TechHub

0 posts0 participants0 posts today

BoudThe <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> <a href="https://framapiaf.org/tags/reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#reproducibility</a> system for scientific research papers that starts from a minimal POSIX-like host OS does not yet build [1] the <a href="https://framapiaf.org/tags/GNUCLibrary" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GNUCLibrary</a> = <a href="https://framapiaf.org/tags/GLibC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GLibC</a> . We have a draft implementation building glibc *after* <a href="https://framapiaf.org/tags/GCC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GCC</a> [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] <a href="https://savannah.nongnu.org/task/?15390" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://savannah.nongnu.org/task/?15390</a> [2] <a href="https://gitlab.com/maneage/project-dev/-/blob/glibc/reproduce/software/make/core-gnu.mk#L718" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://gitlab.com/maneage/project-dev/-/blob/glibc/reproduce/software/make/core-gnu.mk#L718</a>

BoudIs a peer-reviewed <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> 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?). <a href="https://framapiaf.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Reproducibility</a>[1] <a href="https://peerj.com/articles/11856" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://peerj.com/articles/11856</a> [2] <a href="https://codeberg.org/boud/subpoisson/src/branch/202503_reproduce_merge_maneage" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/boud/subpoisson/src/branch/202503_reproduce_merge_maneage</a> commit f554c7e9 [3] <a href="https://codeberg.org/boud/subpoisson/commit/f554c7e9d5fc224d01b9db1126427afe7fb37784" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/boud/subpoisson/commit/f554c7e9d5fc224d01b9db1126427afe7fb37784</a>

Boud<a href="https://mastodon.social/@leibnizopenscience" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@leibnizopenscience</a> The paper seems to have missed a powerful workflow language: <a href="https://framapiaf.org/tags/Make" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Make</a> [1], with <a href="https://framapiaf.org/tags/GNUMake" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GNUMake</a> [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]. <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> [3][4] uses Make for *both* reproducible software + reproducible workflows.[1] <a href="https://en.wikipedia.org/wiki/Make_%28software%29" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://en.wikipedia.org/wiki/Make_%28software%29</a>[2] <a href="https://gnu.org/software/make" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://gnu.org/software/make</a>[3] <a href="https://maneage.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://maneage.org</a>[4] <a href="https://doi.org/10.1109/MCSE.2021.3072860" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1109/MCSE.2021.3072860</a>

BoudAn official PhD course in <a href="https://framapiaf.org/tags/ReproducibleResearchPapers" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleResearchPapers</a> will start next week [1]. Unofficial participation is welcome in the <a href="https://framapiaf.org/tags/ManeageCommunity" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ManeageCommunity</a> room [2] (curated homeservers [3]), where much of the practical sessions will take place (days/times TBD). The focus is on <a href="https://framapiaf.org/tags/ReproducibleAstronomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ReproducibleAstronomy</a>, but <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> is (in principle) usable in any field of science.<a href="https://a.gup.pe/u/academicchatter" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@academicchatter</a> <a href="https://framapiaf.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> <a href="https://framapiaf.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Reproducibility</a> <a href="https://framapiaf.org/tags/Astronomy" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Astronomy</a>[1] <a href="https://usosweb.umk.pl/kontroler.php?_action=katalog2%2Fprzedmioty%2FpokazPrzedmiot&kod=7404-REPASTR&lang=en" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://usosweb.umk.pl/kontroler.php?_action=katalog2%2Fprzedmioty%2FpokazPrzedmiot&kod=7404-REPASTR&lang=en</a>[2] <a href="https://matrix.to/#/#maneage_community:matrix.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://matrix.to/#/#maneage_community:matrix.org</a>[3] <a href="https://servers.joinmatrix.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://servers.joinmatrix.org</a>

Boud<a href="https://mathstodon.xyz/@Pol" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@Pol</a> FOSS is criterion 8 of the eight <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> 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]"<a href="https://social.sciences.re/@zimoun" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@zimoun</a>[1] <a href="https://maneage.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://maneage.org</a>[2] <a href="https://doi.org/10.1109/MCSE.2021.3072860" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1109/MCSE.2021.3072860</a> = <a href="https://arxiv.org/abs/2006.03018" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://arxiv.org/abs/2006.03018</a> = <a href="https://zenodo.org/records/6533902" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://zenodo.org/records/6533902</a>[f] <a href="https://www.gnu.org/proprietary/proprietary-obsolescence.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.gnu.org/proprietary/proprietary-obsolescence.html</a>

BoudCan <a href="https://framapiaf.org/tags/cosmology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cosmology</a> research papers satisfy all 8 <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> reproducibility criteria?At least 3 cosmology papers have been published using the <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> 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]<a href="https://framapiaf.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a> <a href="https://framapiaf.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Reproducibility</a> <a href="https://a.gup.pe/u/cosmology" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@cosmology</a> [1] <a href="https://astro.umk.pl/en/institute/general-seminar" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://astro.umk.pl/en/institute/general-seminar</a> - <a href="https://vc.umk.pl/b/mar-byg-8yu-z15" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://vc.umk.pl/b/mar-byg-8yu-z15</a>[2] <a href="https://cosmo.torun.pl/~boud/Roukema20240311IANCU.pdf" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://cosmo.torun.pl/~boud/Roukema20240311IANCU.pdf</a>[3] <a href="https://matrix.to/#/#maneage_community:matrix.org" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://matrix.to/#/#maneage_community:matrix.org</a>

Boud<a href="https://hachyderm.io/@ethanwhite" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@ethanwhite</a> <a href="https://ecoevo.social/@tpoisot" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@tpoisot</a> In <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> [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 paperFully reproduce: ./project configure ./project makeExample: [2][1] <a href="https://maneage.org" rel="nofollow noopener noreferrer" target="_blank">https://maneage.org</a> [2] <a href="https://zenodo.org/record/7792910" rel="nofollow noopener noreferrer" target="_blank">https://zenodo.org/record/7792910</a>

Boud<a href="https://toot.aquilenet.fr/@civodul" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@civodul</a> <a href="https://scholar.social/@khinsen" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@khinsen</a> We use <a href="https://framapiaf.org/tags/CosmicVoids" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CosmicVoids</a> in [1][2], which in N-body sims are traced by low num-densities of particles => high noise. Full <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> 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]?<a href="https://framapiaf.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Reproducibility</a> <a href="https://framapiaf.org/tags/ArXiv_2304_00591" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ArXiv_2304_00591</a> <a href="https://framapiaf.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>[1] Frozen record: <a href="https://zenodo.org/record/7792910" rel="nofollow noopener noreferrer" target="_blank">https://zenodo.org/record/7792910</a>[2] Live git: <a href="https://codeberg.org/mpeper/lensing" rel="nofollow noopener noreferrer" target="_blank">https://codeberg.org/mpeper/lensing</a>

Boud<a href="https://framapiaf.org/tags/CosmicVoids" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CosmicVoids</a> should be detectable via their <a href="https://framapiaf.org/tags/GravitationalLensing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GravitationalLensing</a> effects. Check this starting with a floppy-disk sized source snapshot [1]. <a href="https://framapiaf.org/tags/Reproducibility" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Reproducibility</a> is via the <a href="https://framapiaf.org/tags/Maneage" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Maneage</a> template of shell+make files. Full research paper: [2][3][4][5][1] <a href="https://zenodo.org/record/7792910/files/lensing-e4f7af0-snapshot.tar.gz" rel="nofollow noopener noreferrer" target="_blank">https://zenodo.org/record/7792910/files/lensing-e4f7af0-snapshot.tar.gz</a>[2] Preprint: <a href="https://arxiv.org/abs/2304.00591" rel="nofollow noopener noreferrer" target="_blank">https://arxiv.org/abs/2304.00591</a> <a href="https://framapiaf.org/tags/ArXiv_2304_00591" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ArXiv_2304_00591</a>[3] Frozen record: <a href="https://zenodo.org/record/7792910" rel="nofollow noopener noreferrer" target="_blank">https://zenodo.org/record/7792910</a>[4] Live git: <a href="https://codeberg.org/mpeper/lensing" rel="nofollow noopener noreferrer" target="_blank">https://codeberg.org/mpeper/lensing</a>[5] SWH: <a href="https://archive.softwareheritage.org/swh:1:rev:41507a706e16f04075c0c35853ddc226d3c72df5%3borigin=https://codeberg.org/mpeper/lensing" rel="nofollow noopener noreferrer" target="_blank">https://archive.softwareheritage.org/swh:1:rev:41507a706e16f04075c0c35853ddc226d3c72df5%3borigin=https://codeberg.org/mpeper/lensing</a><a href="https://framapiaf.org/tags/Cosmology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Cosmology</a> <a href="https://framapiaf.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OpenScience</a>

Recent searches

Search options

Administered by:

Server stats:

#maneage