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As described in Maneage's commit 2bd2e2f18 (which I found while testing
this project), the existing download recipe had problems when using a local
copy of the input dataset. It was first fixed here, then implemented there.
Also, to clarify things for a new user, some long comments were added at
the top of 'INPUTS.conf' to describe each of the variables, that comment
has also been put here (and is also in commit 2bd2e2f18 of Maneage).
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There were two small warnings that are removed with this commit:
- In the end, when we print the number of words in the PDF, we hadn't
accounted for the fact that 'paper.pdf' doesn't always exist (for
example when './project make clean' is run). So a check was added to
only print the number of words when a PDF exists.
- I noticed that the '$(texdir)/to-publish' directory was being built both
in 'initialize.mk' and in 'demo-plot.mk'. So the one in 'demo-plot.mk'
has been removed.
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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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When the project is being re-built from the tarball (not the Git
repository), the 'tex/build' and 'tex/tikz' addresses are actual
directories, not symbolic links. In this case, when someone runs './project
configure', it will complain about not being able to delete them (it
assumes they are symbolic links!).
So with this commit, we first check if they are deletable without '-r'. If
so, then they are full directories and we rename them to a backup directory
to allow the rest of the project to continue building a link there.
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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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When some files should not be merged, until now we were suggesting to also
add deleted files to the '.gitattributes' file. However, this feature of
Git doesn't work for deleted files and they would still show up in the
'master' branch after a merge.
So with this commit, we have added a simple AWK command to run after a
merge that will automatically detect and delete such files (using the
output of 'git status --porcelain').
Also, two minor typos were corrected in the newly added
'servers-backup.conf' file: the copyright year was wrong and there was no
new-line at the end of the file (a good convention!).
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Until now, Maneage would only build Flock before building everything else
using Make (calling 'basic.mk') in parallel. Flock was necessary to avoid
parallel downloads during the building of software (which could cause
network problems). But after recently trying Maneage on FreeBSD (which is
not yet complete, see bug #58465), we noticed that the BSD implemenation of
Make couldn't parse 'basic.mk' (in particular, complaining with the 'ifeq'
parts) and its shell also had some peculiarities.
It was thus decided to also install our own minimalist shell, Make and
compressor program before calling 'basic.mk'. In this way, 'basic.mk' can
now assume the same GNU Make features that high-level.mk and python.mk
assume. The pre-make building of software is now organized in
'reproduce/software/shell/pre-make-build.sh'.
Another nice feature of this commit is for macOS users: until now the
default macOS Make had problems for parallel building of software, so
'basic.mk' was built in one thread. But now that we can build the core
tools with GNU Make on macOS too, it uses all threads. Furthermore, since
we now run 'basic.mk' with GNU Make, we can use '.ONESHELL' and don't have
to finish every line of a long rule with a backslash to keep variables and
such.
Generally, the pre-make software are now organized like this: first we
build Lzip before anything else: it is downloaded as a simple '.tar' file
that is not compressed (only ~400kb). Once Lzip is built, the pre-make
phase continues with building GNU Make, Dash (a minimalist shell) and
Flock. All of their tarballs are in '.tar.lz'. Maneage then enters
'basic.mk' and the first program it builds is GNU Gzip (itself packaged as
'.tar.lz'). Once Gzip is built, we build all the other compression software
(all downloaded as '.tar.gz'). Afterwards, any compression standard for
other software is fine because we have it.
In the process, a bug related to using backup servers was found in
'reproduce/analysis/bash/download-multi-try' for calling outside of
'basic.mk' and removed Bash-specific features. As a result of that bug-fix,
because we now have multiple servers for software tarballs, the backup
servers now have their own configuration file in
'reproduce/software/config/servers-backup.conf'. This makes it much easier
to maintain the backup server list across the multiple places that we need
it.
Some other minor fixes:
- In building Bzip2, we need to specify 'CC' so it doesn't use 'gcc'.
- In building Zip, the 'generic_gcc' Make option caused a crash on FreeBSD
(which doesn't have GCC).
- We are now using 'uname -s' to specify if we are on a Linux kernel or
not, if not, we are still using the old 'on_mac_os' variable.
- While I was trying to build on FreeBSD, I noticed some further
corrections that could help. For example the 'makelink' Make-function
now takes a third argument which can be a different name compared to the
actual program (used for examle to make a link to '/usr/bin/cc' from
'gcc'.
- Until now we didn't know if the host's Make implementation supports
placing a '@' at the start of the recipe (to avoid printing the actual
commands to standard output). Especially in the tarball download phase,
there are many lines that are printed for each download which was really
annoying. We already used '@' in 'high-level.mk' and 'python.mk' before,
but now that we also know that 'basic.mk' is called with our custom GNU
Make, we can use it at the start for a cleaner stdout.
- Until now, WCSLIB assumed a Fortran compiler, but when the user is on a
system where we can't install GCC (or has activated the '--host-cc'
option), it may not be present and the project shouldn't break because
of this. So with this commit, when a Fortran compiler isn't present,
WCSLIB will be built with the '--disable-fortran' configuration option.
This commit (task #15667) was completed with help/checks by Raul
Infante-Sainz and Boud Roukema.
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Until this commit, when the user have previous TeX tarball already
present, the project crashed when trying to re-configure, if there was a
newer version of TeX. This is because TeX are updated yearly. With this
commit, this bug has been fixed. Now, during the installation of TeX, it
checks if this problem happens. If this is the case, then it moves the
old tarball, download the new one and install it. If not, it will just
install the already present tarball or crash because of any other
reason. This probem was recurrent, and each time TeX was updated, the
previous tarball had to be removed manually. But now, with this commit,
it is done automatically. The detection and fix of this bug has been
possible with the help of Mohammad Akhlaghi, thanks!
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Publishing a paper on reproducible research without making it easy for
readers to read the references would defeat the point. Of course we have to
make some compromises with some journals' reluctance to shift towards the
free world, but to satisfy scientific ethics, we should at least provide
clickable URLs to the references, preferably to the ArXiv version if
available [1], and also to the DOI, again, preferably to an open-access
version of the URL if available.
I was not able to fully get this done in the .bst file, so there's an
sed/tr hack done to the .bbl file in `reproduce/analysis/make/paper.mk` to
tidy up commas and spaces.
This commit also reverts some of the hacks in the Akhlaghi IAU Symposium
`tex/src/references.tex` entry, to match the improved .bst file,
`tex/src/IEEEtran_openaccess.bst`, provided here with a different name to
the original, in order to satisfy the LaTeX licence.
[1] https://cosmo.torun.pl/blog/arXiv_refs
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Until this commit, when the user had a previous TeXLive tarball already
present (in their software-tarball directory) compared to the CTAN server,
the project crashed in the configure phase. This was because TeXLive is
updated yearly and we don't yet install TeXLive from source (currently we
use its own package manager, but we plan to fix this in task #15267).
With this commit, we fix the problem by checking the cause of the crash
during the installation of TeX. If the crash is due to this particular
error, we ignore the old tarball and download the new one and install it
(the old one is still kept in '.build/software/tarballs', but will get a
'-OLD' in its name. This probem was recurrent, and every year that TeXLive
is updated, the previous tarball had to be removed manually! But with this
commit, this is done automatically. The detection and fix of this bug has
been possible with the help of Mohammad Akhlaghi, thanks!
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One of the main reasons to building Maneage is to properly
acknowledge/attribute the authors of software in research. So we have
adopted a standard of never referring to the GNU-based operating systems
running the Linux kernel simply as "Linux", we avoid terms like "Open
Sourse" and use Free Software instead (in the same spirit).
With this commit, a few instances of the cases above have been corrected,
they had slipped through our fingers when we initially imported them into
the project. In the special case of the "Journal for Open Source Software",
we simply replaced it with its abbreviation (JOSS). This was done because
in effect we were generally using journal name abbreviations in almost all
the citations already. To avoid any inconsistancies, the names of the three
other journals that weren't abbreviated are also abbreviated.
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With this commit, Maneage now includes instructions to build the memory
tracing tool Valgrind and the program 'patch' (to apply corrections/patches
in text files and in particular the sources of programs).
For this version of Valgrind, some patches were necessary for an interface
with OpenMPI 2.x (which is the case now). Also note that this version of
Valgrind's checks can fail with GCC 10.1.x (when using '--host-cc'), and
the failures aren't due to internal problems but due to how the tests are
designed (https://bugs.gentoo.org/707598). So currently if any of
Valgrind's checks fail, Maneage still assumes that Valgrind was built and
installed successfully.
While testing on macOS, we noticed that it needs the macOS-specific 'mig'
program which we can't build in Maneage. DESCRIPTION: The mig command
invokes the Mach Interface Generator to generate Remote Procedure Call
(RPC) code for client-server style Mach IPC from specification files. So a
symbolic link to the system's 'mig' is now added to the project's programs
on macOS systems.
This commit's build of Patch and Valgrind has been tested on two GNU/Linux
distributions (Debian and ArchLinux) as well as macOS.
Work on this commit started by Boud Roukema, but also involved tests and
corrections by Mohammad Akhlaghi and Raul Infante-Sainz.
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David reported this problem, it happened right after importing IEEEtran,
but for some reason, it didn't happen for me.
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When entering the name of the "listings" package, I had forgot to add the
final 's', so it wasn't being installed on a clean system! I didn't have a
problem until now, because it remained from previous builds.
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Until now, two of the software BibTeX sources (Matplolib and Sympy) had an
"abstract" entry that was long, not similar to the rest, and not relevant
in this context, so they are removed with this commit.
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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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Following the fact that the DSJ editor decided that this paper doesn't fit
into their scope, we decided to submit it to IEEE's Computing in Science
and Engineering (CiSE). So with this commit the text was re-written to fit
into their style and word-count limitations.
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Until this commit, when the version of Gnuastro doesn't match with the
version that the project was designed to use, the warning message saying
how to run the configure step was not showing the option `-e'. This
situation is normal when updating the version of Gnuastro to the most
recent one (with the project already configured). However, the use of this
option is more convenient than giving the top-build directory, etc, every
time. With this commit, the warning message has been changed in order show
also the option `-e' in the re-configure of the project.
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Until this commit, Scamp was installed with the option
`--enable-plplot=yes' (the default). However, Maneage does not have PLplot
included. As it is possible to install Scamp without PLplot (in that case
it won't generate plots), with this commit this option has been set to
`no'. As a consequence, Scamp will be installed even if the host system
does not have PLplot without crashing (but it won't make any plot).
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Until now Maneage used the host's GNU Gettext if it was present. Gettext is
a relatively low-level software that enables programs to print messages in
different languages based on the host environment. Even though it has not
direct effect on the running of the software for Maneage and the lanugage
environment in Maneage is pre-determined, it is necessary to have it
because if the basic programs see it in the host they will link with it and
will have problems if/when the host's Gettext is updated.
With this commit (which is actually a squashed rebase of 9 commits by Raul
and Mohammad), Gettext and its two extra dependencies (libxml2 and
libunistring) are now installed within Maneage as a basic software and
built before GNU Bash. As a result, all programs built afterwards will
successfully link with our own internal version of Gettext and
libraries. To get this working, some of the basic software dependencies had
to updated and re-ordered and it has been tested in both GNU/Linux and
macoS.
Some other minor issues that are fixed with this commit
- Until this commit, when TeX was not installed, the warning message
saying how to run the configure step in order to re-configure the
project was not showing the option `-e'. However, the use of this option
is more convenient than entering the top-build directory and etc every
time. So with this commit, the warning message has been changed in order
use the option `-e' in the re-configure of the project.
- Until now, on macOS systems, Bash was not linking with our internally
built `libncurses'. With this commit, this has been fixed by setting
`--withcurses=yes' for Bash's configure script.
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Until now there we had manually inserted a `\' before the `_' of sip_tpv
program. However, we also recently added a step in the configure script to
add a `\' before every `_' when writing the final LaTeX macro. This was
because some C compilers (when the host's is used) have an `_' in their
version that we had no control over.
With this commit, the `\' is removed from `sip_tpv' in its build-rule and
we let the backslash be inserted automatically.
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Until now, when you changed the version of a software in an already-built
system, its tarball would be downloaded, but it wouldn't actually
build. The only way would be to force the build by deleting the main target
of that file (under `.local/version-info/TYPE/PROGRAM'). This was because
the tarballs were an order-only prerequisite which was implemented some
time ago based on some theoretical argument that if the tarball dates
changes, the software should not be rebuilt (because we check the
checksum).
However, the problems this causes are more than those it solves: Users may
forget to delete the main target of the program and mistakenly think that
they are using the new version. The fact that all the numbers going into
the paper also contain this number further hides this.
With this commit, tarballs are no longer order-only and any time a version
of a software is updated, it will be automatically built and not cause
confusion and manual intervention by the users. As a result of this change,
I also had to correct the way we find the tarball from the list of
prerequisites.
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The paper is no longer using LuaLaTeX, but raw LaTeX (that saves a DVI), it
is so much faster! Initially I had used LuaLaTeX to use special fonts to
resemble the CODATA Data Science Journal, but all that overhead is no
longer necessary. Therefore I also removed the MANY extra LaTeX packages we
were importing. The paper builds and is able to construct one of its images
(the git-branching figure) with only 7 packages beyond the minimal
TeX/LaTeX installation. Also in terms of processing it is so much faster.
The text is just temporary now, and mainly just a place holder. With the
next commit, I'll fill it with proper text.
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A few small conflicts showed up here and there. They are fixed with this
merge.
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Until this commit, the configure step would fail with an error when
compiling libgit2 on a test system. The origin of this bug, on the OS that
was tested, appears to be that in OpenSSL Version 1.1.1a, openssl/ec.h
fails to include openssl/openconf.h. The bug is described in more detail at
https://savannah.nongnu.org/bugs/index.php?58263
With this commit, this is fixed by manually inserting a necessary
components. In particular, `sed` is used to insert a preprocessor
instruction into `openssl/openconf.h`, defining `DEPRECATED_1_2_0(f)`, for
an arbitrary section of code `f`, to include that code rather than exclude
it or warn about it.
This commit is valid provided that openssl remains at a version earlier
than 1.2.0. Starting at version 1.2.0, deprecation warnings should be run
normally. We have thus moved the version of OpenSSL in `versions.conf' to
the section for programs that need to be manually checked for version
updates with a note to remind the user when reaching that version.
Other packages that use OpenSSL may benefit from this commit, not just
libgit2.
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Until now, if GCC couldn't be built for any reason, Maneage would crash and
the user had no way forward. Since GCC is complicated, it may happen and is
frustrating to wait until the bug is fixed. Also, while debugging Maneage,
when we know GCC has no problem, because it takes so long, it discourages
testing.
With this commit, we have re-activated the `--host-cc' option. It was
already defined in the options of `./project', but its affect was nullified
by hard-coding it to zero in the configure script on GNU/Linux systems. So
with this commit that has been removed and the user can use their own C
compiler on a GNU/Linux operating system also.
Furthermore, to inform the user about this option and its usefulness, when
GCC fails to build, a clear warning message is printed, instructing the
user to post the problem as a bug and telling them how to continue building
the project with the `--host-cc' option.
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Until now, at the end of the configuration step, we would tell the user
this: "To change the configuration later, please re-run './project
configure', DO NOT manually edit the relevant files". However, as Boud
suggested in Bug #58243, this is against our principle to encourage users
to modify Maneage.
With this commit, that explanation has been expanded by a few sentences to
tell the users what to change and warn them in case they decide to change
the build-directory.
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Until now Gnuastro and Astropy where installed by default in any clean
build of Maneage. Gnuastro is used to do the demonstration analysis that is
reported in the paper and Astropy was just there to help in testing the
building of the MANY tools it depends on! It (and its dependencies) also
had several papers that helped show software citation.
However, as Boud suggested in task #15619, the burden of installing them
for a new user may be too much and any future changes will cause merge
conflicts. It may also give the impression that Maneage is only/mainly
written for astronomers.
So with this commit, I am removing Astropy as a default target. But we can
only remove Gnuastro after we include an alternative analysis in the
demonstration `delete-me' files. Following Boud's suggestion in that task,
`TARGETS.conf' was also added to the files to be ignored in any future
merge (in the checklist of `README-hacking.mk'). The solution was already
described there, but mainly focused on the deleted `delete-me' files. So
with this commit, I brought out this item as a more prominent item in the
list. Maybe we can later add the analysis done in the Maneage paper (not
yet published).
In terms of testing the software builds, we already have task #15272
(Single target to build all high-level software, for testing) that aims to
have a single configure option to install ALL high-level software and we
can ask people to try if they like and report errors.
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Similar to the previous commit (e43e3291483699), following a change made
yesterday in the identification of software names from their tarballs, a
few other problematic names are corrected with this commit: `apr-util',
HDF5, TeX Live's installation tarball and `rpcsvc-proto'.
Even though we have visually checked the list of software, other
unidentified similar cases may remain and will be fixed when found in
practice.
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Until Commit 3409a54 (from yesterday), pkg-config was found correctly in
`reproduce/software/make/basic.mk` by searching for `pkg`. However, commit
a21ea20 made an improvement in the regular expression for relating package
names and download filenames, and the string `pkg-config` with the new
regex no longer simplifies to `pkg`. The result of this was that the
basic.mk could not find `pkg-config` in the list of packages, since it was
still listed as `pkg`. This blocked downloading for a system without
pkg-config preloaded.
With this commit (of just a few bytes), the bug is fixed.
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Until now, we wouldn't explicity check for GNU gettext. If it was present
on the system, we would just add a link to it in Maneage's installation
directory. However, in bug #58248, Boud noticed that Git (a basic software)
actually needs it to complete its installation. Unfortunately we haven't
had the tiem to include a build of Gettext in Maneage. Because it is mostly
available on many systems, it hasn't been reported too commonly, it also
has many dependencies which make it a little time consuming to install.
So with this commit, we actually check for GNU gettext right after checking
the compiler and if its not available an informative error message is
written to inform the user of the problem, along with suggestions on fixing
it (how to install GNU gettext from their package manager).
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Until now, the sed script for determining URL download rules in the three
software building Makefiles (`basic.mk', `high-level.mk' and `python.mk')
considered package names such as `fftw-3...` and `fftw2-2.1...` to be
identical. As the example above shows, this would make it hard to include
some software that may hav conflicting non-number names.
With this commit, the SED script that is used to separate the version from
the tarball name only matches numbers that are after a dash
(`-'). Therefore considers `fftw-3...` and `fftw-2...` to be identical, but
`fftw-3-...` and `fftw2-2.1...` to be different. As a result of this
change, the `elif' check for some of the other programs like `m4', or
`help2man' was also corrected in all three Makefiles.
While doing this check on all the software, we noticed that `zlib-version'
is being repeated two times in `version.conf' so it was removed. It caused
no complications, because both were the same number, but could lead to bugs
later.
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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, the comment in the file said that setting the `verify-outputs`
variable to `yes` disables the verification. Looking at
`reproduce/analysis/make/verify.mk` shows that the opposite is true.
With this commit, the word `disable` is replaced with `enable` so that the
user is not confused by the conflict between the source code in the other
file and this comment.
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Until now we only checked for the existance and write-ability of the build
directory. But we recently discovered that if the specified build-directory
is in a non-POSIX compatible partition (for example NTFS), permissions
can't be modified and this can cause crashs in some programs (in
particular, while building Perl, see [1]). The thing that makes this
problem hard to identify is that on such partitions, `chmod' will still
return 0 (so it was hard to find).
With this commit, a check has been added after the user specifies the
build-directory. If the proposed build directory is not able to handle
permissions as expected, the configure script will not continue and will
let the user know and will ask them for another directory.
Also, the two printed characters at the start of error messages were
changed to `**' (instead of `--'). When everything is good, we'll use `--'
to tell the user that their given directory will be used as the build
directory. And since there are multiple checks now, the final message to
specify a new build directory is now moved to the end and not repeated in
every check.
[1] https://savannah.nongnu.org/support/?110220
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[Compared to first submission to DSJ last week with 11436 words in raw PDF,
we have decreased the paper by ~1000 words to 10493 :-)]
As with the previous commits, the moment Boud changed the structure of
sentences, I was able to find the redundancies and remove them! This is a
fascinating feature of collaboration I had never felt before: it is so hard
to find redundancies in my own raw text, but even a minor correction by
someone else suddeny breaks my mental memories/barrier on the sentence,
allowing me to be more critical to it!
Anyway, besides such corrections, I fixed a few other things: 1) In the
DSJ's recently published papers, ther is no `~' between "Figure" and its
number. 2) I noticed that in `tex/src/figure-src-inputconf.tex' I was
actually using manually input strings for the filename, checksum and size!
This was contrary to the whole philosophy of Maneage(!), I must have rushed
and forgot! So LaTeX variables are now defined and used.
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Until now, the message that we printed just before starting to build
software didn't actually print the current directory, but only `pwd'. With
this commit, this is fixed (it uses the `currentdir' variable that is
already found before).
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Until now, the message that we printed just before starting to build
software didn't actually print the current directory, but only `pwd'. With
this commit, this is fixed (it uses the `currentdir' variable that is
already found before).
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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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There weren't any conflicts in this merge.
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Of the GCC dynamically linked libraries we need to manually add RPATH to
all and for `libstdc++' we also need to tell it to link with
`libiconv'. Until now, the conditional to check for libstdc++ was not
working and thus libiconv wasn't been added to it.
With this commit the conditional has been corrected and is now
working. Also, to help in reading the logs, an echo statement was added
after every call to PatchELF.
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Until now, when a the raw tarball of some software wasn't usable, I would
put it under my own webpage, or `akhlaghi.org/reproduce-software'. That
same address was also used as a backup server. However, now the project has
a proper name: Maneage. So I changed the directory on my own server to
`akhlaghi.org/maneage-software'.
With this commit, this new address has replaced the old one. But to avoid
crashes in projects that haven't yet merged with the main Maneage branch,
the old `reproduce-software' still works (its actually a symbolic link to
the new directory now).
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In the previous commit, we remove the `-static' flag from building PatchELF
because it wasn't necessary any more. Howver, the comment for the check
still included it and could be confusing. This is corrected with this
commit. Also, we don't need the `good_static_libc' variable (that was only
defined to pass onto PatchELF). This has also been corrected.
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Until a few commits ago, PatchELF was built statically because it was used
to patch `libstdc++' at the end of the GCC building phase, but PatchELF
also depends on `libstdc++', so it would crash. However, recently when
patching the GCC libraries, we don't directly apply Patchelf to the
library, first we copy it to a temporary place, do the patching, then put
it in its proper place. So the problem above won't happen any more.
With this commit, I am thus removing the static flag from patchelf and
letting it built dynamically all the time. The main problem was that some
systems don't have a static C++ library, so PatchELF couldn't be built
statically. Instead of adding more checks, we just fixed the core
foundation of the problem.
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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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