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2018-11-25More generic naming conventionMohammad Akhlaghi-2/+2
Until now, we were keeping the input file within the reproduction pipeline's directories using the same name as the database/server. Now, we are using a short/summarized filename convention for the input dataset.
2018-11-25Pipeline now downloads and uses an input datasetMohammad Akhlaghi-0/+34
In most analysis situations (except for simulations), an input dataset is necessary, but that part of the pipeline was just left out and a general `SURVEY' variable was set and never used. So with this commit, we actually use a sample FITS file from the FITS standard webpage, show it (as well as its histogram) and do some basic calculations on it. This preparation of the input datasets is done in a generic way to enable easy addition of more datasets if necessary.
2018-11-18Pipeline also installs TeX live and necessary packagesMohammad Akhlaghi-1/+0
Since the final product of the pipeline is a LaTeX-created PDF file, it was necessary to also have LaTeX within the pipeline. With this commit, TeX Live is also built as part of the configuration and all the necessary packages to build the PDF are also installed and mentioned in the paper along with their versions.
2018-11-15Minor corrections in paper's textMohammad Akhlaghi-1/+1
Some minor corrections have been made in the paper's text to make things easier to read and be more formal.
2018-11-14All used software with versions, acknowledgedMohammad Akhlaghi-0/+1
All the used software are now acknowledged in the template paper along with their versions. This section is also mentioned in the check list, so users don't delete it by mistake.
2018-08-11Not using random distribution in demonstration plotMohammad Akhlaghi-2/+2
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.
2018-02-28Header for pages, new font and author managementMohammad Akhlaghi-23/+95
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.
2018-02-27Abstract added to final PDF along with better explanationMohammad Akhlaghi-1/+34
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.
2018-02-27Multicol package no longer used for two column PDFMohammad Akhlaghi-16/+0
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.
2018-02-27Better comments on TeX preamblesMohammad Akhlaghi-13/+44
The comments in the preambles were made more clear and elaborate.
2018-02-27Default PDF now uses PGFPlots and BibLaTeXMohammad Akhlaghi-2/+68
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.
2018-02-27Copyrights and TeX management made more clearMohammad Akhlaghi-15/+92
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'.
2018-02-08Adding title and description also mentioned in README.mdMohammad Akhlaghi-8/+8
The first commit didn't have an explanation on correcting the title of the project in the final PDF or the top-level Makefile, so a pointer was added to the list. Also, some extra dependencies were removed from `README' and its paragraphs were scaled to the new width of 75 characters that is defined in `.dir-locals.el' (for Emacs settings, taken from Gnuastro).
2018-02-07First commit to the reproduction pipeline templateMohammad Akhlaghi-0/+313
Let's start working on this pipeline independently with this first commit. It is based on my previous experiences, but I had never made a skeleton of a pipeline before, it was always within a working analysis. But now that the pipeline has a separate repository for its self, we will be able to work on it and use it as a base for future work and modify it to make it even better. Hopefully in time (and with the help of others), it will grow and become much more robust and useful.