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2018-11-21Fetching pipeline updates explained in README.md checklistMohammad Akhlaghi-7/+26
Since working on the pipeline will evolve along with the projects that use it, it can be useful for projects to fetch updates in the pipeline. So the checklist in `README.md' updated to explain how to do this cleanly.
2018-11-21Updated description of Make in README.mdMohammad Akhlaghi-7/+13
Until now, because we didn't build the dependencies internally, it was important for the pipeline to be usable with any version of Make. But because of the new installation of dependencies (including GNU Make), that is no longer the case. So we can safely use GNU Make and this needs to be mentioned in `README.md'.
2018-11-20GNU Coreutils now built in basic dependenciesMohammad Akhlaghi-4/+6
GNU Coreutils are basic programs that can help in the configuration of higher-level programs. Because of that, it was a dependency of almost all software built in `dependencies.mk'. To make things more clear, easier to read and faster (when building in parallel), the building of Coreutils is now moved to the `dependencies-basic.mk' rules. There, it is built along-side Bash. Since `dependenceis-basic.mk' is run and completed before `dependencies.mk', with this, we can be sure that Coreutils is present by the time we want to build the higher-level programs. Also, Zlib is now added as a dependency of Git also (it is necessary for its build).
2018-11-19Minor corrections for easy applying of checklistMohammad Akhlaghi-26/+30
After going through the checklist for starting a new project based on the pipeline, I noticed some parts that could be modified to be more clear. They are now applied.
2018-11-19Gzip's tarball in tar.gz instead of tar.lzMohammad Akhlaghi-25/+38
Until now, we were using a customized `tar.lz' tarball for Gzip. But on systems that don't have GNU Tar, this will cause a problem (non-GNU Tar doesn't recognize `.tar.lz'). So to keep things simple, we are using the customized gzip in `tar.gz' format. After the internal build of GNU Tar and Lzip, the default method of unpacking (`tar xf XXXXX.tar.XX') will work nicely on all the standard compression algorithms and we don't have to modify our commands based on the algorithm (nice feature of GNU Tar).
2018-11-18Updated README and README.md for new dependency building featuresMohammad Akhlaghi-3/+12
The two README files have been updated to explain the new feature of downloading and building dependencies.
2018-11-14All used software with versions, acknowledgedMohammad Akhlaghi-3/+4
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.
2018-11-13Version of programs checked on each run of pipelineMohammad Akhlaghi-9/+3
The version of all programs is now checked in `reproduce/make/src/initialize.mk' and the pipeline won't complete if any of the program versions change from those listed in `reproduce/config/pipeline/dependency-versions.mk'. Since the pipeline is systematically checking all program versions, we don't need Gnuastro's `--onlyversion' option any more. So it (and all references to it) have been removed.
2018-11-12Dependencies built at the start of the pipelineMohammad Akhlaghi-157/+161
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.
2018-08-24Minor editsMohammad Akhlaghi-10/+13
After a full trial of the checklist, some further minor edits were made to make it more clear.
2018-08-24Minor corrections in README.mdMohammad Akhlaghi-7/+7
Some minor changes were made to be more clear.
2018-08-24Minor edits in README.mdMohammad Akhlaghi-11/+18
A few minor points were corrected in README.md.
2018-08-24Step to check pipeline added in README.md checklistMohammad Akhlaghi-4/+21
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.
2018-08-24Checklist modified to keep pipeline historyMohammad Akhlaghi-34/+55
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).
2018-08-11Emphasized correcting name in copyright notice in checklistMohammad Akhlaghi-1/+2
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.
2018-08-11Minor edits in README.md after some testsMohammad Akhlaghi-21/+7
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.
2018-08-11Single quote corrected in README.mdMohammad Akhlaghi-1/+1
In the previous commit, ` was mistakenly written as '. This was only noticed after pushing and rendering the Markup on the webpage.
2018-08-11Minor edit in README.mdMohammad Akhlaghi-3/+4
A minor edit was made in the copyright correction part of the checklist.
2018-08-11Corrected copyright notice correction description in checklistMohammad Akhlaghi-5/+11
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.
2018-08-11Problem with tabs in .mk file corrected in dir-locals.elMohammad Akhlaghi-3/+2
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.
2018-03-14Some further minor edits to new parts of README.mdMohammad Akhlaghi-14/+16
Going through the text, some further minor edits were made.
2018-03-14Minor edits in README.mdMohammad Akhlaghi-6/+9
Some minor edits to the newly added parts of `README.md'.
2018-03-14Added future plans (and Nix/Guix usage) in README.mdMohammad Akhlaghi-4/+51
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.
2018-03-13Updated link to slidesMohammad Akhlaghi-1/+1
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.
2018-03-09Corrected name to new repository addressMohammad Akhlaghi-3/+3
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.
2018-03-09Minor edits in README.mdMohammad Akhlaghi-5/+6
Some minor corrections were made regarding the output repository.
2018-03-09Minor typo corrected in link in README.mdMohammad Akhlaghi-2/+2
The markup for the link to the final PDF in the `README.md' file was mistakenly written and is now corrected.
2018-03-09Added description of output templateMohammad Akhlaghi-10/+15
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'.
2018-03-09Added tip for pipeline outputsMohammad Akhlaghi-3/+22
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.
2018-03-04Edits in README.mdMohammad Akhlaghi-10/+9
Some futher edits were made to the paragraph describing the contents of `README.md' for a smoother reading.
2018-03-04Minor correction in README.mdMohammad Akhlaghi-7/+8
After the last commit, another minor correction is implemeneted to further simplify the reading.
2018-03-04Minor edits in README.mdMohammad Akhlaghi-51/+70
I reviewed the first few sections of `README.md' and made some small corrections to make it easier to understand/read.
2018-03-02Small edit in README.mdMohammad Akhlaghi-2/+1
A small edit was made at the start of `README.md' to make it easier to read.
2018-02-28Header for pages, new font and author managementMohammad Akhlaghi-2/+5
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.
2018-02-27Minor edits in README.mdMohammad Akhlaghi-4/+4
A few minor corrections were made in `README.md'.
2018-02-27Default PDF now uses PGFPlots and BibLaTeXMohammad Akhlaghi-16/+106
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-4/+13
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'.
2018-02-26Typo corrected and minor edit in README.mdMohammad Akhlaghi-8/+8
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.
2018-02-20Added link to slides on this conceptMohammad Akhlaghi-1/+3
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.
2018-02-20Minor edits in design summary of README.mdMohammad Akhlaghi-11/+12
The points were made more clear.
2018-02-20Minor corrections and edits made in README.mdMohammad Akhlaghi-47/+92
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.
2018-02-20Pipeline architecture described in README.mdMohammad Akhlaghi-3/+108
`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.
2018-02-20Necessary programs checked at configure timeMohammad Akhlaghi-7/+31
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.
2018-02-19Minor edits in README.mdMohammad Akhlaghi-9/+18
A few other minor corrections were applied to the text to be more clear.
2018-02-19Minor edits in README.mdMohammad Akhlaghi-10/+12
Some minor edits and a spellcheck were made in the text to make it easier to understand/read.
2018-02-19Added tips section on version control with taggingMohammad Akhlaghi-8/+37
In the "Tips" section of `README.md', a section on version control was added and a first tip regarding tags was added to guide (new) users on how to effectively define and use tags. As a result, in the checklist, adding a `v0' tag is now also suggested. Some minor typos were also fixed.
2018-02-15Gnuastro's memory mapping is now a local variableMohammad Akhlaghi-8/+14
As described in the commens above `MINMAPSIZE' of `LOCAL.mk.in', the amount of memory to map to HDD/SSD or keep in RAM is a local issue and not relevant to the pipeline's results. So it is now defined in a `gnuastro-local.conf' file. To keep the Makefiles clean, this file is created by the `./configure' script. To do this cleanly, the `./configure' script was also almost fully re-written with better functionality now.
2018-02-14Sanity checks added, local settings now in LOCAL.mk.inMohammad Akhlaghi-18/+18
The choice of whether or not to make a PDF is now also a local system issue, not a general pipeline issue. So it has been put in the new `LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local settings (things that when changed should not be version-controlled) should be defined in this file. A sanity check was added to find if `./configure' has been run before `make' or not (using the `LOCAL.mk' file which is an output of the configuration step). If `LOCAL.mk' doesn't exist, an error will be printed informing the user that `./configure' needs to be run first. The configure script also provides more clear and hopefully better information on its purpose and what must be done. Since `make clean', it is executed even when `./configure' hasn't been run, it will only delete the build directory and its contents when local configuration has been done. A `distclean' target was also added which will first "clean" the pipeline, then delete the `LOCAL.mk.in' file. To allow rules like `make' to be run even if `BDIR' isn't defined (`./configure' hasn't been run yet), a fake `BDIR' is defined in such cases.
2018-02-10Minor typo corrections in README.mdMohammad Akhlaghi-21/+22
While going over parts of the text, some minor typos were found and corrected.
2018-02-10Corrected tips title to be more clearMohammad Akhlaghi-6/+6
The title "Tips on using the pipeline" was a little generic and could be confused with people who want to reproduce the result, not the designers of the pipeline. So it was changed to "Tips on expanding this template (designing your pipeline)". Some minor edits were also made to its first paragraph.