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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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In the checklist, we are now defining the remote host of the repository at
an early stage. This is because we will need it in the `README.md' file
(which now has a placeholder `XXXXXXX' instead of a valid URL).
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The README file was edited to be more clear and easy to understand. In
particular, it is explained that Git is not necessary for getting the
pipeline.
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Until now, in the instructions, we were suggesting to run
`./.local/bin/make', but the `./' part is extra: this is already a
directory and so the shell will be able to find it. So to make things more
clear and easy to read/write, we removed the `./' part from the calls to
our custom Make installation.
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When you point to this project, the `README.md' file is the default file
that opens on GitLab and other online git repositories. Since a
reproduction pipeline project is different from the actual pipeline, its
best for the default text that opens to describe the paper, not the
pipeline. The old `README.md' is also kept, but its now called
`REAME-pipeline.md'.
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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).
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The two README files have been updated to explain the new feature of
downloading and building dependencies.
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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.
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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.
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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.
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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.
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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).
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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.
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