fmesher/inlabru compatibility updates #19
Merged
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I'm the developer and maintainer of the
inlabru
andfmesher
packages. Since middle of last year, all mesh related functions inINLA
were moved to a separate package,fmesher
, and calling those methods inINLA
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 tofmesher
instead. Some of thefmesher
functions were temporarily available in theinlabru
package, but only the minimal set needed for temporary compatibility with CRAN packages are now available as re-exportedfmesher
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/changedfmesher
andinlabru
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.htmlA corresponding pull request for intSDM will be submitted shortly.