diff options
| author | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2026-07-20 20:20:56 +0200 |
|---|---|---|
| committer | Mohammad Akhlaghi <mohammad@akhlaghi.org> | 2026-07-20 22:07:00 +0200 |
| commit | ab5e0aa9fa8a6b94b1306fa120736b6fbb1a2f70 (patch) | |
| tree | 34a36afe78cdc244d22b6ad1f0037dd0c0138db0 /README-hacking.md | |
| parent | 4cfa34b1e101adcd050a476307b7680db8afcd8e (diff) | |
Summary: this commit only affects the analysis of your project in case you
used the 'tex-publish-dir' or 'data-publish-dir' directories. They need to
be renamed to 'figdir' and 'drdir' respectively.
Until now, the directories containing the to-be-published data were
described deep in the middle of 'initialize.mk' (away from the other shared
directories), they also had hard-to-use (long) names. Furthermore,
'README-hacking.md' that is the main documentation of Maneage had grown
organically, such that the checklists were scattered across the file and
some things were repeated or not classified clearly. Finally, some
portability issues were reported by Stergios Amarantidis and Diana Korotun.
With this commit, the to-be-published directories have been renamed to the
more simple names of 'figdir' and 'drdir' respectively and their definition
in 'initialize.mk' has come right under the rest of the top-level
directories (to be easily found). Furthermore, the 'README-hacking.md' has
been fully restructured to be easier to navigate and follow for a new
reader. Finally, the portability issues mentioned above have been
addressed:
- Within the '--help' output of './project', the '--keep-going' option was
listed under "Configure and Make options", while it is only relevant as
a Make option. It was therefore moved under Make options.
- We had not explicitly set the locale of Maneage; causing a crash on one
of the newly tested computers (a macOS with a non-C locale) during the
execution of 'prep-source.sh'. With this commit, all the top-level
Makefiles and scripts of Maneage set 'LC_ALL' to 'C' to ensure the same
locale on any system.
- The 'download-multi-try.sh' script would crash when building basic
software in the following scenario: the downloader was still from the
host, but one of its linked libraries had already been installed in
Maneage and conflicted with the host. A step has been added to catch
such cases and remove the Maneage'd library when this was the problem.
- On macOS, we discovered that 'pkg-config' and 'wget' need a Python
installation, so the necessary conditions have been added.
- The 'apptainer.sh' script did not allow passing the '--debug' or
'--host-cc' options to the execution of './project' within the
container.
- Within 'configure.sh', we wrote the absolute path of the downloader to
use in 'LOCAL.conf'. However, we install both downloaders and it is
safer to use Maneage's own downloader when it has been installed. So the
downloader name in 'LOCAL.conf' now only has the name (without its
absolute path).
Diffstat (limited to 'README-hacking.md')
| -rw-r--r-- | README-hacking.md | 2277 |
1 files changed, 1211 insertions, 1066 deletions
diff --git a/README-hacking.md b/README-hacking.md index dc6e623..929b14c 100644 --- a/README-hacking.md +++ b/README-hacking.md @@ -1,662 +1,51 @@ -Maneage: managing data lineage -============================== +# Maneage development Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2020-2026 Raul Infante-Sainz <infantesainz@gmail.com>\ 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. - - - - - -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. +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)). -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: +[[_TOC_]] - 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. 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. -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. +# Maneage checklists -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. +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. - - - - - - - -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. - -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. - - - - - -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. - - - - - -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 @@ -678,7 +67,7 @@ First custom commit 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 precusor of Maneage was for [Akhlaghi & Ichikawa + 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 @@ -687,7 +76,7 @@ First custom commit 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 branchs). In the commands + 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). @@ -716,8 +105,8 @@ First custom commit $ git branch -D journal ``` - 3. **Prepare to build project**: The `./project configure` command of the - next step will build the different software packages within the + 3. **Prepare for configuration**: The `./harvester 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 @@ -733,23 +122,23 @@ First custom commit ```shell # On another terminal (go to top project source directory, last command above) - $ ./project --check-config + $ ./harvester --check-config ``` 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, + is any problem in the `./harvester configure` or `./harvester make` steps, please contact us to fix the problem before continuing. Since the building of dependencies in configuration can take long, you can take the next few steps (editing the files) while its working (they don't - affect the configuration). After `./project make` is finished, open + affect the configuration). After `./harvester make` is finished, open `paper.pdf`. If it looks fine, you are ready to start customizing the Maneage for your project. But before that, clean all the extra Maneage outputs with `make clean` as shown below. ```shell - $ ./project configure # Build the project's software environment (can take an hour or so). - $ ./project make # Do the processing and build paper (just a simple demo). + $ ./harvester configure # Build the project's software environment (can take an hour or so). + $ ./harvester make # Do the processing and build paper (just a simple demo). # Open 'paper.pdf' and see if everything is ok. ``` @@ -788,7 +177,7 @@ First custom commit to `\begin{document}`. Just note that some core project metadata like 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 + in there. After you are done, run the `./harvester make` command again to see your changes in the final PDF and make sure that your changes don't cause a crash in LaTeX. Of course, if you use a different LaTeX package/style for managing the title and authors (in particular a @@ -844,8 +233,8 @@ First custom commit introduced any errors. ```shell - $ ./project make clean - $ ./project make + $ ./harvester make clean + $ ./harvester make ``` 8. **Ignore changes in some Maneage files**: One of the main advantages of @@ -927,7 +316,7 @@ First custom commit ```shell $ git status # See which files you have changed. $ git diff # Check the lines you have added/changed. - $ ./project make # Make sure everything builds successfully. + $ ./harvester make # Make sure everything builds successfully. $ git add -u # Put all tracked changes in staging area. $ git status # Make sure everything is fine. $ git diff --cached # Confirm all the changes that will be committed. @@ -953,8 +342,12 @@ 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 @@ -1036,16 +429,16 @@ 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 - preparation process completes once, future runs of `./project make` + (when `.build/software/preparation-data.mk` doesn't exist). After the + preparation process completes once, future runs of `./harvester make` will not do the preparation process anymore (will not call `top-prepare.mk`). They will only call `top-make.mk` for the analysis. To manually invoke the preparation process after the first - attempt, the `./project make` script should be run with the + attempt, the `./harvester make` script should be run with the `--prepare-redo` option, or you can delete the special file above. ```shell - $ ./project make --prepare-redo + $ ./harvester make --prepare-redo ``` - **Pre-publication**: add notice on reproducibility**: Add a notice @@ -1057,15 +450,7 @@ Other basic customizations - - - - - - - -Upgrading the Maneage branch of your project -============================================ +## 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 @@ -1103,7 +488,7 @@ $ git pull # Get recent work in Maneage 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 (prevoius step). +start of the `git pull` command outputs (previous step). ```shell $ git log XXXXXXX..YYYYYYY --reverse @@ -1129,7 +514,7 @@ $ git status # Just for a check 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 "Unmerged paths" +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 @@ -1149,9 +534,9 @@ 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 +$ ./harvester make distclean # will DELETE ALL your build-directory!! +$ ./harvester configure -e +$ ./harvester make ``` 6. Once your final product is created at the end of the previous step and @@ -1176,13 +561,30 @@ $ 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). + +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 -===================== + +## 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 @@ -1257,7 +659,7 @@ future. 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 @@ -1268,7 +670,7 @@ 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 @@ -1318,20 +720,26 @@ future. 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:2006.03018](https://arxiv.org/pdf/2006.03018.pdf), it points to - [the data](https://zenodo.org/record/3872248/files/tools-per-year.txt) - that was used to create that figure's left-side 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. + [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 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` @@ -1376,22 +784,22 @@ future. into Git or depended on in the build (it happens!). Ideally, it would be good to try it on a different computer. - - **Confirm if `./project make dist` works**: The special target `dist` + - **Confirm if `./harvester make dist` works**: The special target `dist` tells the project to build a tarball that is ready to compile the LaTeX PDF without having to do the analysis and build software. This is very 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 `./harvester` + 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 `./harvester` (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 @@ -1406,7 +814,7 @@ 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). @@ -1428,7 +836,7 @@ 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 `./project + be buildable. You can generate this tarball easily with `./harvester make dist-software`. * All the figure (and other) output datasets of the project. Don't @@ -1445,7 +853,7 @@ future. 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 (formated + - *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 @@ -1541,8 +949,513 @@ future. -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 `./harvester +make` command). + +```shell +$ ./harvester 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 Harvester software +environment (which you can access through `./harvester 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 `./harvester 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, `./harvester 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 `$(BDIR)`) to host all the +intermediate files (you defined it during `./harvester configure`). This +directory doesn't need to be version controlled or even synchronized, or +backed-up in other servers: its contents are all products, and can be +easily re-created any time. As you define targets for your new rules, it is +thus important to place them all under sub-directories of `$(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 `./harvester configure`) and `reproduce/analysis/config/*.conf` +(for the high-level analysis, when you run `./harvester 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 `./harvester configure` and +`./harvester 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 +`./harvester configure`). They are defined in the configuration-Makefile +`reproduce/software/config/LOCAL.conf` which was also built by `./harvester +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, `./harvester 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 @@ -1550,330 +1463,592 @@ 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). - - - *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 - ``` - - - - - -Maneage 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 very 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: +## 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)-*`. + + + +## 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 @@ -1882,40 +2057,41 @@ this section, the development workflow is described: 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. - - 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 -=================== +## 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, @@ -1962,46 +2138,15 @@ 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 |