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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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Some typos were fixed.
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The edits help it be more clear, and remind the reader to delete any
remaining file in the RAM in the end.
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When you are working with large files and there is some good RAM in the
system (large/powerful computers), it is beneficial to work in the shared
memory directory and not the actual persistent storage (like HDD or
SSD).
With this commit, a fully working demo has been added to
`README-hacking.md' (under the tips of "Make programming") to show how to
effectively work in situations like this.
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The tarball of HEALPix includes multiple languages and doesn't include the
ready-to-run GNU Build System by default, we actually have to build the
`./configure' script for the C/C++ libraries. So it was necessary to also
include GNU Autoconf and GNU Automake as prerequisites of HEALPix.
However, the official GNU Autoconf tarball (dating from 2012) doesn't build
on modern systems, so I just cloned it from its source and bootstrapped it
and built its modern tarball which we are using here.
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The following software are added with this commit: eigency, esutil, flake8,
future, galsim, lsstdesccoord, pybind11 and pyflakes.
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As part of an effort to bring in all the dependencies of the LSST Science
pipeline (which includes the last commit), these software are now available
in the template.
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With this commit these three software packages are now installable with
this template.
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The steps to package the project have been made slightly more clear and
also the temporary directory that is created for packaging is deleted after
the tarball is made.
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Until now, when you ran `make clean', all the directories under
`$(BDIR)/tex/' would be deleted except for `macros' and `build'. This was
good for the single-user mode. But in group mode, this would delete the
user-specific TeX build directory because its called `build-USER', not
`build'.
With this commit, to fix the problem, we define the new `texbtopdir' and
based on the group condition, and use that to specify which directory to
not delete.
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Carlos Morales Socorro reported that his LaTeX build was missing the
`trimspaces' package, so it is now included in the pipeline.
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Until now, some software were using the depreciated ADS URL
(`http://adsabs.harvard.edu....') and some were using the modern one
(`http://ui.adsabs.harvard.edu').
With this commit, to be consistent they all link to the modern URL.
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Until now, this script would always only work with a file-lock. But in some
scenarios, we might want to download in parallel. For example when the
system has multiple ports to the internet.
With this commit, we have added this feature: when the lockfile name is
`nolock', it won't lock and will download in parallel.
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Since ImageMagick can take long to build, we are now building it in
parallel. Also, the part where we replace an `_' with `\_' in the software
version at the end of the configure script was removed. It is more
clear/readable that the actual rule that includes such a name deals with
the underline (as is the case for `sip_tpv' which already dealt with it).
Finally, I noticed that the checks at the start of `top-prepare' were
missing new-lines. I had forgot that the Make single-shell variable isn't
activated in this stage yet.
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A special directory is now defined in `initialize.mk' that can be used in
both the preparation and build phases. Also, the contents of prepared
results can now be conditionally read during `./project make'.
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In many real-world scenarios, `./project make' can really benefit from
having some basic information about the data before being run. For example
when quering a server. If we know how many datasets were downloaded and
their general properties, it can greatly optmize the process when we are
designing the solution to be run in `./project make'.
Therefore with this commit, a new phase has been added to the template's
design: `./project prepare'. In the raw template this is empty, because the
simple analysis done in the template doesn't warrant it. But everything is
ready for projects using the template to add preparation phases prior to
the analysis.
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It was some time since these three software were not updated! With this
commit the template now uses the most recent stable release of these
packages.
Also, the hosting server for ImageMagick was moved to my own webpage
because unfortunately ImageMagick removes its tarballs from its own
version.
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Until now, when the project's source was downloaded from something like
arXiv, in `README.md', we were instructing them to set the executable flags
of all the files that need it. But except for `./project', the reader
shouldn't have to worry about the project internals! Once its executable,
`./project' can easily fix the executable flags of all the files that need
it automatically.
With this commit, in `README.md', we just instruct the reader to set the
executable flag of `./project' and any other file that needs an executable
flag is given one at the start of the set of commands for `./project
configure'. In customized projects, if an author needs executable flags on
any other files, they can easily add it there without involving the user.
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Until now we were calling it `Sextractor', but the official way of writing
it is `SExtractor'. With this commit, this has been corrected.
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Konrad Hinsen pointed out that this part was missing from the instructions
in `README.md' after cloning. So it is added.
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