From 13f40d237fa2cb840ddf6fd284104774c58133b4 Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Fri, 30 Aug 2024 20:29:30 +0100
Subject: [PATCH] Fix environment using micromamba for macosx Arm (#84)

* first attempt at macos m1 environment using micromamba

* scipy==1.13.1 (theislab/scvelo#1260)

* fix switch between environments

* add news
---
 DESCRIPTION                  |   2 +-
 NEWS.md                      |   7 +-
 R/basilisk.R                 | 464 ++++++++++++-----------------------
 inst/envs/M1.yaml            | 197 +++++++++++++++
 inst/envs/format_yaml_to_r.R |   2 +-
 5 files changed, 362 insertions(+), 310 deletions(-)
 create mode 100644 inst/envs/M1.yaml

diff --git a/DESCRIPTION b/DESCRIPTION
index d61dc72..3aa38e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.7
+Version: 1.15.8
 Date: 2024-08-30
 Authors@R: c(person("Kevin", "Rue-Albrecht", role = c("aut", "cre"), email = "kevinrue67@gmail.com", comment = c(ORCID = "0000-0003-3899-3872")),
     person("Aaron", "Lun", role="aut", email="infinite.monkeys.with.keyboards@gmail.com", comment = c(ORCID = '0000-0002-3564-4813')),
diff --git a/NEWS.md b/NEWS.md
index 9f1c65b..204ed56 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,11 @@
+# velociraptor 1.15.8
+
+* Update Conda environment using micromamba for MacOSX Arm.
+* Fix switch between MacOSX and MacOSX Arm environments.
+
 # velociraptor 1.15.7
 
-* Update Conda environment using micromamba for Windows. 
+* Update Conda environment using micromamba for Windows.
 
 # velociraptor 1.15.6
 
diff --git a/R/basilisk.R b/R/basilisk.R
index 6b043d6..9f2b6b2 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -159,110 +159,81 @@
 ## MacOSXArm ----
 
 .scvelo.dependencies.MacOSXArm <- list(
-  channels = c("conda-forge", "bioconda"),
+  channels = c("conda-forge"),
   packages = c(
     'absl-py==2.1.0',
-    'anndata==0.10.7',
-    'annotated-types==0.7.0',
-    'anyio==4.3.0',
-    'aom==3.9.0',
-    'array-api-compat==1.6',
-    'arrow==1.3.0',
-    'beautifulsoup4==4.12.3',
-    'blessed==1.19.1',
-    'blosc==1.21.5',
-    'boto3==1.34.111',
-    'botocore==1.34.111',
+    'anndata==0.10.9',
+    'aom==3.9.1',
+    'array-api-compat==1.8',
+    'blosc==1.21.6',
     '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',
+    'c-ares==1.33.1',
+    'ca-certificates==2024.8.30',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.2.2',
-    'cffi==1.16.0',
+    '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==1.3.15',
+    'contourpy==1.3.0',
     'cycler==0.12.1',
-    'dateutils==0.6.12',
     'dav1d==1.2.1',
-    'deepdiff==7.0.1',
-    'distlib==0.3.8',
-    'dnspython==2.6.1',
     'docrep==0.3.2',
-    'dulwich==0.21.7',
-    'email-validator==2.1.1',
-    'email_validator==2.1.1',
     'et_xmlfile==1.1.0',
-    'etils==1.6.0',
-    'exceptiongroup==1.2.0',
-    'fastapi==0.111.0',
-    'fastapi-cli==0.0.4',
-    'filelock==3.14.0',
-    'flax==0.8.3',
-    'fonttools==4.51.0',
+    'etils==1.9.2',
+    'exceptiongroup==1.2.2',
+    'filelock==3.15.4',
+    'flax==0.9.0',
+    'fonttools==4.53.1',
     'freetype==2.12.1',
-    'fsspec==2023.12.2',
+    '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==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',
-    'itsdangerous==2.2.0',
-    'jaraco.classes==3.4.0',
-    'jax==0.4.27',
-    'jaxlib==0.4.23',
+    'icu==75.1',
+    'idna==3.8',
+    'importlib-metadata==8.4.0',
+    'importlib_metadata==8.4.0',
+    'importlib_resources==6.4.4',
+    'jax==0.4.31',
+    'jaxlib==0.4.31',
     'jinja2==3.1.4',
-    'jmespath==1.0.1',
     'joblib==1.4.2',
-    'keyring==24.3.1',
     'kiwisolver==1.4.5',
-    'krb5==1.21.2',
+    'krb5==1.21.3',
     'lcms2==2.16',
     'legacy-api-wrap==1.4',
     'lerc==4.0.0',
     'libabseil==20240116.2',
     'libaec==1.1.3',
-    'libavif16==1.0.4',
+    'libavif16==1.1.1',
     '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',
+    'libcurl==8.9.1',
+    'libcxx==18.1.8',
+    'libdeflate==1.21',
     'libedit==3.1.20191231',
     'libev==4.33',
+    'libexpat==2.6.2',
     'libffi==3.4.2',
     'libgfortran==5.0.0',
     'libgfortran5==13.2.0',
     'libgrpc==1.62.2',
-    'libhwloc==2.10.0',
+    'libhwloc==2.11.1',
     'libiconv==1.17',
     'libjpeg-turbo==3.0.0',
     'liblapack==3.9.0',
@@ -272,162 +243,116 @@
     'libpng==1.6.43',
     'libprotobuf==4.25.3',
     'libre2-11==2023.09.01',
-    'libsqlite==3.45.3',
+    'libsqlite==3.46.0',
     'libssh2==1.11.0',
     'libtiff==4.6.0',
-    'libtorch==2.3.0',
+    'libtorch==2.4.0',
     'libuv==1.48.0',
     'libwebp-base==1.4.0',
-    'libxcb==1.15',
+    'libxcb==1.16',
     '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',
+    'libzlib==1.3.1',
+    'lightning==2.4.0',
+    'lightning-utilities==0.11.6',
+    'llvm-openmp==18.1.8',
+    'llvmlite==0.43.0',
     'loompy==3.0.6',
     'lz4-c==1.9.4',
     'markdown-it-py==3.0.0',
     'markupsafe==2.1.5',
-    'matplotlib-base==3.8.4',
+    'matplotlib-base==3.9.2',
     'mdurl==0.1.2',
     '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',
+    'mudata==0.3.1',
     'multipledispatch==0.6.0',
     'munkres==1.1.4',
     'natsort==8.4.0',
     'ncurses==6.5',
     'nest-asyncio==1.6.0',
-    'networkx==3.2.1',
+    'networkx==3.3',
     'nomkl==1.0',
-    'numba==0.59.1',
+    'numba==0.60.0',
     'numpy==1.26.4',
-    'numpy_groupies==0.11.1',
-    'numpyro==0.15.0',
+    'numpy_groupies==0.11.2',
+    'numpyro==0.15.2',
     'openjpeg==2.5.2',
-    'openpyxl==3.1.2',
-    'openssl==3.3.0',
+    'openpyxl==3.1.5',
+    'openssl==3.3.1',
     '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',
-    'packaging==24.0',
+    'packaging==24.1',
     'pandas==2.2.2',
     'patsy==0.5.6',
-    'pexpect==4.9.0',
-    'pillow==10.3.0',
-    'pip==24.0',
-    'pkginfo==1.10.0',
-    'platformdirs==4.2.2',
-    'poetry==1.8.3',
-    'poetry-core==1.9.0',
-    'poetry-plugin-export==1.8.0',
+    'pillow==10.4.0',
+    'pip==24.2',
     'protobuf==4.25.3',
-    'psutil==5.9.8',
     'pthread-stubs==0.4',
-    'ptyprocess==0.7.0',
     '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',
-    'pyparsing==3.1.2',
-    'pyproject_hooks==1.1.0',
+    'pynndescent==0.5.13',
+    'pyparsing==3.1.4',
     'pyro-api==0.1.2',
-    'pyro-ppl==1.9.0',
+    'pyro-ppl==1.9.1',
     'pysocks==1.7.1',
-    'python==3.9.12',
-    'python-build==1.2.1',
+    'python==3.11.9',
     'python-dateutil==2.9.0',
-    'python-editor==1.0.4',
-    'python-fastjsonschema==2.19.1',
-    'python-installer==0.7.0',
-    'python-multipart==0.0.9',
     'python-tzdata==2024.1',
-    'python_abi==3.9',
-    'pytorch==2.3.0',
-    'pytorch-lightning==2.2.2',
+    'python_abi==3.11',
+    'pytorch==2.4.0',
+    'pytorch-lightning==2.4.0',
     'pytz==2024.1',
-    'pyyaml==6.0.1',
-    'rapidfuzz==3.9.1',
+    'pyyaml==6.0.2',
+    'qhull==2020.2',
     'rav1e==0.6.6',
     're2==2023.09.01',
-    'readchar==4.1.0',
     'readline==8.2',
-    'requests==2.32.2',
-    'requests-toolbelt==1.0.0',
+    'requests==2.32.3',
     'rich==13.7.1',
-    's3transfer==0.10.1',
-    'scanpy==1.10.1',
+    'scanpy==1.10.2',
     'scikit-learn==1.1.3',
-    'scipy==1.13.0',
+    'scipy==1.13.1',
     'scvelo==0.3.2',
-    'scvi-tools==1.1.2',
+    'scvi-tools==1.1.6',
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
     'session-info==1.0.0',
-    'setuptools==70.0.0',
-    'shellingham==1.5.4',
+    'setuptools==72.2.0',
     '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',
-    'starlette==0.37.2',
-    'starsessions==1.3.0',
+    'sleef==3.6.1',
+    'snappy==1.2.1',
+    'sparse==0.15.4',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'svt-av1==2.1.0',
-    'sympy==1.12',
+    'svt-av1==2.2.1',
+    'sympy==1.13.2',
     'tbb==2021.12.0',
-    'tensorstore==0.1.59',
+    'tensorstore==0.1.62',
     'threadpoolctl==3.5.0',
     'tk==8.6.13',
-    'tomli==2.0.1',
-    'tomlkit==0.12.5',
     'toolz==0.12.1',
     'torchmetrics==1.4.0.post0',
-    'tqdm==4.66.4',
-    'traitlets==5.14.3',
-    'trove-classifiers==2024.5.22',
-    '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',
+    'tqdm==4.66.5',
+    'typing-extensions==4.12.2',
+    'typing_extensions==4.12.2',
     'tzdata==2024a',
-    'ujson==5.10.0',
-    'umap-learn==0.5.5',
-    'unicodedata2==15.1.0',
-    'urllib3==1.26.18',
-    'uvicorn==0.29.0',
-    'virtualenv==20.26.2',
-    'wcwidth==0.2.13',
-    'websocket-client==1.8.0',
-    'websockets==11.0.3',
-    'wheel==0.43.0',
-    'xarray==2024.5.0',
-    'xattr==1.1.0',
-    'xlrd==1.2.0',
+    'umap-learn==0.5.6',
+    'urllib3==2.2.2',
+    '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==3.17.0',
+    'zipp==3.20.1',
+    'zstandard==0.23.0',
     'zstd==1.5.6'
   )
 )
@@ -438,107 +363,78 @@
   channels = c("conda-forge", "bioconda"),
   packages = c(
     'absl-py==2.1.0',
-    'anndata==0.10.7',
-    'annotated-types==0.7.0',
-    'anyio==4.3.0',
-    'aom==3.9.0',
-    'array-api-compat==1.6',
-    'arrow==1.3.0',
-    'beautifulsoup4==4.12.3',
-    'blessed==1.19.1',
-    'blosc==1.21.5',
-    'boto3==1.34.111',
-    'botocore==1.34.111',
+    'anndata==0.10.9',
+    'aom==3.9.1',
+    'array-api-compat==1.8',
+    'blosc==1.21.6',
     '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',
+    'c-ares==1.33.1',
+    'ca-certificates==2024.8.30',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.2.2',
-    'cffi==1.16.0',
+    '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==1.3.15',
+    'contourpy==1.3.0',
     'cycler==0.12.1',
-    'dateutils==0.6.12',
     'dav1d==1.2.1',
-    'deepdiff==7.0.1',
-    'distlib==0.3.8',
-    'dnspython==2.6.1',
     'docrep==0.3.2',
-    'dulwich==0.21.7',
-    'email-validator==2.1.1',
-    'email_validator==2.1.1',
     'et_xmlfile==1.1.0',
-    'etils==1.6.0',
-    'exceptiongroup==1.2.0',
-    'fastapi==0.111.0',
-    'fastapi-cli==0.0.4',
-    'filelock==3.14.0',
-    'flax==0.8.3',
-    'fonttools==4.51.0',
+    'etils==1.9.2',
+    'exceptiongroup==1.2.2',
+    'filelock==3.15.4',
+    'flax==0.9.0',
+    'fonttools==4.53.1',
     'freetype==2.12.1',
-    'fsspec==2023.12.2',
+    '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==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',
-    'itsdangerous==2.2.0',
-    'jaraco.classes==3.4.0',
-    'jax==0.4.27',
-    'jaxlib==0.4.23',
+    'icu==75.1',
+    'idna==3.8',
+    'importlib-metadata==8.4.0',
+    'importlib_metadata==8.4.0',
+    'importlib_resources==6.4.4',
+    'jax==0.4.31',
+    'jaxlib==0.4.31',
     'jinja2==3.1.4',
-    'jmespath==1.0.1',
     'joblib==1.4.2',
-    'keyring==24.3.1',
     'kiwisolver==1.4.5',
-    'krb5==1.21.2',
+    'krb5==1.21.3',
     'lcms2==2.16',
     'legacy-api-wrap==1.4',
     'lerc==4.0.0',
     'libabseil==20240116.2',
     'libaec==1.1.3',
-    'libavif16==1.0.4',
+    'libavif16==1.1.1',
     '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',
+    'libcurl==8.9.1',
+    'libcxx==18.1.8',
+    'libdeflate==1.21',
     'libedit==3.1.20191231',
     'libev==4.33',
+    'libexpat==2.6.2',
     'libffi==3.4.2',
     'libgfortran==5.0.0',
     'libgfortran5==13.2.0',
     'libgrpc==1.62.2',
-    'libhwloc==2.10.0',
+    'libhwloc==2.11.1',
     'libiconv==1.17',
     'libjpeg-turbo==3.0.0',
     'liblapack==3.9.0',
@@ -548,162 +444,116 @@
     'libpng==1.6.43',
     'libprotobuf==4.25.3',
     'libre2-11==2023.09.01',
-    'libsqlite==3.45.3',
+    'libsqlite==3.46.0',
     'libssh2==1.11.0',
     'libtiff==4.6.0',
-    'libtorch==2.3.0',
+    'libtorch==2.4.0',
     'libuv==1.48.0',
     'libwebp-base==1.4.0',
-    'libxcb==1.15',
+    'libxcb==1.16',
     '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',
+    'libzlib==1.3.1',
+    'lightning==2.4.0',
+    'lightning-utilities==0.11.6',
+    'llvm-openmp==18.1.8',
+    'llvmlite==0.43.0',
     'loompy==3.0.6',
     'lz4-c==1.9.4',
     'markdown-it-py==3.0.0',
     'markupsafe==2.1.5',
-    'matplotlib-base==3.8.4',
+    'matplotlib-base==3.9.2',
     'mdurl==0.1.2',
     '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',
+    'mudata==0.3.1',
     'multipledispatch==0.6.0',
     'munkres==1.1.4',
     'natsort==8.4.0',
     'ncurses==6.5',
     'nest-asyncio==1.6.0',
-    'networkx==3.2.1',
+    'networkx==3.3',
     'nomkl==1.0',
-    'numba==0.59.1',
+    'numba==0.60.0',
     'numpy==1.26.4',
-    'numpy_groupies==0.11.1',
-    'numpyro==0.15.0',
+    'numpy_groupies==0.11.2',
+    'numpyro==0.15.2',
     'openjpeg==2.5.2',
-    'openpyxl==3.1.2',
-    'openssl==3.3.0',
+    'openpyxl==3.1.5',
+    'openssl==3.3.1',
     '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',
-    'packaging==24.0',
+    'packaging==24.1',
     'pandas==2.2.2',
     'patsy==0.5.6',
-    'pexpect==4.9.0',
-    'pillow==10.3.0',
-    'pip==24.0',
-    'pkginfo==1.10.0',
-    'platformdirs==4.2.2',
-    'poetry==1.8.3',
-    'poetry-core==1.9.0',
-    'poetry-plugin-export==1.8.0',
+    'pillow==10.4.0',
+    'pip==24.2',
     'protobuf==4.25.3',
-    'psutil==5.9.8',
     'pthread-stubs==0.4',
-    'ptyprocess==0.7.0',
     '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',
-    'pyparsing==3.1.2',
-    'pyproject_hooks==1.1.0',
+    'pynndescent==0.5.13',
+    'pyparsing==3.1.4',
     'pyro-api==0.1.2',
-    'pyro-ppl==1.9.0',
+    'pyro-ppl==1.9.1',
     'pysocks==1.7.1',
-    'python==3.9.12',
-    'python-build==1.2.1',
+    'python==3.11.9',
     'python-dateutil==2.9.0',
-    'python-editor==1.0.4',
-    'python-fastjsonschema==2.19.1',
-    'python-installer==0.7.0',
-    'python-multipart==0.0.9',
     'python-tzdata==2024.1',
-    'python_abi==3.9',
-    'pytorch==2.3.0',
-    'pytorch-lightning==2.2.2',
+    'python_abi==3.11',
+    'pytorch==2.4.0',
+    'pytorch-lightning==2.4.0',
     'pytz==2024.1',
-    'pyyaml==6.0.1',
-    'rapidfuzz==3.9.1',
+    'pyyaml==6.0.2',
+    'qhull==2020.2',
     'rav1e==0.6.6',
     're2==2023.09.01',
-    'readchar==4.1.0',
     'readline==8.2',
-    'requests==2.32.2',
-    'requests-toolbelt==1.0.0',
+    'requests==2.32.3',
     'rich==13.7.1',
-    's3transfer==0.10.1',
-    'scanpy==1.10.1',
+    'scanpy==1.10.2',
     'scikit-learn==1.1.3',
-    'scipy==1.13.0',
+    'scipy==1.13.1',
     'scvelo==0.3.2',
-    'scvi-tools==1.1.2',
+    'scvi-tools==1.1.6',
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
     'session-info==1.0.0',
-    'setuptools==70.0.0',
-    'shellingham==1.5.4',
+    'setuptools==72.2.0',
     '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',
-    'starlette==0.37.2',
-    'starsessions==1.3.0',
+    'sleef==3.6.1',
+    'snappy==1.2.1',
+    'sparse==0.15.4',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'svt-av1==2.1.0',
-    'sympy==1.12',
+    'svt-av1==2.2.1',
+    'sympy==1.13.2',
     'tbb==2021.12.0',
-    'tensorstore==0.1.59',
+    'tensorstore==0.1.62',
     'threadpoolctl==3.5.0',
     'tk==8.6.13',
-    'tomli==2.0.1',
-    'tomlkit==0.12.5',
     'toolz==0.12.1',
     'torchmetrics==1.4.0.post0',
-    'tqdm==4.66.4',
-    'traitlets==5.14.3',
-    'trove-classifiers==2024.5.22',
-    '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',
+    'tqdm==4.66.5',
+    'typing-extensions==4.12.2',
+    'typing_extensions==4.12.2',
     'tzdata==2024a',
-    'ujson==5.10.0',
-    'umap-learn==0.5.5',
-    'unicodedata2==15.1.0',
-    'urllib3==1.26.18',
-    'uvicorn==0.29.0',
-    'virtualenv==20.26.2',
-    'wcwidth==0.2.13',
-    'websocket-client==1.8.0',
-    'websockets==11.0.3',
-    'wheel==0.43.0',
-    'xarray==2024.5.0',
-    'xattr==1.1.0',
-    'xlrd==1.2.0',
+    'umap-learn==0.5.6',
+    'urllib3==2.2.2',
+    '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==3.17.0',
+    'zipp==3.20.1',
+    'zstandard==0.23.0',
     'zstd==1.5.6'
   )
 )
@@ -868,10 +718,10 @@ if (basilisk.utils::isWindows()) {
   .scvelo_dependencies <- .scvelo.dependencies.Windows
 } else if (basilisk.utils::isLinux()) {
   .scvelo_dependencies <- .scvelo.dependencies.Linux
-} else if (basilisk.utils::isMacOSX()) {
-  .scvelo_dependencies <- .scvelo.dependencies.MacOSX
 } else if (basilisk.utils::isMacOSXArm()) {
   .scvelo_dependencies <- .scvelo.dependencies.MacOSXArm
+} else if (basilisk.utils::isMacOSX()) {
+  .scvelo_dependencies <- .scvelo.dependencies.MacOSX
 } else {
   stop("Unsupported operating system or architecture.\n  Please open an issue at <https://github.com/kevinrue/velociraptor/issues> to request support.")
 }
diff --git a/inst/envs/M1.yaml b/inst/envs/M1.yaml
new file mode 100644
index 0000000..a9fe0be
--- /dev/null
+++ b/inst/envs/M1.yaml
@@ -0,0 +1,197 @@
+name: scvelo
+channels:
+- conda-forge
+dependencies:
+- absl-py=2.1.0=pyhd8ed1ab_0
+- anndata=0.10.9=pyhd8ed1ab_0
+- aom=3.9.1=h7bae524_0
+- array-api-compat=1.8=pyhd8ed1ab_0
+- blosc=1.21.6=h5499902_0
+- brotli=1.1.0=hb547adb_1
+- brotli-bin=1.1.0=hb547adb_1
+- brotli-python=1.1.0=py311ha891d26_1
+- bzip2=1.0.8=h99b78c6_7
+- c-ares=1.33.1=hd74edd7_0
+- ca-certificates=2024.8.30=hf0a4a13_0
+- cached-property=1.5.2=hd8ed1ab_1
+- cached_property=1.5.2=pyha770c72_1
+- certifi=2024.7.4=pyhd8ed1ab_0
+- cffi=1.17.0=py311h3a79f62_1
+- charset-normalizer=3.3.2=pyhd8ed1ab_0
+- chex=0.1.86=pyhd8ed1ab_0
+- click=8.1.7=unix_pyh707e725_0
+- colorama=0.4.6=pyhd8ed1ab_0
+- contextlib2=21.6.0=pyhd8ed1ab_0
+- contourpy=1.3.0=py311h2c37856_0
+- cycler=0.12.1=pyhd8ed1ab_0
+- dav1d=1.2.1=hb547adb_0
+- docrep=0.3.2=pyh44b312d_0
+- et_xmlfile=1.1.0=pyhd8ed1ab_0
+- etils=1.9.2=pyhd8ed1ab_0
+- exceptiongroup=1.2.2=pyhd8ed1ab_0
+- filelock=3.15.4=pyhd8ed1ab_0
+- flax=0.9.0=pyhd8ed1ab_0
+- fonttools=4.53.1=py311hd3f4193_0
+- freetype=2.12.1=hadb7bae_2
+- fsspec=2024.6.1=pyhff2d567_0
+- get-annotations=0.1.2=pyhd8ed1ab_0
+- gmp=6.3.0=h7bae524_2
+- gmpy2=2.1.5=py311h1e33d93_1
+- h2=4.1.0=pyhd8ed1ab_0
+- h5py=3.11.0=nompi_py311hd41bb03_102
+- hdf5=1.14.3=nompi_hec07895_105
+- hpack=4.0.0=pyh9f0ad1d_0
+- hyperframe=6.0.1=pyhd8ed1ab_0
+- icu=75.1=hfee45f7_0
+- idna=3.8=pyhd8ed1ab_0
+- importlib-metadata=8.4.0=pyha770c72_0
+- importlib_metadata=8.4.0=hd8ed1ab_0
+- importlib_resources=6.4.4=pyhd8ed1ab_0
+- jax=0.4.31=pyhd8ed1ab_0
+- jaxlib=0.4.31=cpu_py311he9b4290_0
+- jinja2=3.1.4=pyhd8ed1ab_0
+- joblib=1.4.2=pyhd8ed1ab_0
+- kiwisolver=1.4.5=py311h2c37856_2
+- krb5=1.21.3=h237132a_0
+- lcms2=2.16=ha0e7c42_0
+- legacy-api-wrap=1.4=pyhd8ed1ab_1
+- lerc=4.0.0=h9a09cb3_0
+- libabseil=20240116.2=cxx17_h00cdb27_1
+- libaec=1.1.3=hebf3989_0
+- libavif16=1.1.1=ha4d98b1_1
+- libblas=3.9.0=23_osxarm64_openblas
+- libbrotlicommon=1.1.0=hb547adb_1
+- libbrotlidec=1.1.0=hb547adb_1
+- libbrotlienc=1.1.0=hb547adb_1
+- libcblas=3.9.0=23_osxarm64_openblas
+- libcurl=8.9.1=hfd8ffcc_0
+- libcxx=18.1.8=h3ed4263_6
+- libdeflate=1.21=h99b78c6_0
+- libedit=3.1.20191231=hc8eb9b7_2
+- libev=4.33=h93a5062_2
+- libexpat=2.6.2=hebf3989_0
+- libffi=3.4.2=h3422bc3_5
+- libgfortran=5.0.0=13_2_0_hd922786_3
+- libgfortran5=13.2.0=hf226fd6_3
+- libgrpc=1.62.2=h9c18a4f_0
+- libhwloc=2.11.1=default_h7685b71_1000
+- libiconv=1.17=h0d3ecfb_2
+- libjpeg-turbo=3.0.0=hb547adb_1
+- liblapack=3.9.0=23_osxarm64_openblas
+- libllvm14=14.0.6=hd1a9a77_4
+- libnghttp2=1.58.0=ha4dd798_1
+- libopenblas=0.3.27=openmp_h517c56d_1
+- libpng=1.6.43=h091b4b1_0
+- libprotobuf=4.25.3=hbfab5d5_0
+- libre2-11=2023.09.01=h7b2c953_2
+- libsqlite=3.46.0=hfb93653_0
+- libssh2=1.11.0=h7a5bd25_0
+- libtiff=4.6.0=hf8409c0_4
+- libtorch=2.4.0=cpu_generic_h15ee98c_1
+- libuv=1.48.0=h93a5062_0
+- libwebp-base=1.4.0=h93a5062_0
+- libxcb=1.16=hc9fafa5_1
+- libxml2=2.12.7=h01dff8b_4
+- libzlib=1.3.1=hfb2fe0b_1
+- lightning=2.4.0=pyhd8ed1ab_0
+- lightning-utilities=0.11.6=pyhd8ed1ab_0
+- llvm-openmp=18.1.8=hde57baf_1
+- llvmlite=0.43.0=py311h02e79e2_0
+- loompy=3.0.6=py_0
+- lz4-c=1.9.4=hb7217d7_0
+- markdown-it-py=3.0.0=pyhd8ed1ab_0
+- markupsafe=2.1.5=py311h460d6c5_1
+- matplotlib-base=3.9.2=py311hba6b155_0
+- mdurl=0.1.2=pyhd8ed1ab_0
+- ml-collections=0.1.1=pyhd8ed1ab_0
+- ml_dtypes=0.4.0=py311h4b4568b_1
+- mpc=1.3.1=h91ba8db_0
+- mpfr=4.2.1=h1cfca0a_2
+- mpmath=1.3.0=pyhd8ed1ab_0
+- msgpack-python=1.0.8=py311h6bde47b_0
+- mudata=0.3.1=pyhd8ed1ab_0
+- multipledispatch=0.6.0=pyhd8ed1ab_1
+- munkres=1.1.4=pyh9f0ad1d_0
+- natsort=8.4.0=pyhd8ed1ab_0
+- ncurses=6.5=h7bae524_1
+- nest-asyncio=1.6.0=pyhd8ed1ab_0
+- networkx=3.3=pyhd8ed1ab_1
+- nomkl=1.0=h5ca1d4c_0
+- numba=0.60.0=py311h9506ed5_0
+- numpy=1.26.4=py311h7125741_0
+- numpy_groupies=0.11.2=pyhd8ed1ab_0
+- numpyro=0.15.2=pyhd8ed1ab_0
+- openjpeg=2.5.2=h9f1df11_0
+- openpyxl=3.1.5=py311h1fc4b72_0
+- openssl=3.3.1=h8359307_3
+- opt-einsum=3.3.0=hd8ed1ab_2
+- opt_einsum=3.3.0=pyhc1e730c_2
+- optax=0.2.2=pyhd8ed1ab_1
+- orbax-checkpoint=0.4.4=pyhd8ed1ab_0
+- packaging=24.1=pyhd8ed1ab_0
+- pandas=2.2.2=py311h4b4568b_1
+- patsy=0.5.6=pyhd8ed1ab_0
+- pillow=10.4.0=py311hd7951ec_0
+- pip=24.2=pyh8b19718_1
+- protobuf=4.25.3=py311hd7a3543_1
+- pthread-stubs=0.4=h27ca646_1001
+- pybind11-abi=4=hd8ed1ab_3
+- pycparser=2.22=pyhd8ed1ab_0
+- pygments=2.18.0=pyhd8ed1ab_0
+- pynndescent=0.5.13=pyhff2d567_0
+- pyparsing=3.1.4=pyhd8ed1ab_0
+- pyro-api=0.1.2=pyhd8ed1ab_0
+- pyro-ppl=1.9.1=pyhd8ed1ab_0
+- pysocks=1.7.1=pyha2e5f31_6
+- python=3.11.9=h932a869_0_cpython
+- python-dateutil=2.9.0=pyhd8ed1ab_0
+- python-tzdata=2024.1=pyhd8ed1ab_0
+- python_abi=3.11=5_cp311
+- pytorch=2.4.0=cpu_generic_py311h8ecd042_1
+- pytorch-lightning=2.4.0=pyhd8ed1ab_0
+- pytz=2024.1=pyhd8ed1ab_0
+- pyyaml=6.0.2=py311hd3f4193_0
+- qhull=2020.2=h420ef59_5
+- rav1e=0.6.6=h69fbcac_2
+- re2=2023.09.01=h4cba328_2
+- readline=8.2=h92ec313_1
+- requests=2.32.3=pyhd8ed1ab_0
+- rich=13.7.1=pyhd8ed1ab_0
+- scanpy=1.10.2=pyhd8ed1ab_0
+- scikit-learn=1.1.3=py311hba7d9bc_1
+- scipy=1.13.1=py311hceeca8c_0
+- scvelo=0.3.2=pyhd8ed1ab_1
+- scvi-tools=1.1.6=pyhd8ed1ab_1
+- seaborn=0.13.2=hd8ed1ab_2
+- seaborn-base=0.13.2=pyhd8ed1ab_2
+- session-info=1.0.0=pyhd8ed1ab_0
+- setuptools=72.2.0=pyhd8ed1ab_0
+- six=1.16.0=pyh6c4a22f_0
+- sleef=3.6.1=h7783ee8_3
+- snappy=1.2.1=hd02b534_0
+- sparse=0.15.4=pyhd8ed1ab_0
+- statsmodels=0.14.2=py311h5d790af_0
+- stdlib-list=0.10.0=pyhd8ed1ab_0
+- svt-av1=2.2.1=ha39b806_0
+- sympy=1.13.2=pypyh2585a3b_103
+- tbb=2021.12.0=h7b3277c_4
+- tensorstore=0.1.62=py311h888675e_0
+- threadpoolctl=3.5.0=pyhc1e730c_0
+- tk=8.6.13=h5083fa2_1
+- toolz=0.12.1=pyhd8ed1ab_0
+- torchmetrics=1.4.0.post0=pyhd8ed1ab_0
+- tqdm=4.66.5=pyhd8ed1ab_0
+- typing-extensions=4.12.2=hd8ed1ab_0
+- typing_extensions=4.12.2=pyha770c72_0
+- tzdata=2024a=h8827d51_1
+- umap-learn=0.5.6=py311h267d04e_1
+- urllib3=2.2.2=pyhd8ed1ab_1
+- wheel=0.44.0=pyhd8ed1ab_0
+- xarray=2024.7.0=pyhd8ed1ab_0
+- xorg-libxau=1.0.11=hb547adb_0
+- xorg-libxdmcp=1.1.3=h27ca646_0
+- xz=5.2.6=h57fd34a_0
+- yaml=0.2.5=h3422bc3_2
+- zipp=3.20.1=pyhd8ed1ab_0
+- zstandard=0.23.0=py311h4a6b76e_0
+- zstd=1.5.6=hb46c0d2_0
diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R
index 9120aa8..3ca1244 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("Windows.yaml")
+yaml_data <- yaml::read_yaml("inst/envs/M1.yaml")
 r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies)
 cat(paste0(
   "c(",