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add pip dependencies
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@kevinrue
kevinrue committed Aug 30, 2024
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180 changes: 68 additions & 112 deletions R/basilisk.R
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Original file line number Diff line number Diff line change
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## Windows ----

.scvelo.dependencies.Windows <- list(
channels = c("conda-forge", "bioconda"),
channels = c("conda-forge"),
packages = c(
'anndata==0.9.2',
'array-api-compat==1.8',
'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',
'click==8.1.7',
'colorama==0.4.6',
'contourpy==1.1.1',
'cycler==0.12.1',
'exceptiongroup==1.2.2',
'fonttools==4.53.1',
'freetype==2.12.1',
'get-annotations==0.1.2',
'gettext==0.22.5',
'gettext-tools==0.22.5',
'glib==2.80.2',
'glib-tools==2.80.2',
'gst-plugins-base==1.21.3',
'gstreamer==1.21.3',
'h2==4.1.0',
'h5py==3.9.0',
'hdf5==1.14.0',
'hpack==4.0.0',
'hyperframe==6.0.1',
'icu==70.1',
'idna==3.7',
'importlib-metadata==8.4.0',
'importlib-resources==6.4.4',
'importlib_resources==6.4.4',
'hdf5==1.14.3',
'intel-openmp==2024.2.1',
'joblib==1.4.2',
'jpeg==9e',
'kiwisolver==1.4.5',
'krb5==1.20.1',
'lcms2==2.12',
'legacy-api-wrap==1.4',
'krb5==1.21.3',
'lcms2==2.16',
'lerc==4.0.0',
'libaec==1.1.3',
'libasprintf==0.22.5',
'libasprintf-devel==0.22.5',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libclang==15.0.7',
'libclang13==15.0.7',
'libcurl==8.1.2',
'libcurl==8.9.1',
'libdeflate==1.21',
'libexpat==2.6.2',
'libffi==3.4.2',
'libgettextpo==0.22.5',
'libgettextpo-devel==0.22.5',
'libglib==2.80.2',
'libhwloc==2.11.1',
'libiconv==1.17',
'libintl==0.22.5',
'libintl-devel==0.22.5',
'libjpeg-turbo==2.1.4',
'libjpeg-turbo==3.0.0',
'liblapack==3.9.0',
'libogg==1.3.5',
'libpng==1.6.43',
'libsqlite==3.46.0',
'libssh2==1.10.0',
'libtiff==4.2.0',
'libvorbis==1.3.7',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libwebp-base==1.4.0',
'libxcb==1.16',
'libxml2==2.12.7',
'libzlib==1.2.13',
'llvmlite==0.41.1',
'loompy==3.0.6',
'libzlib==1.3.1',
'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==3.7.2',
'matplotlib-base==3.7.2',
'matplotlib-base==3.9.2',
'mkl==2024.1.0',
'msys2-conda-epoch==20160418',
'numpy_groupies==0.11.2',
'openjpeg==2.5.2',
'openssl==3.3.1',
'pthread-stubs==0.4',
'pthreads-win32==2.9.1',
'python==3.12.5',
'python-tzdata==2024.1',
'python_abi==3.12',
'qhull==2020.2',
'seaborn-base==0.13.2',
'tbb==2021.12.0',
'tk==8.6.13',
'typing_extensions==4.12.2',
'ucrt==10.0.22621.0',
'vc==14.3',
'vc14_runtime==14.40.33810',
'vs2015_runtime==14.40.33810',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'zstd==1.5.6'
),
pip = c(
'anndata==0.10.9',
'array-api-compat==1.8',
'cached-property==1.5.2',
'certifi==2024.7.4',
'click==8.1.7',
'colorama==0.4.6',
'contourpy==1.3.0',
'cycler==0.12.1',
'exceptiongroup==1.2.2',
'fonttools==4.53.1',
'get-annotations==0.1.2',
'h5py==3.11.0',
'joblib==1.4.2',
'kiwisolver==1.4.5',
'legacy-api-wrap==1.4',
'llvmlite==0.43.0',
'loompy==3.0.6',
'matplotlib==3.9.2',
'munkres==1.1.4',
'natsort==8.4.0',
'networkx==3.1',
'numba==0.58.1',
'numpy==1.24.4',
'numpy_groupies==0.9.22',
'olefile==0.47',
'openjpeg==2.4.0',
'openssl==1.1.1w',
'networkx==3.3',
'numba==0.60.0',
'numpy==1.26.4',
'numpy-groupies==0.11.2',
'packaging==24.1',
'pandas==2.0.3',
'pandas==2.2.2',
'patsy==0.5.6',
'pcre2==10.43',
'pillow==8.2.0',
'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==3.0.9',
'pyqt==5.15.7',
'pyqt5-sip==12.11.0',
'pysocks==1.7.1',
'python==3.8.0',
'pyparsing==3.1.4',
'python-dateutil==2.9.0',
'python-tzdata==2024.1',
'python_abi==3.8',
'pytz==2024.1',
'qhull==2020.2',
'qt-main==5.15.6',
'requests==2.32.3',
'scanpy==1.10.2',
'scikit-learn==1.3.2',
'scipy==1.10.1',
'scikit-learn==1.5.1',
'scipy==1.14.1',
'scvelo==0.2.5',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==72.2.0',
'sip==6.7.12',
'six==1.16.0',
'sqlite==3.46.0',
'statsmodels==0.14.1',
'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==6.4.1',
'tqdm==4.66.5',
'typing_extensions==4.12.2',
'tzdata==2024a',
'ucrt==10.0.22621.0',
'typing-extensions==4.12.2',
'tzdata==2024.1',
'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==3.20.0',
'zlib==1.2.13',
'zstandard==0.23.0',
'zstd==1.5.6'
'wheel==0.44.0'
)
)

## MacOSXArm ----

.scvelo.dependencies.MacOSXArm <- list(
channels = c("conda-forge", "bioconda"),
pip = character(0),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.7',
Expand Down Expand Up @@ -446,6 +400,7 @@

.scvelo.dependencies.MacOSX <- list(
channels = c("conda-forge", "bioconda"),
pip = character(0),
packages = c(
'absl-py==2.1.0',
'anndata==0.10.7',
Expand Down Expand Up @@ -722,6 +677,7 @@

.scvelo.dependencies.Linux <- list(
channels = c("anaconda", "conda-forge", "bioconda"),
pip = character(0),
packages = c(
'_libgcc_mutex==0.1',
'_openmp_mutex==4.5',
Expand Down Expand Up @@ -889,4 +845,4 @@ if (basilisk.utils::isWindows()) {
#' @importFrom basilisk BasiliskEnvironment
#' @importFrom zellkonverter AnnDataDependencies
velo.env <- BasiliskEnvironment("env", "velociraptor",
packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels)
packages=.scvelo_dependencies$packages, channels = .scvelo_dependencies$channels, pip = .scvelo_dependencies$pip)
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