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fmesher/inlabru compatibility updates #19

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merged 6 commits into from
Nov 22, 2024

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finnlindgren
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I'm the developer and maintainer of the inlabru and fmesher packages. Since middle of last year, all mesh related functions in INLA were moved to a separate package, fmesher, and calling those methods in INLA was deprecated, but with temporary translation functions for backwards compatibility. However, as those transition functions are deprecated and unmaintained, users of those functions should move to fmesher instead. Some of the fmesher functions were temporarily available in the inlabru package, but only the minimal set needed for temporary compatibility with CRAN packages are now available as re-exported fmesher functions.

inlabru version 2.12.0 has just been submitted to CRAN, and includes the minimal amount of re-exports etc to support the CRAN versions of PointedSDMs and intSDM with those package test passing. However, some of the temporary workarounds will be removed in the future, and this PointedSDMs update upgrades the PointedSDMs code and tests to avoid the deprecated/changed fmesher and inlabru features, and to avoid some internal inlabru data structure details that may change in the future but have well-defined interface accessors; there may be more such cases that I didn't find, but at least the tests now succeed.

Note that the github tests won't succeed until inlabru 2.12.0 is available via CRAN, so you may wish to wait with merging until that point.
You can test locally by installing both the stable and development versions from github; see https://inlabru-org.github.io/inlabru/ for details.

For further details on fmesher, see https://inlabru-org.github.io/fmesher/index.html

A corresponding pull request for intSDM will be submitted shortly.

@PhilipMostert PhilipMostert merged commit 53a56bf into PhilipMostert:main Nov 22, 2024
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@PhilipMostert
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Dear Finn,

Thank you very much for your help with this transition! Everything looks great and is running perfectly well.

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