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2022-01-21IMPORTANT: Updates to almost all softwareMohammad Akhlaghi-21/+40
This commit primarily affects the configuration step of Maneage'd projects, and in particular, updated versions of the many of the software (see P.S.). So it shouldn't affect your high-level analysis other than the version bumps of the software you use (and the software's possibly improve/changed behavior). The following software (and thus their dependencies) couldn't be updated as described below: - Cryptography: isn't building because it depends on a new setuptools-rust package that has problems (https://savannah.nongnu.org/bugs/index.php?61731), so it has been commented in 'versions.conf'. - SecretStorage: because it depends on Cryptography. - Keyring: because it depends on SecretStorage. - Astroquery: because it depends on Keyring. This is a "squashed" commit after rebasing a development branch of 60 commits corresponding to a roughly two-month time interval. The following people contributed to this branch. - Boudewijn Roukema added all the R software infrastructure and the R packages, as well as greatly helping in fixing many bugs during the update. - Raul Infante-Sainz helped in testing and debugging the build. - Pedram Ashofteh Ardakani found and fixed a bug. - Zahra Sharbaf helped in testing and found several bugs. Below a description of the most noteworthy points is given. - Software tarballs: all updated software now have a unified format tarball (ustar; if not possible, pax) and unified compression (Lzip) in Maneage's software repository in Zenodo (https://doi.org/10.5281/zenodo.3883409). For more on this See https://savannah.nongnu.org/task/?15699 . This won't affect any extra software you would like to add; you can use any format recognized by GNU Tar, and all common compression algorithms. This new requirement is only for software that get merged to the core Maneage branch. - Metastore (and thus libbsd and libmd) moved to highlevel: Metastore (and the packages it depends on) is a high-level product that is only relevant during the project development (like Emacs!): when the user wants the file meta data (like dates) to be unchanged after checking out branches. So it should be considered a high-level software, not basic. Metastore also usually causes many more headaches and error messages, so personally, I have stopped using it! Instead I simply merge my branches in a separate clone, then pull the merge commit: in this way, the files of my project aren't re-written during the checkout phase and therefore their dates are untouched (which can conflict with Make's dates on configuration files). - The un-official cloned version of Flex (2.6.4-91 until this commit) was causing problems in the building of Netpbm, so with this commit, it has been moved back to version 2.6.4. - Netpbm's official page had version 10.73.38 as the latest stable tarball that was just released in late 2021. But I couldn't find our previously-used version 10.86.99 anywhere (to see when it was released and why we used it! Its at last more than one year old!). So the official stable version is being used now. - Improved instructions in 'README.md' for building software environment in a Docker container (while having project source and output data products on the local system; including the usage of the host's '/dev/shm' to speed up temporary operations). - Until now, the convention in Maneage was to put eight SPACE characters before the comment lines within recipes. This was done because by default GNU Emacs (also many other editors) show a TAB as eight characters. However, in other text editors, online browsers, or even the Git diff, a TAB can correspond to a different number of characters. In such cases, the Maneage recipes wouldn't look too interesting (the comments and the recipe commands would show a different indentation!). With this commit, all the comment lines in the Makefiles within the core Maneage branch have a hash ('#') as their first character and a TAB as the second. This allows the comment lines in recipes to have the same indentation as code; making the code much more easier to read in a general scenario including a 'git diff' (editor agnostic!). P.S. List of updated software with their old and new versions - Software with no version update are not mentioned. - The old version of newly added software are shown with '--'. Name (Basic) Old version New version ------------ ----------- ----------- Bzip2 1.0.6 1.0.8 CURL 7.71.1 7.79.1 Dash 0.5.10.2 0.5.11.5 File 5.39 5.41 Flock 0.2.3 0.4.0 GNU Bash 5.0.18 5.1.8 GNU Binutils 2.35 2.37 GNU Coreutils 8.32 9.0 GNU GCC 10.2.0 11.2.0 GNU M4 1.4.18 1.4.19 GNU Readline 8.0 8.1.1 GNU Tar 1.32 1.34 GNU Texinfo 6.7 6.8 GNU diffutils 3.7 3.8 GNU findutils 4.7.0 4.8.0 GNU gmp 6.2.0 6.2.1 GNU grep 3.4 3.7 GNU gzip 1.10 1.11 GNU libunistring 0.9.10 1.0 GNU mpc 1.1.0 1.2.1 GNU mpfr 4.0.2 4.1.0 GNU nano 5.2 6.0 GNU ncurses 6.2 6.3 GNU wget 1.20.3 1.21.2 Git 2.28.0 2.34.0 Less 563 590 Libxml2 2.9.9 2.9.12 Lzip 1.22-rc2 1.22 OpenSLL 1.1.1a 3.0.0 Patchelf 0.10 0.13 Perl 5.32.0 5.34.0 Podlators -- 4.14 Name (Highlevel) Old version New version ---------------- ----------- ----------- Apachelog4cxx 0.10.0-603 0.12.1 Astrometry.net 0.80 0.85 Boost 1.73.0 1.77.0 CFITSIO 3.48 4.0.0 Cmake 3.18.1 3.21.4 Eigen 3.3.7 3.4.0 Expat 2.2.9 2.4.1 FFTW 3.3.8 3.3.10 Flex 2.6.4-91 2.6.4 Fontconfig 2.13.1 2.13.94 Freetype 2.10.2 2.11.0 GNU Astronomy Utilities 0.12 0.16.1-e0f1 GNU Autoconf 2.69.200-babc 2.71 GNU Automake 1.16.2 1.16.5 GNU Bison 3.7 3.8.2 GNU Emacs 27.1 27.2 GNU GDB 9.2 11.1 GNU GSL 2.6 2.7 GNU Help2man 1.47.11 1.48.5 Ghostscript 9.52 9.55.0 ICU -- 70.1 ImageMagick 7.0.8-67 7.1.0-13 Libbsd 0.10.0 0.11.3 Libffi 3.2.1 3.4.2 Libgit2 1.0.1 1.3.0 Libidn 1.36 1.38 Libjpeg 9b 9d Libmd -- 1.0.4 Libtiff 4.0.10 4.3.0 Libx11 1.6.9 1.7.2 Libxt 1.2.0 1.2.1 Netpbm 10.86.99 10.73.38 OpenBLAS 0.3.10 0.3.18 OpenMPI 4.0.4 4.1.1 Pixman 0.38.0 0.40.0 Python 3.8.5 3.10.0 R 4.0.2 4.1.2 SWIG 3.0.12 4.0.2 Util-linux 2.35 2.37.2 Util-macros 1.19.2 1.19.3 Valgrind 3.15.0 3.18.1 WCSLIB 7.3 7.7 Xcb-proto 1.14 1.14.1 Xorgproto 2020.1 2021.5 Name (Python) Old version New version ------------- ----------- ----------- Astropy 4.0 5.0 Beautifulsoup4 4.7.1 4.10.0 Beniget -- 0.4.1 Cffi 1.12.2 1.15.0 Cryptography 2.6.1 36.0.1 Cycler 0.10.0 0.11.0+} Cython 0.29.21 0.29.24 Esutil 0.6.4 0.6.9 Extension-helpers -- 0.1 Galsim 2.2.1 2.3.3 Gast -- 0.5.3 Jinja2 -- 3.0.3 MPI4py 3.0.3 3.1.3 Markupsafe -- 2.0.1 Numpy 1.19.1 1.21.3 Packaging -- 21.3 Pillow -- 8.4.0 Ply -- 3.11 Pyerfa -- 2.0.0.1 Pyparsing 2.3.1 3.0.4 Pythran -- 0.11.0 Scipy 1.5.2 1.7.3 Setuptools 41.6.0 58.3.0 Six 1.12.0 1.16.0 Uncertainties 3.1.2 3.1.6 Wheel -- 0.37.0 Name (R) Old version New version -------- ----------- ----------- Cli -- 2.5.0 Colorspace -- 2.0-1 Cowplot -- 1.1.1 Crayon -- 1.4.1 Digest -- 0.6.27 Ellipsis -- 0.3.2 Fansi -- 0.5.0 Farver -- 2.1.0 Ggplot2 -- 3.3.4 Glue -- 1.4.2 GridExtra -- 2.3 Gtable -- 0.3.0 Isoband -- 0.2.4 Labeling -- 0.4.2 Lifecycle -- 1.0.0 Magrittr -- 2.0.1 MASS -- 7.3-54 Mgcv -- 1.8-36 Munsell -- 0.5.0 Pillar -- 1.6.1 R-Pkgconfig -- 2.0.3 R6 -- 2.5.0 RColorBrewer -- 1.1-2 Rlang -- 0.4.11 Scales -- 1.1.1 Tibble -- 3.1.2 Utf8 -- 1.2.1 Vctrs -- 0.3.8 ViridisLite -- 0.4.0 Withr -- 2.4.2
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-21/+21
Having entered 2021, it was necessary to update the copyright years at the top of the source files. We recommend that you do this for all your project-specific source files also.
2020-05-25Unified reference to GNU/Linux and free softwareMohammad Akhlaghi-5/+5
One of the main reasons to building Maneage is to properly acknowledge/attribute the authors of software in research. So we have adopted a standard of never referring to the GNU-based operating systems running the Linux kernel simply as "Linux", we avoid terms like "Open Sourse" and use Free Software instead (in the same spirit). With this commit, a few instances of the cases above have been corrected, they had slipped through our fingers when we initially imported them into the project. In the special case of the "Journal for Open Source Software", we simply replaced it with its abbreviation (JOSS). This was done because in effect we were generally using journal name abbreviations in almost all the citations already. To avoid any inconsistancies, the names of the three other journals that weren't abbreviated are also abbreviated.
2020-05-22Software citation: removed abstract entry from BibTeX infoMohammad Akhlaghi-7/+0
Until now, two of the software BibTeX sources (Matplolib and Sympy) had an "abstract" entry that was long, not similar to the rest, and not relevant in this context, so they are removed with this commit.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-0/+7
In time, some of the copyright license description had been mistakenly shortened to two paragraphs instead of the original three that is recommended in the GPL. With this commit, they are corrected to be exactly in the same three paragraph format suggested by GPL. The following files also didn't have a copyright notice, so one was added for them: reproduce/software/make/README.md reproduce/software/bibtex/healpix.tex reproduce/analysis/config/delete-me-num.conf reproduce/analysis/config/verify-outputs.conf
2020-02-24MissFITS is now added to the templateSurena Fatemi-0/+18
MissFITS is package for manipulating FITS files. I added it as my first commit to the project for educational purposes.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-19/+19
Now that its 2020, its necessary to include this year in the copyright statements.
2019-10-29lmfit and its dependencies added, Python tarballs as prerequisiteMohammad Akhlaghi-0/+19
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.
2019-10-28HEALPix, Autoconf and Automake now in libraryMohammad Akhlaghi-0/+18
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.
2019-10-24Several more LSST pipeline dependencies are addedMohammad Akhlaghi-0/+27
The following software are added with this commit: eigency, esutil, flake8, future, galsim, lsstdesccoord, pybind11 and pyflakes.
2019-10-07Software citations now use modern ADS link for adsurlMohammad Akhlaghi-9/+9
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.
2019-09-15SExtractor BibTex entry updated with ADS's exported formatMohammad Akhlaghi-10/+13
Until now the SExtractor BibTeX entry has the first-name and family name in the same field, while the family-name should be in curly braces. Also, it was missing an ADS URL. So the default ADS generated BibTeX entry for SExtractor is now used instead of the old one.
2019-06-29Added citation for TIDES, sorted progs alphabeticallyMohammad Akhlaghi-0/+19
While reviewing Prasenjit's commits, I noticed that we had forgot to add the citation for TIDES, also to make things clear, the program/library build rules are now sorted alphabetically. Finally, I noticed that after building the TiKZ PDF figures, it is crashing (like on Prasenjit's computer). After looking around, I noticed its because we were setting the of the `TEXINPUTS' environment variable to be the installed TeX Live directory (which was ultimately redundant because by default TeX will look into where it was installed). The important thing is just that we remove any possible value the host system has, not to set new directories.
2019-05-27Added paper citation of ImfitRaul Infante-Sainz-0/+24
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.
2019-04-24Added copyright notice for sip_tpv.texMohammad Akhlaghi-1/+7
The BibTeX data for `sip_tpv' didn't have a copyright notice, so one was added for it.
2019-04-24Added paper citation of sip_tpv Python packageRaul Infante-Sainz-0/+16
Until now, we were not citing the paper of `sip_tpv' package. With this commit, we have been fix this issue.
2019-04-23Python package SymPy added into the templateRaul Infante-Sainz-0/+23
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.
2019-04-22SCAMP and cdsclient have been added into the projectRaul Infante-Sainz-0/+18
With this commit, we add SCAMP into the project. This program is part of the Astromatic software and the main purpose is to make the fine astrometry and the distorsion correction astronomical images. In principle, SCAMP needs ATLAS library to be able to work (that is what the documentation says). However, we had some problems with ATLAS libraries on Mac OS system, and due to that, we set the option `--enable-openblas' in the configure step. By doing that, we are be able to install SCAMP with no problems. One dependency of SCAMP is `cdsclient', it has been also added with this commit. The `cdsclient' package is a set of C and shell routines which can be built on Unix stations or PCs running Linux, which once compiled allow to query some databases located at CDS or on mirrors over the network.
2019-04-17SExtractor is now included into the projectRaul Infante-Sainz-0/+18
With this commit, we add SExtractor to be installed into the project. It is a widely used program to detect object and build catalogues from astronomical images. We had some problems when installing it because it could not link with some ATLAS libraries. But, since we have OpenBLAS installed, we can use it to override the problem with ATLAS.
2019-04-17Corrected bibtex entry for Astrometry-net and SwarpRaul Infante-Sainz-11/+10
Until now, there were erros in the citation of Astrometry-net and Scamp papers. With this commit, we fix these problems. The Swarp bibtex has also been modify to follow the stetic of the citation style we have right now in the project. We also added the `dependency-bib.tex' as a prerequisite of `paper.bbl'.
2019-04-17SWarp is now into the pipelineRaul Infante-Sainz-25/+39
SWarp resamples and co-adds together FITS images using any arbitrary astrometric projection defined in the WCS standard. It is a very useful program for astronomy and that is why we added it to the pipeline. With this commit, we also cite the paper for Astrometry-net that until now was missing.
2019-04-16Astrometry-net and all its dependencies are now in the projectRaul Infante-Sainz-0/+25
With this commit, we include Astrometry-net software and one remaining dependency of it (Swig). In principle it should work as far as we tested all of this software in GNU/Linux, but we need to test also in Mac OS. As a result, this commit is just for setting all the rules and dependencies, but more tests are necessaries to ensure it works properly, specially in Mac OS systems.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+260
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).