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Some minor conflicts (all expected from the commit messages in the Maneage
branch) occurred but were easily fixed.
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Summary:
- Use the new name of this variable in your Makefiles.
- In 'metadata.conf', remove fixed URL prefixes for DOIs
('https://doi.org/') or arXiv ('https://arxiv.org/abs').
Until now, the Make variable that would print the general metadata (of
whole project) into each to-be-published dataset was called
'print-copyright'! But it now does much more than simply printing the
copyright, it will also print a lot of metadata like arXiv ID, Zenodo DOI
and etc into plain-text outputs. The out-dated name could thus be
misleading and cause confusions.
With this commit, the variable is therefore called
'print-general-metadata'. After merging your project with the Maneage
branch, please replace any usage of 'print-copyright' to
'print-general-metadata'.
Also with this commit, 'README-hacking.md' mentions 'metadata.conf' and
'print-general-metadata' in the "Publication checklist" section and reminds
you to keep the first up to date, and use the second in your
to-be-published datasets.
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In the project's 'metadata.conf', we also have an option to store the
journal DOI of the project (that will later be printed in the output file
products). So now that the paper's DOI has been set by the journal, it was
time to add it in the project too.
While looking at the usage of the metadata, I noticed that the "Publication
checklist" of 'README-hacking.md' didn't talk about it. In fact, the part
about putting metadata went into a lot of detail without even mentioning
the generic 'print-general-metadata' variable (previously called
'print-copyright') that is created in 'initialize.mk'. So I removed those
extra points and just recommended using this variable for plain-text files
and putting similar info in other formats.
Some other minor changes were made:
- The metadata now doesn't need the fixed 'https://doi.org/' prefix (to
make it consistent with the arXiv identifier). Inside 'initialize.mk',
there are now two variables called 'doi-prefix-url' and
'arxiv-prefix-url' that contain the fixed prefix.
- The 'print-copyright' name was clearly outdated for all the extra
metadata that this variable created (including the copyright). So its
name was changed to 'print-general-metadata'.
The generic Maneage changes will be taken into Maneage after this (they
were tested here).
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In the previous commit, some Gnuastro-specific initializations were
removed but a few more cases remained that are removed with this
commit.
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Until now, important LaTeX packages like 'caption' (for managing figure
captions), 'hyperref' (for managing links) and 'xcolor' (for managing
colors) were being loaded inside the optional
'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove
this file from loading when you use custom journal sytels. However, these
packages will often be necessary after loading special journal styles also.
With this commit, these packages are now loaded into LaTeX as part of the
'tex/src/preamble-project.tex' file. This file is in charge of LaTeX
settings that are custom to the project and independent of its style.
Several other small corrections are made with this commit:
- I noticed that './project make texclean' crashes if no PDF exists in the
working directory! So a '-f' was added to the 'rm' command of the
'texclean' rule.
- As part of the LaTeX Hyperref, we can set general metadata or properties
for the PDF (that aren't written into the printable PDF, but into the
file metadata). They can be viewed in many PDF viewers as PDF
properties. Until now, we were only using the '\projecttitle' macro here
to write the paper's title. However, thanks to the recently added
'reproduce/analysis/config/metadata.conf', we now have a lot of useful
information that can also go here. So the 'metadata-copyright-owner' is
now used to define the PDF author, and the project's
'metadata-git-repository' and commit hash are written into the PDF
subject. But to import these, it was necessary to define them as LaTeX
macros, hence the addition of these macros in 'initialize.mk'.
- Some extra packages that aren't necessary to build the default PDF were
removed in 'preamble-project.tex'.
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Until now, when you ran './project make dist', first it would delete the
temporary files (like files ending in '~' or '.swp' created by some
editors), then it had a place to add project-specific operations for the
distribution.
However, in the process of cleaning the temporary files, it would 'cd' into
the directory that would later be packaged. So project-specific operations
would first have to 'cd' back into the top source directory. This was prone
to hard-to-find bugs.
With this commit, to avoid the problem the project-specific operations are
now placed before the cleaning phase. This is also technically good because
in the project-specific operations there may also be temporary files that
shouldn't go into the distribution tarball.
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There was a single conflict in the comments of one part of 'configure.sh'
that has been fixed.
There was also a single place that needed to convert 'BDIR' to 'badir' in
this project (so after the merge, it also built easily).
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Until now, the build directory contained a 'software/' directory (that
hosted all the built software), a 'tex/' subdirectory for the final
building of the paper, and many other directories containing
intermediate/final data of the specific project. But this mixing of built
software and data is against our modularity and minimal complexity
principles: built software and built data are separate things and keeping
them separate will enable many optimizations.
With this commit, the build directory of the core Maneage branch will only
contain two sub-directories: 'software/' and 'analysis/'. The 'software/'
directory has the same contents as before and is not touched in this
commit. However, the 'analysis/' directory is new and everything created in
the './project make' phase of the project will be created inside of this
directory.
To facilitate easy access to these top-level built directories, two new
variables are defined at the top of 'initialize.mk': 'badir', which is
short for "built-analysis directory" and 'bsdir', which is short for
"built-software directory".
HOW TO IMPLEMENT THIS CHANGE IN YOUR PROJECT. It is easy: simply replace
all occurances of '$(BDIR)' in your project's subMakefiles (except the ones
below) to '$(badir)'. To confirm if everything is fine before building your
project from scratch after merging, you can run the following command to
see where 'BDIR' is used and confirm the only remaning cases.
$ grep -r BDIR reproduce/analysis/*
--> make/verify.mk: innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \
--> make/initialize.mk:badir=$(BDIR)/analysis
--> make/initialize.mk:bsdir=$(BDIR)/software
--> make/initialize.mk: $$sys_rm -rf $(BDIR)
--> make/top-prepare.mk:all: $(BDIR)/software/preparation-done.mk
'BDIR' should only be present in lines of the files above. If you see
'$(BDIR)' used anywhere else, simply change it to '$(badir)'. Ofcourse, if
your project assumes BDIR in other contexts, feel free to keep it, it will
not conflict. If anything un-expected happens, please post a comment on the
link below (you need to be registered on Savannah to post a comment):
https://savannah.nongnu.org/task/?15855
One consequence of this change is that the 'analysis/' subdirectory can be
optionally mounted on a separate partition. The need for this actually came
up for some new users of Maneage in a Docker image. Docker can fix
portability problems on systems that we haven't yet supported (even
Windows!), or had a chance to fix low-level issues on. However, Docker
doesn't have a GUI interface. So to see the built PDF or intermediate data,
it was necessary to copy the built data to the host system after every
change, which is annoying during working on a project. It would also need
two copies of the source: one in the host, one in the container. All these
frustrations can be fixed with this new feature.
To describe this scenario, README.md now has a new section titled "Only
software environment in the Docker image". It explains step-by-step how you
can make a Docker image to only host the built software environment. While
your project's source, software tarballs and 'BDIR/analysis' directories
are on your host operating system. It has been tested before this commit
and works very nicely.
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Since the addition of the appendix bibliography we hadn't checked the 'make
dist' command, as a result the PDF couldn't be built. With this commit, in
the 'dist' rule, we are now also copying 'appendix.bbl' and the created
tarball could build the PDF properly. Also the 'peer-review' directory is
now also included in the tarball created by './project make dist'.
I also found a small typo in the description of Occam (an 'a' was missing)
and fixed it.
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There were only three very small conflicts that have been fixed.
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Until now, the build strategy of the paper was to have a single output PDF
that either contains (1) the full paper with appendices in the same paper
(2) only the main body of the paper with no appencies.
But the editor in chief of CiSE recently recommended publishing the
appendices as supplements that is a separate PDF (on its webpage). So with
this commit, the project can make either (1) a single PDF (containing both
the main body and the appendices) that will be published on arXiv and will
be the default output (this is the same as before). (2) two PDFs: one that
is only the main body of the paper and another that is only the appendices.
Since the appendices will be printed as a PDF in any case now, the old
'--no-appendix' option has been replaced by '--supplement'. Also, the
internal shell/TeX variable 'noappendix' has been renamed to
'separatesupplement'.
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Until now there was only a 'clean' (to delete all files created during the
'make' phase) and the 'distclean' (to delete all files during configuration
and make). But sometimes we don't want to delete all the files created
during the full 'make' phase, we only want to delete the files that were
created by LaTeX for building the paper.
Witht this commit, a new target has been added for this job. You can now
run the following command for this job:
./project make texclean
Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz'
directory under that location is recreated, ready for a future build).
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Having entered 2021, it was necessary to update the copyright years at the
top of the source files. We recommend that you do this for all your
project-specific source files also.
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Until now, there was no warning when the 'maneage' branch didn't exist in
the Git history. This can happen when you forget to push the 'maneage'
branch to a remote for your project, and you later clone your project from
that remote (for example on another computer). We use the 'maneage' branch
to report the latest commit hash and date in the final paper (which can
greatly help future readers). Since we check the 'maneage' branch on every
run of './project make' (in 'initialize.mk') this would result in a printed
statement like this:
fatal: Not a valid object name maneage
Also until now, the description of what to do when TeXLive wasn't installed
properly wasn't complete: it didn't mention that it is necessary to delete
the TeXLive target files. This could confuse users (they would re-run
'./project configure -e', but with no effect).
With this commit, for the 'maneage' branch issue a complete warning will be
printed. Telling the user what to do to get the 'maneage' branch (and thus
fix this warning). Also, the LaTeX macros that go in the paper are now red
when the 'maneage' branch doesn't exist, telling the user to see the
printed warning (thus encouraging the user to get the branch). For the
TeXLive issue, the necessary commands to run are now also printed in the
warning.
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Some minor conflicts that came up during the merge were fixed.
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Until now, Maneage only provided the commit hashes (of the project and
Maneage) as LaTeX macros to use in your paper. However, they are too
cryptic and not really human friendly (unless you have access to the Git
history on a computer).
With this commit, to make things easier for the readers, the date of both
commits are also available as LaTeX macros for use in the paper. The date
of the Maneage commit is also included in the acknowledgements.
Also, the paragraph above the acknowledgements has been updated with better
explanation on why adding this acknowledgement in the science papers is
good/necessary.
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A new directory has been added at the top of the project's source called
'peer-review'. The raw reviews of the paper by the editors and referees has
been added there as '1-review.txt'. All the main points raised by the
referees have been listed in a numbered list and addressed (mostly) in
'1-answers.txt'. The text of the paper now also includes all the
implemented answers to the various points.
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With the optional appendices added recently to the paper, it was important
to go through them and make them more fitting into the paper.
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The LaTeX macro files for these two subMakefiles are created on every run
of './project make'. So their commands are also printed every time and
hardly ever will a normal user want to modify or change these.
So to avoid populating the standard output of a Maneaged project with all
these extra lines every time (possibly getting mixed with the important
analysis or LaTeX outputs), an '@' has been placed at the start of the
recipes. With an '@' at the start of the recipe, Make is instructed to not
print the commands it wants to run in the standard output.
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Until now, the core Maneage branch included some configuration files for
Gnuastro's programs. This was actually a remnant of the distant past when
Maneage didn't actually build its own software and we had to rely on the
host's software versions. This file contained the configuration files
specific to Gnuastro for this project and also had a feature to avoid
checking the host's own configuration files.
However, we now build all our software ourselves with fixed configuration
files (for the version that is being installed and its version is
stored). So those extra configuration files were just extra and caused
confusion and problems in some scenarios. With this commit, those extra
files are now removed.
Also, two small issues are also addressed in parallel with this commit:
- When running './project make clean', the 'hardware-parameters.tex' macro
file (which is created by './project configure' is not deleted.
- The project title is now written into the default output's PDF's
properties (through 'hypersetup' in 'tex/src/preamble-header.tex')
through the LaTeX macro.
All these issues were found and fixed with the help of Samane Raji.
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Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.
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One of the LaTeX macros reported by 'initialize.mk' is the git commit hash
of the most recent 'maneage' branch that the project has been branched
from. However, not all projects will retain the maneage reference. This can
happen for example when people don't push the 'maneage' reference to their
repository and then clone from their own repository to a second
computer. Therefore, until now, in such situations, Maneage would break
with an error.
With this commit, in such scenarios, a place holder string is used instead,
clearly highlighting that there is no 'maneage' reference.
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Until this commit, the '$(project-package-contents)' rules in
'reproduce/analysis/make/initialize.mk' included a line to provide all
contents, recursively, of the directory 'reproduce/' in the package for
further distribution.
This could potentially lead to the distribution of private working files
that are used during development and not intended for general distribution.
With this commit, only those files in 'reproduce/' and 'tex/src' that are
under version control are copied to the temporary directory (that is later
used for creating an archive). With this change, the archiving commands
actually became more clean (we don't have to manually remove 'LOCAL.conf'
or other temporary files). Extensive comments have also been added above
each step to clarify each step's purpose and method.
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Until now the './project make dist' command implicitly assumed that the
'tex/tikz' directory always contains PDF files (because of the 'cp
tex/tikz/*.pdf $$dir/tex/tikz' line). This was annoying for projects that
don't use TiKZ or PGFPlots to generate their plots, and they had to
manually comment this line.
With this commit a check has been placed to see if any PDF files exist in
there at all. If there aren't PDF files, the 'cp' command above is ignored.
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To help in the documentation, the Git hash of the Maneage branch commit
that the project has most recently merged with (or branched from) is now
also provided as a LaTeX macro ('\maneageversion').
It is calculated in 'reproduce/analysis/make/initialize.mk' (in the recipe
to 'initialize.tex').
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Until now, when the user wanted to complete remove all built files
(including software), the './project make distclean' command would fail if
the git hooks weren't installed. They are present when the project's
configuration has been successfully finished, but this bug can happen when
trying to re-do an incomplete build.
With this commit, this is fixed by adding an '-f' has been added before the
'rm' command for the Git hooks.
This commit was also done in the core Maneage branch.
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Until now, when the user wanted to complete remove all built files
(including software), the './project make distclean' command would fail if
the git hooks weren't installed. They are present when the project's
configuration has been successfully finished, but this bug can happen when
trying to re-do an incomplete build.
With this commit, this is fixed by adding an '-f' has been added before the
'rm' command for the Git hooks.
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Until now, the Zenodo identifier was manually written in the paper. But now
we have the Zenodo DOI in 'metadata.conf', so its much more robust to get
it from there (in case updated versions of the paper is published).
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Only two conflicts came up in the newly added comments of 'paper.mk' in the
Maneage branch. It happened because in this project we don't use
'pdflatex', but 'latex' alone.
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Until this commit, the file `BDIR/software/preparation-done.mk' were not
removed when cleaning the project with `./project make clean'. This file
is generated in the preparation of the data during the analysis step.
However, the cleaning is expected to remove anything generated in the
analysis process! Step by step, with the commands:
./project make ---> Will make the preparation and analysis
./project make clean ---> Will remove all analysis outputs (but
not `preparation-done.mk')
./project make ---> Won't do the preparation, only analysis!
However, in the last step it should do the preparation again, because
the input data could have change for any reason. With this commit, the
file `BDIR/software/preparation-done.mk' is removed when cleaning the
project, and consequently, in the analysis step the input data is
prepared.
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When publishing a project, it is necessary to also publish the source code
of all necessary software of the project. We had recently added a new
'./project make' target called 'dist-software' for this job, but had
forgotten to add it in the output of './project --help'! There was also a
small bug inside of it that didn't allow the successful copying of the
created tarball to the top project directory.
With this commit, an explanation for this target has been added in the
output of './project --help' and that bug has been fixed.
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Until now, in the 'print-copyright' function of 'initialize.mk' (that
prints a fixed set of common meta necessary in plain-text files), we were
simply printing this line:
# Pre-print server: arXiv:1234.56789
But given that all the other elements are click-able URLs, it now prints:
# Pre-print server: https://arxiv.org/abs/1234.56789
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Some minor conflicts came up in 'initialize.mk' and 'verify.mk'. For the
former, I chose the version on Maneage, for the latter, I kept the 'master'
version on the checksums of this project, but kept the Maneage version for
the rest of the improvements there (like printing the verified files as
LaTeX comments in 'verify.tex'.
While testing the conflicts, I noticed a bug (in the LaTeX macro for the
number of years in the Menke+20 paper) in the previous build, thanks to the
verification step :-)! Fortunately it wasn't actually printed in the PDF,
so a normal reader won't recognize.
The bug was caused by the recently added meta-data/commented lines in the
'tools-per-year.txt' file: when calculating the number of years studied in
that paper, we were simply counting all the lines and we had forgot to
correct this after adding comments. As a result, the un-used LaTeX macro
file was saying that they have studied 47 years instead of the real 31
years! This element was actually used in the very first (+40 page!) draft
of the paper that was summarized to fit into the journal limits.
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Possible semantic conflicts (that may not show up as Git conflicts but may
cause a crash in your project after the merge):
1) The project title (and other basic metadata) should be set in
'reproduce/analysis/conf/metadata.conf'. Please include this file in
your merge (if it is ignored because of '.gitattributes'!).
2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if
you have added all analysis Makefiles to the '.gitattributes' file
(thus not merging any change in them with your branch). For example
with this command:
git diff master...maneage -- reproduce/analysis/make/initialize.mk
3) The old 'verify-txt-no-comments-leading-space' function has been
replaced by 'verify-txt-no-comments-no-space'. The new function will
also remove all white-space characters between the columns (not just
white space characters at the start of the line). Thus the resulting
check won't involve spacing between columns.
A common set of steps are always necessary to prepare a project for
publication. Until now, we would simply look at previous submissions and
try to follow them, but that was prone to errors and could cause
confusion. The internal infrastructure also didn't have some useful
features to make good publication possible. Now that the submission of a
paper fully devoted to the founding criteria of Maneage is complete
(arXiv:2006.03018), it was time to formalize the necessary steps for easier
submission of a project using Maneage and implement some low-level features
that can make things easier.
With this commit a first draft of the publication checklist has been added
to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018
and zenodo.3872248. To help guide users on implementing the good practices
for output datasets, the outputs of the default project shown in the paper
now use the new features). After reading the checklist, please inspect
these.
Some other relevant changes in this commit:
- The publication involves a copy of the necessary software
tarballs. Hence a new target ('dist-software') was also added to
package all the project's software tarballs in one tarball for easy
distribution.
- A new 'dist-lzip' target has been defined for those who want to
distribute an Lzip-compressed tarball.
- The '\includetikz' LaTeX macro now has a second argument to allow
configuring the '\includegraphics' call when the plot should not be
built, but just imported.
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This paper doesn't use pdflatex or biblatex, so it was necessary to make
some small corrections in the make-dist rule of initialize.mk. Also, while
testing the upload on arXiv, I noticed that it complains about an empty
'verify.tex' file, so that is also corrected.
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All the steps following the to-be-added (in 'README-hacking.md')
publication checklist prior to the final check from new clone have been
added:
- 'README.md' file has been set.
- "Reproducible supplement" was added just above the keywords, pointing to
Zenodo.
- A link to the to-be-uploaded data underlying the plot was added in the
caption of the tools-per-year plot.
- A new meta-data configuration file was added to store basic project
metadata to be used throughout the project. This will later be taken
into Maneage. For examle the project title is now stored here and
written into the paper's LaTeX source and output datasets automatically.
- Verification was activated and plot's data and LaTeX macro files are now
automatically verified.
- A complete metadata was added for the data underlying the plot.
- A generic function was added in 'initialize.mk' that will automatically
write project info and copyright in all plain-text outputs.
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The minor conflict was with 'reproduce/software/make/high-level.mk', and in
particular because we implemented the fix to Maneage's Task #15664 in this
project first. After it was moved to the main Maneage branch some minor
stylistic corrections were done to it, thus causing the conflict. To
resolve the conflict, I simply imported the full Maneage version of the
file with this command:
git checkout maneage -- reproduce/software/make/high-level.mk
The other conflicts were due to the deleted files (that were resolved as
described in 'README-hacking.md') and the LaTeX files that I had told
'.gitattributes' to ignore from the Maneage branch.
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In time, some of the copyright license description had been mistakenly
shortened to two paragraphs instead of the original three that is
recommended in the GPL. With this commit, they are corrected to be exactly
in the same three paragraph format suggested by GPL.
The following files also didn't have a copyright notice, so one was added
for them:
reproduce/software/make/README.md
reproduce/software/bibtex/healpix.tex
reproduce/analysis/config/delete-me-num.conf
reproduce/analysis/config/verify-outputs.conf
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A few small conflicts showed up here and there. They are fixed with this
merge.
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Recently (in Commit 8eb0892e) the Gnuastro configuration files moved under
"reproduce/analysis/config/gnuastro" directory (before that they were in
`reproduce/software/config/gnuastro)'. But this hadn't been reflected in it
the variable that defines this directory in `initialize.mk'.
With this commit, the address of the Gnuastro configuration files directory
is corrected, allowing Gnuastro programs to operate properly when it is
used.
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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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A few minor conflicts came up that were easily fixed.
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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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Since the journal doesn't accept supplementary files during initial
submission, I have put this link on the PDF for the referee and editors to
access if they want.
Also the `tex/img' file was added to the distribution tarball.
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I was using some special Bash feature before to ignore the distribution
directory itself when copying the files, but that had some problems, so I
just used a simple for loop over a `find' command to ignore it. Also, for
now, we don't need BibLaTeX sources in the project (that is primarily for
arXiv), so to help the referee see a more cleaner contents of this
supplement file.
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TeXLive recently transitioned from its 2019 version to its 2020 version
thanks to Elham Saremi's trial of the this project. The fact that
traditionally Maneage installs all TeXLive packages in a per-year directory
is very annoying and required an update in the core Maneage system every
year. So I suddently recognized that we can fix this by setting a different
name for the directory holding the release year. This has been implemented
with this commit.
I have also done this change in the main Maneage branch for other projects
to also benefit from this correction.
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It is this time of year again: TeXLive has transitioned to its 2020 release
and the year is imprinted into the installation directory of TeXLive. Until
now, we have had to manually change this year and it caused complications
and was very annoying.
With this commit, the explicit year has been removed from TeXLive's
installation and we now simply put a `maneage' instead of the year. I tried
this on another system and it worked nicely. Until the time that we can
fully install LaTeX packages from source tarballs, this is the best thing
we could do for now.
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A few minor conflicts occurred and were fixed.
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Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.
With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.
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Until now, the project would first ask for the basic directories, then it
would start testing the compiler. But that was problematic because the
build directory can come from a previous setting (with `./project configure
-e'). Also, it could confuse users to first ask for details, then suddently
tell them that you don't have a working C library! We also need to store
the CPATH variable in the `LOCAL.conf' because in some cases, the compiler
won't work without it.
With this commit, the compiler checking has been moved at the start of the
configure script. Instead of putting the test program in the build
directory, we now make a temporary hidden directory in the source directory
and delete that directory as soon as the tests are done.
In the process, I also noticed that the copyright year of the two hidden
files weren't updated and corrected them.
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