project.git - Core Maneage branch (where all projects derive from)

Age	Commit message (Collapse)	Author	Lines
2022-01-21	IMPORTANT: Updates to almost all software	Mohammad Akhlaghi	-1/+1
	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
2021-01-02	Copyright year updated in all source files	Mohammad Akhlaghi	-1/+1
	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.
2020-01-01	Copyright statements updated to include 2020	Mohammad Akhlaghi	-1/+1
	Now that its 2020, its necessary to include this year in the copyright statements.
2019-10-07	Software citations now use modern ADS link for adsurl	Mohammad Akhlaghi	-1/+1
	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.
2019-04-22	SCAMP and cdsclient have been added into the project	Raul 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.

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

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.

Now that its 2020, its necessary to include this year in the copyright statements.

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.

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.