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2018-02-15Ignoring .nfs* files from GitMohammad Akhlaghi-0/+1
On some servers, `.nfs*' files are also created during the processing, so to keep the Git repo clean (avoid an un-necessary `-dirty' prefix), we are adding these files to the `.gitignore'.
2018-02-15Backup file ending with ~ is also deleted in configureMohammad Akhlaghi-2/+3
Some editors put a copy of their input file into another file ending with `~' (for backup). So now, the `./configure' script also cleans this file along with the temporary file.
2018-02-15Wildcard for mmap files made more genericMohammad Akhlaghi-1/+1
In some systems, the fact that `.gnuastro' and `reproduce/config/gnuastro' are the same is not recognized by Git in `.gitignore' and so the `mmap' files will be treated as un-commit files. So we now simply ignore all files starting with `mmap_*' and removed the directory information before it.
2018-02-15Configure script starts with bin/bash shebangMohammad Akhlaghi-1/+8
While trying the pipeline on a remote server (which runs on Debian), the configure script had an `Syntax error: "(" unexpected' error. This is caused by the fact that in the Debian world (and its derivate OSs), the default shell is not Bash but Dash which has much fewer features for fast loading. It was thus necessary to start the configure script explicity with the `/bin/bash' shebang.
2018-02-15Minor typo corrections in Gnuastro's config fileMohammad Akhlaghi-2/+2
Two minor typo corrections in the comments were made in Gnuastro's configuration file to make it more clear.
2018-02-15Gnuastro's memory mapping is now a local variableMohammad Akhlaghi-72/+180
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.
2018-02-15Choice to build final PDF removed from LOCAL settingsMohammad Akhlaghi-27/+22
The previous change where we had set the building of the PDF as a local (and thus not version controlled) setting was not good, because different commits might be made without the high-level preparations for the final PDF (especially during the initial/testing phases of a research). Therefore, if the runner of the pipeline is ignorant to this, they may hit some errors in LaTeX which can be frustrating. To have a clean reproduction, it is thus necessary to have the choice of pdf-building under version control along with the rest of the pipeline.
2018-02-14clean-mmap now a dependency of cleanMohammad Akhlaghi-2/+2
Until now, Gnuastro's `mmap' files were included in the `rm' commands of `clean*' rules two times. But by setting `clean-mmap' as a dependency of `clean', it is now only necessary to have them in the Makefile once. This also makes the code much more cleaner.
2018-02-14Some extra space in alert when no PDF is createdMohammad Akhlaghi-0/+2
To help view that everything is OK and that there were no errors, an extra blank line followed by one with `----' is added to the notice when we won't be making a PDF. These two lines help the eye more clearly see everything is fine (given that above it, there are MANY commands and outputs).
2018-02-14Symbolic link to build directory now permanently addedMohammad Akhlaghi-46/+32
Managing this symbolic link as a prerequisite that may or maynot be defined just made the code too dirty. It is almost always needed, so it is now a super-high-level prerequisite (first dependency of the `all' target, even before the final PDF). In this way, we can be sure it is always built and that nothing else depends on it. If the user doesn't want it, they can simply remove it from the top `Makefile'.
2018-02-14Sanity checks added, local settings now in LOCAL.mk.inMohammad Akhlaghi-78/+135
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.
2018-02-08Minor typos corrected in README.mdMohammad Akhlaghi-70/+75
Some minor typos were found and corrected. In other cases, the text was slightly edited to be more clear.
2018-02-08Initialization results now a .PHONY targetMohammad Akhlaghi-6/+10
Recently the filename keeping TeX macros for the versions was changed from `versions.tex' to `initialization.tex' (since it also contained the build directory). However, it was forgotten to correct the change of name in the `.PHONY' targets, so it was not being rebuilt every time. This is corrected now.
2018-02-08Instructions to delete README.md before startingMohammad Akhlaghi-0/+5
`README.md' is for this pipeline, not the research project that is using it. Therefore it might be confused with the `README' that is devoted to the research project. So in the checklist, a point was added to delete this file before making the first new commit.
2018-02-08Usage of configure command added to READMEMohammad Akhlaghi-10/+5
The README file didn't match the current way to set the top-level directories (through `./configure'), it was still the old-fashioned way of manually finding and opening the file. The explanation is now corrected.
2018-02-08Basic titles now corrected after copyright in README.mdMohammad Akhlaghi-18/+16
The basic title, short description and author section of the checklist was moved immediately after copyright because it is more related to it. The description of Gnuastro is now before `README' because the user will confront Gnuastro in `README' and this will provide a good introduction on what to do with it.
2018-02-08Moved creation of a new Git repo to the end of the checklistMohammad Akhlaghi-23/+30
The creation of a new Git repo is now moved to the end of the checklist. It was not in place as the third step before. Now, the user makes all the standard changes and just before they start going into the details of their research, they define their new repository.
2018-02-08Minor edits in README.mdMohammad Akhlaghi-4/+7
The description of adding a title and authors was made slightly more clear.
2018-02-08Adding title and description also mentioned in README.mdMohammad Akhlaghi-77/+69
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/+1465
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.