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During the configuration step several new programs that were necessary for
a more complete controlled environment are now also downloaded and built
statically.
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The host web address of most of the necessary packages was blank (filled
with `WWWWWWWWWWWWWWWW' as a place holder). They now point to the correct
webpages.
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To enable easy/proper reproduction of results, all the high-level
dependencies are now built within the pipeline and installed in a fixed
directory that is added to the PATH of the Makefile. This includes GNU Bash
and GNU Make, which are then used to run the pipeline.
The `./configure' script will first build Bash and Make within itself, then
it will build
All the dependencies are also built to be static. So after they are built,
changing of the system's low-level libraries (like C library) won't change
the tarballs.
Currently the C library and C compiler aren't built within the pipeline,
but we'll hopefully add them to the build process also.
With this change, we now have full control of the shell and Make that will
be used in the pipeline, so we can safely remove some of the generalities
we had before.
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After a full trial of the checklist, some further minor edits were made to
make it more clear.
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Some minor changes were made to be more clear.
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A few minor points were corrected in README.md.
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A step was added close to the top of the checklist to remind people to
check the pipeline before making any changes. Also, the `--origin' option
was removed from the `git clone' command into a separate command to rename
the origin branch. This helps in readability.
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Until now, in the check list of `README.md', we were recommending to delete
the history of the pipeline and start your own history from that. But this
disables users of the pipeline to keep it up to date with new features that
are added to it.
With this commit, the main branch is now called `pipeline' (to allow users
to use `master' for their own research) and in the clone command, the
pipeline's remote is now called `pipeline-origin' (to allow the user to use
`origin' for their own remote).
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While trying the checklist, I noticed that I had forgot to add my name
after the copyright year and that `reproduce/src/make/paper.mk' still had
my own name on it, the copyright notice also said `script' instead of
`Makefile' which is now corrected.
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While testing the reproduction pipeline on a small project, I noticed some
parts of the checklist that were either repetative or needed to be
corrected. This is done with this commit.
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We had previously started the `configure' script with `/bin/bash'. But this
script is meant to check for Bash inside of it. So to be run-able (on a
system which may not have Bash), the `configure' script has to be run by
`/bin/sh'.
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In the previous commit, ` was mistakenly written as '. This was only
noticed after pushing and rendering the Markup on the webpage.
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A minor edit was made in the copyright correction part of the checklist.
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To be more generic (and avoid listing file names in `README.md'), a command
is now used to find the files where the name has to be added to the
copyright notice. Also, I noticed that `reproduce/src/make/paper.mk' lacked
a placeholder name/email, so one was added.
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To be more easy to read/understand, the comments in `.dir-locals.el' were
edited and made a little more elaborate.
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Previously we had tried to corrected the problem that `.mk' files use space
instead of TAB by setting them to be read into makefile-mode at the
start. However, for some reason, this caused a problem in reading the
maximum line length (the value of 75 wasn't read by Emacs).
So after some playing around, I found out that the problem is that the
`nil' setting (for all other files) must be defined in the end, not the
start of the basic settings and this solved this problem.
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Different implementations of AWK may use different random number
generators, so even setting the seed will not ensure a reproducible
result. Because of this, the random plot may be different when the
pipeline runs on different systems and this can confuse early users
(its contrary to the exact reproducibility that is the whole purpose
of this pipeline).
The plot is just a simple X^2 plot, showing the squared value of the X
axis on the Y axis. It is very simple, but atleast it will be
identical on all systems. Also, there may be too many complicated
things in the pipeline already for an early user, and its just a
demonstration, so the easier/simpler, the better.
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While we had set the default Makefile SHELL to be bash, we weren't
actually checking if `bash' is available on the system. With this
commit, it is also checked at configure time.
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On some systems, the default shell `/bin/sh' doesn't point to Bash and
this can cause problems and failures when the designer uses its
features. Bash (and its extra features) make things very easy and it
is very ubiquitous, so it is safe to assume users will have it.
This problem was reported by Alejandro Serrano Borlaff.
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Since version 26.1, apparently Emacs doesn't tream `.mk' files in
Makefile-mode. So thanks to Mosè Giordano, a line was added in the
`.dir-locals.el' file so we can be sure they are always treated as
Makefiles and make things more convenient for Emacs users.
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Going through the text, some further minor edits were made.
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Some minor edits to the newly added parts of `README.md'.
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A section was added to `README.md' for describing possible future steps
that we can take to make this pipeline even more robust. In it, I added a
first interesting thing that I think would be really exciting to add, but I
don't have time to do now.
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The link to the slides describing the context was the old address (which
still works, but is just a symbolic link to the new address). It was thus
corrected to point to the proper filename.
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The main online repository name has been changed to `reproducible-paper'
from `reproduction-pipeline-template'. So the cloning command in
`README.md' had to be corrected.
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Some minor corrections were made regarding the output repository.
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The markup for the link to the final PDF in the `README.md' file was
mistakenly written and is now corrected.
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A template was made to keep the output of this pipeline as a demonstration
and it is now added to the description in `README.md'.
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While doing my own project (which has grown to a processing time of about
half an hour), I felt that it would be very convenient to a record of the
outputs at major points also. But we don't want to bloat the pipeline by
commiting PDF files or large datasets that get fully changed and are just
by-products. So it occurred to me to have a separate pipeline only for
outputs and after trying it out, it indeed seemds to be a good solution.
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Some futher edits were made to the paragraph describing the contents of
`README.md' for a smoother reading.
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After the last commit, another minor correction is implemeneted to further
simplify the reading.
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I reviewed the first few sections of `README.md' and made some small
corrections to make it easier to understand/read.
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A small edit was made at the start of `README.md' to make it easier to
read.
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The old comments could be a little confusing, so they are now more clear
and describe where to look for how this variable is used.
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The computer modern font that was designed by Donald Knuth and is the
default of LaTeX is indeed a very good, elegant and nice font in
print. However, most journals choose the roman fonts and thus the computer
modern font doesn't (subjectively) fit into the journal format nicely. So
the default font of this pipeline's paper now uses LaTeX's `newtx' package
for a roman style font.
Also, a set of preamble settings were added to allow headers in the pages
of the paper to make the result resemble more like a journal paper
(familiar to the eye), while also adding important information. A new
header was made for this job. This new header now also contains the title
and author settings (after all, these are also a type of header).
Finally, the LaTeX `authblk' package was used to organize authors and their
affiliations.
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An abstract is also something most research reports will need, so a simple
macro was defined to make it easy (not too many code lines within the text
of the main body) to implement an abstract.
The title was also moved up a little to better use the extra white space at
the top of the page.
Finally, the `\highlightchanges' along with its explanation (both as
comments and within the text with examples) was added in `paper.tex' to
demonstrate how useful the `\new' and `\tonote' macros are.
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Until now, we were using the `multicol' package which is mainly designed
for more than two columns. Instead, we are just passing a `twocolumn'
option to the article document class.
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A few minor corrections were made in `README.md'.
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The comments needed to be corrected to fit and explain the new logic (LaTeX
being run within another directory).
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The comments in the preambles were made more clear and elaborate.
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Having a look at the TeX source, some minor edits were made to the comments
so it is more clear.
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Making plots and including references are integral parts of a scientific
paper. Therefore to demonstrate how cleanly they can be used within the
pipeline, they are now used to produce the final PDF.
To use PGFPlots a random dataset is made (using AWK's random function) and
is plotted using PGFPlots. The minimum and maximum values of the dataset
are also included in the text to further show how such calculations can go
into the macros and text.
For the references, the NoiseChisel paper was added as a reference to cite
when using this pipeline along with the MUSE UDF paper I, which uses this
pipeline for two sections. Following this discussion, citation is also
discussed in `README.md` and the NoiseChisel paper is also added as a
published work with a reproduction pipeline.
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Until now, the copyright statement was left empty for the users of the
pipeline to fill. However, the files have already been created and have an
author (or contributing authors) before the user starts using the
pipeline. So the original authors of the files are added along with the
year. The user can add their own name to the existing files under the
"Contributing author" when they start and they will be the "Original
author" of the new files they create.
Several changes were also made to the TeX management:
- LaTeX is run within a `reproduce/build/tex/build' directory now. Not in
the top reproduction pipeline directory. This helps keep all the
auxiliary TeX files and directories in that directory and keep the top
reproduction pipeline directory clean. After the final PDF is built, a
copy is put in the top reproduction pipeline directory for easy viewing.
- The PGFPlots preamble was also made more useful, allowing the name of
the `.tex' file to also be the name of the final plot that is
produced. This is a GREAT feature, because without it, the TiKZ
externalization would be based on order of the plots within the
paper. But now, order is irrelevant and we can even delete the TiKZ
files within the processing workhorse-Makefiles so the plots are
definitly rebuilt on the next run.
- The paper is now in a two-column format to be more similar to published
papers.
A tip on debugging Make was added to `README.md'.
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A typo (" ... followed b checklist ...") was found and corrected in
`README.md'. Also, after re-reading the paragraph, it was made slightly
more clear with some minor edits in the text.
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I had made some slides for a talk here at Lyon Observatory a little over a
week ago and I thought it may be useful to add them in the `README.md' file
to help demonstrate the general concept before having to read such long
texts.
Later, we should be adding some figures to this `README.md' file to make it
more easier to understand.
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The points were made more clear.
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The published works using the pipeline now have a separate section for them
selves in the introduction and some of the explanation was made more clear.
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`README.md' didn't contain a general description of the pipeline's design
architecture. So a few paragraphs have been added to help someone new to it
to understand it better.
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The mandatory and optional (for example downloader) dependencies are now
checked at configure time so users can know what they may be missing before
the processing starts. Since its recommended to be run in parallel, it can
be hard to find what you are missing after running the pipeline. As part of
these checks, the program to use for downloading is now also set at
configure time, it is only used as a pre-defined (in `LOCAL.mk') variable
during Make's processing.
A small title was also added to discus the pipeline architecture that will
be filled in the next commit.
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A few other minor corrections were applied to the text to be more clear.
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