#maneage — Public Fediverse posts

@civodul #Maneage is still under the radar :P.

https://matrix.to/#/#maneage_community:matrix.org

#Reproducibility in numerical #GalaxyFormation with #Maneage [1] - ongoing lab course [2]. A 5-yr old reproducible paper (Roukema+Peper2021) [3] was not as trivially reproducible as hoped, but now seems OK in 2026 with commit 024d1f21 [4] maneage #AstroRelatedPython updates [5].

@cosmology @makhlaghi

[1] https://maneage.org

[2] https://cosmo.torun.pl/Cosmo/GalaxyFormationCourse

[3] https://ui.adsabs.harvard.edu/abs/2021MNRAS.505.1223P = https://arxiv.org/abs/2010.03742 = https://zenodo.org/records/4699702

[4] https://codeberg.org/boud/elaphrocentre/commit/17c7d9033abda74fe5e8bf029119565b8a0be2ce

[5] https://savannah.nongnu.org/task/index.php?16740

The #Maneage #reproducibility system for scientific research papers that starts from a minimal POSIX-like host OS does not yet build [1] the #GNUCLibrary = #GLibC . We have a draft implementation building glibc *after* #GCC [2]; and an alternative proposal arguing that building glibc *first* and gcc second would be more long-term sustainable [[1] comment18].

Should GLibC be built first? Why (or why not)?

[1] https://savannah.nongnu.org/task/?15390
[2] https://gitlab.com/maneage/project-dev/-/blob/glibc/reproduce/software/make/core-gnu.mk#L718

Is a peer-reviewed #Maneage paper [1] (software + full results) reproducible from scratch?

Same author+machine; OS Debian stable updated 2021...2025.

Reproduction to final pdf by merge to current maneage 'software/' +minor hacks +disable a few verifications [2].

Result: final pdf has small but scientifically negligible diffs [3]; (due to python/numpy int or float changes?).

#Reproducibility

[1] https://peerj.com/articles/11856
[2] https://codeberg.org/boud/subpoisson/src/branch/202503_reproduce_merge_maneage commit f554c7e9
[3] https://codeberg.org/boud/subpoisson/commit/f554c7e9d5fc224d01b9db1126427afe7fb37784

@leibnizopenscience

The paper seems to have missed a powerful workflow language: #Make [1], with #GNUMake [2] being the canonical example. It's stable and nearly half a century old. Learn and use it now and your scientific grandchildren will be able to reproduce your workflow in 2075 [3]. #Maneage [3][4] uses Make for *both* reproducible software + reproducible workflows.

[1] https://en.wikipedia.org/wiki/Make_%28software%29

[2] https://gnu.org/software/make

[3] https://maneage.org

[4] https://doi.org/10.1109/MCSE.2021.3072860

An official PhD course in #ReproducibleResearchPapers will start next week [1]. Unofficial participation is welcome in the #ManeageCommunity room [2] (curated homeservers [3]), where much of the practical sessions will take place (days/times TBD). The focus is on #ReproducibleAstronomy, but #Maneage is (in principle) usable in any field of science.

@academicchatter #OpenScience #Reproducibility #Astronomy

[1] https://usosweb.umk.pl/kontroler.php?_action=katalog2%2Fprzedmioty%2FpokazPrzedmiot&kod=7404-REPASTR&lang=en

[2] https://matrix.to/#/#maneage_community:matrix.org

[3] https://servers.joinmatrix.org

@Pol

FOSS is criterion 8 of the eight #Maneage criteria for long-term archivable reproducibility [1][2].

Proprietary software is not reproducible because it "typically cannot be distributed, inspected, or modified by others. [It is], thus, reliant on a single supplier (even without payments) and prone to proprietary obsolescence. [f]"

@zimoun

[1] https://maneage.org

[2] https://doi.org/10.1109/MCSE.2021.3072860 = https://arxiv.org/abs/2006.03018 = https://zenodo.org/records/6533902

[f] https://www.gnu.org/proprietary/proprietary-obsolescence.html

Can #cosmology research papers satisfy all 8 #Maneage reproducibility criteria?

At least 3 cosmology papers have been published using the #Maneage shell/make template.

All welcome in my online+f2f seminar (BBB) [1] tomorrow (CET) at 10:15 UTC = 11:15 CET Monday 11 March 2024.

* pdf [2]
* Matrix [3]

#OpenScience #Reproducibility
@cosmology

[1] https://astro.umk.pl/en/institute/general-seminar - https://vc.umk.pl/b/mar-byg-8yu-z15

[2] https://cosmo.torun.pl/~boud/Roukema20240311IANCU.pdf

[3] https://matrix.to/#/#maneage_community:matrix.org

@ethanwhite @tpoisot

In #Maneage [1], level 4+ is different:

* in analysis/ we use 'make' for the higher-level workflow, encouraging bash scripts for details;

* in software/ we use 'make' to build all the software with sha512sum checks on the downloads, starting from a minimal unix-like system;

* the makefiles initialize.mk and paper.mk are the workflow for the paper

Fully reproduce:
./project configure
./project make

Example: [2]

[1] https://maneage.org
[2] https://zenodo.org/record/7792910

@civodul @khinsen

We use #CosmicVoids in [1][2], which in N-body sims are traced by low num-densities of particles => high noise. Full #Maneage controls + fixed seed rng's. We still have intramachine + (higher) intermachine randomness. Statistical upper limits to results OK. But still untraced sources of randomness.

Any clues for remaining randomness [2]?

#Reproducibility #ArXiv_2304_00591 #OpenScience

[1] Frozen record: https://zenodo.org/record/7792910

[2] Live git: https://codeberg.org/mpeper/lensing

#CosmicVoids should be detectable via their #GravitationalLensing effects.
Check this starting with a floppy-disk sized source snapshot [1].
#Reproducibility is via the #Maneage template of shell+make files.
Full research paper: [2][3][4][5]

[1] https://zenodo.org/record/7792910/files/lensing-e4f7af0-snapshot.tar.gz

[2] Preprint: https://arxiv.org/abs/2304.00591 #ArXiv_2304_00591

[3] Frozen record: https://zenodo.org/record/7792910

[4] Live git: https://codeberg.org/mpeper/lensing

[5] SWH: https://archive.softwareheritage.org/swh:1:rev:41507a706e16f04075c0c35853ddc226d3c72df5%3borigin=https://codeberg.org/mpeper/lensing

#Cosmology #OpenScience

@Eldeberen @sebsauvage

Dans le cadre de la #reproducibility des projets de recherche à la #maneage, voilà où nous sommes pour installer un .tar.gz d'un paquet python après vérification du checksum - en gros c'est 'bdist_wheel' + 'installer' :

python setup.py bdist_wheel
python -m installer dist/*.whl

Discussion et commits ici :
* https://savannah.nongnu.org/task/?16268

#Maneage talk for tomorrow morning 10:00 UTC+2 Fri 16 Sep 2022 at the Ten Years of Guix meeting [1], in principle live-streamed [2]:

https://cosmo.torun.pl/~boud/Roukema20220916TYG.pdf

[1] https://10years.guix.gnu.org/program

[2] https://10years.guix.gnu.org/live

#OpenScience
#Reproducibility
@civodul

On Friday, we'll have talks on using #Guix for research, but also on other people & tools sharing common goals: #Maneage, #Nix, #SoftwareHeritage, #OCaml #bootstrapping, #bioinformatics, and more.

Cosmology research paper reproducible from plain text source on a #Mobian #Pinephone using the #Maneage template/git tree:

* preprint: https://arXiv.org/abs/2112.14174

* full source + pdf: https://zenodo.org/record/5806028

* live git: https://codeberg.org/boud/gevcurvtest

* archived git: https://archive.softwareheritage.org/swh:1:rev:54398b720ddbac269ede30bf1e27fe27f07567f7

#Reproducibility on pinephone (or other): download sources, compile, non-root install, run simulations, analyse results, verify checksums, produce final pdf.

Please post bug reports at #codeberg !

@civodul @mobian @PINE64

Science #reproducibility challenge: does your project fully reproduce on a Unix-like phone?

A science project that branches off #Maneage commit 5a6e6e6 fully reproduced on my #Mobian #arm64 #pinephone: downloading source, configuring/compiling, running cosmology simulations, analysing+plotting results, producing a pdf (nearly) ready for peer review. :))

https://savannah.nongnu.org/bugs/?61026 - patches upstreamed to #Maneage.

PS: sms/phone/camera work fine too :P

#OpenScience

#TLDRBHTWL (too long, didn't read, but happy to watch and listen)?
Good overviews of #Maneage by Mohammad Akhlaghi :

20 minute presentation June 2020 - https://peertube.stream/videos/watch/f8b1b565-0e8d-4279-b7c5-f20e51e1d8da

80 minute longer presentation , including questions, March 2021 - https://peertube.stream/videos/watch/e7fdf27b-61b8-40cd-8306-482d79e4d6c5

#PeerTube #Reproducibility #OpenScience

Here's a Nature Astronomy News & Views description of why our #Reproducibility criteria for longevity are "rigorous" and "onerous", by #MichelleKuttel. There's a nice description of #Maneage, with a warning that Maneage does not seem to cater to Windows users (oh dear!), and that "bells and whistles" for the #TyrannyOfConvenience generation are lacking.

Privacy disclaimer: https://rdcu.be/cmYVx gives the subscription-only pdf but requires something like chromium with absolutely no protection!

Apparently #Reproducibility is very popular at #CiSE (Computing in Science and Engineering). The #IEEE host server for CiSE claims [1] that our #Maneage paper, formally published a few days ago (Akhlaghi+2021, CiSE, 23, 82 [2]), is currently CiSE's sixth most popular article!

[1] https://ieeexplore.ieee.org/xpl/topAccessedArticles.jsp?punumber=5992
(archives: https://web.archive.org/web/20210620130655if_/https://ieeexplore.ieee.org/xpl/topAccessedArticles.jsp?punumber=5992 https://archive.today/c0olT)

[2] https://zenodo.org/record/4913277
https://arxiv.org/abs/2006.03018
https://archive.softwareheritage.org/swh:1:rev:1cfb83e01b9ab6375727da5afd89bb3e744b9894%3Borigin=http://git.maneage.org/paper-concept.git

#OpenScience

@VickyRampin @remram44

Mohammad (Akhlaghi, the real main author, not just alphabetically favoured) accepted my changes based on your comments on ReproZip, with minor adjustments:

http://git.maneage.org/paper-concept.git/commit/?id=f88b104f6ed0f

https://upload.disroot.org/r/PaJyxAQD#MTpx0hT9hFx0qqJ6gF90NNgWen4FUPvO97O7kvwWuqs

You're acknowledged on p7; the extended ReproZip section is App B.T on p 24.

I'm not sure you'll be completely happy, but I did circulate the draft on my fediverse account a year ago... #Maneage (2020-06-05, 2020-09-24, 2020-11-27)

@VickyRampin

Our #Maneage paper in CiSE (https://oadoi.org/10.1109/MCSE.2021.3072860) on criteria for reproducible scientific papers states in section T of Appendix B what ReproZip is and why it doesn't satisfy our criteria (sorry!). In Appendix A.D, there's a paragraph on git #ScholarlyEphemera. See https://codeberg.org/maneage/paper-concept (currently the ephemera paragraph is in branch 'appA_archiving'). [Not yet updated: https://arxiv.org/abs/2006.03018 https://doi.org/10.5281/zenodo.4291207 ]

#OpenScience #reproducibility

@civodul

Que pensent les organisateurs d'une éventuelle présentation de #Maneage le mardi entre 11h30 et 12h00 ? [1] On déplacerait alors la table ronde un peu. L'article de base, ArXiv:2006.03018, vient d'être accepté, et deux articles scientifiques sous Maneage, ArXiv:2007.11779 et ArXiv:2010.03742, ont passé la prèmiere phase du peer review. ArXiv:2007.11779 a déjà eu presque deux mille téléchargements (mille vues) sur Zenodo : https://zenodo.org/record/4432080 .

[1] https://maneage.org

@civodul

Reproducibility without the legal right to develop a scientific project further wastes time and threatens copyright attacks against similar projects.

The 8 #Maneage criteria [1] are more favourable for community development:
* completeness (no non-POSIX dep., no root, network optional, plain text);
* modular design;
* minimal complexity;
* scalability;
* verifiable inputs and outputs;
* version control;
* linking analysis with narrative;
* free software.

[1] https://doi.org/10.5281/zenodo.3911395

#OpenScience #Cosmology #Reproducibility @civodul

Make your own #galaxies starting from a POSIX system, and check our results with our #Maneage pipeline:

"The role of the elaphrocentre in low surface brightness galaxy formation"

* #ArXiv preprint: https://arxiv.org/abs/2010.03742
* #Zenodo: https://zenodo.org/record/4062461
* live git #codeberg: https://codeberg.org/boud/elaphrocentre
* archived git #swh: https://archive.softwareheritage.org/swh:1:dir:c4770e81288f340083dd8aa9fe017103c4eaf476

Default resources for 128^3 particles, levelmax=12, 4 cores: 8 hours, 14.8 Gb RAM, 162 Gb disk.

@fribbledom This is for the #Maneage #reproducibility system for science research papers - https://maneage.org https://arxiv.org/abs/2006.03018 - in case you or anyone wants to know the relevance. :)