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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.
With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.
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Until now, the preparation phase was always executed before the final build
phase when running `./project make'. But when it becomes necessary, project
preparation can be slow and will un-necessarily slow down the project while
the project is growing (focus is on the analysis that is done after
preparation).
With this commit, preparation will be done automatically the first time
that the project is run (`.build/software/preparation-done.mk' doesn't
exist). However, after preperation is complete once, future runs of
`./project make' won't do preparation any more (by calling
`top-prepare.mk'). They will directly call `top-make.mk' for the analysis.
To manually invoke preparation after the first attempt, the `./project
make' script should be run with the new `--prepare-redo' option.
Also, since the preparation phase is now automatically done before the
analysis phase, the long notice that describes running `./project make' at
the end of the preparation phase has been removed in `top-prepare.mk'. It
now just prints a short line, saying the preparation has been complete.
Finally, when the project has not been run with the proper group
configuration, it ends with an `exit 1' so the main `./project' script
doesn't proceed any further.
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Since ImageMagick can take long to build, we are now building it in
parallel. Also, the part where we replace an `_' with `\_' in the software
version at the end of the configure script was removed. It is more
clear/readable that the actual rule that includes such a name deals with
the underline (as is the case for `sip_tpv' which already dealt with it).
Finally, I noticed that the checks at the start of `top-prepare' were
missing new-lines. I had forgot that the Make single-shell variable isn't
activated in this stage yet.
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A special directory is now defined in `initialize.mk' that can be used in
both the preparation and build phases. Also, the contents of prepared
results can now be conditionally read during `./project make'.
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In many real-world scenarios, `./project make' can really benefit from
having some basic information about the data before being run. For example
when quering a server. If we know how many datasets were downloaded and
their general properties, it can greatly optmize the process when we are
designing the solution to be run in `./project make'.
Therefore with this commit, a new phase has been added to the template's
design: `./project prepare'. In the raw template this is empty, because the
simple analysis done in the template doesn't warrant it. But everything is
ready for projects using the template to add preparation phases prior to
the analysis.
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