v4.0.1 #843
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v4.0.1 #843
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Switch references to suite_modular to suite
Change: `cell_ids` param removed in favor of `random_subset`, `set_seed`, and `seed_number` params in `calculateHVF()` This way, the random subsetting is entirely internalized and the user does not have to do it in order to get a subset of cell_IDs to pass
- See if the issue is related to irlba no longer being installed - update to contribution page
irlba did not fix it, so it will be removed again. try setting to Matrix >= 1.6.3. The breaking change causing our issues might have been introduced in 1.6.2 - add set_seed and seed_number params to runGiottoHarmony() - Update runGiottoHarmony() to use
- Add contribution page section about imports - Add higher terra version requirement - Remove soft deprecated items from re-exports - Add some missing functions to re-exports
- See if the issue is related to irlba no longer being installed - update to contribution page
irlba did not fix it, so it will be removed again. try setting to Matrix >= 1.6.3. The breaking change causing our issues might have been introduced in 1.6.2 - add set_seed and seed_number params to runGiottoHarmony() - Update runGiottoHarmony() to use
- Add contribution page section about imports - Add higher terra version requirement - Remove soft deprecated items from re-exports - Add some missing functions to re-exports
This reverts commit d6b08d2.
rcmdcheck is still finding errors - new naming scheme applied - changes in some other module functions - loss of access to internal functions requires further examination - testthat also throwing errors - suite re-exports updated
- change `1:length()` to `seq_along()` - docs fixes - Rcmd check shows a failure in merfish testing, 0 warnings, 5 notes. There appears to be no more issues with missing exported functions from other modules
- Removing offending line that prevented access to py functions
- Slower than normal for smaller datasets
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Breaking Changes
cell_idsparam forcalculateHVFin favor of simplerrandom_subsetAdded
parse_affine()for interpreting affine transform matricesrunGiottoHarmony()calculateHVF()when a future plan is setChanges
createGiottoXeniumObject()feature metadata reading for.jsonfilerunGiottoHarmony()to callharmony::RunHarmony()