R/basilisk.R
In kevinrue/velociraptor: Toolkit for Single-Cell Velocity
## Windows ----
.scvelo.dependencies.Windows <- 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'
)
)
## LinuxAarch64 ----
.scvelo.dependencies.LinuxAarch64 <- list(
channels = c("conda-forge"),
packages = c(
'ipywidgets==8.1.2',
'libtiff==4.5.1',
'pillow==10.0.0',
'scipy==1.13.1',
'scvelo==0.3.2',
'tqdm==4.66.5'
)
)
## Linux ----
.scvelo.dependencies.Linux <- list(
channels = c("conda-forge"),
packages = c(
'_libgcc_mutex==0.1',
'_openmp_mutex==4.5',
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'asttokens==2.4.1',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.8.30',
'cffi==1.17.1',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'comm==0.2.2',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'decorator==5.1.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.4',
'exceptiongroup==1.2.2',
'executing==2.1.0',
'filelock==3.16.1',
'flax==0.9.0',
'fonttools==4.54.1',
'freetype==2.12.1',
'fsspec==2024.9.0',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.10',
'importlib-metadata==8.5.0',
'importlib_metadata==8.5.0',
'importlib_resources==6.4.5',
'ipython==8.27.0',
'ipywidgets==8.1.2',
'jax==0.4.27',
'jaxlib==0.4.23',
'jedi==0.19.1',
'jinja2==3.1.4',
'joblib==1.4.2',
'jupyterlab_widgets==3.0.13',
'keyutils==1.6.1',
'kiwisolver==1.4.7',
'krb5==1.21.3',
'lcms2==2.15',
'ld_impl_linux-64==2.43',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20230802.1',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.10.1',
'libdeflate==1.18',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.3',
'libffi==3.4.2',
'libgcc==14.1.0',
'libgcc-ng==14.1.0',
'libgfortran==14.1.0',
'libgfortran-ng==14.1.0',
'libgfortran5==14.1.0',
'libgomp==14.1.0',
'libgrpc==1.58.2',
'libhwloc==2.11.1',
'libiconv==1.17',
'libjpeg-turbo==2.1.5.1',
'liblapack==3.9.0',
'libllvm14==14.0.6',
'libnghttp2==1.58.0',
'libnsl==2.0.1',
'libopenblas==0.3.27',
'libpng==1.6.44',
'libprotobuf==4.24.3',
'libre2-11==2023.09.01',
'libsqlite==3.46.1',
'libssh2==1.11.0',
'libstdcxx==14.1.0',
'libstdcxx-ng==14.1.0',
'libtiff==4.5.1',
'libuuid==2.38.1',
'libuv==1.49.0',
'libwebp-base==1.4.0',
'libxcb==1.15',
'libxcrypt==4.4.36',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.3.3',
'lightning-utilities==0.11.7',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'matplotlib-inline==0.1.7',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.5.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.1.0',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.3',
'openjpeg==2.5.0',
'openpyxl==3.1.5',
'openssl==3.3.2',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.3',
'parso==0.8.4',
'patsy==0.5.6',
'pexpect==4.9.0',
'pickleshare==0.7.5',
'pillow==10.0.0',
'pip==24.2',
'prompt-toolkit==3.0.48',
'protobuf==4.24.3',
'pthread-stubs==0.4',
'ptyprocess==0.7.0',
'pure_eval==0.2.3',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.10',
'python-dateutil==2.9.0',
'python-tzdata==2024.2',
'python_abi==3.11',
'pytorch==2.0.0',
'pytorch-lightning==2.3.3',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.8.1',
'scanpy==1.10.3',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6.post1',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==75.1.0',
'six==1.16.0',
'sleef==3.7',
'snappy==1.2.1',
'sparse==0.15.4',
'stack_data==0.6.2',
'statsmodels==0.14.3',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.13.0',
'tensorstore==0.1.44',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.2',
'tqdm==4.66.5',
'traitlets==5.14.3',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.3',
'wcwidth==0.2.13',
'wheel==0.44.0',
'widgetsnbextension==4.0.13',
'xarray==2024.9.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.2',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
## MacOSXArm ----
.scvelo.dependencies.MacOSXArm <- list(
channels = c("conda-forge"),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'asttokens==2.4.1',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.8.30',
'cffi==1.17.1',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'comm==0.2.2',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'decorator==5.1.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.4',
'exceptiongroup==1.2.2',
'executing==2.1.0',
'filelock==3.16.0',
'flax==0.9.0',
'fonttools==4.53.1',
'freetype==2.12.1',
'fsspec==2024.9.0',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.8',
'importlib-metadata==8.4.0',
'importlib_resources==6.4.4',
'ipython==8.27.0',
'ipywidgets==8.1.5',
'jax==0.4.31',
'jaxlib==0.4.31',
'jedi==0.19.1',
'jinja2==3.1.4',
'joblib==1.4.2',
'jupyterlab_widgets==3.0.13',
'kiwisolver==1.4.7',
'krb5==1.21.3',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.9.1',
'libcxx==18.1.8',
'libdeflate==1.21',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.3',
'libffi==3.4.2',
'libgfortran==5.0.0',
'libgfortran5==13.2.0',
'libgrpc==1.62.2',
'libhwloc==2.11.1',
'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==3.46.1',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libtorch==2.4.0',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.4.0',
'lightning-utilities==0.11.7',
'llvm-openmp==18.1.8',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'matplotlib-inline==0.1.7',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.3.2',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.2',
'parso==0.8.4',
'patsy==0.5.6',
'pexpect==4.9.0',
'pickleshare==0.7.5',
'pillow==10.4.0',
'pip==24.2',
'prompt-toolkit==3.0.47',
'protobuf==4.25.3',
'pthread-stubs==0.4',
'ptyprocess==0.7.0',
'pure_eval==0.2.3',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.9',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python_abi==3.11',
'pytorch==2.4.0',
'pytorch-lightning==2.4.0',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.7.1',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==73.0.1',
'six==1.16.0',
'sleef==3.6.1',
'snappy==1.2.1',
'sparse==0.15.4',
'stack_data==0.6.2',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.13.0',
'tensorstore==0.1.62',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.5',
'traitlets==5.14.3',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.2',
'wcwidth==0.2.13',
'wheel==0.44.0',
'widgetsnbextension==4.0.13',
'xarray==2024.7.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.1',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
## MacOSX ----
.scvelo.dependencies.MacOSX <- list(
channels = c("conda-forge", "bioconda"),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.7.4',
'cffi==1.17.0',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.2',
'exceptiongroup==1.2.2',
'filelock==3.15.4',
'flax==0.9.0',
'fonttools==4.53.1',
'freetype==2.12.1',
'fsspec==2024.6.1',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.8',
'importlib-metadata==8.4.0',
'importlib_metadata==8.4.0',
'importlib_resources==6.4.4',
'jax==0.4.31',
'jaxlib==0.4.31',
'jinja2==3.1.4',
'joblib==1.4.2',
'kiwisolver==1.4.5',
'krb5==1.21.3',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.9.1',
'libcxx==18.1.8',
'libdeflate==1.21',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.2',
'libffi==3.4.2',
'libgfortran==5.0.0',
'libgfortran5==13.2.0',
'libgrpc==1.62.2',
'libhwloc==2.11.1',
'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==3.46.0',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libtorch==2.4.0',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.4.0',
'lightning-utilities==0.11.6',
'llvm-openmp==18.1.8',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.3.1',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.2',
'patsy==0.5.6',
'pillow==10.4.0',
'pip==24.2',
'protobuf==4.25.3',
'pthread-stubs==0.4',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.9',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python_abi==3.11',
'pytorch==2.4.0',
'pytorch-lightning==2.4.0',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.7.1',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==72.2.0',
'six==1.16.0',
'sleef==3.6.1',
'snappy==1.2.1',
'sparse==0.15.4',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.12.0',
'tensorstore==0.1.62',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.5',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.2',
'wheel==0.44.0',
'xarray==2024.7.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.1',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
# Switch environment ----
if (basilisk.utils::isWindows()) {
.scvelo_dependencies <- .scvelo.dependencies.Windows
} else if (basilisk.utils::isLinuxAarch64()) {
.scvelo_dependencies <- .scvelo.dependencies.LinuxAarch64
} else if (basilisk.utils::isLinux()) {
.scvelo_dependencies <- .scvelo.dependencies.Linux
} else if (basilisk.utils::isMacOSXArm()) {
.scvelo_dependencies <- .scvelo.dependencies.MacOSXArm
} else if (basilisk.utils::isMacOSX()) {
.scvelo_dependencies <- .scvelo.dependencies.MacOSX
} 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$packages, channels = .scvelo_dependencies$channels)
kevinrue/velociraptor documentation built on Oct. 12, 2024, 10:38 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
## Windows ----
.scvelo.dependencies.Windows <- 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'
)
)
## LinuxAarch64 ----
.scvelo.dependencies.LinuxAarch64 <- list(
channels = c("conda-forge"),
packages = c(
'ipywidgets==8.1.2',
'libtiff==4.5.1',
'pillow==10.0.0',
'scipy==1.13.1',
'scvelo==0.3.2',
'tqdm==4.66.5'
)
)
## Linux ----
.scvelo.dependencies.Linux <- list(
channels = c("conda-forge"),
packages = c(
'_libgcc_mutex==0.1',
'_openmp_mutex==4.5',
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'asttokens==2.4.1',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.8.30',
'cffi==1.17.1',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'comm==0.2.2',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'decorator==5.1.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.4',
'exceptiongroup==1.2.2',
'executing==2.1.0',
'filelock==3.16.1',
'flax==0.9.0',
'fonttools==4.54.1',
'freetype==2.12.1',
'fsspec==2024.9.0',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.10',
'importlib-metadata==8.5.0',
'importlib_metadata==8.5.0',
'importlib_resources==6.4.5',
'ipython==8.27.0',
'ipywidgets==8.1.2',
'jax==0.4.27',
'jaxlib==0.4.23',
'jedi==0.19.1',
'jinja2==3.1.4',
'joblib==1.4.2',
'jupyterlab_widgets==3.0.13',
'keyutils==1.6.1',
'kiwisolver==1.4.7',
'krb5==1.21.3',
'lcms2==2.15',
'ld_impl_linux-64==2.43',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20230802.1',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.10.1',
'libdeflate==1.18',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.3',
'libffi==3.4.2',
'libgcc==14.1.0',
'libgcc-ng==14.1.0',
'libgfortran==14.1.0',
'libgfortran-ng==14.1.0',
'libgfortran5==14.1.0',
'libgomp==14.1.0',
'libgrpc==1.58.2',
'libhwloc==2.11.1',
'libiconv==1.17',
'libjpeg-turbo==2.1.5.1',
'liblapack==3.9.0',
'libllvm14==14.0.6',
'libnghttp2==1.58.0',
'libnsl==2.0.1',
'libopenblas==0.3.27',
'libpng==1.6.44',
'libprotobuf==4.24.3',
'libre2-11==2023.09.01',
'libsqlite==3.46.1',
'libssh2==1.11.0',
'libstdcxx==14.1.0',
'libstdcxx-ng==14.1.0',
'libtiff==4.5.1',
'libuuid==2.38.1',
'libuv==1.49.0',
'libwebp-base==1.4.0',
'libxcb==1.15',
'libxcrypt==4.4.36',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.3.3',
'lightning-utilities==0.11.7',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'matplotlib-inline==0.1.7',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.5.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.1.0',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.3',
'openjpeg==2.5.0',
'openpyxl==3.1.5',
'openssl==3.3.2',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.3',
'parso==0.8.4',
'patsy==0.5.6',
'pexpect==4.9.0',
'pickleshare==0.7.5',
'pillow==10.0.0',
'pip==24.2',
'prompt-toolkit==3.0.48',
'protobuf==4.24.3',
'pthread-stubs==0.4',
'ptyprocess==0.7.0',
'pure_eval==0.2.3',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.10',
'python-dateutil==2.9.0',
'python-tzdata==2024.2',
'python_abi==3.11',
'pytorch==2.0.0',
'pytorch-lightning==2.3.3',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.8.1',
'scanpy==1.10.3',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6.post1',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==75.1.0',
'six==1.16.0',
'sleef==3.7',
'snappy==1.2.1',
'sparse==0.15.4',
'stack_data==0.6.2',
'statsmodels==0.14.3',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.13.0',
'tensorstore==0.1.44',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.2',
'tqdm==4.66.5',
'traitlets==5.14.3',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.3',
'wcwidth==0.2.13',
'wheel==0.44.0',
'widgetsnbextension==4.0.13',
'xarray==2024.9.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.2',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
## MacOSXArm ----
.scvelo.dependencies.MacOSXArm <- list(
channels = c("conda-forge"),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'asttokens==2.4.1',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.8.30',
'cffi==1.17.1',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'comm==0.2.2',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'decorator==5.1.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.4',
'exceptiongroup==1.2.2',
'executing==2.1.0',
'filelock==3.16.0',
'flax==0.9.0',
'fonttools==4.53.1',
'freetype==2.12.1',
'fsspec==2024.9.0',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.8',
'importlib-metadata==8.4.0',
'importlib_resources==6.4.4',
'ipython==8.27.0',
'ipywidgets==8.1.5',
'jax==0.4.31',
'jaxlib==0.4.31',
'jedi==0.19.1',
'jinja2==3.1.4',
'joblib==1.4.2',
'jupyterlab_widgets==3.0.13',
'kiwisolver==1.4.7',
'krb5==1.21.3',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.9.1',
'libcxx==18.1.8',
'libdeflate==1.21',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.3',
'libffi==3.4.2',
'libgfortran==5.0.0',
'libgfortran5==13.2.0',
'libgrpc==1.62.2',
'libhwloc==2.11.1',
'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==3.46.1',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libtorch==2.4.0',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.4.0',
'lightning-utilities==0.11.7',
'llvm-openmp==18.1.8',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'matplotlib-inline==0.1.7',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.3.2',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.2',
'parso==0.8.4',
'patsy==0.5.6',
'pexpect==4.9.0',
'pickleshare==0.7.5',
'pillow==10.4.0',
'pip==24.2',
'prompt-toolkit==3.0.47',
'protobuf==4.25.3',
'pthread-stubs==0.4',
'ptyprocess==0.7.0',
'pure_eval==0.2.3',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.9',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python_abi==3.11',
'pytorch==2.4.0',
'pytorch-lightning==2.4.0',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.7.1',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==73.0.1',
'six==1.16.0',
'sleef==3.6.1',
'snappy==1.2.1',
'sparse==0.15.4',
'stack_data==0.6.2',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.13.0',
'tensorstore==0.1.62',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.5',
'traitlets==5.14.3',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.2',
'wcwidth==0.2.13',
'wheel==0.44.0',
'widgetsnbextension==4.0.13',
'xarray==2024.7.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.1',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
## MacOSX ----
.scvelo.dependencies.MacOSX <- list(
channels = c("conda-forge", "bioconda"),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.9',
'aom==3.9.1',
'array-api-compat==1.8',
'blosc==1.21.6',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.33.1',
'ca-certificates==2024.8.30',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.7.4',
'cffi==1.17.0',
'charset-normalizer==3.3.2',
'chex==0.1.86',
'click==8.1.7',
'colorama==0.4.6',
'contextlib2==21.6.0',
'contourpy==1.3.0',
'cycler==0.12.1',
'dav1d==1.2.1',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'etils==1.9.2',
'exceptiongroup==1.2.2',
'filelock==3.15.4',
'flax==0.9.0',
'fonttools==4.53.1',
'freetype==2.12.1',
'fsspec==2024.6.1',
'get-annotations==0.1.2',
'gmp==6.3.0',
'gmpy2==2.1.5',
'h2==4.1.0',
'h5py==3.11.0',
'hdf5==1.14.3',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==75.1',
'idna==3.8',
'importlib-metadata==8.4.0',
'importlib_metadata==8.4.0',
'importlib_resources==6.4.4',
'jax==0.4.31',
'jaxlib==0.4.31',
'jinja2==3.1.4',
'joblib==1.4.2',
'kiwisolver==1.4.5',
'krb5==1.21.3',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.1.1',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.9.1',
'libcxx==18.1.8',
'libdeflate==1.21',
'libedit==3.1.20191231',
'libev==4.33',
'libexpat==2.6.2',
'libffi==3.4.2',
'libgfortran==5.0.0',
'libgfortran5==13.2.0',
'libgrpc==1.62.2',
'libhwloc==2.11.1',
'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==3.46.0',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libtorch==2.4.0',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxml2==2.12.7',
'libzlib==1.3.1',
'lightning==2.4.0',
'lightning-utilities==0.11.6',
'llvm-openmp==18.1.8',
'llvmlite==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib-base==3.9.2',
'mdurl==0.1.2',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'mudata==0.3.1',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.3',
'nomkl==1.0',
'numba==0.60.0',
'numpy==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.15.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.3.1',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'packaging==24.1',
'pandas==2.2.2',
'patsy==0.5.6',
'pillow==10.4.0',
'pip==24.2',
'protobuf==4.25.3',
'pthread-stubs==0.4',
'pybind11-abi==4',
'pycparser==2.22',
'pygments==2.18.0',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'pysocks==1.7.1',
'python==3.11.9',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python_abi==3.11',
'pytorch==2.4.0',
'pytorch-lightning==2.4.0',
'pytz==2024.1',
'pyyaml==6.0.2',
'qhull==2020.2',
'rav1e==0.6.6',
're2==2023.09.01',
'readline==8.2',
'requests==2.32.3',
'rich==13.7.1',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==1.1.6',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==72.2.0',
'six==1.16.0',
'sleef==3.6.1',
'snappy==1.2.1',
'sparse==0.15.4',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.2.1',
'sympy==1.13.2',
'tbb==2021.12.0',
'tensorstore==0.1.62',
'threadpoolctl==3.5.0',
'tk==8.6.13',
'toolz==0.12.1',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.5',
'typing-extensions==4.12.2',
'typing_extensions==4.12.2',
'tzdata==2024a',
'umap-learn==0.5.6',
'urllib3==2.2.2',
'wheel==0.44.0',
'xarray==2024.7.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zipp==3.20.1',
'zstandard==0.23.0',
'zstd==1.5.6'
)
)
# Switch environment ----
if (basilisk.utils::isWindows()) {
.scvelo_dependencies <- .scvelo.dependencies.Windows
} else if (basilisk.utils::isLinuxAarch64()) {
.scvelo_dependencies <- .scvelo.dependencies.LinuxAarch64
} else if (basilisk.utils::isLinux()) {
.scvelo_dependencies <- .scvelo.dependencies.Linux
} else if (basilisk.utils::isMacOSXArm()) {
.scvelo_dependencies <- .scvelo.dependencies.MacOSXArm
} else if (basilisk.utils::isMacOSX()) {
.scvelo_dependencies <- .scvelo.dependencies.MacOSX
} 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$packages, channels = .scvelo_dependencies$channels)
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