aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorLines
2020-11-25Points 33-35 handled in answer to reviewersBoud Roukema-14/+27
This commit only modifies "peer-review/1-answer.txt", giving answers to Reviewer 4; these mostly take into account David's email list of proposed answers. No changes are done to "paper.tex".
2020-11-25Reviewer points 16 to 32Boud Roukema-37/+49
Copyediting of points 16 to 32 (paper.tex + peer-review/1-answer.txt) is done in this commit. TODO list: 2. paper lacking focus 9. tidy up README-hacking.md for appearance on website App B.G. similar to Figure ?? - ref missing 29. website: README-hacking.md and tutorial "on same page"
2020-11-25Reviewer points 1-15; appendix clickable linksBoud Roukema-113/+142
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.
2020-11-25Copyedit; no-abstract word count 6084Boud Roukema-31/+37
This commit tidies up minor aspects of the language in the text marked by "\new", e.g. a "wokflow" would be fine for Chinese cooking, but is a little off-topic for Maneage. :) The word count is reduced by about 7 words. I haven't yet got to the serious part: checked that we've responded to the referees' points, and completing the responses which we haven't yet done.
2020-11-24List of answers - minor copyeditBoud Roukema-18/+21
This commit does a minor copyedit of "peer-review/1-answer.txt", mostly just at the top, plus some hashes to highlight an unanswered concern; and removes the @ symbols (and full stops) from email addresses in the peer review email in order to reduce our feeding of email harvesters (spiders that collect email addresses for spammers).
2020-11-23Minor edits and correctionsMohammad Akhlaghi-12/+15
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.
2020-11-23Minor corrections to the final paper documentRaul Infante-Sainz-20/+17
With this commit, I make several minor changes to the text of the final paper. They are not important, but minor modifications like avoiding contractions (don't -> do not, and so on).
2020-11-23Minor corrections to referees answerRaul Infante-Sainz-6/+13
With this commit, I am just adding several minor corrections to the answer to the referees. They are very minor typos. I would only emphasize the fact that in Maneage there is the "Minimal complexity" criteria, and because of that, even if the project is not able to be executed in the future, the interested reader could have a look at the analysis steps (because it is in plain text). Note that I put "Raul" at the beginning of the line, so my name should have to be removed in the final document to be sent to the referees.
2020-11-23First draft of all the points addressed by the refereesMohammad Akhlaghi-94/+2309
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-16/+34
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-320/+350
With the optional appendices added recently to the paper, it was important to go through them and make them more fitting into the paper.
2020-11-04Appendix of long paper added, optionally we can disable itMohammad Akhlaghi-314/+1044
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.
2020-09-14Add machine class related argument and fix small typosMohammadreza Khellat-14/+12
Before this commit, there were no arguments regarding machine related specifications in the manuscript. This was needed as Mohammad Akhlaghi came across a review of the artcile by Dylan Aïssi in which Dylan mentioned the need for discussing CPU architecture dependence in pursuing a long-trem archivable workflow. With this commit, the required argument has been added in Sec.IV POC: Maneage in the paragraph in which it is explained how 'macro files build the core skeleton of Maneage'. Furthermore, few typos in different places have been fixed and the 'pre-make-build.sh' has been updated with the latest fix in Maneage core project.
2020-09-09Imported recent important fixes in Maneage, no conflictsMohammad Akhlaghi-15/+34
There weren't any conflicts in this merge.
2020-09-09R is built without tcl/tk (for GUI) dependenceBoud Roukema-0/+19
Tcl/Tk are a set of tools to provide Graphic User Interface (GUI) support in some software. But they are not yet natively built within Maneage, primarily because we have higher-priority work right now. GUI tools in general aren't high on our priority list right now because GUI tools are generally good for human interaction (which is contrary to the reproducible philosophy), not automatic analysis (a core concept in reproducibility). So even later, when we do include Tcl/Tk in Maneage, their direct usage will be discouraged. Until this commit, because we don't yet build Tcl/Tk, the default maneage install of the statistical package R failed on a Debian Stretch, with 6227 repeats of the line: '/usr/lib//tcl8.5/tclConfig.sh: line 2: dpkg-architecture: command not found' To fix this problem (atleast until Tcl/Tk is installed within Maneage), R is now configured with the '--without-tcltk' option which fixed the problem. Please see the description above the R installation instructions in 'reproduce/software/make/high-level.mk' for more.
2020-09-08Removed all occurances of IFS in low-level scriptsMohammad Akhlaghi-11/+11
Following the previous commit, we recognized that the 'IFS' terms are not necessary and can be even cause problems. So all their occurances in the scripts of Maneage have been removed with this commit.
2020-09-07Software installation: removed IFS statements in pre-make-build.shMohammad Akhlaghi-4/+4
Until a recent commit, the IFS='"' was added at the start of the variables in this shell script and as a result, the SPACE character wasn't being used as a delimiter. This caused a major problem when downloading the tarballs (all the backup servers were considered as the top link). With this commit we removed these 'IFS' statements). Because we now check for the existance of meta-characters in the build directory name, there is no more problem, and also generally both the calling command and internally, we have double-qutations around the variable names. So removal of IFS will not affect the result in this scenario. This bug was found by Mohammadreza Khellat.
2020-09-04Minor correction in first sentence of abstractMohammad Akhlaghi-2/+1
This paper is generally about data analysis pipelines, so the abstract now starts with "Analysis pipelines" instead of "Reproducible workflows". I also noticed that the sentence was mistakenly broken into multiple lines.
2020-09-03Imported recent work in Maneage, minor conflicts fixedMohammad Akhlaghi-179/+362
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'.
2020-09-03Added example of DockerHub deleting unused Docker imagesMohammad Akhlaghi-1/+3
I saw this link today in the news (to be implemented from November 1st, 2020), and because it is directly related to this work, I added it. Many people assume that simply pushing a Docker image to DockerHub is enough to preserve it, but ignore how much it costs to maintain the storage and network capacity.
2020-08-28Edited README.md to remove installation of a text editorMohammad Akhlaghi-10/+7
With the previous commit, we now build Nano by default within Maneage, and project authors can ask to install Emacs and Vim within 'TARGETS.conf'. So in the instructions to build within a Docker image have been removed.
2020-08-28Plain text editors: nano in basic, emacs and vim in high-levelMohammad Akhlaghi-18/+87
While a project is under development, the raw analysis software are not the only necessary software in a project. We also need tools to all the edit plain-text files within the Maneaged project. Usually people use their operating system's plain-text editor. However, when working on the project on a new computer, or in a container, the plain-text editors will have different versions, or may not be present at all! This can be very annoying and frustrating! With this commit, Maneage now installs GNU Nano as part of the basic tools. GNU Nano is a very simple and small plain text editor (the installed size is only ~3.5MB, and it is friendly to new users). Therefore, any Maneaged project can assume atleast Nano will be present (in particular when no editor is available on the running system!). GNU Emacs and VIM (both without extra dependencies, in particular without GUI support) are also optionally available in 'high-level.mk' (by adding them to 'TARGETS.conf'). The basic idea for the more advanced editors (Emacs and VIM) is that project authors can add their favorite editor while they are working on the project, but upon publication they can remove them from 'TARGETS.conf'. A few other minor things came up during this work and are now also fixed: - The 'file' program and its libraries like 'libmagic' were linking to system's 'libseccomp'! This dependency then leaked into Nano (which depends on 'libmagic'). But this is just an extra feature of 'file', only for the Linux kernel. Also, we have no dependency on it so far. So 'file' is not configured to not build with 'libseccomp'. - A typo was fixed in the line where the physical core information is being read on macOS. - The top-level directories when running './project shell' are now quoted (in case they have special characters).
2020-08-27Machine architecture and byte-order available as LaTeX macroMohammadreza Khellat-161/+265
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.
2020-08-25README.md: added explanation on copying files from Docker imageMohammad Akhlaghi-2/+17
When building Maneage inside a Docker container, in the end the users want to extract the final outputs from the container into their host operating system to inspect more comfortably. So with this commit, a short examplanation has been added on how to do this. We also noticed that it is much better if the 'Dockerfile' is stored and run in an empty directory, otherwise, it will start parsing the full directory and its subdirectories as the docker image's environment.
2020-08-20Data lineage and replicated plot in one rowMohammad Akhlaghi-40/+276
Until now, the replicated plot had the width of the full page and the data lineage graph was under it. Together they were covering more than half of the height of the page! But the plot showing the number of papers with tools really doesn't have too much detail, and all the space was being wasted. With this commit, the plot is now much much thinner and the data lineage graph has been fitted to the right of it.
2020-08-20Imported recent updates in Maneage, minor conflicts fixedMohammad Akhlaghi-372/+641
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'.
2020-08-13--check-config option now prints names of last 5 installedMohammad Akhlaghi-3/+54
Until now, './project --check-config' would only print the names of the software that were being built. Besides that, it is also useful to know which packages have most recently finished. With this commit, we now print the last 5 built software packages with '--check-config' also, and the output has also been placed in a row of '='s to help separate it in each round. Also some more sanity checks have been added so it doesn't print error messages.
2020-08-08Software tarballs saved as symlinks if already in filesystemMohammad Akhlaghi-5/+18
Until now, if the software source tarballs already existed on the system they would be copied inside the project. However, the software source tarballs are sometimes/mostly larger than their actual product and can consume significant space (~375 MB in the core branch!). With this commit, when the software are present on the system, their symbolic link will be placed in 'BDIR/software/tarballs', not a full copy. Also, because the tarballs in software tarball directory may themselves be links, we use 'realpath' to find the final place of the actual file and link to that location. Therefore if 'realpath' can't be found (prior to installing Coreutils in Maneage), we will copy the tarballs from the given software tarball directory. After Maneage has installed Coreutils, the project's own 'realpath' will be used. Of course, if the software are downloaded, their full downloaded copy will be kept in 'BDIR/software/tarballs', nothing has changed in the downloading scenario.
2020-08-08IMPORTANT: New software versions (17 basic, 16 high-level and 7 Python)Mohammad Akhlaghi-170/+187
It was a long time that the Maneage software versions hadn't been updated. With this commit, the versions of all basic software were checked and 17 of that had newer versions were updated. Also, 16 high-level programs and libraries were updated as well as 7 Python modules. The full list is available below. Basic Software (affecting all projects) --------------------------------------- bash 5.0.11 -> 5.0.18 binutils 2.32 -> 2.35 coreutils 8.31 -> 8.32 curl 7.65.3 -> 7.71.1 file 5.36 -> 5.39 gawk 5.0.1 -> 5.1.0 gcc 9.2.0 -> 10.2.0 gettext 0.20.2 -> 0.21 git 2.26.2 -> 2.28.0 gmp 6.1.2 -> 6.2.0 grep 3.3 -> 3.4 libbsd 0.9.1 -> 0.10.0 ncurses 6.1 -> 6.2 perl 5.30.0 -> 5.32.0 sed 4.7 -> 4.8 texinfo 6.6 -> 6.7 xz 5.2.4 -> 5.2.5 Custom programs/libraries ------------------------- astrometrynet 0.77 -> 0.80 automake 0.16.1 -> 0.16.2 bison 3.6 -> 3.7 cfitsio 3.47 -> 3.48 cmake 3.17.0 -> 3.18.1 freetype 2.9 -> 2.10.2 gdb 8.3 -> 9.2 ghostscript 9.50 -> 9.52 gnuastro 0.11 -> 0.12 libgit2 0.28.2 -> 1.0.1 libidn 1.35 -> 1.36 openmpi 4.0.1 -> 4.0.4 R 3.6.2 -> 4.0.2 python 3.7.4 -> 3.8.5 wcslib 6.4 -> 7.3 yaml 0.2.2 -> 0.2.5 Python modules -------------- cython 0.29.6 -> 0.29.21 h5py 2.9.0 -> 2.10.0 matplotlib 3.1.1 -> 3.3.0 mpi4py 3.0.2 -> 3.0.3 numpy 1.17.2 -> 1.19.1 pybind11 2.4.3 -> 2.5.0 scipy 1.3.1 -> 1.5.2
2020-08-08Configuration fail if gfortran necessary, but not built or availableBoud Roukema-25/+41
When the host C compiler is used (either by calling '--host-cc' or on OSs that we can't build the GNU C Compiler), Maneage will also not build the Fortran compiler 'gfortran'. Until now, the './project configure' script would give a big warning about the need for 'gfortran' and the fact that it is missing, and would for 5 seconds, but it would continue anyway. For projects that don't need 'gfortran', this can be confusing to the users and for those that need 'gfortran', it means that a lot of time and cpu cycles are wasted compiling non-fortran software that are unusable in the end. With this commit, the 'need_gfortarn' variable has been added 'reproduce/software/shell/configure.sh', in a new part that is devoted to project-specific features. If it equals '0', then the 'gfortran' test (and message!) isn't done at all, but if it is set to '1', then the configure stage will halt immediately gfortran is not found and not built. The default operations of the core Maneage branch don't need 'gfortran', so by default it is set to 0. But 'gfortran' is necessary for all projects that use Numpy (Python's numeric library) for example. So if your project needs 'gfortran', please set this new variable to 1. As mentioned in the comments of 'configure.sh', ideally we should detect this automatically, but we haven't had the time to implement it yet.
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.
2020-08-02OpenMPI build with slurm compatibilityBoud Roukema-1/+4
Prior to this commit, compilation of OpenMPI used the default OpenMPI choices of deciding which libraries should be used in relating to a job scheduler [1] (such as Slurm [2]). Given that the user on a multi-user cluster has to accept the sysadmin's choice of a job scheduler, the question of whether to (1) link with OpenMPI's own libraries (and increase the reproducibility of the science project) or rather (2) link with the sysadmin managed libraries (more likely to be compatible with the host's job scheduler), is an open question of which the best strategy for reproducibility needs to be debated and studied. In this commit, strategy (1) is adopted. The options '--withpmix=internal' and '--with-hwloc=internal' are added to the configure command. The working assumption is that the Maneage version of OpenMPI is likely to be modern enough to be compatible with the native job scheduler such as Slurm. Compilation without any 'pmix' option gave a fail in at least one case; it appears that an external pmix library was sought by the configure script. As of OpenMPI 4.0.1, the internal libevent library is used by default, so there appears to be no option to force it to be chosen internally. This commit also includes the option '--without-verbs'. This option removes a library related to "infiniband", "verbs", "openib" and "BTL"; this library appears to be deprecated. See [3], [4] for discussion. Please add feedback and discussion to the Maneage task about openmpi linking strategies (1) (internal) and (2) (external) at Savannah [5]. [1] https://en.wikipedia.org/wiki/Job_scheduler#Batch_queuing_for_HPC_clusters [2] https://en.wikipedia.org/wiki/Slurm_Workload_Manager - To avoid a name clash, 'slurm-wlm' is the metapackage in Debian for the client commands, the compute node daemon, and the central node daemon. An unrelated package 'slurm' also exists. [3] https://www-lb.open-mpi.org/faq/?category=openfabrics#ofa-device-error [4] https://www-lb.open-mpi.org/faq/?category=building [5] https://savannah.nongnu.org/task/index.php?15737
2020-07-28README-hacking.md: added new paper using Maneage (arXiv:2007.11779)Boud Roukema-4/+15
Roukema+2020 (arXiv:2007.11779) is a newly published (as preprint) paper that uses Maneage, so it is being added to the list of published or submitted papers in 'README-hacking.md'. The Software Heritage URL sticks out way beyond the standard number of columns in the plain text form of the updated 'README-hacking.md' file, when rendered using markdown, it shouldn't look so bad. Also, see the related task https://savannah.nongnu.org/task/index.php?15736 (Raul+2020 should be Infante-Sainz+2020) for a suggestion of a more standard machine-readable format. It should be mentioned and emphasised to the reader that one should very carefully and obediently note and pay attention to the noteworthy fact that a few distracting words [1] such as "Note that" are removed in this commit. ;) [1] https://en.wiktionary.org/wiki/pontification
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-10/+25
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.
2020-07-17README.md now has description of building project in DockerMohammad Akhlaghi-0/+218
Docker is a "container" technology that allows an almost independent operating system run on the host. It is useful when the host OS doesn't support some features or has internal problems (for example its C library or C compiler have problems). Fortunately a Maneaged project can easily be built within a Docker image and a minimal image operating system. With this commit, a section has been added to 'README.md' to describe this process. Each step of the Dockerfile is explined, to help users that may not be too familiar with Docker, or help Docker user who are not familiar with Maneage.
2020-07-07Fixed typo that lead to crash when building healpyMarius Peper-1/+1
Until now, if a project needed the healpy software package, Maneage would crash with the following error message (abridged for full name in build directory). This was caused by a typo in the version of 'healpix' (the dependency of 'healpy'). make: *** No rule to make target '.../version-info/proglib/healpix-' With this commit, the typo in line 334 of 'python.mk' is fixed, so that when '$(ipydir)/healpy-$(healpy-version)' gets called it correctly searches for a rule to make '$(ibidir)/healpix-$(healpix-version)'.
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.
2020-07-05Configure script prefers clang for macOS systemsMohammad Akhlaghi-96/+129
In the previous commit (Commit 1bc00c9: Only using clang in macOS systems that also have GCC) we set the used C compiler for high-level programs to be 'clang' on macOS systems. But I forgot to do the same kind of change in the configure script (to prefer 'clang' when we are testing for a C compiler on the host). With this commit, the compiler checking phases of the configure script have been improved, so on macOS systems, we now first search for 'clang', then search for 'gcc'. While doing this, I also noticed that the 'rpath' checking command was done before we actually define 'instdir'!!! So in effect, the 'rpath' directory was being set to '/lib'! So with this commit, this test has been taken to after defining 'instdir'.
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.
2020-07-05Only using clang in macOS systems that also have GCCMohammad Akhlaghi-27/+58
Until now, when Maneage was built on a macOS that had both a clang and GCC, we would make links to both. But this cause many conflicts in some high-level programs (for example Numpy and etc, all the programs where we have explicity set 'export CC=clang' before the build recipe). This happens because the GCC that is built on a macOS isn't complete for some operations. To fix this problem, when we are on a macOS, we explicity set 'gcc' to point to 'clang' and 'g++' to point to 'clang++'. We also don't link to the host's C-preprocessor ('cpp') on macOS systems because this is only a GNU feature and using the GNU CPP is also known to have some basic problems. For example this was reported by Mahdieh Nabavi (which was the main trigger for this work): ld: Symbol not found: ___keymgr_global Referenced from: /Users/Mahdieh/build/software/installed/bin/cpp Expected in: /usr/lib/libSystem.B.dylib Also, to avoid linking to another link on the host tools (in the 'makelink' function of 'basic.mk'), we are now using 'realpath'.
2020-07-04Commit hash of Maneage branch used to build project as LaTeX macroMohammad Akhlaghi-12/+19
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-29/+33
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.
2020-07-04Some command line messages of ./project didn't mention shellMohammad Akhlaghi-2/+3
Until now, the 'shell' mode of the './project' script was missing in the top output of './project --help' and in the error message printed when no operation was given, or when more than one operation was given. This is now corrected.
2020-07-04Improved comments in paper.mk and README.mdMohammad Akhlaghi-8/+14
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.
2020-07-04Citing Maneage paper in acknowledgmentsMohammad Akhlaghi-10/+10
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.
2020-07-04Corrected Acknowledgments section in default paperMohammad Akhlaghi-14/+14
Until now, the acknowledgment section didn't contain the new name of Maneage and it also included an acknowledgment of Gnuastro (which is not appropriate for a general project which may not use Gnuastro). With this commit this is fixed.
2020-07-03Edits in REAME.md on Docker images and internet for TeXLiveMohammad Akhlaghi-9/+13
The explanation was made more clear.