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With this commit a description of these two important parts have been added
to the project, along with several figures showing various parts of the
files that are discussed. I also done some other restructuring of the
figures and files to make things fit better into the the description of the
paper.
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Until now, I was mistakenly multiplying the fraction of papers in that
journal. This is corrected with this commit.
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In order to make the description more clear and readable, the rules in the
demonstrated Makefile (and their links to the data lineage plot) were made
more clear.
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Until now, there was no explanation on an actual analysis phase, therefore
with this commit an example scenario with a readable Makefile is included.
The Data lineage graph was also simplified to both be more readable, and
also to correspond to this new explanation and subMakefile.
Some random edits/typos were also corrected and some references added for
discussion.
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This was done just to get going with describing the analysis process.
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The main problems with this dataset was the names of the journals (which
sometimes have single quotes or apostrophes in them that is really annoying
for SED)! But ultimately, for the simple study we want to do here, the
journal names are irrelevant, so in the end I just ignored the names. Later
we can set an identifier for the journals if necessary.
But now we have the basic information in a way that is usable in a plot to
show in this paper.
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Until now, there was no easy way to read/write `.xlsx' files (Microsoft
Excel spreadsheets) within the template. But XLSX I/O provides to simple
programs and some libraries to easily convert `.xlsx' files to CSV that can
easily be read by any tool.
This has also been implemented in the core template branch.
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The text was slightly improved/edited and I also recently came up to the
Menke et al. 2020 (DOI:10.1101/2020.01.15.908111) which also has some good
datasets we can use as a demonstration here.
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While reading over the already written parts (and hopefully complete the
paper), they were edited/corrected to be more clear.
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Some edits were made after rereading of some parts.
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With this commit, the general outline of the analysis phase is given, as
well as a description of the LaTeX macros and their relation to the paper
and thier verification.
Also, the data-lineage figure was updated to have references.tex also and
some resizing of the folders in file-architecture to be more clear.
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In the last few days I have been writing these two sections in the middle
of other work. But I am making this commit because it has already become a
lot! I am now going onto the description of `./project make'.
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Until now the file architecture plot at the directories ontop of the
top-level files. This made it hard to visually identify the top-level
files. They are not placed ontop of the sub-directories and some space is
added to highlight the files in the top-level directory and those in the
subdirectories.
Two other changes were made:
- The symbolic links created in the top source directory are also shown.
- The coding of this figure was made much more elegant by defining a
PGFPlots node class and just changing the things that are direrent
between each directory.
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It was a little hard to describe the file structure so instead of using a
standard listing as most papers do, I thought of showing the file and
directory structure as boxes within each other (modeled on the Gnome
disk-utility).
Some other polishing was done throughout the paper also.
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Until now, I was writing the paper without the template. But we will soon
be adding a tutorial to the template, and I thought it will be good to have
an example demonstration here too. So I just brought the hole project into
the template structure, allowing us to add the template analysis later when
its ready, and also allowing us to easily reproduce this paper ofcourse
(without having to worry about the host's TeXLive installation.
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The unnecessary parts were removed and the project now runs.
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Until now the actual journal webpage was used for Raul's paper. However,
the journal webpage needs authorized access for people to read it,
therefore its will be inaccessible for many people. A better and more well
known place for the paper (atleast in astronomy) is the ADS link. In the
ADS link, if someone has access to the journal, they will get the journal's
version and if not, they will get the arXiv version. It also has a common
BibTeX export tool for all journals. We had also done this for the other
papers in that list.
With this commit, I thus changed the URL for the paper, and also removed
the "issue" number (4 in this case), since that is mostly irrelevant, only
the volume and page numbers are usually used for the other papers too.
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The "SDSS extended PSFs" paper was already included as an example of
papers wich uses this template. However, the reference was the arXiv
one. With this commit, since the paper has been finally published, it
has been added the final reference to the journal.
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Until this commit, the checking of X11 installation done to ensure that
it is already available in the host system was crashing in macOS
systems. The reason is that the place of the X11 libraries use to be
`/opt/X11/lib' in macOS systems. With this commit, this issue has been
fixed by adding this directory to the LDFLAGS.
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Newer versions of Astropy package has been released. With this commit,
it has been updated. It has been increased from v3.2.1 to v4.0
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In markdown, to specify that part of the text should be shown as code we
need to put it between two `. But in `reproduce/software/make/README.md',
the code parts started with ` and finished in ' (like the file name above).
With this commit, this has been corrected and it will display properly on
web browsers.
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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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In the previous commit, I had forgot to update a small part in the
checklist (when modifying `top-make.mk') which is now corrected.
I also added a few sentences in the description of how to customize the
verification to make it easier to understand.
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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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In the previous commit, we added the files to ignore from the template
branch, but only the files that had been deleted. With this commit,
`paper.tex' is also added to the files that must be ignored from the
template branch (the file remains in the project, but in the template
branch, its contents are just dummy place-holders).
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During the checklist we guide the user to delete the dummy `delete-me*'
files from their custom branch. Later, if the dummy files are updated in
the template's master branch, if the user merges with the template branch,
these files will be written back into their project! This is very annoying!
With this commit, a step was added in the `README-hacking.md' checklist,
just after deleting the dummy files to avoid this problem using the
`.gitattributes' file, telling Git to keep the changes as implemented in
the merging branch (`ours').
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until this commit, the number `2' was missing in the checksum variable
name of that library. It was `libxml-checksum' but it should be
`libxml2-checksum'. With this commit, this issue has been fixed.
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An extra backslash in the prerequisites of Jeepney Python package was
causing a crash in the installation of that software. With this commit,
this problem has been fixed by removing the backslash.
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OpenMP takes a LONG TIME to build, so to keep things reproducible we are
explicitly disabling OpenMP, if a user needs OpenMP, its trivial to just
add it as a prerequisite of R. The problem is that in some scenarios (based
on other dependencies and when they were built in the build directory),
OpenMP may be present when R is being installed and in other it may not. We
don't want the result to be different between the two builds.
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With this commit, we now have the core R interpretter within the
template. We should later include instructions to install R packages
(possibly in a separate top-level Makefile like Python).
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Recent builds of the template need these three packages to build the PDF.
This was reported by Hamed Altafi.
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Until now we weren't including this package, but Alberto Madrigal recently
reported that his build of the template failed because it needed it.
With this commit, it is now being installed with the template.
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Until now, while building Perl, the `-Dlddlflags="-shared $$LDFLAGS"'
option was being used for all systems. However, this caused `symbol(s) not
found for architecture x86_64' problems on macOS systems.
With this commit, this configure option is only passed for GNU/Linux
systems. With it, Perl can be built nicely on both GNU/Linux and macOS.
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Newer versions of these packages have recently come out with major
improvements, so they have been updated in the template.
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Until now, Ghostscript was using some host system's X11 libraries during
its build (and later at run-time). We should ideally install all these
necessary libraries within the template (Task #15481). But right now we are
too busy.
As a temporary work-around we try building a small dummy program that links
with some of those libraries before attempting to built Ghostscript. If it
fails, then a notice is printed with the cause and explaining a temporary
solution is suggested: how to install those libraries on the system when
you have root access.
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Until now, when an input dataset already exists in `INDIR', the template
would just make a symbolic link to it in the build directory. However, in
many cases, the files in INDIR will actually be links to other locations on
the filesystem and some programs have problems following too many links.
With this commit, the template is now using the `readlink' program (part of
GNU Coreutils) to follow a possible link and point the link in the build
directory directly to an actual non-link file.
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Until now, after removing all environment variables, we were just giving
Make the top Makefile to execute. By default, for every target, Make will
try many built-in rules (which is good when compiling programs, but
redundant in other cases). All these checkings also populate the debugging
output of Make (with `-d'). So its easier and slightly faster to just tell
Make to ignore builtin rules and variables.
With this commit, to address this issue, the `project' script runs
`.local/bin/make' with `--no-builtin-rules' and `--no-builtin-variables'.
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Until now when building Matplotlib on macOS systems, we were using the
default C compiler. However, while Yahya Sefidbakht (previously) and
Mahdieh Nabavi (now) were trying to build the template, on their macOS
using the GNU Compiler Collection (GCC), we found that Matplotlib needs
special macOS headers that GCC doesn't recognize.
With this commit, when Matplotlib is being built on macOS systems, it uses
`clang' and this fixed the problem (so far checked on Mahdieh's machine).
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While working on a different branch to build the GNU C Library, I noticed a
few places in the template that need corrections which are now applied:
1. A new-line character after the "C compiler works" notice at the start
of the configure script.
2. Removing possible `::' in the `LD_LIBRARY_PATH' definition of
`basic.mk'. Note that its not necessary in the other steps because we
don't use any outside-defined `LD_LIBRARY_PATH'.
3. Building GMP for C++ and also with `--enable-fat'.
4. Removing the unpacked Perl tarball directory after its installation.
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These two packages are necessary to build the GNU C Library.
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Perl is necessary to build Texinfo and later to build LaTeX. Until now we
were just using the host operating system's installation of Perl, but in
some instances that Perl can be too old and not suppor the features
necessary. With this commit, Perl is now built from source during the basic
installation step of the template.
This was reported by Idafen Santana Pérez, after trying the pipeline on an
Amazon AWS EC2 system (a Linux distro by Amazon for its cloud services).
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Raul's paper (that uses this template) was just published on arXiv today
(congratulations Raul!). So it has been added to the list of papers using
this template.
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Since we got the RDA Adoption grant, it was necessary to add it in the
acknowledgements.
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When building the log4cxx tarball from its Git history, I noticed that
files with very long names are not packaged by tar (because by default
Automake uses the ancient v7 tar format that only supports file names less
than 99 characters).
So I build the tarball with the `tar-ustar' option to Automake (by
modifying the log4cxx source) and the resulting tarball was able to compile
and run successfully. This has been described above the rule to build
log4cxx and I also sent an email to their developing mailing list to inform
them of this problem. If they address it, I will remove the note on the
necessary corrections.
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Some minor corrections were made in the template:
- When making the distribution, `.swp' files (created by Vim) are also
removed.
- Autoconf is set as a prerequisite of Automake
I was also trying to add the Apache log4cxx, but its default 0.10.0 tarball
needs some patches, so I have just left it half done until someone actually
needs it and we apply the patch.
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Since adding this new step, I had forgot to mention it in the checklist of
`README-hacking.md'. It is added with this commit.
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Until now, the tarballs were the first normal prerequisite of the
software. As a result if their date changed, the whole software would be
re-built. However, for tarballs specifically, we actually check their
contents with a checksum, so their date is irrelevant (if its newer than
the built program, but has the same checksum, there is no need to re-build
the software).
Also, calling the tarball name as an argument to the building process (for
example `gbuild') was redundant. It is now automatically found from the
list of order-only prerequisites within `gbuild' and `cbuild' (similar to
how it was previously found in the `pybuild' for Python building).
A `README.md' file has also been placed in `reproduce/software/make' to
help describe the shared properties of the software building
Makefiles. This will hopefully grow much larger in the future.
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Python's `lmfit' module and all its major dependencies (`asteval',
`corner', `emcee' and `uncertainties') have been included in the template.
While doing this I noticed that if the tarballs are the last prerequisite
of each software building rule, then when building in parallel, the
template will immediately start building packages as soon as the first one
is downloaded. Not like the current way that it will attempt to download
several, then start building. For now, this has been implemented in the
Python build rules for all the modules and we'll later do the same for the
other programs and libraries. This also motivated a simplification of the
`pybuild' function: it now internally looks into the prerequisites and
selects the tarball from the prerequisite that is in the tarballs
directory.
This isn't a problem for the build, but I just don't understand why Python
can't recognize the version of `emcee', Python reads the version of `emcee'
as `0.0.0'! But it doesn't cause any crash in the build, so for now its
fine.
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The part on using shared memory was edited for a few things that weren't
clear.
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