From 17bccb001c507ce0be737baed8f9bdfe688c865c Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Wed, 12 Jun 2024 10:17:35 +0100
Subject: [PATCH] update conda environments and workflows to fix issue similar
 to devel

---
 DESCRIPTION                |    6 +-
 NEWS.md                    |    7 +
 R/basilisk.R               | 1066 +++++++++++++++++++++++++++++++++---
 R/scvelo.R                 |   83 ++-
 man/scvelo.Rd              |   35 +-
 vignettes/velociraptor.Rmd |   15 +-
 6 files changed, 1110 insertions(+), 102 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index db6054c..17f9ab1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.14.0
-Date: 2024-01-29
+Version: 1.14.1
+Date: 2024-06-12
 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')),
@@ -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
diff --git a/NEWS.md b/NEWS.md
index d8c7dd3..a29231b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# velociraptor 1.14.1
+
+* Update scvelo environment to version `0.3.2` on Linux/Mac.
+* Update scvelo environment to version `0.2.5` on Windows.
+* 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=`.
diff --git a/R/basilisk.R b/R/basilisk.R
index c3c2898..5078521 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -1,77 +1,997 @@
-# scvelo 0.2.2 and latest version of dependencies in zellkonverter::AnnDataDependencies() succesfully tested.
-.scvelo_dependencies <- c("alabaster==0.7.12",
-    "anndata==0.7.4",
-    "Babel==2.8.0",
-    "brotlipy==0.7.0",
-    "certifi==2020.6.20",
-    "cffi==1.14.1",
-    "chardet==3.0.4",
-    "colorama==0.4.3",
-    "cryptography==3.1",
-    "cycler==0.10.0",
-    "decorator==4.4.2",
-    "docutils==0.16",
-    "h5py==2.10.0",
-    "idna==2.10",
-    "imagesize==1.2.0",
-    "importlib-metadata==1.7.0",
-    "Jinja2==2.11.2",
-    "joblib==0.16.0",
-    "kiwisolver==1.2.0",
-    "llvmlite==0.34.0",
-    "loompy==2.0.16",
-    "MarkupSafe==1.1.1",
-    "matplotlib==3.3.1",
-    "mock==4.0.2",
-    "natsort==7.0.1",
-    "networkx==2.5",
-    "numba==0.51.2",
-    "numexpr==2.7.1",
-    "numpy==1.19.1",
-    "olefile==0.46",
-    "packaging==20.4",
-    "pandas==1.1.2",
-    "patsy==0.5.1",
-    "Pillow==7.2.0",
-    "pip==20.2.3",
-    "pycparser==2.20",
-    "Pygments==2.7.0",
-    "pyOpenSSL==19.1.0",
-    "pyparsing==2.4.7",
-    "PySocks==1.7.1",
-    "python==3.8",
-    "python-dateutil==2.8.1",
-    "pytz==2020.1",
-    "requests==2.24.0",
-    "scanpy==1.6.0",
-    "scikit-learn==0.23.2",
-    "scipy==1.5.2",
-    "scvelo==0.2.2",
-    "seaborn==0.11.0",
-    "setuptools-scm==4.1.2",
-    "sinfo==0.3.1",
-    "six==1.15.0",
-    "snowballstemmer==2.0.0",
-    "Sphinx==3.2.1",
-    "sphinxcontrib-applehelp==1.0.2",
-    "sphinxcontrib-devhelp==1.0.2",
-    "sphinxcontrib-htmlhelp==1.0.3",
-    "sphinxcontrib-jsmath==1.0.1",
-    "sphinxcontrib-qthelp==1.0.3",
-    "sphinxcontrib-serializinghtml==1.1.4",
-    "statsmodels==0.12.0",
-    "stdlib-list==0.6.0",
-    "threadpoolctl==2.1.0",
-    "toml==0.10.1",
-    "tornado==6.0.4",
-    "tqdm==4.49.0",
-    "typing_extensions==3.10.0.0",
-    "umap-learn==0.4.6",
-    "urllib3==1.25.10",
-    "wheel==0.35.1",
-    "zipp==3.1.0")
+.scvelo.dependencies.Windows <- list(
+  channels = c("bioconda", "conda-forge"),
+  packages = c(
+    'anndata==0.10.5.post1',
+    'array-api-compat==1.6',
+    'blosc==1.21.5',
+    'brotli==1.1.0',
+    'brotli-bin==1.1.0',
+    'bzip2==1.0.8',
+    'ca-certificates==2024.2.2',
+    'cached-property==1.5.2',
+    'cached_property==1.5.2',
+    'certifi==2024.2.2',
+    'colorama==0.4.6',
+    'contourpy==1.2.1',
+    'cycler==0.12.1',
+    'exceptiongroup==1.2.0',
+    'fonttools==4.51.0',
+    'freetype==2.12.1',
+    'glib==2.80.2',
+    'glib-tools==2.80.2',
+    'gst-plugins-base==1.24.3',
+    'gstreamer==1.24.3',
+    'h5py==3.8.0',
+    'hdf5==1.14.0',
+    'icu==73.2',
+    'importlib-metadata==7.1.0',
+    'importlib_metadata==7.1.0',
+    'intel-openmp==2024.1.0',
+    'joblib==1.4.2',
+    'kiwisolver==1.4.5',
+    'krb5==1.21.2',
+    'lcms2==2.16',
+    'legacy-api-wrap==1.4',
+    'lerc==4.0.0',
+    'libaec==1.1.3',
+    'libblas==3.9.0',
+    'libbrotlicommon==1.1.0',
+    'libbrotlidec==1.1.0',
+    'libbrotlienc==1.1.0',
+    'libcblas==3.9.0',
+    'libclang13==18.1.5',
+    'libcurl==8.8.0',
+    'libdeflate==1.20',
+    'libffi==3.4.2',
+    'libglib==2.80.2',
+    'libhwloc==2.10.0',
+    'libiconv==1.17',
+    'libintl==0.22.5',
+    'libintl-devel==0.22.5',
+    'libjpeg-turbo==3.0.0',
+    'liblapack==3.9.0',
+    'libogg==1.3.4',
+    'libpng==1.6.43',
+    'libsqlite==3.45.3',
+    'libssh2==1.11.0',
+    'libtiff==4.6.0',
+    'libvorbis==1.3.7',
+    'libwebp-base==1.4.0',
+    'libxcb==1.15',
+    'libxml2==2.12.7',
+    'libzlib==1.2.13',
+    'llvmlite==0.40.1',
+    'loompy==2.0.16',
+    'lz4-c==1.9.4',
+    'm2w64-gcc-libgfortran==5.3.0',
+    'm2w64-gcc-libs==5.3.0',
+    'm2w64-gcc-libs-core==5.3.0',
+    'm2w64-gmp==6.1.0',
+    'm2w64-libwinpthread-git==5.0.0.4634.697f757',
+    'matplotlib==3.6.3',
+    'matplotlib-base==3.6.3',
+    'mkl==2024.1.0',
+    'msys2-conda-epoch==20160418',
+    'munkres==1.0.7',
+    'natsort==8.4.0',
+    'networkx==3.2',
+    'numba==0.57.1',
+    'numexpr==2.7.3',
+    'numpy==1.21.1',
+    'openjpeg==2.5.2',
+    'openssl==3.3.0',
+    'packaging==24.0',
+    'pandas==1.5.2',
+    'patsy==0.5.6',
+    'pcre2==10.43',
+    'pillow==10.3.0',
+    'pip==24.0',
+    'ply==3.11',
+    'pthread-stubs==0.4',
+    'pthreads-win32==2.9.1',
+    'pynndescent==0.5.12',
+    'pyparsing==3.1.2',
+    'pyqt==5.15.9',
+    'pyqt5-sip==12.12.2',
+    'pytables==3.7.0',
+    'python==3.9.12',
+    'python-dateutil==2.9.0',
+    'python_abi==3.9',
+    'pytz==2024.1',
+    'qt-main==5.15.8',
+    'scanpy==1.7.2',
+    'scikit-learn==1.5.0',
+    'scipy==1.13.1',
+    'scvelo==0.2.5',
+    'seaborn==0.13.2',
+    'seaborn-base==0.13.2',
+    'setuptools==70.0.0',
+    'setuptools-scm==8.1.0',
+    'setuptools_scm==8.1.0',
+    'sinfo==0.3.1',
+    'sip==6.7.12',
+    'six==1.16.0',
+    'snappy==1.2.0',
+    'sqlite==3.45.3',
+    'statsmodels==0.14.2',
+    'stdlib-list==0.10.0',
+    'tbb==2021.12.0',
+    'threadpoolctl==3.5.0',
+    'tk==8.6.13',
+    'toml==0.10.2',
+    'tomli==2.0.1',
+    'tornado==6.4',
+    'tqdm==4.66.4',
+    'typing==3.10.0.0',
+    'typing-extensions==4.11.0',
+    'typing_extensions==4.11.0',
+    'tzdata==2024a',
+    'ucrt==10.0.22621.0',
+    'umap-learn==0.5.5',
+    'unicodedata2==15.1.0',
+    'vc==14.3',
+    'vc14_runtime==14.38.33135',
+    'vs2015_runtime==14.38.33135',
+    'wheel==0.43.0',
+    'xorg-libxau==1.0.11',
+    'xorg-libxdmcp==1.1.3',
+    'xz==5.2.6',
+    'zipp==3.17.0',
+    'zstd==1.5.6'
+  )
+)
+
+.scvelo.dependencies.MacOSXArm <- list(
+  channels = c("conda-forge", "bioconda"),
+  packages = c(
+    'absl-py==2.1.0',
+    'anndata==0.10.7',
+    'annotated-types==0.7.0',
+    'anyio==4.3.0',
+    'aom==3.9.0',
+    'array-api-compat==1.6',
+    'arrow==1.3.0',
+    'beautifulsoup4==4.12.3',
+    'blessed==1.19.1',
+    'blosc==1.21.5',
+    'boto3==1.34.111',
+    'botocore==1.34.111',
+    'brotli==1.1.0',
+    'brotli-bin==1.1.0',
+    'brotli-python==1.1.0',
+    'bzip2==1.0.8',
+    'c-ares==1.28.1',
+    'ca-certificates==2024.2.2',
+    'cachecontrol==0.14.0',
+    'cachecontrol-with-filecache==0.14.0',
+    'cached-property==1.5.2',
+    'cached_property==1.5.2',
+    'certifi==2024.2.2',
+    'cffi==1.16.0',
+    'charset-normalizer==3.3.2',
+    'chex==0.1.86',
+    'cleo==2.1.0',
+    'click==8.1.7',
+    'colorama==0.4.6',
+    'contextlib2==21.6.0',
+    'contourpy==1.2.1',
+    'crashtest==0.4.1',
+    'croniter==1.3.15',
+    'cycler==0.12.1',
+    'dateutils==0.6.12',
+    'dav1d==1.2.1',
+    'deepdiff==7.0.1',
+    'distlib==0.3.8',
+    'dnspython==2.6.1',
+    'docrep==0.3.2',
+    'dulwich==0.21.7',
+    'email-validator==2.1.1',
+    'email_validator==2.1.1',
+    'et_xmlfile==1.1.0',
+    'etils==1.6.0',
+    'exceptiongroup==1.2.0',
+    'fastapi==0.111.0',
+    'fastapi-cli==0.0.4',
+    'filelock==3.14.0',
+    'flax==0.8.3',
+    'fonttools==4.51.0',
+    'freetype==2.12.1',
+    'fsspec==2023.12.2',
+    'get-annotations==0.1.2',
+    'gmp==6.3.0',
+    'gmpy2==2.1.5',
+    'h11==0.14.0',
+    'h2==4.1.0',
+    'h5py==3.11.0',
+    'hdf5==1.14.3',
+    'hpack==4.0.0',
+    'httpcore==1.0.5',
+    'httpx==0.27.0',
+    'hyperframe==6.0.1',
+    'icu==73.2',
+    'idna==3.7',
+    'importlib-metadata==7.1.0',
+    'importlib-resources==6.4.0',
+    'importlib_metadata==7.1.0',
+    'importlib_resources==6.4.0',
+    'inquirer==3.1.4',
+    'itsdangerous==2.2.0',
+    'jaraco.classes==3.4.0',
+    'jax==0.4.27',
+    'jaxlib==0.4.23',
+    'jinja2==3.1.4',
+    'jmespath==1.0.1',
+    'joblib==1.4.2',
+    'keyring==24.3.1',
+    'kiwisolver==1.4.5',
+    'krb5==1.21.2',
+    'lcms2==2.16',
+    'legacy-api-wrap==1.4',
+    'lerc==4.0.0',
+    'libabseil==20240116.2',
+    'libaec==1.1.3',
+    'libavif16==1.0.4',
+    'libblas==3.9.0',
+    'libbrotlicommon==1.1.0',
+    'libbrotlidec==1.1.0',
+    'libbrotlienc==1.1.0',
+    'libcblas==3.9.0',
+    'libcurl==8.8.0',
+    'libcxx==17.0.6',
+    'libdeflate==1.20',
+    'libedit==3.1.20191231',
+    'libev==4.33',
+    'libffi==3.4.2',
+    'libgfortran==5.0.0',
+    'libgfortran5==13.2.0',
+    'libgrpc==1.62.2',
+    'libhwloc==2.10.0',
+    'libiconv==1.17',
+    'libjpeg-turbo==3.0.0',
+    'liblapack==3.9.0',
+    'libllvm14==14.0.6',
+    'libnghttp2==1.58.0',
+    'libopenblas==0.3.27',
+    'libpng==1.6.43',
+    'libprotobuf==4.25.3',
+    'libre2-11==2023.09.01',
+    'libsqlite==3.45.3',
+    'libssh2==1.11.0',
+    'libtiff==4.6.0',
+    'libtorch==2.3.0',
+    'libuv==1.48.0',
+    'libwebp-base==1.4.0',
+    'libxcb==1.15',
+    'libxml2==2.12.7',
+    'libzlib==1.2.13',
+    'lightning==2.0.4',
+    'lightning-cloud==0.5.69',
+    'lightning-utilities==0.11.2',
+    'llvm-openmp==18.1.5',
+    'llvmlite==0.42.0',
+    'loompy==3.0.6',
+    'lz4-c==1.9.4',
+    'markdown-it-py==3.0.0',
+    'markupsafe==2.1.5',
+    'matplotlib-base==3.8.4',
+    'mdurl==0.1.2',
+    'ml-collections==0.1.1',
+    'ml_dtypes==0.4.0',
+    'more-itertools==10.2.0',
+    'mpc==1.3.1',
+    'mpfr==4.2.1',
+    'mpmath==1.3.0',
+    'msgpack-python==1.0.8',
+    'mudata==0.2.3',
+    'multipledispatch==0.6.0',
+    'munkres==1.1.4',
+    'natsort==8.4.0',
+    'ncurses==6.5',
+    'nest-asyncio==1.6.0',
+    'networkx==3.2.1',
+    'nomkl==1.0',
+    'numba==0.59.1',
+    'numpy==1.26.4',
+    'numpy_groupies==0.11.1',
+    'numpyro==0.15.0',
+    'openjpeg==2.5.2',
+    'openpyxl==3.1.2',
+    'openssl==3.3.0',
+    'opt-einsum==3.3.0',
+    'opt_einsum==3.3.0',
+    'optax==0.2.2',
+    'orbax-checkpoint==0.4.4',
+    'ordered-set==4.1.0',
+    'orjson==3.10.3',
+    'packaging==24.0',
+    'pandas==2.2.2',
+    'patsy==0.5.6',
+    'pexpect==4.9.0',
+    'pillow==10.3.0',
+    'pip==24.0',
+    'pkginfo==1.10.0',
+    'platformdirs==4.2.2',
+    'poetry==1.8.3',
+    'poetry-core==1.9.0',
+    'poetry-plugin-export==1.8.0',
+    'protobuf==4.25.3',
+    'psutil==5.9.8',
+    'pthread-stubs==0.4',
+    'ptyprocess==0.7.0',
+    'pybind11-abi==4',
+    'pycparser==2.22',
+    'pydantic==2.7.1',
+    'pydantic-core==2.18.2',
+    'pygments==2.18.0',
+    'pyjwt==2.8.0',
+    'pynndescent==0.5.12',
+    'pyparsing==3.1.2',
+    'pyproject_hooks==1.1.0',
+    'pyro-api==0.1.2',
+    'pyro-ppl==1.9.0',
+    'pysocks==1.7.1',
+    'python==3.9.12',
+    'python-build==1.2.1',
+    'python-dateutil==2.9.0',
+    'python-editor==1.0.4',
+    'python-fastjsonschema==2.19.1',
+    'python-installer==0.7.0',
+    'python-multipart==0.0.9',
+    'python-tzdata==2024.1',
+    'python_abi==3.9',
+    'pytorch==2.3.0',
+    'pytorch-lightning==2.2.2',
+    'pytz==2024.1',
+    'pyyaml==6.0.1',
+    'rapidfuzz==3.9.1',
+    'rav1e==0.6.6',
+    're2==2023.09.01',
+    'readchar==4.1.0',
+    'readline==8.2',
+    'requests==2.32.2',
+    'requests-toolbelt==1.0.0',
+    'rich==13.7.1',
+    's3transfer==0.10.1',
+    'scanpy==1.10.1',
+    'scikit-learn==1.1.3',
+    'scipy==1.13.0',
+    'scvelo==0.3.2',
+    'scvi-tools==1.1.2',
+    'seaborn==0.13.2',
+    'seaborn-base==0.13.2',
+    'session-info==1.0.0',
+    'setuptools==70.0.0',
+    'shellingham==1.5.4',
+    'six==1.16.0',
+    'sleef==3.5.1',
+    'snappy==1.2.0',
+    'sniffio==1.3.1',
+    'soupsieve==2.5',
+    'sparse==0.15.3',
+    'sqlite==3.45.3',
+    'starlette==0.37.2',
+    'starsessions==1.3.0',
+    'statsmodels==0.14.2',
+    'stdlib-list==0.10.0',
+    'svt-av1==2.1.0',
+    'sympy==1.12',
+    'tbb==2021.12.0',
+    'tensorstore==0.1.59',
+    'threadpoolctl==3.5.0',
+    'tk==8.6.13',
+    'tomli==2.0.1',
+    'tomlkit==0.12.5',
+    'toolz==0.12.1',
+    'torchmetrics==1.4.0.post0',
+    'tqdm==4.66.4',
+    'traitlets==5.14.3',
+    'trove-classifiers==2024.5.22',
+    'typer==0.12.3',
+    'typer-slim==0.12.3',
+    'typer-slim-standard==0.12.3',
+    'types-python-dateutil==2.9.0.20240316',
+    'typing-extensions==4.11.0',
+    'typing_extensions==4.11.0',
+    'tzdata==2024a',
+    'ujson==5.10.0',
+    'umap-learn==0.5.5',
+    'unicodedata2==15.1.0',
+    'urllib3==1.26.18',
+    'uvicorn==0.29.0',
+    'virtualenv==20.26.2',
+    'wcwidth==0.2.13',
+    'websocket-client==1.8.0',
+    'websockets==11.0.3',
+    'wheel==0.43.0',
+    'xarray==2024.5.0',
+    'xattr==1.1.0',
+    'xlrd==1.2.0',
+    'xorg-libxau==1.0.11',
+    'xorg-libxdmcp==1.1.3',
+    'xz==5.2.6',
+    'yaml==0.2.5',
+    'zipp==3.17.0',
+    'zstd==1.5.6'
+  )
+)
+
+.scvelo.dependencies.MacOSX <- list(
+  channels = c("conda-forge", "bioconda"),
+  packages = c(
+    'absl-py==2.1.0',
+    'anndata==0.10.7',
+    'annotated-types==0.7.0',
+    'anyio==4.3.0',
+    'aom==3.9.0',
+    'array-api-compat==1.6',
+    'arrow==1.3.0',
+    'beautifulsoup4==4.12.3',
+    'blessed==1.19.1',
+    'blosc==1.21.5',
+    'boto3==1.34.111',
+    'botocore==1.34.111',
+    'brotli==1.1.0',
+    'brotli-bin==1.1.0',
+    'brotli-python==1.1.0',
+    'bzip2==1.0.8',
+    'c-ares==1.28.1',
+    'ca-certificates==2024.2.2',
+    'cachecontrol==0.14.0',
+    'cachecontrol-with-filecache==0.14.0',
+    'cached-property==1.5.2',
+    'cached_property==1.5.2',
+    'certifi==2024.2.2',
+    'cffi==1.16.0',
+    'charset-normalizer==3.3.2',
+    'chex==0.1.86',
+    'cleo==2.1.0',
+    'click==8.1.7',
+    'colorama==0.4.6',
+    'contextlib2==21.6.0',
+    'contourpy==1.2.1',
+    'crashtest==0.4.1',
+    'croniter==1.3.15',
+    'cycler==0.12.1',
+    'dateutils==0.6.12',
+    'dav1d==1.2.1',
+    'deepdiff==7.0.1',
+    'distlib==0.3.8',
+    'dnspython==2.6.1',
+    'docrep==0.3.2',
+    'dulwich==0.21.7',
+    'email-validator==2.1.1',
+    'email_validator==2.1.1',
+    'et_xmlfile==1.1.0',
+    'etils==1.6.0',
+    'exceptiongroup==1.2.0',
+    'fastapi==0.111.0',
+    'fastapi-cli==0.0.4',
+    'filelock==3.14.0',
+    'flax==0.8.3',
+    'fonttools==4.51.0',
+    'freetype==2.12.1',
+    'fsspec==2023.12.2',
+    'get-annotations==0.1.2',
+    'gmp==6.3.0',
+    'gmpy2==2.1.5',
+    'h11==0.14.0',
+    'h2==4.1.0',
+    'h5py==3.11.0',
+    'hdf5==1.14.3',
+    'hpack==4.0.0',
+    'httpcore==1.0.5',
+    'httpx==0.27.0',
+    'hyperframe==6.0.1',
+    'icu==73.2',
+    'idna==3.7',
+    'importlib-metadata==7.1.0',
+    'importlib-resources==6.4.0',
+    'importlib_metadata==7.1.0',
+    'importlib_resources==6.4.0',
+    'inquirer==3.1.4',
+    'itsdangerous==2.2.0',
+    'jaraco.classes==3.4.0',
+    'jax==0.4.27',
+    'jaxlib==0.4.23',
+    'jinja2==3.1.4',
+    'jmespath==1.0.1',
+    'joblib==1.4.2',
+    'keyring==24.3.1',
+    'kiwisolver==1.4.5',
+    'krb5==1.21.2',
+    'lcms2==2.16',
+    'legacy-api-wrap==1.4',
+    'lerc==4.0.0',
+    'libabseil==20240116.2',
+    'libaec==1.1.3',
+    'libavif16==1.0.4',
+    'libblas==3.9.0',
+    'libbrotlicommon==1.1.0',
+    'libbrotlidec==1.1.0',
+    'libbrotlienc==1.1.0',
+    'libcblas==3.9.0',
+    'libcurl==8.8.0',
+    'libcxx==17.0.6',
+    'libdeflate==1.20',
+    'libedit==3.1.20191231',
+    'libev==4.33',
+    'libffi==3.4.2',
+    'libgfortran==5.0.0',
+    'libgfortran5==13.2.0',
+    'libgrpc==1.62.2',
+    'libhwloc==2.10.0',
+    'libiconv==1.17',
+    'libjpeg-turbo==3.0.0',
+    'liblapack==3.9.0',
+    'libllvm14==14.0.6',
+    'libnghttp2==1.58.0',
+    'libopenblas==0.3.27',
+    'libpng==1.6.43',
+    'libprotobuf==4.25.3',
+    'libre2-11==2023.09.01',
+    'libsqlite==3.45.3',
+    'libssh2==1.11.0',
+    'libtiff==4.6.0',
+    'libtorch==2.3.0',
+    'libuv==1.48.0',
+    'libwebp-base==1.4.0',
+    'libxcb==1.15',
+    'libxml2==2.12.7',
+    'libzlib==1.2.13',
+    'lightning==2.0.4',
+    'lightning-cloud==0.5.69',
+    'lightning-utilities==0.11.2',
+    'llvm-openmp==18.1.5',
+    'llvmlite==0.42.0',
+    'loompy==3.0.6',
+    'lz4-c==1.9.4',
+    'markdown-it-py==3.0.0',
+    'markupsafe==2.1.5',
+    'matplotlib-base==3.8.4',
+    'mdurl==0.1.2',
+    'ml-collections==0.1.1',
+    'ml_dtypes==0.4.0',
+    'more-itertools==10.2.0',
+    'mpc==1.3.1',
+    'mpfr==4.2.1',
+    'mpmath==1.3.0',
+    'msgpack-python==1.0.8',
+    'mudata==0.2.3',
+    'multipledispatch==0.6.0',
+    'munkres==1.1.4',
+    'natsort==8.4.0',
+    'ncurses==6.5',
+    'nest-asyncio==1.6.0',
+    'networkx==3.2.1',
+    'nomkl==1.0',
+    'numba==0.59.1',
+    'numpy==1.26.4',
+    'numpy_groupies==0.11.1',
+    'numpyro==0.15.0',
+    'openjpeg==2.5.2',
+    'openpyxl==3.1.2',
+    'openssl==3.3.0',
+    'opt-einsum==3.3.0',
+    'opt_einsum==3.3.0',
+    'optax==0.2.2',
+    'orbax-checkpoint==0.4.4',
+    'ordered-set==4.1.0',
+    'orjson==3.10.3',
+    'packaging==24.0',
+    'pandas==2.2.2',
+    'patsy==0.5.6',
+    'pexpect==4.9.0',
+    'pillow==10.3.0',
+    'pip==24.0',
+    'pkginfo==1.10.0',
+    'platformdirs==4.2.2',
+    'poetry==1.8.3',
+    'poetry-core==1.9.0',
+    'poetry-plugin-export==1.8.0',
+    'protobuf==4.25.3',
+    'psutil==5.9.8',
+    'pthread-stubs==0.4',
+    'ptyprocess==0.7.0',
+    'pybind11-abi==4',
+    'pycparser==2.22',
+    'pydantic==2.7.1',
+    'pydantic-core==2.18.2',
+    'pygments==2.18.0',
+    'pyjwt==2.8.0',
+    'pynndescent==0.5.12',
+    'pyparsing==3.1.2',
+    'pyproject_hooks==1.1.0',
+    'pyro-api==0.1.2',
+    'pyro-ppl==1.9.0',
+    'pysocks==1.7.1',
+    'python==3.9.12',
+    'python-build==1.2.1',
+    'python-dateutil==2.9.0',
+    'python-editor==1.0.4',
+    'python-fastjsonschema==2.19.1',
+    'python-installer==0.7.0',
+    'python-multipart==0.0.9',
+    'python-tzdata==2024.1',
+    'python_abi==3.9',
+    'pytorch==2.3.0',
+    'pytorch-lightning==2.2.2',
+    'pytz==2024.1',
+    'pyyaml==6.0.1',
+    'rapidfuzz==3.9.1',
+    'rav1e==0.6.6',
+    're2==2023.09.01',
+    'readchar==4.1.0',
+    'readline==8.2',
+    'requests==2.32.2',
+    'requests-toolbelt==1.0.0',
+    'rich==13.7.1',
+    's3transfer==0.10.1',
+    'scanpy==1.10.1',
+    'scikit-learn==1.1.3',
+    'scipy==1.13.0',
+    'scvelo==0.3.2',
+    'scvi-tools==1.1.2',
+    'seaborn==0.13.2',
+    'seaborn-base==0.13.2',
+    'session-info==1.0.0',
+    'setuptools==70.0.0',
+    'shellingham==1.5.4',
+    'six==1.16.0',
+    'sleef==3.5.1',
+    'snappy==1.2.0',
+    'sniffio==1.3.1',
+    'soupsieve==2.5',
+    'sparse==0.15.3',
+    'sqlite==3.45.3',
+    'starlette==0.37.2',
+    'starsessions==1.3.0',
+    'statsmodels==0.14.2',
+    'stdlib-list==0.10.0',
+    'svt-av1==2.1.0',
+    'sympy==1.12',
+    'tbb==2021.12.0',
+    'tensorstore==0.1.59',
+    'threadpoolctl==3.5.0',
+    'tk==8.6.13',
+    'tomli==2.0.1',
+    'tomlkit==0.12.5',
+    'toolz==0.12.1',
+    'torchmetrics==1.4.0.post0',
+    'tqdm==4.66.4',
+    'traitlets==5.14.3',
+    'trove-classifiers==2024.5.22',
+    'typer==0.12.3',
+    'typer-slim==0.12.3',
+    'typer-slim-standard==0.12.3',
+    'types-python-dateutil==2.9.0.20240316',
+    'typing-extensions==4.11.0',
+    'typing_extensions==4.11.0',
+    'tzdata==2024a',
+    'ujson==5.10.0',
+    'umap-learn==0.5.5',
+    'unicodedata2==15.1.0',
+    'urllib3==1.26.18',
+    'uvicorn==0.29.0',
+    'virtualenv==20.26.2',
+    'wcwidth==0.2.13',
+    'websocket-client==1.8.0',
+    'websockets==11.0.3',
+    'wheel==0.43.0',
+    'xarray==2024.5.0',
+    'xattr==1.1.0',
+    'xlrd==1.2.0',
+    'xorg-libxau==1.0.11',
+    'xorg-libxdmcp==1.1.3',
+    'xz==5.2.6',
+    'yaml==0.2.5',
+    'zipp==3.17.0',
+    'zstd==1.5.6'
+  )
+)
+
+.scvelo.dependencies.Linux <- list(
+  channels = c("conda-forge", "bioconda"),
+  packages = c(
+    c(
+      '_libgcc_mutex==0.1',
+      '_openmp_mutex==4.5',
+      'absl-py==2.1.0',
+      'anndata==0.10.7',
+      'annotated-types==0.7.0',
+      'anyio==4.3.0',
+      'aom==3.9.0',
+      'array-api-compat==1.6',
+      'arrow==1.3.0',
+      'beautifulsoup4==4.12.3',
+      'blessed==1.19.1',
+      'blosc==1.21.5',
+      'boto3==1.34.111',
+      'botocore==1.34.111',
+      'brotli==1.1.0',
+      'brotli-bin==1.1.0',
+      'brotli-python==1.1.0',
+      'bzip2==1.0.8',
+      'c-ares==1.28.1',
+      'ca-certificates==2024.2.2',
+      'cachecontrol==0.14.0',
+      'cachecontrol-with-filecache==0.14.0',
+      'cached-property==1.5.2',
+      'cached_property==1.5.2',
+      'certifi==2024.2.2',
+      'cffi==1.16.0',
+      'charset-normalizer==3.3.2',
+      'chex==0.1.86',
+      'cleo==2.1.0',
+      'click==8.1.7',
+      'colorama==0.4.6',
+      'contextlib2==21.6.0',
+      'contourpy==1.2.1',
+      'crashtest==0.4.1',
+      'croniter==1.3.15',
+      'cryptography==42.0.7',
+      'cycler==0.12.1',
+      'dateutils==0.6.12',
+      'dav1d==1.2.1',
+      'dbus==1.13.6',
+      'deepdiff==7.0.1',
+      'distlib==0.3.8',
+      'dnspython==2.6.1',
+      'docrep==0.3.2',
+      'dulwich==0.21.7',
+      'email-validator==2.1.1',
+      'email_validator==2.1.1',
+      'et_xmlfile==1.1.0',
+      'etils==1.6.0',
+      'exceptiongroup==1.2.0',
+      'expat==2.6.2',
+      'fastapi==0.111.0',
+      'fastapi-cli==0.0.4',
+      'filelock==3.14.0',
+      'flax==0.8.3',
+      'fonttools==4.51.0',
+      'freetype==2.12.1',
+      'fsspec==2023.12.2',
+      'get-annotations==0.1.2',
+      'gmp==6.3.0',
+      'gmpy2==2.1.5',
+      'h11==0.14.0',
+      'h2==4.1.0',
+      'h5py==3.11.0',
+      'hdf5==1.14.3',
+      'hpack==4.0.0',
+      'httpcore==1.0.5',
+      'httpx==0.27.0',
+      'hyperframe==6.0.1',
+      'icu==73.2',
+      'idna==3.7',
+      'importlib-metadata==7.1.0',
+      'importlib-resources==6.4.0',
+      'importlib_metadata==7.1.0',
+      'importlib_resources==6.4.0',
+      'inquirer==3.1.4',
+      'itsdangerous==2.2.0',
+      'jaraco.classes==3.4.0',
+      'jax==0.4.27',
+      'jaxlib==0.4.23',
+      'jeepney==0.8.0',
+      'jinja2==3.1.4',
+      'jmespath==1.0.1',
+      'joblib==1.4.2',
+      'keyring==24.3.1',
+      'keyutils==1.6.1',
+      'kiwisolver==1.4.5',
+      'krb5==1.21.2',
+      'lcms2==2.16',
+      'ld_impl_linux-64==2.40',
+      'legacy-api-wrap==1.4',
+      'lerc==4.0.0',
+      'libabseil==20240116.2',
+      'libaec==1.1.3',
+      'libavif16==1.0.4',
+      'libblas==3.9.0',
+      'libbrotlicommon==1.1.0',
+      'libbrotlidec==1.1.0',
+      'libbrotlienc==1.1.0',
+      'libcblas==3.9.0',
+      'libcurl==8.8.0',
+      'libdeflate==1.20',
+      'libedit==3.1.20191231',
+      'libev==4.33',
+      'libexpat==2.6.2',
+      'libffi==3.4.2',
+      'libgcc-ng==13.2.0',
+      'libgfortran-ng==13.2.0',
+      'libgfortran5==13.2.0',
+      'libglib==2.80.2',
+      'libgomp==13.2.0',
+      'libgrpc==1.62.2',
+      'libhwloc==2.10.0',
+      'libiconv==1.17',
+      'libjpeg-turbo==3.0.0',
+      'liblapack==3.9.0',
+      'libllvm14==14.0.6',
+      'libnghttp2==1.58.0',
+      'libnsl==2.0.1',
+      'libopenblas==0.3.27',
+      'libpng==1.6.43',
+      'libprotobuf==4.25.3',
+      'libre2-11==2023.09.01',
+      'libsqlite==3.45.3',
+      'libssh2==1.11.0',
+      'libstdcxx-ng==13.2.0',
+      'libtiff==4.6.0',
+      'libtorch==2.3.0',
+      'libuuid==2.38.1',
+      'libuv==1.48.0',
+      'libwebp-base==1.4.0',
+      'libxcb==1.15',
+      'libxml2==2.12.7',
+      'libzlib==1.2.13',
+      'lightning==2.0.4',
+      'lightning-cloud==0.5.69',
+      'lightning-utilities==0.11.2',
+      'llvmlite==0.42.0',
+      'loompy==3.0.6',
+      'lz4-c==1.9.4',
+      'markdown-it-py==3.0.0',
+      'markupsafe==2.1.5',
+      'matplotlib-base==3.8.4',
+      'mdurl==0.1.2',
+      'ml-collections==0.1.1',
+      'ml_dtypes==0.4.0',
+      'more-itertools==10.2.0',
+      'mpc==1.3.1',
+      'mpfr==4.2.1',
+      'mpmath==1.3.0',
+      'msgpack-python==1.0.8',
+      'mudata==0.2.3',
+      'multipledispatch==0.6.0',
+      'munkres==1.1.4',
+      'natsort==8.4.0',
+      'ncurses==6.5',
+      'nest-asyncio==1.6.0',
+      'networkx==3.2.1',
+      'nomkl==1.0',
+      'numba==0.59.1',
+      'numpy==1.26.4',
+      'numpy_groupies==0.11.1',
+      'numpyro==0.15.0',
+      'openjpeg==2.5.2',
+      'openpyxl==3.1.2',
+      'openssl==3.3.0',
+      'opt-einsum==3.3.0',
+      'opt_einsum==3.3.0',
+      'optax==0.2.2',
+      'orbax-checkpoint==0.4.4',
+      'ordered-set==4.1.0',
+      'orjson==3.10.3',
+      'packaging==24.0',
+      'pandas==2.2.2',
+      'patsy==0.5.6',
+      'pcre2==10.43',
+      'pexpect==4.9.0',
+      'pillow==10.3.0',
+      'pip==24.0',
+      'pkginfo==1.10.0',
+      'platformdirs==4.2.2',
+      'poetry==1.8.3',
+      'poetry-core==1.9.0',
+      'poetry-plugin-export==1.8.0',
+      'protobuf==4.25.3',
+      'psutil==5.9.8',
+      'pthread-stubs==0.4',
+      'ptyprocess==0.7.0',
+      'pybind11-abi==4',
+      'pycparser==2.22',
+      'pydantic==2.7.1',
+      'pydantic-core==2.18.2',
+      'pygments==2.18.0',
+      'pyjwt==2.8.0',
+      'pynndescent==0.5.12',
+      'pyparsing==3.1.2',
+      'pyproject_hooks==1.1.0',
+      'pyro-api==0.1.2',
+      'pyro-ppl==1.9.0',
+      'pysocks==1.7.1',
+      'python==3.9.12',
+      'python-build==1.2.1',
+      'python-dateutil==2.9.0',
+      'python-editor==1.0.4',
+      'python-fastjsonschema==2.19.1',
+      'python-installer==0.7.0',
+      'python-multipart==0.0.9',
+      'python-tzdata==2024.1',
+      'python_abi==3.9',
+      'pytorch==2.3.0',
+      'pytorch-lightning==2.2.2',
+      'pytz==2024.1',
+      'pyyaml==6.0.1',
+      'rapidfuzz==3.9.1',
+      'rav1e==0.6.6',
+      're2==2023.09.01',
+      'readchar==4.1.0',
+      'readline==8.2',
+      'requests==2.32.2',
+      'requests-toolbelt==1.0.0',
+      'rich==13.7.1',
+      's3transfer==0.10.1',
+      'scanpy==1.10.1',
+      'scikit-learn==1.1.3',
+      'scipy==1.13.0',
+      'scvelo==0.3.2',
+      'scvi-tools==1.1.2',
+      'seaborn==0.13.2',
+      'seaborn-base==0.13.2',
+      'secretstorage==3.3.3',
+      'session-info==1.0.0',
+      'setuptools==70.0.0',
+      'shellingham==1.5.4',
+      'six==1.16.0',
+      'sleef==3.5.1',
+      'snappy==1.2.0',
+      'sniffio==1.3.1',
+      'soupsieve==2.5',
+      'sparse==0.15.3',
+      'sqlite==3.45.3',
+      'starlette==0.37.2',
+      'starsessions==1.3.0',
+      'statsmodels==0.14.2',
+      'stdlib-list==0.10.0',
+      'svt-av1==2.1.0',
+      'sympy==1.12',
+      'tbb==2021.12.0',
+      'tensorstore==0.1.59',
+      'threadpoolctl==3.5.0',
+      'tk==8.6.13',
+      'tomli==2.0.1',
+      'tomlkit==0.12.5',
+      'toolz==0.12.1',
+      'torchmetrics==1.4.0.post0',
+      'tqdm==4.66.4',
+      'traitlets==5.14.3',
+      'trove-classifiers==2024.5.22',
+      'typer==0.12.3',
+      'typer-slim==0.12.3',
+      'typer-slim-standard==0.12.3',
+      'types-python-dateutil==2.9.0.20240316',
+      'typing-extensions==4.11.0',
+      'typing_extensions==4.11.0',
+      'tzdata==2024a',
+      'ujson==5.10.0',
+      'umap-learn==0.5.5',
+      'unicodedata2==15.1.0',
+      'urllib3==1.26.18',
+      'uvicorn==0.29.0',
+      'virtualenv==20.26.2',
+      'wcwidth==0.2.13',
+      'websocket-client==1.8.0',
+      'websockets==11.0.3',
+      'wheel==0.43.0',
+      'xarray==2024.5.0',
+      'xlrd==1.2.0',
+      'xorg-libxau==1.0.11',
+      'xorg-libxdmcp==1.1.3',
+      'xz==5.2.6',
+      'yaml==0.2.5',
+      'zipp==3.17.0',
+      'zstd==1.5.6'
+    )
+  )
+)
+
+if (basilisk.utils::isWindows()) {
+  .scvelo_dependencies <- .scvelo.dependencies.Windows
+} else if (basilisk.utils::isLinux()) {
+  .scvelo_dependencies <- .scvelo.dependencies.Linux
+} else if (basilisk.utils::isMacOSX()) {
+  .scvelo_dependencies <- .scvelo.dependencies.MacOSX
+} else if (basilisk.utils::isMacOSXArm()) {
+  .scvelo_dependencies <- .scvelo.dependencies.MacOSXArm
+} else {
+  stop("Unsupported operating system or architecture.\n  Please open an issue at <https://github.com/kevinrue/velociraptor/issues> to request support.")
+}
 
 #' @importFrom basilisk BasiliskEnvironment
 #' @importFrom zellkonverter AnnDataDependencies
 velo.env <- BasiliskEnvironment("env", "velociraptor",
-    packages=.scvelo_dependencies, channels = c("bioconda", "conda-forge"))
+  packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels)
diff --git a/R/scvelo.R b/R/scvelo.R
index 85387f8..fe8548c 100644
--- a/R/scvelo.R
+++ b/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:
@@ -124,12 +149,12 @@
 #'
 #' # make scvelo use 10 rather than the default 30 neighbors to compute moments for velocity estimation:
 #' out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced),
-#'               scvelo.params=list(moments=list(n_neighbors=10L)))
+#'               scvelo.params=list(neighbors=list(n_neighbors=10L)))
 #'
 #' @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
 NULL
 
@@ -138,6 +163,7 @@ NULL
 #' @importFrom BiocSingular bsparam runPCA
 #' @importFrom BiocParallel SerialParam
 #' @importFrom Matrix t
+#' @importFrom zellkonverter AnnData2SCE
 .scvelo <- function(x, subset.row=NULL,
     sf.X=NULL, sf.spliced=NULL, sf.unspliced=NULL,
     use.theirs=FALSE,
@@ -148,35 +174,35 @@ NULL
     spliced <- x$spliced
     unspliced <- x$unspliced
     X <- x$X
-
+    
     refdim <- as.integer(dim(spliced))
     if (!identical(refdim, as.integer(dim(unspliced))) || !identical(refdim, as.integer(dim(X)))) {
         stop("matrices in 'x' must have the same dimensions")
     }
-
+    
     if (!use.theirs) {
         X <- normalizeCounts(X, sf.X, log=TRUE)
         spliced <- normalizeCounts(spliced, sf.spliced, log=FALSE)
         unspliced <- normalizeCounts(unspliced, sf.unspliced, log=FALSE)
-
+        
         if (!is.null(subset.row)) {
             X <- X[subset.row,,drop=FALSE]
             spliced <- spliced[subset.row,,drop=FALSE]
             unspliced <- unspliced[subset.row,,drop=FALSE]
         }
-
+        
         if (is.null(dimred)) {
             dimred <- runPCA(t(X), rank=ncomponents, BSPARAM=BSPARAM, BPPARAM=BPPARAM)$x
         }
     }
-
+    
     mode <- match.arg(mode)
     output <- basiliskRun(env=velo.env, fun=.run_scvelo,
         X=X, spliced=spliced, unspliced=unspliced,
         use.theirs=use.theirs, mode=mode,
         scvelo.params=scvelo.params,
         dimred=dimred, testload = c("scvelo", "anndata"))
-
+    
     output
 }
 
@@ -184,42 +210,61 @@ NULL
     X <- t(velociraptor:::.make_np_friendly(X))
     spliced <- t(velociraptor:::.make_np_friendly(spliced))
     unspliced <- t(velociraptor:::.make_np_friendly(unspliced))
-
+    
     and <- reticulate::import("anndata")
     scv <- reticulate::import("scvelo")
+    sc <- reticulate::import("scanpy")
     adata <- and$AnnData(X, layers=list(spliced=spliced, unspliced=unspliced))
     adata$obs_names <- rownames(spliced)
     adata$var_names <- colnames(spliced)
-
+    
     ## A supplied dimred will be used even if use.theirs=TRUE
     if (!is.null(dimred)) {
         dimred <- velociraptor:::.make_np_friendly(dimred)
         adata$obsm <- list(X_pca = dimred)
     }
-
+    
     if (use.theirs) {
         do.call(scv$pp$filter_and_normalize, c(list(data=adata), scvelo.params$filter_and_normalize))
     }
-
+    
+    do.call(sc$pp$neighbors, c(list(adata), scvelo.params$neighbors))
+    
+    if (!is.null(scvelo.params$moments)) {
+        if (!is.null(scvelo.params$moments$n_neighbors)) {
+            stop("scvelo.params$moments$n_neighbors is deprecated; use scvelo.params$neighbors$n_neighbors instead")
+        }
+        if (!is.null(scvelo.params$moments$n_pcs)) {
+            stop("scvelo.params$moments$n_pcs is deprecated; use scvelo.params$neighbors$n_pcs instead")
+        }
+    } else {
+        # if unspecified, set to NULL (= None)
+        # see https://github.com/theislab/scvelo/issues/1212
+        scvelo.params$moments <- list(
+            n_neighbors = NULL,
+            n_pcs = NULL
+        )
+    }
+    
     do.call(scv$pp$moments, c(list(data=adata), scvelo.params$moments))
-
+    
     if (mode=="dynamical") {
         do.call(scv$tl$recover_dynamics, c(list(data=adata), scvelo.params$recover_dynamics))
     }
-
+    
     scvelo.params$velocity$mode <- mode
     do.call(scv$tl$velocity, c(list(data=adata), scvelo.params$velocity))
-
+    
     do.call(scv$tl$velocity_graph, c(list(data=adata), scvelo.params$velocity_graph))
-
+    
     do.call(scv$tl$velocity_pseudotime, c(list(adata=adata), scvelo.params$velocity_pseudotime))
-
+    
     if (mode=="dynamical") {
         do.call(scv$tl$latent_time, c(list(data=adata), scvelo.params$latent_time))
     }
-
+    
     do.call(scv$tl$velocity_confidence, c(list(data=adata), scvelo.params$velocity_confidence))
-
+    
     zellkonverter::AnnData2SCE(adata)
 }
 
diff --git a/man/scvelo.Rd b/man/scvelo.Rd
index 2158660..512c46a 100644
--- a/man/scvelo.Rd
+++ b/man/scvelo.Rd
@@ -93,7 +93,7 @@ containing the velocity pseudotime for each cell.
 containing the velocity vectors for each cell.
 }
 The output will always have number of columns equal to the number of cells supplied in \code{x},
-though the number of rows will depend on whether any subsetting (if \code{subset.row} is supplied) 
+though the number of rows will depend on whether any subsetting (if \code{subset.row} is supplied)
 or feature selection (if \code{use.theirs=TRUE}) was performed.
 }
 \description{
@@ -167,6 +167,33 @@ The PCA is not performed if \code{dimred} or \code{use.dimred} is already suppli
 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}).
+}
+}
+}
+
 \examples{
 # Using mock data to demonstrate the process:
 library(scuttle)
@@ -179,13 +206,13 @@ unspliced <- counts(sce2)
 out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced))
 
 # make scvelo use 10 rather than the default 30 neighbors to compute moments for velocity estimation:
-out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced), 
-              scvelo.params=list(moments=list(n_neighbors=10L))) 
+out <- scvelo(list(X=spliced, spliced=spliced, unspliced=unspliced),
+              scvelo.params=list(neighbors=list(n_neighbors=10L)))
 
 }
 \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
+Aaron Lun, Charlotte Soneson, Kevin Rue-Albrecht
 }
diff --git a/vignettes/velociraptor.Rmd b/vignettes/velociraptor.Rmd
index f5e6329..18b4297 100644
--- a/vignettes/velociraptor.Rmd
+++ b/vignettes/velociraptor.Rmd
@@ -64,11 +64,20 @@ top.hvgs <- getTopHVGs(dec, n=2000)
 
 We can plug these choices into the `scvelo()` function with our `SingleCellExperiment` object.
 By default, `scvelo()` uses the steady-state approach to estimate velocities,
-though the stochastic and dynamical models implemented in `r basilisk::PyPiLink("scvelo")` can also be used by modifying the `mode` argument. 
+though the stochastic and dynamical models implemented in `r basilisk::PyPiLink("scvelo")` can also be used by modifying the `mode` argument.
+
+Note that automatic neighbor calculation is deprecated since scvelo==0.4.0 and will be removed in a future version.
+Instead, `r BiocStyle::Biocpkg("velociraptor")` computes neighbors with Scanpy (as per [scVelo recommendations](https://github.com/theislab/scvelo/blob/f21651c3b122860d8ae6b5a5173f242ba91c8761/scvelo/preprocessing/moments.py#L66)), and the number of neighbors should be supplied to [scanpy.pp.neighbors](https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html) as demonstrated below.
+
+In particular, the default number of neighbors was 30 for [scvelo.pp.moments](https://scvelo.readthedocs.io/en/stable/scvelo.pp.moments.html) while it is 15 for [scanpy.pp.neighbors](https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html).
+Users should use `scvelo.params=list(neighbors=list(n_neighbors=30L)` to reproduce earlier results.
 
 ```{r}
 library(velociraptor)
-velo.out <- scvelo(sce, subset.row=top.hvgs, assay.X="spliced")
+velo.out <- scvelo(
+  sce, subset.row=top.hvgs, assay.X="spliced",
+  scvelo.params=list(neighbors=list(n_neighbors=30L))
+)
 velo.out
 ```
 
@@ -88,7 +97,7 @@ library(scater)
 
 set.seed(100)
 sce <- runPCA(sce, subset_row=top.hvgs)
-sce <- runTSNE(sce, dimred="PCA")
+sce <- runTSNE(sce, dimred="PCA", perplexity = 30)
 
 sce$velocity_pseudotime <- velo.out$velocity_pseudotime
 plotTSNE(sce, colour_by="velocity_pseudotime")