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Until now, the '$(project-commit-hash)' Make variable of 'initialize.mk'
simply called 'git' to find the commit hash. However, due to one of the
recent software updates, we noticed that this command is no longer working
(and the project commit hash wasn't getting printed in the PDF)! The
problem was that Maneage's Git, couldn't find the 'libiconv' library that
it was built with.
With this commit, the '$(shell' command that calls Git, first exports
'LD_LIBRARY_PATH' to Maneage's software build directory. As a result, the
Git command can work and will report the commit as a LaTeX macro to be used
in the paper. To avoid relying on PATH outside of Make recipes, we now also
directly call the Git executable with Maneage.
Some other minor issues have been found and fixed in this commit:
- README-hacking.md: some minor edits and typo corrections.
- initialize.mk: the '$(curdir)' variable is now used in several places
that we were calling 'pwd'.
- versions.conf: 'xlsxio-version' now included with other programs. Until
now it was commented because GCC 11.1.0 had issues with it. However, GCC
11.2.0 doesn't have a problem any more, so it has been returned to the
list of all high-level programs.
- xorg.mk: used same format to comment recipe lines as the other Makefiles
(a '#' followed by a TAB).
- preamble-pgfplots.tex: lines to comment for building an EPS figure with
PGFPlots have been re-formatted to be more human-readable.
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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
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Until now, important LaTeX packages like 'caption' (for managing figure
captions), 'hyperref' (for managing links) and 'xcolor' (for managing
colors) were being loaded inside the optional
'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove
this file from loading when you use custom journal sytels. However, these
packages will often be necessary after loading special journal styles also.
With this commit, these packages are now loaded into LaTeX as part of the
'tex/src/preamble-project.tex' file. This file is in charge of LaTeX
settings that are custom to the project and independent of its style.
Several other small corrections are made with this commit:
- I noticed that './project make texclean' crashes if no PDF exists in the
working directory! So a '-f' was added to the 'rm' command of the
'texclean' rule.
- As part of the LaTeX Hyperref, we can set general metadata or properties
for the PDF (that aren't written into the printable PDF, but into the
file metadata). They can be viewed in many PDF viewers as PDF
properties. Until now, we were only using the '\projecttitle' macro here
to write the paper's title. However, thanks to the recently added
'reproduce/analysis/config/metadata.conf', we now have a lot of useful
information that can also go here. So the 'metadata-copyright-owner' is
now used to define the PDF author, and the project's
'metadata-git-repository' and commit hash are written into the PDF
subject. But to import these, it was necessary to define them as LaTeX
macros, hence the addition of these macros in 'initialize.mk'.
- Some extra packages that aren't necessary to build the default PDF were
removed in 'preamble-project.tex'.
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Having entered 2021, it was necessary to update the copyright years at the
top of the source files. We recommend that you do this for all your
project-specific source files also.
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This only concerns the TeX sources in the default branch. In case you don't
use them, there should only be a clean conflict in 'paper.tex' (that is
obvious and easy to fix). Conflicts may only happen in some of the
'tex/src/preamble-*.tex' files if you have actually changed them for your
project. But generally any conflict that does arise by this commit with
your project branch should be very clear and easy to fix and test.
In short, from now on things will even be easier: any LaTeX configuration
that you want to do for your project can be done in
'tex/src/preamble-project.tex', so you don't have to worry about any other
LaTeX preamble file. They are either templates (like the ones for PGFPlots
and BibLaTeX) or low-level things directly related to Maneage. Until now,
this distinction wasn't too clear.
Here is a summary of the improvements:
- Two new options to './project make': with '--highlight-new' and
'--highlight-notes' it is now possible to activate highlighting on the
command-line. Until now, there was a LaTeX macro for this at the start
of 'paper.tex' (\highlightchanges). But changing that line would change
the Git commit hash, making it hard for the readers to trust that this
is the same PDF. With these two new run-time options, the printed commit
hash will not changed.
- paper.tex: the sentences are formatted as one sentence per line (and one
line per sentence). This helps in version controlling narrative and
following the changes per sentence. A description of this format (and
its advantages) is also included in the default text.
- The internal Maneage preambles have been modified:
- 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have
been merged into one preamble file called
'tex/src/preamble-maneage-default-style.tex'. This helps a lot in
simply removing it when you use a journal style file for example.
- Things like the options to highlight parts of the text are now put in
a special 'tex/src/preamble-maneage.tex'. This helps highlight that
these are Maneage-specific features that are independent of the style
used in the paper.
- There is a new 'tex/src/preamble-project.tex' that is the place you
can add your project-specific customizations.
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Until now, the core Maneage branch included some configuration files for
Gnuastro's programs. This was actually a remnant of the distant past when
Maneage didn't actually build its own software and we had to rely on the
host's software versions. This file contained the configuration files
specific to Gnuastro for this project and also had a feature to avoid
checking the host's own configuration files.
However, we now build all our software ourselves with fixed configuration
files (for the version that is being installed and its version is
stored). So those extra configuration files were just extra and caused
confusion and problems in some scenarios. With this commit, those extra
files are now removed.
Also, two small issues are also addressed in parallel with this commit:
- When running './project make clean', the 'hardware-parameters.tex' macro
file (which is created by './project configure' is not deleted.
- The project title is now written into the default output's PDF's
properties (through 'hypersetup' in 'tex/src/preamble-header.tex')
through the LaTeX macro.
All these issues were found and fixed with the help of Samane Raji.
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Until now, the dataset's configuration names had a 'WFPC2' prefix. But this
very alien to anyone that is not familiar with the history of the Hubble
Space Telescope (the camera is no longer used! Its just used here since its
one of the standard FITS files from the FITS standard webpage).
With this commit the variable names have been modified to be more readable
and clear (having a 'DEMO-' prefix). Also the comments of 'INPUTS.conf'
(describing the purpose of each variable) were edited and made more clear.
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In the previous commit, the modified abstract of the acknowledgments only
included the URL of Maneage, but its more formal to cite the Maneage paper,
the URL is already present in the paper.
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The default 'paper.tex' starts by defining some macros and comments
describing them. Until now, the text was not too clear and could be
confusing for someone that is not at all familiar with Maneage.
With this commit, the comments have been edited to be more clear for a
first-time reader. For example they all start with FULL CAPS
summaries.
Two other small things were corrected in 'tex/src/preamble-necessary.tex':
- Until now 'project.tex' was included in this preamble. However, because
of its importance in Maneage, and prominent place in the demonstration
plot of the paper introducing Maneage, it is now included directly in
'paper.tex'. This also allows users to safely ignore/delete this
preamble file if their LaTeX style is different.
- I noticed that some macros for some astronomical software names from the
very first commits in Maneage were still present here! They are no
longer used, so they have been removed.
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The text of the default paper hadn't been changed for a very long time! In
this time, three papers using Maneage have been published (which can be
very good as an example), Maneage also now has a webpage!
With these commit these examples and the webpage have been added and
generally it was also polished a little to hopefully be more useful.
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Possible semantic conflicts (that may not show up as Git conflicts but may
cause a crash in your project after the merge):
1) The project title (and other basic metadata) should be set in
'reproduce/analysis/conf/metadata.conf'. Please include this file in
your merge (if it is ignored because of '.gitattributes'!).
2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if
you have added all analysis Makefiles to the '.gitattributes' file
(thus not merging any change in them with your branch). For example
with this command:
git diff master...maneage -- reproduce/analysis/make/initialize.mk
3) The old 'verify-txt-no-comments-leading-space' function has been
replaced by 'verify-txt-no-comments-no-space'. The new function will
also remove all white-space characters between the columns (not just
white space characters at the start of the line). Thus the resulting
check won't involve spacing between columns.
A common set of steps are always necessary to prepare a project for
publication. Until now, we would simply look at previous submissions and
try to follow them, but that was prone to errors and could cause
confusion. The internal infrastructure also didn't have some useful
features to make good publication possible. Now that the submission of a
paper fully devoted to the founding criteria of Maneage is complete
(arXiv:2006.03018), it was time to formalize the necessary steps for easier
submission of a project using Maneage and implement some low-level features
that can make things easier.
With this commit a first draft of the publication checklist has been added
to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018
and zenodo.3872248. To help guide users on implementing the good practices
for output datasets, the outputs of the default project shown in the paper
now use the new features). After reading the checklist, please inspect
these.
Some other relevant changes in this commit:
- The publication involves a copy of the necessary software
tarballs. Hence a new target ('dist-software') was also added to
package all the project's software tarballs in one tarball for easy
distribution.
- A new 'dist-lzip' target has been defined for those who want to
distribute an Lzip-compressed tarball.
- The '\includetikz' LaTeX macro now has a second argument to allow
configuring the '\includegraphics' call when the plot should not be
built, but just imported.
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In time, some of the copyright license description had been mistakenly
shortened to two paragraphs instead of the original three that is
recommended in the GPL. With this commit, they are corrected to be exactly
in the same three paragraph format suggested by GPL.
The following files also didn't have a copyright notice, so one was added
for them:
reproduce/software/make/README.md
reproduce/software/bibtex/healpix.tex
reproduce/analysis/config/delete-me-num.conf
reproduce/analysis/config/verify-outputs.conf
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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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Until now, the only verification that the template provided was the
published PDF. Users had to manually compare the published and generated
PDFs (numbers, plots, tables) and see if they obtained the same
result. However, this type of manual verification is not good and is prone
to frustration and missing important differences.
With this commit, a new Makefile has been added in the analysis steps:
`verify.mk'. It provides facilities to easily verify the results that go
into the paper. For example tables that go into making the paper's plots,
or the LaTeX macros that blend into the text. See the updated parts in
`README-hacking.md` for a more complete explanation.
This completes task #15497.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until now, we weren't explicitly asking for BibLaTeX to build the citations
with only initial of the author's given names. Therefore when one BibTeX
entry had a full given name and another had only initials, this would also
be reflected in the paper's bibliography.
With this commit, the `giveninits=true' option is given to BibLaTeX to
always only print the initial character of an author's given name.
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In some cases, users of the template may not need the other template
headers, they may only want `preamble-biblatex.tex'. But `xcolor' needs to
be loaded before being able to load the various colors we use in the
references. So to be self-consistent, it is loaded.
Also, the default style was also printing the month of the publication
which is not common. So a line was added to clear the `month' field before
building the Bibliography.
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Until now, the paper's title and author information were set it
`tex/src/preamble-header.tex'. But they are actually shown in the final PDF
paper and a much better place to keep them is the top-level `paper.tex'.
With this commit, the setting of the title and author names has been moved
to `paper.tex', just after importing all the preambles. However, the basic
package importation and low-level settings are still set in
`tex/src/preamble-header.tex', because they are relatively low-level.
This task was suggested by Deepak (Indian Institute of Astrophysics).
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In the warnings output by LaTeX during the building of a project, I noticed
that `csquotes' is recommended for some features of BibLaTeX (a warning was
printed) so it is added with this commit.
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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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All occurances of "pipeline" have been chanaged to "project" or "template"
withint the text (comments, READMEs, and comments) of the template. The
main template branch is now also named `template'.
This was all because `pipeline' is too generic and couldn't be
distinguished from the base, and customized project.
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Until now, the files where the people were meant to change didn't have a
proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was
wrong because the license does not convey copyright ownership. So the name
of the file's original author must always be included and when people
modify it (and add their own copyright-able modifications).
With this commit, the file's original author (and email) are added to the
copyright notice and when more than one person modified a file, both names
have their individual copyright notice.
Based on this, the description for adding a copyright notice in
`README-hacking.md' has also been modified.
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Until now, there was a single `tex/src/references.tex' file that housed the
BibTex entries for everything (software and non-software).
Since we have started to include the BibTeX entry for more software, it
will be hard to manage the large (sometime unused) BibTeX entries of the
software in the middle of the non-software related citations in the text of
the paper.
Therefore, with this commit, a `tex/dependencies' directory has been made
which has a separate BibTeX entry file for each software that needs
one. After the software is built, this file is copied to the new
`.local/version-info/cite' directory. At the end, the configure script will
concatenate all the files in this directory into one file which will later
be used with `tex/src/references.tex' by BibLaTeX.
This greatly simplifies managing of citations. Allowing us to focus on the
software-building and paper-writing citations separately/cleanly (and thus
be more efficient in both).
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Some recent corrections that were done by Raul are now merged into the
pipeline. There weren't any conflicts.
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Until now, the Scipy citation was only one paper and not the correct one
(it was the online manual).
With this commit, Scipy is properly cited using the two papers. Also
some modifications in the `tex/src/references.tex' have been done
(remove last page number).
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Until now, name and version of all Python packages were indicated in the
final paper, but not the main paper of them (if it exists).
With this commit, some Python packages (Cython, Matplotlib, Numpy and
Scipy) are now properly acknoledged by citating the source paper.
`mpi4py' is also cited although this package is not yet included into
the pipeline.
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With this commit, we are applying the new style of citing software within
the build rule of Gnuastro.
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After doing a systematic search for files without a copyright notice, a few
more were found that didn't have a notice. So a notice was added for them.
I used this Bash command to find the files:
for f in $(find ./ -type f); do \
if [[ $f != *.git* ]]; then \
n=$(grep -i copyright $f | wc -l); \
echo "$n $f"; \
fi; \
done | awk '$1==0'
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In order to be more clear, a copyright statement was added to all the LaTeX
and README files.
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Raul Infante-Sainz added the building of Python (along with the Numpy and
Astropy packages) into the pipeline. That work is now being merged into the
main pipeline branch.
There was only this small problem that needed to be fixed: the Python
tarball's name after unpacking is actually `Python-X.X.X' (with a captial
P), not `python-X.X.X'. This has been corrected with this merge.
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Astropy was added and one very important thing is that we have to
use the pypi tarball (https://pypi.org/) (which is bootstrapped)
and not the github tarball.
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In order to collaborate effectively in the project, even project members
that don't necessarily want (or have the capacity) to do the whole analysis
must be able to contribute to the project. Until now, the users of the
distributed tarball could only modify the text and not the figures (built
with PGFPlots) of the paper.
With this commit, the management of TeX source files in the pipeline was
slightly modified to allow this as cleanly as I could think of now! In
short, the hand-written TeX files are now kept in `tex/src' and for the
pipeline's generated TeX files (in particular the old `tex/pipeline.tex'),
we now have a `tex/pipeline' symbolic-link/directory that points to the
`tex' directory under the build directory.
When packaging the project, `tex/pipeline' will be a full directory with a
copy of all the necessary files. Therefore as far as LaTeX is concerned,
having a build-directory is no longer relevant. Many other small changes
were made to do this job cleanly which will just make this commit message
too long!
Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as
in the standard GNU Build system).
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