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There is an answer for all the referee points now. I also did some minor
edits in the paper. But we are still over the limit by around 250 words.
The only remaining point that is not yet addressed (and has '####' around
it) is the discussion on parallelization and its effect on reproducibility.
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This commit updates "paper.tex" and "peer-review/1-answer.txt"
for the first 15 (out of 59!) reviewer points, excluding
points 2 (not yet done) and 9 (README-hacking.md needs
tidying).
A fix to "reproduce/analysis/make/paper.mk" for the
links in the appendices is also done in this commit (the same
algorithm as for paper.tex is added). The links in the appendices
are not (yet) clickable.
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Raul's added point on the answer to the referee was very good, so I edited
it a little to be more clear (and removed his name).
Also, after looking in a few parts of the text, I fixed a few typos.
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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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Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro
that defines two LaTeX macros: '\new' and '\tonote'.
When '\highlightchanges' was defined, anything that was written within
'\new' became dark green (highlighting new things that have been
added). Also, anything that was written in '\tonote' was put within a '[]'
and became dark red (to show that there is a note here that should be
addressed later).
When '\highlightchanges' wasn't defined, anything within the '\new' element
would be black (like the rest of the text), and the things in '\tonote'
would not be shown at all.
Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex'
(to toggle the modes above) would create a different Git hash and has to be
committed.
But this different commit hash could create a false sense in the reader
that other things have also been changed and the only way they could
confirm was to actually go and look into the project history (which they
will not usually have time to do, and thus won't be able to trust the two
modes of the text).
Also, the added highlights and the note highlights were bundeled together
into one macro, so you couldn't only have one of them.
With this commit, the choice of highlighting either one of the two is now
done as two new run-time options to the './project' script (which are
passed to the Makefiles, and written into the 'project.tex' file which is
loaded into 'paper.tex'). In this way, we can generate two PDFs with the
same Git commit (project's state): one with the selected highlights and
another one without it.
This issue actually came up for me while implementing the changes here: we
need to submit one PDF to the journal/referees with highlights on the added
features. But we also need to submit another PDF to arXiv and Zenodo
without any highlights. If the PDFs have different commit hashes, the
referees may associate it with other changes in any part of the work. For
example https://oadoi.org/10.22541/au.159724632.29528907 that mentions
"Another version of the manuscript was published on arXiv: 2006.03018",
while the only difference was a few words in the abstract after the journal
complained on the abstract word-count of our first submission (where the
commit hashes matched with arXiv/Zenodo).
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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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Given the referee reports, after discussing with the editors of CiSE, we
decided that it is important to include the complete appendix we had before
that included a thorough review of existing tools and methods. However, the
appendix will not be published in the paper (due to the strict word-count
limit). It will only be used in the arXiv/Zenodo versions of the paper.
This actually created a technical problem: we want the commit hash of the
project source to remain the same when the paper is built with an appendix
or without it.
To fix this problem the choice of including an appendix has gone into the
'project' script as a run-time option called '--no-appendix'. So by default
(when someone just runs './project make'), the PDF will have an appendix,
but when we want to submit to the journal, or when the appendix isn't
needed for a certain reason, we can use this new option. The appendix also
has its own separate bibliography.
Some other corrections made in this commit:
1. Some new references were added that had an '_' in their source, they
were corrected in 'references.tex'.
2. I noticed that 'preamble-style.tex' is not actually used in this paper,
so it has been deleted.
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There weren't any conflicts in this merge.
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Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support
in some software. But they are not yet natively built within Maneage,
primarily because we have higher-priority work right now. GUI tools in
general aren't high on our priority list right now because GUI tools are
generally good for human interaction (which is contrary to the reproducible
philosophy), not automatic analysis (a core concept in reproducibility). So
even later, when we do include Tcl/Tk in Maneage, their direct usage will
be discouraged.
Until this commit, because we don't yet build Tcl/Tk, the default maneage
install of the statistical package R failed on a Debian Stretch, with 6227
repeats of the line:
'/usr/lib//tcl8.5/tclConfig.sh: line 2: dpkg-architecture:
command not found'
To fix this problem (atleast until Tcl/Tk is installed within Maneage), R
is now configured with the '--without-tcltk' option which fixed the
problem. Please see the description above the R installation instructions
in 'reproduce/software/make/high-level.mk' for more.
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Following the previous commit, we recognized that the 'IFS' terms are not
necessary and can be even cause problems. So all their occurances in the
scripts of Maneage have been removed with this commit.
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Until a recent commit, the IFS='"' was added at the start of the variables
in this shell script and as a result, the SPACE character wasn't being used
as a delimiter. This caused a major problem when downloading the tarballs
(all the backup servers were considered as the top link).
With this commit we removed these 'IFS' statements). Because we now check
for the existance of meta-characters in the build directory name, there is
no more problem, and also generally both the calling command and
internally, we have double-qutations around the variable names. So removal
of IFS will not affect the result in this scenario.
This bug was found by Mohammadreza Khellat.
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Only two small conflicts came up:
* The addition of the hardware architecture macro in 'paper.tex' (which
was removed for now, but will be added as the referee has requested
within the text).
* The usage of "" around directory variables in 'paper.mk'.
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While a project is under development, the raw analysis software are not the
only necessary software in a project. We also need tools to all the edit
plain-text files within the Maneaged project. Usually people use their
operating system's plain-text editor. However, when working on the project
on a new computer, or in a container, the plain-text editors will have
different versions, or may not be present at all! This can be very annoying
and frustrating!
With this commit, Maneage now installs GNU Nano as part of the basic
tools. GNU Nano is a very simple and small plain text editor (the installed
size is only ~3.5MB, and it is friendly to new users). Therefore, any
Maneaged project can assume atleast Nano will be present (in particular
when no editor is available on the running system!). GNU Emacs and VIM
(both without extra dependencies, in particular without GUI support) are
also optionally available in 'high-level.mk' (by adding them to
'TARGETS.conf').
The basic idea for the more advanced editors (Emacs and VIM) is that
project authors can add their favorite editor while they are working on the
project, but upon publication they can remove them from 'TARGETS.conf'.
A few other minor things came up during this work and are now also fixed:
- The 'file' program and its libraries like 'libmagic' were linking to
system's 'libseccomp'! This dependency then leaked into Nano (which
depends on 'libmagic'). But this is just an extra feature of 'file',
only for the Linux kernel. Also, we have no dependency on it so far. So
'file' is not configured to not build with 'libseccomp'.
- A typo was fixed in the line where the physical core information is
being read on macOS.
- The top-level directories when running './project shell' are now quoted
(in case they have special characters).
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Until now, no machine-related specifications were being documented in the
workflow. This information can become helpful when observing differences in
the outcome of both software and analysis segments of the workflow by
others (some software may behave differently based on host machine).
With this commit, the host machine's 'hardware class' and 'byte-order' are
collected and now available as LaTeX macros for the authors to use in the
paper. Currently it is placed in the acknowledgments, right after
mentioning the Maneage commit.
Furthermore, the project and configuration scripts are now capable of
dealing with input directory names that have SPACE (and other special
characters) by putting them inside double-quotes. However, having spaces
and metacharacters in the address of the build directory could cause
build/install failure for some software source files which are beyond the
control of Maneage. So we now check the user's given build directory
string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(',
')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different
directory.
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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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The '.bbl' suffix in the comment of one call to LaTeX was incorrectly
written as '.bb'.
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Until now, if the software source tarballs already existed on the system
they would be copied inside the project. However, the software source
tarballs are sometimes/mostly larger than their actual product and can
consume significant space (~375 MB in the core branch!).
With this commit, when the software are present on the system, their
symbolic link will be placed in 'BDIR/software/tarballs', not a full
copy. Also, because the tarballs in software tarball directory may
themselves be links, we use 'realpath' to find the final place of the
actual file and link to that location. Therefore if 'realpath' can't be
found (prior to installing Coreutils in Maneage), we will copy the tarballs
from the given software tarball directory. After Maneage has installed
Coreutils, the project's own 'realpath' will be used. Of course, if the
software are downloaded, their full downloaded copy will be kept in
'BDIR/software/tarballs', nothing has changed in the downloading scenario.
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It was a long time that the Maneage software versions hadn't been updated.
With this commit, the versions of all basic software were checked and 17 of
that had newer versions were updated. Also, 16 high-level programs and
libraries were updated as well as 7 Python modules. The full list is
available below.
Basic Software (affecting all projects)
---------------------------------------
bash 5.0.11 -> 5.0.18
binutils 2.32 -> 2.35
coreutils 8.31 -> 8.32
curl 7.65.3 -> 7.71.1
file 5.36 -> 5.39
gawk 5.0.1 -> 5.1.0
gcc 9.2.0 -> 10.2.0
gettext 0.20.2 -> 0.21
git 2.26.2 -> 2.28.0
gmp 6.1.2 -> 6.2.0
grep 3.3 -> 3.4
libbsd 0.9.1 -> 0.10.0
ncurses 6.1 -> 6.2
perl 5.30.0 -> 5.32.0
sed 4.7 -> 4.8
texinfo 6.6 -> 6.7
xz 5.2.4 -> 5.2.5
Custom programs/libraries
-------------------------
astrometrynet 0.77 -> 0.80
automake 0.16.1 -> 0.16.2
bison 3.6 -> 3.7
cfitsio 3.47 -> 3.48
cmake 3.17.0 -> 3.18.1
freetype 2.9 -> 2.10.2
gdb 8.3 -> 9.2
ghostscript 9.50 -> 9.52
gnuastro 0.11 -> 0.12
libgit2 0.28.2 -> 1.0.1
libidn 1.35 -> 1.36
openmpi 4.0.1 -> 4.0.4
R 3.6.2 -> 4.0.2
python 3.7.4 -> 3.8.5
wcslib 6.4 -> 7.3
yaml 0.2.2 -> 0.2.5
Python modules
--------------
cython 0.29.6 -> 0.29.21
h5py 2.9.0 -> 2.10.0
matplotlib 3.1.1 -> 3.3.0
mpi4py 3.0.2 -> 3.0.3
numpy 1.17.2 -> 1.19.1
pybind11 2.4.3 -> 2.5.0
scipy 1.3.1 -> 1.5.2
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When the host C compiler is used (either by calling '--host-cc' or on OSs
that we can't build the GNU C Compiler), Maneage will also not build the
Fortran compiler 'gfortran'. Until now, the './project configure' script
would give a big warning about the need for 'gfortran' and the fact that it
is missing, and would for 5 seconds, but it would continue anyway.
For projects that don't need 'gfortran', this can be confusing to the users
and for those that need 'gfortran', it means that a lot of time and cpu
cycles are wasted compiling non-fortran software that are unusable in the
end.
With this commit, the 'need_gfortarn' variable has been added
'reproduce/software/shell/configure.sh', in a new part that is devoted to
project-specific features. If it equals '0', then the 'gfortran' test (and
message!) isn't done at all, but if it is set to '1', then the configure
stage will halt immediately gfortran is not found and not built.
The default operations of the core Maneage branch don't need 'gfortran', so
by default it is set to 0. But 'gfortran' is necessary for all projects
that use Numpy (Python's numeric library) for example. So if your project
needs 'gfortran', please set this new variable to 1. As mentioned in the
comments of 'configure.sh', ideally we should detect this automatically,
but we haven't had the time to implement it yet.
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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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Prior to this commit, compilation of OpenMPI used the default OpenMPI
choices of deciding which libraries should be used in relating to a job
scheduler [1] (such as Slurm [2]). Given that the user on a multi-user
cluster has to accept the sysadmin's choice of a job scheduler, the
question of whether to (1) link with OpenMPI's own libraries (and increase
the reproducibility of the science project) or rather (2) link with the
sysadmin managed libraries (more likely to be compatible with the host's
job scheduler), is an open question of which the best strategy for
reproducibility needs to be debated and studied.
In this commit, strategy (1) is adopted. The options '--withpmix=internal'
and '--with-hwloc=internal' are added to the configure command. The working
assumption is that the Maneage version of OpenMPI is likely to be modern
enough to be compatible with the native job scheduler such as
Slurm. Compilation without any 'pmix' option gave a fail in at least one
case; it appears that an external pmix library was sought by the configure
script.
As of OpenMPI 4.0.1, the internal libevent library is used by default, so
there appears to be no option to force it to be chosen internally.
This commit also includes the option '--without-verbs'. This option
removes a library related to "infiniband", "verbs", "openib" and "BTL";
this library appears to be deprecated. See [3], [4] for discussion.
Please add feedback and discussion to the Maneage task about openmpi
linking strategies (1) (internal) and (2) (external) at Savannah [5].
[1] https://en.wikipedia.org/wiki/Job_scheduler#Batch_queuing_for_HPC_clusters
[2] https://en.wikipedia.org/wiki/Slurm_Workload_Manager - To avoid a name
clash, 'slurm-wlm' is the metapackage in Debian for the client
commands, the compute node daemon, and the central node daemon. An
unrelated package 'slurm' also exists.
[3] https://www-lb.open-mpi.org/faq/?category=openfabrics#ofa-device-error
[4] https://www-lb.open-mpi.org/faq/?category=building
[5] https://savannah.nongnu.org/task/index.php?15737
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There are many different directory trees involved in Maneage system: the
top directory, the 'reproduce/' directory and its sub-directories,
'.build/' (that point to a user-defined build area), and a possibly
user-defined input directory. Until now, in the case of a download checksum
failure, it was not immediately obvious [1] to the user *where* the file
with a failed checksum is.
To clarify to the user *where* the suspicious file is now located, this
commit adds a line to 'reproduce/analysis/make/download.mk' to print out
this full path location: '$$unchecked' along with the expected and
calculated checksums.
[1] Euphemism for me spending lots of time debugging and being confused.
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This commit clarifies the initial usage of Zenodo for reserving a Zenodo
identifier and starting an 'unpublished' upload. Some other minor wording
changes are done here.
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Until this commit, the '$(project-package-contents)' rules in
'reproduce/analysis/make/initialize.mk' included a line to provide all
contents, recursively, of the directory 'reproduce/' in the package for
further distribution.
This could potentially lead to the distribution of private working files
that are used during development and not intended for general distribution.
With this commit, only those files in 'reproduce/' and 'tex/src' that are
under version control are copied to the temporary directory (that is later
used for creating an archive). With this change, the archiving commands
actually became more clean (we don't have to manually remove 'LOCAL.conf'
or other temporary files). Extensive comments have also been added above
each step to clarify each step's purpose and method.
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Until now, if a project needed the healpy software package, Maneage would
crash with the following error message (abridged for full name in build
directory). This was caused by a typo in the version of 'healpix' (the
dependency of 'healpy').
make: *** No rule to make target '.../version-info/proglib/healpix-'
With this commit, the typo in line 334 of 'python.mk' is fixed, so that
when '$(ipydir)/healpy-$(healpy-version)' gets called it correctly searches
for a rule to make '$(ibidir)/healpix-$(healpix-version)'.
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Until now the './project make dist' command implicitly assumed that the
'tex/tikz' directory always contains PDF files (because of the 'cp
tex/tikz/*.pdf $$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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In the previous commit (Commit 1bc00c9: Only using clang in macOS systems
that also have GCC) we set the used C compiler for high-level programs to
be 'clang' on macOS systems. But I forgot to do the same kind of change in
the configure script (to prefer 'clang' when we are testing for a C
compiler on the host).
With this commit, the compiler checking phases of the configure script have
been improved, so on macOS systems, we now first search for 'clang', then
search for 'gcc'.
While doing this, I also noticed that the 'rpath' checking command was done
before we actually define 'instdir'!!! So in effect, the 'rpath' directory
was being set to '/lib'! So with this commit, this test has been taken to
after defining 'instdir'.
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Until now, when the bibliography file ('paper.bbl') had a LaTeX-related
error (for example the journal name was a LaTeX macro that isn't defined),
the first 'pdflatex' command that is run before 'biber' would crash, not
allowing the project to reach 'biber'. So the user would have to manually
remove 'paper.bbl' before running './project make'.
With this commit, we remove any possibly existing 'paper.bbl' file before
rebuilding it. Generally, this also helps in keeping things clean during
the generation of the new bibliography.
This bug was found by Mahdieh Nabavi.
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Until now, when Maneage was built on a macOS that had both a clang and GCC,
we would make links to both. But this cause many conflicts in some
high-level programs (for example Numpy and etc, all the programs where we
have explicity set 'export CC=clang' before the build recipe). This happens
because the GCC that is built on a macOS isn't complete for some
operations.
To fix this problem, when we are on a macOS, we explicity set 'gcc' to
point to 'clang' and 'g++' to point to 'clang++'. We also don't link to the
host's C-preprocessor ('cpp') on macOS systems because this is only a GNU
feature and using the GNU CPP is also known to have some basic
problems. For example this was reported by Mahdieh Nabavi (which was the
main trigger for this work):
ld: Symbol not found: ___keymgr_global
Referenced from: /Users/Mahdieh/build/software/installed/bin/cpp
Expected in: /usr/lib/libSystem.B.dylib
Also, to avoid linking to another link on the host tools (in the 'makelink'
function of 'basic.mk'), we are now using 'realpath'.
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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, the dataset's configuration names had a 'WFPC2' prefix. But this
very alien to anyone that is not familiar with the history of the Hubble
Space Telescope (the camera is no longer used! Its just used here since its
one of the standard FITS files from the FITS standard webpage).
With this commit the variable names have been modified to be more readable
and clear (having a 'DEMO-' prefix). Also the comments of 'INPUTS.conf'
(describing the purpose of each variable) were edited and made more clear.
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In 'README.md' I tried to explain a little better that TeXLive will only
install its necessary packages, not the full TeXLive library! Also in
paper.mk, I slightly improved the comments with very minor edits.
Both these parts are slated to go into the core Maneage branch, so its
important to maintain them here for now.
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Until now, when reading the host's PATH environment variable we weren't
accounting for directory names with a space character. This was most
prominently visible in the 'low-level-links' step where we put links to
some core system components into the project's build directory (mainly for
prorietary systems like macOS).
To address the problem, double quotations have been placed around the part
that we extract 'ccache' from the PATH, and the part where we make the
symbolic link. In the process the comments above 'makelink' were made more
clear and 'low-level-links' now depends on 'grep' (which is the
highest-level program it uses).
This bug was reported by Mahdieh Navabi.
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Until this commit, once Libidn was installed, insted of its own name and
version, the name and version of Libjpeg were saved (in the target if
Libidn). This robably come from a copy/paste of the rule.
With this commit, this minor bug has been corrected. I also added my name
as an author of `reproduce/software/make/xorg.mk' Makefile since I added
some code there.
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There weren't any conflicts in this merge.
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After recently adding util-linux to Maneage build-tree, we had forgot to
delete the unpacked and built source directory after it was installed! This
has been corrected with this commit.
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Until now, when the user specified an input and software directory, the raw
string they entered was used. But when this string was a relative location,
this could be problematic in general scenarios.
With this commit, the same function that finds the absolute location of the
build directory is used to find the absolute address of the data and
software directories.
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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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There weren't any conflicts in this merge.
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Until now, in order to build Ghostscript, the project used the host's Xorg
libraries. This was because we hadn't yet added the necessary build rules
for them.
With this commit, the instructions to build the necessary Xorg libraries
for Ghostscript have also been added. Also, the shared Ghostscript library
has been built with this commit and two sets of standard fonts are also
included, setting us on the path to build TeXLive from source later.
This task was done with the help and support of Raul Infante-Sainz.
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Until this commit, there was a problem when building Bison in parallel in
macOS systems. With this commit, this problem has been fixed by updating
Bison to its most recent version (3.6).
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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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POSSIBLE EFFECT ON YOUR PROJECT: The changes in this commit may only cause
conflicts to your project if you have changed the software building
Makefiles in your project's branch (e.g., 'basic.mk', 'high-level.mk' and
'python.mk'). If your project has only added analysis, it shouldn't be
affected.
This is a large commit, involving a long series of corrections in a
differnt branch which is now finally being merged into the core Maneage
branch. All changes were related and came up naturally as the low-level
infrastructure was improved. So separating them in the end for the final
merge would have been very time consuming and we are merging them as one
commit.
In general, the software building Makefiles are now much more easier to
read, modify and use, along with several new features that have been
added. See below for the full list.
- Until now, Maneage needed the host to have a 'make' implementation
because Make was necessary to build Lzip. Lzip is then used to
uncompress the source of our own GNU Make. However, in the
minimalist/slim versions of operating systems (for example used to build
Docker images) Make isn't included by default. Since Lzip was the only
program before our own GNU Make was installed, we consulting Antonio
Diaz Diaz (creator of Lzip) and he kindly added the necessary
functionality to a new version of Lzip, which we are using now. Hence we
don't need to assume a Make implementation on the host any more. With
this commit, Lzip and GNU Make are built without Make, allowing
everything else to be safely built with our own custom version of GNU
Make and not using the host's 'make' at all.
- Until recently (Commit 3d8aa5953c4) GNU Make was built in
'basic.mk'. Therefore 'basic.mk' was written in a way that it can be
used with other 'make' implementations also (i.e., important shell
commands starting with '&&' and ending in '\' without any comments
between them!). Furthermore, to help in style uniformity, the rules in
'high-level.mk' and 'python.mk' also followed a similar structure. But
due to the point above, we can now guarantee that GNU Make is used from
the very first Makefile, so this hard-to-read structure has been removed
in the software build recipes and they are much more readable and
edit-friendly now.
- Until now, the default backup servers where at some fixed URLs, on our
own pages or on Gitlab. But recently we uploaded all the necessary
software to Zenodo (https://doi.org/10.5281/zenodo.3883409) which is
more suitable for this task (it promises longevity, has a fixed DOI,
while allowing us to add new content, or new software tarball
versions). With this commit, a small script has been written to extract
the most recent Zenodo upload link from the Zenodo DOI and use it for
downloading the software source codes.
- Until now, we primarily used the webpage of each software for
downloading its tarball. But this caused many problems: 1) Some of them
needed Javascript before the download, 2) Some URLs had a complex
dependency on the version number, 3) some servers would be randomly down
for maintenance and etc. So thanks to the point above, we now use the
Zenodo server as the primary download location. However, if a user wants
to use a custom software that is not (yet!) in Zenodo, the download
script gives priority to a custom URL that the users can give as Make
variables. If that variable is defined, then the script will use that
URL before going onto Zenodo. We now have a special place for such URLs:
'reproduce/software/config/urls.conf'. The old URLs (which are a good
documentation themselves) are preserved here, but are commented by
default.
- The software source code downloading and checksum verification step has
been moved into a Make function called 'import-source' (defined in the
'build-rules.mk' and loaded in all software Makefiles). Having taken all
the low-level steps there, I noticed that there is no more need for
having the tarball as a separate target! So with this commit, a single
rule is the only place that needs to be edited/added (greatly
simplifying the software building Makefiles).
- Following task #15272, A new option has been added to the './project'
script called '--all-highlevel'. When this option is given, the contents
of 'TARGETS.conf' are ignored and all the software in Maneage are built
(selected by parsing the 'versions.conf' file). This new option was
added to confirm the extensive changes made in all the software building
recipes and is great for development/testing purposes.
- Many of the software hadn't been tested for a long time! So after using
the newly added '--all-highlevel', we noticed that some need to be
updated. In general, with this commit, 'libpaper' and 'pcre' were added
as new software, and the versions of the following software was updated:
'boost', 'flex', 'libtirpc', 'openblas' and 'lzip'. A 'run-parts.in'
shell script was added in 'reproduce/software/shell/' which is installed
with 'libpaper'.
- Even though we intentionally add the necessary flags to add RPATH inside
the built executable at compilation time, some software don't do it
(different software on different operating systems!). Until now, for
historical reasons this check was done in different ways for different
software on GNU/Linux sytems. But now it is unified: if 'patchelf' is
present we apply it. Because of this, 'patchelf' has been put as a
top-level prerequisite, right after Tar and is installed before anything
else.
- In 'versions.conf', GNU Libtool is recognized as 'libtool', but in
'basic.mk', it was 'glibtool'! This caused many confusions and is
corrected with this commit (in 'basic.mk', it is also 'libtool').
- A new argument is added to the './project' script to allow easy loading
of the project's shell and environment for fast/temporary testing of
things in the same environment as the project. Before activating the
project's shell, we completely remove all host environment variables to
simulate the project's environment. It can be called with this command:
'./project shell'. A simple prompt has also been added to highlight that
the user is using the Maneage shell!
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Until now, Maneage would accept the given build directory, regardless of
the free memory available there. This could cause confusing situations for
new users who don't know about the minimum storage requirement.
With this commit, after all other checks on the given build directory are
completed, the configure script will check the available space and warns
the user if there is less than almost 5GB free space available in the build
directory (with a 5 second delay).
It won't cause a crash because some projects may require roughly smaller
than this space (the default only needs roughly 2GB). But we also don't
want the host's partition to get too close to being full, causing them
problems elsewhere. We can change the behavior as desired in future
commits.
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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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In Commit 105467fe6402 (Software tarballs are downloaded even if not
built), we introduced tests to download the tarballs of software even if
they don't need to be built on the respective host. However some small
typos in the checks existed that could cause a crash on macOS. In
particular in the building of PatchELF and libbsd we had forgot to add the
necessary 'x' before the 'yes' in the conditional to check if a we are on
macOS or not.
With this commit these two checks have been corrected. Also, in the
building of 'isl' and 'mpc', we now check for 'host_cc' (signifying that
the user wants to use their host C compiler for the high-level step)
instead of 'on_mac_os'. The reason is that even on non-macOS systems, a
user may not want to build the C compiler from scratch and use the
'--host-cc' option. In such cases, they don't need to compile 'isl' and
'mpc'.
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Until now, the English texts that embeds the list of software to
acknowledge in the paper was hard-wired into the low-level coding
('reproduce/software/shell/configure.sh' to be more specific). But this
file is very low-level, thus discouraging users to modify this surrounding
text.
While the list of software packages can be considered to be 'data' and is
fixed, the surrounding text to describe the lists is something the authors
should decide on. Authors of a scientific research paper take
responsibility for the full paper, including for the style of the
acknowledgments, even if these may well evolve into some standard text.
With this commit, authors who do *not* modify
'reproduce/software/config/acknowledge_software.sh' will have a default
text, with only a minor English correction from earlier versions of
Maneage. However, Authors choosing to use their own wording should be able
to modify the text parameters in
`reproduce/software/config/acknowledge_software.sh` in the obvious
way. This is much more modular than asking project authors to go looking
into the long and technical 'configure.sh' script.
Systematic issues: the file
`reproduce/software/config/acknowledge_software.sh` is an executable shell
script, because it has to be called by
`reproduce/software/shell/configure.sh`, which, in principle, does not yet
have access to `GNU make` (if I understand the bootstrap sequence
correctly). It is placed in `config/` rather than `shell/`, because the
user will expect to find configuration files in `config/`, not in `shell/`.
A possible alternative to avoid having a shell script as a configure file
would be to let `reproduce/software/config/acknowledge_software.sh` appear
to be a `make` file, but analyse it in `configure.sh` using `sed` to remove
whitespace around `=`, and adding other hacks to switch from `make` syntax
to `shell` syntax. However, this risks misleading the user, who will not
know whether s/he should follow `make` conventions or `shell` conventions.
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The 'pdflatex' program is used to build the default Maneage-branch paper.
But since the default paper uses PGFPlots to build the figures within LaTeX
as an external PDF, PGFPlots requires 'pdflatex' to be called with the
'-shell-escape' option. Generally, this option can be considered as a
security risk (in particular when 'pdflatex' is being run by an external
LaTeX file: a malicious LaTeX writer may embed commands in the LaTeX source
that will be executed on the host if this option is present).
This is not too serious of an issue in Maneage, because when someone runs
Maneage, they intentionally let it run many on their system. Hence if
someone wants to exploit a host system, they can add the necessary commands
long before 'pdflatex' is run. After all, all commands in Maneage are run
with the calling user's permissions, hence they have access to many parts
of the user's accounts. If someone is worried about security on a
non-trusted Maneage project they should act the same as they do with any
software: define a new user for it, and call it with that user (as a
weak-level security), or run it in a virtual machine or container.
However, since this option has been explicity mentioned as a security risk
before, it helps if we have a comment explaining its usage in 'paper.mk'.
With this commit, the concerned user will read a brief explanation and can
read the brief discussion at [1] and possibly re-open the discussion or
propose ways of mitigating the security risk(s).
[1] https://savannah.nongnu.org/task/?15694
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