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diff --git a/README-hacking.md b/README-hacking.md index 475f2ca..99cb6c2 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,551 +1,51 @@ -Maneage: managing data lineage -============================== +# Maneage development -Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2020-2021 Raul Infante-Sainz <infantesainz@gmail.com>\ +Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ See the end of the file for license conditions. -Maneage is a **fully working template** for doing reproducible research (or -writing a reproducible paper) as defined in the link below. If the link -below is not accessible at the time of reading, please see the appendix at -the end of this file for a portion of its introduction. Some -[slides](http://akhlaghi.org/pdf/reproducible-paper.pdf) are also available -to help demonstrate the concept implemented here. - - http://akhlaghi.org/reproducible-science.html - -Maneage is created with the aim of supporting reproducible research by -making it easy to start a project in this framework. As shown below, it is -very easy to customize Maneage for any particular (research) project and -expand it as it starts and evolves. It can be run with no modification (as -described in `README.md`) as a demonstration and customized for use in any -project as fully described below. - -A project designed using Maneage will download and build all the necessary -libraries and programs for working in a closed environment (highly -independent of the host operating system) with fixed versions of the -necessary dependencies. The tarballs for building the local environment are -also collected in a [separate -repository](http://git.maneage.org/tarballs-software.git/tree/). The final -output of the project is [a -paper](http://git.maneage.org/output-raw.git/plain/paper.pdf). Notice the -last paragraph of the Acknowledgments where all the necessary software are -mentioned with their versions. - -Below, we start with a discussion of why Make was chosen as the high-level -language/framework for project management and how to learn and master Make -easily (and freely). The general architecture and design of the project is -then discussed to help you navigate the files and their contents. This is -followed by a checklist for the easy/fast customization of Maneage to your -exciting research. We continue with some tips and guidelines on how to -manage or extend your project as it grows based on our experiences with it -so far. There is also a publication checklist, describing the recommended -steps to publish your data/code. The main body concludes with a description -of possible future improvements that are planned for Maneage (but not yet -implemented). As discussed above, we end with a short introduction on the -necessity of reproducible science in the appendix. +Maneage (Managing data lineage) is a customizable workflow controller +program, providing low-level control over a project's data lineage and its +history for a designing and operating fully reproducible project. Maneage +is formally defined in [Akhlaghi et +al. 2021](https://scixplorer.org/abs/2021CSE....23c..82A) (Computing in +Science & Engineering, vol. 23, issue 3, pp. 82-91; +DOI:[10.1109/MCSE.2021.3072860](https://doi.org/10.1109/MCSE.2021.3072860)). The +Maneage webpage at https://maneage.org contains a 30 minute video +presentation of Maneage that you can also watch for a fast introduction. + +This `README-hacking.md` file is targeted at those who want to develop +their projects within Maneage (by "hacking", or modifying, it), not just +execute it. The `README.md` file that is also in this directory contains +the instructions for those who only need to run/execute it. Please don't forget to share your thoughts, suggestions and criticisms. Maintaining and designing Maneage is itself a separate project, -so please join us if you are interested. Once it is mature enough, we will -describe it in a paper (written by all contributors) for a formal -introduction to the community. +so please join us if you are interested. The "Development Workflow" section +below describes our general development workflow. One of our planned tasks +is to write a fully featured documentation (similar to the [Gnuastro +documentation](https://www.gnu.org/software/gnuastro/manual)). +[[_TOC_]] -Why Make? ---------- -When batch processing is necessary (no manual intervention, as in a -reproducible project), shell scripts are usually the first solution that -come to mind. However, the inherent complexity and non-linearity of -progress in a scientific project (where experimentation is key) make it -hard to manage the script(s) as the project evolves. For example, a script -will start from the top/start every time it is run. So if you have already -completed 90% of a research project and want to run the remaining 10% that -you have newly added, you have to run the whole script from the start -again. Only then will you see the effects of the last new steps (to find -possible errors, or better solutions and etc). - -It is possible to manually ignore/comment parts of a script to only do a -special part. However, such checks/comments will only add to the complexity -of the script and will discourage you to play-with/change an already -completed part of the project when an idea suddenly comes up. It is also -prone to very serious bugs in the end (when trying to reproduce from -scratch). Such bugs are very hard to notice during the work and frustrating -to find in the end. - -The Make paradigm, on the other hand, starts from the end: the final -*target*. It builds a dependency tree internally, and finds where it should -start each time the project is run. Therefore, in the scenario above, a -researcher that has just added the final 10% of steps of her research to -her Makefile, will only have to run those extra steps. With Make, it is -also trivial to change the processing of any intermediate (already written) -*rule* (or step) in the middle of an already written analysis: the next -time Make is run, only rules that are affected by the changes/additions -will be re-run, not the whole analysis/project. - -This greatly speeds up the processing (enabling creative changes), while -keeping all the dependencies clearly documented (as part of the Make -language), and most importantly, enabling full reproducibility from scratch -with no changes in the project code that was working during the -research. This will allow robust results and let the scientists get to what -they do best: experiment and be critical to the methods/analysis without -having to waste energy and time on technical problems that come up as a -result of that experimentation in scripts. - -Since the dependencies are clearly demarcated in Make, it can identify -independent steps and run them in parallel. This further speeds up the -processing. Make was designed for this purpose. It is how huge projects -like all Unix-like operating systems (including GNU/Linux or Mac OS -operating systems) and their core components are built. Therefore, Make is -a highly mature paradigm/system with robust and highly efficient -implementations in various operating systems perfectly suited for a complex -non-linear research project. - -Make is a small language with the aim of defining *rules* containing -*targets*, *prerequisites* and *recipes*. It comes with some nice features -like functions or automatic-variables to greatly facilitate the management -of text (filenames for example) or any of those constructs. For a more -detailed (yet still general) introduction see the article on Wikipedia: - - https://en.wikipedia.org/wiki/Make_(software) - -Make is a +40 year old software that is still evolving, therefore many -implementations of Make exist. The only difference in them is some extra -features over the [standard -definition](https://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html) -(which is shared in all of them). Maneage is primarily written in GNU Make -(which it installs itself, you don't have to have it on your system). GNU -Make is the most common, most actively developed, and most advanced -implementation. Just note that Maneage downloads, builds, internally -installs, and uses its own dependencies (including GNU Make), so you don't -have to have it installed before you try it out. - - - - - -How can I learn Make? ---------------------- - -The GNU Make book/manual (links below) is arguably the best place to learn -Make. It is an excellent and non-technical book to help get started (it is -only non-technical in its first few chapters to get you started easily). It -is freely available and always up to date with the current GNU Make -release. It also clearly explains which features are specific to GNU Make -and which are general in all implementations. So the first few chapters -regarding the generalities are useful for all implementations. - -The first link below points to the GNU Make manual in various formats and -in the second, you can download it in PDF (which may be easier for a first -time reading). - - https://www.gnu.org/software/make/manual/ - - https://www.gnu.org/software/make/manual/make.pdf - -If you use GNU Make, you also have the whole GNU Make manual on the -command-line with the following command (you can come out of the "Info" -environment by pressing `q`). - -```shell - $ info make -``` - -If you aren't familiar with the Info documentation format, we strongly -recommend running `$ info info` and reading along. In less than an hour, -you will become highly proficient in it (it is very simple and has a great -manual for itself). Info greatly simplifies your access (without taking -your hands off the keyboard!) to many manuals that are installed on your -system, allowing you to be much more efficient as you work. If you use the -GNU Emacs text editor (or any of its variants), you also have access to all -Info manuals while you are writing your projects (again, without taking -your hands off the keyboard!). - - - - - -Published works using Maneage ------------------------------ - -The list below shows some of the works that have already been published -with (earlier versions of) Maneage, and some that have been recently -submitted for peer review. The previous version of Maneage was called -"Reproducible paper template", with a separate git tree. Maneage is -evolving rapidly, so some details will differ between the different -versions. The more recent papers will tend to be the most useful as good -working examples. - - - Peper & Roukema ([2020](https://arxiv.org/abs/2010.03742), - arXiv:2010.03742): The live version of the controlled source is [at - Codeberg](https://codeberg.org/boud/elaphrocentre); the main input - dataset, a software snapshot, the software tarballs, the project - outputs and editing history are available at - [zenodo.4062461](https://zenodo.org/record/4062461); and the - archived git history is available at - [swh:1:dir:c4770e81288f340083dd8aa9fe017103c4eaf476](https://archive.softwareheritage.org/swh:1:dir:c4770e81288f340083dd8aa9fe017103c4eaf476). - - - Roukema ([2020](https://arxiv.org/abs/2007.11779), - arXiv:2007.11779): The live version of the controlled source is [at - Codeberg](https://codeberg.org/boud/subpoisson); the main input - dataset, a software snapshot, the software tarballs, the project - outputs and editing history are available at - [zenodo.3951152](https://zenodo.org/record/3951152); and the - archived git history is available at - [swh:1:dir:fcc9d6b111e319e51af88502fe6b233dc78d5166](https://archive.softwareheritage.org/swh:1:dir:fcc9d6b111e319e51af88502fe6b233dc78d5166). - - - Akhlaghi et al. ([2020](https://arxiv.org/abs/2006.03018), - arXiv:2006.03018): The project's version controlled source is [on - Gitlab](https://gitlab.com/makhlaghi/maneage-paper), necessary software, - outputs and backup of history is available in - [zenodo.3872248](https://doi.org/10.5281/zenodo.3872248). - - - Infante-Sainz et - al. ([2020](https://ui.adsabs.harvard.edu/abs/2020MNRAS.491.5317I), - MNRAS, 491, 5317): The version controlled project source is available - [on GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) - and is also archived on Zenodo with all the necessary software tarballs: - [zenodo.3524937](https://zenodo.org/record/3524937). - - - Akhlaghi ([2019](https://arxiv.org/abs/1909.11230), IAU Symposium - 355). The version controlled project source is available [on - GitLab](https://gitlab.com/makhlaghi/iau-symposium-355) and is also - archived on Zenodo with all the necessary software tarballs: - [zenodo.3408481](https://doi.org/10.5281/zenodo.3408481). - - - Section 7.3 of Bacon et - al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A - 608, A1): The version controlled project source is available [on - GitLab](https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes) - and a snapshot of the project along with all the necessary input - datasets and outputs is available in - [zenodo.1164774](https://doi.org/10.5281/zenodo.1164774). - - - Section 4 of Bacon et - al. ([2017](http://adsabs.harvard.edu/abs/2017A%26A...608A...1B), A&A, - 608, A1): The version controlled project is available [on - GitLab](https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry) and - a snapshot of the project along with all the necessary input datasets is - available in [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746). - - - Akhlaghi & Ichikawa - ([2015](http://adsabs.harvard.edu/abs/2015ApJS..220....1A), ApJS, 220, - 1): The version controlled project is available [on - GitLab](https://gitlab.com/makhlaghi/NoiseChisel-paper). This is the - very first (and much less mature!) incarnation of Maneage: the history - of Maneage started more than two years after this paper was - published. It is a very rudimentary/initial implementation, thus it is - only included here for historical reasons. However, the project source - is complete, accurate and uploaded to arXiv along with the paper. - - - - - -Citation --------- - -If you use Maneage in your project please cite Akhlaghi et -al. ([2020](https://arxiv.org/abs/2006.03018), arXiv:2006.03018). It has -been submitted and is under peer review. - -Also, when your paper is published, don't forget to add a notice in your -own paper (in coordination with the publishing editor) that the paper is -fully reproducible and possibly add a sentence or paragraph in the end of -the paper shortly describing the concept. This will help spread the word -and encourage other scientists to also manage and publish their projects in -a reproducible manner. - - - - - - - - - - -Project architecture -==================== - -In order to customize Maneage to your research, it is important to first -understand its architecture so you can navigate your way in the directories -and understand how to implement your research project within its framework: -where to add new files and which existing files to modify for what -purpose. But if this the first time you are using Maneage, before reading -this theoretical discussion, please run Maneage once from scratch without -any changes (described in `README.md`). You will see how it works (note that -the configure step builds all necessary software, so it can take long, but -you can continue reading while its working). - -The project has two top-level directories: `reproduce` and -`tex`. `reproduce` hosts all the software building and analysis -steps. `tex` contains all the final paper's components to be compiled into -a PDF using LaTeX. - -The `reproduce` directory has two sub-directories: `software` and -`analysis`. As the name says, the former contains all the instructions to -download, build and install (independent of the host operating system) the -necessary software (these are called by the `./project configure` -command). The latter contains instructions on how to use those software to -do your project's analysis. - -After it finishes, `./project configure` will create the following symbolic -links in the project's top source directory: `.build` which points to the -top build directory and `.local` for easy access to the custom built -software installation directory. With these you can easily access the build -directory and project-specific software from your top source directory. For -example if you run `.local/bin/ls` you will be using the `ls` of Maneage, -which is probably different from your system's `ls` (run them both with -`--version` to check). - -Once the project is configured for your system, `./project make` will do -the basic preparations and run the project's analysis with the custom -version of software. The `project` script is just a wrapper, and with the -`make` argument, it will first call `top-prepare.mk` and `top-make.mk` -(both are in the `reproduce/analysis/make` directory). - -In terms of organization, `top-prepare.mk` and `top-make.mk` have an -identical design, only minor differences. So, let's continue Maneage's -architecture with `top-make.mk`. Once you understand that, you'll clearly -understand `top-prepare.mk` also. These very high-level files are -relatively short and heavily commented so hopefully the descriptions in -each comment will be enough to understand the general details. As you read -this section, please also look at the contents of the mentioned files and -directories to fully understand what is going on. - -Before starting to look into the top `top-make.mk`, it is important to -recall that Make defines dependencies by files. Therefore, the -input/prerequisite and output of every step/rule must be a file. Also -recall that Make will use the modification date of the prerequisite(s) and -target files to see if the target must be re-built or not. Therefore during -the processing, _many_ intermediate files will be created (see the tips -section below on a good strategy to deal with large/huge files). - -To keep the source and (intermediate) built files separate, the user _must_ -define a top-level build directory variable (or `$(BDIR)`) to host all the -intermediate files (you defined it during `./project configure`). This -directory doesn't need to be version controlled or even synchronized, or -backed-up in other servers: its contents are all products, and can be -easily re-created any time. As you define targets for your new rules, it is -thus important to place them all under sub-directories of `$(BDIR)`. As -mentioned above, you always have fast access to this "build"-directory with -the `.build` symbolic link. Also, beware to *never* make any manual change -in the files of the build-directory, just delete them (so they are -re-built). - -In this architecture, we have two types of Makefiles that are loaded into -the top `Makefile`: _configuration-Makefiles_ (only independent -variables/configurations) and _workhorse-Makefiles_ (Makefiles that -actually contain analysis/processing rules). - -The configuration-Makefiles are those that satisfy these two wildcards: -`reproduce/software/config/*.conf` (for building the necessary software -when you run `./project configure`) and `reproduce/analysis/config/*.conf` -(for the high-level analysis, when you run `./project make`). These -Makefiles don't actually have any rules, they just have values for various -free parameters throughout the configuration or analysis. Open a few of -them to see for yourself. These Makefiles must only contain raw Make -variables (project configurations). By "raw" we mean that the Make -variables in these files must not depend on variables in any other -configuration-Makefile. This is because we don't want to assume any order -in reading them. It is also very important to *not* define any rule, or -other Make construct, in these configuration-Makefiles. - -Following this rule-of-thumb enables you to set these configure-Makefiles -as a prerequisite to any target that depends on their variable -values. Therefore, if you change any of their values, all targets that -depend on those values will be re-built. This is very convenient as your -project scales up and gets more complex. - -The workhorse-Makefiles are those satisfying this wildcard -`reproduce/software/make/*.mk` and `reproduce/analysis/make/*.mk`. They -contain the details of the processing steps (Makefiles containing -rules). Therefore, in this phase *order is important*, because the -prerequisites of most rules will be the targets of other rules that will be -defined prior to them (not a fixed name like `paper.pdf`). The lower-level -rules must be imported into Make before the higher-level ones. -All processing steps are assumed to ultimately (usually after many rules) -end up in some number, image, figure, or table that will be included in the -paper. The writing of these results into the final report/paper is managed -through separate LaTeX files that only contain macros (a name given to a -number/string to be used in the LaTeX source, which will be replaced when -compiling it to the final PDF). So the last target in a workhorse-Makefile -is a `.tex` file (with the same base-name as the Makefile, but in -`$(BDIR)/tex/macros`). As a result, if the targets in a workhorse-Makefile -aren't directly a prerequisite of other workhorse-Makefile targets, they -can be a prerequisite of that intermediate LaTeX macro file and thus be -called when necessary. Otherwise, they will be ignored by Make. -Maneage also has a mode to share the build directory between several -users of a Unix group (when working on large computer clusters). In this -scenario, each user can have their own cloned project source, but share the -large built files between each other. To do this, it is necessary for all -built files to give full permission to group members while not allowing any -other users access to the contents. Therefore the `./project configure` and -`./project make` steps must be called with special conditions which are -managed in the `--group` option. -Let's see how this design is implemented. Please open and inspect -`top-make.mk` it as we go along here. The first step (un-commented line) is -to import the local configuration (your answers to the questions of -`./project configure`). They are defined in the configuration-Makefile -`reproduce/software/config/LOCAL.conf` which was also built by `./project -configure` (based on the `LOCAL.conf.in` template of the same directory). -The next non-commented set of the top `Makefile` defines the ultimate -target of the whole project (`paper.pdf`). But to avoid mistakes, a sanity -check is necessary to see if Make is being run with the same group settings -as the configure script (for example when the project is configured for -group access using the `./for-group` script, but Make isn't). Therefore we -use a Make conditional to define the `all` target based on the group -permissions. -Having defined the top/ultimate target, our next step is to include all the -other necessary Makefiles. However, order matters in the importing of -workhorse-Makefiles and each must also have a TeX macro file with the same -base name (without a suffix). Therefore, the next step in the top-level -Makefile is to define the `makesrc` variable to keep the base names -(without a `.mk` suffix) of the workhorse-Makefiles that must be imported, -in the proper order. +# Maneage checklists -Finally, we import all the necessary remaining Makefiles: 1) All the -analysis configuration-Makefiles with a wildcard. 2) The software -configuration-Makefile that contains their version (just in case its -necessary). 3) All workhorse-Makefiles in the proper order using a Make -`foreach` loop. +This section contians some checklists to help in various stages of your +project: from the first commit, to the final publication. If you notice +anything missing or any in-correct part (probably a change that has not +been explained here), please let us know to correct it. -In short, to keep things modular, readable and manageable, follow these -recommendations: 1) Set clear-to-understand names for the -configuration-Makefiles, and workhorse-Makefiles, 2) Only import other -Makefiles from top Makefile. These will let you know/remember generally -which step you are taking before or after another. Projects will scale up -very fast. Thus if you don't start and continue with a clean and robust -convention like this, in the end it will become very dirty and hard to -manage/understand (even for yourself). As a general rule of thumb, break -your rules into as many logically-similar but independent steps as -possible. -The `reproduce/analysis/make/paper.mk` Makefile must be the final Makefile -that is included. This workhorse Makefile ends with the rule to build -`paper.pdf` (final target of the whole project). If you look in it, you -will notice that this Makefile starts with a rule to create -`$(mtexdir)/project.tex` (`mtexdir` is just a shorthand name for -`$(BDIR)/tex/macros` mentioned before). As you see, the only dependency of -`$(mtexdir)/project.tex` is `$(mtexdir)/verify.tex` (which is the last -analysis step: it verifies all the generated results). Therefore, -`$(mtexdir)/project.tex` is _the connection_ between the -processing/analysis steps of the project, and the steps to build the final -PDF. -During the research, it often happens that you want to test a step that is -not a prerequisite of any higher-level operation. In such cases, you can -(temporarily) define that processing as a rule in the most relevant -workhorse-Makefile and set its target as a prerequisite of its TeX -macro. If your test gives a promising result and you want to include it in -your research, set it as prerequisites to other rules and remove it from -the list of prerequisites for TeX macro file. In fact, this is how a -project is designed to grow in this framework. - - - - - -File modification dates (meta data) ------------------------------------ - -While Git does an excellent job at keeping a history of the contents of -files, it makes no effort in keeping the file meta data, and in particular -the dates of files. Therefore when you checkout to a different branch, -files that are re-written by Git will have a newer date than the other -project files. However, file dates are important in the current design of -Maneage: Make checks the dates of the prerequisite files and target files -to see if the target should be re-built. - -To fix this problem, for Maneage we use a forked version of -[Metastore](https://github.com/mohammad-akhlaghi/metastore). Metastore use -a binary database file (which is called `.file-metadata`) to keep the -modification dates of all the files under version control. This file is -also under version control, but is hidden (because it shouldn't be modified -by hand). During the project's configuration, Maneage installs to Git hooks -to run Metastore 1) before making a commit to update its database with the -file dates in a branch, and 2) after doing a checkout, to reset the -file-dates after the checkout is complete and re-set the file dates back to -what they were. - -In practice, Metastore should work almost fully invisibly within your -project. The only place you might notice its presence is that you'll see -`.file-metadata` in the list of modified/staged files (commonly after -merging your branches). Since its a binary file, Git also won't show you -the changed contents. In a merge, you can simply accept any changes with -`git add -u`. But if Git is telling you that it has changed without a merge -(for example if you started a commit, but canceled it in the middle), you -can just do `git checkout .file-metadata` and set it back to its original -state. - - - - - -Summary -------- - -Based on the explanation above, some major design points you should have in -mind are listed below. - - - Define new `reproduce/analysis/make/XXXXXX.mk` workhorse-Makefile(s) - with good and human-friendly name(s) replacing `XXXXXX`. - - - Add `XXXXXX`, as a new line, to the values in `makesrc` of the top-level - `Makefile`. - - - Do not use any constant numbers (or important names like filter names) - in the workhorse-Makefiles or paper's LaTeX source. Define such - constants as logically-grouped, separate configuration-Makefiles in - `reproduce/analysis/config/XXXXX.conf`. Then set this - configuration-Makefiles file as a prerequisite to any rule that uses - the variable defined in it. - - - Through any number of intermediate prerequisites, all processing steps - should end in (be a prerequisite of) `$(mtexdir)/verify.tex` (defined in - `reproduce/analysis/make/verify.mk`). `$(mtexdir)/verify.tex` is the sole - dependency of `$(mtexdir)/project.tex`, which is the bridge between the - processing steps and PDF-building steps of the project. - - - - - - - - - - -Customization checklist -======================= - -Take the following steps to fully customize Maneage for your research -project. After finishing the list, be sure to run `./project configure` and -`project make` to see if everything works correctly. If you notice anything -missing or any in-correct part (probably a change that has not been -explained here), please let us know to correct it. - -As described above, the concept of reproducibility (during a project) -heavily relies on [version -control](https://en.wikipedia.org/wiki/Version_control). Currently Maneage -uses Git as its main version control system. If you are not already -familiar with Git, please read the first three chapters of the [ProGit -book](https://git-scm.com/book/en/v2) which provides a wonderful practical -understanding of the basics. You can read later chapters as you get more -advanced in later stages of your work. - -First custom commit -------------------- +## First custom commit 1. **Get this repository and its history** (if you don't already have it): Arguably the easiest way to start is to clone Maneage and prepare for @@ -553,7 +53,7 @@ First custom commit the default `origin` remote server to specify that this is Maneage's remote server. This will allow you to use the conventional `origin` name for your own project as shown in the next steps. Second, you will - create and go into the conventional `master` branch to start + create and go into the conventional `main` branch to start committing in your project later. ```shell @@ -561,12 +61,55 @@ First custom commit $ mv project my-project # Change the name to your project's name. $ cd my-project # Go into the cloned directory. $ git remote rename origin origin-maneage # Rename current/only remote to "origin-maneage". - $ git checkout -b master # Create and enter your own "master" branch. + $ git checkout -b main # Create and enter your own "main" branch. $ pwd # Just to confirm where you are. ``` - 2. **Prepare to build project**: The `./project configure` command of the - next step will build the different software packages within the + 2. The final job of Maneage is to create your paper's PDF. By default it + uses a custom LaTeX style that resembles that of the Astrophysical + Journal (because the precursor of Maneage was for [Akhlaghi & Ichikawa + 2015](https://ui.adsabs.harvard.edu/abs/2015ApJS..220....1A)). The + journal you plan to submit your paper to will have its own separate + style. So it is best that you start your project by writing in the + desired style. We have already customized Maneage for the official + styles of some journals. To find them, run `git branch -r | grep + journal`. If your planned journal is one of them, you can take the + following steps to start your project based on that journal's style. If + it is not in these, you can ignore this step for now and customize the + style later (you can model based on these branches). In the commands + below, we'll assume you want to prepare for the Astronomy and + Astrophysics journal (A&A). + + ```shell + $ git checkout -b journal origin-maneage/journal-a-and-a + $ git log -1 --oneline | awk '{print $1}' # To keep the commit hash + $ git rebase -i main # See description below + ``` + + In the first text editor that opens after the last command, change all + (except the first) `pick`s into `squash`, then save the change and + close the editor. If you notice any conflicts during the rebase, always + prefer the `HEAD` (or latest `maneage` branch) version for non-TeX + related files; then run `git rebase --continue`. Once the rebase is + finished, the editor will be pre-filled with all the commit messages in + that branch. You do not need those, so you can delete everything and + write a commit message like the following: `A&A journal (commit XXXXX + of Maneage's journal-a-and-a branch)`. Just replace the `XXXXX` with + the output of the second command above. The commit hash is important to + be stored here since it allows you to later check if any updates have + been made in that branch in the future. After completing the git rebase + operation (last command above), run the following commands below to put + the new commit in your `main` branch (and continue working based on + that). + + ```shell + $ git checkout main + $ git merge journal + $ git branch -D journal + ``` + + 3. **Prepare for configuration**: The `./project configure` command of + the next step will build the different software packages within the "build" directory (that you will specify). Nothing else on your system will be touched. However, since it takes long, it is useful to see what it is being built at every instant (its almost impossible to tell @@ -585,7 +128,7 @@ First custom commit $ ./project --check-config ``` - 3. **Test Maneage**: Before making any changes, it is important to test it + 4. **Test Maneage**: Before making any changes, it is important to test it and see if everything works properly with the commands below. If there is any problem in the `./project configure` or `./project make` steps, please contact us to fix the problem before continuing. Since the @@ -603,7 +146,7 @@ First custom commit # Open 'paper.pdf' and see if everything is ok. ``` - 4. **Setup the remote**: You can use any [hosting + 5. **Setup the remote**: You can use any [hosting facility](https://en.wikipedia.org/wiki/Comparison_of_source_code_hosting_facilities) that supports Git to keep an online copy of your project's version controlled history. We recommend [GitLab](https://gitlab.com) because @@ -616,7 +159,7 @@ First custom commit a new project which is bad in this scenario, and will not allow you to push to it). It will give you a URL (usually starting with `git@` and ending in `.git`), put this URL in place of `XXXXXXXXXX` in the first - command below. With the second command, "push" your `master` branch to + command below. With the second command, "push" your `main` branch to your `origin` remote, and (with the `--set-upstream` option) set them to track/follow each other. However, the `maneage` branch is currently tracking/following your `origin-maneage` remote (automatically set @@ -627,15 +170,15 @@ First custom commit ```shell git remote add origin XXXXXXXXXX # Newly created repo is now called 'origin'. - git push --set-upstream origin master # Push 'master' branch to 'origin' (with tracking). + git push --set-upstream origin main # Push 'main' branch to 'origin' (with tracking). git push origin maneage # Push 'maneage' branch to 'origin' (no tracking). ``` - 5. **Title**, **short description** and **author**: You can start adding + 6. **Title**, **short description** and **author**: You can start adding your name (with your possible coauthors) and tentative abstract in `paper.tex`. You should see the relevant place in the preamble (prior to `\begin{document}`. Just note that some core project metadata like - the project tile are actually set in + the project title are actually set in `reproduce/analysis/config/metadata.conf`. So set your project title in there. After you are done, run the `./project make` command again to see your changes in the final PDF and make sure that your changes @@ -644,7 +187,7 @@ First custom commit specific journal's style), please feel free to use it your own methods after finishing this checklist and doing your first commit. - 6. **Delete dummy parts**: Maneage contains some parts that are only for + 7. **Delete dummy parts**: Maneage contains some parts that are only for the initial/test run, mainly as a demonstration of important steps, which you can use as a reference to use in your own project. But they not for any real analysis, so you should remove these parts as @@ -664,14 +207,22 @@ First custom commit - `reproduce/analysis/make/top-make.mk`: Delete the `delete-me` line in the `makesrc` definition. Just make sure there is no empty line - between the `download \` and `verify \` lines (they should be + between the `initialize \` and `verify \` lines (they should be directly under each other). - - `reproduce/analysis/make/verify.mk`: In the final recipe, under the - commented line `Verify TeX macros`, remove the full line that - contains `delete-me`, and set the value of `s` in the line for - `download` to `XXXXX` (any temporary string, you'll fix it in the - end of your project, when its complete). + - `reproduce/analysis/make/initialize.mk`: in the very end of this + file, you will see a set of lines between `delete the lines below + this` and `delete the lines above this`. Delete this whole group of + lines (including the two instruction lines). + + - `reproduce/analysis/config/verify-outputs.conf`: Disable + verification of outputs by changing the `yes` (the value of + `verify-outputs`) to `no`. Later, when you are ready to submit your + paper, or publish the dataset, activate verification and make the + proper corrections in this file (described under the "Other basic + customizations" section below). This is a critical step and only + takes a few minutes when your project is finished. So DON'T FORGET + to activate it in the end. - Delete all `delete-me*` files in the following directories: @@ -681,14 +232,6 @@ First custom commit $ rm reproduce/analysis/config/delete-me* ``` - - Disable verification of outputs by removing the `yes` from - `reproduce/analysis/config/verify-outputs.conf`. Later, when you are - ready to submit your paper, or publish the dataset, activate - verification and make the proper corrections in this file (described - under the "Other basic customizations" section below). This is a - critical step and only takes a few minutes when your project is - finished. So DON'T FORGET to activate it in the end. - - Re-make the project (after a cleaning) to see if you haven't introduced any errors. @@ -697,9 +240,9 @@ First custom commit $ ./project make ``` - 7. **Ignore changes in some Maneage files**: One of the main advantages of + 8. **Ignore changes in some Maneage files**: One of the main advantages of Maneage is that you can later update your infra-structure by merging - your `master` branch with the `maneage` branch. This is good for many + your `main` branch with the `maneage` branch. This is good for many low-level features that you will likely never modify yourself. But it is not desired for some files like `paper.tex` (you don't want changes in Maneage's default `paper.tex` to cause conflicts with all the text @@ -729,7 +272,7 @@ First custom commit $ git add .gitattributes ``` - 8. **Copyright and License notice**: It is necessary that _all_ the + 9. **Copyright and License notice**: It is necessary that _all_ the "copyright-able" files in your project (those larger than 10 lines) have a copyright and license notice. Please take a moment to look at several existing files to see a few examples. The copyright notice is @@ -743,15 +286,15 @@ First custom commit add a copyright notice in your name under the existing one(s), like the line with capital letters below. To start with, add this line with your name and email address to `paper.tex`, - `tex/src/preamble-header.tex`, `reproduce/analysis/make/top-make.mk`, + `tex/src/preamble-project.tex`, `reproduce/analysis/make/top-make.mk`, and generally, all the files you modified in the previous step. ``` - Copyright (C) 2018-2021 Existing Name <existing@email.address> - Copyright (C) 2021 YOUR NAME <YOUR@EMAIL.ADDRESS> + Copyright (C) 2018-2026 Existing Name <existing@email.address> + Copyright (C) 2026-2026 YOUR NAME <YOUR@EMAIL.ADDRESS> ``` - 9. **Configure Git for fist time**: If this is the first time you are + 10. **Configure Git for fist time**: If this is the first time you are running Git on this system, then you have to configure it with some basic information in order to have essential information in the commit messages (ignore this step if you have already done it). Git will @@ -765,8 +308,8 @@ First custom commit $ git config --global core.editor nano ``` - 10. **Your first commit**: You have already made some small and basic - changes in the steps above and you are in your project's `master` + 11. **Your first commit**: You have already made some small and basic + changes in the steps above and you are in your project's `main` branch. So, you can officially make your first commit in your project's history and push it. But before that, you need to make sure that there are no problems in the project. This is a good habit to @@ -784,7 +327,7 @@ First custom commit $ git push # Push your commit to your remote. ``` - 11. **Read the publication checklist**: The publication checklist below is + 12. **Read the publication checklist**: The publication checklist below is very similar to this one, but for the final phase of your project. For now, you don't have to do any of its steps, but reading it will give you good insight into the later stages of your project. If you already @@ -794,7 +337,7 @@ First custom commit Making it much easier to complete that checklist when you are ready for submission. - 12. **Start your exciting research**: You are now ready to add flesh and + 13. **Start your exciting research**: You are now ready to add flesh and blood to this raw skeleton by further modifying and adding your exciting research steps. You can use the "published works" section in the introduction (above) as some fully working models to learn @@ -802,8 +345,12 @@ First custom commit questions. -Other basic customizations --------------------------- + +## Other basic customizations + +The checklist for the first commit above does not include other basic +customizations that will be necessary once you start using maneaging your +project. Here, we list some of the other steps that are usually necessary. - **High-level software**: Maneage installs all the software that your project needs. You can specify which software your project needs in @@ -823,24 +370,12 @@ Other basic customizations Gnuastro, go through the analysis steps in `reproduce/analysis` and remove all its use cases (clearly marked). - - **Input dataset**: The input datasets are managed through the - `reproduce/analysis/config/INPUTS.conf` file. It is best to gather all - the information regarding all the input datasets into this one central - file. To ensure that the proper dataset is being downloaded and used - by the project, it is also recommended get an [MD5 - checksum](https://en.wikipedia.org/wiki/MD5) of the file and include - that in `INPUTS.conf` so the project can check it automatically. The - preparation/downloading of the input datasets is done in - `reproduce/analysis/make/download.mk`. Have a look there to see how - these values are to be used. This information about the input datasets - is also used in the initial `configure` script (to inform the users), - so also modify that file. You can find all occurrences of the demo - dataset with the command below and replace it with your input's - dataset. - - ```shell - $ grep -ir wfpc2 ./* - ``` + - **Input datasets**: The input datasets are managed through the + `reproduce/analysis/config/INPUTS.conf` file. It is best to gather the + following information regarding all the input datasets into this one + central file: 1) the SHA256 checksum of the file, 2) the URL where the + file can be downloaded online. Please read the comments at the start + of `reproduce/analysis/config/INPUTS.conf` carefully. - **`README.md`**: Correct all the `XXXXX` place holders (name of your project, your own name, address of your project's online/remote @@ -897,7 +432,7 @@ Other basic customizations whole project while the project is under development (focus is on the analysis that is done after preparation). Because of this, preparation will be done automatically for the first time that the project is run - (when `.build/software/preparation-done.mk` doesn't exist). After the + (when `.build/software/preparation-data.mk` doesn't exist). After the preparation process completes once, future runs of `./project make` will not do the preparation process anymore (will not call `top-prepare.mk`). They will only call `top-make.mk` for the @@ -918,15 +453,141 @@ Other basic customizations +## Upgrading the Maneage branch + +In time, Maneage is going to become more and more mature and robust (thanks +to your feedback and the feedback of other users). Bugs will be fixed and +new/improved features will be added. So every once and a while, you can run +the commands below to pull new work that is done in Maneage. If the changes +are useful for your work, you can merge them with your project to benefit +from them. + +0. Before going into the technicalities of upgrading your project's +Maneage, it may happen that you don't have the `maneage` branch and +`origin-maneage` remote any more! This can happen when you clone your own +project on a different system, or a colleague clones it to collaborate with +you: the clone won't have the `origin-maneage` remote that you started the +project with. If this is the case, you can add the `origin-maneage` remote +and define the `maneage` branch from it using the steps below: + +```shell +$ git remote add origin-maneage https://git.maneage.org/project.git +$ git fetch origin-maneage maneage +$ git checkout -b maneage --track origin-maneage/maneage +``` + +1. Pull the latest changes on the `maneage` branch and read the commit +message (full description) of all new changes with the commands below. Just +be sure that you have already committed any changes in your branch +(otherwise the checkout command will fail). + +```shell +# Go to the 'maneage' branch and import updates. +$ git checkout maneage +$ git pull # Get recent work in Maneage +``` + +2. Read all the commit messages of the newly imported features/changes. In +particular pay close attention to the ones starting with 'IMPORTANT': these +may cause a crash in your project (changing something fundamental in +Maneage). Replace the `XXXXXXX..YYYYYYY` with hashs mentioned close to +start of the `git pull` command outputs (previous step). + +```shell +$ git log XXXXXXX..YYYYYYY --reverse +``` + +3. If you find the updates useful, go to your project's `main` branch and +import all the updates into it with the commands below. Don't worry about +the printed outputs (in particular the `CONFLICT`s), we'll clean them up in +the next step. + +```shell +$ git checkout main +$ git merge maneage + +# Ignore conflicting Maneage files that you had previously deleted +# in the customization checklist (mostly demonstration files). +$ git status # Just for a check +$ git status --porcelain | awk '/^DU/{system("git rm "$NF)}' +$ git status # Just for a check +``` + +4. Files with conflicts will be visible from the output of the last command +above) with the classification `both modified:`. Open one of these files +with your favorite text editor and correct the conflict (placed in between +`<<<<<<<`, `=======` and `>>>>>>>`). Once all conflicts in a file are +removed, the file will be automatically removed from the "Un-merged paths" +of `git status`. So run `git status` after correcting the conflicts of each +file just to make sure things are clean. TIP: If you want the changes in +one file to be only from a special branch (`maneage` or `main`, completely +ignoring changes in the other), use this command: + +```shell +$ git checkout <BRANCH-NAME> -- <FILENAME> +``` + +5. Once all the Git conflicts are fixed, it is important to make sure that +"semantic conflicts" (that don't show up in Git, but can potentially break +your project) are also fixed. For example updates to software versions +(their behavior may have changed), or to internal Maneage structure. Hence +read the commit messages of `git log` carefully to see what has changed. In +case you see a commit with `IMPORTANT` in its title, the best way is to +delete your build directory and let the software and project be executed +from scratch. + +```shell +$ ./project make distclean # will DELETE ALL your build-directory!! +$ ./project configure -e +$ ./project make +``` + +6. Once your final product is created at the end of the previous step and +its contents are what you expect, you are ready to commit the merge. In the +commit message, Explain any conflicts that you fixed. + +```shell +$ git add -u +$ git commit +``` + +7. When everything is OK, before continuing with your project's work, don't +forget to push both your `main` branch and your updated `maneage` branch to +your remote server. + +```shell +$ git push +$ git push origin maneage +``` +## Citing Maneage +If you use Maneage in your project please cite Akhlaghi et al. 2025, +published in Computing in Science & Engineering, vol. 23, issue 3, +pp. 82-91; +arXiv: [2006.03018](https://arxiv.org/abs/2006.03018); +Bibcode: +[2021CSE....23c..82A](https://scixplorer.org/abs/2021CSE....23c..82A); +DOI:[10.1109/MCSE.2021.3072860](https://doi.org/10.1109/MCSE.2021.3072860). -Publication checklist -===================== +The default `paper.tex` file contains example citation and how to +acknowledge all the software that are used. + +Also, when your paper is published, don't forget to add a notice that you +paper is fully reproducible and add a sentence or paragraph in the end of +the paper shortly describing the concept. This will help spread the word +and encourage other scientists to also manage and publish their projects in +a correctly scientific (reproducible) manner. + + + + + +## Publication checklist Once your project is complete and you are ready to submit/publish the project, we recommend the following steps to ensure the maximum FAIRness of @@ -945,14 +606,14 @@ effectively no cost in keeping multiple redundancies on different servers, just in case one (or more) of them are discontinued in the (near/far) future. - - **Reserve a DOI for your dataset**: There are multiple data servers that - give this functionality, one of the most well known and (currently!) - well-funded is [Zenodo](https://zenodo.org) so we'll focus on it - here. Of course, you can use any other service that provides a similar - functionality. Once you complete these steps, you can start using/citing - your dataset's DOI in the source of your project to finalize the rest of - the points. With Zenodo, you can even use the given identifier - for things like downloading. + - **Reserve a DOI for your datasets**: There are multiple data servers + that give this functionality, one of the most well known and + (currently!) well-funded is [Zenodo](https://zenodo.org) so we'll focus + on it here. Of course, you can use any other service that provides a + similar functionality. Once you complete these steps, you can start + using/citing your dataset's DOI in the source of your project to + finalize the rest of the points. With Zenodo, you can even use the given + identifier for things like downloading. * *Start new upload*: After you log in to Zenodo, you can start a new upload by clicking on the "New Upload button". @@ -961,16 +622,23 @@ future. Identifier", click on the "Reserve DOI" button. * *Fill basic info*: You need to at least fill in the "required fields" - (marked with a red star). You will always be able to change any - metadata (even after you "Publish"), so don't worry too much about - values in the fields, at this phase, its just important that they - are not empty. + (marked with a red star). You will always be able to change any + metadata (even after you "Publish"), so don't worry too much about + values in the fields, at this phase, its just important that they are + not empty. * *Save your project but do not yet publish*: Press the "Save" button - (at the top or bottom of the page). Do not yet press "Publish" - though, since that would make the project public, and freeze the DOI - with any possible file you may have uploaded already. We will get to - the publication phase in the next steps. + (at the top or bottom of the page). Do not yet press "Publish" though, + since that would make the project public, and freeze the DOI with any + possible file you may have uploaded already. We will get to the + publication phase in the next steps. + + - **Record the metadata**: Maneage comes with a file to store all the + project's metadata: `reproduce/analysis/config/metadata.conf`. Open this + file and store all the information that you currently have: for example + the Zenodo DOI, project's Git repository, Copyright owner and license of + the data after it becomes public. Keep the empty fields in mind and + after obtaining them, don't forget to fill them up. - **Request archival on SoftwareHeritage**: [Software Heritage](https://archive.softwareheritage.org/save/) is an online @@ -989,12 +657,12 @@ future. - **Zenodo/SoftwareHeritage links in paper**: put links to the Zenodo-DOI (and SoftwareHeritage source when you make it public) in your - paper. Somewhere close the start, maybe under the keywords/abstract, + paper. Somewhere close to the start, maybe under the keywords/abstract, highlighting that they are supplements for reproducibility. These help readers easily access these resources for supplementary material directly from your PDF paper (sources on SoftwareHeritage and data/software on Zenodo). These links are more trusted/reliable in terms - of longevity than Git repositories or private webpages. + of longevity than Git repositories or private web pages. - **Identify and properly format output data**: If you have a plot, figure or table in your paper, you need to verify that data later and publish @@ -1005,7 +673,7 @@ future. * *Keep published data in a special place*: it helps if you keep the to-be-published data files in a special sub-directory under your build directory. In this way, irrespective of which subMakefile builds a - published dataset, they won't be lost/scatterred in the middle of all + published dataset, they won't be lost/scattered in the middle of all the project's intermediate-built files. * *In plain-text*: If the data are in tabular form (for example the X @@ -1013,14 +681,14 @@ future. (for example with columns separated by white-space characters) or in the more formal [Comma-separated values](https://en.wikipedia.org/wiki/Comma-separated_values) or CSV, - format). In the former case, its best to set the suffixes to `.txt` - (because most browsers/OSs will automatically know they are plain-text - and open them without needing any other software. If you have other - types of data (for example images, or very large tables with millions - of rows/columns that can be inconvenient in plain-text), feel free to - use custom binary formats, but later, in the description of your - project on the server, add a note, explaining what software they - should use to open them. + format). Generally, its best to set the suffixes to `.txt` (because + most browsers/OSs will automatically know they are plain-text and open + them without needing any other software). If you have other types of + data (for example images, or very large tables with millions of + rows/columns that can be inconvenient in plain-text), feel free to use + custom binary formats, but later, in the description of your project + on the server, add a note, explaining what software they should use to + open them. * *Descriptive names*: In some papers there are many files and having cryptic names will only confuse your readers (actually, yourself in @@ -1033,65 +701,48 @@ future. to rename everything related to each figure (which is very frustrating and prone to errors). - * *Good metadata*: Raw data are not too useful merely as a series of + * *Good metadata*: Raw data are not too useful merely as a series of raw numbers! So don't forget to have **good metadata in every file**. If its a plain-text file, usually lines starting with a `#` are ignored. So in the command that generates each dataset, add some extra - information about the dataset as lines starting with `#`. A minimal - set of recommended metadata are listed below. Feel free to add - more. You can use a configuration file to keep this information in one - place and automatically include them in all your output files. - - * *Project Title and authors*: This is very important to give a - general perspective of the figure. - - * *Links to project*: For example Zenodo-DOI, Journal-DOI (after it is - accepted), SoftwareHeritage page, arXiv-ID (or any other pre-print - server) and ofcourse, your Git repository. - - * *Commit hash* of the project that produced the dataset. This - directly links the dataset to a particular point in your project's - history. It is stored in the `$(project-commit-hash)` variable that - is defined in `initialize.mk`. So you can use it anywhere in your - project. - - * *Same commit hashes*: each dataset may have been created at - different phases of your project's history. If you simply upload the - produced datasets, they may therefore have different commits on - them. To avoid confusing your readers (and your self in the future), - it is best that they all have the same commit hash (which will also - be the commit hash printed in the paper). So upon publication, we - recommend deleting all of them and running `./project make` to build - them all with the same commit hash. - - * *Copyright as metadata*: people need to know if they can "use" the - dataset (i.e., modify it), or possibly re-distribute it and their - derived products. They also need to know how they can contact the - creator of the datset (who is usually also the copyright owner). So - as another metadata element, also add your name and email-address - (or the name of the person and email of the person who was in charge - of that part of the project), and the copyright license name and - standard link to the fully copyright license. + information (the more the better!) about the dataset as lines starting + with `#`. Based on `reproduce/analysis/config/metadata.conf`, in + `initialize.mk`, Maneage will produce a default set of basic + information for plain-text data and will put it in the + `$(print-general-metadata)` variable. It is thus recommended to print + this variable into your plain-text file before printing the actual + data (so it shows on top of the file). For a real-world example, see + its usage in `reproduce/analysis/make/delete-me.mk` (in the `maneage` + branch). If you are publishing your data in binary formats, please add + all the metadata you see in `$(print-general-metadata)` into each + dataset file (for example keywords in the FITS format). If there are + many files, its easy to define a tiny shell-script to do the job on + each dataset. - **Link to figure datasets in caption**: all the datasets that go into the plots should be uploaded directly to Zenodo so they can be viewed/downloaded with a simple link in the caption. For example see the last sentence of the caption of Figure 1 in - [arXiv:2006.03018v1](https://arxiv.org/pdf/2006.03018v1.pdf), it points - to [the + [Akhlaghi+2021](https://scixplorer.org/abs/2021CSE....23c..82A), it + points to [the data](https://zenodo.org/record/3872248/files/tools-per-year.txt) that - was used to create that figure's top plot. As you see, this will allow - your paper's readers (again, most probably your future-self!) to - directly access the numbers of each visualization (plot/figure) with a - simple click in a trusted server. This also shows the major advantage of - having your data as simple plain-text where possible, as described - above. To help you keep all your to-be-visualized datasets in a single - place, Maneage has the two `tex-publish-dir` and `data-publish-dir` - directories that are defined in `reproduce/analysis/make/initialize.mk`, - see the comments above their definition for more. + was used to create that figure's left-side plot. A more complete example + is [Eskandarlou+2026](https://scixplorer.org/abs/2026A&A...709A.210E); + where the underlying data of all figures are linked in Appendix E. As + you see, this will allow your paper's readers (again, most probably your + future-self!) to directly access the numbers of each visualization + (plot/figure) with a simple click in a trusted server. This also shows + the major advantage of having your data as simple plain-text where + possible, as described above. To help you keep all your to-be-visualized + datasets in a single place, Maneage has the two `figdir` (for + figures/plots) and `drdir` (for data release) directories that are + defined in `reproduce/analysis/make/initialize.mk`, see the comments + above their definition for more. Upon publication, you can just publish + the contents of these two directories. Therefore, be sure to only keep + the actual data in these directories, not intermediate files. - **Verification step**: It is very important to automatically verify the - outptus of your project. Recall from the customization checklist (above) + outputs of your project. Recall from the customization checklist (above) that you can activate verification by setting the `verify-outputs` variable to `yes` in `reproduce/analysis/config/verify-outputs.conf`. So please activate it and look into the `reproduce/analysis/make/verify.mk` @@ -1127,7 +778,7 @@ future. - **Confirm if your project builds from scratch**: Before publishing anything, you should see if your project can indeed reproduce itself! You may be mistakenly using temporarily created files that aren't built - when teh project is built from scratch (this happens a lot and is very + when the project is built from scratch (this happens a lot and is very dangerous for the integrity of your project!). So, go to a temporary directory, clone your project from its repository and try configuring and building it from scratch in a new-temporary build-directory. It is @@ -1142,16 +793,16 @@ future. useful for servers like arXiv, or some journals. This tarball is also one of the deliverables you want to publish on Zenodo. Once the tarball is created, copy it to a temporary directory outside of Maneage, unpack - it and run `make` (completely ignoring Maneage's `./project` script). If - you plan to submit your paper to arXiv, the best test is to actually - start a test submission on arXiv to upload the tarball there to see if - it can build your PDF. Once it works, you can delete that temporary - submission for now. Afterwards, try configuring and building it with the - tarball by running its `./project` (from scratch and without the Git - history!). If there is a problem in any of these tests, you can modify - what goes into this tarball in `reproduce/analysis/make/initialize.mk`: - go through the steps and add the necessary components until the checks - pass. + it and run `make` (completely ignoring Maneage's `./project` + script). If you plan to submit your paper to arXiv, the best test is to + actually start a test submission on arXiv to upload the tarball there to + see if it can build your PDF. Once it works, you can delete that + temporary submission for now. Afterwards, try configuring and building + it with the tarball by running its `./project` (from scratch and + without the Git history!). If there is a problem in any of these tests, + you can modify what goes into this tarball in + `reproduce/analysis/make/initialize.mk`: go through the steps and add + the necessary components until the checks pass. - **Upload all deliverables to Zenodo**: With the datasets ready, you can now upload the following deliverables to Zenodo. Except for the data @@ -1166,7 +817,7 @@ future. * **paper-XXXXXXX.pdf**: you shouldn't just download data to the data server, also upload your paper's PDF so its there with the other raw - formats. It will greatly help yourself and others. Most datacenters + formats. It will greatly help yourself and others. Most data centers (like Zenodo) actually also have a PDF viewer that will load automatically before the list of data files. For example see [zenodo.3408481](https://doi.org/10.5281/zenodo.3408481). @@ -1188,8 +839,8 @@ future. `.build/software/tarballs`. It is necessary to upload these with your project to avoid relying on third party servers. In the future any one of those servers may go down and if so, your project won't - be buildable. You can generate this tarball easily with `make - dist-software`. + be buildable. You can generate this tarball easily with `./project + make dist-software`. * All the figure (and other) output datasets of the project. Don't rename these files, let them have the same descriptive name @@ -1201,9 +852,12 @@ future. initial/final submission to your desired journal. But we'll just add the necessary points for arXiv submission here: - * *Necessary links in comments*: put a link to your project's Git - repository, Zenodo-DOI (this is not your paper's DOI, its the - data/resources DOI), and/or SoftwareHeritage link in the comments. + * *Necessary links in comments*: put a link to your project's Git + repository, Zenodo-DOI (this is not your paper's DOI, its the + data/resources DOI), and/or SoftwareHeritage link in the comments. + + - *Update `metadata.conf`*: Once you have your final arXiv ID (formatted + as: `1234.56789`) put it in `reproduce/analysis/config/metadata.conf`. - **Submission to a journal**: different journals accept submissions in different formats, some accept LaTeX, some only want a PDF, or etc. It @@ -1212,6 +866,50 @@ future. are public). If not, you can mention that everything is ready for such a submission after acceptance. + * Some journals (like the "Astronomy and Astrophysics" journal) + require that only a single LaTeX file be submitted without any + commens (along with all the figures). In other words, they do not + want any sub-directories: only a single LaTeX file, one `.bbl` file + and one PDF per figure. Here is how you can do this: + ```shell + # If you don't already have 'latexpand' in your OS, install it: + $ tlmgr install latexpand + + # Unpack the tarball and make a directory for a single-LaTeX source. + $ tar -xf maneaged-XXXXXXX.tar.gz + $ cd maneaged-XXXXXXX.tar.gz + $ mkdir one-latex + + ## The '--empty-comments' and subsequent call to AWK (that removes + ## lines starting with '%') is because we need the lines ending in a + ## '%' for some LaTeX macros). + $ latexpand paper.tex --output=one-latex/paper-0.tex \ + --empty-comments + $ awk '!/^%/' one-latex/paper-0.tex > one-latex/paper.tex + $ rm one-latex/paper-0.tex + + ## Copy the other necessary files (if you are using specific journal + ## style files, also copy them). + $ cp paper.bbl one-latex/ + $ cp tex/tikz/*.pdf one-latex/ + + ## Correct the location of the images. + $ sed -i -e's|tex/tikz/|./|' one-latex/paper.tex + ``` + + * You can confirm the contents of the `one-latex` directory made + above by running `pdflatex paper` inside that directory. Your + operating system's LaTeX may not have all the necessary packages, + in that case run `tlmgr install XXXXX` (where `XXXXX` is the + value of `texlive-packages` in + `reproduce/software/config/texlive-packages.conf`. Afterwards, + clean up all the temporary files with this command: + ```shell + $ rm *.log *.aux *.auxlock *.bcf *.out *.xml + ``` + + * Upload the contents of this `one-latex` directory to the journal. + - **Future versions**: Both Zenodo and arXiv allow uploading new versions after your first publication. So it is recommended to put more recent versions of your published projects later (for example after applying @@ -1221,14 +919,546 @@ future. the DOI (so you don't need to upload a new version if you just want to update the metadata). + - **After acceptance (before publication)**: Congratulations on the + acceptance! The main science content of your paper can't be changed any + more, but the paper will now go to the publication editor (for language + and style). Your approval of the final proof is necessary before the + paper is finally published. Use this period to finalize the final + metadata of your project: the journal's DOI. Some journals associate + your paper's DOI during this process. So before approving the final + proof do these steps: + + * Add the Journal DOI in `reproduce/analysis/config/metadata.conf`, + and re-build your final data products, so this important metadata is + added. + + * Once you get the final proof, and if everything is OK for you, + implement all the good language corrections/edits they have made + inside your own copy here and commit it into your project. This will + be the final commit of your project before publication. + + * Submit your final project as a new version to Zenodo (and + arXiv). The Zenodo one is most important because your plots will + link to it and you want the commit hash in the data files that + readers will get from Zenodo to be the same hash as the paper. + + * Tell the journal's publication editor to correct the hash and Zenodo + ID in your final proof confirmation (so the links point to the + correct place). Recall that on every new version upload in Zenodo, + you get a new DOI (or Zenodo ID). + + + -Tips for designing your project -=============================== + +# Maneage development tools + +Maneage does not define a new programming language. By design, it uses +existing and time-tested tools/software. In this section, we review the +purpose of each tool and include recommendations on how to learn them. The +"Published works using Maneage" section below lists published papers that +have been written within Maneage. Once you have a good knowledge of the +necessary tools listed below, you can try reading the source of previously +published papers as demos to help in the optimal design your own project. + + + +### GNU Info + +The distinguishing feature of a good developer is not memorizing more of a +tool's features, but to know where to look (for the details) when they need +something. Documentation is therefore very important in any development +environment. As part of Maneage's software environment configuration, we +also install any documentation that each software installs (mostly in the +Info documentation format). This includes many of the basic software in +Maneage like Make, AWK, SED, Coreutils (that provides commands such as +`ls`, `cp` and etc), as well as high-level software like GNU Scientific +Library (GSL) and GNU Astronomy Utilities (Gnuastro). + +Info greatly simplifies your access (without taking your hands off the +keyboard!) to many manuals that are installed in your Maneage'd software +environment, allowing you to be much more efficient as you work. Another +nice thing with the Info documentation is that it corresponds the same +version that you are using in your analysis and you do not need any +internet connection. + +If you are not familiar with this documentation format, the good news is +that it has a very nice manual for itself that you can easily enter with +the second command below. The first command takes you into the interactive +Maneage'd software environment. In case you have the software environment +within a container, include the `--sif` option (just like the `./project +make` command). + +```shell +$ ./project shell +$ info info +``` + +We strongly recommend reading this manual: it will open a world of +knowledge for you that is always available, even when you are offline. In +less than an hour, you will become familiar and proficient in the Info +documentation. You can then use Info when reading the documentation of +other software you may want to learn when using Maneage (like Make, AWK, +SED or Gnuastro), and you'll see how powerful and convenient it is. + +If you use the GNU Emacs text editor (or any of its variants), you also +have access to all Info manuals while you are writing your code (again, +without taking your hands off the keyboard!): simply run `Ctrl-h i` inside +Emacs. Emacs (along with Vim) is available within the Project software +environment (which you can access through `./project shell`). + + + +### GNU Make + +When batch processing is necessary (no manual intervention, as in a +reproducible project), shell (or Python) scripts are usually the first +solution for most people. However, the inherent complexity and +non-linearity of progress in a scientific project (where experimentation is +key) make it hard to manage them as the project evolves. For example, a +script will start from the top/start every time it is run. So if you have +already completed 90% of the project and want to run the remaining 10% that +you have newly added, you have to run the whole script from the start +again. + +It is possible to manually ignore/comment parts of a script to only do a +special part. However, such checks/comments will only add to the complexity +of the script and will discourage you from experimenting on an already +completed part of the project when an idea suddenly comes up. It is also +prone to very serious bugs in the end (when trying to reproduce from +scratch); for example you forget to un-comment or remove a temporary +change. Such bugs are very hard to notice during the work and frustrating +to find in the end. + +Make is the solution to these problems. It starts from the end: the final +*target*. Dependencies and recipes (shell scripts) are defined for every +target and using them, Make builds a dependency tree internally. Using +that, Make finds where it should start each time the project is +run. Therefore, in the scenario above, a researcher that has just added the +final 10% of the project, will only have to run those extra steps: without +any modification to previously executed code. With Make, it is also trivial +to change the processing of any intermediate (already written) *rule* (or +step) in the middle of an already written analysis: the next time Make is +run, only rules that are affected by the changes/additions will be re-run, +not the whole analysis/project. + +This greatly speeds up the processing (enabling creative changes), while +keeping all the dependencies clearly documented (as part of the Make +language), and most importantly, enabling full reproducibility from scratch +with no changes in the project code that was working during the +research. This will allow robust results and let the scientists get to what +they do best: experiment and be critical to the methods/analysis without +having to waste energy and time on technical problems that come up as a +result of using scripts alone. + +Furthermore, since the dependencies are clearly demarcated in Make, it can +identify independent steps and run them in parallel. This further speeds up +the processing. Make was designed for this purpose. It is how huge projects +like all Unix-like operating systems (including GNU/Linux or Mac OS +operating systems) and their core components are built. Therefore, Make is +a highly mature paradigm/system with robust and highly efficient +implementations in various operating systems perfectly suited for a complex +non-linear research project. + +Make is a small language with the aim of defining *rules* that are composed +of *targets*, *prerequisites* and *recipes*. It comes with some nice +features like functions or automatic-variables to greatly facilitate the +management of text (filenames for example) or any of those constructs. For +a more detailed (yet still general) introduction see the [Make article on +Wikipedia](https://en.wikipedia.org/wiki/Make_(software)). + +As of 2026, Make is a 50 year old software that is still getting better, +therefore many implementations of Make exist. The only difference in them +is some extra features over the [standard +definition](https://pubs.opengroup.org/onlinepubs/009695399/utilities/make.html) +(which is shared in all of them). Maneage is primarily written in GNU Make +that is the most common, most actively developed, and most advanced +implementation. Just note that Maneage downloads, builds, internally +installs, and uses its own dependencies (including GNU Make), so you don't +have to have it installed before you try it out. + +The recipes (operations) that are applied on the dependencies of each +target to build the target are simple shell scripts in Maneage. In case you +are more comfortable with Python, Perl or R scripts, you can save them in +your project's source and simply call them in the recipe. + +The [GNU Make book](https://www.gnu.org/software/make/manual) is arguably +the best place to learn Make. As mentioned in the "Info documentation" +section above, you also have the manual within your Maneage'd software +environment. The main caveat of the GNU Make manual is that all its +examples and demonstrations are based on compiling programs in C; not data +analysis. But fortunately beyond the first chapter, the rest of the +examples in the manual are sufficiently generic. + +To replace the first chapter (and give examples of how Make can be used in +data analysis), along with some early adopters of Maneage and as part of +the IAC's Short Meetings on Astro-Computing Knowledge (SMACK) series, we +prepared [a hands-on video +demonstration](https://peertube.stream/w/iJitjS3r232Z8UPMxKo6jq) that you +can watch. In it we show how you can write your Make recipes in any +high-level scripting language. + +Once you have watched the video above, read the GNU Make manual at least +until the end of Chapter 8 (called "Functions for transforming text"). You +can use the Info format manual within Maneage (as described in the "Info +documentation" section above) with `info make`. + + + +### GNU Bash + +The main shell that is installed within Maneage is GNU Bash. Like GNU Make, +it also has an Info manual, but unfortunately it is not written with +beginners in mind: it digs deep into very technical details from the +start. In case you are using Gnuastro in your analysis, its [general +tutorial](https://www.gnu.org/software/gnuastro/manual/html_node/General-program-usage-tutorial.html) +also includes many useful tips on the shell. We have also prepared the +following hands-on SMACK videos to introduce the shell + +- SMACK 2: [More on the command-line](https://peertube.stream/w/d16286ee-fc46-444f-acb8-645f9de6c7b7). +- SMACK 4: [Shell scripting](https://peertube.stream/w/18d2e386-2ca2-4a1f-a949-c7ca5dcee8ff). + + + +### Git + +Git is the version control system used in Maneage to allow easy tracking of +changes during the development of the project, collaborate with colleagues +and also to import improvements from the core branch into individual +projects. Without Git, such operations become so tedious and prone to human +error that the development of any software-based project with more than one +developer would be practically impossible. + +If you are not yet familiar with Git, the best resource is the free and +open source [Pro Git](https://git-scm.com/book/en) book. Don't be alarmed +by the number of chapters in the Pro Git book. The majority of the book is +for very advanced usages of Git, including setting up servers (that is not +relevant in Maneage). To comfortably use Maneage, mastering the following +chapters is enough + +- Chapter 1: Getting Started +- Chapter 2: Git Basics +- Chapter 3: Git Branching +- Chapter 5: Distributed Git + +After mastering these chapters, you will get a very good feeling of any +further chapters in case you need them. Of course, [Git's own +manual](https://git-scm.com/docs/user-manual.html) is also available for +further details when necessary. + + + + + + + + + + +# Maneage directory architecture + +In order to customize Maneage to your research, it is important to first +understand its souce and build directory architectures. This will help +navigate your way in the directories and understand how to implement your +research project: where to add new files and which existing files to modify +for what purpose. But if this the first time you are using Maneage, before +reading this theoretical discussion, please run Maneage once from scratch +without any changes (described in `README.md`). This will show you how it +works and will allow you to make test changes/edits in the code to test +what you read here. + +A core concept in Maneage is that that there is a very strong distinction +between the "source" (hand-written, plain-text files: most valuable of them +all) and "build" (for downloaded, or automatically generated +datasets/files) directories. + +## Source directory (hand-written files) + +The directory that is hosting this file in your operating system is the +"source" directory. This is where all hand-written files of your project +(the most valuable) are saved and it is fully under version control. The +source directory has two top-level directories: + +- `reproduce/`: contains all the "code" (assuming LaTeX is not "code") and + has two high-level sub-directories for the two high-level phases of + Maneage: + + - `software/`: all the instructions to download, build and install + (independent of the host operating system) the necessary + software. These are executed when you ran the `./project configure`. + + - `analysis/`: all the analysis steps of your project: that are executed + with the `./project make` command. + +- `tex/` contains all the final paper's components to be compiled into a + PDF using LaTeX. After building Maneage once, two symbolic links to the + build directory are placed here that are described in the corresponding + sub-section below. But they are not under version control, the place to + keep any extra hand-written LaTeX source is under the `src/` + sub-directory here. + +At the end of its configuration, Maneage also creates some symbolic links +for easy access to the build directory from your top source directory. See +the corresponding sub-section below for more on those: they are very useful +while you are developing your project. + +Once the project is configured for your system, `./project make` will do +the basic preparations and run the project's analysis with the custom +version of software. The `project` script is just a wrapper, and with the +`make` argument, it will first call `top-prepare.mk` and `top-make.mk` +(both are in the `reproduce/analysis/make` directory). + +In terms of organization, `top-prepare.mk` and `top-make.mk` have an +identical design, only minor differences. So, let's continue Maneage's +architecture with `top-make.mk`. Once you understand that, you'll clearly +understand `top-prepare.mk` also. These very high-level files are +relatively short and heavily commented so hopefully the descriptions in +each comment will be enough to understand the general details. As you read +this section, please also look at the contents of the mentioned files and +directories to fully understand what is going on. + +Before starting to look into the top `top-make.mk`, it is important to +recall that Make defines dependencies by files. Therefore, the +input/prerequisite and output of every step/rule must be a file. Also +recall that Make will use the modification date of the prerequisite(s) and +target files to see if the target must be re-built or not. Therefore during +the processing, _many_ intermediate files will be created (see the tips +section below on a good strategy to deal with large/huge files). + +To keep the source and (intermediate) built files separate, the user _must_ +define a top-level build directory variable (or `$(BDIR)`) to host all the +intermediate files (you defined it during `./project configure`). This +directory doesn't need to be version controlled or even synchronized, or +backed-up in other servers: its contents are all products, and can be +easily re-created any time. As you define targets for your new rules, it is +thus important to place them all under sub-directories of `$(BDIR)`. As +mentioned above, you always have fast access to this "build"-directory with +the `.build` symbolic link. Also, beware to *never* make any manual change +in the files of the build-directory, just delete them (so they are +re-built). + +In this architecture, we have two types of Makefiles that are loaded into +the top `Makefile`: _configuration-Makefiles_ (only independent +variables/configurations) and _workhorse-Makefiles_ (Makefiles that +actually contain analysis/processing rules). + +The configuration-Makefiles are those that satisfy these two wildcards: +`reproduce/software/config/*.conf` (for building the necessary software +when you run `./project configure`) and `reproduce/analysis/config/*.conf` +(for the high-level analysis, when you run `./project make`). These +Makefiles don't actually have any rules, they just have values for various +free parameters throughout the configuration or analysis. Open a few of +them to see for yourself. These Makefiles must only contain raw Make +variables (project configurations). By "raw" we mean that the Make +variables in these files must not depend on variables in any other +configuration-Makefile. This is because we don't want to assume any order +in reading them. It is also very important to *not* define any rule, or +other Make construct, in these configuration-Makefiles. + +Following this rule-of-thumb enables you to set these configure-Makefiles +as a prerequisite to any target that depends on their variable +values. Therefore, if you change any of their values, all targets that +depend on those values will be re-built. This is very convenient as your +project scales up and gets more complex. + +The workhorse-Makefiles are those satisfying this wildcard +`reproduce/software/make/*.mk` and `reproduce/analysis/make/*.mk`. They +contain the details of the processing steps (Makefiles containing +rules). Therefore, in this phase *order is important*, because the +prerequisites of most rules will be the targets of other rules that will be +defined prior to them (not a fixed name like `paper.pdf`). The lower-level +rules must be imported into Make before the higher-level ones. + +All processing steps are assumed to ultimately (usually after many rules) +end up in some number, image, figure, or table that will be included in the +paper. The writing of these results into the final report/paper is managed +through separate LaTeX files that only contain macros (a name given to a +number/string to be used in the LaTeX source, which will be replaced when +compiling it to the final PDF). So the last target in a workhorse-Makefile +is a `.tex` file (with the same base-name as the Makefile, but in +`$(BDIR)/tex/macros`). As a result, if the targets in a workhorse-Makefile +aren't directly a prerequisite of other workhorse-Makefile targets, they +can be a prerequisite of that intermediate LaTeX macro file and thus be +called when necessary. Otherwise, they will be ignored by Make. + +Maneage also has a mode to share the build directory between several +users of a Unix group (when working on large computer clusters). In this +scenario, each user can have their own cloned project source, but share the +large built files between each other. To do this, it is necessary for all +built files to give full permission to group members while not allowing any +other users access to the contents. Therefore the `./project configure` and +`./project make` steps must be called with special conditions which are +managed in the `--group` option. + +Let's see how this design is implemented. Please open and inspect +`top-make.mk` it as we go along here. The first step (un-commented line) is +to import the local configuration (your answers to the questions of +`./project configure`). They are defined in the configuration-Makefile +`reproduce/software/config/LOCAL.conf` which was also built by `./project +configure` (based on the `LOCAL.conf.in` template of the same directory). + +The next non-commented set of the top `Makefile` defines the ultimate +target of the whole project (`paper.pdf`). But to avoid mistakes, a sanity +check is necessary to see if Make is being run with the same group settings +as the configure script (for example when the project is configured for +group access using the `./for-group` script, but Make isn't). Therefore we +use a Make conditional to define the `all` target based on the group +permissions. + +Having defined the top/ultimate target, our next step is to include all the +other necessary Makefiles. However, order matters in the importing of +workhorse-Makefiles and each must also have a TeX macro file with the same +base name (without a suffix). Therefore, the next step in the top-level +Makefile is to define the `makesrc` variable to keep the base names +(without a `.mk` suffix) of the workhorse-Makefiles that must be imported, +in the proper order. + +Finally, we import all the necessary remaining Makefiles: 1) All the +analysis configuration-Makefiles with a wildcard. 2) The software +configuration-Makefile that contains their version (just in case its +necessary). 3) All workhorse-Makefiles in the proper order using a Make +`foreach` loop. + +In short, to keep things modular, readable and manageable, follow these +recommendations: 1) Set clear-to-understand names for the +configuration-Makefiles, and workhorse-Makefiles, 2) Only import other +Makefiles from top Makefile. These will let you know/remember generally +which step you are taking before or after another. Projects will scale up +very fast. Thus if you don't start and continue with a clean and robust +convention like this, in the end it will become very dirty and hard to +manage/understand (even for yourself). As a general rule of thumb, break +your rules into as many logically-similar but independent steps as +possible. + +The `reproduce/analysis/make/paper.mk` Makefile must be the final Makefile +that is included. This workhorse Makefile ends with the rule to build +`paper.pdf` (final target of the whole project). If you look in it, you +will notice that this Makefile starts with a rule to create +`$(mtexdir)/project.tex` (`mtexdir` is just a shorthand name for +`$(BDIR)/tex/macros` mentioned before). As you see, the only dependency of +`$(mtexdir)/project.tex` is `$(mtexdir)/verify.tex` (which is the last +analysis step: it verifies all the generated results). Therefore, +`$(mtexdir)/project.tex` is _the connection_ between the +processing/analysis steps of the project, and the steps to build the final +PDF. + +During the research, it often happens that you want to test a step that is +not a prerequisite of any higher-level operation. In such cases, you can +(temporarily) define that processing as a rule in the most relevant +workhorse-Makefile and set its target as a prerequisite of its TeX +macro. If your test gives a promising result and you want to include it in +your research, set it as prerequisites to other rules and remove it from +the list of prerequisites for TeX macro file. In fact, this is how a +project is designed to grow in this framework. + +## Build directory (automatically generated files) + +The build directory has the same sub-directories as the `reproduce/` +sub-directory of the source. + +- `software/`: all the automatically built products during the Maneage + configuration phase. It includes the following sub-directories: + - `config/`: all the local configurations for your system. The + `LOCAL.conf` file of this directory can contain your server user ID + and password (used when your input data are in servers that need + authentication). + - `installed/`: the top-level software environment of Maneage. Just like + your Unix-based operating system, it has sub-directories like `bin/` + (for executable software), `lib/` (for libraries) and etc. + - `locks/`: This directory is used to keep file locks when necessary (it + may be removed later). File locks are useful to stop the + parallelization. for example when we want all the steps to be done in + parallel, but not for steps like downloading (where the + network/servers can be a bottleneck and actually decrease the speed of + a parallelized operation compared to its serial operation). + - `tarballs/`: The source tarballs of all the software that were used to + build the software environment. If they were in the directory given to + `--software-dir`, they will be symbolic links to the files in that + directory. Otherwise (if they were downloaded), they will be normal + files. +- `analysis/`: all the analysis outputs. The default (in the `maneage` + branch) will create two sub-directories here when you run `./project + make`: + - `inputs/`: all the input files to the project. Similar to the + `tarballs/` directory above, if the files were present on the host + file system (in a directory given to `--input-dir`), a symbolic link + will be placed. Otherwise (if they were downloaded), the raw file will + be present. You can use this distinction (being a symbolic link or + not) to see which files were not on your system and copy them into a + dedicated directory to avoid needing the internet on every new run. + + - `tex/`: This directory contains the built files that are necessary for + LaTeX aspect of you final PDF. It is recommended to not keep large + data files here, only that absolute minimum that you need to create + the final PDF (the contents of this directory will need to be uploaded + to publication severs like arXiv). The following sub-directories are + assumed to always be present here: + - `build\`: the directory that LaTeX actually executes in. The + `paper.tex` (of the top source directory) will be copied here and + the directories containing the other LaTeX files are included into + as directories under the `tex/` directory of the top-level source. + - `macros\`: all the macros from the various stages of the software + and analysis will be present as different files here. As described + in the source directory descriptions, these are the backbone of + Maneage's operation (one for every sub-Makefile). + - `to-publish\`: will contain the raw tables behind every figure. For + example, see Appendix E of [Eskandarlou et + al. 2026](https://scixplorer.org/abs/2026A%26A...709A.210E). + + +## Easy access to build directory from source + +After it finishes, `./project configure` will create the following symbolic +links (also directories) in the project's top source directory for easy +access to the build directory. + +- `.build` points to the top build directory. This is very useful for fast + access to the build directory without having to worry about which system + is hosting your maneage'd project: in one system, your build directory + can be in one location and on another system in another directory. But + thanks to this symbolic link, you do not have to worry which system you + are developing on. + +- `.local` for easy access to the custom built software installation + directory. For example the `ls` command of your project can be accessed + outside of Maneage with `.local/bin/ls`. This is useful when you want to + run your Maneage'd software outside of maneage (although using `./project + shell` is a much better strategy for that). + +There are also two symbolic links under the `tex/` directory of the source +that are listed below. When running `./project make dist`, the contents of +these symbolic links will be copied into the tarball. In this way, +publishers (like arXiv) do not have to run Maneage, they just run LaTeX and +have all the products that are necessary). + +- `tex/build` for direct access to the `analysis/tex/build` directory. As + described above, this directory will contain all the files that go into + the TeX source of the paper. + +- `tex/tikz` for the outputs of [PGF & TiKZ](https://ctan.org/pkg/pgf) (or + [PGFPLots](https://ctan.org/pkg/pgfplots), that is based on it). These + packages can generate plots within LaTeX. Therefore, they use the same + font, line width and colors of the paper, making your plots fit very + nicely (visually) in the final paper. Another nice aspect is that with + these software, you do not need to generate the plots/figures separate + from the paper (PGFPlots can directly read the tables you put in the + `to-publish/` subdirectory mentioned under the build directory. + + + + + + + + + + +# Maneagement tips The following is a list of design points, tips, or recommendations that have been learned after some experience with this type of project @@ -1236,427 +1466,699 @@ management. Please don't hesitate to share any experience you gain after using it with us. In this way, we can add it here (with full giving credit) for the benefit of others. - - **Modularity**: Modularity is the key to easy and clean growth of a - project. So it is always best to break up a job into as many - sub-components as reasonable. Here are some tips to stay modular. - - - *Short recipes*: if you see the recipe of a rule becoming more than a - handful of lines which involve significant processing, it is probably - a good sign that you should break up the rule into its main - components. Try to only have one major processing step per rule. - - - *Context-based (many) Makefiles*: For maximum modularity, this design - allows easy inclusion of many Makefiles: in - `reproduce/analysis/make/*.mk` for analysis steps, and - `reproduce/software/make/*.mk` for building software. So keep the - rules for closely related parts of the processing in separate - Makefiles. - - - *Descriptive names*: Be very clear and descriptive with the naming of - the files and the variables because a few months after the - processing, it will be very hard to remember what each one was - for. Also this helps others (your collaborators or other people - reading the project source after it is published) to more easily - understand your work and find their way around. - - - *Naming convention*: As the project grows, following a single standard - or convention in naming the files is very useful. Try best to use - multiple word filenames for anything that is non-trivial (separating - the words with a `-`). For example if you have a Makefile for - creating a catalog and another two for processing it under models A - and B, you can name them like this: `catalog-create.mk`, - `catalog-model-a.mk` and `catalog-model-b.mk`. In this way, when - listing the contents of `reproduce/analysis/make` to see all the - Makefiles, those related to the catalog will all be close to each - other and thus easily found. This also helps in auto-completions by - the shell or text editors like Emacs. - - - *Source directories*: If you need to add files in other languages for - example in shell, Python, AWK or C, keep the files in the same - language in a separate directory under `reproduce/analysis`, with the - appropriate name. - - - *Configuration files*: If your research uses special programs as part - of the processing, put all their configuration files in a devoted - directory (with the program's name) within - `reproduce/software/config`. It is much cleaner and readable (thus - less buggy) to avoid mixing the configuration files, even if there is - no technical necessity. - - - - **Contents**: It is good practice to follow the following - recommendations on the contents of your files, whether they are source - code for a program, Makefiles, scripts or configuration files - (copyrights aren't necessary for the latter). - - - *Copyright*: Always start a file containing programming constructs - with a copyright statement like the ones that Maneage starts with - (for example in the top level `Makefile`). - - - *Comments*: Comments are vital for readability (by yourself in two - months, or others). Describe everything you can about why you are - doing something, how you are doing it, and what you expect the result - to be. Write the comments as if it was what you would say to describe - the variable, recipe or rule to a friend sitting beside you. When - writing the project it is very tempting to just steam ahead with - commands and codes, but be patient and write comments before the - rules or recipes. This will also allow you to think more about what - you should be doing. Also, in several months when you come back to - the code, you will appreciate the effort of writing them. Just don't - forget to also read and update the comment first if you later want to - make changes to the code (variable, recipe or rule). As a general - rule of thumb: first the comments, then the code. - - - *File title*: In general, it is good practice to start all files with - a single line description of what that particular file does. If - further information about the totality of the file is necessary, add - it after a blank line. This will help a fast inspection where you - don't care about the details, but just want to remember/see what that - file is (generally) for. This information must of course be commented - (its for a human), but this is kept separate from the general - recommendation on comments, because this is a comment for the whole - file, not each step within it. - - - - **Make programming**: Here are some experiences that we have come to - learn over the years in using Make and are useful/handy in research - contexts. - - - *Environment of each recipe*: If you need to define a special - environment (or aliases, or scripts to run) for all the recipes in - your Makefiles, you can use a Bash startup file - `reproduce/software/shell/bashrc.sh`. This file is loaded before every - Make recipe is run, just like the `.bashrc` in your home directory is - loaded every time you start a new interactive, non-login terminal. See - the comments in that file for more. - - - *Automatic variables*: These are wonderful and very useful Make - constructs that greatly shrink the text, while helping in - read-ability, robustness (less bugs in typos for example) and - generalization. For example even when a rule only has one target or - one prerequisite, always use `$@` instead of the target's name, `$<` - instead of the first prerequisite, `$^` instead of the full list of - prerequisites and etc. You can see the full list of automatic - variables - [here](https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html). If - you use GNU Make, you can also see this page on your command-line: - - ```shell - $ info make "automatic variables" - ``` - - - *Debug*: Since Make doesn't follow the common top-down paradigm, it - can be a little hard to get accustomed to why you get an error or - un-expected behavior. In such cases, run Make with the `-d` - option. With this option, Make prints a full list of exactly which - prerequisites are being checked for which targets. Looking - (patiently) through this output and searching for the faulty - file/step will clearly show you any mistake you might have made in - defining the targets or prerequisites. - - - *Large files*: If you are dealing with very large files (thus having - multiple copies of them for intermediate steps is not possible), one - solution is the following strategy (Also see the next item on "Fast - access to temporary files"). Set a small plain text file as the - actual target and delete the large file when it is no longer needed - by the project (in the last rule that needs it). Below is a simple - demonstration of doing this. In it, we use Gnuastro's Arithmetic - program to add all pixels of the input image with 2 and create - `large1.fits`. We then subtract 2 from `large1.fits` to create - `large2.fits` and delete `large1.fits` in the same rule (when its no - longer needed). We can later do the same with `large2.fits` when it - is no longer needed and so on. - ``` - large1.fits.txt: input.fits - astarithmetic $< 2 + --output=$(subst .txt,,$@) - echo "done" > $@ - large2.fits.txt: large1.fits.txt - astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@) - rm $(subst .txt,,$<) - echo "done" > $@ - ``` - A more advanced Make programmer will use Make's [call - function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html) - to define a wrapper in `reproduce/analysis/make/initialize.mk`. This - wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be - possible to greatly simplify this repetitive statement and make the - code even more readable throughout the whole project. - - - *Fast access to temporary files*: Most Unix-like operating systems - will give you a special shared-memory device (directory): on systems - using the GNU C Library (all GNU/Linux system), it is `/dev/shm`. The - contents of this directory are actually in your RAM, not in your - persistence storage like the HDD or SSD. Reading and writing from/to - the RAM is much faster than persistent storage, so if you have enough - RAM available, it can be very beneficial for large temporary files to - be put there. You can use the `mktemp` program to give the temporary - files a randomly-set name, and use text files as targets to keep that - name (as described in the item above under "Large files") for later - deletion. For example, see the minimal working example Makefile below - (which you can actually put in a `Makefile` and run if you have an - `input.fits` in the same directory, and Gnuastro is installed). - ``` - .ONESHELL: - .SHELLFLAGS = -ec - all: mean-std.txt - shm-maneage := /dev/shm/$(shell whoami)-maneage-XXXXXXXXXX - large1.txt: input.fits - out=$$(mktemp $(shm-maneage)) - astarithmetic $< 2 + --output=$$out.fits - echo "$$out" > $@ - large2.txt: large1.txt - input=$$(cat $<) - out=$$(mktemp $(shm-maneage)) - astarithmetic $$input.fits 2 - --output=$$out.fits - rm $$input.fits $$input - echo "$$out" > $@ - mean-std.txt: large2.txt - input=$$(cat $<) - aststatistics $$input.fits --mean --std > $@ - rm $$input.fits $$input - ``` - The important point here is that the temporary name template - (`shm-maneage`) has no suffix. So you can add the suffix - corresponding to your desired format afterwards (for example - `$$out.fits`, or `$$out.txt`). But more importantly, when `mktemp` - sets the random name, it also checks if no file exists with that name - and creates a file with that exact name at that moment. So at the end - of each recipe above, you'll have two files in your `/dev/shm`, one - empty file with no suffix one with a suffix. The role of the file - without a suffix is just to ensure that the randomly set name will - not be used by other calls to `mktemp` (when running in parallel) and - it should be deleted with the file containing a suffix. This is the - reason behind the `rm $$input.fits $$input` command above: to make - sure that first the file with a suffix is deleted, then the core - random file (note that when working in parallel on powerful systems, - in the time between deleting two files of a single `rm` command, many - things can happen!). When using Maneage, you can put the definition - of `shm-maneage` in `reproduce/analysis/make/initialize.mk` to be - usable in all the different Makefiles of your analysis, and you won't - need the three lines above it. **Finally, BE RESPONSIBLE:** after you - are finished, be sure to clean up any possibly remaining files (due - to crashes in the processing while you are working), otherwise your - RAM may fill up very fast. You can do it easily with a command like - this on your command-line: `rm -f /dev/shm/$(whoami)-*`. - - - - **Software tarballs and raw inputs**: It is critically important to - document the raw inputs to your project (software tarballs and raw - input data): - - - *Keep the source tarball of dependencies*: After configuration - finishes, the `.build/software/tarballs` directory will contain all - the software tarballs that were necessary for your project. You can - mirror the contents of this directory to keep a backup of all the - software tarballs used in your project (possibly as another version - controlled repository) that is also published with your project. Note - that software web-pages are not written in stone and can suddenly go - offline or not be accessible in some conditions. This backup is thus - very important. If you intend to release your project in a place like - Zenodo, you can upload/keep all the necessary tarballs (and data) - there with your - project. [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746) is - one example of how the data, Gnuastro (main software used) and all - major Gnuastro's dependencies have been uploaded with the project's - source. Just note that this is only possible for [free - software](https://www.gnu.org/philosophy/free-sw.html). - - - *Keep your input data*: The input data is also critical to the - project's reproducibility, so like the above for software, make sure - you have a backup of them, or their persistent identifiers (PIDs). - - - **Version control**: Version control is a critical component of - Maneage. Here are some tips to help in effectively using it. - - - *Regular commits*: It is important (and extremely useful) to have the - history of your project under version control. So try to make commits - regularly (after any meaningful change/step/result). - - - *Keep Maneage up-to-date*: In time, Maneage is going to become more - and more mature and robust (thanks to your feedback and the feedback - of other users). Bugs will be fixed and new/improved features will be - added. So every once and a while, you can run the commands below to - pull new work that is done in Maneage. If the changes are useful for - your work, you can merge them with your project to benefit from - them. Just pay **very close attention** to resolving possible - **conflicts** which might happen in the merge. In particular the - "semantic conflicts" that don't show up in Git, but can potentially - break your project, for example updates to software versions, or to - internal Maneage structure. Hence read the commit messages of `git - log` carefully to **see what has changed**. The best way to check is - to first complete the steps below, then build your project from - scratch (from `./project configure` in a new build-directory). - - ```shell - # Go to the 'maneage' branch and import updates. - $ git checkout maneage - $ git pull # Get recent work in Maneage - - # Read all the commit messages of the newly imported - # features/changes. In particular pay close attention to the ones - # starting with 'IMPORTANT': these may cause a crash in your - # project (changing something fundamental in Maneage). - # - # Replace the XXXXXXX..YYYYYYY with hashs mentioned close to start - # of the 'git pull' command outputs. - $ git log XXXXXXX..YYYYYYY --reverse - - # Have a look at the commits in the 'maneage' branch in relation - # with your project. - $ git log --oneline --graph --decorate --all # General view of branches. - - # Go to your 'master' branch and import all the updates into - # 'master', don't worry about the printed outputs (in particular - # the 'CONFLICT's), we'll clean them up in the next step. - $ git checkout master - $ git merge maneage - - # Ignore conflicting Maneage files that you had previously deleted - # in the customization checklist (mostly demonstration files). - $ git status # Just for a check - $ git status --porcelain | awk '/^DU/{system("git rm "$NF)}' - $ git status # Just for a check - - # If any files have conflicts, open a text editor and correct the - # conflict (placed in between '<<<<<<<', '=======' and '>>>>>>>'. - # Once all conflicts in a file are remoted, the file will be - # automatically removed from the "Unmerged paths", so run this - # command after correcting the conflicts of each file just to make - # sure things are clean. - git status - - # TIP: If you want the changes in one file to be only from a - # special branch ('maneage' or 'master', completely ignoring - # changes in the other), use this command: - # $ git checkout <BRANCH-NAME> -- <FILENAME> - - # When there are no more "Unmerged paths", you can commit the - # merge. In the commit message, Explain any conflicts that you - # fixed. - git commit - - # Do a clean build of your project (to check for "Semanic - # conflicts" (not detected as a conflict by Git, but may cause a - # crash in your project). You can backup your build directory - # before running the 'distclean' target. - # - # Any error in the build will be due to low-level changes in - # Maneage, so look closely at the commit messages in the Maneage - # branch and especially those where the title starts with - # 'IMPORTANT'. - ./project make distclean # will DELETE ALL your build-directory!! - ./project configure -e - ./project make - - # When everything is OK, before continuing with your project's - # work, don't forget to push both your 'master' branch and your - # updated 'maneage' branch to your remote server. - git push - git push origin maneage - ``` - - - *Adding Maneage to a fork of your project*: As you and your colleagues - continue your project, it will be necessary to have separate - forks/clones of it. But when you clone your own project on a - different system, or a colleague clones it to collaborate with you, - the clone won't have the `origin-maneage` remote that you started the - project with. As shown in the previous item above, you need this - remote to be able to pull recent updates from Maneage. The steps - below will setup the `origin-maneage` remote, and a local `maneage` - branch to track it, on the new clone. - - ```shell - $ git remote add origin-maneage https://git.maneage.org/project.git - $ git fetch origin-maneage - $ git checkout -b maneage --track origin-maneage/maneage - ``` - - - *Commit message*: The commit message is a very important and useful - aspect of version control. To make the commit message useful for - others (or yourself, one year later), it is good to follow a - consistent style. Maneage already has a consistent formatting - (described below), which you can also follow in your project if you - like. You can see many examples by running `git log` in the `maneage` - branch. If you intend to push commits to Maneage, for the consistency - of Maneage, it is necessary to follow these guidelines. 1) No line - should be more than 75 characters (to enable easy reading of the - message when you run `git log` on the standard 80-character - terminal). 2) The first line is the title of the commit and should - summarize it (so `git log --oneline` can be useful). The title should - also not end with a point (`.`, because its a short single sentence, - so a point is not necessary and only wastes space). 3) After the - title, leave an empty line and start the body of your message - (possibly containing many paragraphs). 4) Describe the context of - your commit (the problem it is trying to solve) as much as possible, - then go onto how you solved it. One suggestion is to start the main - body of your commit with "Until now ...", and continue describing the - problem in the first paragraph(s). Afterwards, start the next - paragraph with "With this commit ...". - - - *Project outputs*: During your research, it is possible to checkout a - specific commit and reproduce its results. However, the processing - can be time consuming. Therefore, it is useful to also keep track of - the final outputs of your project (at minimum, the paper's PDF) in - important points of history. However, keeping a snapshot of these - (most probably large volume) outputs in the main history of the - project can unreasonably bloat it. It is thus recommended to make a - separate Git repo to keep those files and keep your project's source - as small as possible. For example if your project is called - `my-exciting-project`, the name of the outputs repository can be - `my-exciting-project-output`. This enables easy sharing of the output - files with your co-authors (with necessary permissions) and not - having to bloat your email archive with extra attachments also (you - can just share the link to the online repo in your - communications). After the research is published, you can also - release the outputs repository, or you can just delete it if it is - too large or un-necessary (it was just for convenience, and fully - reproducible after all). For example Maneage's output is available - for demonstration in [a - separate](http://git.maneage.org/output-raw.git/) repository. - - - *Full Git history in one file*: When you are publishing your project - (for example to Zenodo for long term preservation), it is more - convenient to have the whole project's Git history into one file to - save with your datasets. After all, you can't be sure that your - current Git server (for example GitLab, Github, or Bitbucket) will be - active forever. While they are good for the immediate future, you - can't rely on them for archival purposes. Fortunately keeping your - whole history in one file is easy with Git using the following - commands. To learn more about it, run `git help bundle`. - - - "bundle" your project's history into one file (just don't forget to - change `my-project-git.bundle` to a descriptive name of your - project): - - ```shell - $ git bundle create my-project-git.bundle --all - ``` - - - You can easily upload `my-project-git.bundle` anywhere. Later, if - you need to un-bundle it, you can use the following command. - - ```shell - $ git clone my-project-git.bundle - ``` - - - - - - - - - - -Future improvements -=================== + + +## Modularity + +Modularity is the key to easy and clean growth of a project. So it is +always best to break up a job into as many sub-components as +reasonable. Here are some tips to stay modular. + +- *Short recipes*: if you see the recipe of a rule becoming more than a + handful of lines which involve significant processing, it is probably a + good sign that you should break up the rule into its main + components. Try to only have one major processing step per rule. + +- *Context-based (many) Makefiles*: For maximum modularity, this design + allows easy inclusion of many Makefiles: in + `reproduce/analysis/make/*.mk` for analysis steps, and + `reproduce/software/make/*.mk` for building software. So keep the rules + for closely related parts of the processing in separate Makefiles. + +- *Descriptive names*: Be very clear and descriptive with the naming of the + files and the variables because a few months after the processing, it + will be very hard to remember what each one was for. Also this helps + others (your collaborators or other people reading the project source + after it is published) to more easily understand your work and find + their way around. + +- *Naming convention*: As the project grows, following a single standard or + convention in naming the files is very useful. Try best to use multiple + word filenames for anything that is non-trivial (separating the words + with a `-`). For example if you have a Makefile for creating a catalog + and another two for processing it under models A and B, you can name + them like this: `catalog-create.mk`, `catalog-model-a.mk` and + `catalog-model-b.mk`. In this way, when listing the contents of + `reproduce/analysis/make` to see all the Makefiles, those related to the + catalog will all be close to each other and thus easily found. This also + helps in auto-completions by the shell or text editors like Emacs. + +- *Source directories*: If you need to add files in other languages for + example in shell, Python, AWK or C, keep the files in the same language + in a separate directory under `reproduce/analysis`, with the appropriate + name. + +- *Configuration files*: If your research uses special programs as part of + the processing, put all their configuration files in a devoted directory + (with the program's name) within `reproduce/software/config`. It is much + cleaner and readable (thus less buggy) to avoid mixing the configuration + files, even if there is no technical necessity. + + + +## Contents of source files + +It is good practice to follow the following recommendations on the contents +of your files, whether they are source code for a program, Makefiles, +scripts or configuration files (copyrights aren't necessary for the +latter). + +- *Copyright*: Always start a file containing programming constructs with a + copyright statement like the ones that Maneage starts with (for example + in the top level `Makefile`). + +- *Comments*: Comments are vital for readability (by yourself in two + months, or others). Describe everything you can about why you are doing + something, how you are doing it, and what you expect the result to + be. Write the comments as if it was what you would say to describe the + variable, recipe or rule to a friend sitting beside you. When writing + the project it is very tempting to just steam ahead with commands and + codes, but be patient and write comments before the rules or + recipes. This will also allow you to think more about what you should be + doing. Also, in several months when you come back to the code, you will + appreciate the effort of writing them. Just don't forget to also read + and update the comment first if you later want to make changes to the + code (variable, recipe or rule). As a general rule of thumb: first the + comments, then the code. + +- *File title*: In general, it is good practice to start all files with a + single line description of what that particular file does. If further + information about the totality of the file is necessary, add it after a + blank line. This will help a fast inspection where you don't care about + the details, but just want to remember/see what that file is (generally) + for. This information must of course be commented (its for a human), but + this is kept separate from the general recommendation on comments, + because this is a comment for the whole file, not each step within it. + + + +## Make programming + +Here are some experiences that we have come to learn over the years in +using Make and are useful/handy in research contexts. + +### Environment of each recipe + +If you need to define a special environment (or aliases, or scripts to run) +for all the recipes in your Makefiles, you can use a Bash startup file +`reproduce/software/shell/bashrc.sh`. This file is loaded before every Make +recipe is run, just like the `.bashrc` in your home directory is loaded +every time you start a new interactive, non-login terminal. See the +comments in that file for more. + +### Automatic variables + +These are wonderful and very useful Make constructs that greatly shrink the +text, while helping in read-ability, robustness (less bugs in typos for +example) and generalization. For example even when a rule only has one +target or one prerequisite, always use `$@` instead of the target's name, +`$<` instead of the first prerequisite, `$^` instead of the full list of +prerequisites and etc. You can see the full list of automatic variables +[here](https://www.gnu.org/software/make/manual/html_node/Automatic-Variables.html). If +you use GNU Make, you can also see this page on your command-line: + +```shell +$ info make "automatic variables" +``` + +### Debugging Make dependencies + +Since Make doesn't follow the common top-down paradigm, it can be a little +hard to get accustomed to why you get an error or un-expected behavior. In +such cases, run Make with the `-d` option. With this option, Make prints a +full list of exactly which prerequisites are being checked for which +targets. Looking (patiently) through this output and searching for the +faulty file/step will clearly show you any mistake you might have made in +defining the targets or prerequisites. + +### Large files + +If you are dealing with very large files (thus having multiple copies of +them for intermediate steps is not possible), one solution is the following +strategy (Also see the next item on "Fast access to temporary files"). Set +a small plain text file as the actual target and delete the large file when +it is no longer needed by the project (in the last rule that needs +it). Below is a simple demonstration of doing this. In it, we use +Gnuastro's Arithmetic program to add all pixels of the input image with 2 +and create `large1.fits`. We then subtract 2 from `large1.fits` to create +`large2.fits` and delete `large1.fits` in the same rule (when its no longer +needed). We can later do the same with `large2.fits` when it is no longer +needed and so on. + +```make +large1.fits.txt: input.fits + astarithmetic $< 2 + --output=$(subst .txt,,$@) + echo "done" > $@ +large2.fits.txt: large1.fits.txt + astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@) + rm $(subst .txt,,$<) + echo "done" > $@ +``` + +A more advanced Make +programmer will use Make's [call +function](https://www.gnu.org/software/make/manual/html_node/Call-Function.html) +to define a wrapper in `reproduce/analysis/make/initialize.mk`. This +wrapper will replace `$(subst .txt,,XXXXX)`. Therefore, it will be possible +to greatly simplify this repetitive statement and make the code even more +readable throughout the whole project. + +### Fast access to temporary files + +Most Unix-like operating systems will give you a special shared-memory +device (directory): on systems using the GNU C Library (all GNU/Linux +system), it is `/dev/shm`. The contents of this directory are actually in +your RAM, not in your persistence storage like the HDD or SSD. Reading and +writing from/to the RAM is much faster than persistent storage, so if you +have enough RAM available, it can be very beneficial for large temporary +files to be put there. You can use the `mktemp` program to give the +temporary files a randomly-set name, and use text files as targets to keep +that name (as described in the item above under "Large files") for later +deletion. For example, see the minimal working example Makefile below +(which you can actually put in a `Makefile` and run if you have an +`input.fits` in the same directory, and Gnuastro is installed). + +```make +.ONESHELL: +.SHELLFLAGS = -ec +all: mean-std.txt +shm-maneage := /dev/shm/$(shell whoami)-maneage-XXXXXXXXXX +large1.txt: input.fits + out=$$(mktemp $(shm-maneage)) + astarithmetic $< 2 + --output=$$out.fits + echo "$$out" > $@ +large2.txt: large1.txt + input=$$(cat $<) + out=$$(mktemp $(shm-maneage)) + astarithmetic $$input.fits 2 - --output=$$out.fits + rm $$input.fits $$input + echo "$$out" > $@ +mean-std.txt: large2.txt + input=$$(cat $<) + aststatistics $$input.fits --mean --std > $@ + rm $$input.fits $$input +``` + +The important point here is that the temporary name template +(`shm-maneage`) has no suffix. So you can add the suffix corresponding to +your desired format afterwards (for example `$$out.fits`, or +`$$out.txt`). But more importantly, when `mktemp` sets the random name, it +also checks if no file exists with that name and creates a file with that +exact name at that moment. So at the end of each recipe above, you'll have +two files in your `/dev/shm`, one empty file with no suffix one with a +suffix. The role of the file without a suffix is just to ensure that the +randomly set name will not be used by other calls to `mktemp` (when running +in parallel) and it should be deleted with the file containing a +suffix. This is the reason behind the `rm $$input.fits $$input` command +above: to make sure that first the file with a suffix is deleted, then the +core random file (note that when working in parallel on powerful systems, +in the time between deleting two files of a single `rm` command, many +things can happen!). When using Maneage, you can put the definition of +`shm-maneage` in `reproduce/analysis/make/initialize.mk` to be usable in +all the different Makefiles of your analysis, and you won't need the three +lines above it. **Finally, BE RESPONSIBLE:** after you are finished, be +sure to clean up any possibly remaining files (due to crashes in the +processing while you are working), otherwise your RAM may fill up very +fast. You can do it easily with a command like this on your command-line: +`rm -f /dev/shm/$(whoami)-*`. + +### Pattern rules with multiple components + +In a large pipeline, as you go from the lower-level to higher-level +targets, the higher-level targets can depend on multiple lower-level +files. However, Make's [pattern +rules](https://www.gnu.org/software/make/manual/html_node/Pattern-Rules.html) +only allow the extraction of a single component. The minimal working +example below shows how to account for such situations. + +The targets in this minimal working example are in the format of +`file-*.fits`. The low-level files only have one character instead of the +`*` (for example `file-1.fits`). The high-level targets have three +characters there (with `-` as a delimiter; for example +`file-1-a.fits`). This Makefile will ensure that `file-1-a.fits` is always +built as soon as `file-1.fits` and `file-a.fits` have been created. As +described in the comments ontop of the `$(targets)` rule, this uses GNU +Make's [secondary +expansion](https://www.gnu.org/software/make/manual/html_node/Secondary-Expansion.html). + +```make +# Low-level target file components. +numbers = 1 2 3 4 +letters = a b c d + +# Ultimate (first) target that depends on the last target in this Makefile +# to simplify the writing of the rest (in a human-friendly manner: +# redundant for Make). This is not necessray in Maneage; only to help the +# readability of this file. +all: final +.PHONY: all final + +# This allows using functions in prequisite lists as described below. +.SECONDEXPANSION: + +# Rule to build the alphabetical low-level files. +alphabets := $(foreach i,$(letters),file-$(i).fits) +$(alphabets): file-%.fits: + @echo "Making $@"; touch $@ + +# Rule to build the numeric low-level files. +numerics := $(foreach i,$(numbers),file-$(i).fits) +$(numerics): file-%.fits: + @echo "Making $@"; touch $@ + +# Rule to build the high-level target: each high-level target depends on an +# alphabetic and numeric low-level target. All functions in the +# prerequisite need '$$(...)' instead of '$(...)' to avoid expansion in +# the first parsing of the file and let it get expanded in the second +# parsing (thus necessity of '.SECONDEXPANSION' above). +targets := $(foreach i,$(numbers), \ + $(foreach j,$(letters), \ + file-$(i)-$(j).fits) ) +$(targets): file-%.fits: file-$$(word 1,$$(subst -, ,%)).fits \ + file-$$(word 2,$$(subst -, ,%)).fits + @echo "Prequisities of $@ are: $^" + +# Dependency of 'all' +final: $(targets) +``` + + + +## Inputs (software tarballs and data) + +It is critically important to document the raw inputs to your project +(software tarballs and raw input data): + +- *Keep the source tarball of dependencies*: After configuration finishes, + the `.build/software/tarballs` directory will contain all the software + tarballs that were necessary for your project. You can mirror the + contents of this directory to keep a backup of all the software tarballs + used in your project (possibly as another version controlled repository) + that is also published with your project. Note that software web-pages + are not written in stone and can suddenly go offline or not be + accessible in some conditions. This backup is thus very important. If + you intend to release your project in a place like Zenodo, you can + upload/keep all the necessary tarballs (and data) there with your + project. [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746) is one + example of how the data, Gnuastro (main software used) and all major + Gnuastro's dependencies have been uploaded with the project's + source. Just note that this is only possible for [free + software](https://www.gnu.org/philosophy/free-sw.html). + +- *Keep your input data*: The input data is also critical to the project's + reproducibility, so like the above for software, make sure you have a + backup of them, or their persistent identifiers (PIDs). + + + +## Project outputs + +During your research, it is possible to checkout a specific commit and +reproduce its results. However, the processing can be time +consuming. Therefore, it is useful to also keep track of the final outputs +of your project (at minimum, the paper's PDF) in important points of +history. However, keeping a snapshot of these (most probably large volume) +outputs in the main history of the project can unreasonably bloat it. It is +thus recommended to make a separate Git repo to keep those files and keep +your project's source as small as possible. For example if your project is +called `my-exciting-project`, the name of the outputs repository can be +`my-exciting-project-output`. This enables easy sharing of the output files +with your co-authors (with necessary permissions) and not having to bloat +your email archive with extra attachments also (you can just share the link +to the online repo in your communications). After the research is +published, you can also release the outputs repository, or you can just +delete it if it is too large or un-necessary (it was just for convenience, +and fully reproducible after all). For example Maneage's output is +available for demonstration in [a +separate](http://git.maneage.org/output-raw.git/) repository. + + + +## Git and version control + +Version control is a critical component of Maneage. Here are some tips to +help in effectively using it. + +### Committing + +Every commit is a significant point in the history of your project: when +you consider one component of the job to be complete and ready to move to +the next component. This significance is very subjective: it can be a +significant change in one part of one file, or many files, or even a +temporal criteria: a milestone is reaching and you need to change +topic. Here are some tips on good habits in committing. + +- *Regular commits*: It is important (and extremely useful) to have the + history of your project under version control. So try to make commits + regularly (after any meaningful change/step/result). + +- *Commit message*: The commit message is a very important and useful + aspect of version control. To make the commit message useful for others + (or yourself, one year later), it is good to follow a consistent + style. Maneage already has a consistent formatting (described below), + which you can also follow in your project if you like. You can see many + examples by running `git log` in the `maneage` branch. If you intend to + push commits to Maneage, for the consistency of Maneage, it is necessary + to follow these guidelines. 1) No line should be more than 75 characters + (to enable easy reading of the message when you run `git log` on the + standard 80-character terminal). 2) The first line is the title of the + commit and should summarize it (so `git log --oneline` can be + useful). The title should also not end with a point (`.`, because its a + short single sentence, so a point is not necessary and only wastes + space). 3) After the title, leave an empty line and start the body of + your message (possibly containing many paragraphs). 4) Describe the + context of your commit (the problem it is trying to solve) as much as + possible, then go onto how you solved it. One suggestion is to start the + main body of your commit with "Until now ...", and continue describing + the problem in the first paragraph(s). Afterwards, start the next + paragraph with "With this commit ...". + +### Full Git history in one file + +When you are publishing your project (for example to Zenodo for long term +preservation), it is more convenient to have the whole project's Git +history into one file to save with your datasets. After all, you can't be +sure that your current Git server (for example GitLab, Github, or +Bitbucket) will be active forever. While they are good for the immediate +future, you can't rely on them for archival purposes. Fortunately keeping +your whole history in one file is easy with Git using the following +commands. To learn more about it, run `git help bundle`. + +Run the following command to "bundle" your project's history into one file +(just don't forget to change `my-project-git.bundle` to a descriptive name +of your project): + +```shell +$ git bundle create my-project-git.bundle --all +``` + +You can easily upload `my-project-git.bundle` anywhere. Later, if you need +to un-bundle it, you can use the following command. + +```shell +$ git clone my-project-git.bundle +``` + +### File modification dates (meta data) + +While Git does an excellent job at keeping a history of the contents of +files, it makes no effort in keeping the file meta data, and in particular +the dates of files. Therefore when you checkout to a different branch, +files that are re-written by Git will have a newer date than the other +project files. However, file dates are important in the current design of +Maneage: Make checks the dates of the prerequisite files and target files +to see if the target should be re-built. + +This is relevant, for example, in the `analysis/` side of calculations when +a rule in a `reproduce/analysis/make/SOMETHING.mk` is dependent on +`reproduce/analysis/conf/SOMETHING.conf` (where `SOMETHING` is one of the +science pipeline steps that you have prepared). Switching back and forth +between git branches will update the timestamp on `SOMETHING.conf`, +incorrectly implying, according to the Make rules, that a rule in +SOMETHING.mk has to be run again. + +To address this problem, you can use the `touch` command to backdate the +timestamp of files that you want to be considered to be old. For example +with the command below: + +```shell +$ touch --date=2000-01-01 reproduce/analysis/conf/SOMETHING.conf +$ ls -l reproduce/analysis/conf/SOMETHING.conf # to check +``` + +You may want to use a date that is obviously (to you) fake, so that you +don't accidentally believe the date later on. + + + + + + + + + + +# Maneaged papers already published + +The list below shows some of the works that have already been published +with (earlier versions of) Maneage, and some that have been recently +submitted for peer review. Maneage is evolving rapidly, so some details +will differ between the different versions. The more recent papers will +tend to be the most useful as good working examples if you are just +starting. + +In the list below, by clicking on the paper's publication year, you will be +taken to the paper's indexed page on the [SciX Digital +Library](https://scixplorer.org) (successor to the [NASA +ADS](https://ui.adsabs.harvard.edu)) which contains further bibliographic +information like title, DOI and etc, in a unified format (independent of +which journal the paper is published in). + + - Eskandarlou et + al. ([2026](https://scixplorer.org/abs/2026A%26A...709A.210E), A&A + Volume 709, id.A210, 17 pp; + arXiv:[2603.22166](https://arxiv.org/abs/2603.22166)). The + project's version controlled source is on + [Gitlab](https://gitlab.com/sepideh.esk/alba), necessary software, + outputs and backup of history are available at + [zenodo.17674805](http://doi.org/10.5281/zenodo.17674805); and the + archived git history is available at + [swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99](https://archive.softwareheritage.org/swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99;origin=https://gitlab.com/Sepideh.Esk/alba;visit=swh:1:snp:adc584ff3540ea3151de6ebc8462805e8818b1f4;anchor=swh:1:rev:f9d0f9cb25c80415107c962cc53d369a650e9b82). + - Eskandarlou et + al. ([2026](https://scixplorer.org/abs/2026A%26A...705A..67E), A&A, + Volume 705, id.A67, 14 pp; + arXiv:[2510.12940](https://arxiv.org/abs/2510.12940)). The project's + version controlled source is on + [Gitlab](https://gitlab.com/sepideh.esk/psf-j-plus), necessary software, + outputs and backup of history are available at + [zenodo.17348653](http://doi.org/10.5281/zenodo.17348653); and the + archived git history is available at + [swh:1:dir:fc95ed9ad173de6fa64690e3d71ab041c630f32c](https://archive.softwareheritage.org/swh:1:dir:fc95ed9ad173de6fa64690e3d71ab041c630f32c;origin=https://gitlab.com/Sepideh.Esk/psf-j-plus;visit=swh:1:snp:31bb4550902f7902a0a65d0674106271de776d3e;anchor=swh:1:rev:4860c70d6285a60300e429889e8637e98568a915). + - Saremi et al. ([2025](https://scixplorer.org/abs/2025A%26A...701A.116S), + A&A, Volume 701, id.A116, 18 pp.; + arXiv:[2508.02780](https://arxiv.org/abs/2508.02780)). The project's + version controlled source is on + [Gitlab](https://gitlab.com/nasim-projects/pipeline), necessary + software, outputs and backup of history are available at + [zenodo.16152699](https://doi.org/10.5281/zenodo.16152699); and the + archived git history is available at + [swh:1:dir:b3657cfb6053fd976695bd63c15cb99e5095648a](https://archive.softwareheritage.org/swh:1:dir:b3657cfb6053fd976695bd63c15cb99e5095648a;origin=https://gitlab.com/nasim-projects/pipeline;visit=swh:1:snp:ab7c6f0b9999f42d77154103c1bc082fa23b325c;anchor=swh:1:rev:afeb282c01983cba2a11eb4b2f25d5a40d35c164). + - Eskandarlou & Akhlaghi + ([2024](https://scixplorer.org/abs/2024RNAAS...8..168E), RNAAS, Volume + 8, Issue 6, id.168; + arXiv:[2406.14619](https://arxiv.org/abs/2406.14619)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `polar-plot` + branch). Necessary software, outputs and backup of history are available + at [zenodo.11403643](https://doi.org/10.5281/zenodo.11403643); and the + archived git history is available at + [swh:1:dir:4e09bf85f9f87336fa55920bf67e7bcf6d58bbd5](https://archive.softwareheritage.org/swh:1:dir:4e09bf85f9f87336fa55920bf67e7bcf6d58bbd5;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:557ee1a90de465659659ecc46df0c5ce29d0bb61;anchor=swh:1:rev:375e12e52080006be6a28e10980e79ef54d13d1d). + - Infante-Sainz et + al. ([2024](https://scixplorer.org/abs/2024RNAAS...8...22I), RNAAS, + Volume 8, Issue 1, id.22; + arXiv:[2401.05303](https://arxiv.org/abs/2401.05303)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `radial-profile` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10124582](https://doi.org/10.5281/zenodo.10124582); and the + archived git history is available at + [swh:1:dir:d5029e066916cb64f0d95d20eb88294acc78b2b1](https://archive.softwareheritage.org/swh:1:dir:d5029e066916cb64f0d95d20eb88294acc78b2b1;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:b065324c2ef3b48bc26e8f30e48102a1abd2052f;anchor=swh:1:rev:61764447b16da44538e5ddbf7fb69937ba138e81). + - Infante-Sainz & Akhlaghi + ([2024](https://scixplorer.org/abs/2024RNAAS...8...10I), RNAAS, Volume + 8, Issue 1, id.10; + arXiv:[2401.03814](https://arxiv.org/abs/2401.03814)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `color-faint-gray` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10058165](https://doi.org/10.5281/zenodo.10058165); and the + archived git history is available at + [swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d](https://archive.softwareheritage.org/swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:a083ff647c571f895d1ccc9f7432fa1b9a1d03a8;anchor=swh:1:rev:ff77b619daa50b05ddd83206d979d1f8a53d040b). + - Peper, Roukema & Bolejko + ([2023](https://scixplorer.org/abs/2023MNRAS.525...91P), MNRAS, 525, 91, + DOI:10.1093/mnras/stad2246, + arXiv:[2304.00591](https://arxiv.org/abs/2304.00591)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/mpeper/lensing); the main input + dataset, a software snapshot, the software tarballs, the project outputs + and editing history are available at + [zenodo.8103985](https://zenodo.org/record/8103985); and the archived + git history is available at + [swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914](https://archive.softwareheritage.org/swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914;origin=https://codeberg.org/mpeper/lensing;visit=swh:1:snp:984413c49bb02ee0eec88c3ac01614808d57beb7;anchor=swh:1:rev:185c36f1b6263588526be3881078626869041882). + - Eskandarlou et + al. ([2023](https://scixplorer.org/abs/2023RNAAS...7..269E), RNAAS, + Volume 7, Issue 12, id.269; + arXiv:[2312.04263](https://arxiv.org/abs/2312.04263)). The project's + version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the `zeropoint` + branch). Necessary software, outputs and backup of history are available + at [zenodo.10256845](https://doi.org/10.5281/zenodo.10256845); and the + archived git history is available at + [swh:1:dir:8b2d1f63be96de3de03aa3e2bb68fa7fa52df56f](https://archive.softwareheritage.org/swh:1:dir:8b2d1f63be96de3de03aa3e2bb68fa7fa52df56f;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:e37e226bab517eef24d854467682b2fcf5d7dc32;anchor=swh:1:rev:ea682783d83707c0e1d114a5de74a100be9f545d). + - Akhlaghi ([2023](https://scixplorer.org/abs/2023RNAAS...7..211A), RNAAS), Volume 7, Issue + 10, id.211; arXiv:[2310.15006](https://arxiv.org/abs/2310.15006)). The + project's version controlled source is on + [Codeberg](https://codeberg.org/gnuastro/papers) (the + `pointing-simulate` branch). + - Borkowska & Roukema + ([2022](https://scixplorer.org/abs/2022CQGra..39u5007B), Classical and + Quantum Gravity, Volume 39, Issue 21, id.215007, 29 pp; + arXiv:[2112.14174](https://arxiv.org/abs/2112.14174)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/boud/gevcurvtest); the main input + dataset, a software snapshot, the software tarballs, the project outputs + and editing history are available at + [zenodo.5806027](https://doi.org/10.5281/zenodo.5806027); and the + archived git history is available at + [swh:1:rev:54398b720ddbac269ede30bf1e27fe27f07567f7](https://archive.softwareheritage.org/browse/revision/54398b720ddbac269ede30bf1e27fe27f07567f7). + - Peper & Roukema ([2021](https://scixplorer.org/abs/2021MNRAS.505.1223P), + MNRAS, 505, 1223; arXiv:[2010.03742](https://arxiv.org/abs/2010.03742)): + The live version of the controlled source is [at + Codeberg](https://codeberg.org/boud/elaphrocentre); the main input + dataset, a software snapshot, the software tarballs, the project outputs + and editing history are available at + [zenodo.4699702](https://zenodo.org/record/4699702); and the archived + git history is available at + [swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e](https://archive.softwareheritage.org/swh:1:rev:a029edd32d5cd41dbdac145189d9b1a08421114e). + - Roukema ([2021](https://scixplorer.org/abs/2021PeerJ...911856R), PeerJ, + Vol. 9, article id. e11856; + arXiv:[2007.11779](https://arxiv.org/abs/2007.11779)): The live version + of the controlled source is [at + Codeberg](https://codeberg.org/boud/subpoisson); the main input dataset, + a software snapshot, the software tarballs, the project outputs and + editing history are available at + [zenodo.4765705](https://zenodo.org/record/4765705); and the archived + git history is available at + [swh:1:rev:72242ca8eade9659031ea00394a30e0cc5cc1c37](https://archive.softwareheritage.org/swh:1:rev:72242ca8eade9659031ea00394a30e0cc5cc1c37). + - Akhlaghi et al. ([2021](https://scixplorer.org/abs/2021CSE....23c..82A), + CiSE, 23(3), 82; arXiv:[2006.03018](https://arxiv.org/abs/2006.03018)): + The project's version controlled source is [on + Gitlab](https://gitlab.com/makhlaghi/maneage-paper), necessary software, + outputs and backup of history are available at + [zenodo.3872248](https://doi.org/10.5281/zenodo.3872248); and the + archived git history is available at + [swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717](https://archive.softwareheritage.org/swh:1:dir:45a9e282a86145fe9babef529c8fce52ffe8d717). + - Infante-Sainz et + al. ([2020](https://scixplorer.org/abs/2020MNRAS.491.5317I), MNRAS, 491, + 5317; arXiv:[1911.01430](https://arxiv.org/abs/1911.01430)): The version + controlled project source is available [on + GitLab](https://gitlab.com/infantesainz/sdss-extended-psfs-paper) and is + also archived on Zenodo with all the necessary software tarballs: + [zenodo.3524937](https://zenodo.org/record/3524937). + - Akhlaghi ([2019](https://scixplorer.org/abs/2019arXiv190911230A), IAU + Symposium 355; + arXiv:[1909.11230](https://arxiv.org/abs/1909.11230)). The version + controlled project source is available [on + GitLab](https://gitlab.com/makhlaghi/iau-symposium-355) and is also + archived on Zenodo with all the necessary software tarballs: + [zenodo.3408481](https://doi.org/10.5281/zenodo.3408481). + +The items below were the precursors to Maneage. In other words, the work to +have reproducible results in the items below lead to what is now +Maneage. They are therefore much less complete than what Maneage is today, +but are important from a historical perspective. + - Section 7.3 of Bacon et + al. ([2017](https://scixplorer.org/abs/2017A%26A...608A...1B), A&A 608, + A1; arXiv:[1710.03002](https://arxiv.org/abs/1710.03002)): The version + controlled project source is available [on + GitLab](https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes) + and a snapshot of the project along with all the necessary input + datasets and outputs is available in + [zenodo.1164774](https://doi.org/10.5281/zenodo.1164774). + - Section 4 of Bacon et + al. ([2017](https://scixplorer.org/abs/2017A%26A...608A...1B), A&A, 608, + A1; arXiv:[1710.03002](https://arxiv.org/abs/1710.03002)): The version + controlled project is available [on + GitLab](https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry) and + a snapshot of the project along with all the necessary input datasets is + available in [zenodo.1163746](https://doi.org/10.5281/zenodo.1163746). + - Akhlaghi & Ichikawa + ([2015](https://scixplorer.org/abs/2015ApJS..220....1A), ApJS, 220, 1; + arXiv:[1505.01664](https://arxiv.org/abs/1505.01664)): The version + controlled project is available [on + GitLab](https://gitlab.com/makhlaghi/NoiseChisel-paper). This is the + very first (and much less mature!) incarnation of Maneage: the history + of Maneage started more than two years after this paper was + published. It is a very rudimentary/initial implementation, thus it is + only included here for historical reasons. However, the project source + is complete, accurate and uploaded to arXiv along with the paper. + + + + + + + + + + +# Maneage Development + +This section describes Maneage's own development workflow, not the workflow +of your Maneage-based projects (where you are free to select any workflow +model that you prefer). So it is only intended for those who would like to +contribute to the core Maneage project, not those who only develop their +own project. + +## Development workflow + +Maneage users can only use it by developing it, therefore Maneage is a very +unique software: the boundary between a user and developer is blurry by +design/philosophy. We hope that all users can contribute to the `maneage` +branch for project-agnostic bugs/features that they fix/add. In this +section, the development workflow is described: + - At any point that you find a bug or want to share a fix, anyone is + welcome to open a "Bug" or "Task" on GNU Savannah (which is the main + project management interface of Maneage). In case the submitter already + has a commit to merge, they can fork Maneage (similar to [this forking + tutorial](https://www.gnu.org/software/gnuastro/manual/html_node/Forking-tutorial.html)) + and share their commit in the Savannah post. + - The review of bugs and merge requests will happen at the earliest + possible time for the maintainer. At this point, the maintainer will + create a new development branch over the `maneage` branch in a + development repository (not the main Maneage repository) and all + separate merge requests will be rebased over that branch. Finally, all + the commits in that branch will be `squash`ed into a single commit that + will be merged over the `maneage` branch. Of course, every contributor + will be acknowledged in the squashed commit for their contribution. + - The `squash`ing into a single commit is intentionally done because the + `maneage` branch is shared between all projects that use Maneage and + we do not want to introduce complexity in their history by preserving + all the various development commits that were done before the + merge. + - After the merge, the development branch may be deleted from the + development repository: any historically relevant point that you find + when making a commit should be written as comments within the source + (to be preserved during the squash) and not in the commit message. + - Checklist for the maintainer: + - Make sure all contributors are properly acknowledged. + - In case any software was added in the 'maneage' branch or the version + of existing software was updated, upload/push the new tarballs to all + the backup repositories (in + `reproduce/software/config/servers-backup.conf`). + - The final commit amend (done to edit the final text of the commit + message) should be like this: `git commit --amend --date=now`. This + helps have a date on the commit that matches the merge (independent of + which development commit was squashed first). + +## Future improvements This is an evolving project and as time goes on, it will evolve and become more robust. Some of the most prominent issues we plan to implement in the future are listed below, please join us if you are interested. -Package management ------------------- +### Full documentation in Info + +Currently the only documentation for Maneage's development is this file! +But this format is not too convenient for a complete documentation: README +files are only meant to point readers to the proper place of the manual, +not be the whole documentation themselves! This choice was due to time +constraints. Work has already started on this in the +`[texibook](https://gitlab.com/maneage/project-dev/-/tree/texibook)` branch +that will build a professional manual in info, HTML and PDF formats using +Texinfo during the configuration phase. But this still needs to be +finished. + +### Package management It is important to have control of the environment of the project. Maneage currently builds the higher-level programs (for example GNU Bash, GNU Make, @@ -1703,46 +2205,15 @@ commonly have large overlaps in lower-level programs). -Appendix: Necessity of exact reproduction in scientific research -================================================================ - -In case [the link above](http://akhlaghi.org/reproducible-science.html) is -not accessible at the time of reading, here is a copy of the introduction -of that link, describing the necessity for a reproducible project like this -(copied on February 7th, 2018): - -The most important element of a "scientific" statement/result is the fact -that others should be able to falsify it. The Tsunami of data that has -engulfed astronomers in the last two decades, combined with faster -processors and faster internet connections has made it much more easier to -obtain a result. However, these factors have also increased the complexity -of a scientific analysis, such that it is no longer possible to describe -all the steps of an analysis in the published paper. Citing this -difficulty, many authors suffice to describing the generalities of their -analysis in their papers. - -However, It is impossible to falsify (or even study) a result if you can't -exactly reproduce it. The complexity of modern science makes it vitally -important to exactly reproduce the final result. Because even a small -deviation can be due to many different parts of an analysis. Nature is -already a black box which we are trying so hard to comprehend. Not letting -other scientists see the exact steps taken to reach a result, or not -allowing them to modify it (do experiments on it) is a self-imposed black -box, which only exacerbates our ignorance. - -Other scientists should be able to reproduce, check and experiment on the -results of anything that is to carry the "scientific" label. Any result -that is not reproducible (due to incomplete information by the author) is -not scientific: the readers have to have faith in the subjective experience -of the authors in the very important choice of configuration values and -order of operations: this is contrary to the scientific spirit. +# Copyright information +Contributors:\ +Copyright (C) 2020-2026 Raul Infante-Sainz <infantesainz@gmail.com>\ +Copyright (C) 2021-2026 Boud Roukema <boud@astro.uni.torun.pl> -Copyright information ---------------------- This file is part of Maneage (https://maneage.org). This file is free software: you can redistribute it and/or modify it |