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2022-01-21IMPORTANT: Updates to almost all softwareMohammad 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
2021-01-02Copyright year updated in all source filesMohammad 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.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-8/+12
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
2020-04-20Maneage instead of Template in README-hacking.md and copyright noticesMohammad Akhlaghi-12/+9
Until now, throughout Maneage we were using the old name of "Reproducible Paper Template". But we have finally decided to use Maneage, so to avoid confusion, the name has been corrected in `README-hacking.md' and also in the copyright notices. Note also that in `README-hacking.md', the main Maneage branch is now called `maneage', and the main Git remote has been changed to `https://gitlab.com/maneage/project' (this is a new GitLab Group that I have setup for all Maneage-related projects). In this repository there is only one `maneage' branch to avoid complications with the `master' branch of the projects using Maneage later.
2020-04-01Added a README.md file under the top-level tex/ directoryMohammad Akhlaghi-0/+59
The subdirectories here (and the fact that they may be symbolic links) may be confusing for some early project users, so a `README.md' file was added there describing them and when they are links, when directories and when some may not yet exist.