paper-concept.git/tex/src, branch master Paper (Towards Long-term and Archivable Reproducibility) Imported recent updates in Maneage, conflicts fixed 2022-05-09T21:52:29+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2022-05-09T11:32:47+00:00 9fdeebaacd06d57c479cd69e9937c4bfe5d0a286 Until now, Maneage had undergone some updates. With this commit, those updates have been imported and the conflicts that resulted were fixed. They were all cosmetic and had no effect on the analysis. The most significant one was about the change in the format of 'INPUTS.conf'. In the process, I also noticed that the IEEEtran LaTeX package is now called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing). 
Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).
IMPORTANT: Updates to almost all software 2022-01-21T00:15:24+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2021-10-04T00:51:45+00:00 8463df97c6f26ec4d22cd5828bb0574fd5e450d2 This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2 
This commit primarily affects the configuration step of Maneage'd projects,
and in particular, updated versions of the many of the software (see
P.S.). So it shouldn't affect your high-level analysis other than the
version bumps of the software you use (and the software's possibly
improve/changed behavior).

The following software (and thus their dependencies) couldn't be updated as
described below:
  - Cryptography: isn't building because it depends on a new
    setuptools-rust package that has problems
    (https://savannah.nongnu.org/bugs/index.php?61731), so it has been
    commented in 'versions.conf'.
  - SecretStorage: because it depends on Cryptography.
  - Keyring: because it depends on SecretStorage.
  - Astroquery: because it depends on Keyring.

This is a "squashed" commit after rebasing a development branch of 60
commits corresponding to a roughly two-month time interval. The following
people contributed to this branch.
  - Boudewijn Roukema added all the R software infrastructure and the R
    packages, as well as greatly helping in fixing many bugs during the
    update.
  - Raul Infante-Sainz helped in testing and debugging the build.
  - Pedram Ashofteh Ardakani found and fixed a bug.
  - Zahra Sharbaf helped in testing and found several bugs.

Below a description of the most noteworthy points is given.

  - Software tarballs: all updated software now have a unified format
    tarball (ustar; if not possible, pax) and unified compression (Lzip) in
    Maneage's software repository in Zenodo
    (https://doi.org/10.5281/zenodo.3883409). For more on this See
    https://savannah.nongnu.org/task/?15699 . This won't affect any extra
    software you would like to add; you can use any format recognized by
    GNU Tar, and all common compression algorithms. This new requirement is
    only for software that get merged to the core Maneage branch.

  - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore
    (and the packages it depends on) is a high-level product that is only
    relevant during the project development (like Emacs!): when the user
    wants the file meta data (like dates) to be unchanged after checking
    out branches. So it should be considered a high-level software, not
    basic. Metastore also usually causes many more headaches and error
    messages, so personally, I have stopped using it! Instead I simply
    merge my branches in a separate clone, then pull the merge commit: in
    this way, the files of my project aren't re-written during the checkout
    phase and therefore their dates are untouched (which can conflict with
    Make's dates on configuration files).

  - The un-official cloned version of Flex (2.6.4-91 until this commit) was
    causing problems in the building of Netpbm, so with this commit, it has
    been moved back to version 2.6.4.

  - Netpbm's official page had version 10.73.38 as the latest stable
    tarball that was just released in late 2021. But I couldn't find our
    previously-used version 10.86.99 anywhere (to see when it was released
    and why we used it! Its at last more than one year old!). So the
    official stable version is being used now.

  - Improved instructions in 'README.md' for building software environment
    in a Docker container (while having project source and output data
    products on the local system; including the usage of the host's
    '/dev/shm' to speed up temporary operations).

  - Until now, the convention in Maneage was to put eight SPACE characters
    before the comment lines within recipes. This was done because by
    default GNU Emacs (also many other editors) show a TAB as eight
    characters. However, in other text editors, online browsers, or even
    the Git diff, a TAB can correspond to a different number of
    characters. In such cases, the Maneage recipes wouldn't look too
    interesting (the comments and the recipe commands would show a
    different indentation!).

    With this commit, all the comment lines in the Makefiles within the
    core Maneage branch have a hash ('#') as their first character and a
    TAB as the second. This allows the comment lines in recipes to have the
    same indentation as code; making the code much more easier to read in a
    general scenario including a 'git diff' (editor agnostic!).

P.S. List of updated software with their old and new versions
 - Software with no version update are not mentioned.
 - The old version of newly added software are shown with '--'.

Name (Basic)              Old version    New version
------------              -----------    -----------
Bzip2                     1.0.6          1.0.8
CURL                      7.71.1         7.79.1
Dash                      0.5.10.2       0.5.11.5
File                      5.39           5.41
Flock                     0.2.3          0.4.0
GNU Bash                  5.0.18         5.1.8
GNU Binutils              2.35           2.37
GNU Coreutils             8.32           9.0
GNU GCC                   10.2.0         11.2.0
GNU M4                    1.4.18         1.4.19
GNU Readline              8.0            8.1.1
GNU Tar                   1.32           1.34
GNU Texinfo               6.7            6.8
GNU diffutils             3.7            3.8
GNU findutils             4.7.0          4.8.0
GNU gmp                   6.2.0          6.2.1
GNU grep                  3.4            3.7
GNU gzip                  1.10           1.11
GNU libunistring          0.9.10         1.0
GNU mpc                   1.1.0          1.2.1
GNU mpfr                  4.0.2          4.1.0
GNU nano                  5.2            6.0
GNU ncurses               6.2            6.3
GNU wget                  1.20.3         1.21.2
Git                       2.28.0         2.34.0
Less                      563            590
Libxml2                   2.9.9          2.9.12
Lzip                      1.22-rc2       1.22
OpenSLL                   1.1.1a         3.0.0
Patchelf                  0.10           0.13
Perl                      5.32.0         5.34.0
Podlators                 --             4.14

Name (Highlevel)          Old version    New version
----------------          -----------    -----------
Apachelog4cxx             0.10.0-603     0.12.1
Astrometry.net            0.80           0.85
Boost                     1.73.0         1.77.0
CFITSIO                   3.48           4.0.0
Cmake                     3.18.1         3.21.4
Eigen                     3.3.7          3.4.0
Expat                     2.2.9          2.4.1
FFTW                      3.3.8          3.3.10
Flex                      2.6.4-91       2.6.4
Fontconfig                2.13.1         2.13.94
Freetype                  2.10.2         2.11.0
GNU Astronomy Utilities   0.12           0.16.1-e0f1
GNU Autoconf              2.69.200-babc  2.71
GNU Automake              1.16.2         1.16.5
GNU Bison                 3.7            3.8.2
GNU Emacs                 27.1           27.2
GNU GDB                   9.2            11.1
GNU GSL                   2.6            2.7
GNU Help2man              1.47.11        1.48.5
Ghostscript               9.52           9.55.0
ICU                       --             70.1
ImageMagick               7.0.8-67       7.1.0-13
Libbsd                    0.10.0         0.11.3
Libffi                    3.2.1          3.4.2
Libgit2                   1.0.1          1.3.0
Libidn                    1.36           1.38
Libjpeg                   9b             9d
Libmd                     --             1.0.4
Libtiff                   4.0.10         4.3.0
Libx11                    1.6.9          1.7.2
Libxt                     1.2.0          1.2.1
Netpbm                    10.86.99       10.73.38
OpenBLAS                  0.3.10         0.3.18
OpenMPI                   4.0.4          4.1.1
Pixman                    0.38.0         0.40.0
Python                    3.8.5          3.10.0
R                         4.0.2          4.1.2
SWIG                      3.0.12         4.0.2
Util-linux                2.35           2.37.2
Util-macros               1.19.2         1.19.3
Valgrind                  3.15.0         3.18.1
WCSLIB                    7.3            7.7
Xcb-proto                 1.14           1.14.1
Xorgproto                 2020.1         2021.5

Name (Python)             Old version    New version
-------------             -----------    -----------
Astropy                   4.0            5.0
Beautifulsoup4            4.7.1          4.10.0
Beniget                   --             0.4.1
Cffi                      1.12.2         1.15.0
Cryptography              2.6.1          36.0.1
Cycler                    0.10.0         0.11.0+}
Cython                    0.29.21        0.29.24
Esutil                    0.6.4          0.6.9
Extension-helpers         --             0.1
Galsim                    2.2.1          2.3.3
Gast                      --             0.5.3
Jinja2                    --             3.0.3
MPI4py                    3.0.3          3.1.3
Markupsafe                --             2.0.1
Numpy                     1.19.1         1.21.3
Packaging                 --             21.3
Pillow                    --             8.4.0
Ply                       --             3.11
Pyerfa                    --             2.0.0.1
Pyparsing                 2.3.1          3.0.4
Pythran                   --             0.11.0
Scipy                     1.5.2          1.7.3
Setuptools                41.6.0         58.3.0
Six                       1.12.0         1.16.0
Uncertainties             3.1.2          3.1.6
Wheel                     --             0.37.0

Name (R)                  Old version    New version
--------                  -----------    -----------
Cli                       --             2.5.0
Colorspace                --             2.0-1
Cowplot                   --             1.1.1
Crayon                    --             1.4.1
Digest                    --             0.6.27
Ellipsis                  --             0.3.2
Fansi                     --             0.5.0
Farver                    --             2.1.0
Ggplot2                   --             3.3.4
Glue                      --             1.4.2
GridExtra                 --             2.3
Gtable                    --             0.3.0
Isoband                   --             0.2.4
Labeling                  --             0.4.2
Lifecycle                 --             1.0.0
Magrittr                  --             2.0.1
MASS                      --             7.3-54
Mgcv                      --             1.8-36
Munsell                   --             0.5.0
Pillar                    --             1.6.1
R-Pkgconfig               --             2.0.3
R6                        --             2.5.0
RColorBrewer              --             1.1-2
Rlang                     --             0.4.11
Scales                    --             1.1.1
Tibble                    --             3.1.2
Utf8                      --             1.2.1
Vctrs                     --             0.3.8
ViridisLite               --             0.4.0
Withr                     --             2.4.2
Copyedits in appendices, suggested by Antonio Dı́az Dı́az 2021-07-02T19:57:18+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2021-07-02T19:47:47+00:00 ae5fb4d3d3af8b3e851589449566286098fd1470 Antonio kindly proposed these corrections (mostly in Appendix A, but one also at the start of Appendix B). They are fixed with this commit. 
Antonio kindly proposed these corrections (mostly in Appendix A, but one
also at the start of Appendix B). They are fixed with this commit.
Appendix A: minor edits to clarify text 2021-06-24T16:17:52+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2021-06-24T16:17:52+00:00 c61d44efba38ad7ef87b19c26b7b71141b3aa8a5 While having a fast glance at Appendix A, I noticed two small parts that could be improved by adding a 'from' and using 'Maneage' instead of "the proposed solution". They are corrected with this commit. 
While having a fast glance at Appendix A, I noticed two small parts that
could be improved by adding a 'from' and using 'Maneage' instead of "the
proposed solution". They are corrected with this commit.
Futher copyediting on the apendices 2021-06-14T23:56:20+00:00 Boud Roukema boud@cosmo.torun.pl 2021-06-14T23:31:46+00:00 ccce0fb9f9229d015e942b00073f39fc16130dc7 In the discussion on criteria that Popper lacks, the last mentioned criteria "including the narrative" is written in such a way that can confuse readers into thinking that only a single criteria is lacking. Hyphenating ('including-the-narrative') has been applied to make the sentence less likely to be misunderstood. The ending of the first paragraph in the "Generational gaps" item in Appendix A.G ("... every few years is not practically possible.") sounds like "not almost possible". So it can cause confusions. Endings that are much clearer include: * is impractical. * is not possible in practice. * is not practical. * is not possible practically. [meaning 2. is less likely in this case] I've selected the first option, also replacing "they" by "scientists" to avoid the misinterpretation that "programming languages ... have their own science field to focus on". This commit and the previous one were "amended" by Mohammad (compared to the original commits that Boud had sent). 
In the discussion on criteria that Popper lacks, the last mentioned
criteria "including the narrative" is written in such a way that can
confuse readers into thinking that only a single criteria is
lacking. Hyphenating ('including-the-narrative') has been applied to make
the sentence less likely to be misunderstood.

The ending of the first paragraph in the "Generational gaps" item in
Appendix A.G ("... every few years is not practically possible.") sounds
like "not almost possible". So it can cause confusions. Endings that are
much clearer include:

  * is impractical.
  * is not possible in practice.
  * is not practical.
  * is not possible practically.
    [meaning 2. is less likely in this case]

I've selected the first option, also replacing "they" by "scientists" to
avoid the misinterpretation that "programming languages ... have their own
science field to focus on".

This commit and the previous one were "amended" by Mohammad (compared to
the original commits that Boud had sent).
Copyediting of appendices 2021-06-14T22:39:03+00:00 Boud Roukema boud@cosmo.torun.pl 2021-06-14T20:58:52+00:00 d3ee5799299660b42d7b6211b09ad4b707744e77 This commit does several small copyediting fixes in the body of the appandices which should improve their readability. 
This commit does several small copyediting fixes in the body of the
appandices which should improve their readability.
Replace archive.today with archive.org in footnote URL 2021-06-13T17:05:53+00:00 Boud Roukema boud@cosmo.torun.pl 2021-06-13T15:29:38+00:00 ba7792ff2322a96b08737452964c9ef0c739a38d Based on a reasonable suggestion on ethical reasoning [1], this commit replaces the git.sdf.org + archive.today pair of URLs in the footnote on Github's unethical aspects, with a single archive.org URL, which contains the original URL, making this sufficient for readers wishing to check either the live or archived versions. [1] https://social.privacytools.io/@resist1984/106403926114506533 https://social.privacytools.io/@resist1984/106403932399114639 
Based on a reasonable suggestion on ethical reasoning [1], this commit
replaces the git.sdf.org + archive.today pair of URLs in the footnote on
Github's unethical aspects, with a single archive.org URL, which contains
the original URL, making this sufficient for readers wishing to check
either the live or archived versions.

[1] https://social.privacytools.io/@resist1984/106403926114506533
    https://social.privacytools.io/@resist1984/106403932399114639
Add GHTorrent, some https, notabug 2021-06-13T14:09:19+00:00 Boud Roukema boud@cosmo.torun.pl 2021-06-12T23:56:45+00:00 a77bba6249f03062eb9849997c77245ad403d027 This commit adds a few sentences in relation to the first known attempt to store and make available git repository hosting ephemera (GHTorrent, introduced to us by Roberto Di Cosmo). Since one of the two sponsors of GHTorrent is Microsoft, both the ethics and practical aspects of this in the context of reproducibility and scientific ethics as expressed by the international scientific community are rather unclear, so a link to one of the well-known lists of practical and ethical issues with Github is included. A minor fix is made in 'tex/src/appendix-existing-solutions.tex', since the word 'data' is plural (singular is 'datum'). 
This commit adds a few sentences in relation to the first known attempt to
store and make available git repository hosting ephemera (GHTorrent,
introduced to us by Roberto Di Cosmo). Since one of the two sponsors of
GHTorrent is Microsoft, both the ethics and practical aspects of this in
the context of reproducibility and scientific ethics as expressed by the
international scientific community are rather unclear, so a link to one of
the well-known lists of practical and ethical issues with Github is
included.

A minor fix is made in 'tex/src/appendix-existing-solutions.tex', since the
word 'data' is plural (singular is 'datum').
Published version in CiSE 2021-06-11T20:48:10+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2021-06-11T20:37:45+00:00 313db0b04bd3499f83d9e79fd7e92578cd367c2b This is the version of the project that will be published in Computing in Science and Engineering (CiSE), Volume 23, Issue 3, Pages 82--91. 
This is the version of the project that will be published in Computing in
Science and Engineering (CiSE), Volume 23, Issue 3, Pages 82--91.
Minor edits and updated first-page Software Heritage ID 2021-06-08T18:11:11+00:00 Mohammad Akhlaghi mohammad@akhlaghi.org 2021-06-08T18:02:47+00:00 a0a51763a611faad22b7b2bc8ebbb5094b3377af After going through Boud's corrections and edits in the previous commit, I thought some minor clarifications would be necessary, and they are implemented in this commit. Also, in preparation for submission to the journal, the top-level software heritage ID has been corrected to the latest commit on Software Heritage. 
After going through Boud's corrections and edits in the previous commit, I
thought some minor clarifications would be necessary, and they are
implemented in this commit.

Also, in preparation for submission to the journal, the top-level software
heritage ID has been corrected to the latest commit on Software Heritage.