Update scvelo to 0.3.2

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.20'}
+          - { os: windows-latest, r: 'devel', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.13.1
-Date: 2024-01-29
+Version: 1.15.1
+Date: 2024-05-24
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="[email protected]", comment = c(ORCID = '0000-0002-3564-4813')),
     person("Charlotte", "Soneson", role="aut", email="[email protected]", comment = c(ORCID = '0000-0003-3833-2169')),
@@ -46,7 +46,7 @@ Suggests:
 StagedInstall: no
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 URL: https://github.com/kevinrue/velociraptor
 BugReports: https://github.com/kevinrue/velociraptor/issues
 biocViews: SingleCell, GeneExpression, Sequencing, Coverage

NEWS.md

@@ -1,3 +1,12 @@
+# velociraptor 1.15.1
+
+* Fix issue #63.
+* Update `scvelo` to 0.3.2 (conda-forge) for macOS (M1) and Linux.
+* Update `scvelo` to 0.2.5 (bioconda) for Windows.
+* Add mechanism to switch Conda environment (and scvelo version) based on operating system and architecture.
+* Use `scanpy.pp.neighbors` to calculate neighbors due to deprecation of automatic neighbor calculation in `scvelo.pp.moments`.
+* Update vignette to document the change of default value for `n_neighbors` from scvelo (30) to scanpy (15).
+
 # velociraptor 1.13.1
 
 * Robust fallback mechanism using `basiliskRun` option `testload=`.