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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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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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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, 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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The 'pdflatex' program is used to build the default Maneage-branch paper.
But since the default paper uses PGFPlots to build the figures within LaTeX
as an external PDF, PGFPlots requires 'pdflatex' to be called with the
'-shell-escape' option. Generally, this option can be considered as a
security risk (in particular when 'pdflatex' is being run by an external
LaTeX file: a malicious LaTeX writer may embed commands in the LaTeX source
that will be executed on the host if this option is present).
This is not too serious of an issue in Maneage, because when someone runs
Maneage, they intentionally let it run many on their system. Hence if
someone wants to exploit a host system, they can add the necessary commands
long before 'pdflatex' is run. After all, all commands in Maneage are run
with the calling user's permissions, hence they have access to many parts
of the user's accounts. If someone is worried about security on a
non-trusted Maneage project they should act the same as they do with any
software: define a new user for it, and call it with that user (as a
weak-level security), or run it in a virtual machine or container.
However, since this option has been explicity mentioned as a security risk
before, it helps if we have a comment explaining its usage in 'paper.mk'.
With this commit, the concerned user will read a brief explanation and can
read the brief discussion at [1] and possibly re-open the discussion or
propose ways of mitigating the security risk(s).
[1] https://savannah.nongnu.org/task/?15694
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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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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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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.
This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).
With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:
$ ./project configure
$ ./project make
To work on the project with other users in a group these commands can be
used:
$ ./project configure --group=GROUPNAME
$ ./project make --group=GROUPNAME
The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:
$ ./project configure -e --host-cc
$ ./project make -j8
The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.
On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).
This fixes bug #56682.
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While reviewing Prasenjit's commits, I noticed that we had forgot to add
the citation for TIDES, also to make things clear, the program/library
build rules are now sorted alphabetically.
Finally, I noticed that after building the TiKZ PDF figures, it is crashing
(like on Prasenjit's computer). After looking around, I noticed its because
we were setting the of the `TEXINPUTS' environment variable to be the
installed TeX Live directory (which was ultimately redundant because by
default TeX will look into where it was installed). The important thing is
just that we remove any possible value the host system has, not to set new
directories.
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Until now, the `tex/build' symbolic link was put in the clone/source tree
when the build-directory's `tex' directory was being built. Thanks to
Roberto Baena, we just found a bug because of this behavior: when a second
group member is trying to build the pipeline, since the build directory's
`tex' directory already exists, no `tex/build' will be put in their
clone/source directory. As a result, the PDF building will crash.
To fix this (and keep things organized), the two `tex/build' and `tex/tikz'
links (to the build directory) are now built in the configure step while it
is building all the top-level directories. They are no longer built within
the Makefiles.
Also, a comment was added on top of every directory built during the
configuration phase to be clear.
This fixes bug #56362.
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When we need to quote the new-line character we end the line with a
backslash (`\'). Until now, our convention has been to put all such
backslashes under each other to help in visual inspection.
But this causes a lot of confusion in version control: if only one line's
length is larger, the whole block will be marked as changed and thus makes
it hard to visually see the actual change. It also makes debuging the code
(adding some temporary lines) hard.
With this commit, I went through all the files and tried to fix all such
cases so only a single white space character is between the last command
character and the backslash. Where there was an empty line (ending with a
backslash, to help in visually separating the code into blocks), I put the
backslash right under the previous line's.
This completes task #15259.
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Until now, there were erros in the citation of Astrometry-net and Scamp
papers.
With this commit, we fix these problems. The Swarp bibtex has also been
modify to follow the stetic of the citation style we have right now in
the project.
We also added the `dependency-bib.tex' as a prerequisite of `paper.bbl'.
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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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