aboutsummaryrefslogtreecommitdiff
path: root/README-hacking.md
AgeCommit message (Collapse)AuthorLines
2019-07-26Better explanation of suggested commit messages in REAME-hacking.mdMohammad Akhlaghi-19/+25
Until now the description of the commit message guidelines wasn't clear enough and could cause confusion, in particular because it didn't describe why some basic formatting issues are mandatory. With this commit, it is explained that the main reason we require contributors for follow this format is "consistency" within the project. Also generally it was edited to become more elaborate and explain the points more clearly. I also ran a spell check over the whole file and fixed a few typos. This correction was suggested by Mohammad-reza Khellat.
2019-07-07Commit message format tip added to README-hacking.mdMohammad Akhlaghi-0/+16
Until now there was no guideline in `README-hacking.md' to describe/suggest a good format for commit messages. With this commit a point has been added in the "Tips" section to help new developers contribute more smoothly. The necessity of this paragraph was pointed out by Mohammad-reza Khellat.
2019-06-14Minor correction in README-hacking.md for better web-renderingMohammad Akhlaghi-5/+5
The new command-box wasn't being rendered properly, so another correction is made here. I also added the prompt `$' sign in another box of commands.
2019-06-14Minor correction is code demonstration in previous commitMohammad Akhlaghi-1/+2
After checking the previous commit on Gitlab (to see how it is rendered), I noticed that the code has come in the same line, not as a sperate box. Hopefully this commit will fix it.
2019-06-14Software building status check tip added to README-hacking.mdMohammad Akhlaghi-0/+18
It is useful to visually see how the building of software is progressing when running configure. I have been using a simple Bash `while' loop for this, so I added it in the `README-hacking.md' to be useful for others too.
2019-05-21README-hacking.md: corrected typoMohammad Akhlaghi-1/+1
A title in the checklist was mistakenly using "project" (customized template) instead of "template".
2019-05-02Updated to TeXLive 2019Mohammad Akhlaghi-0/+10
Since we just download the binary source of TeXLive, we need to keep it up to date with the server. So it has been incremented to 2019 (TeXLive 2019 was released April 29th). A note was also added in the Checklist to keep the users informed on how to update TeXLive if necessary.
2019-04-22High-level software now specified in TARGETS.mkMohammad Akhlaghi-26/+18
Until now, to specify which high-level software you want the project to contain, it was necessary to go into the `high-level.mk' Makefile that is complicated and can create bugs. With this commit, a new `reproduce/software/config/installation/TARGETS.mk' file has been created that is easily/cleanly in charge of documenting the final high-level software that must be built for the project. Also, until now, FFTW was set as a dependency of Numpy while we couldn't actually get Numpy to use it! It was just there for future reference and to justify its build rule. But now that many software won't be built and there is no problem with having rules even though a project might not use them, it has been removed.
2019-04-15Minor typo corrections in README-hacking.mdMohammad Akhlaghi-3/+7
In two places, I had mistakenly put a <'> instead of a <`>, causing bad highlighting in the markdown rendering. They have been corrected. Also, one long line in was broken up into several.
2019-04-15Correction in customization checklistMohammad Akhlaghi-22/+22
Until now, the customization checklist of `README-hacking.md' had the same name for the base template's remote and branch. This was confusing and would cause Git to print a warning. With this commit, like before, the template's remote is now called `template-origin', and `template' is only the branch name.
2019-04-15Template's main branch is now masterMohammad Akhlaghi-25/+44
Until now, the main template branch was called `template'. However, the standard Git convention is that the main branch of a project be called `master'. Many systems rely on this default and it is also easier for new users (who have been accustomed to this convention). So with this commit, the main template branch is `master', but in `README-hacking.mk', we instruct the users on how to rename it to `template' as part of their customization. This is infact better, because when we are actually developing the template in a separate fork, we can refer/use the `master' branch like any other project. And when we are working on a project that uses this template, we will be referring to the main template branch as `template'.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-125/+133
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).
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-242/+238
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.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-20/+23
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.
2019-04-11.file-metadata also given a copyright in top READMEMohammad Akhlaghi-16/+16
Since `.file-metadata' is a binary file and we couldn't put a copyright notice within it, it has been mentioned in `README.md' to have the same copyright. Also, the copyright modification step in `README-hacking.md' was brought to a later step to be more clear that it should always be done (on new files or files that are changed).
2019-04-07Copyright notice added to all files missing oneMohammad Akhlaghi-10/+12
Until now, for short files, we only had a license notice, not an actual copyright notice. With this commit, a copyright notice has also been added. We use this new command to find these files, suggested by `ineiev@gnu.org'.
2019-04-04Better option-reading in configure, using .build to access BDIRMohammad Akhlaghi-76/+70
Until now, the steps to manage the command-line options of the configure script were limited (couldn't accept an equal sign or space between the option name and value). With this commit, it can now also accept optional equal signs between the option name and value. Thus not causing many confusions. Also, it is more logically consistent for the link to the build-directory to be placed in the top directory (as a hidden file like `.local' until now), and not as a visible directory like `reproduce/build' (which we used until now). Therefore, with this commit, the link to easily access the build-directory is `.build' in the top source directory. Finally, because `minmapsize' is too specific to Gnuastro and has now been given its default value at the start of the configure script, the description for `minmapsize' has been removed (to not confuse users who don't use Gnuastro). If anyone is familiar enough with Gnuastro to change it, they already know it from its book.
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-0/+25
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-03-01Elaboration in README-hacking.mk's future improvements sectionMohammad Akhlaghi-30/+43
This section was a little outdated and since then, a more clear/exact image of using the Nix experience for the reproducible paper template has been added.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-17/+10
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).
2019-02-01Group name is now part of the local configurationMohammad Akhlaghi-21/+13
Until now, the group name to build the project actually went into the Git source of the project! This doesn't allow exact reproducibility on different machines (where the group name may be different). With this commit, the `for-group' script has been modified to accept the group name as its first argument and pass that onto `configure' and Make. This is much better now, because not only the existance of a group installation is checked, but also the name of the group. It also made things simpler (in particular in `LOCAL.mk.in').
2019-01-23New note to checklist for including pipeline-origin in new cloneMohammad Akhlaghi-0/+16
I needed to take these steps in a few occasions on a project I am building over this pipeline. This will commonly happen when a team starts using this pipeline, so it was added to make things easier.
2019-01-23README-pipeline.md is now called README-hacking.mdMohammad Akhlaghi-0/+999
To be more generic and recognizable, the `README-pipeline.md' script was renamed to `README-hacking.md'. In essence, it is just that: to hack the existing pipeline for your own project. We follow a similar naming convention in many GNU software.