From 58cda9c87212de081262567d7beae280b164ff52 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Wed, 22 May 2024 15:49:26 +0100
Subject: [PATCH] Revert "pin all package versions"

This reverts commit 75035b2f29cf0a32de81f8ad16d6fb369195454a.
---
 R/basilisk.R | 263 ++-------------------------------------------------
 1 file changed, 6 insertions(+), 257 deletions(-)

diff --git a/R/basilisk.R b/R/basilisk.R
index 7b1e151..6bf7735 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -1,265 +1,14 @@
 # scvelo 0.2.5
 # and dependencies pinned to fix various issues linked below
 .scvelo_dependencies <- c(
-    'absl-py==2.1.0',
-    'anndata==0.10.7',
-    'annotated-types==0.7.0',
-    'anyio==4.3.0',
-    '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',
-    'boto3==1.34.109',
-    'botocore==1.34.110',
-    'Brotli==1.1.0',
-    'build==1.2.1',
-    'CacheControl==0.14.0',
-    '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',
-    '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',
-    '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',
-    'fastjsonschema==2.19.1',
-    'filelock==3.14.0',
-    'flax==0.8.3',
-    'fonttools==4.51.0',
-    'fqdn==1.5.1',
-    'fsspec==2023.12.2',
-    'get-annotations==0.1.2',
-    'gmpy2==2.1.5',
-    'h11==0.14.0',
-    'h2==4.1.0',
-    'h5py==3.11.0',
-    'hpack==4.0.0',
-    'httpcore==1.0.5',
-    'httpx==0.27.0',
-    'hyperframe==6.0.1',
-    'idna==3.7',
-    'importlib_metadata==7.1.0',
-    'importlib_resources==6.4.0',
-    'inquirer==3.1.4',
-    'installer==0.7.0',
-    '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.dev20240522',
-    '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',
-    'jupyter_client==8.6.1',
-    'jupyter_core==5.7.2',
-    'jupyter-events==0.10.0',
-    'jupyter-lsp==2.2.5',
-    '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',
-    'legacy-api-wrap==1.4',
-    'lightning==2.0.4',
-    'lightning_cloud==0.5.69',
-    'lightning-utilities==0.11.2',
-    'llvmlite==0.42.0',
-    'loompy==3.0.6',
-    'markdown-it-py==3.0.0',
-    'MarkupSafe==2.1.5',
-    'matplotlib==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',
-    'mpmath==1.3.0',
-    'msgpack==1.0.8',
-    'mudata==0.2.3',
-    'multipledispatch==0.6.0',
-    'munkres==1.1.4',
-    'natsort==8.4.0',
-    'nbclient==0.10.0',
-    'nbconvert==7.16.4',
-    'nbformat==5.10.4',
-    'nest_asyncio==1.6.0',
-    'networkx==3.2.1',
-    'notebook_shim==0.2.4',
-    'numba==0.59.1',
-    'numpy==1.23.1',
-    'numpy-groupies==0.11.1',
-    'numpyro==0.15.0',
-    'openpyxl==3.1.2',
-    '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',
-    'ptyprocess==0.7.0',
-    'pure-eval==0.2.2',
-    '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+f02dfb9',
-    'PySocks==1.7.1',
-    'python-dateutil==2.9.0',
-    'python-editor==1.0.4',
-    'python-json-logger==2.0.7',
-    'python-multipart==0.0.9',
-    'pytorch-lightning==2.2.2',
-    'pytz==2024.1',
-    'PyYAML==6.0.1',
-    'pyzmq==26.0.3',
-    'rapidfuzz==3.9.1',
-    'readchar==4.1.0.dev3',
-    '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',
-    'Send2Trash==1.8.3',
-    'session-info==1.0.0',
-    'setuptools==70.0.0',
-    'shellingham==1.5.4',
-    'six==1.16.0',
-    'sniffio==1.3.1',
-    'soupsieve==2.5',
-    'sparse==0.15.3',
-    'stack-data==0.6.2',
-    'starlette==0.37.2',
-    'starsessions==1.3.0',
-    'statsmodels==0.14.2',
-    'stdlib-list==0.10.0',
-    'sympy==1.12',
-    'tensorstore==0.1.59',
-    'terminado==0.18.1',
-    'threadpoolctl==3.5.0',
-    'tinycss2==1.3.0',
-    'tomli==2.0.1',
-    'tomlkit==0.12.5',
-    'toolz==0.12.1',
-    'torch==2.3.0',
-    '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',
-    'types-python-dateutil==2.9.0.20240316',
-    'typing_extensions==4.11.0',
-    'typing-utils==0.1.0',
-    'tzdata==2024.1',
-    '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',
-    'zipp==3.17.0'
+    "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
 )
 
-# Note:
-# c(
-#     "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",