NEWS.md

In kevinrue/velociraptor: Toolkit for Single-Cell Velocity

velociraptor 1.15.13

• Add separate environment (untested) for Linux Aarch64. Cannot break that platform more than it already is.

velociraptor 1.15.12

• Update Conda environment for Linux to avoid Anaconda channel.

velociraptor 1.15.11

• Re-enable plotVelocityStream() with a warning.

velociraptor 1.15.10

• Temporarily disable plotVelocityStream() due to unexplained issue related to metr::geom_streamline()

velociraptor 1.15.9

• Update Conda environment for Linux and MacOSX Arm.
• Patch GitHub Action to use GitHub version of remotes.

velociraptor 1.15.8

• Update Conda environment using micromamba for MacOSX Arm.
• Fix switch between MacOSX and MacOSX Arm environments.

velociraptor 1.15.7

• Update Conda environment using micromamba for Windows.

velociraptor 1.15.6

• Update Conda environment to use anaconda channel on Linux. Passed GitHub Action https://github.com/kevinrue/velociraptor/actions/runs/10612115572/job/29413105915.

velociraptor 1.15.5

• Update Conda environment to svelo==0.3.2 on Linux.

velociraptor 1.15.4

• Set scvelo version triggering deprecation error to 0.3.1.

velociraptor 1.15.3

• Revert environment for Linux to the one of Bioconductor release 3.18.

velociraptor 1.15.2

• Add environment for macOS (Intel); same environment as macos (M1).

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=.

velociraptor 1.9.3

• Pin python version in conda environment.

velociraptor 1.9.2

• Remove column names from reduced dimension matrix in gridVectors().

velociraptor 1.5.2

• Remove column names of reduced dimension representation before velocity embedding.

velociraptor 1.5.1

• Add example for scvelo.params argument.

velociraptor 1.3.1

• Add typing_extensions to environment.

velociraptor 1.1.6

• Move sanity check vignette to inst/.

velociraptor 1.1.5

• Add Michael Stadler to package authors.

velociraptor 1.1.4

• Fix typo in documentation.

velociraptor 1.1.3

• Add vignette subdirectory with sanity checks.

velociraptor 1.1.2

• Add functions plotVelocity and plotVelocityStream.

velociraptor 1.1.1

• Refresh cached environments.

velociraptor 1.1.0

• Bioconductor release 1.1.0.

velociraptor 0.99.9

• Converted various functions to S4 generics for easier use with SingleCellExperiment objects.

velociraptor 0.99.8

• Trigger new build to repeat ExperimentHub download.

velociraptor 0.99.7

• Delete empty line to force cache update. See https://github.com/rubocop-hq/rubocop/pull/4342#issuecomment-305449759.

velociraptor 0.99.6

• Set autoscale=FALSE in the call to scvelo function velocity_embedding to avoid issue related to Qt and plotting.

velociraptor 0.99.5

• Trigger new build to check if Windows issue resolved itself.

velociraptor 0.99.4

• Trigger new build to check whether TIMEOUT issue on Windows is reproducible.

velociraptor 0.99.3

• Explicitly declare all Conda dependencies for scvelo.

velociraptor 0.99.2

• Add hexsticker.

velociraptor 0.99.1

• Remove .Rproj file from git repository.

velociraptor 0.99.0

• First submission to Bioconductor.

kevinrue/velociraptor documentation built on Oct. 12, 2024, 10:38 a.m.