver has no effect.
  bug #64544: Arithmetic crashes with tofilefree operator value has a
  bug #64545: Accounting for CFITSIO silently appending '.gz' when file
              doesn't exist. Reported by Sepideh Eskandarlou.

[3] 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:

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

  $ tar xf gnuastro-0.20.60-d994.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-0.20.60-d994.tar.lz | tar -xf -'):

  $ lzip -d gnuastro-0.20.60-d994.tar.lz
  $ tar xf gnuastro-0.20.60-d994.tar

[4] 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-0.20.60-d994.tar.lz.sig

The signature should match the fingerprint of the following key:

  pub   rsa4096 2018-12-08 [SC]
        52B0 4484 D806 C90D CB52  7249 71E8 9901 2D17 4B66
  uid           [ unknown] Mohammad Akhlaghi <>

If that command fails because you don't have the required public key, or that public key has expired, try the following commands to retrieve or refresh it, and then rerun the 'gpg --verify' command.

  gpg --recv-keys 71E899012D174B66

As a last resort to find the key, you can try the official GNU keyring:

  wget -q
  gpg --keyring gnu-keyring.gpg --verify gnuastro-0.20.60-d994.tar.lz.sig

[5] 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 7.0.3
  Autoconf 2.71
  Automake 1.16.5
  Help2man 1.49.3
  ImageMagick 7.1.1-15
  Gnulib v0.1-6638-gd820198e8a
  Autoconf archives v2023.02.20-29-g5001091

The dependencies to build Gnuastro from this tarball on your system are
described here:

[6] To get the base64 SHA256 checksum, you can use the command below (assuming you already have the 'openssl' command-line program).

  cat gnuastro-0.20.60-d994.tar.lz \
      | openssl dgst -binary -sha256 | openssl base64 -A

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