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woops updated env in R code too
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@kevinrue
kevinrue committed Aug 30, 2024
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208 changes: 94 additions & 114 deletions R/basilisk.R
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.scvelo.dependencies.Windows <- list(
channels = c("bioconda", "conda-forge"),
packages = c(
'_libgcc_mutex==0.1',
'_openmp_mutex==4.5',
'absl-py==2.1.0',
'anndata==0.10.9',
'array-api-compat==1.8',
'blas==1.0',
'bottleneck==1.3.7',
'brotli==1.0.9',
'brotli-bin==1.0.9',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'bzip2==1.0.8',
'c-ares==1.19.1',
'ca-certificates==2024.7.2',
'chex==0.1.5',
'click==8.1.7',
'contextlib2==21.6.0',
'contourpy==1.2.0',
'cycler==0.11.0',
'dm-tree==0.1.7',
'docrep==0.3.2',
'et_xmlfile==1.1.0',
'exceptiongroup==1.2.0',
'filelock==3.13.1',
'flax==0.6.1',
'fonttools==4.51.0',
'ca-certificates==2024.7.4',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.7.4',
'colorama==0.4.6',
'contourpy==1.3.0',
'cycler==0.12.1',
'exceptiongroup==1.2.2',
'fonttools==4.53.1',
'freetype==2.12.1',
'fsspec==2024.3.1',
'get-annotations==0.1.2',
'gmp==6.2.1',
'gmpy2==2.1.2',
'glib==2.80.3',
'glib-tools==2.80.3',
'gst-plugins-base==1.24.6',
'gstreamer==1.24.6',
'h5py==3.11.0',
'hdf5==1.12.1',
'jax==0.3.25',
'jaxlib==0.3.25',
'jinja2==3.1.4',
'hdf5==1.14.3',
'icu==73.2',
'intel-openmp==2024.2.1',
'joblib==1.4.2',
'jpeg==9e',
'kiwisolver==1.4.4',
'krb5==1.20.1',
'lcms2==2.12',
'ld_impl_linux-64==2.38',
'kiwisolver==1.4.5',
'krb5==1.21.3',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==3.0',
'lerc==4.0.0',
'libaec==1.1.3',
'libblas==3.9.0',
'libbrotlicommon==1.0.9',
'libbrotlidec==1.0.9',
'libbrotlienc==1.0.9',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==7.88.1',
'libdeflate==1.17',
'libedit==3.1.20230828',
'libev==4.33',
'libffi==3.4.4',
'libgcc==14.1.0',
'libgcc-ng==14.1.0',
'libgfortran-ng==11.2.0',
'libgfortran5==11.2.0',
'libgomp==14.1.0',
'libllvm14==14.0.6',
'libnghttp2==1.57.0',
'libopenblas==0.3.21',
'libpng==1.6.39',
'libprotobuf==3.20.3',
'libclang13==18.1.8',
'libcurl==8.9.1',
'libdeflate==1.21',
'libexpat==2.6.2',
'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',
'libstdcxx==14.1.0',
'libstdcxx-ng==14.1.0',
'libtiff==4.5.1',
'libuuid==1.41.5',
'libwebp-base==1.3.2',
'lightning-utilities==0.9.0',
'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==0.43.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==2.2.0',
'markupsafe==2.1.3',
'matplotlib-base==3.8.4',
'mdurl==0.1.0',
'ml-collections==0.1.1',
'mpc==1.1.0',
'mpfr==4.0.2',
'mpmath==1.3.0',
'msgpack-python==1.0.3',
'mudata==0.3.0',
'multipledispatch==0.6.0',
'natsort==7.1.1',
'ncurses==6.4',
'loompy==2.0.16',
'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==3.3',
'numba==0.60.0',
'numexpr==2.8.7',
'numpy==1.26.4',
'numpy-base==1.26.4',
'numpy_groupies==0.11.2',
'numpyro==0.13.2',
'openjpeg==2.5.2',
'openpyxl==3.1.5',
'openssl==3.0.14',
'opt_einsum==3.3.0',
'optax==0.1.4',
'openssl==3.3.1',
'packaging==24.1',
'pandas==2.2.2',
'pandas==1.5.2',
'patsy==0.5.6',
'pcre2==10.44',
'pillow==10.4.0',
'pip==24.2',
'pybind11-abi==4',
'pygments==2.15.1',
'pynndescent==0.5.10',
'pyparsing==3.0.9',
'pyro-api==0.1.2',
'pyro-ppl==1.9.1',
'ply==3.11',
'pthread-stubs==0.4',
'pthreads-win32==2.9.1',
'pynndescent==0.5.13',
'pyparsing==3.1.4',
'pyqt==5.15.9',
'pyqt5-sip==12.12.2',
'python==3.11.9',
'python-dateutil==2.9.0post0',
'python-tzdata==2023.3',
'python-dateutil==2.9.0',
'python_abi==3.11',
'pytorch==2.3.0',
'pytorch-lightning==1.9.5',
'pytz==2024.1',
'pyyaml==6.0.1',
'readline==8.2',
'rich==13.7.1',
'qt-main==5.15.8',
'scanpy==1.10.2',
'scikit-learn==1.1.3',
'scikit-learn==1.5.1',
'scipy==1.13.1',
'scvelo==0.3.2',
'scvi-tools==0.20.3',
'scvelo==0.2.5',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'session-info==1.0.0',
'setuptools==72.1.0',
'setuptools==72.2.0',
'sip==6.7.12',
'six==1.16.0',
'sqlite==3.45.3',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'sympy==1.12',
'tbb==2021.12.0',
'threadpoolctl==3.5.0',
'tk==8.6.14',
'toolz==0.12.0',
'torchmetrics==1.4.0.post0',
'tqdm==4.66.4',
'typing-extensions==4.11.0',
'typing_extensions==4.11.0',
'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',
'tzdata==2024a',
'umap-learn==0.5.3',
'unicodedata2==15.1.0',
'wheel==0.43.0',
'xz==5.4.6',
'yaml==0.2.5',
'zlib==1.2.13',
'zstd==1.5.5'
'ucrt==10.0.22621.0',
'umap-learn==0.5.6',
'vc==14.3',
'vc14_runtime==14.40.33810',
'vs2015_runtime==14.40.33810',
'wheel==0.44.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'zstd==1.5.6'
)
)

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2 changes: 1 addition & 1 deletion inst/envs/format_yaml_to_r.R
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library(yaml)
yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml")
yaml_data <- yaml::read_yaml("Windows.yaml")
r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies)
cat(paste0(
"c(",
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