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[task #16244] Software update 2022-2

From: Mohammad Akhlaghi
Subject: [task #16244] Software update 2022-2
Date: Fri, 5 Aug 2022 20:20:27 -0400 (EDT)


                 Summary: Software update 2022-2
                 Project: Maneage
               Submitter: makhlaghi
               Submitted: Sat 06 Aug 2022 01:20:26 AM BST
         Should Start On: Sat 06 Aug 2022 12:00:00 AM BST
   Should be Finished on: Sat 06 Aug 2022 12:00:00 AM BST
                Category: Software
                Priority: 5 - Normal
                  Status: In Progress
                 Privacy: Public
        Percent Complete: 50%
             Assigned to: makhlaghi
             Open/Closed: Open
         Discussion Lock: Any
                  Effort: 0.00


Follow-up Comments:

Date: Sat 06 Aug 2022 01:20:26 AM BST By: Mohammad Akhlaghi <makhlaghi>
It is almost one year since the last general Maneage software update (that was
done in the autumn of 2021; see task #16103). 

To start this round of updates, I just updated almost all of the basic
software with a version increase, and some of the default ones. The job is
being done on the 'update-software' branch of the development repository

Currently there is only one commit (Commit 504e79d3cb
<>), the commit
message details all the version updates and is in the P.S. of this post. I
will hopefully merge this branch into Maneage in one week (Saturday April 13th
2022). It would be great if you can test this branch on your systems and help
fix any bugs that you may find. Also, in case there are software you would
like to update, please feel free to add them as commits over this branch until
the deadline ;-).

As mentioned in the first comment of task #16103, updating non-default Maneage
software needs to be done by those who use/need them (in particular Python or
R packages, which have a completely different, and evolving build system). I
will be happy to test and ultimately merge them once they build on a
sufficient number of systems. But due to time constraints, I can't update them

P.S. Commit message of first set of software updates in this round.

    IMPORTANT: Updates to many default software
    New versions of many of the Maneage software had come since the last
    update in Maneage (almost one year ago)! With this commit, the software
    the P.S. have been updated, and a new software (PLplot) has been added.
    Besides the updates in the core software, the followimg improvements have
    also been implemented in this commit:
     - When you run './project shell':
       - A welcome message is printed that will remind the caller that they
         have entered a new environment, it will print the location of 'HOME'
         and the location of the shell startup file.
       - The 'reproduce/software/shell/' is loaded as a startup
         file. This allows you to customize your interactive Maneage shell. A
         default step has already been placed there that will put the git
         branch name (in green) within the shell prompt (which was
         purple). This greatly helps when dealing with directories under Git
         version control. These settings won't bother with Maneage's default
         operations: through environment variables we make sure that these
         './project shell' features will not slow-down the calls to the shell
         within the non-interactive Make calls.
       - The host's 'COLORTERM' is passed to the Maneage environment. It is
         used by some programs that can have color outputs on the terminal.
     - The host's 'ldd' is linked inside the custom environment. This belongs
       to the GNU C Library (which is not yet installed in Maneage). But
       in checking the linking status of the binaries.
     - The Zip and Unzip programs have been moved as high-level software that
       have to be manually requested when necessary. This is because they are
       not used by any of the basic software anymore. They were just
       as dependencies of GNU Tar to be close the other compression
       programs. Also, in the past we would use the original tarballs, and
       (for example Numpy) were distributed in Zip format. However, by
       we now use a custom Lzip tarball and don't need Zip or Unzip. This was
       suggested by Zahra Sharbaf and Raul Infante-Sainz.
     - Some minor edits in 'reproduce/software/shell/'. In
       particular the 'awk' command was effectively just replacing a '_' with
       '-', so it just uses a simple SED expression instead.
    P.S. List of software:
    Basic software:
       cURL                                7.79.1    -->  7.84.0
       Dash                        -->  0.5.11-057cd65
       File                                5.41      -->  5.42
       Git                                 2.36.0    -->  2.37.1
       GNU AWK                             5.1.0     -->  5.1.1
       GNU Bash                            5.1.8     -->  5.2-rc2
       GNU Gzip                            1.11      -->  1.12
       GNU Nano                            6.0       -->  6.4
       GNU Libtool                         2.4.6     -->  2.4.7
       GNU libiconv                        0.16      -->  0.17
       GNU Readline                        8.1.1     -->  8.2-rc2
       GNU Binutils                        2.37      -->  2.39
       GNU Findutils                       4.8.0     -->  4.9.0
       GNU Integer Set Library (ISL)       0.18      -->  0.24
       GNU Compiler Collection (GCC)       11.2.1    -->  12.1.0
       PatchELF                            0.13      -->  0.15.0
       Perl                                5.34.0    -->  5.36.0
    High-level software:
       Libjpeg                             9d        -->  9e
       Libtiff                             4.3.0     -->  4.4.0
       CFITSIO                             4.0.0     -->  4.1.0
       Ghostscript                         9.55.0    -->  9.56.1
       GNU Astronomy Utilities (Gnuastro)  0.16.1    -->  0.18
       PLplot                              n/a       -->  5.15.0
       SCAMP                               2.6.7     -->  2.10.0
       SWarp                               2.38.0    -->  2.41.5
       WCSLIB                              7.7       -->  7.11


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