aboutsummaryrefslogtreecommitdiff
path: root/reproduce/analysis
AgeCommit message (Collapse)AuthorLines
2021-04-17Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-20/+42
Some minor conflicts (all expected from the commit messages in the Maneage branch) occurred but were easily fixed.
2021-04-17IMPORTANT: print-general-metadata new name for print-copyrightMohammad Akhlaghi-13/+36
Summary: - Use the new name of this variable in your Makefiles. - In 'metadata.conf', remove fixed URL prefixes for DOIs ('https://doi.org/') or arXiv ('https://arxiv.org/abs'). Until now, the Make variable that would print the general metadata (of whole project) into each to-be-published dataset was called 'print-copyright'! But it now does much more than simply printing the copyright, it will also print a lot of metadata like arXiv ID, Zenodo DOI and etc into plain-text outputs. The out-dated name could thus be misleading and cause confusions. With this commit, the variable is therefore called 'print-general-metadata'. After merging your project with the Maneage branch, please replace any usage of 'print-copyright' to 'print-general-metadata'. Also with this commit, 'README-hacking.md' mentions 'metadata.conf' and 'print-general-metadata' in the "Publication checklist" section and reminds you to keep the first up to date, and use the second in your to-be-published datasets.
2021-04-17Finally published journal DOI addedMohammad Akhlaghi-9/+11
In the project's 'metadata.conf', we also have an option to store the journal DOI of the project (that will later be printed in the output file products). So now that the paper's DOI has been set by the journal, it was time to add it in the project too. While looking at the usage of the metadata, I noticed that the "Publication checklist" of 'README-hacking.md' didn't talk about it. In fact, the part about putting metadata went into a lot of detail without even mentioning the generic 'print-general-metadata' variable (previously called 'print-copyright') that is created in 'initialize.mk'. So I removed those extra points and just recommended using this variable for plain-text files and putting similar info in other formats. Some other minor changes were made: - The metadata now doesn't need the fixed 'https://doi.org/' prefix (to make it consistent with the arXiv identifier). Inside 'initialize.mk', there are now two variables called 'doi-prefix-url' and 'arxiv-prefix-url' that contain the fixed prefix. - The 'print-copyright' name was clearly outdated for all the extra metadata that this variable created (including the copyright). So its name was changed to 'print-general-metadata'. The generic Maneage changes will be taken into Maneage after this (they were tested here).
2021-04-09Changed all gitlab.com URLs to git.maneage.orgMohammad Akhlaghi-1/+1
Until now, we were primarily linking people to the Gitlab fork of this paper. However, since this paper is part of Maneage, its main repository is on Maneage's own server at http://git.maneage.org/paper-concept.git With this commit therefore, all the gitlab.com URLs have been corrected to owr own Git server. While looking into Git-related points, I also noticed that in the demo code listing showing how to clone Maneage and start a new project, we were using Git's old/depreciated 'master' name. Git (and almost all common repositories) now use 'main' as the default branch name, so this has also been corrected here.
2021-03-28Configuration: corrected check of group nameMohammad Akhlaghi-3/+3
When built in 'group' mode, the write permissions of all created files will be activated for a certain group of users in the host operating system. The user specifies the name of the group with the '--group' option at configure time. At the very start, the './project' script checks to see if the given group name actually exists or not (to avoid hard-to-debug errors popping up later). Until now, the checking 'sg' command (that was used to build the project with group-writable permissions) would always fail due to the excessive number of redirections. Therefore, it would always print the error message and abort. With this commit, the output of 'sg' is no longer re-directed (which also helps users in debuggin). If the group does actually exist, it will just print a small statement saying so, and if it fails, the error message is printed. This fixed the problem, allowing maneage to be built in group-mode. I also noticed that the variable name keeping the group name ('reproducible_paper_group_name') used the old name for the project (which was "Reproducible paper template"! So it has been changed/corrected to 'maneage_group_name'.
2021-03-26Initialization: removed other Gnuastro-specific featuresMohammad Akhlaghi-8/+3
In the previous commit, some Gnuastro-specific initializations were removed but a few more cases remained that are removed with this commit.
2021-01-12Default LaTeX preamble: some packages moved to preamble-project.texMohammad Akhlaghi-1/+3
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'.
2021-01-10make dist: removing temp files moved after project-specific filesMohammad Akhlaghi-6/+7
Until now, when you ran './project make dist', first it would delete the temporary files (like files ending in '~' or '.swp' created by some editors), then it had a place to add project-specific operations for the distribution. However, in the process of cleaning the temporary files, it would 'cd' into the directory that would later be packaged. So project-specific operations would first have to 'cd' back into the top source directory. This was prone to hard-to-find bugs. With this commit, to avoid the problem the project-specific operations are now placed before the cleaning phase. This is also technically good because in the project-specific operations there may also be temporary files that shouldn't go into the distribution tarball.
2021-01-09Imported recent changes in Maneage, minor single conflict fixedMohammad Akhlaghi-22/+35
There was a single conflict in the comments of one part of 'configure.sh' that has been fixed. There was also a single place that needed to convert 'BDIR' to 'badir' in this project (so after the merge, it also built easily).
2021-01-09IMPORTANT: analysis outputs written in BDIR/analysisMohammad Akhlaghi-21/+34
Until now, the build directory contained a 'software/' directory (that hosted all the built software), a 'tex/' subdirectory for the final building of the paper, and many other directories containing intermediate/final data of the specific project. But this mixing of built software and data is against our modularity and minimal complexity principles: built software and built data are separate things and keeping them separate will enable many optimizations. With this commit, the build directory of the core Maneage branch will only contain two sub-directories: 'software/' and 'analysis/'. The 'software/' directory has the same contents as before and is not touched in this commit. However, the 'analysis/' directory is new and everything created in the './project make' phase of the project will be created inside of this directory. To facilitate easy access to these top-level built directories, two new variables are defined at the top of 'initialize.mk': 'badir', which is short for "built-analysis directory" and 'bsdir', which is short for "built-software directory". HOW TO IMPLEMENT THIS CHANGE IN YOUR PROJECT. It is easy: simply replace all occurances of '$(BDIR)' in your project's subMakefiles (except the ones below) to '$(badir)'. To confirm if everything is fine before building your project from scratch after merging, you can run the following command to see where 'BDIR' is used and confirm the only remaning cases. $ grep -r BDIR reproduce/analysis/* --> make/verify.mk: innobdir=$$(echo $$infile | sed -e's|$(BDIR)/||g'); \ --> make/initialize.mk:badir=$(BDIR)/analysis --> make/initialize.mk:bsdir=$(BDIR)/software --> make/initialize.mk: $$sys_rm -rf $(BDIR) --> make/top-prepare.mk:all: $(BDIR)/software/preparation-done.mk 'BDIR' should only be present in lines of the files above. If you see '$(BDIR)' used anywhere else, simply change it to '$(badir)'. Ofcourse, if your project assumes BDIR in other contexts, feel free to keep it, it will not conflict. If anything un-expected happens, please post a comment on the link below (you need to be registered on Savannah to post a comment): https://savannah.nongnu.org/task/?15855 One consequence of this change is that the 'analysis/' subdirectory can be optionally mounted on a separate partition. The need for this actually came up for some new users of Maneage in a Docker image. Docker can fix portability problems on systems that we haven't yet supported (even Windows!), or had a chance to fix low-level issues on. However, Docker doesn't have a GUI interface. So to see the built PDF or intermediate data, it was necessary to copy the built data to the host system after every change, which is annoying during working on a project. It would also need two copies of the source: one in the host, one in the container. All these frustrations can be fixed with this new feature. To describe this scenario, README.md now has a new section titled "Only software environment in the Docker image". It explains step-by-step how you can make a Docker image to only host the built software environment. While your project's source, software tarballs and 'BDIR/analysis' directories are on your host operating system. It has been tested before this commit and works very nicely.
2021-01-05appendix.bbl is now included in make dist tarballMohammad Akhlaghi-4/+7
Since the addition of the appendix bibliography we hadn't checked the 'make dist' command, as a result the PDF couldn't be built. With this commit, in the 'dist' rule, we are now also copying 'appendix.bbl' and the created tarball could build the PDF properly. Also the 'peer-review' directory is now also included in the tarball created by './project make dist'. I also found a small typo in the description of Occam (an 'a' was missing) and fixed it.
2021-01-03Updated copyrights of project-specific copyrightsMohammad Akhlaghi-2/+2
Having entered 2021, it was necessary to update the years of all the copyright statements.
2021-01-03Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-24/+43
There were only three very small conflicts that have been fixed.
2021-01-02Supplement (containing appendices) optionally built separatelyMohammad Akhlaghi-47/+55
Until now, the build strategy of the paper was to have a single output PDF that either contains (1) the full paper with appendices in the same paper (2) only the main body of the paper with no appencies. But the editor in chief of CiSE recently recommended publishing the appendices as supplements that is a separate PDF (on its webpage). So with this commit, the project can make either (1) a single PDF (containing both the main body and the appendices) that will be published on arXiv and will be the default output (this is the same as before). (2) two PDFs: one that is only the main body of the paper and another that is only the appendices. Since the appendices will be printed as a PDF in any case now, the old '--no-appendix' option has been replaced by '--supplement'. Also, the internal shell/TeX variable 'noappendix' has been renamed to 'separatesupplement'.
2021-01-02./project make: new texclean targetMohammad Akhlaghi-1/+6
Until now there was only a 'clean' (to delete all files created during the 'make' phase) and the 'distclean' (to delete all files during configuration and make). But sometimes we don't want to delete all the files created during the full 'make' phase, we only want to delete the files that were created by LaTeX for building the paper. Witht this commit, a new target has been added for this job. You can now run the following command for this job: ./project make texclean Only the files in '$(BDIR)/tex/build' will be deleted (and the 'tikz' directory under that location is recreated, ready for a future build).
2021-01-02Copyright year updated in all source filesMohammad Akhlaghi-14/+14
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.
2020-12-14Better warnings when maneage branch not present and PDF not builtMohammad Akhlaghi-12/+31
Until now, there was no warning when the 'maneage' branch didn't exist in the Git history. This can happen when you forget to push the 'maneage' branch to a remote for your project, and you later clone your project from that remote (for example on another computer). We use the 'maneage' branch to report the latest commit hash and date in the final paper (which can greatly help future readers). Since we check the 'maneage' branch on every run of './project make' (in 'initialize.mk') this would result in a printed statement like this: fatal: Not a valid object name maneage Also until now, the description of what to do when TeXLive wasn't installed properly wasn't complete: it didn't mention that it is necessary to delete the TeXLive target files. This could confuse users (they would re-run './project configure -e', but with no effect). With this commit, for the 'maneage' branch issue a complete warning will be printed. Telling the user what to do to get the 'maneage' branch (and thus fix this warning). Also, the LaTeX macros that go in the paper are now red when the 'maneage' branch doesn't exist, telling the user to see the printed warning (thus encouraging the user to get the branch). For the TeXLive issue, the necessary commands to run are now also printed in the warning.
2020-12-01Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-158/+32
Some minor conflicts that came up during the merge were fixed.
2020-12-01Default paper: macros available for date of commits citedMohammad Akhlaghi-1/+5
Until now, Maneage only provided the commit hashes (of the project and Maneage) as LaTeX macros to use in your paper. However, they are too cryptic and not really human friendly (unless you have access to the Git history on a computer). With this commit, to make things easier for the readers, the date of both commits are also available as LaTeX macros for use in the paper. The date of the Maneage commit is also included in the acknowledgements. Also, the paragraph above the acknowledgements has been updated with better explanation on why adding this acknowledgement in the science papers is good/necessary.
2020-12-01IMPORTANT: organizational improvements in Maneage TeX sourcesMohammad Akhlaghi-2/+15
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.
2020-11-27Fix paper.bbl flaw; reduce long author lists: save 70 wordsBoud Roukema-10/+21
This commit fixes the error of trying to run bibtex on appendix.tex when the --no-appendix option is selected. A hardwired hack, appropriate only for this specific paper, replaces the more-than-three-author parts of two long author lists by "et al." To test this without having to redownload the menke file, first do "rm -fv .build/tex/build/*.aux .build/tex/build/*.bbl" and then "./project make --no-appendix" a few times. This commit should reduce the word length by about 70 words.
2020-11-26All the referee points have been answeredMohammad Akhlaghi-1/+1
There is an answer for all the referee points now. I also did some minor edits in the paper. But we are still over the limit by around 250 words. The only remaining point that is not yet addressed (and has '####' around it) is the discussion on parallelization and its effect on reproducibility.
2020-11-25Reviewer points 1-15; appendix clickable linksBoud Roukema-0/+7
This commit updates "paper.tex" and "peer-review/1-answer.txt" for the first 15 (out of 59!) reviewer points, excluding points 2 (not yet done) and 9 (README-hacking.md needs tidying). A fix to "reproduce/analysis/make/paper.mk" for the links in the appendices is also done in this commit (the same algorithm as for paper.tex is added). The links in the appendices are not (yet) clickable.
2020-11-23Minor edits and correctionsMohammad Akhlaghi-1/+1
Raul's added point on the answer to the referee was very good, so I edited it a little to be more clear (and removed his name). Also, after looking in a few parts of the text, I fixed a few typos.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-2/+8
A new directory has been added at the top of the project's source called 'peer-review'. The raw reviews of the paper by the editors and referees has been added there as '1-review.txt'. All the main points raised by the referees have been listed in a numbered list and addressed (mostly) in '1-answers.txt'. The text of the paper now also includes all the implemented answers to the various points.
2020-11-20Highlighting changes can now be toggled at run-timeMohammad Akhlaghi-1/+11
Until now, the core Maneage 'paper.tex' had a '\highlightchanges' macro that defines two LaTeX macros: '\new' and '\tonote'. When '\highlightchanges' was defined, anything that was written within '\new' became dark green (highlighting new things that have been added). Also, anything that was written in '\tonote' was put within a '[]' and became dark red (to show that there is a note here that should be addressed later). When '\highlightchanges' wasn't defined, anything within the '\new' element would be black (like the rest of the text), and the things in '\tonote' would not be shown at all. Commenting the '\newcommand{\highlightchanges}{}' line within 'paper.tex' (to toggle the modes above) would create a different Git hash and has to be committed. But this different commit hash could create a false sense in the reader that other things have also been changed and the only way they could confirm was to actually go and look into the project history (which they will not usually have time to do, and thus won't be able to trust the two modes of the text). Also, the added highlights and the note highlights were bundeled together into one macro, so you couldn't only have one of them. With this commit, the choice of highlighting either one of the two is now done as two new run-time options to the './project' script (which are passed to the Makefiles, and written into the 'project.tex' file which is loaded into 'paper.tex'). In this way, we can generate two PDFs with the same Git commit (project's state): one with the selected highlights and another one without it. This issue actually came up for me while implementing the changes here: we need to submit one PDF to the journal/referees with highlights on the added features. But we also need to submit another PDF to arXiv and Zenodo without any highlights. If the PDFs have different commit hashes, the referees may associate it with other changes in any part of the work. For example https://oadoi.org/10.22541/au.159724632.29528907 that mentions "Another version of the manuscript was published on arXiv: 2006.03018", while the only difference was a few words in the abstract after the journal complained on the abstract word-count of our first submission (where the commit hashes matched with arXiv/Zenodo).
2020-11-15First edits on the newly added appendices in new formMohammad Akhlaghi-2/+3
With the optional appendices added recently to the paper, it was important to go through them and make them more fitting into the paper.
2020-11-15Building final PDF: pdf-build-final has to be given an explicit yesMohammad Akhlaghi-15/+15
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.
2020-11-04Appendix of long paper added, optionally we can disable itMohammad Akhlaghi-2/+15
Given the referee reports, after discussing with the editors of CiSE, we decided that it is important to include the complete appendix we had before that included a thorough review of existing tools and methods. However, the appendix will not be published in the paper (due to the strict word-count limit). It will only be used in the arXiv/Zenodo versions of the paper. This actually created a technical problem: we want the commit hash of the project source to remain the same when the paper is built with an appendix or without it. To fix this problem the choice of including an appendix has gone into the 'project' script as a run-time option called '--no-appendix'. So by default (when someone just runs './project make'), the PDF will have an appendix, but when we want to submit to the journal, or when the appendix isn't needed for a certain reason, we can use this new option. The appendix also has its own separate bibliography. Some other corrections made in this commit: 1. Some new references were added that had an '_' in their source, they were corrected in 'references.tex'. 2. I noticed that 'preamble-style.tex' is not actually used in this paper, so it has been deleted.
2020-10-18Recipes for final initialize and verify targets not on stdoutMohammad Akhlaghi-4/+11
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.
2020-09-24Gnuastro's analysis configuration files removedMohammad Akhlaghi-133/+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.
2020-09-03Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-5/+6
Only two small conflicts came up: * The addition of the hardware architecture macro in 'paper.tex' (which was removed for now, but will be added as the referee has requested within the text). * The usage of "" around directory variables in 'paper.mk'.
2020-08-27Machine architecture and byte-order available as LaTeX macroMohammadreza Khellat-4/+5
Until now, no machine-related specifications were being documented in the workflow. This information can become helpful when observing differences in the outcome of both software and analysis segments of the workflow by others (some software may behave differently based on host machine). With this commit, the host machine's 'hardware class' and 'byte-order' are collected and now available as LaTeX macros for the authors to use in the paper. Currently it is placed in the acknowledgments, right after mentioning the Maneage commit. Furthermore, the project and configuration scripts are now capable of dealing with input directory names that have SPACE (and other special characters) by putting them inside double-quotes. However, having spaces and metacharacters in the address of the build directory could cause build/install failure for some software source files which are beyond the control of Maneage. So we now check the user's given build directory string, and if the string has any '@', '#', '$', '%', '^', '&', '*', '(', ')', '+', ';', and ' ' (SPACE), it will ask the user to provide a different directory.
2020-08-20Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-34/+82
Some very minor conflicts came up and were easily corrected. They were mostly in parts that are also shared with the demonstration in the core Maneage branch.
2020-08-17Minor typo correction in comments of paper.mkMohammad Akhlaghi-1/+1
The '.bbl' suffix in the comment of one call to LaTeX was incorrectly written as '.bb'.
2020-08-02initialize.mk: accounting for no maneage branchBoud Roukema-3/+8
One of the LaTeX macros reported by 'initialize.mk' is the git commit hash of the most recent 'maneage' branch that the project has been branched from. However, not all projects will retain the maneage reference. This can happen for example when people don't push the 'maneage' reference to their repository and then clone from their own repository to a second computer. Therefore, until now, in such situations, Maneage would break with an error. With this commit, in such scenarios, a place holder string is used instead, clearly highlighting that there is no 'maneage' reference.
2020-07-21Printing location when downloaded input data checksum is differentBoud Roukema-0/+1
There are many different directory trees involved in Maneage system: the top directory, the 'reproduce/' directory and its sub-directories, '.build/' (that point to a user-defined build area), and a possibly user-defined input directory. Until now, in the case of a download checksum failure, it was not immediately obvious [1] to the user *where* the file with a failed checksum is. To clarify to the user *where* the suspicious file is now located, this commit adds a line to 'reproduce/analysis/make/download.mk' to print out this full path location: '$$unchecked' along with the expected and calculated checksums. [1] Euphemism for me spending lots of time debugging and being confused.
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.
2020-07-20make dist: only archive files that are under version controlBoud Roukema-17/+31
Until this commit, the '$(project-package-contents)' rules in 'reproduce/analysis/make/initialize.mk' included a line to provide all contents, recursively, of the directory 'reproduce/' in the package for further distribution. This could potentially lead to the distribution of private working files that are used during development and not intended for general distribution. With this commit, only those files in 'reproduce/' and 'tex/src' that are under version control are copied to the temporary directory (that is later used for creating an archive). With this change, the archiving commands actually became more clean (we don't have to manually remove 'LOCAL.conf' or other temporary files). Extensive comments have also been added above each step to clarify each step's purpose and method.
2020-07-07Project distribution tarball can account for no PDFs in tex/tikzMohammad Akhlaghi-1/+6
Until now the './project make dist' command implicitly assumed that the 'tex/tikz' directory always contains PDF files (because of the 'cp tex/tikz/*.pdf $$dir/tex/tikz' line). This was annoying for projects that don't use TiKZ or PGFPlots to generate their plots, and they had to manually comment this line. With this commit a check has been placed to see if any PDF files exist in there at all. If there aren't PDF files, the 'cp' command above is ignored.
2020-07-05Removing possibly existing paper.bbl before remaking itMohammad Akhlaghi-0/+6
Until now, when the bibliography file ('paper.bbl') had a LaTeX-related error (for example the journal name was a LaTeX macro that isn't defined), the first 'pdflatex' command that is run before 'biber' would crash, not allowing the project to reach 'biber'. So the user would have to manually remove 'paper.bbl' before running './project make'. With this commit, we remove any possibly existing 'paper.bbl' file before rebuilding it. Generally, this also helps in keeping things clean during the generation of the new bibliography. This bug was found by Mahdieh Nabavi.
2020-07-04Commit hash of Maneage branch used to build project as LaTeX macroMohammad Akhlaghi-0/+6
To help in the documentation, the Git hash of the Maneage branch commit that the project has most recently merged with (or branched from) is now also provided as a LaTeX macro ('\maneageversion'). It is calculated in 'reproduce/analysis/make/initialize.mk' (in the recipe to 'initialize.tex').
2020-07-04Better names and comments in INPUTS.confMohammad Akhlaghi-28/+32
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.
2020-07-04Improved comments in paper.mk and README.mdMohammad Akhlaghi-1/+5
In 'README.md' I tried to explain a little better that TeXLive will only install its necessary packages, not the full TeXLive library! Also in paper.mk, I slightly improved the comments with very minor edits. Both these parts are slated to go into the core Maneage branch, so its important to maintain them here for now.
2020-06-30The distclean target accounts for non-existance of git hooksMohammad Akhlaghi-1/+1
Until now, when the user wanted to complete remove all built files (including software), the './project make distclean' command would fail if the git hooks weren't installed. They are present when the project's configuration has been successfully finished, but this bug can happen when trying to re-do an incomplete build. With this commit, this is fixed by adding an '-f' has been added before the 'rm' command for the Git hooks. This commit was also done in the core Maneage branch.
2020-06-30The distclean target accounts for non-existance of git hooksMohammad Akhlaghi-1/+1
Until now, when the user wanted to complete remove all built files (including software), the './project make distclean' command would fail if the git hooks weren't installed. They are present when the project's configuration has been successfully finished, but this bug can happen when trying to re-do an incomplete build. With this commit, this is fixed by adding an '-f' has been added before the 'rm' command for the Git hooks.
2020-06-28Zenodo identifier is extracted automatically from metadata.confMohammad Akhlaghi-1/+5
Until now, the Zenodo identifier was manually written in the paper. But now we have the Zenodo DOI in 'metadata.conf', so its much more robust to get it from there (in case updated versions of the paper is published).
2020-06-27Imported recent work in master, minor conflict fixed in paper.mkMohammad Akhlaghi-6/+14
Only two conflicts came up in the newly added comments of 'paper.mk' in the Maneage branch. It happened because in this project we don't use 'pdflatex', but 'latex' alone.
2020-06-19Removing preparation-done.mk when cleaning by ./project make cleanRaul Infante-Sainz-0/+1
Until this commit, the file `BDIR/software/preparation-done.mk' were not removed when cleaning the project with `./project make clean'. This file is generated in the preparation of the data during the analysis step. However, the cleaning is expected to remove anything generated in the analysis process! Step by step, with the commands: ./project make ---> Will make the preparation and analysis ./project make clean ---> Will remove all analysis outputs (but not `preparation-done.mk') ./project make ---> Won't do the preparation, only analysis! However, in the last step it should do the preparation again, because the input data could have change for any reason. With this commit, the file `BDIR/software/preparation-done.mk' is removed when cleaning the project, and consequently, in the analysis step the input data is prepared.
2020-06-17Security risk of LaTeX's -shell-escape option explained in commentBoud Roukema-0/+9
The 'pdflatex' program is used to build the default Maneage-branch paper. But since the default paper uses PGFPlots to build the figures within LaTeX as an external PDF, PGFPlots requires 'pdflatex' to be called with the '-shell-escape' option. Generally, this option can be considered as a security risk (in particular when 'pdflatex' is being run by an external LaTeX file: a malicious LaTeX writer may embed commands in the LaTeX source that will be executed on the host if this option is present). This is not too serious of an issue in Maneage, because when someone runs Maneage, they intentionally let it run many on their system. Hence if someone wants to exploit a host system, they can add the necessary commands long before 'pdflatex' is run. After all, all commands in Maneage are run with the calling user's permissions, hence they have access to many parts of the user's accounts. If someone is worried about security on a non-trusted Maneage project they should act the same as they do with any software: define a new user for it, and call it with that user (as a weak-level security), or run it in a virtual machine or container. However, since this option has been explicity mentioned as a security risk before, it helps if we have a comment explaining its usage in 'paper.mk'. With this commit, the concerned user will read a brief explanation and can read the brief discussion at [1] and possibly re-open the discussion or propose ways of mitigating the security risk(s). [1] https://savannah.nongnu.org/task/?15694