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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.
2020-10-18Recipes for final initialize and verify targets not on stdoutMohammad Akhlaghi-2/+6
The LaTeX macro files for these two subMakefiles are created on every run of './project make'. So their commands are also printed every time and hardly ever will a normal user want to modify or change these. So to avoid populating the standard output of a Maneaged project with all these extra lines every time (possibly getting mixed with the important analysis or LaTeX outputs), an '@' has been placed at the start of the recipes. With an '@' at the start of the recipe, Make is instructed to not print the commands it wants to run in the standard output.
2020-07-20README-hacking.md: clarify Zenodo usage in publication checklistBoud Roukema-2/+2
This commit clarifies the initial usage of Zenodo for reserving a Zenodo identifier and starting an 'unpublished' upload. Some other minor wording changes are done here.
2020-06-10IMPORTANT: bug fix in default data download script of download.mkMohammad Akhlaghi-1/+1
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.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-13/+36
Possible semantic conflicts (that may not show up as Git conflicts but may cause a crash in your project after the merge): 1) The project title (and other basic metadata) should be set in 'reproduce/analysis/conf/metadata.conf'. Please include this file in your merge (if it is ignored because of '.gitattributes'!). 2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if you have added all analysis Makefiles to the '.gitattributes' file (thus not merging any change in them with your branch). For example with this command: git diff master...maneage -- reproduce/analysis/make/initialize.mk 3) The old 'verify-txt-no-comments-leading-space' function has been replaced by 'verify-txt-no-comments-no-space'. The new function will also remove all white-space characters between the columns (not just white space characters at the start of the line). Thus the resulting check won't involve spacing between columns. A common set of steps are always necessary to prepare a project for publication. Until now, we would simply look at previous submissions and try to follow them, but that was prone to errors and could cause confusion. The internal infrastructure also didn't have some useful features to make good publication possible. Now that the submission of a paper fully devoted to the founding criteria of Maneage is complete (arXiv:2006.03018), it was time to formalize the necessary steps for easier submission of a project using Maneage and implement some low-level features that can make things easier. With this commit a first draft of the publication checklist has been added to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018 and zenodo.3872248. To help guide users on implementing the good practices for output datasets, the outputs of the default project shown in the paper now use the new features). After reading the checklist, please inspect these. Some other relevant changes in this commit: - The publication involves a copy of the necessary software tarballs. Hence a new target ('dist-software') was also added to package all the project's software tarballs in one tarball for easy distribution. - A new 'dist-lzip' target has been defined for those who want to distribute an Lzip-compressed tarball. - The '\includetikz' LaTeX macro now has a second argument to allow configuring the '\includegraphics' call when the plot should not be built, but just imported.
2020-05-22Corrected copyright notices to fit GPL suggested formatMohammad Akhlaghi-8/+11
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-11/+8
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.
2020-01-20IMPORTANT!!! Configuration Makefiles now have a .conf suffixMohammad Akhlaghi-1/+1
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.
2020-01-18README-hacking.md: edits and corrections for easier customizationMohammad Akhlaghi-2/+2
The checklist descriptions were slightly edited to be more clear. Also, while following them, I noticed that while removing the "delete-me" parts on `verify.mk', would cause an error: the `if [ $$m == delete-me ];' statement we were saying to delete cause an error because `elif' was the first statement Bash would see. So with this commit, the `download' conditional (which isn't instructed to be deleted) was set to be the top (with an `if') and the `delete-me' conditional now has an `elif'.
2020-01-01Verification function checks if file existsMohammad Akhlaghi-3/+13
Until now, if the file to be verified didn't exist, a different checksum would be generated, and it would stop, but it wasn't immediately clear if the differing checksum is because the file doesn't exist at all! With this commit, before calculating the checksum, we first make sure if the file exists. If it doesn't exist an explicit error is printed and thus will help the project editor to find the cause of the problem.
2020-01-01Verification of output values and data added within templateMohammad Akhlaghi-0/+116
Until now, the only verification that the template provided was the published PDF. Users had to manually compare the published and generated PDFs (numbers, plots, tables) and see if they obtained the same result. However, this type of manual verification is not good and is prone to frustration and missing important differences. With this commit, a new Makefile has been added in the analysis steps: `verify.mk'. It provides facilities to easily verify the results that go into the paper. For example tables that go into making the paper's plots, or the LaTeX macros that blend into the text. See the updated parts in `README-hacking.md` for a more complete explanation. This completes task #15497.