[CODE] NNPDF/nnpdf: 4.1.0

While not attached to a PDF release, this is a major release of the framework as many things have changed in the backend and legacy code has been removed. What follows is a (non-exhaustive) list of breaking changes and most important differences. This tag allow us to branch off a stable 4.0.x branch where bugs might be back-ported and the 4.1.0 series which will not attempt to be completely backwards compatible with 4.0 (although compatibility at the level of runcards will be attempted). Library changes Only pineappl >= 1 allowed Only eko >= 0.15 allowed (and ekos constructed with eko >= 0.14) parallel_models=true is now the default when running more than one replica at once Diagonal covmat #2301 now fully implemented and will eventually be made default ekos are now downloaded independently by vp-get eko to its own folder Breaking changes All dataset names must follow the new naming conventions, old naming is no longer allowed. Older theories have been removed, except for those used for PDF releases. separate_multiplicative defaults to False resample_pseudodata defaults to False (negative pseudodata no longer resampled by default) Pseudodata is now generated using the t0 PDF by default What's Changed Update docs, citations by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2296 Positivity fktables at Q2 = 10 by @comane in https://github.com/NNPDF/nnpdf/pull/2285 Merge all pytest workflows by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2298 Add faketheoryid by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2297 Prepare a coverage report in the CI by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2299 some things used in alphas studies by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2302 Define theory settings for 4.1 by @felixhekhorn in https://github.com/NNPDF/nnpdf/pull/2295 Remove all old theories by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2304 C-factors in the API extension by @achiefa in https://github.com/NNPDF/nnpdf/pull/2307 Fix rapidity in SIHP-pp by @Radonirinaunimi in https://github.com/NNPDF/nnpdf/pull/2310 Hotfix for macos 15.4 , rsync -> openrsync by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2311 Miscellaneous improvements to docs and tests by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2305 Modify how losses are computed in a multi-replicas hyperopt by @Radonirinaunimi in https://github.com/NNPDF/nnpdf/pull/2145 Introduce frag scale to theory card by @t7phy in https://github.com/NNPDF/nnpdf/pull/2308 True Positive and Negative rates in multiclosure weighted fits by @comane in https://github.com/NNPDF/nnpdf/pull/2258 reactivate use_t0_sampling by @comane in https://github.com/NNPDF/nnpdf/pull/2300 Modify the theory metadata for ATLAS_Z0J_8TEV_PT-M by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2316 Use eko v0.15 by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2181 Make parallel_models=true the default by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2313 Data update 250521 by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2321 Add an option to drop filter rules for a given dataset by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2309 Modified label in theory covariance matrix by @enocera in https://github.com/NNPDF/nnpdf/pull/2324 update scalevariationtheoryids for alphas fits by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2327 Remove accidental 's' from commondata by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2329 loop over replica_ folders rather than replica numbers starting from 0 by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2328 Update PineAPPL version to v1 by @Radonirinaunimi in https://github.com/NNPDF/nnpdf/pull/2217 Diagonal covmat by @jacoterh in https://github.com/NNPDF/nnpdf/pull/2301 Evolution of hessian sets and refactor of evolven3fit by @tgiani in https://github.com/NNPDF/nnpdf/pull/2325 fix photon replica treatment if replica is equal to the number of replicas in the luxset by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2333 Use new theories and names for tests and examples by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2303 don't resample L2 pseudodata by @RoyStegeman in https://github.com/NNPDF/nnpdf/pull/2275 Separate the ekos into its own folder by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2331 Remove a bunch of deprecated functions and options by @scarlehoff in https://github.com/NNPDF/nnpdf/pull/2334 Full Changelog: https://github.com/NNPDF/nnpdf/compare/4.0.10...4.1.0

Zaharid, Juan M. Cruz-Martinez, Roy Stegeman, Stefano Carrazza, Cameron Voisey, wilsonmr, Mark Nestor Costantini, Andrea Barontini, Niccolò Laurenti, Nathan Hartland, Aron Jansen, Tanjona R. Rabemananjara, Giacomo Magni, Amedeo Chiefa, Emanuele R. Nocera, Luca Rottoli, Rabah Khalek, Emma Slade, Rosalyn Pearson, … Giovanni De Crescenzo. (2025). NNPDF/nnpdf: 4.1.0 (4.1.0). Zenodo. https://doi.org/10.5281/zenodo.15691478