From c3d9afe91629220167006ed7d49a3c6fb534acdc Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Wed, 28 Aug 2024 13:20:33 +0100 Subject: [PATCH] replace env in R code --- R/basilisk.R | 101 ++++++--------------------------------------------- 1 file changed, 12 insertions(+), 89 deletions(-) diff --git a/R/basilisk.R b/R/basilisk.R index 913eb65..66df06b 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -704,87 +704,53 @@ '_openmp_mutex==4.5', 'absl-py==2.1.0', 'anndata==0.10.8', - 'annotated-types==0.7.0', - 'anyio==4.4.0', 'aom==3.9.1', 'array-api-compat==1.8', - 'arrow==1.3.0', - 'backoff==2.2.1', - 'beautifulsoup4==4.12.3', - 'blessed==1.19.1', 'blosc==1.21.6', - 'boto3==1.35.3', - 'botocore==1.35.3', 'brotli==1.1.0', 'brotli-bin==1.1.0', 'brotli-python==1.1.0', 'bzip2==1.0.8', - 'c-ares==1.33.0', + 'c-ares==1.33.1', 'ca-certificates==2024.7.4', - 'cachecontrol==0.14.0', - 'cachecontrol-with-filecache==0.14.0', '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', - 'cleo==2.1.0', 'click==8.1.7', 'colorama==0.4.6', 'contextlib2==21.6.0', 'contourpy==1.2.1', - 'crashtest==0.4.1', - 'croniter==1.4.1', - 'cryptography==43.0.0', 'cycler==0.12.1', - 'dateutils==0.6.12', 'dav1d==1.2.1', - 'dbus==1.13.6', - 'deepdiff==7.0.1', - 'distlib==0.3.8', - 'dnspython==2.6.1', 'docrep==0.3.2', - 'dulwich==0.21.7', - 'email-validator==2.2.0', - 'email_validator==2.2.0', 'et_xmlfile==1.1.0', 'etils==1.9.2', 'exceptiongroup==1.2.2', - 'expat==2.6.2', - 'fastapi==0.112.1', - 'fastapi-cli==0.0.5', 'filelock==3.15.4', - 'flax==0.8.5', + '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', - 'h11==0.14.0', 'h2==4.1.0', 'h5py==3.11.0', 'hdf5==1.14.3', 'hpack==4.0.0', - 'httpcore==1.0.5', - 'httpx==0.27.0', 'hyperframe==6.0.1', 'icu==75.1', - 'idna==3.7', + 'idna==3.8', 'importlib-metadata==8.4.0', 'importlib_metadata==8.4.0', 'importlib_resources==6.4.4', - 'inquirer==3.1.4', - 'itsdangerous==2.2.0', - 'jaraco.classes==3.4.0', 'jax==0.4.31', 'jaxlib==0.4.31', - 'jeepney==0.8.0', 'jinja2==3.1.4', - 'jmespath==1.0.1', 'joblib==1.4.2', - 'keyring==24.3.1', 'keyutils==1.6.1', 'kiwisolver==1.4.5', 'krb5==1.21.3', @@ -806,10 +772,11 @@ 'libev==4.33', 'libexpat==2.6.2', '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', - 'libglib==2.80.3', 'libgomp==14.1.0', 'libgrpc==1.62.2', 'libhwloc==2.11.1', @@ -825,9 +792,10 @@ 'libre2-11==2023.09.01', 'libsqlite==3.46.0', 'libssh2==1.11.0', + 'libstdcxx==14.1.0', 'libstdcxx-ng==14.1.0', 'libtiff==4.6.0', - 'libtorch==2.3.1', + 'libtorch==2.4.0', 'libuuid==2.38.1', 'libuv==1.48.0', 'libwebp-base==1.4.0', @@ -835,8 +803,7 @@ 'libxcrypt==4.4.36', 'libxml2==2.12.7', 'libzlib==1.3.1', - 'lightning==2.0.9.post0', - 'lightning-cloud==0.5.70', + 'lightning==2.4.0', 'lightning-utilities==0.11.6', 'llvmlite==0.43.0', 'loompy==3.0.6', @@ -847,7 +814,6 @@ 'mdurl==0.1.2', 'ml-collections==0.1.1', 'ml_dtypes==0.4.0', - 'more-itertools==10.4.0', 'mpc==1.3.1', 'mpfr==4.2.1', 'mpmath==1.3.0', @@ -871,59 +837,35 @@ 'opt_einsum==3.3.0', 'optax==0.2.2', 'orbax-checkpoint==0.4.4', - 'ordered-set==4.1.0', - 'orjson==3.10.7', 'packaging==24.1', 'pandas==2.2.2', 'patsy==0.5.6', - 'pcre2==10.44', - 'pexpect==4.9.0', 'pillow==10.4.0', 'pip==24.2', - 'pkginfo==1.11.1', - 'platformdirs==4.2.2', - 'poetry==1.8.3', - 'poetry-core==1.9.0', - 'poetry-plugin-export==1.8.0', 'protobuf==4.25.3', - 'psutil==6.0.0', 'pthread-stubs==0.4', - 'ptyprocess==0.7.0', 'pybind11-abi==4', 'pycparser==2.22', - 'pydantic==2.1.1', - 'pydantic-core==2.4.0', 'pygments==2.18.0', - 'pyjwt==2.9.0', 'pynndescent==0.5.13', - 'pyparsing==3.1.2', - 'pyproject_hooks==1.1.0', + 'pyparsing==3.1.4', 'pyro-api==0.1.2', 'pyro-ppl==1.9.1', 'pysocks==1.7.1', 'python==3.11.9', - 'python-build==1.2.1', 'python-dateutil==2.9.0', - 'python-editor==1.0.4', - 'python-fastjsonschema==2.20.0', - 'python-installer==0.7.0', - 'python-multipart==0.0.9', 'python-tzdata==2024.1', 'python_abi==3.11', - 'pytorch==2.3.1', + 'pytorch==2.4.0', 'pytorch-lightning==2.4.0', 'pytz==2024.1', 'pyyaml==6.0.2', 'qhull==2020.2', - 'rapidfuzz==3.9.6', 'rav1e==0.6.6', 're2==2023.09.01', - 'readchar==4.2.0', 'readline==8.2', 'requests==2.32.3', - 'requests-toolbelt==1.0.0', 'rich==13.7.1', - 's3transfer==0.10.2', 'scanpy==1.10.2', 'scikit-learn==1.1.3', 'scipy==1.13.1', @@ -931,54 +873,35 @@ 'scvi-tools==1.1.6', 'seaborn==0.13.2', 'seaborn-base==0.13.2', - 'secretstorage==3.3.3', 'session-info==1.0.0', 'setuptools==72.2.0', - 'shellingham==1.5.4', 'six==1.16.0', 'sleef==3.6.1', 'snappy==1.2.1', - 'sniffio==1.3.1', - 'soupsieve==2.5', 'sparse==0.15.4', - 'starlette==0.38.2', - 'starsessions==1.3.0', 'statsmodels==0.14.2', 'stdlib-list==0.10.0', - 'svt-av1==2.1.2', + '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', - 'tomli==2.0.1', - 'tomlkit==0.13.2', 'toolz==0.12.1', 'torchmetrics==1.4.0.post0', 'tqdm==4.66.5', - 'traitlets==5.14.3', - 'trove-classifiers==2024.7.2', - 'typer==0.12.4', - 'typer-slim==0.12.4', - 'typer-slim-standard==0.12.4', - 'types-python-dateutil==2.9.0.20240821', 'typing-extensions==4.12.2', 'typing_extensions==4.12.2', 'tzdata==2024a', 'umap-learn==0.5.6', 'urllib3==2.2.2', - 'uvicorn==0.30.6', - 'virtualenv==20.26.3', - 'wcwidth==0.2.13', - 'websocket-client==1.8.0', - 'websockets==12.0', '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==3.20.0', + 'zipp==3.20.1', 'zstandard==0.23.0', 'zstd==1.5.6' )