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2019-04-02Python packages are installed as high level program dependenciesRaul Infante-Sainz-51/+6
Until this commit, the installation of all Python packages were done in a separate Makefile. With this commit, the pipeline install Python packages as part of the hight level software. All Python packages rules them remain in a separate Makefile, but this Makefile is included in the high level dependency `reproduce/src/make/dependencies.mk'.
2019-04-02Numpy and Scipy using OpenBLAS instead of ATLASRaul Infante-Sainz-8/+16
We could not get ATLAS shared libraries on Mac (while the static ATLAS libraries are built and can be used successfully on Mac). So, the pipeline now builds OpenBLAS, which both Numpy and Scipy can use on Mac and GNU/Linux. We also added FFTW as a dependency of Numpy. Altough Numpy is not linking to FFTW for some reason. However, since FFTW is a low level library used by many programs, we have kept it as a dependency of Numpy anyway for now.
2019-03-29Disabling ATLAS shared libraries on Mac OSRaul Infante-Sainz-9/+5
The Makefile that build the shared libraries comes from Arch Linux so it does not work easily on Mac. But the full ATLAS build goes successfully for static libraries. For now we are disabling shared libraries on Mac. Python was built explicity with `clang' on Mac.
2019-03-27GCC is now built on a Mac, not yet ATLASRaul Infante-Sainz-1/+4
Until now, we were simply using the host's GCC for Mac systems. But we found that except for a single step (to fixing `rpath'), it works on Mac!!! So, GCC is now part of the Mac build as well. However, we are still having some problems in building ATLAS on Mac. It works on GNU/Linux, but not in Mac. So for the time being (just temporarily), we are avoiding ATLAS (and thus Scipy) on Mac systems. We just filed an issue on the ATLAS discussion list to hopefully fix the problem soon.
2019-03-22H5py added and setuptools as main Python module dependencyRaul Infante-Sainz-27/+36
In this commit we add `h5py' Python package. We also include `setuptools' as a main dependency of Python because with the previous commit it (as well as `pip') is no longer installed with Python. Numpy version also has been incremented.
2019-03-21ATLAS and Scipy working on GNU/LinuxRaul Infante-Sainz-17/+34
Numpy needs ATLAS as shared libraries. So we also need to build Python with shared libraries. We also need to define site.cfg for numpy and scipy so we define a master template: `reproduce/config/pipeline/dependency-numpy-scipy.cfg' Also `Openssl' did not have rpath so we added with this commit.
2019-03-20Including ATLAS in the pipeline, not yet completeRaul Infante-Sainz-3/+0
An initial installation of atlas is now included in the pipeline, but we are still trying to make it compile and build smoothly. In the process, we found that GCC also needs some modifications (for example rpath issues).
2019-03-07Several new Python packages added for full buildMohammad Akhlaghi-12/+70
To ensure that we have all the necessary Python dependencies, I done an offline build and noticed that several packages were also necessary for the `./configure' step to finish (`libffi', `asn1crypto', `cffi', `jeepney', `pycparser' and `secretstorage'). With this commit they are added.
2019-03-06Reseting Python environment variables also when building PythonMohammad Akhlaghi-1/+20
Until now, we were only resetting the Python environment variables in the actual processing Makefiles, not in the Makefile that build Python and its modules. They are now added there also.
2019-03-06Astroquery, astropy, matplotlib and numpy are now in the pipelineRaul Infante-Sainz-0/+1
Until this commit, we had some of the python packages intalled but they did not work properly because of the `PYTHONPATH' variables. That is, the pipeline's `python' was the `python' of the system instead of the pipeline's `python'. With this commit this issue has been fixed by setting the correct `PYTHONPATH'. In this commit we also modify the installation of `bzip2' because `CMake' was complaining about some libraries built statically.
2019-02-28Python installation and related packages have been splitRaul Infante-Sainz-1/+13
Until now the installation of Python and its packages (numpy, astropy, astroquery, etc.) were done in the same `makefile'. With this commit the installation of Python and its packages have been split and now it is independent of the other programs. The installation of all Python packages needs to be written explicitely because pip is not used anymore.
2019-02-21Matplotlib is now in the pipelineRaul Infante-Sainz-5/+63
As matplotlib is a general package for plotting and it is widely used in science, we have added it to the pipeline. When installing a dependency of matplotlib `python-dateutil', we found a conflict in the download of the tarball. This is because the name has a dash (-) in the middle. In addition, the name starts with 'python', so it is the same as the python itself. Now it is possible to install any package with any name, just adding an elif in before the URL direction.
2019-02-20Installed astroquery in the pipelineRaul Infante-Sainz-0/+294
All dependencies for building astroquery package have been done. Until nowthe Python dependencies were built in the same Makefile as the high level libraries and programs. But, because astroquery has many dependencies we split the Python and Python packages installation in a new Makefile. The installation of differents packages are done using Python and not pip, because we found some problems when doing it with pip. Apparently there are some interferences between the packages installed by the pip of the system and the pip installed as part of Python in the pipeline.