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SUMMARY: just house-cleaning, no need to do anything major in your
branch. Just update the copyright years in files that you have added.
Until now, the latest copyright years of the whole Maneage source code was
2022! As of this commit, we have already moved to 2023 for 5 months!
Furthermore, there were a few other minor issues that needed correction:
- The URL to download input datasets wasn't quoted in 'initialize.mk' or
the download script! As a result, when the input URL had characters that
are meaningful to the shell (like '&'), the download command would not
work.
- The only program that had 'make check' in the 'basic.mk' programs was
MPFR. At that stage, we still haven't built our own compiler at this
stage, this is not accurate.
- The 'pyerfa' and 'extension-helpers' packages in Python need
'setuptools_scm' on some systems. But until now, it was not in the list
of their prerequisites.
With this commit, all the issues above have been corrected.
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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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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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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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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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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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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 only build Flock before building everything else
using Make (calling 'basic.mk') in parallel. Flock was necessary to avoid
parallel downloads during the building of software (which could cause
network problems). But after recently trying Maneage on FreeBSD (which is
not yet complete, see bug #58465), we noticed that the BSD implemenation of
Make couldn't parse 'basic.mk' (in particular, complaining with the 'ifeq'
parts) and its shell also had some peculiarities.
It was thus decided to also install our own minimalist shell, Make and
compressor program before calling 'basic.mk'. In this way, 'basic.mk' can
now assume the same GNU Make features that high-level.mk and python.mk
assume. The pre-make building of software is now organized in
'reproduce/software/shell/pre-make-build.sh'.
Another nice feature of this commit is for macOS users: until now the
default macOS Make had problems for parallel building of software, so
'basic.mk' was built in one thread. But now that we can build the core
tools with GNU Make on macOS too, it uses all threads. Furthermore, since
we now run 'basic.mk' with GNU Make, we can use '.ONESHELL' and don't have
to finish every line of a long rule with a backslash to keep variables and
such.
Generally, the pre-make software are now organized like this: first we
build Lzip before anything else: it is downloaded as a simple '.tar' file
that is not compressed (only ~400kb). Once Lzip is built, the pre-make
phase continues with building GNU Make, Dash (a minimalist shell) and
Flock. All of their tarballs are in '.tar.lz'. Maneage then enters
'basic.mk' and the first program it builds is GNU Gzip (itself packaged as
'.tar.lz'). Once Gzip is built, we build all the other compression software
(all downloaded as '.tar.gz'). Afterwards, any compression standard for
other software is fine because we have it.
In the process, a bug related to using backup servers was found in
'reproduce/analysis/bash/download-multi-try' for calling outside of
'basic.mk' and removed Bash-specific features. As a result of that bug-fix,
because we now have multiple servers for software tarballs, the backup
servers now have their own configuration file in
'reproduce/software/config/servers-backup.conf'. This makes it much easier
to maintain the backup server list across the multiple places that we need
it.
Some other minor fixes:
- In building Bzip2, we need to specify 'CC' so it doesn't use 'gcc'.
- In building Zip, the 'generic_gcc' Make option caused a crash on FreeBSD
(which doesn't have GCC).
- We are now using 'uname -s' to specify if we are on a Linux kernel or
not, if not, we are still using the old 'on_mac_os' variable.
- While I was trying to build on FreeBSD, I noticed some further
corrections that could help. For example the 'makelink' Make-function
now takes a third argument which can be a different name compared to the
actual program (used for examle to make a link to '/usr/bin/cc' from
'gcc'.
- Until now we didn't know if the host's Make implementation supports
placing a '@' at the start of the recipe (to avoid printing the actual
commands to standard output). Especially in the tarball download phase,
there are many lines that are printed for each download which was really
annoying. We already used '@' in 'high-level.mk' and 'python.mk' before,
but now that we also know that 'basic.mk' is called with our custom GNU
Make, we can use it at the start for a cleaner stdout.
- Until now, WCSLIB assumed a Fortran compiler, but when the user is on a
system where we can't install GCC (or has activated the '--host-cc'
option), it may not be present and the project shouldn't break because
of this. So with this commit, when a Fortran compiler isn't present,
WCSLIB will be built with the '--disable-fortran' configuration option.
This commit (task #15667) was completed with help/checks by Raul
Infante-Sainz and Boud Roukema.
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