diff --git a/R/basilisk.R b/R/basilisk.R index 29860f4..5b6c4cb 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -3,152 +3,132 @@ .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' ) ) diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R index d147eb2..9120aa8 100644 --- a/inst/envs/format_yaml_to_r.R +++ b/inst/envs/format_yaml_to_r.R @@ -1,5 +1,5 @@ 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(",