docs, version bump and news

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.0
-Date: 2024-01-29
+Version: 1.15.1
+Date: 2024-05-24
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "kevinrue67@gmail.com", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="infinite.monkeys.with.keyboards@gmail.com", comment = c(ORCID = '0000-0002-3564-4813')),
     person("Charlotte", "Soneson", role="aut", email="charlottesoneson@gmail.com", comment = c(ORCID = '0000-0003-3833-2169')),

NEWS.md

@@ -1,3 +1,10 @@
+# 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.
+
 # velociraptor 1.13.1
 
 * Robust fallback mechanism using `basiliskRun` option `testload=`.

R/basilisk.R

@@ -712,24 +712,9 @@ if (basilisk.utils::isWindows()) {
 } else if (basilisk.utils::isMacOSXArm()) {
   .scvelo_dependencies <- .scvelo.dependencies.MacOSXArm
 } else {
-  stop("Unsupported OS type: ", .Platform$OS.type)
+  stop("Unsupported operating system or architecture.\n  Please open an issue at <https://github.com/kevinrue/velociraptor/issues> to request support.")
 }
 
-# Note:
-
-# macOS
-# "matplotlib==3.7.3", # https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no
-# "numpy==1.23.1" # https://github.com/OpenTalker/video-retalking/issues/35
-# "tqdm==4.66.4", # required for progress bar, optional
-# "ipywidgets==8.1.2", # required for progress bar, optional
-# "jupyterlab==4.2.0", # required for progress bar, optional
-
-# Windows:
-# 'scvelo==0.2.5', # last version compatible with Windows before move to bioconda and dependency on jaxlib unsupported on windows
-# 'matplotlib==3.6.3',
-# 'pandas==1.5.2', # https://stackoverflow.com/questions/76234312/importerror-cannot-import-name-is-categorical-from-pandas-api-types
-# 'numpy==1.21.1' # https://github.com/theislab/scvelo/issues/1109
-
 #' @importFrom basilisk BasiliskEnvironment
 #' @importFrom zellkonverter AnnDataDependencies
 velo.env <- BasiliskEnvironment("env", "velociraptor",

R/scvelo.R

@@ -98,6 +98,31 @@
 #' }
 #' See the \pkg{scVelo} documentation for more details about the available arguments and the examples below for a syntax example.
 #'
+#' @section Supported operating systems and architectures:
+#' \pkg{scVelo} dependencies are pinned in a Conda environment to ensure reproducibility.
+#' 
+#' Differences in packages and versions available from Conda require different environments for different operating systems and architectures.
+#' \pkg{basilisk.utils} is used to determine the operating system and architecture of the computer used to run \code{scvelo()}, using to the appropriate Conda environment.
+#' 
+#' As of the latest \pkg{velociraptor} update (24 May 2024):
+#' 
+#' \describe{
+#' \item{Linux}{\pkg{scVelo} v0.3.2 from conda-forge is used.
+#' This is the latest version available to date.
+#' Note that
+#' \pkg{matplotlib} is pinned to v3.7.3 (\url{https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no})
+#' and \pkg{numpy} is pinned to v1.23.1 (\url{https://github.com/OpenTalker/video-retalking/issues/35})}
+#' \item{MacOS Arm}{\pkg{scVelo} v0.3.2 from conda-forge is used.
+#' This is the latest version available to date.
+#' Tested on M1.}
+#' \item{Windows}{\pkg{scVelo} v0.2.5 from bioconda is used.
+#' Later versions of \pkg{scVelo} depend on \pkg{jaxlib} which is not supported on Windows (\url{https://github.com/google/jax/issues/438}).
+#' Note that \pkg{matplotlib} is pinned to v3.6.3 (\url{https://github.com/scverse/scanpy/issues/2411}),
+#' \pkg{pandas} is pinned to v1.5.2 (\url{https://stackoverflow.com/questions/76234312/importerror-cannot-import-name-is-categorical-from-pandas-api-types}),
+#' and \pkg{numpy} is pinned to v1.21.1 (\url{https://github.com/theislab/scvelo/issues/1109}).
+#' }
+#' }
+#'
 #' @return
 #' A \linkS4class{SingleCellExperiment} is returned containing the output of the velocity calculations.
 #' Of particular interest are:
@@ -129,7 +154,7 @@
 #' @references
 #' Bergen, V., Lange, M., Peidli, S. et al. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol 38, 1408–1414 (2020). \url{https://doi.org/10.1038/s41587-020-0591-3}
 #'
-#' @author Aaron Lun, Charlotte Soneson
+#' @author Aaron Lun, Charlotte Soneson, Kevin Rue-Albrecht
 #' @name scvelo
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