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On some Fedora systems, libffi installs under `lib64', not `lib'. As a
result, Python's Setuptools can't find it and will not built (complaining
about not finding the `_ctypes' module).
With this commit, we fix this problem by explicitly putting a copy of
libffi's installed libraries within the `lib' directory.
This issue was found while testing the pipeline with Elham Saremi and Hamed
Altafi.
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Until this commit, the name of the decompressed tarball directory of
PyYAML Python package was wrong. It has to be `PyYAML-version' instead
of `pyyaml-version'. When I run the installation on Mac OS system it
went up to the end of the installation with no error. However, when I
tried to install it on a GNU/Linux system, it complained about no
finding the `pyyaml-version' directory, which is the expected because
the name was wrong!
With this commit, I have fixed this issue by writting correctly the name
of the decompressed tarball directory.
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With this commit, PyYAML Python package has been added into the project.
It is widely used in the Python community and the goal is to have human
readable configuration files. As in the web page
(https://pypi.org/project/PyYAML/) says:
YAML is a data serialization format designed for human readability and
interaction with scripting languages. PyYAML is a YAML parser and
emitter for Python.
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Matplotlib can optionally use LaTeX and Ghostscript as dependencies to
render text with LaTeX.
Since we already have their build rules, with this commit, they have been
added as its prerequisites.
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With this commit, ImageMagick program has been set as prerequisite of
Matplotlib Python package. Since some submodules of Matplotlib rely on
ImageMagick programs (for example, those to make image animations), and
now we have ImageMagick into the project, it is good to install
ImageMagick when Matplotlib is requested to be installed.
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Especially because of the new convention regarding backslashes, there were
many conflicts that are now fixed. But none were substantial.
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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, we were missing `numpy' and `six' as prerequisites of `h5py'.
Because we did the configure step with all cores, `numpy' and `six'
allways were built before `h5py' with any crash. However, in a single
thread configure run we noticed that we were missing these two
dependencies.
With this commit, we fix this issue by setting `numpy' and `six' as
prerequisites of `h5py'.
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Until this commit, the prerequisites of `sip_tpv' were `mpmath' and
`sympy'. However, the real prerequisites of `sip_tpv' are `astropy',
`numpy' and `sympy'.
With this commit, we fix this issue, and now `mpmath' is only a
prerequisite of `sympy'.
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Until now, we were not citing the paper of `sip_tpv' package.
With this commit, we have been fix this issue.
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With this commit, we add `sip_tpv' Python package into the template.
This is a small package to convert SIP distorsion coefficients into PV
distorsion coefficients, and the other way around.
This package is useful in a astronomical context, specially when `swarp'
is going to be used in order to resample images. The reason is that
`swarp' only can understand PV distorsion coefficients.
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With this commit, we add `sympy' Python package into the template. This
is a package to do symbolic mathematics.
The motivation is that it is a prerequisite of `sip_tpv' Python package,
which is useful to convert SIP distorsion coefficients into PV
coefficients (in the context of astronomical images). However, the
availability of `sympy' in the template will be useful for anyone
interested in this package.
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With this commit, we add `mpmath' Python package into the template. This
package is a prerequisite of `sympy', a package to do symbolic
mathematics.
The motivation of adding this package is because it is a dependency of
`sympy', which is more widely used into the Python science community.
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Until now, to specify which high-level software you want the project to
contain, it was necessary to go into the `high-level.mk' Makefile that is
complicated and can create bugs.
With this commit, a new `reproduce/software/config/installation/TARGETS.mk'
file has been created that is easily/cleanly in charge of documenting the
final high-level software that must be built for the project.
Also, until now, FFTW was set as a dependency of Numpy while we couldn't
actually get Numpy to use it! It was just there for future reference and to
justify its build rule. But now that many software won't be built and there
is no problem with having rules even though a project might not use them,
it has been removed.
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Until this commit, we were using `python3' when calling Python (because
we were using Python version 3.6.8). This will force us to change the
name in the future. For example, when `python4' were available and into
the pipeline.
With this commit, at the end of the Python installation it creates a
symbolic link to the Python bin executable with the new name `python'.
As a consecuence, whatever version of Python was installed, into the
project we will use allways `python' to invoke it.
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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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