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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.
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In a few cases, I had used a signle quote to close `. This would not
display properly on the Gitlab webpage, so they are corrected.
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If the `./for-group' script is not used properly, it can lead to the whole
pipeline being re-run. Therefore it is important to do a sanity check
immediately at the start of Make's processing and inform the user if there
is a problem.
With this commit, `./for-group' exports the `reproducible_paper_for_group'
variable which is used by both the initial `./configure' script, and later
in each call to Make. The `./configure' script will use it to write a value
in `reproduce/config/pipeline/LOCAL.mk' and Make will use it to compare
with the value in `reproduce/config/pipeline/LOCAL.mk'.
If there is an inconsistency, Make will not even attempt to build anything
and will just print a message and abort.
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On large projects, its often necessary to share the build directory between
the various users of the pipeline. To simplify the process a `for-group'
script is now added to the pipeline which is just a wrapper over the
`./configure' and `.local/bin/make' commands to make sure that the group
owner of the outputs and the permission flags are set properly.
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A closing double-quotation was missing in the command to read about
Automatic variables in Make.
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A minor correction was made in the checklist (since we only have one
`foreach' loop in the top-level Makefile) and also the version of Gnuastro
was incremented.
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An extra line regarding the removal of Gnuastro in the checklist was
removed (we don't report the Gnuastro version at the start of the paper any
more).
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To avoid redundant steps in the the top-level Makefile and make it simpler
and easier to follow, we now define the base names of all the Makefiles in
the `makesrc' variable of the top-level Makefile. `makesrc' is then used to
define the Makefiles to include and the necessary TeX macros at the same
time. This is much more clear and obvious than the previous case were we
had to list the Makefiles and TeX macro files separately in the top level
Makefile.
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A step has been added to the checklist to correct the template's input
dataset into the custom dataset necessary for each research.
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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.
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There was an extra line (probably created by Emacs in a wrong command!) in
the end of `README-pipeline.md' that has been removed.
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A spellcheck was run on the two README files.
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A placeholder link is now used in `README.md' to encourage the pipeline
designers to keep a backup of all the dependencies they use.
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Until now, were were advising the users to rename the two README files
after cloning the project. This was because online Git browsers usually
display the `README.md' file, so we wanted the description of the pipeline
to be visible in the pipeline, and later when a project adopts it, they can
have their own `README.md'. But the problem is that any change in
`REAME.md' will later cause conflicts with a project's `README.md'. So we
are now using the same naming convention as the papers that use the
pipeline.
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