Get scvelo going on Windows using reticulate and conda

velocity_windows.R

# Install R infrastructure
pkg_install <- c("reticulate", "zellkonverter")
BiocManager::install(pkg_install, update = FALSE)

# Install conda itself via the reticulate package, takes time...
reticulate::install_miniconda()

# Create an environment for velocity with a specific python version that is required
# to install a downgraded matplotlib, see below
reticulate::conda_create(envname = "velocity", python_version = "3.8.19")

# Directly from https://github.com/kevinrue/velociraptor/blob/devel/R/basilisk.R#L3C1-L157C2
# because manual install always resulted in conflicts with matplotlib, see https://github.com/theislab/scvelo/issues/1124
velocity_env_conda <- list(
  channels = c("bioconda", "conda-forge"),
  packages = c(
    'anndata==0.9.2',
    'blosc==1.21.6',
    'brotli==1.1.0',
    'brotli-bin==1.1.0',
    'brotli-python==1.1.0',
    'bzip2==1.0.8',
    'ca-certificates==2024.7.4',
    'cached-property==1.5.2',
    'cached_property==1.5.2',
    'certifi==2024.7.4',
    'cffi==1.17.0',
    'charset-normalizer==3.3.2',
    'colorama==0.4.6',
    'contourpy==1.1.1',
    'cycler==0.12.1',
    'fonttools==4.53.1',
    'freetype==2.12.1',
    'glib==2.80.3',
    'glib-tools==2.80.3',
    'gst-plugins-base==1.24.6',
    'gstreamer==1.24.6',
    'h2==4.1.0',
    'h5py==3.8.0',
    'hdf5==1.14.0',
    'hpack==4.0.0',
    'hyperframe==6.0.1',
    'icu==73.2',
    'idna==3.8',
    'importlib-metadata==8.4.0',
    'importlib_metadata==8.4.0',
    'intel-openmp==2024.2.1',
    'jinja2==3.0.3',
    'joblib==1.4.2',
    'kiwisolver==1.4.5',
    'krb5==1.21.3',
    '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==18.1.8',
    'libcurl==8.9.1',
    'libdeflate==1.21',
    'libffi==3.4.2',
    'libglib==2.80.3',
    'libhwloc==2.11.1',
    'libiconv==1.17',
    'libintl==0.22.5',
    'libintl-devel==0.22.5',
    'libjpeg-turbo==3.0.0',
    'liblapack==3.9.0',
    'libogg==1.3.5',
    'libpng==1.6.43',
    'libsqlite==3.46.0',
    'libssh2==1.11.0',
    'libtiff==4.6.0',
    'libvorbis==1.3.7',
    'libwebp-base==1.4.0',
    'libxcb==1.16',
    'libxml2==2.12.7',
    'libzlib==1.3.1',
    'llvmlite==0.39.1',
    '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',
    'markupsafe==2.1.5',
    '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==3.1',
    'numba==0.56.4',
    'numexpr==2.7.3',
    'numpy==1.21.1',
    'openjpeg==2.5.2',
    'openssl==3.3.1',
    'packaging==24.1',
    'pandas==1.5.2',
    'patsy==0.5.6',
    'pcre2==10.44',
    'pillow==10.4.0',
    'pip==24.2',
    'platformdirs==4.2.2',
    'ply==3.11',
    'pooch==1.8.2',
    'pthread-stubs==0.4',
    'pthreads-win32==2.9.1',
    'pycparser==2.22',
    'pynndescent==0.5.13',
    'pyparsing==3.1.4',
    'pyqt==5.15.9',
    'pyqt5-sip==12.12.2',
    'pysocks==1.7.1',
    'pytables==3.7.0',
    'python==3.8.19',
    'python-dateutil==2.9.0',
    'python_abi==3.8',
    'pytz==2024.1',
    'qt-main==5.15.8',
    'requests==2.32.3',
    'scanpy==1.7.2',
    'scikit-learn==1.2.2',
    'scipy==1.10.1',
    'scvelo==0.2.5',
    'seaborn==0.13.2',
    'seaborn-base==0.13.2',
    'setuptools==72.2.0',
    'setuptools-scm==8.1.0',
    'setuptools_scm==8.1.0',
    'sinfo==0.3.1',
    'sip==6.7.12',
    'six==1.16.0',
    'snappy==1.2.1',
    'statsmodels==0.13.5',
    '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==6.4.1',
    'tqdm==4.66.5',
    'typing==3.10.0.0',
    'typing-extensions==4.12.2',
    'typing_extensions==4.12.2',
    'ucrt==10.0.22621.0',
    'umap-learn==0.5.6',
    'unicodedata2==15.1.0',
    'urllib3==2.2.2',
    'vc==14.3',
    'vc14_runtime==14.40.33810',
    'vs2015_runtime==14.40.33810',
    'wheel==0.44.0',
    'win_inet_pton==1.1.0',
    'xorg-libxau==1.0.11',
    'xorg-libxdmcp==1.1.3',
    'xz==5.2.6',
    'zipp==3.20.1',
    'zstandard==0.23.0',
    'zstd==1.5.6'
  )
)

# Install scvelo into this environment using the above package tree
reticulate::conda_install(
  envname = "velocity", 
  packages = velocity_env_conda$packages,
  channel = velocity_env_conda$channels
)

# Load scvelo
reticulate::use_miniconda(condaenv = "velocity")
scv <- reticulate::import("scvelo")
scanpy <- reticulate::import("scanpy")

# ...