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2020-11-15Building final PDF: pdf-build-final has to be given an explicit yesMohammad Akhlaghi-5/+5
Until now, when the 'pdf-build-final' configuration variable (defined in 'reproduce/analysis/config/pdf-build.conf') was given any string a PDF would be built. This was very confusing, because people could put a 'no' and the PDF would still be built! With this commit, only when this variable has a value of 'yes' will the PDF be built. If given any other string (or no string at all), it will not produce a PDF. This issue was reported by Zahra Sharbaf.
2020-09-24Gnuastro's analysis configuration files removedMohammad Akhlaghi-128/+0
Until now, the core Maneage branch included some configuration files for Gnuastro's programs. This was actually a remnant of the distant past when Maneage didn't actually build its own software and we had to rely on the host's software versions. This file contained the configuration files specific to Gnuastro for this project and also had a feature to avoid checking the host's own configuration files. However, we now build all our software ourselves with fixed configuration files (for the version that is being installed and its version is stored). So those extra configuration files were just extra and caused confusion and problems in some scenarios. With this commit, those extra files are now removed. Also, two small issues are also addressed in parallel with this commit: - When running './project make clean', the 'hardware-parameters.tex' macro file (which is created by './project configure' is not deleted. - The project title is now written into the default output's PDF's properties (through 'hypersetup' in 'tex/src/preamble-header.tex') through the LaTeX macro. All these issues were found and fixed with the help of Samane Raji.
2020-07-04Better names and comments in INPUTS.confMohammad 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.
2020-06-10IMPORTANT: bug fix in default data download script of download.mkMohammad 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.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-1/+26
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-2/+16
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
2020-04-26verify-outputs.conf: typo correction in comment to avoid confusionBoud Roukema-1/+1
Until now, the comment in the file said that setting the `verify-outputs` variable to `yes` disables the verification. Looking at `reproduce/analysis/make/verify.mk` shows that the opposite is true. With this commit, the word `disable` is replaced with `enable` so that the user is not confused by the conflict between the source code in the other file and this comment.
2020-04-17IMPORTANT: software config directly under reproduce/software/configMohammad Akhlaghi-0/+128
Until now the software configuration parameters were defined under the `reproduce/software/config/installation/' directory. This was because the configuration parameters of analysis software (for example Gnuastro's configurations) were placed under there too. But this was terribly confusing, because the run-time options of programs falls under the "analysis" phase of the project. With this commit, the Gnuastro configuration files have been moved under the new `reproduce/analysis/config/gnuastro' directory and the software configuration files are directly under `reproduce/software/config'. A clean build was done with this change and it didn't crash, but it may cause crashes in derived projects, so after merging with Maneage, please re-configure your project to see if anything has been missed. Please let us know if there is a problem.
2020-01-20IMPORTANT!!! Configuration Makefiles now have a .conf suffixMohammad Akhlaghi-1/+0
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.
2020-01-01Verification of output values and data added within templateMohammad Akhlaghi-0/+3
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.
2020-01-01Copyright statements updated to include 2020Mohammad Akhlaghi-2/+2
Now that its 2020, its necessary to include this year in the copyright statements.
2019-06-29Added citation for TIDES, sorted progs alphabeticallyMohammad Akhlaghi-1/+1
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.
2019-06-28tides library addedPrasenjit Saha-1/+1
TIDES is an ODE integrator with multiple-precision arithmetic.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-0/+38
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).