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2019-06-12Imported recent work on Imfit, minor conflicts fixedMohammad Akhlaghi-0/+0
The recent work by Raul to import Imfit is now merged into the master branch. Only a few minor conflicts came up due to the update with CFITSIO (that Raul also done in parallel on this branch).
2019-06-10TeXlive: allows for updating itself and removes old version fileMohammad Akhlaghi-0/+0
Until now, TeXlive would only attempt to download/update LaTeX packages, but after some time, it will be necessary for it to update itself. When this happens, it complains about running it with `update --self'. To fix this problem, before installing/updating the LaTeX packages, we will first update tlmgr in any case. Also, we weren't removing the TeXlive package version file before appending the values to it. So it was just repeating the packages every time it was updated. With this commit, it is being removed on every new build. Finally, the version of Git was updated to its most recent version.
2019-05-31Modified Imfit installation to not consider default and host pathsRaul Infante-Sainz-0/+0
Until this commit, 'imfit' was installed using proper flags in order to use our own libraries. However, it looks first of all to the default system. As a consecuence, `imfit' program was linked to the host system libraries, even when we told to use our own libraries!! With this commit, the installation of `imfit' has been modified in order to remove the default paths already set in the `SConstruct' script. By doing this, only our paths are take into account for compiling the program. It has been tested on Mac OS laptop and it works fine. Test on GNU/Linux systems remain before merge into the main project branch.
2019-05-31Building single and double precission float libraries of FFTWRaul Infante-Sainz-0/+0
Until this commit, `fftw' was building single precission float library because `scamp' had problem on using the default double precission library. However,`imfit' and maybe other programs will use double precission float libraries. With this commit, `fftw' installation is done twice in order to build single and double precission float libraries. It does not complain and goes up to the end without crashing. However, more tests are needed in order to ensure that there is not problem on having both libraries because in principle, they share the same header file and that could cause problems.
2019-05-31Fixing rpath problem in CFITSIO installationRaul Infante-Sainz-0/+0
`cfitsio' was recently updated and it cames up with a problem when trying to build shared libraries (on Mac OS system laptop). This is because the `configure' script for building `cfitsio' include by default `rpath'. With this commit, this issue is fixed by modifying the installation of `cfitsio'. Using `sed', each ocurrence of `@rpath' in `configure' is replaced by `$(ildir)'. Once it has been done, the installation of `cfitsio' goes as normal. In this commit, the version of the `cfitsio' has been also updated to the most recent one.
2019-05-28Corrected typo in Imfit installation, but not working yetRaul Infante-Sainz-0/+0
With this commit, I have corrected a typo in the installation of `imfit'. In principle it is working on Mac OS system but when I tried to install it in GNU/Linux system it crashed. It complains about a problem with the `cfitsio' library: /pathto/libcfitsio.a: error adding symbols: File format not recognized As in the last commits done by Mohammad in the project, `cfitsio' installation has been upgraded and also the installation has been modified, I am going to try this new version. I will also check if it is a problem about dynamic/static library. It also seems that the installation is taking libraries and variables from the host system, so I will check that everything used is from our own programs/libraries.
2019-05-27Software: CFITSIO 3.47, implemented many common standardsMohammad Akhlaghi-0/+0
Until now, CFITSIO had several peculiar features which needed special attention: 1) Its tarball didn't have a `.' in the version name and would sometimes have extra `0's. 2) When unpacked it was just `cfitsio'. 3) It hard coded the directory to search for cURL library. All of these forced us to do a lot of extra steps for CFITSIO. So I got in touch with them and fortunately they were very open to correcting these issues and with version 3.47 all such issues have been addressed in the tarball. Thanks to these changes, with this commit, CFITSIO's build rule is now very similar to many other programs. I also noticed that it has an optional `--with-bz2' feature to enable unpacking `.fits.bz2' files. So this feature is also added.
2019-05-27Added paper citation of ImfitRaul Infante-Sainz-0/+0
Until this commit, `imfit' paper was not included into the acknowledgements. With this commit, a bib tex file for `imfit' has been added. So, now it is properly cited into the final paper.
2019-05-27Added Imfit into the projectRaul Infante-Sainz-0/+0
With this commit, `imfit' has been included into the project. As described in the official webpage (http://www.mpe.mpg.de/~erwin/code/imfit/): Imfit is a program for fitting astronomical images -- especially images of galaxies, though it can in principle be used for fitting other sources. This program uses the `scons' program to build itself (not the traditional GNU `configure' and `make' system). I have tested it by using an example that can be found in the `examples' directory of the decompressed tarball. It works fine without any error on my Mac OS system.
2019-05-27Adding SCons into the projectRaul Infante-Sainz-0/+0
With this commit, SCons has been included into the project. As in the official webpage of this program says: SCons is an Open Source software construction tool—that is, a next-generation build tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software. The motivation for including this software into the project is because there are some software that use this system for the installation. In particular, the necessity of installing it comes from Imfit. This is an astronomical software that uses this system so that is why it has been included into the project. In principle it is simple, and I have tested it on Mac OS sytem without any problem.
2019-05-24PyYAML decompressed tarball directory name fixedRaul Infante-Sainz-0/+0
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.
2019-05-24Added PyYAML Python package into the projectRaul Infante-Sainz-0/+0
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.
2019-05-24Added LibYAML library into the projectRaul Infante-Sainz-0/+0
With this commit, LibYAML library has been added. This library is a prerequisite of the Python package PyYAML, which is widely used in the Python community when configuration scripts are needed.
2019-05-24Shared CFITSIO installation includedMohammad Akhlaghi-0/+0
By default (when you run `make' within CFITSIO), it only builds a static library. So until now, the template would only install a static version of this library. To be more clear about which libraries are used during the linking of programs that use CFITSIO, it would be helpful to have shared library versions also. Also, if the system has problems with static libraries (like macOS systems), then it won't go looking outside the template to link with them (these paths are hardcoded in the linker, which we don't build on macOS and just use the system's tools). With this commit, we are explicity running `make shared' in the CFITSIO installation to have shared CFITSIO also. I also removed the old `static' element (which we don't use anymore in any of the programs and have to remove some time later!).
2019-05-22Removing extra spaces in variable definition in configure scriptRaul Infante-Sainz-0/+0
With this commit, extra spaces in the definition of two variables in the `configure' script have been removed. Since they are defined in a `shell' context (not in `make'), variable assignation is not allow to have any space at both sides of the `=' character. I detected these typos when trying to run `./configure' in a particular project.
2019-05-22TeXLive and Ghostscript also added as dependencies of MatplotlibMohammad Akhlaghi-0/+0
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.
2019-05-21Imported Matplotlib installation, no conflictsMohammad Akhlaghi-0/+0
There weren't any conflicts in this merge.
2019-05-21README-hacking.md: corrected typoMohammad Akhlaghi-0/+0
A title in the checklist was mistakenly using "project" (customized template) instead of "template".
2019-05-21ImageMagick put as prerequisite of MatplotlibRaul Infante-Sainz-0/+0
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.
2019-05-21ImageMagick is now included into the projectRaul Infante-Sainz-0/+0
With this commit, ImageMagick software has been added into the project. This software is useful to deal and treat images from the command line. Since it is widely used and a lot of other programs rely on it, it is worth to have it into the project.
2019-05-21Source directory links to build directory all managed in configureMohammad Akhlaghi-0/+0
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.
2019-05-15for-group script using internal chmodMohammad Akhlaghi-0/+0
Until now, the `for-group' script was using the system's `chmod' at the end of its operation. But when `for-group' reaches this level, we already have our own custom `chmod'. With this commit, for a consistent operation, we are now using our custom `chmod' program for this final step.
2019-05-09Typo, space instead of TAB, corrected in recipe of MetastoreMohammad Akhlaghi-0/+0
In the previous commits where Metastore's recipe was updated, all the `TAB's in the recipe were saved as spaces just before the commit (due to a copying and pasting from the terminal, not the text editor). With this commit, I am correcting this.
2019-05-06Disabled X Window System in netpbm installation for GNU/Linux systemsRaul Infante-Sainz-0/+0
Until this commit, we were installing `netpbm' without disabling the X Windows System in GNU/Linux. That is the default option in the configure step of `netpbm'. However, we are not installing the necessary libraries (X11) and headers for that. As a consecuence, when testing in a system where we don't have these libraries/headers (Ubuntu 14.04), it crashes. With this commit, we disable the X Windows System option in `netpbm' by giving the answer `none' to one of the last answers to that question in the configure step.
2019-05-01Disabled X Window System in Cairo installationRaul Infante-Sainz-0/+0
Until this commit, we were installing `cairo' without disabling the X Windows System. That is the default option in the configure step of `cairo'. However, we are not installing the necessaries libraries (X11) and headers for that. As a consecuence, when testing in a system where we don't have these libraries/headers (Ubuntu 14.04), it crashes. With this commit, we disable the X Windows System option in `cairo' configure step by setting the option `--with-x=no'.
2019-05-01Corrected typo in netpbm tarball extensionRaul Infante-Sainz-0/+0
In the last imported work about fixing all backslashes, the extension of `netpbm' tarball was not the correct one. Now we are using `.tar.gz' instead of `.tgz'. With this commit, we fix this typo by replacing the `.tgz' by `.tar.gz' in the rule of `netpbm'.
2019-04-29Added M4 as prerequisite of GMPRaul Infante-Sainz-0/+0
Until this commit, `m4' was not a prerequisite of `gmp'. However, during a test in Ubuntu 14.04 using one single core in the configure step, it crashed complaining about not having `m4' installed. With this commit, we set `m4' as a prerequisite of `gmp'.
2019-04-29Corrected spaces/TAB in some rulesRaul Infante-Sainz-0/+0
In some rules there were some spaces when we should use TAB, and also the other way around. We were using TAB instead using spaces. With this commit, we fix that spaces/TAB in the necessary rules.
2019-04-29Added numpy and six as prerequisites of h5pyRaul Infante-Sainz-0/+0
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'.
2019-04-29Modified copyright information of some filesRaul Infante-Sainz-0/+0
With this commit, the copyright information of some files have been modify in order to include the work of Raul Infante-Sainz.
2019-04-29Modified sip_tpv Python package prerequisitesRaul Infante-Sainz-0/+0
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'.
2019-04-27Astrometry-net installation modified to avoid two reporting stepsRaul Infante-Sainz-0/+0
Until this commit, we had a problem in the installation of Astrometry-net in Mac OS systems. During the runing of the Makefile, it stopped at the reporting stage because it tried to do a couple of steps that in Mac OS are not possible: $ cat /proc/cpuinfo $ free The reason is that `/proc/cpuinfo' and `free' doesn't exist in Mac OS. With this commit, we override these two steps. Since they are only for reporting, they are not mandatory. So, we avoid doing them by using `sed' before running the Makefile.
2019-04-27Libpng updated (version 1.6.37)Raul Infante-Sainz-0/+0
Until this commit, we were using `libpng' version 1.4.22 (out dated). The reason is that with `libpng` versions > 1.5, there was some problems with `netpbm'. But we have update `netpbm' version and now there is no conflict betweem them. With this commit, we increase the version of `libpng' to have the most recent one.
2019-04-27Modified netpbm installation answers for Mac OS systemsRaul Infante-Sainz-0/+0
Until now, we installed `netpbm' by setting the default paths to libraries and headers. That worked fine for GNU/Linux systems, however, in Mac OS systems we have to explicity say to `netpbm' questions what are the paths to the libraries and headers. We found this problem because we tried to run `solve-field' to obtain the astrometry of some images, and then it goes to use `pnmfile', a program that failed because it was not properly linked with `libnetpmb'. With this commit, we fix this problem by answering properly the questions in the configure step of `netpbm' and setting explicity where we want to place the libraries and headers. With this commit, we also update `netpbm' version. To do that, we have to download the last version, for which it doesn't exist a tarball. So, we built this tarball and put it in the Mohammad's webpage.
2019-04-27Lack of semicolons in Binutils installation rule for Mac OS fixedRaul Infante-Sainz-0/+0
Until this commit, in Mac OS we were installing `binutils' as symbolic links of various programs (`as', `ar', `ld', `nm',` ps' and `ranlib'). However, there was a missing semicolon at the end of each line. As a consecuence, the installation of `binutils' on Mac OS systems failed. With this commit, we fix this problem by typing a semicolon at the end of each makelink line.
2019-04-25Added --enable-single option in FFTW installationRaul Infante-Sainz-0/+0
Until this commit, FFTW was installed by default, without the single precission option. However, when installing `sextractor' in a new system we found an error in the installation complaining about not having single precission files of FFTW. More explicity the error was: "FFTW single precision library files not found in [...]". With this commit, we fix this problem by passing the option `--enable-single' in the installation of FFTW.
2019-04-24Added paper citation of sip_tpv Python packageRaul Infante-Sainz-0/+0
Until now, we were not citing the paper of `sip_tpv' package. With this commit, we have been fix this issue.
2019-04-24Removed sip_tpv from TARGETS, now it is an optional packageRaul Infante-Sainz-0/+0
With this commit, we let the Python package `sip_tpv' to be optional in order to not install it by default. It is a very specific package and I forgot to remove it from `TARGETS.mk' in the previous commit.
2019-04-23Python package sip_tpv added into the templateRaul Infante-Sainz-0/+0
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.
2019-04-23Python package SymPy added into the templateRaul Infante-Sainz-0/+0
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.
2019-04-23Python package mpmath added into the templateRaul Infante-Sainz-0/+0
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.
2019-04-23Awk, coreutils and sed are now prerequisites of metastoreRaul Infante-Sainz-0/+0
Until now, `metastore' did not depend on the necessaries programs that we use to install it (`awk', `coreutils' and `sed'). They are not official dependencies of `metastore', but we need them to install it. With this commit, we put these programs as prerequisites of `metastore' in order to be able to install it without any problem.
2019-04-15Minor typo corrections in README-hacking.mdMohammad Akhlaghi-0/+0
In two places, I had mistakenly put a <'> instead of a <`>, causing bad highlighting in the markdown rendering. They have been corrected. Also, one long line in was broken up into several.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+0
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).
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-0/+0
All occurances of "pipeline" have been chanaged to "project" or "template" withint the text (comments, READMEs, and comments) of the template. The main template branch is now also named `template'. This was all because `pipeline' is too generic and couldn't be distinguished from the base, and customized project.
2019-04-14Corrected copyright information for .file-metadataMohammad Akhlaghi-0/+0
Since `.file-metadata' is a binary file, we can't include a copyright inside of it so we have to use `README.md' to mention its copyright and license notice. However, this was not done clearly and is now corrected.
2019-04-14Added citation for FFTWMohammad Akhlaghi-0/+0
Until now we weren't including the citation for FFTW (one of the template's optional packages). With this commit, it is added.
2019-04-12Dependency BibTeX entries included only when necessaryMohammad Akhlaghi-0/+0
Until now, there was a single `tex/src/references.tex' file that housed the BibTex entries for everything (software and non-software). Since we have started to include the BibTeX entry for more software, it will be hard to manage the large (sometime unused) BibTeX entries of the software in the middle of the non-software related citations in the text of the paper. Therefore, with this commit, a `tex/dependencies' directory has been made which has a separate BibTeX entry file for each software that needs one. After the software is built, this file is copied to the new `.local/version-info/cite' directory. At the end, the configure script will concatenate all the files in this directory into one file which will later be used with `tex/src/references.tex' by BibLaTeX. This greatly simplifies managing of citations. Allowing us to focus on the software-building and paper-writing citations separately/cleanly (and thus be more efficient in both).
2019-04-12File is built as a dependency of GCCRaul Infante-Sainz-0/+0
Until now, we did not have `file'. It was in other project, where a problem with `Astrometry-net' software, ends up with the necessity of having `file' into the pipeline. With this commit, we add `file' to the project. Since it is a low level program, it is set in `dependencies-basic.mk' as a prerequisite of GCC.
2019-04-12Fixed some Scipy-related packages citationsRaul Infante-Sainz-0/+0
Until now, the Scipy citation was only one paper and not the correct one (it was the online manual). With this commit, Scipy is properly cited using the two papers. Also some modifications in the `tex/src/references.tex' have been done (remove last page number).