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SUMMARY: Nothing special is necessary for your existing projects. This
commit just addds two new features (read the commit description for more):
1. To provide a user and password to servers that need authentication
before they allow downloading of proprietary data,
2. To use the FITS Standard's DATASUM for file verification (for cases
where the file is not static on the server, and is generated upon
receiving your download request).
Until now, Maneage didn't have any infrastructure for databases that
require authentication (through a user or password, when calling
'wget'). Furthermore, when the downloaded file is automatically generated
by the server upon request, the server usually adds metadata (like file
date, or query number and etc) in the header. Therefore the simple SHA256
checksum of the file would differ on every download! This made it very hard
to verify if the data (not headers) are unchanged.
With this commit, both these problems have been addressed:
- Server authentication: the 'reproduce/software/config/LOCAL.conf' now
contains three new variables for this purpose. With them, you can give
your username and password, along with the authentication method of the
server. The comments on top of these three variables give a full
description of their usage.
- Verifying only the data in a file (ignoring the headers): The
'reproduce/analysis/config/INPUTS.conf' now accepts two new optional
variables for each input file using the FITS standard's DATASUM
convention: 'INPUT-%-fitsdatasum' and 'INPUT-%-fitshdu'. If the SHA256
isn't specified for a file, Maneage will use these to verify the
file. With the latter, you specify the HDU of the data you want to
verify and with the former you give the DATASUM value for that HDU. As
the name suggests, this is only valid for FITS files. If we find other
formats that support a similar behavior, we can add this feature for
those formats also. This is also thoroughly discussed in the comments of
'reproduce/analysis/config/INPUTS.conf'.
This commit was done with the help of Pedram Ashofte Ardakani, Sepideh
Eskandarlou and Mohammadreza Khellat.
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SUMMARY: This is a software update to make Maneage more portable and up to
date. It does not involve any Maneage infrastructure changes. You should
just re-build your project to make sure the updated software haven't
removed/changed any of their features that you were using. In particular,
for Astrometry.net users, please see the respective note in P.S.2 below.
Until now, there have been many updates in the software that are built
within Maneage. The last software upadte was almost one year ago.
With this commit, the software in the P.S.1 have been updated. A
description of notable changes in the software environment is given in
P.S.2. This software environment has been tested on an Arch GNU/Linux,
Debian, CentOS-7 and macOS.
This commit is the merging of 24 individual commits by Raul Infante-Sainz
(who put a lot of energy on porting the software below for macOS, and
updating citations), Boudewijn Roukema (who helped with memory checking for
GCC, and testing on Debian and CentOS), Sepideh Eskandarlou (who tested the
environment) and myself.
Besides the updates in the core software, the followimg improvements have
also been implemented in this commit:
- When you run './project shell':
- A welcome message is printed that will remind the caller that they
have entered a new environment, it will print the location of 'HOME'
and the location of the shell startup file.
- The 'reproduce/software/shell/bashrc.sh' is loaded as a startup
file. This allows you to customize your interactive Maneage shell. A
default step has already been placed there that will put the git
branch name (in green) within the shell prompt (which was
purple). This greatly helps when dealing with directories under Git
version control. These settings won't bother with Maneage's default
operations: through environment variables we make sure that these
'./project shell' features will not slow-down the calls to the shell
within the non-interactive Make calls.
- The host's 'COLORTERM' is passed to the Maneage environment. It is
used by some programs that can have color outputs on the terminal.
- Updates to citations:
- Numpy and Scipy (as requested on their pages):
https://numpy.org/citing-numpy and https://scipy.org/citing-scipy
- Gnuastro: Added https://arxiv.org/abs/1909.11230 which describes major
updates to Gnuastro after 10 releases.
- When a software's paper is indexed in the SAO/NASA Astrophysics Data
System (ADS), Maneage now use the BibTeX entries provided by ADS. This
helps to give a unified format to most software, and more information
(like ADS+arXiv hyperlinks in the BibLaTeX compilation of the default
bibliography).
- We were able to build this version of Maneage on a Debian system from
2010 (+12 years ago!). Only three downgrades were necessary in the
"basic" software (not affecting the high-level science software!). A
description of the necessary downgrades for such old systems has been
added in 'README.md'.
P.S.1 List of updated software:
Basic software:
cURL 7.79.1 --> 7.84.0
Dash 0.5.11.5 --> 0.5.11-057cd65
File 5.41 --> 5.42
GNU AWK 5.1.0 --> 5.1.1
GNU Bash 5.1.8 --> 5.2-rc2
GNU Binutils 2.37 --> 2.39
GNU Compiler Collection (GCC) 11.2.1 --> 12.1.0
GNU Findutils 4.8.0 --> 4.9.0
GNU Gzip 1.11 --> 1.12
GNU Help2man 1.48.5 --> 1.49.2
GNU Integer Set Library (ISL) 0.18 --> 0.24
GNU Libtool 2.4.6 --> 2.4.7
GNU Nano 6.0 --> 6.4
GNU Readline 8.1.1 --> 8.2-rc2
GNU libiconv 0.16 --> 0.17
Git 2.36.0 --> 2.37.1
OpenSSL 3.0.0 --> 3.0.5
PatchELF 0.13 --> 0.15.0
Perl 5.34.0 --> 5.36.0
High-level software:
Astrometry.net 0.89 --> 0.91
CFITSIO 4.0.0 --> 4.1.0
CMake 3.21.4 --> 3.24.0
GNU Astronomy Utilities (Gnuastro) 0.16.1 --> 0.18
GPL Ghostscript 9.55.0 --> 9.56.1
HDF5 1.10.5 --> 1.13.1
Libjpeg 9d --> 9e
Libtiff 4.3.0 --> 4.4.0
OpenBLAS 0.3.18 --> 0.3.21
PLplot n/a --> 5.15.0
Python 3.10.0 --> 3.10.6
SCAMP 2.6.7 --> 2.10.0
SWarp 2.38.0 --> 2.41.5
Util-Linux 2.37.2 --> 2.38.1
Vim 8.2 --> 9.0
WCSLIB 7.7 --> 7.11
X.org packages (used by graphical software like Ghostscript and LaTeX):
Fontconfig 2.13.94 --> 2.14.0
LibX11 1.7.2 --> 1.8
LibXCB 1.14 --> 1.15
XCB-proto 1.14.1 --> 1.15
Xorg-proto 2021.5 --> 2022.1
Python modules:
Astropy 5.0 --> 5.1
GalSim 2.3.3 --> 2.3.5
P.S.2: Notable points regarding the software environment:
- Two new links from the host's low-level tools are now included in
Maneage's build environment:
- On GNU/Linux systems, the host's 'ldd' is linked inside the custom
environment. This belongs to the GNU C Library (which is not yet
installed in Maneage). But helps in checking the linking status of the
binaries on GNU/Linux systems.
- On macOS: the 'codesign' binary is included, which is used by GNU
Emacs on macOS to sign the built executable.
- GNU Bison has been moved in basic software (necessary for GNU Binutils).
- The Zip and Unzip programs have been moved as high-level software that
have to be manually requested when necessary. This is because they are
not used by any of the basic software anymore. They were just installed
as dependencies of GNU Tar to be close the other compression
programs. Also, in the past we would use the original tarballs, and some
(for example Numpy) were distributed in Zip format. However, by default,
we now use a custom Lzip tarball and don't need Zip or Unzip. This was
suggested by Zahra Sharbaf and Raul Infante-Sainz.
- Some minor edits in 'reproduce/software/shell/tarball-prepare.sh'. In
particular the 'awk' command was effectively just replacing a '_' with
'-', so it just uses a simple SED expression instead.
- Fixed bug 62700 (https://savannah.nongnu.org/bugs/index.php?62700) by
compiling 'xz' with a patched version of the xz source file
'src/liblzma/liblzma.map'.
- Astrometry.net doesn't depend on NetPBM any more. NetPBM (and its
dependencies) were causing many crashes on macOS and it also a very
strange build system that is hard to maintain. Astrometry.net uses it to
take images as input. However, it isn't necessary when you provide
Astrometry.net with a catalog. Therefore, Raul added some instructions
on how to run astrometry from your own custom X-Y catalog. These
instruction can be seen on top of the build rule of Astrometry.net in
'reproduce/software/make/high-level.mk'.
- h5py has been removed as a dependency of Astropy. It is an optional
dependency to write tables into HDF5 format. But since we couldn't get
it to build on macOS it has been removed. None of the current Maneage
users/developers also use this feature of Astropy!
- PLplot is added a new software, but not a default pre-requisite of SCAMP
(which can use it to generate figures), because there were many build
problems on macOS. Instructions have been added on top of SCAMP on how
to add PLplot as a dependency.
- With the aim of being able to install Plplot on macOS, we have wrote
several lines to fix header problems. However, we didn't succeed. In any
case we are leaving these lines in case they are useful in the future.
- The '-Wno-nullability-completeness' compiler flag (which is primarily
necessary for macOS) is now only added for macOS systems. It was causing
many warnings of un-recognized option in GNU/Linux systems.
- The 'mkswap' program of Util-Linux has been disabled because it caused
crashes on older kernels. Generally, its not necessary for a Maneage
project because it needs root permissions to run!
- LibXT (of the x.org software) has been added as a dependency of Cairo.
- ImageMagick and Lzip were using the host's C++ standard library! But on
GNU/Linux we build our own C++ Standard Library with GCC, so with this
commit, they properly link with Maneage's C++ standard library.
- ImageMagick on macOS couldn't properly link with Maneage's Ghostscript
library! This has been fixed using macOS's install_name_tool.
- Necessary RAM to build GCC on GNU/Linux systems changed to ~8GB, see
https://savannah.nongnu.org/task/?16244#comment12
- Pythran is no longer as prerequisite of Scipy. Until now, Pythran was a
prerequisite of Scipy. But we noticed that it is optional and was
causing problems on macOS.
- The URLs of some of the software have been updated in
'reproduce/software/config/urls.conf'. By default, these are all
commented, but they can be useful when searching for new versions or
when a project needs custom software that is not (yet) in Maneage.
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Until now, astrometry.net didn't explicitly depend on Astropy! However,
astrometry.net does depend on it (or pyfits) and will crash later when
running if astropy or pyfits aren't installed. We hadn't noticed this until
now because of the data reduction projects we had built Astropy
independently of astrometry.net! We noticed this bug in a project that
didn't use astropy!
With this commit, astropy is built as a dependency of astrometry.net and
afterwards (during the analysis), astrometry.net was able to run without
any crash.
This bug was found with the help of Zohreh Ghaffari.
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Until now, SCons (a high-level Python package builder) was using the OS
PATH when building packages (like Imfit that use SCons), not Maneage's
PATH. This happened even though 'reproduce/software/make/high-level.mk'
completely removes the host's PATH to avoid any host OS dependency.
After some investigation, we recognized that SCons hard-codes operating
system directories into its source! This doesn't let the user (Maneage in
this case; that builds packages that use SCons) customize the search
directories. As a result, even though we have our own linker and compiler
in Maneage, SCons would go and use the operating system's linker and
compiler, causing a leak in the controlled environment we plan to achieve
in Maneage. Not letting users customize such critical components of a
software and hard-coding parameters is bad program design!
This wasn't noticed until now because most operating systems we tested on
were relatively recent and the versions of Maneage's linker and the OS
linker weren't too different! However, after testing on a much older
operating system (GNU/Linux 4.4.0-143-generic X86_64), the operating
system's linker couldn't build Imfit (that uses SCons) and would crash.
With this commit, after unpacking SCons's source (but before building or
installing it), we have added a step to modify SCons's source and replace
the hard-coded PATH directories with Maneage's PATH. This fixed the
problem.
This bug has been fixed with the help of Mohammad Akhlaghi.
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SUMMARY: no special action should be necessary; but its an important update
in low-level Maneage infra-structure (related with downloading and setting
input checksums).
Until now, we had a separate 'download.mk' as one of the default
sub-Makefiles that should have been loaded in all the 'top-*.mk' files
after 'initialize.mk'. This was due to historic reasons: until Commit
91799fe4b6d, we had to manually make some changes in 'download.mk' for
every input file we defined in 'INPUTS.mk' (which was very inconvenient,
and not easily possible for a large number of files!). But since Commit
91799fe4b6d, those manual changes are no longer necessary, and a normal
user will hardly ever need to touch the contents of 'download.mk' (which
also had one effective rule).
Furthermore, based on shared projects with Zohre Ghaffari and Sepideh
Eskandarlou (which involved a large number of large files), we recognized
that it is very inconvenient to download a file once, update its checksum,
and re-run Maneage (so the validation works). A robust solution was
necesary to let project authors download the data and automatically update
the checksum.
With this commit, to help in high-level project management in Maneage, the
single, and generic rule of 'download.mk' has been moved to
'initialize.mk', enabling us to fully remove this extra sub-Makefile from
Maneage's source.
Furthermore, with this commit, a usable solution to the automatic updating
of the checksum has also been implemented (which has been described in the
comments of 'INPUTS.conf'): the users can now set the checksum to
'--auto-replace--'. In this case, the download rule (now in
'initialize.mk') will automatically update that line of 'INPUTS.conf' and
add the checksum instead.
After './project make' is complete, when the user runs 'git diff', they can
see all the updated checksums in the source of their project and commit the
updated 'INPUTS.conf' into the source so this will not be necessary later.
Two other smaller issues have also been addressed in this commit:
- There was an extra ',' in the call to 'filter-out' when we defined
'prepare-dep' in 'reproduce/analysis/make/prepare.mk'. This would cause
a crash (with Make complaining that there is no rule for target
'initialize.mk,': notice the extra ','). With this commit, that extra
',' has been removed and the problem was solved.
- The build recipe of Imfit (in 'reproduce/software/make/high-level.mk'),
had two SPACE characters after '--no-openmp' which would make the
reading hard. They have been updated to one SPACE.
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Until now, we never had the opportunity of testing Maneage in a macOS
laptop with an Apple M1 CPU (tested on macOS Monterey; version 12.3). The
way of getting the number of cores for this type of CPU is different from
other macOSs. It was therefore necessary to change the parameters of the
'sysctl' for properly accounting this CPU.
Furthermore, until now, GhostScript and ImageMagick were built
independently. However, they were not linked. As a consequence, when trying
to obtain an image with the program 'convert' (that belongs to
ImageMagick'), it complains about not having some fonts. This can be fixed
by letting 'ImakeMagick' know that 'GhostScript' libraries are available.
With this commit, GhostScript has been set as a dependency of ImageMagick,
and ImageMagick is configured with the '--with-gslib' flag. Furthermore, to
read the number of M1 CPU cores, we distinguish between the Apple M1 and
all other CPU types. However, Maneage still does not successfully build all
the software until the end of the configure step. There are other problems
that need to be fixed for Apple's M1.
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Until now, there were several portability issues in Maneage:
1. Maneage would crash on older operating systems (checked on Debian 6),
where Wget didn't have the '--no-use-server-timestamps'.
2. On a Linux kernel 2.6.32 (of the same Debian 6 above) some features in
'util-linux' (like 'swapon' or 'libmount') wouldn't build and wouldn't
let 'util-linux' complete. These features need root permissions to be
useful, so the wouldn't be used in Maneage any way! But they wouldn't
let Maneage get built
3. The './project shell' command would still read the host's '~/.bashrc',
letting the host environment leak-in to Maneage's interactive shell.
4. The building of Flex 2.64 wouldn't complete due to a segmentation
fault an Ubuntu, but NetPBM (which depends on Flex) would crash with a
wrong usage of 'yyunput'. This had actually caused a non-update to
Flex in a previous Maneage software update.
5. The update Astrometry.net would assume SExtractor's executable name is
'source-extractor'; causing a crash in usage. This forced the users to
manually create a 'source-extractor' symbolic link in the '.local/bin'
directory.
6. The 'reproduce/software/shell/tarball-prepare.sh' script (that is used
for making Maneage-standard tarballs) wouldn't accept option values
with an '=' between the option name and value! It also didnt' print
sufficiently informative messages and errors (for example it would say
"skipping ..." (making the user think there is a problem!), but it was
actually that the file already existed!
7. The 'reproduce/analysis/make/prepare.mk' and
'reproduce/analysis/make/verify.mk' Makefiles that needed to reject
some of the 'makesrc' sub-Makefiles would simply substitute their names
with nothing. But this would cause problems when the name is part of
the name of another sub-Makefile.
8. On the Debian 6 system mentioned above the raw 'df' command's output
wasn't in the expected format; so Maneage would fail to properly detect
the free space in the disk.
With these commit, all the issues above have been solved: for 1, A check
has been added to avoid using that option. For 2, those 'util-linux'
features have been disabled. For 3, the '--norc' and '--noprofile' options
have beed added to the call to Bash. For 4, see below. For 5, the symbolic
link is now automatically made with SExtractor. For 6, the option reading
components of that script have been fully re-written and more robust sanity
checks are also added, with more informative warnings. For 7, the 'subst'
function of Make was replaced with 'filter-out' and this fixed the
problem. For 8, 'df' is called with the '-P' option so it has a unified
format in all versions.
For 4, the versions of 'flex' and 'netpbm' have been updated. Since they
were the dependency of 'astrometrynet', that has also been updated. In the
process, we discovered that 'lzip' has a new version which claims to be
faster, so that is also updated.
lzip 1.22 --> 1.23
astrometrynet 0.85 --> 0.89
flex 2.6.4 --> 2.6.4-410-74a89fd
netpbm 10.73.39 --> 10.73.39
NetPBM needed some manual manipulation in its source (to remove the extra
line), so the necessary steps have been added to its build recipe in
'reproduce/software/make/high-level.mk'.
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Until now, Maneage failed to build the 'file' program on at least one
machine running CentOS version 7.9.2009 (with Linux kernel 3.10.0, and GCC
4.8.5) when running './project configure'.
With this commit (as suggested by the error message issued by the
compiler), the '-std=c99' is passed to the compiler in the 'file' recipe
(within 'basic.mk'). This flag puts the compiler in C99 mode, which forces
it to compile code according to the 1999 edition of the C standard. This
was necessary for older versions of GCC (for example GCC 4.8.5 was released
in June 2015); hence why others hadn't reported this issue until now.
After this fix, File compiles succesfully on such systems; without causing
any problem with newer GCC versions (tested in GCC 12.1.0).
This issue was solved with the help of Pedram Ashofte Ardakani and Mohammad
Akhlaghi.
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Until now, the '$(project-commit-hash)' Make variable of 'initialize.mk'
simply called 'git' to find the commit hash. However, due to one of the
recent software updates, we noticed that this command is no longer working
(and the project commit hash wasn't getting printed in the PDF)! The
problem was that Maneage's Git, couldn't find the 'libiconv' library that
it was built with.
With this commit, the '$(shell' command that calls Git, first exports
'LD_LIBRARY_PATH' to Maneage's software build directory. As a result, the
Git command can work and will report the commit as a LaTeX macro to be used
in the paper. To avoid relying on PATH outside of Make recipes, we now also
directly call the Git executable with Maneage.
Some other minor issues have been found and fixed in this commit:
- README-hacking.md: some minor edits and typo corrections.
- initialize.mk: the '$(curdir)' variable is now used in several places
that we were calling 'pwd'.
- versions.conf: 'xlsxio-version' now included with other programs. Until
now it was commented because GCC 11.1.0 had issues with it. However, GCC
11.2.0 doesn't have a problem any more, so it has been returned to the
list of all high-level programs.
- xorg.mk: used same format to comment recipe lines as the other Makefiles
(a '#' followed by a TAB).
- preamble-pgfplots.tex: lines to comment for building an EPS figure with
PGFPlots have been re-formatted to be more human-readable.
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Until now, one had to follow the instructions from [1] to prepare a
standard software tarball before merging with the low-level
tarballs-software repository [2]. The script only worked for '.tar.gz'
suffix and was only available as a comment on Savannah (in [1]).
With this commit, the script has been imported into Maneage as
'reproduce/software/shell/tarball-prepare.sh' to simplify future software
updates. It work with all supported '.tar.*' suffixes (of the upstream
tarball repository) and will convert the tarballs to Maneage's standard
format. Also, this script has a minimal argument parser and can skip the
tarballs that are already unpacked, allowing faster tests.
This script was used to update the versions of:
Coreutiles 9.0 --> 9.1
Git 2.34 --> 2.36
Emacs 27.2 --> 28.1
The main motive behind this update was Git which announced a vulnerability
issue [3] and suggested an update to the latest version as soon as
possible. More detail is described in this github blog [4], but in summary,
it was a security issue on multi-user systems that has been found and fixed
by Git developers. Since Maneage is often installed on such shared systems,
it was important to make this update. GNU Coreutils and GNU Emacs were also
updated because they are also commonly used.
The following improvements have also done with this commit:
- .gitignore: ignore emacs auto-save files (that end with a '#')
- README-hacking.md: In the checklist for updating the Maneage branch, the
no-longer-necessary '--decorate' option of Git was removed from the
command to check the general branch history.
[1] https://savannah.nongnu.org/task/?15699
[2] https://git.maneage.org/tarballs-software.git/
[3] https://lore.kernel.org/git/xmqqv8veb5i6.fsf@gitster.g/
[4] https://github.blog/2022-04-12-git-security-vulnerability-announced/
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This commit primarily affects the configuration step of Maneage'd projects,
and in particular, updated versions of the many of the software (see
P.S.). So it shouldn't affect your high-level analysis other than the
version bumps of the software you use (and the software's possibly
improve/changed behavior).
The following software (and thus their dependencies) couldn't be updated as
described below:
- Cryptography: isn't building because it depends on a new
setuptools-rust package that has problems
(https://savannah.nongnu.org/bugs/index.php?61731), so it has been
commented in 'versions.conf'.
- SecretStorage: because it depends on Cryptography.
- Keyring: because it depends on SecretStorage.
- Astroquery: because it depends on Keyring.
This is a "squashed" commit after rebasing a development branch of 60
commits corresponding to a roughly two-month time interval. The following
people contributed to this branch.
- Boudewijn Roukema added all the R software infrastructure and the R
packages, as well as greatly helping in fixing many bugs during the
update.
- Raul Infante-Sainz helped in testing and debugging the build.
- Pedram Ashofteh Ardakani found and fixed a bug.
- Zahra Sharbaf helped in testing and found several bugs.
Below a description of the most noteworthy points is given.
- Software tarballs: all updated software now have a unified format
tarball (ustar; if not possible, pax) and unified compression (Lzip) in
Maneage's software repository in Zenodo
(https://doi.org/10.5281/zenodo.3883409). For more on this See
https://savannah.nongnu.org/task/?15699 . This won't affect any extra
software you would like to add; you can use any format recognized by
GNU Tar, and all common compression algorithms. This new requirement is
only for software that get merged to the core Maneage branch.
- Metastore (and thus libbsd and libmd) moved to highlevel: Metastore
(and the packages it depends on) is a high-level product that is only
relevant during the project development (like Emacs!): when the user
wants the file meta data (like dates) to be unchanged after checking
out branches. So it should be considered a high-level software, not
basic. Metastore also usually causes many more headaches and error
messages, so personally, I have stopped using it! Instead I simply
merge my branches in a separate clone, then pull the merge commit: in
this way, the files of my project aren't re-written during the checkout
phase and therefore their dates are untouched (which can conflict with
Make's dates on configuration files).
- The un-official cloned version of Flex (2.6.4-91 until this commit) was
causing problems in the building of Netpbm, so with this commit, it has
been moved back to version 2.6.4.
- Netpbm's official page had version 10.73.38 as the latest stable
tarball that was just released in late 2021. But I couldn't find our
previously-used version 10.86.99 anywhere (to see when it was released
and why we used it! Its at last more than one year old!). So the
official stable version is being used now.
- Improved instructions in 'README.md' for building software environment
in a Docker container (while having project source and output data
products on the local system; including the usage of the host's
'/dev/shm' to speed up temporary operations).
- Until now, the convention in Maneage was to put eight SPACE characters
before the comment lines within recipes. This was done because by
default GNU Emacs (also many other editors) show a TAB as eight
characters. However, in other text editors, online browsers, or even
the Git diff, a TAB can correspond to a different number of
characters. In such cases, the Maneage recipes wouldn't look too
interesting (the comments and the recipe commands would show a
different indentation!).
With this commit, all the comment lines in the Makefiles within the
core Maneage branch have a hash ('#') as their first character and a
TAB as the second. This allows the comment lines in recipes to have the
same indentation as code; making the code much more easier to read in a
general scenario including a 'git diff' (editor agnostic!).
P.S. List of updated software with their old and new versions
- Software with no version update are not mentioned.
- The old version of newly added software are shown with '--'.
Name (Basic) Old version New version
------------ ----------- -----------
Bzip2 1.0.6 1.0.8
CURL 7.71.1 7.79.1
Dash 0.5.10.2 0.5.11.5
File 5.39 5.41
Flock 0.2.3 0.4.0
GNU Bash 5.0.18 5.1.8
GNU Binutils 2.35 2.37
GNU Coreutils 8.32 9.0
GNU GCC 10.2.0 11.2.0
GNU M4 1.4.18 1.4.19
GNU Readline 8.0 8.1.1
GNU Tar 1.32 1.34
GNU Texinfo 6.7 6.8
GNU diffutils 3.7 3.8
GNU findutils 4.7.0 4.8.0
GNU gmp 6.2.0 6.2.1
GNU grep 3.4 3.7
GNU gzip 1.10 1.11
GNU libunistring 0.9.10 1.0
GNU mpc 1.1.0 1.2.1
GNU mpfr 4.0.2 4.1.0
GNU nano 5.2 6.0
GNU ncurses 6.2 6.3
GNU wget 1.20.3 1.21.2
Git 2.28.0 2.34.0
Less 563 590
Libxml2 2.9.9 2.9.12
Lzip 1.22-rc2 1.22
OpenSLL 1.1.1a 3.0.0
Patchelf 0.10 0.13
Perl 5.32.0 5.34.0
Podlators -- 4.14
Name (Highlevel) Old version New version
---------------- ----------- -----------
Apachelog4cxx 0.10.0-603 0.12.1
Astrometry.net 0.80 0.85
Boost 1.73.0 1.77.0
CFITSIO 3.48 4.0.0
Cmake 3.18.1 3.21.4
Eigen 3.3.7 3.4.0
Expat 2.2.9 2.4.1
FFTW 3.3.8 3.3.10
Flex 2.6.4-91 2.6.4
Fontconfig 2.13.1 2.13.94
Freetype 2.10.2 2.11.0
GNU Astronomy Utilities 0.12 0.16.1-e0f1
GNU Autoconf 2.69.200-babc 2.71
GNU Automake 1.16.2 1.16.5
GNU Bison 3.7 3.8.2
GNU Emacs 27.1 27.2
GNU GDB 9.2 11.1
GNU GSL 2.6 2.7
GNU Help2man 1.47.11 1.48.5
Ghostscript 9.52 9.55.0
ICU -- 70.1
ImageMagick 7.0.8-67 7.1.0-13
Libbsd 0.10.0 0.11.3
Libffi 3.2.1 3.4.2
Libgit2 1.0.1 1.3.0
Libidn 1.36 1.38
Libjpeg 9b 9d
Libmd -- 1.0.4
Libtiff 4.0.10 4.3.0
Libx11 1.6.9 1.7.2
Libxt 1.2.0 1.2.1
Netpbm 10.86.99 10.73.38
OpenBLAS 0.3.10 0.3.18
OpenMPI 4.0.4 4.1.1
Pixman 0.38.0 0.40.0
Python 3.8.5 3.10.0
R 4.0.2 4.1.2
SWIG 3.0.12 4.0.2
Util-linux 2.35 2.37.2
Util-macros 1.19.2 1.19.3
Valgrind 3.15.0 3.18.1
WCSLIB 7.3 7.7
Xcb-proto 1.14 1.14.1
Xorgproto 2020.1 2021.5
Name (Python) Old version New version
------------- ----------- -----------
Astropy 4.0 5.0
Beautifulsoup4 4.7.1 4.10.0
Beniget -- 0.4.1
Cffi 1.12.2 1.15.0
Cryptography 2.6.1 36.0.1
Cycler 0.10.0 0.11.0+}
Cython 0.29.21 0.29.24
Esutil 0.6.4 0.6.9
Extension-helpers -- 0.1
Galsim 2.2.1 2.3.3
Gast -- 0.5.3
Jinja2 -- 3.0.3
MPI4py 3.0.3 3.1.3
Markupsafe -- 2.0.1
Numpy 1.19.1 1.21.3
Packaging -- 21.3
Pillow -- 8.4.0
Ply -- 3.11
Pyerfa -- 2.0.0.1
Pyparsing 2.3.1 3.0.4
Pythran -- 0.11.0
Scipy 1.5.2 1.7.3
Setuptools 41.6.0 58.3.0
Six 1.12.0 1.16.0
Uncertainties 3.1.2 3.1.6
Wheel -- 0.37.0
Name (R) Old version New version
-------- ----------- -----------
Cli -- 2.5.0
Colorspace -- 2.0-1
Cowplot -- 1.1.1
Crayon -- 1.4.1
Digest -- 0.6.27
Ellipsis -- 0.3.2
Fansi -- 0.5.0
Farver -- 2.1.0
Ggplot2 -- 3.3.4
Glue -- 1.4.2
GridExtra -- 2.3
Gtable -- 0.3.0
Isoband -- 0.2.4
Labeling -- 0.4.2
Lifecycle -- 1.0.0
Magrittr -- 2.0.1
MASS -- 7.3-54
Mgcv -- 1.8-36
Munsell -- 0.5.0
Pillar -- 1.6.1
R-Pkgconfig -- 2.0.3
R6 -- 2.5.0
RColorBrewer -- 1.1-2
Rlang -- 0.4.11
Scales -- 1.1.1
Tibble -- 3.1.2
Utf8 -- 1.2.1
Vctrs -- 0.3.8
ViridisLite -- 0.4.0
Withr -- 2.4.2
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This commit provides a hack/correction to the unwrapped GCC source files
that sym-links the generic file 'libgcc/unwind-generic.h' to the two
directories in which a file includes "unwind.h" or <unwind.h>. The aim is
that the gcc compilation system uses this header file from the internal gcc
source files instead of searching for a system-level file 'unwind.h'.
This commit also unaliases two 'ls' commands in some build recipes of
'basic.mk' in case the host system (normally at user level) has aliased the
command to something like 'ls -F'. In the situation that sometimes occurs
of library files being given executable status, the '-F' decorative option
could lead to an asterisk being included in a string that is not expected
to contain asterisks. If the system shell does not contain the 'alias'
command at all, then a fallback of 'true' should provide safe
behaviour. The notation of the 'sed' command is also clarified.
This solves bug #61240: https://savannah.nongnu.org/bugs/index.php?61240
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Until now, the 'RPATH' variable (specifying where to look for shared
libraries) wasn't being set in the 'libcrypto' library of OpenSSL (it was
only set for the 'libssl' library).
Also, Gettext used the host Emacs for some operations during installation
that could cause the following crash (because we are giving priority to
local libraries, which the host Emacs doesn't recognize):
emacs: /BDIR/libcrypto.so.1.1: version `OPENSSL_1_1_1b' not found
(required by /lib64/libk5crypto.so.3)
With this commit both these bugs have been fixed: 1) Patchelf is run on the
'libcrypto' library also and 2) we pass the '--without-emacs' configuration
option to the configure script of Gettext.
These bugs were found by Elham Saremi.
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On systems that allow it (like GNU/Linux systems), Maneage will build the
necessary software in shared memory (a directory that is actually in the
RAM, not on an SSD/HDD, on GNU/Linux systems, it is '/dev/shm'). This
allows Maneage to operate faster and not harm the HDD/SSD with all the
temporary writing of many small files.
Until now, we would only check that this directory exists and that it has
enough space. However, some systems also set the 'noexec' flag on shared
memory for security reasons [1]. This causes Maneage to crash upon building
of the software in later phases.
With this commit, at the very start of the configuration step, and after
all other shared-memory checks are done, a dummy executable script file is
created there and its execution is tested. If it doesn't work, shared
memory will not be used at all.
In the process, the steps dealing with the software building directory in
the configure script have been brought in one place and comments were added
to further clarify every step.
This commit was initially done by Boud Roukema and later edited by Mohammad
Akhlaghi.
[1] https://web.archive.org/web/20210624192819/https://serverfault.com/questions/72356/how-useful-is-mounting-tmp-noexec
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Once a year, the texlive update system becomes incompatible with the
version from the previous year. Since a texlive install failure is
considered non-fatal by 'high-level.mk', so until now, the user could miss
the printed message and mistakenly believe that the configure is valid.
This commit explicitly adds a 10-second delay that should be enough for a
user who does the 'configure --existing-conf' step alone to notice that
there is a TeX Live problem. It also adds the explicit instruction of how
to allow an update from an earlier year's texlive installer to the warning
message (by deleting '.build/software/tarballs/install-tl-unx.tar.gz'). I
had to rediscover this a few times for old Maneage installs.
Also, a few lines in 'reproduce/software/shell/configure.sh' were indented
with a TAB (that is not recommended because TAB is displayed with different
widths on different browsers). So while doing this commit, those TABs were
also converted to a space.
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When built in 'group' mode, the write permissions of all created files will
be activated for a certain group of users in the host operating system. The
user specifies the name of the group with the '--group' option at configure
time. At the very start, the './project' script checks to see if the given
group name actually exists or not (to avoid hard-to-debug errors popping up
later).
Until now, the checking 'sg' command (that was used to build the project
with group-writable permissions) would always fail due to the excessive
number of redirections. Therefore, it would always print the error message
and abort.
With this commit, the output of 'sg' is no longer re-directed (which also
helps users in debuggin). If the group does actually exist, it will just
print a small statement saying so, and if it fails, the error message is
printed. This fixed the problem, allowing maneage to be built in
group-mode.
I also noticed that the variable name keeping the group name
('reproducible_paper_group_name') used the old name for the project (which
was "Reproducible paper template"! So it has been changed/corrected to
'maneage_group_name'.
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Until now the SWIG software would use the host operating system's packages
to find the TCL configuraiton (which we don't install yet in Maneage). In
particular, you can see the error during its configuration here:
....
checking for pkg-config... pkg-config
checking for Tcl configuration... found /usr/lib/tclConfig.sh
/usr/lib/tclConfig.sh: line 2: dpkg-architecture: command not found
/usr/lib//tcl8.6/tclConfig.sh: line 2: dpkg-architecture: com. not found
With this commit, TCL has been disabled when building SWIG with the
'--without-tcl' option. Later, when we add TCL in Maneage, we can remove
this option.
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With a recent update of macOS systems (macOS Big Sur 11.2.3 and Xcode
12.4), there are many warnings when building C programs (for example the
simple program we compile to check the compiler, or some of the software
like `gzip'). It prints hundreds of warning lines for every source file
that are irrelevant for our builds, but really clutters the output.
With this commit, these warnings are disabled by adding
`-Wno-nullability-completeness' to the 'CPPFLAGS' environment
variable. This has also been added to the very first check of the C
compiler in the configure step.
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Until now, each time there was a problem in the configuration of Maneage'd
projects and debugging was necessary, we had to take the following changes:
- Run the configuration on a single thread ('-j1') to see the building of
only the problematic software.
- Disable the Zenodo check manually by commenting those parts of
'reproduce/software/shell/configure.sh'. Because the internet connection
wastes a few seconds and is thus very annoying during repeated runs!
- Manually remove the '-k' option that was passed to Make (when building
the software). With the '-k', Make keeps going with the execution of
other targets if something crashes and this usually causes confusions
during the debugging.
Doing the manual changes within the code was both very annoying and prone
to errors (forgetting to correct it!).
With this commit, the existing '--debug' option has been generalized to the
software configuration phase of Maneage also. Until now, it was only
available in the analysis phase (and would directly be passed to the 'make'
command that would run the analysis). When this option is used, and the
project is in the software configuration phase, the Zenodo check won't be
done, it will use one single thread ('-j1'), and it will stop the execution
as soon as an error occurs (Make is not run with '-k').
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Until now when making a link to the system's 'dl' and 'pthread' libraries
we were simply linking the installed location on the system (in
'/usr/lib'). However, in some systems, these may themselves be links to
other locations and this could cause linking problems.
With this commit, we now use 'realpath' to extract the absolute address of
the final file that the libraries may link to, and directly link to them.
A minor cosmetic correction was also made in the build rule for CFITSIO:
the long line was broken into two!
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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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Until now, when building GNU Binutils on GNU Linux operating systems, we
would simply put a link to the host's core C library components (the
'*crt*' files). However, the symbolic link wasn't "forced"! So if it
already existed in the build directory, it would crash.
With this commit a '-f' option has been added to the 'ln' command and this
fixed the problem.
This bug was reported by Zahra Sharbaf.
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After correctly setting Less to depend on 'ncurses', I noticed its still
not linking to Maneage's 'ncurses', but pointing to my host system's
'ncurses' (that happens to have the same version! So it would crash on a
system with a different version). This shows that like some other software,
we need to manually correct the RPATH inside Less.
With this command, the necessary call to 'patchelf' has been added and with
it, the installed 'less' command properly linked to Maneage's internal
build of 'ncurses'.
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Until now, the 'less' software package (used to view large files easily on
the command-line and used by Git for things like 'git diff' or 'git log')
only depended on 'patchelf' (which is a very low-level software).
However, as Boud reported in bug #59811 [1], building less would crash with
an error saying "Cannot find terminal libraries" in some systems (including
the proposed Docker image of 'README.md' which I confirmed
afterwards). Looking into the 'configure' script of 'less', I noticed that
'less' is actually just checking for some functions provided by the ncurses
library!
With this commit, 'less' depends on 'ncurses'. I was able to confirm that
with this change, 'less' successfully builds within the Docker image.
[1] https://savannah.nongnu.org/bugs/?59811
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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, when building the high-level (optional) software, we would give
both 'CPPFLAGS' and 'C_INCLUDE_PATH' the same value/directory in
'high-level.mk'. But we recently found that on macOS's C compiler
('clang'), if a directory is included in both 'CPPFLAGS' and
'C_INCLUDE_PATH', then that directory is ignored in 'CPPFLAGS' (which has
higher priority). This caused linking problems when the version of a
software on the host was different from the Maneage version.
With this commit, 'C_INCLUDE_PATH' is not set on macOS any more and this
fixed the problem on the reported systems.
This bug was fixed with the help of Mohammad Akhlaghi and Mahdieh Navabi.
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Less is rarely used in non-interactive mode and is primarily intended for
interactively viewing large files. So its need within Maneage (for batch
processing) wasn't often felt until now. However, when running './project
shell' (which completely closes-off the outside environment), or building a
Maneage'd project within a minimal container that doesn't have less, it
becomes hard to use Git (and in particular its 'diff' output which depends
on 'less').
With this commit, Less has been added as a dependency of Git in
'basic.mk'. In total its built product is roughly 800KB and builds within a
second or two. So it isn't a burden on any project. But it can be very
useful when the projects are being developed within the Maneage environment
itself.
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In a recent build on a macOS, we recognized that Texinfo needs the
'libintl.h' headers of Gettext. However, Gettext depends on M4, and until
now we had set M4 to depend on Texinfo. Therefore adding Gettext as a
dependency of Texinfo would cause a circular dependency.
On the macOS, we temporarily disabled M4's Texinfo dependency, and the
build went through. I also checked on my GNU/Linux system: temporarily
renamed all Texinfo built files from my system and done a clean build of M4
and it succeeded. To be further safe, I built Maneage from this commit
(where M4 doesn't depend on Texinfo) in a Docker container, and it went
through with no problems. So the current M4 version indeed doesn't need
Texinfo. I think adding Texinfo as a dependency of M4 was a historic issue
from the early days.
In the process, I also cleaned 'basic.mk' a little:
- A "# Level N" comment was added on top of each group of software that
can be built in parallel (generally).
- GNU Nano was moved to the end of the file (to be "Level 6").
- Some comments were edited in some places.
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After a fresh build of Maneage with a newly downloaded TeXLive, I noticed
that it is complaining about not finding 'xstring.sty', apparently some
package that depeneded on it is no longer including it itself!
It is thus now added to the packages that are built by Maneage's TeXLive.
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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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Until now, during the configure step it was checked if the host Operative
System were GNU/Linux, and if not, we assumed it is macOS. However, it can
be any other different OS! With this commit, now we explicity check if the
system is GNU/Linux or Darwin (macOS). If it is not any of them, a warning
message says to the user that the host system is different from which we
have checked so far (and invite to contact us if there is any problem).
In addition to this, if the system is macOS, now it checks if Xcode is
already installed in the host system. If it is not installed, a warning
message informs the user to do that in case a problem/crash in the
configure step occurs. We have found that it is convenient to have Xcode
installed in order to avoid some problems.
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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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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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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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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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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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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 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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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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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, 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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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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