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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: 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, 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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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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The LaTeX macro files for these two subMakefiles are created on every run
of './project make'. So their commands are also printed every time and
hardly ever will a normal user want to modify or change these.
So to avoid populating the standard output of a Maneaged project with all
these extra lines every time (possibly getting mixed with the important
analysis or LaTeX outputs), an '@' has been placed at the start of the
recipes. With an '@' at the start of the recipe, Make is instructed to not
print the commands it wants to run in the standard output.
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This commit clarifies the initial usage of Zenodo for reserving a Zenodo
identifier and starting an 'unpublished' upload. Some other minor wording
changes are done here.
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Summary of possible semantic conflicts
1. The recipe to download input datasets has been modified. You have to
re-set the old 'origname' variable to 'localname' (to avoid confusion)
and the default dataset URL should now be complete (including the
actual filename). See the newly added descriptions in 'INPUTS.conf' for
more on this.
Until now, when the dataset was already present on the host system, a link
couldn't be made to it, causing the project to crash in the checksum
phase. This has been fixed with properly naming the main variable as
'localname' to avoid the confusion that caused it.
Some other problems have been fixed in this recipe in the meantime:
- When the checksum is different, the expected and calculated checksums
are printed.
- In the default paper, we now print the full URL of the dataset, not just
the server, so the checksum of the 'download.tex' step has been updated.
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Possible semantic conflicts (that may not show up as Git conflicts but may
cause a crash in your project after the merge):
1) The project title (and other basic metadata) should be set in
'reproduce/analysis/conf/metadata.conf'. Please include this file in
your merge (if it is ignored because of '.gitattributes'!).
2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if
you have added all analysis Makefiles to the '.gitattributes' file
(thus not merging any change in them with your branch). For example
with this command:
git diff master...maneage -- reproduce/analysis/make/initialize.mk
3) The old 'verify-txt-no-comments-leading-space' function has been
replaced by 'verify-txt-no-comments-no-space'. The new function will
also remove all white-space characters between the columns (not just
white space characters at the start of the line). Thus the resulting
check won't involve spacing between columns.
A common set of steps are always necessary to prepare a project for
publication. Until now, we would simply look at previous submissions and
try to follow them, but that was prone to errors and could cause
confusion. The internal infrastructure also didn't have some useful
features to make good publication possible. Now that the submission of a
paper fully devoted to the founding criteria of Maneage is complete
(arXiv:2006.03018), it was time to formalize the necessary steps for easier
submission of a project using Maneage and implement some low-level features
that can make things easier.
With this commit a first draft of the publication checklist has been added
to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018
and zenodo.3872248. To help guide users on implementing the good practices
for output datasets, the outputs of the default project shown in the paper
now use the new features). After reading the checklist, please inspect
these.
Some other relevant changes in this commit:
- The publication involves a copy of the necessary software
tarballs. Hence a new target ('dist-software') was also added to
package all the project's software tarballs in one tarball for easy
distribution.
- A new 'dist-lzip' target has been defined for those who want to
distribute an Lzip-compressed tarball.
- The '\includetikz' LaTeX macro now has a second argument to allow
configuring the '\includegraphics' call when the plot should not be
built, but just imported.
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In time, some of the copyright license description had been mistakenly
shortened to two paragraphs instead of the original three that is
recommended in the GPL. With this commit, they are corrected to be exactly
in the same three paragraph format suggested by GPL.
The following files also didn't have a copyright notice, so one was added
for them:
reproduce/software/make/README.md
reproduce/software/bibtex/healpix.tex
reproduce/analysis/config/delete-me-num.conf
reproduce/analysis/config/verify-outputs.conf
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Until now, throughout Maneage we were using the old name of "Reproducible
Paper Template". But we have finally decided to use Maneage, so to avoid
confusion, the name has been corrected in `README-hacking.md' and also in
the copyright notices.
Note also that in `README-hacking.md', the main Maneage branch is now
called `maneage', and the main Git remote has been changed to
`https://gitlab.com/maneage/project' (this is a new GitLab Group that I
have setup for all Maneage-related projects). In this repository there is
only one `maneage' branch to avoid complications with the `master' branch
of the projects using Maneage later.
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Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).
To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.
The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.
THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
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The checklist descriptions were slightly edited to be more clear. Also,
while following them, I noticed that while removing the "delete-me" parts
on `verify.mk', would cause an error: the `if [ $$m == delete-me ];'
statement we were saying to delete cause an error because `elif' was the
first statement Bash would see. So with this commit, the `download'
conditional (which isn't instructed to be deleted) was set to be the top
(with an `if') and the `delete-me' conditional now has an `elif'.
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Until now, if the file to be verified didn't exist, a different checksum
would be generated, and it would stop, but it wasn't immediately clear if
the differing checksum is because the file doesn't exist at all!
With this commit, before calculating the checksum, we first make sure if
the file exists. If it doesn't exist an explicit error is printed and thus
will help the project editor to find the cause of the problem.
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Until now, the only verification that the template provided was the
published PDF. Users had to manually compare the published and generated
PDFs (numbers, plots, tables) and see if they obtained the same
result. However, this type of manual verification is not good and is prone
to frustration and missing important differences.
With this commit, a new Makefile has been added in the analysis steps:
`verify.mk'. It provides facilities to easily verify the results that go
into the paper. For example tables that go into making the paper's plots,
or the LaTeX macros that blend into the text. See the updated parts in
`README-hacking.md` for a more complete explanation.
This completes task #15497.
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