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update scvelo to 0.2.5
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@kevinrue
kevinrue committed May 22, 2024
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353 changes: 347 additions & 6 deletions R/basilisk.R
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# scvelo 0.2.5
# and dependencies pinned to fix various issues linked below
.scvelo_dependencies <- c(
"scvelo==0.2.5",
"matplotlib==3.7.3", # https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no
"tqdm==4.66.4", # required for progress bar
"ipywidgets==8.1.2", # required for progress bar
"jupyterlab==4.2.0", # required for progress bar
"numpy==1.23.1" # https://github.com/OpenTalker/video-retalking/issues/35
'absl-py==2.1.0',
'anndata==0.10.7',
'annotated-types==0.7.0',
'anyio==4.3.0',
'aom==3.9.0',
'appnope==0.1.4',
'argon2-cffi==23.1.0',
'argon2-cffi-bindings==21.2.0',
'array-api-compat==1.6',
'arrow==1.3.0',
'asttokens==2.4.1',
'async-lru==2.0.4',
'attrs==23.2.0',
'babel==2.14.0',
'beautifulsoup4==4.12.3',
'bleach==6.1.0',
'blessed==1.19.1',
'blosc==1.21.5',
'boto3==1.34.109',
'botocore==1.34.110',
'brotli==1.1.0',
'brotli-bin==1.1.0',
'brotli-python==1.1.0',
'bzip2==1.0.8',
'c-ares==1.28.1',
'ca-certificates==2024.2.2',
'cachecontrol==0.14.0',
'cachecontrol-with-filecache==0.14.0',
'cached-property==1.5.2',
'cached_property==1.5.2',
'certifi==2024.2.2',
'cffi==1.16.0',
'charset-normalizer==3.3.2',
'chex==0.1.83',
'cleo==2.1.0',
'click==8.1.7',
'colorama==0.4.6',
'comm==0.2.2',
'contextlib2==21.6.0',
'contourpy==1.2.1',
'crashtest==0.4.1',
'croniter==1.3.15',
'cycler==0.12.1',
'dateutils==0.6.12',
'dav1d==1.2.1',
'debugpy==1.8.1',
'decorator==5.1.1',
'deepdiff==7.0.1',
'defusedxml==0.7.1',
'distlib==0.3.8',
'dm-tree==0.1.8',
'dnspython==2.6.1',
'docrep==0.3.2',
'dulwich==0.21.7',
'email-validator==2.1.1',
'email_validator==2.1.1',
'entrypoints==0.4',
'et_xmlfile==1.1.0',
'etils==1.6.0',
'exceptiongroup==1.2.0',
'executing==2.0.1',
'fastapi==0.111.0',
'fastapi-cli==0.0.4',
'filelock==3.14.0',
'flax==0.8.3',
'fonttools==4.51.0',
'fqdn==1.5.1',
'freetype==2.12.1',
'fsspec==2023.12.2',
'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==73.2',
'idna==3.7',
'importlib-metadata==7.1.0',
'importlib-resources==6.4.0',
'importlib_metadata==7.1.0',
'importlib_resources==6.4.0',
'inquirer==3.1.4',
'ipykernel==6.29.3',
'ipython==8.18.1',
'ipywidgets==8.1.2',
'isoduration==20.11.0',
'itsdangerous==2.2.0',
'jaraco.classes==3.4.0',
'jax==0.4.27',
'jaxlib==0.4.23',
'jedi==0.19.1',
'jinja2==3.1.4',
'jmespath==1.0.1',
'joblib==1.4.2',
'json5==0.9.25',
'jsonpointer==2.4',
'jsonschema==4.22.0',
'jsonschema-specifications==2023.12.1',
'jsonschema-with-format-nongpl==4.22.0',
'jupyter-lsp==2.2.5',
'jupyter_client==8.6.1',
'jupyter_core==5.7.2',
'jupyter_events==0.10.0',
'jupyter_server==2.14.0',
'jupyter_server_terminals==0.5.3',
'jupyterlab==4.2.0',
'jupyterlab_pygments==0.3.0',
'jupyterlab_server==2.27.1',
'jupyterlab_widgets==3.0.10',
'keyring==24.3.1',
'kiwisolver==1.4.5',
'krb5==1.21.2',
'lcms2==2.16',
'legacy-api-wrap==1.4',
'lerc==4.0.0',
'libabseil==20240116.2',
'libaec==1.1.3',
'libavif16==1.0.4',
'libblas==3.9.0',
'libbrotlicommon==1.1.0',
'libbrotlidec==1.1.0',
'libbrotlienc==1.1.0',
'libcblas==3.9.0',
'libcurl==8.8.0',
'libcxx==17.0.6',
'libdeflate==1.20',
'libedit==3.1.20191231',
'libev==4.33',
'libffi==3.4.2',
'libgfortran==5.0.0',
'libgfortran5==13.2.0',
'libgrpc==1.62.2',
'libhwloc==2.10.0',
'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',
'libsodium==1.0.18',
'libsqlite==3.45.3',
'libssh2==1.11.0',
'libtiff==4.6.0',
'libtorch==2.3.0',
'libuv==1.48.0',
'libwebp-base==1.4.0',
'libxcb==1.15',
'libxml2==2.12.7',
'libzlib==1.2.13',
'lightning==2.0.4',
'lightning-cloud==0.5.69',
'lightning-utilities==0.11.2',
'llvm-openmp==18.1.5',
'llvmlite==0.42.0',
'loompy==3.0.6',
'lz4-c==1.9.4',
'markdown-it-py==3.0.0',
'markupsafe==2.1.5',
'matplotlib==3.7.3',
'matplotlib-base==3.7.3',
'matplotlib-inline==0.1.7',
'mdurl==0.1.2',
'mistune==3.0.2',
'ml-collections==0.1.1',
'ml_dtypes==0.4.0',
'more-itertools==10.2.0',
'mpc==1.3.1',
'mpfr==4.2.1',
'mpmath==1.3.0',
'msgpack-python==1.0.8',
'mudata==0.2.3',
'multipledispatch==0.6.0',
'munkres==1.1.4',
'natsort==8.4.0',
'nbclient==0.10.0',
'nbconvert-core==7.16.4',
'nbformat==5.10.4',
'ncurses==6.5',
'nest-asyncio==1.6.0',
'networkx==3.2.1',
'nomkl==1.0',
'notebook-shim==0.2.4',
'numba==0.59.1',
'numpy==1.23.1',
'numpy_groupies==0.11.1',
'numpyro==0.15.0',
'openjpeg==2.5.2',
'openpyxl==3.1.2',
'openssl==3.3.0',
'opt-einsum==3.3.0',
'opt_einsum==3.3.0',
'optax==0.2.2',
'orbax-checkpoint==0.4.4',
'ordered-set==4.1.0',
'orjson==3.10.3',
'overrides==7.7.0',
'packaging==24.0',
'pandas==2.2.2',
'pandocfilters==1.5.0',
'parso==0.8.4',
'patsy==0.5.6',
'pexpect==4.9.0',
'pickleshare==0.7.5',
'pillow==10.3.0',
'pip==24.0',
'pkginfo==1.10.0',
'pkgutil-resolve-name==1.3.10',
'platformdirs==4.2.2',
'poetry==1.8.3',
'poetry-core==1.9.0',
'poetry-plugin-export==1.8.0',
'prometheus_client==0.20.0',
'prompt-toolkit==3.0.42',
'protobuf==4.25.3',
'psutil==5.9.8',
'pthread-stubs==0.4',
'ptyprocess==0.7.0',
'pure_eval==0.2.2',
'pybind11-abi==4',
'pycparser==2.22',
'pydantic==2.7.1',
'pydantic-core==2.18.2',
'pygments==2.18.0',
'pyjwt==2.8.0',
'pynndescent==0.5.12',
'pyobjc-core==10.2',
'pyobjc-framework-cocoa==10.2',
'pyparsing==3.1.2',
'pyproject_hooks==1.1.0',
'pyro-api==0.1.2',
'pyro-ppl==1.9.0',
'pysocks==1.7.1',
'python==3.9.12',
'python-build==1.2.1',
'python-dateutil==2.9.0',
'python-editor==1.0.4',
'python-fastjsonschema==2.19.1',
'python-installer==0.7.0',
'python-json-logger==2.0.7',
'python-multipart==0.0.9',
'python-tzdata==2024.1',
'python_abi==3.9',
'pytorch==2.3.0',
'pytorch-lightning==2.2.2',
'pytz==2024.1',
'pyyaml==6.0.1',
'pyzmq==26.0.3',
'rapidfuzz==3.9.1',
'rav1e==0.6.6',
're2==2023.09.01',
'readchar==4.1.0',
'readline==8.2',
'referencing==0.35.1',
'requests==2.32.2',
'requests-toolbelt==1.0.0',
'rfc3339-validator==0.1.4',
'rfc3986-validator==0.1.1',
'rich==13.7.1',
'rpds-py==0.18.1',
's3transfer==0.10.1',
'scanpy==1.10.1',
'scikit-learn==1.5.0',
'scipy==1.13.0',
'scvelo==0.2.5',
'scvi-tools==1.1.2',
'seaborn==0.13.2',
'seaborn-base==0.13.2',
'send2trash==1.8.3',
'session-info==1.0.0',
'setuptools==70.0.0',
'shellingham==1.5.4',
'six==1.16.0',
'sleef==3.5.1',
'snappy==1.2.0',
'sniffio==1.3.1',
'soupsieve==2.5',
'sparse==0.15.3',
'sqlite==3.45.3',
'stack_data==0.6.2',
'starlette==0.37.2',
'starsessions==1.3.0',
'statsmodels==0.14.2',
'stdlib-list==0.10.0',
'svt-av1==2.1.0',
'sympy==1.12',
'tbb==2021.12.0',
'tensorstore==0.1.59',
'terminado==0.18.1',
'threadpoolctl==3.5.0',
'tinycss2==1.3.0',
'tk==8.6.13',
'tomli==2.0.1',
'tomlkit==0.12.5',
'toolz==0.12.1',
'torchmetrics==1.4.0.post0',
'tornado==6.4',
'tqdm==4.66.4',
'traitlets==5.14.3',
'trove-classifiers==2024.5.17',
'typer==0.12.3',
'typer-slim==0.12.3',
'typer-slim-standard==0.12.3',
'types-python-dateutil==2.9.0.20240316',
'typing-extensions==4.11.0',
'typing_extensions==4.11.0',
'typing_utils==0.1.0',
'tzdata==2024a',
'ujson==5.10.0',
'umap-learn==0.5.5',
'unicodedata2==15.1.0',
'uri-template==1.3.0',
'urllib3==1.26.18',
'uvicorn==0.29.0',
'virtualenv==20.26.2',
'wcwidth==0.2.13',
'webcolors==1.13',
'webencodings==0.5.1',
'websocket-client==1.8.0',
'websockets==11.0.3',
'wheel==0.43.0',
'widgetsnbextension==4.0.10',
'xarray==2024.5.0',
'xattr==1.1.0',
'xlrd==1.2.0',
'xorg-libxau==1.0.11',
'xorg-libxdmcp==1.1.3',
'xz==5.2.6',
'yaml==0.2.5',
'zeromq==4.3.5',
'zipp==3.17.0',
'zstd==1.5.6'
)

# Note:

# "matplotlib==3.7.3", # https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no
# "tqdm==4.66.4", # required for progress bar
# "ipywidgets==8.1.2", # required for progress bar
# "jupyterlab==4.2.0", # required for progress bar
# "numpy==1.23.1" # https://github.com/OpenTalker/video-retalking/issues/35

#' @importFrom basilisk BasiliskEnvironment
#' @importFrom zellkonverter AnnDataDependencies
velo.env <- BasiliskEnvironment("env", "velociraptor",
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7 changes: 4 additions & 3 deletions R/scvelo.R
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Original file line number Diff line number Diff line change
Expand Up @@ -206,13 +206,14 @@ NULL

if (!is.null(scvelo.params$moments)) {
if (!is.null(scvelo.params$moments$n_neighbors)) {
scvelo.params$moments$n_neighbors <- NULL
stop("scvelo.params$moments$n_neighbors is deprecated; use scvelo.params$neighbors$n_neighbors instead")
}
if (!is.null(scvelo.params$moments$n_pcs)) {
scvelo.params$moments$n_pcs <- NULL
stop("scvelo.params$moments$n_pcs is deprecated; use scvelo.params$neighbors$n_pcs instead")
}
} else {
warning("setting moments")
# if unspecified, set to NULL (= None)
# see https://github.com/theislab/scvelo/issues/1212
scvelo.params$moments <- list(
n_neighbors = NULL,
n_pcs = NULL
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