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Until now, the Zenodo identifier for the project was for the second arXiv
release (after the first referee reports). However, since the paper has
been published, it hasn't been updated on arXiv and its necessary to make a
"final" arXiv publication.
With this commit, a new Zenodo DOI has been reserved for the third release
and is now being used.
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Until now, Maneage had undergone some updates.
With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.
In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).
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Until now, the './project make clean' command would only clean (remove) the
PDF file from the top source directory. However, if a user would run LaTeX
outside of Maneage, many extra latex output such as *.aux, *.log, *.synctex
and etc would be produced in the top source directory. These files can
interfere with './project make'.
With this commit, when './project make clean' is run, any possibly existing
LaTeX temporary files will also be deleted from the top source directory.
This problem was first reported by Matin Torkian.
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SUMMARY: it is necessary to update your 'INPUTS.conf' and 'download.mk'.
Until now, adding an input file involved several steps that needed manual
(and inconvenient!) intervention: for every file, you needed to define four
variables in 'INPUTS.conf', and in 'reproduce/analysis/make/download.mk'
you had to use a (complex for large number of files) shell 'if/elif/else'
condition to link the names of the input files to those variables. Besides
inconvenience, this could cause bugs (typos!). Furthermore, a basic MD5
checksum was used for verifying the files.
With this commit, a new structure has been defined for 'INPUTS.conf' that
(thanks to some pretty useful GNU Make features), removes the need for
users to manually edit 'reproduce/analysis/make/download.mk', and reduces
the number of variables necessary for each file to three (from
four). Furthermore, we now use the SHA256 checksum for input data
validation.
Regarding the trick used in 'INPUTS.conf' (form the newly added description
in 'download.mk'): In GNU Make, '.VARIABLES' "... expands to a list of the
names of all global variables defined so far" (from the "Other Special
Variables" section of the GNU Make manual). Assuming that the pattern
'INPUT-%-sha256' is only used for input files, we find all the variables
that contain the input file names (the '%' is the filename). Finally, using
the pattern-substitution function ('patsubst'), we remove the fixed string
at the start and end of the variable name.
Steps you need to take:
- INPUTS.conf: translate your old format to the new format (after
carefully reading the description in the comments at the start of the
file). After applying the new standards, you don't need to use the
variables of 'INPUTS.conf' directly in your Makefiles! For example if
one of your input datasets is called 'abc.fits', the checksum variable
will be 'INPUT-abc.fits-sha256' and in your high-level Makefiles, you
can simply set '$(indir)/abc.fits' as a prerequisite (like you probably
did already).
- reproduce/analysis/make/download.mk: for the definition and rule of
'inputdatasets', simply use the Maneage branch, and remove anything you
had added in your project.
In the process, I also noticed that 'README-hacking.md' still referred to
'master' as the main project branch, while we have used 'main' in the paper
(and is the common convention with Git).
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Until now, the definition of the prepare directory was wrong (not in the
'analysis' directory of the build directory). I noticed this after an
update of the Maneage branch of one project that requires the prepare step.
With this commit, this problem has been fixed.
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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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I just(!) noticed that in the CiSE version of the paper, they replaced the
"Towards" (first word in the title) with "Toward" (removing the
's'). According to thorough history provided by the Merriam-Webster
dictionary[1], the difference is mainly because of US/British English.
Also, they have slightly changed the capitalizations of the "long-term"
phrase, from "Long-term" that we had initially used to "Long-Term". I have
no particular opinion on this and accept their judgement.
To keep things in line with the published paper, I am correcting both these
issues in our version of the paper also (that will later go in arXiv).
https://www.merriam-webster.com/words-at-play/toward-towards-usage
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David made suggested some minor edits that are now implemented (most
importantly that he would not like to be associated with an ORCID ID).
I also "saved" a new Zenodo DOI for the final submission of this paper to
Zenodo, but "after" obtaining the page number information and other minor
things.
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Some minor conflicts (all expected from the commit messages in the Maneage
branch) occurred but were easily fixed.
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Summary:
- Use the new name of this variable in your Makefiles.
- In 'metadata.conf', remove fixed URL prefixes for DOIs
('https://doi.org/') or arXiv ('https://arxiv.org/abs').
Until now, the Make variable that would print the general metadata (of
whole project) into each to-be-published dataset was called
'print-copyright'! But it now does much more than simply printing the
copyright, it will also print a lot of metadata like arXiv ID, Zenodo DOI
and etc into plain-text outputs. The out-dated name could thus be
misleading and cause confusions.
With this commit, the variable is therefore called
'print-general-metadata'. After merging your project with the Maneage
branch, please replace any usage of 'print-copyright' to
'print-general-metadata'.
Also with this commit, 'README-hacking.md' mentions 'metadata.conf' and
'print-general-metadata' in the "Publication checklist" section and reminds
you to keep the first up to date, and use the second in your
to-be-published datasets.
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In the project's 'metadata.conf', we also have an option to store the
journal DOI of the project (that will later be printed in the output file
products). So now that the paper's DOI has been set by the journal, it was
time to add it in the project too.
While looking at the usage of the metadata, I noticed that the "Publication
checklist" of 'README-hacking.md' didn't talk about it. In fact, the part
about putting metadata went into a lot of detail without even mentioning
the generic 'print-general-metadata' variable (previously called
'print-copyright') that is created in 'initialize.mk'. So I removed those
extra points and just recommended using this variable for plain-text files
and putting similar info in other formats.
Some other minor changes were made:
- The metadata now doesn't need the fixed 'https://doi.org/' prefix (to
make it consistent with the arXiv identifier). Inside 'initialize.mk',
there are now two variables called 'doi-prefix-url' and
'arxiv-prefix-url' that contain the fixed prefix.
- The 'print-copyright' name was clearly outdated for all the extra
metadata that this variable created (including the copyright). So its
name was changed to 'print-general-metadata'.
The generic Maneage changes will be taken into Maneage after this (they
were tested here).
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Until now, we were primarily linking people to the Gitlab fork of this
paper. However, since this paper is part of Maneage, its main repository is
on Maneage's own server at http://git.maneage.org/paper-concept.git
With this commit therefore, all the gitlab.com URLs have been corrected to
owr own Git server.
While looking into Git-related points, I also noticed that in the demo code
listing showing how to clone Maneage and start a new project, we were using
Git's old/depreciated 'master' name. Git (and almost all common
repositories) now use 'main' as the default branch name, so this has also
been corrected here.
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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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In the previous commit, some Gnuastro-specific initializations were
removed but a few more cases remained that are removed with this
commit.
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Until now, important LaTeX packages like 'caption' (for managing figure
captions), 'hyperref' (for managing links) and 'xcolor' (for managing
colors) were being loaded inside the optional
'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove
this file from loading when you use custom journal sytels. However, these
packages will often be necessary after loading special journal styles also.
With this commit, these packages are now loaded into LaTeX as part of the
'tex/src/preamble-project.tex' file. This file is in charge of LaTeX
settings that are custom to the project and independent of its style.
Several other small corrections are made with this commit:
- I noticed that './project make texclean' crashes if no PDF exists in the
working directory! So a '-f' was added to the 'rm' command of the
'texclean' rule.
- As part of the LaTeX Hyperref, we can set general metadata or properties
for the PDF (that aren't written into the printable PDF, but into the
file metadata). They can be viewed in many PDF viewers as PDF
properties. Until now, we were only using the '\projecttitle' macro here
to write the paper's title. However, thanks to the recently added
'reproduce/analysis/config/metadata.conf', we now have a lot of useful
information that can also go here. So the 'metadata-copyright-owner' is
now used to define the PDF author, and the project's
'metadata-git-repository' and commit hash are written into the PDF
subject. But to import these, it was necessary to define them as LaTeX
macros, hence the addition of these macros in 'initialize.mk'.
- Some extra packages that aren't necessary to build the default PDF were
removed in 'preamble-project.tex'.
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Until now, when you ran './project make dist', first it would delete the
temporary files (like files ending in '~' or '.swp' created by some
editors), then it had a place to add project-specific operations for the
distribution.
However, in the process of cleaning the temporary files, it would 'cd' into
the directory that would later be packaged. So project-specific operations
would first have to 'cd' back into the top source directory. This was prone
to hard-to-find bugs.
With this commit, to avoid the problem the project-specific operations are
now placed before the cleaning phase. This is also technically good because
in the project-specific operations there may also be temporary files that
shouldn't go into the distribution tarball.
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There was a single conflict in the comments of one part of 'configure.sh'
that has been fixed.
There was also a single place that needed to convert 'BDIR' to 'badir' in
this project (so after the merge, it also built easily).
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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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Since the addition of the appendix bibliography we hadn't checked the 'make
dist' command, as a result the PDF couldn't be built. With this commit, in
the 'dist' rule, we are now also copying 'appendix.bbl' and the created
tarball could build the PDF properly. Also the 'peer-review' directory is
now also included in the tarball created by './project make dist'.
I also found a small typo in the description of Occam (an 'a' was missing)
and fixed it.
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Having entered 2021, it was necessary to update the years of all the
copyright statements.
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There were only three very small conflicts that have been fixed.
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Until now, the build strategy of the paper was to have a single output PDF
that either contains (1) the full paper with appendices in the same paper
(2) only the main body of the paper with no appencies.
But the editor in chief of CiSE recently recommended publishing the
appendices as supplements that is a separate PDF (on its webpage). So with
this commit, the project can make either (1) a single PDF (containing both
the main body and the appendices) that will be published on arXiv and will
be the default output (this is the same as before). (2) two PDFs: one that
is only the main body of the paper and another that is only the appendices.
Since the appendices will be printed as a PDF in any case now, the old
'--no-appendix' option has been replaced by '--supplement'. Also, the
internal shell/TeX variable 'noappendix' has been renamed to
'separatesupplement'.
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Until now there was only a 'clean' (to delete all files created during the
'make' phase) and the 'distclean' (to delete all files during configuration
and make). But sometimes we don't want to delete all the files created
during the full 'make' phase, we only want to delete the files that were
created by LaTeX for building the paper.
Witht this commit, a new target has been added for this job. You can now
run the following command for this job:
./project make texclean
Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz'
directory under that location is recreated, ready for a future build).
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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, there was no warning when the 'maneage' branch didn't exist in
the Git history. This can happen when you forget to push the 'maneage'
branch to a remote for your project, and you later clone your project from
that remote (for example on another computer). We use the 'maneage' branch
to report the latest commit hash and date in the final paper (which can
greatly help future readers). Since we check the 'maneage' branch on every
run of './project make' (in 'initialize.mk') this would result in a printed
statement like this:
fatal: Not a valid object name maneage
Also until now, the description of what to do when TeXLive wasn't installed
properly wasn't complete: it didn't mention that it is necessary to delete
the TeXLive target files. This could confuse users (they would re-run
'./project configure -e', but with no effect).
With this commit, for the 'maneage' branch issue a complete warning will be
printed. Telling the user what to do to get the 'maneage' branch (and thus
fix this warning). Also, the LaTeX macros that go in the paper are now red
when the 'maneage' branch doesn't exist, telling the user to see the
printed warning (thus encouraging the user to get the branch). For the
TeXLive issue, the necessary commands to run are now also printed in the
warning.
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Some minor conflicts that came up during the merge were fixed.
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Until now, Maneage only provided the commit hashes (of the project and
Maneage) as LaTeX macros to use in your paper. However, they are too
cryptic and not really human friendly (unless you have access to the Git
history on a computer).
With this commit, to make things easier for the readers, the date of both
commits are also available as LaTeX macros for use in the paper. The date
of the Maneage commit is also included in the acknowledgements.
Also, the paragraph above the acknowledgements has been updated with better
explanation on why adding this acknowledgement in the science papers is
good/necessary.
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This only concerns the TeX sources in the default branch. In case you don't
use them, there should only be a clean conflict in 'paper.tex' (that is
obvious and easy to fix). Conflicts may only happen in some of the
'tex/src/preamble-*.tex' files if you have actually changed them for your
project. But generally any conflict that does arise by this commit with
your project branch should be very clear and easy to fix and test.
In short, from now on things will even be easier: any LaTeX configuration
that you want to do for your project can be done in
'tex/src/preamble-project.tex', so you don't have to worry about any other
LaTeX preamble file. They are either templates (like the ones for PGFPlots
and BibLaTeX) or low-level things directly related to Maneage. Until now,
this distinction wasn't too clear.
Here is a summary of the improvements:
- Two new options to './project make': with '--highlight-new' and
'--highlight-notes' it is now possible to activate highlighting on the
command-line. Until now, there was a LaTeX macro for this at the start
of 'paper.tex' (\highlightchanges). But changing that line would change
the Git commit hash, making it hard for the readers to trust that this
is the same PDF. With these two new run-time options, the printed commit
hash will not changed.
- paper.tex: the sentences are formatted as one sentence per line (and one
line per sentence). This helps in version controlling narrative and
following the changes per sentence. A description of this format (and
its advantages) is also included in the default text.
- The internal Maneage preambles have been modified:
- 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have
been merged into one preamble file called
'tex/src/preamble-maneage-default-style.tex'. This helps a lot in
simply removing it when you use a journal style file for example.
- Things like the options to highlight parts of the text are now put in
a special 'tex/src/preamble-maneage.tex'. This helps highlight that
these are Maneage-specific features that are independent of the style
used in the paper.
- There is a new 'tex/src/preamble-project.tex' that is the place you
can add your project-specific customizations.
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This commit fixes the error of trying to run bibtex on
appendix.tex when the --no-appendix option is selected.
A hardwired hack, appropriate only for this specific paper,
replaces the more-than-three-author parts of two long author
lists by "et al." To test this without having to redownload
the menke file, first do
"rm -fv .build/tex/build/*.aux .build/tex/build/*.bbl"
and then "./project make --no-appendix" a few times.
This commit should reduce the word length by about 70 words.
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There is an answer for all the referee points now. I also did some minor
edits in the paper. But we are still over the limit by around 250 words.
The only remaining point that is not yet addressed (and has '####' around
it) is the discussion on parallelization and its effect on reproducibility.
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This commit updates "paper.tex" and "peer-review/1-answer.txt"
for the first 15 (out of 59!) reviewer points, excluding
points 2 (not yet done) and 9 (README-hacking.md needs
tidying).
A fix to "reproduce/analysis/make/paper.mk" for the
links in the appendices is also done in this commit (the same
algorithm as for paper.tex is added). The links in the appendices
are not (yet) clickable.
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Raul's added point on the answer to the referee was very good, so I edited
it a little to be more clear (and removed his name).
Also, after looking in a few parts of the text, I fixed a few typos.
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A new directory has been added at the top of the project's source called
'peer-review'. The raw reviews of the paper by the editors and referees has
been added there as '1-review.txt'. All the main points raised by the
referees have been listed in a numbered list and addressed (mostly) in
'1-answers.txt'. The text of the paper now also includes all the
implemented answers to the various points.
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Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro
that defines two LaTeX macros: '\new' and '\tonote'.
When '\highlightchanges' was defined, anything that was written within
'\new' became dark green (highlighting new things that have been
added). Also, anything that was written in '\tonote' was put within a '[]'
and became dark red (to show that there is a note here that should be
addressed later).
When '\highlightchanges' wasn't defined, anything within the '\new' element
would be black (like the rest of the text), and the things in '\tonote'
would not be shown at all.
Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex'
(to toggle the modes above) would create a different Git hash and has to be
committed.
But this different commit hash could create a false sense in the reader
that other things have also been changed and the only way they could
confirm was to actually go and look into the project history (which they
will not usually have time to do, and thus won't be able to trust the two
modes of the text).
Also, the added highlights and the note highlights were bundeled together
into one macro, so you couldn't only have one of them.
With this commit, the choice of highlighting either one of the two is now
done as two new run-time options to the './project' script (which are
passed to the Makefiles, and written into the 'project.tex' file which is
loaded into 'paper.tex'). In this way, we can generate two PDFs with the
same Git commit (project's state): one with the selected highlights and
another one without it.
This issue actually came up for me while implementing the changes here: we
need to submit one PDF to the journal/referees with highlights on the added
features. But we also need to submit another PDF to arXiv and Zenodo
without any highlights. If the PDFs have different commit hashes, the
referees may associate it with other changes in any part of the work. For
example https://oadoi.org/10.22541/au.159724632.29528907 that mentions
"Another version of the manuscript was published on arXiv: 2006.03018",
while the only difference was a few words in the abstract after the journal
complained on the abstract word-count of our first submission (where the
commit hashes matched with arXiv/Zenodo).
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With the optional appendices added recently to the paper, it was important
to go through them and make them more fitting into the paper.
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Until now, when the 'pdf-build-final' configuration variable (defined in
'reproduce/analysis/config/pdf-build.conf') was given any string a PDF
would be built. This was very confusing, because people could put a 'no'
and the PDF would still be built!
With this commit, only when this variable has a value of 'yes' will the PDF
be built. If given any other string (or no string at all), it will not
produce a PDF.
This issue was reported by Zahra Sharbaf.
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Given the referee reports, after discussing with the editors of CiSE, we
decided that it is important to include the complete appendix we had before
that included a thorough review of existing tools and methods. However, the
appendix will not be published in the paper (due to the strict word-count
limit). It will only be used in the arXiv/Zenodo versions of the paper.
This actually created a technical problem: we want the commit hash of the
project source to remain the same when the paper is built with an appendix
or without it.
To fix this problem the choice of including an appendix has gone into the
'project' script as a run-time option called '--no-appendix'. So by default
(when someone just runs './project make'), the PDF will have an appendix,
but when we want to submit to the journal, or when the appendix isn't
needed for a certain reason, we can use this new option. The appendix also
has its own separate bibliography.
Some other corrections made in this commit:
1. Some new references were added that had an '_' in their source, they
were corrected in 'references.tex'.
2. I noticed that 'preamble-style.tex' is not actually used in this paper,
so it has been deleted.
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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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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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Only two small conflicts came up:
* The addition of the hardware architecture macro in 'paper.tex' (which
was removed for now, but will be added as the referee has requested
within the text).
* The usage of "" around directory variables in 'paper.mk'.
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Until now, no machine-related specifications were being documented in the
workflow. This information can become helpful when observing differences in
the outcome of both software and analysis segments of the workflow by
others (some software may behave differently based on host machine).
With this commit, the host machine's 'hardware class' and 'byte-order' are
collected and now available as LaTeX macros for the authors to use in the
paper. Currently it is placed in the acknowledgments, right after
mentioning the Maneage commit.
Furthermore, the project and configuration scripts are now capable of
dealing with input directory names that have SPACE (and other special
characters) by putting them inside double-quotes. However, having spaces
and metacharacters in the address of the build directory could cause
build/install failure for some software source files which are beyond the
control of Maneage. So we now check the user's given build directory
string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(',
')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different
directory.
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Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.
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The '.bbl' suffix in the comment of one call to LaTeX was incorrectly
written as '.bb'.
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One of the LaTeX macros reported by 'initialize.mk' is the git commit hash
of the most recent 'maneage' branch that the project has been branched
from. However, not all projects will retain the maneage reference. This can
happen for example when people don't push the 'maneage' reference to their
repository and then clone from their own repository to a second
computer. Therefore, until now, in such situations, Maneage would break
with an error.
With this commit, in such scenarios, a place holder string is used instead,
clearly highlighting that there is no 'maneage' reference.
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There are many different directory trees involved in Maneage system: the
top directory, the 'reproduce/' directory and its sub-directories,
'.build/' (that point to a user-defined build area), and a possibly
user-defined input directory. Until now, in the case of a download checksum
failure, it was not immediately obvious [1] to the user *where* the file
with a failed checksum is.
To clarify to the user *where* the suspicious file is now located, this
commit adds a line to 'reproduce/analysis/make/download.mk' to print out
this full path location: '$$unchecked' along with the expected and
calculated checksums.
[1] Euphemism for me spending lots of time debugging and being confused.
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This commit clarifies the initial usage of Zenodo for reserving a Zenodo
identifier and starting an 'unpublished' upload. Some other minor wording
changes are done here.
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Until this commit, the '$(project-package-contents)' rules in
'reproduce/analysis/make/initialize.mk' included a line to provide all
contents, recursively, of the directory 'reproduce/' in the package for
further distribution.
This could potentially lead to the distribution of private working files
that are used during development and not intended for general distribution.
With this commit, only those files in 'reproduce/' and 'tex/src' that are
under version control are copied to the temporary directory (that is later
used for creating an archive). With this change, the archiving commands
actually became more clean (we don't have to manually remove 'LOCAL.conf'
or other temporary files). Extensive comments have also been added above
each step to clarify each step's purpose and method.
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Until now the './project make dist' command implicitly assumed that the
'tex/tikz' directory always contains PDF files (because of the 'cp
tex/tikz/*.pdf $$dir/tex/tikz' line). This was annoying for projects that
don't use TiKZ or PGFPlots to generate their plots, and they had to
manually comment this line.
With this commit a check has been placed to see if any PDF files exist in
there at all. If there aren't PDF files, the 'cp' command above is ignored.
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Until now, when the bibliography file ('paper.bbl') had a LaTeX-related
error (for example the journal name was a LaTeX macro that isn't defined),
the first 'pdflatex' command that is run before 'biber' would crash, not
allowing the project to reach 'biber'. So the user would have to manually
remove 'paper.bbl' before running './project make'.
With this commit, we remove any possibly existing 'paper.bbl' file before
rebuilding it. Generally, this also helps in keeping things clean during
the generation of the new bibliography.
This bug was found by Mahdieh Nabavi.
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To help in the documentation, the Git hash of the Maneage branch commit
that the project has most recently merged with (or branched from) is now
also provided as a LaTeX macro ('\maneageversion').
It is calculated in 'reproduce/analysis/make/initialize.mk' (in the recipe
to 'initialize.tex').
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