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

Age	Commit message (Collapse)	Author	Lines
2022-06-10	Housekeeping: some portability issues fixed; four software updates	Mohammad Akhlaghi	-1/+1
	Until now, there were several portability issues in Maneage: 1. Maneage would crash on older operating systems (checked on Debian 6), where Wget didn't have the '--no-use-server-timestamps'. 2. On a Linux kernel 2.6.32 (of the same Debian 6 above) some features in 'util-linux' (like 'swapon' or 'libmount') wouldn't build and wouldn't let 'util-linux' complete. These features need root permissions to be useful, so the wouldn't be used in Maneage any way! But they wouldn't let Maneage get built 3. The './project shell' command would still read the host's '~/.bashrc', letting the host environment leak-in to Maneage's interactive shell. 4. The building of Flex 2.64 wouldn't complete due to a segmentation fault an Ubuntu, but NetPBM (which depends on Flex) would crash with a wrong usage of 'yyunput'. This had actually caused a non-update to Flex in a previous Maneage software update. 5. The update Astrometry.net would assume SExtractor's executable name is 'source-extractor'; causing a crash in usage. This forced the users to manually create a 'source-extractor' symbolic link in the '.local/bin' directory. 6. The 'reproduce/software/shell/tarball-prepare.sh' script (that is used for making Maneage-standard tarballs) wouldn't accept option values with an '=' between the option name and value! It also didnt' print sufficiently informative messages and errors (for example it would say "skipping ..." (making the user think there is a problem!), but it was actually that the file already existed! 7. The 'reproduce/analysis/make/prepare.mk' and 'reproduce/analysis/make/verify.mk' Makefiles that needed to reject some of the 'makesrc' sub-Makefiles would simply substitute their names with nothing. But this would cause problems when the name is part of the name of another sub-Makefile. 8. On the Debian 6 system mentioned above the raw 'df' command's output wasn't in the expected format; so Maneage would fail to properly detect the free space in the disk. With these commit, all the issues above have been solved: for 1, A check has been added to avoid using that option. For 2, those 'util-linux' features have been disabled. For 3, the '--norc' and '--noprofile' options have beed added to the call to Bash. For 4, see below. For 5, the symbolic link is now automatically made with SExtractor. For 6, the option reading components of that script have been fully re-written and more robust sanity checks are also added, with more informative warnings. For 7, the 'subst' function of Make was replaced with 'filter-out' and this fixed the problem. For 8, 'df' is called with the '-P' option so it has a unified format in all versions. For 4, the versions of 'flex' and 'netpbm' have been updated. Since they were the dependency of 'astrometrynet', that has also been updated. In the process, we discovered that 'lzip' has a new version which claims to be faster, so that is also updated. lzip 1.22 --> 1.23 astrometrynet 0.85 --> 0.89 flex 2.6.4 --> 2.6.4-410-74a89fd netpbm 10.73.39 --> 10.73.39 NetPBM needed some manual manipulation in its source (to remove the extra line), so the necessary steps have been added to its build recipe in 'reproduce/software/make/high-level.mk'.
2022-04-15	IMPORTANT: more generic, robust and secure INPUTS.conf and download.mk	Mohammad Akhlaghi	-41/+68
	SUMMARY: it is necessary to update your 'INPUTS.conf' and 'download.mk'. Until now, adding an input file involved several steps that needed manual (and inconvenient!) intervention: for every file, you needed to define four variables in 'INPUTS.conf', and in 'reproduce/analysis/make/download.mk' you had to use a (complex for large number of files) shell 'if/elif/else' condition to link the names of the input files to those variables. Besides inconvenience, this could cause bugs (typos!). Furthermore, a basic MD5 checksum was used for verifying the files. With this commit, a new structure has been defined for 'INPUTS.conf' that (thanks to some pretty useful GNU Make features), removes the need for users to manually edit 'reproduce/analysis/make/download.mk', and reduces the number of variables necessary for each file to three (from four). Furthermore, we now use the SHA256 checksum for input data validation. Regarding the trick used in 'INPUTS.conf' (form the newly added description in 'download.mk'): In GNU Make, '.VARIABLES' "... expands to a list of the names of all global variables defined so far" (from the "Other Special Variables" section of the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only used for input files, we find all the variables that contain the input file names (the '%' is the filename). Finally, using the pattern-substitution function ('patsubst'), we remove the fixed string at the start and end of the variable name. Steps you need to take: - INPUTS.conf: translate your old format to the new format (after carefully reading the description in the comments at the start of the file). After applying the new standards, you don't need to use the variables of 'INPUTS.conf' directly in your Makefiles! For example if one of your input datasets is called 'abc.fits', the checksum variable will be 'INPUT-abc.fits-sha256' and in your high-level Makefiles, you can simply set '$(indir)/abc.fits' as a prerequisite (like you probably did already). - reproduce/analysis/make/download.mk: for the definition and rule of 'inputdatasets', simply use the Maneage branch, and remove anything you had added in your project. In the process, I also noticed that 'README-hacking.md' still referred to 'master' as the main project branch, while we have used 'main' in the paper (and is the common convention with Git).
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.
2020-07-04	Better names and comments in INPUTS.conf	Mohammad Akhlaghi	-20/+23
	Until now, the dataset's configuration names had a 'WFPC2' prefix. But this very alien to anyone that is not familiar with the history of the Hubble Space Telescope (the camera is no longer used! Its just used here since its one of the standard FITS files from the FITS standard webpage). With this commit the variable names have been modified to be more readable and clear (having a 'DEMO-' prefix). Also the comments of 'INPUTS.conf' (describing the purpose of each variable) were edited and made more clear.
2020-06-10	IMPORTANT: bug fix in default data download script of download.mk	Mohammad Akhlaghi	-3/+39
	Summary of possible semantic conflicts 1. The recipe to download input datasets has been modified. You have to re-set the old 'origname' variable to 'localname' (to avoid confusion) and the default dataset URL should now be complete (including the actual filename). See the newly added descriptions in 'INPUTS.conf' for more on this. Until now, when the dataset was already present on the host system, a link couldn't be made to it, causing the project to crash in the checksum phase. This has been fixed with properly naming the main variable as 'localname' to avoid the confusion that caused it. Some other problems have been fixed in this recipe in the meantime: - When the checksum is different, the expected and calculated checksums are printed. - In the default paper, we now print the full URL of the dataset, not just the server, so the checksum of the 'download.tex' step has been updated.
2020-01-20	IMPORTANT!!! Configuration Makefiles now have a .conf suffix	Mohammad Akhlaghi	-0/+15
	Until now, the configuration Makefiles (in `reproduce/software/config/installation' and `reproduce/analysis/config') had a `.mk' suffix, similar to the workhorse Makefiles. Although they are indeed Makefiles, but given their nature (to only keep configuration parameters), it is confusing (especially to early users) for them to also have a `.mk' (similar to the analysis or software building Makefiles). To address this issue, with this commit, all the configuration Makefiles (in those directories) are now given a `.conf' suffix. This is also assumed for all the files that are loaded. The configuration (software building) and running of the template have been checked with this change from scratch, but please report any error that may not have been noticed. THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.

Until now, there were several portability issues in Maneage: 1. Maneage would crash on older operating systems (checked on Debian 6), where Wget didn't have the '--no-use-server-timestamps'. 2. On a Linux kernel 2.6.32 (of the same Debian 6 above) some features in 'util-linux' (like 'swapon' or 'libmount') wouldn't build and wouldn't let 'util-linux' complete. These features need root permissions to be useful, so the wouldn't be used in Maneage any way! But they wouldn't let Maneage get built 3. The './project shell' command would still read the host's '~/.bashrc', letting the host environment leak-in to Maneage's interactive shell. 4. The building of Flex 2.64 wouldn't complete due to a segmentation fault an Ubuntu, but NetPBM (which depends on Flex) would crash with a wrong usage of 'yyunput'. This had actually caused a non-update to Flex in a previous Maneage software update. 5. The update Astrometry.net would assume SExtractor's executable name is 'source-extractor'; causing a crash in usage. This forced the users to manually create a 'source-extractor' symbolic link in the '.local/bin' directory. 6. The 'reproduce/software/shell/tarball-prepare.sh' script (that is used for making Maneage-standard tarballs) wouldn't accept option values with an '=' between the option name and value! It also didnt' print sufficiently informative messages and errors (for example it would say "skipping ..." (making the user think there is a problem!), but it was actually that the file already existed! 7. The 'reproduce/analysis/make/prepare.mk' and 'reproduce/analysis/make/verify.mk' Makefiles that needed to reject some of the 'makesrc' sub-Makefiles would simply substitute their names with nothing. But this would cause problems when the name is part of the name of another sub-Makefile. 8. On the Debian 6 system mentioned above the raw 'df' command's output wasn't in the expected format; so Maneage would fail to properly detect the free space in the disk. With these commit, all the issues above have been solved: for 1, A check has been added to avoid using that option. For 2, those 'util-linux' features have been disabled. For 3, the '--norc' and '--noprofile' options have beed added to the call to Bash. For 4, see below. For 5, the symbolic link is now automatically made with SExtractor. For 6, the option reading components of that script have been fully re-written and more robust sanity checks are also added, with more informative warnings. For 7, the 'subst' function of Make was replaced with 'filter-out' and this fixed the problem. For 8, 'df' is called with the '-P' option so it has a unified format in all versions. For 4, the versions of 'flex' and 'netpbm' have been updated. Since they were the dependency of 'astrometrynet', that has also been updated. In the process, we discovered that 'lzip' has a new version which claims to be faster, so that is also updated. lzip 1.22 --> 1.23 astrometrynet 0.85 --> 0.89 flex 2.6.4 --> 2.6.4-410-74a89fd netpbm 10.73.39 --> 10.73.39 NetPBM needed some manual manipulation in its source (to remove the extra line), so the necessary steps have been added to its build recipe in 'reproduce/software/make/high-level.mk'.

SUMMARY: it is necessary to update your 'INPUTS.conf' and 'download.mk'. Until now, adding an input file involved several steps that needed manual (and inconvenient!) intervention: for every file, you needed to define four variables in 'INPUTS.conf', and in 'reproduce/analysis/make/download.mk' you had to use a (complex for large number of files) shell 'if/elif/else' condition to link the names of the input files to those variables. Besides inconvenience, this could cause bugs (typos!). Furthermore, a basic MD5 checksum was used for verifying the files. With this commit, a new structure has been defined for 'INPUTS.conf' that (thanks to some pretty useful GNU Make features), removes the need for users to manually edit 'reproduce/analysis/make/download.mk', and reduces the number of variables necessary for each file to three (from four). Furthermore, we now use the SHA256 checksum for input data validation. Regarding the trick used in 'INPUTS.conf' (form the newly added description in 'download.mk'): In GNU Make, '.VARIABLES' "... expands to a list of the names of all global variables defined so far" (from the "Other Special Variables" section of the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only used for input files, we find all the variables that contain the input file names (the '%' is the filename). Finally, using the pattern-substitution function ('patsubst'), we remove the fixed string at the start and end of the variable name. Steps you need to take: - INPUTS.conf: translate your old format to the new format (after carefully reading the description in the comments at the start of the file). After applying the new standards, you don't need to use the variables of 'INPUTS.conf' directly in your Makefiles! For example if one of your input datasets is called 'abc.fits', the checksum variable will be 'INPUT-abc.fits-sha256' and in your high-level Makefiles, you can simply set '$(indir)/abc.fits' as a prerequisite (like you probably did already). - reproduce/analysis/make/download.mk: for the definition and rule of 'inputdatasets', simply use the Maneage branch, and remove anything you had added in your project. In the process, I also noticed that 'README-hacking.md' still referred to 'master' as the main project branch, while we have used 'main' in the paper (and is the common convention with Git).

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.

Until now, the dataset's configuration names had a 'WFPC2' prefix. But this very alien to anyone that is not familiar with the history of the Hubble Space Telescope (the camera is no longer used! Its just used here since its one of the standard FITS files from the FITS standard webpage). With this commit the variable names have been modified to be more readable and clear (having a 'DEMO-' prefix). Also the comments of 'INPUTS.conf' (describing the purpose of each variable) were edited and made more clear.

Summary of possible semantic conflicts 1. The recipe to download input datasets has been modified. You have to re-set the old 'origname' variable to 'localname' (to avoid confusion) and the default dataset URL should now be complete (including the actual filename). See the newly added descriptions in 'INPUTS.conf' for more on this. Until now, when the dataset was already present on the host system, a link couldn't be made to it, causing the project to crash in the checksum phase. This has been fixed with properly naming the main variable as 'localname' to avoid the confusion that caused it. Some other problems have been fixed in this recipe in the meantime: - When the checksum is different, the expected and calculated checksums are printed. - In the default paper, we now print the full URL of the dataset, not just the server, so the checksum of the 'download.tex' step has been updated.

Until now, the configuration Makefiles (in `reproduce/software/config/installation' and `reproduce/analysis/config') had a `.mk' suffix, similar to the workhorse Makefiles. Although they are indeed Makefiles, but given their nature (to only keep configuration parameters), it is confusing (especially to early users) for them to also have a `.mk' (similar to the analysis or software building Makefiles). To address this issue, with this commit, all the configuration Makefiles (in those directories) are now given a `.conf' suffix. This is also assumed for all the files that are loaded. The configuration (software building) and running of the template have been checked with this change from scratch, but please report any error that may not have been noticed. THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.