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2021-01-12Default LaTeX preamble: some packages moved to preamble-project.texMohammad Akhlaghi-69/+39
Until now, important LaTeX packages like 'caption' (for managing figure captions), 'hyperref' (for managing links) and 'xcolor' (for managing colors) were being loaded inside the optional 'tex/src/preamble-maneagge-defualt-style.tex' file. We recommend to remove this file from loading when you use custom journal sytels. However, these packages will often be necessary after loading special journal styles also. With this commit, these packages are now loaded into LaTeX as part of the 'tex/src/preamble-project.tex' file. This file is in charge of LaTeX settings that are custom to the project and independent of its style. Several other small corrections are made with this commit: - I noticed that './project make texclean' crashes if no PDF exists in the working directory! So a '-f' was added to the 'rm' command of the 'texclean' rule. - As part of the LaTeX Hyperref, we can set general metadata or properties for the PDF (that aren't written into the printable PDF, but into the file metadata). They can be viewed in many PDF viewers as PDF properties. Until now, we were only using the '\projecttitle' macro here to write the paper's title. However, thanks to the recently added 'reproduce/analysis/config/metadata.conf', we now have a lot of useful information that can also go here. So the 'metadata-copyright-owner' is now used to define the PDF author, and the project's 'metadata-git-repository' and commit hash are written into the PDF subject. But to import these, it was necessary to define them as LaTeX macros, hence the addition of these macros in 'initialize.mk'. - Some extra packages that aren't necessary to build the default PDF were removed in 'preamble-project.tex'.
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-8/+8
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.
2020-12-01IMPORTANT: organizational improvements in Maneage TeX sourcesMohammad Akhlaghi-159/+173
This only concerns the TeX sources in the default branch. In case you don't use them, there should only be a clean conflict in 'paper.tex' (that is obvious and easy to fix). Conflicts may only happen in some of the 'tex/src/preamble-*.tex' files if you have actually changed them for your project. But generally any conflict that does arise by this commit with your project branch should be very clear and easy to fix and test. In short, from now on things will even be easier: any LaTeX configuration that you want to do for your project can be done in 'tex/src/preamble-project.tex', so you don't have to worry about any other LaTeX preamble file. They are either templates (like the ones for PGFPlots and BibLaTeX) or low-level things directly related to Maneage. Until now, this distinction wasn't too clear. Here is a summary of the improvements: - Two new options to './project make': with '--highlight-new' and '--highlight-notes' it is now possible to activate highlighting on the command-line. Until now, there was a LaTeX macro for this at the start of 'paper.tex' (\highlightchanges). But changing that line would change the Git commit hash, making it hard for the readers to trust that this is the same PDF. With these two new run-time options, the printed commit hash will not changed. - paper.tex: the sentences are formatted as one sentence per line (and one line per sentence). This helps in version controlling narrative and following the changes per sentence. A description of this format (and its advantages) is also included in the default text. - The internal Maneage preambles have been modified: - 'tex/src/preamble-header.tex' and 'tex/src/preamble-style.tex' have been merged into one preamble file called 'tex/src/preamble-maneage-default-style.tex'. This helps a lot in simply removing it when you use a journal style file for example. - Things like the options to highlight parts of the text are now put in a special 'tex/src/preamble-maneage.tex'. This helps highlight that these are Maneage-specific features that are independent of the style used in the paper. - There is a new 'tex/src/preamble-project.tex' that is the place you can add your project-specific customizations.
2020-09-24Gnuastro's analysis configuration files removedMohammad Akhlaghi-2/+2
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-1/+1
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.
2020-07-04Citing Maneage paper in acknowledgmentsMohammad Akhlaghi-1/+1
In the previous commit, the modified abstract of the acknowledgments only included the URL of Maneage, but its more formal to cite the Maneage paper, the URL is already present in the paper.
2020-06-14Better comments for the top macros of paper.texMohammad Akhlaghi-20/+0
The default 'paper.tex' starts by defining some macros and comments describing them. Until now, the text was not too clear and could be confusing for someone that is not at all familiar with Maneage. With this commit, the comments have been edited to be more clear for a first-time reader. For example they all start with FULL CAPS summaries. Two other small things were corrected in 'tex/src/preamble-necessary.tex': - Until now 'project.tex' was included in this preamble. However, because of its importance in Maneage, and prominent place in the demonstration plot of the paper introducing Maneage, it is now included directly in 'paper.tex'. This also allows users to safely ignore/delete this preamble file if their LaTeX style is different. - I noticed that some macros for some astronomical software names from the very first commits in Maneage were still present here! They are no longer used, so they have been removed.
2020-06-10Updated text of default paper.tex, putting more recent examplesMohammad Akhlaghi-22/+78
The text of the default paper hadn't been changed for a very long time! In this time, three papers using Maneage have been published (which can be very good as an example), Maneage also now has a webpage! With these commit these examples and the webpage have been added and generally it was also polished a little to hopefully be more useful.
2020-06-06IMPORTANT: Added publication checklist, improved relevant infrastructureMohammad Akhlaghi-10/+21
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-44/+67
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-77/+56
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.
2020-01-01Verification of output values and data added within templateMohammad Akhlaghi-1/+1
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-8/+8
Now that its 2020, its necessary to include this year in the copyright statements.
2019-09-15BibLaTeX configured to only print initials of given namesMohammad Akhlaghi-0/+1
Until now, we weren't explicitly asking for BibLaTeX to build the citations with only initial of the author's given names. Therefore when one BibTeX entry had a full given name and another had only initials, this would also be reflected in the paper's bibliography. With this commit, the `giveninits=true' option is given to BibLaTeX to always only print the initial character of an author's given name.
2019-09-07Updates in BibLaTeX preambleMohammad Akhlaghi-0/+8
In some cases, users of the template may not need the other template headers, they may only want `preamble-biblatex.tex'. But `xcolor' needs to be loaded before being able to load the various colors we use in the references. So to be self-consistent, it is loaded. Also, the default style was also printing the month of the publication which is not common. So a line was added to clear the `month' field before building the Bibliography.
2019-08-22Paper's title and author information moved to main paper.texMohammad Akhlaghi-12/+0
Until now, the paper's title and author information were set it `tex/src/preamble-header.tex'. But they are actually shown in the final PDF paper and a much better place to keep them is the top-level `paper.tex'. With this commit, the setting of the title and author names has been moved to `paper.tex', just after importing all the preambles. However, the basic package importation and low-level settings are still set in `tex/src/preamble-header.tex', because they are relatively low-level. This task was suggested by Deepak (Indian Institute of Astrophysics).
2019-05-08TeXLive csquotes packages (needed by BibLaTeX) has been addedMohammad Akhlaghi-0/+7
In the warnings output by LaTeX during the building of a project, I noticed that `csquotes' is recommended for some features of BibLaTeX (a warning was printed) so it is added with this commit.
2019-04-15New architecture to separate software-building and analysis stepsMohammad Akhlaghi-5/+5
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).
2019-04-14Replaced all occurances of pipeline in textMohammad Akhlaghi-2/+2
All occurances of "pipeline" have been chanaged to "project" or "template" withint the text (comments, READMEs, and comments) of the template. The main template branch is now also named `template'. This was all because `pipeline' is too generic and couldn't be distinguished from the base, and customized project.
2019-04-13Corrected copyright notices and info about adding copyright infoMohammad Akhlaghi-30/+9
Until now, the files where the people were meant to change didn't have a proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was wrong because the license does not convey copyright ownership. So the name of the file's original author must always be included and when people modify it (and add their own copyright-able modifications). With this commit, the file's original author (and email) are added to the copyright notice and when more than one person modified a file, both names have their individual copyright notice. Based on this, the description for adding a copyright notice in `README-hacking.md' has also been modified.
2019-04-12Dependency BibTeX entries included only when necessaryMohammad Akhlaghi-250/+9
Until now, there was a single `tex/src/references.tex' file that housed the BibTex entries for everything (software and non-software). Since we have started to include the BibTeX entry for more software, it will be hard to manage the large (sometime unused) BibTeX entries of the software in the middle of the non-software related citations in the text of the paper. Therefore, with this commit, a `tex/dependencies' directory has been made which has a separate BibTeX entry file for each software that needs one. After the software is built, this file is copied to the new `.local/version-info/cite' directory. At the end, the configure script will concatenate all the files in this directory into one file which will later be used with `tex/src/references.tex' by BibLaTeX. This greatly simplifies managing of citations. Allowing us to focus on the software-building and paper-writing citations separately/cleanly (and thus be more efficient in both).
2019-04-12Imported recent corrections, no conflictsMohammad Akhlaghi-0/+115
Some recent corrections that were done by Raul are now merged into the pipeline. There weren't any conflicts.
2019-04-12Fixed some Scipy-related packages citationsRaul Infante-Sainz-12/+42
Until now, the Scipy citation was only one paper and not the correct one (it was the online manual). With this commit, Scipy is properly cited using the two papers. Also some modifications in the `tex/src/references.tex' have been done (remove last page number).
2019-04-12Acknowledged Scipy-related packages: Cython, Matplotlib, Numpy and ScipyRaul Infante-Sainz-0/+85
Until now, name and version of all Python packages were indicated in the final paper, but not the main paper of them (if it exists). With this commit, some Python packages (Cython, Matplotlib, Numpy and Scipy) are now properly acknoledged by citating the source paper. `mpi4py' is also cited although this package is not yet included into the pipeline.
2019-04-12Gnuastro's citation included in its build targetMohammad Akhlaghi-1/+1
With this commit, we are applying the new style of citing software within the build rule of Gnuastro.
2019-04-02Copyright notice added to remaining filesMohammad Akhlaghi-0/+21
After doing a systematic search for files without a copyright notice, a few more were found that didn't have a notice. So a notice was added for them. I used this Bash command to find the files: for f in $(find ./ -type f); do \ if [[ $f != *.git* ]]; then \ n=$(grep -i copyright $f | wc -l); \ echo "$n $f"; \ fi; \ done | awk '$1==0'
2019-03-29Added Copyright to all TeX and README filesMohammad Akhlaghi-8/+134
In order to be more clear, a copyright statement was added to all the LaTeX and README files.
2019-02-13Imported recent work on building Python within the pipelineMohammad Akhlaghi-0/+94
Raul Infante-Sainz added the building of Python (along with the Numpy and Astropy packages) into the pipeline. That work is now being merged into the main pipeline branch. There was only this small problem that needed to be fixed: the Python tarball's name after unpacking is actually `Python-X.X.X' (with a captial P), not `python-X.X.X'. This has been corrected with this merge.
2019-02-13Astropy installed in the pipelineRaul Infante-Sainz-0/+94
Astropy was added and one very important thing is that we have to use the pypi tarball (https://pypi.org/) (which is bootstrapped) and not the github tarball.
2019-02-06Better management for .tex directories to build from tarballMohammad Akhlaghi-0/+617
In order to collaborate effectively in the project, even project members that don't necessarily want (or have the capacity) to do the whole analysis must be able to contribute to the project. Until now, the users of the distributed tarball could only modify the text and not the figures (built with PGFPlots) of the paper. With this commit, the management of TeX source files in the pipeline was slightly modified to allow this as cleanly as I could think of now! In short, the hand-written TeX files are now kept in `tex/src' and for the pipeline's generated TeX files (in particular the old `tex/pipeline.tex'), we now have a `tex/pipeline' symbolic-link/directory that points to the `tex' directory under the build directory. When packaging the project, `tex/pipeline' will be a full directory with a copy of all the necessary files. Therefore as far as LaTeX is concerned, having a build-directory is no longer relevant. Many other small changes were made to do this job cleanly which will just make this commit message too long! Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as in the standard GNU Build system).