diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index 5699751..dc6aef9 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -216,6 +216,11 @@ jobs:
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
+      - name: Install reticulate patch
+        run: |
+          remotes::install_github("rstudio/reticulate")
+        shell: Rscript {0}
+
       - name: Install BiocGenerics
         if:  env.has_RUnit == 'true'
         run: |
diff --git a/DESCRIPTION b/DESCRIPTION
index 3aa38e3..80df7af 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: velociraptor
 Title: Toolkit for Single-Cell Velocity
-Version: 1.15.8
+Version: 1.15.9
 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 204ed56..ee6c97f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# velociraptor 1.15.9
+
+* Update Conda environment for Linux and MacOSX Arm.
+* Patch GitHub Action to use GitHub version of `remotes`.
+
 # velociraptor 1.15.8
 
 * Update Conda environment using micromamba for MacOSX Arm.
diff --git a/R/basilisk.R b/R/basilisk.R
index 9f2b6b2..a28649f 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -165,6 +165,7 @@
     'anndata==0.10.9',
     'aom==3.9.1',
     'array-api-compat==1.8',
+    'asttokens==2.4.1',
     'blosc==1.21.6',
     'brotli==1.1.0',
     'brotli-bin==1.1.0',
@@ -174,25 +175,28 @@
     'ca-certificates==2024.8.30',
     'cached-property==1.5.2',
     'cached_property==1.5.2',
-    'certifi==2024.7.4',
-    'cffi==1.17.0',
+    'certifi==2024.8.30',
+    'cffi==1.17.1',
     'charset-normalizer==3.3.2',
     'chex==0.1.86',
     'click==8.1.7',
     'colorama==0.4.6',
+    'comm==0.2.2',
     'contextlib2==21.6.0',
     'contourpy==1.3.0',
     'cycler==0.12.1',
     'dav1d==1.2.1',
+    'decorator==5.1.1',
     'docrep==0.3.2',
     'et_xmlfile==1.1.0',
-    'etils==1.9.2',
+    'etils==1.9.4',
     'exceptiongroup==1.2.2',
-    'filelock==3.15.4',
+    'executing==2.1.0',
+    'filelock==3.16.0',
     'flax==0.9.0',
     'fonttools==4.53.1',
     'freetype==2.12.1',
-    'fsspec==2024.6.1',
+    'fsspec==2024.9.0',
     'get-annotations==0.1.2',
     'gmp==6.3.0',
     'gmpy2==2.1.5',
@@ -204,13 +208,16 @@
     'icu==75.1',
     'idna==3.8',
     'importlib-metadata==8.4.0',
-    'importlib_metadata==8.4.0',
     'importlib_resources==6.4.4',
+    'ipython==8.27.0',
+    'ipywidgets==8.1.5',
     'jax==0.4.31',
     'jaxlib==0.4.31',
+    'jedi==0.19.1',
     'jinja2==3.1.4',
     'joblib==1.4.2',
-    'kiwisolver==1.4.5',
+    'jupyterlab_widgets==3.0.13',
+    'kiwisolver==1.4.7',
     'krb5==1.21.3',
     'lcms2==2.16',
     'legacy-api-wrap==1.4',
@@ -228,7 +235,7 @@
     'libdeflate==1.21',
     'libedit==3.1.20191231',
     'libev==4.33',
-    'libexpat==2.6.2',
+    'libexpat==2.6.3',
     'libffi==3.4.2',
     'libgfortran==5.0.0',
     'libgfortran5==13.2.0',
@@ -243,7 +250,7 @@
     'libpng==1.6.43',
     'libprotobuf==4.25.3',
     'libre2-11==2023.09.01',
-    'libsqlite==3.46.0',
+    'libsqlite==3.46.1',
     'libssh2==1.11.0',
     'libtiff==4.6.0',
     'libtorch==2.4.0',
@@ -253,7 +260,7 @@
     'libxml2==2.12.7',
     'libzlib==1.3.1',
     'lightning==2.4.0',
-    'lightning-utilities==0.11.6',
+    'lightning-utilities==0.11.7',
     'llvm-openmp==18.1.8',
     'llvmlite==0.43.0',
     'loompy==3.0.6',
@@ -261,6 +268,7 @@
     'markdown-it-py==3.0.0',
     'markupsafe==2.1.5',
     'matplotlib-base==3.9.2',
+    'matplotlib-inline==0.1.7',
     'mdurl==0.1.2',
     'ml-collections==0.1.1',
     'ml_dtypes==0.4.0',
@@ -282,18 +290,24 @@
     'numpyro==0.15.2',
     'openjpeg==2.5.2',
     'openpyxl==3.1.5',
-    'openssl==3.3.1',
+    'openssl==3.3.2',
     'opt-einsum==3.3.0',
     'opt_einsum==3.3.0',
     'optax==0.2.2',
     'orbax-checkpoint==0.4.4',
     'packaging==24.1',
     'pandas==2.2.2',
+    'parso==0.8.4',
     'patsy==0.5.6',
+    'pexpect==4.9.0',
+    'pickleshare==0.7.5',
     'pillow==10.4.0',
     'pip==24.2',
+    'prompt-toolkit==3.0.47',
     'protobuf==4.25.3',
     'pthread-stubs==0.4',
+    'ptyprocess==0.7.0',
+    'pure_eval==0.2.3',
     'pybind11-abi==4',
     'pycparser==2.22',
     'pygments==2.18.0',
@@ -324,28 +338,32 @@
     'seaborn==0.13.2',
     'seaborn-base==0.13.2',
     'session-info==1.0.0',
-    'setuptools==72.2.0',
+    'setuptools==73.0.1',
     'six==1.16.0',
     'sleef==3.6.1',
     'snappy==1.2.1',
     'sparse==0.15.4',
+    'stack_data==0.6.2',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
     'svt-av1==2.2.1',
     'sympy==1.13.2',
-    'tbb==2021.12.0',
+    'tbb==2021.13.0',
     'tensorstore==0.1.62',
     'threadpoolctl==3.5.0',
     'tk==8.6.13',
     'toolz==0.12.1',
     'torchmetrics==1.4.0.post0',
     'tqdm==4.66.5',
+    'traitlets==5.14.3',
     'typing-extensions==4.12.2',
     'typing_extensions==4.12.2',
     'tzdata==2024a',
     'umap-learn==0.5.6',
     'urllib3==2.2.2',
+    'wcwidth==0.2.13',
     'wheel==0.44.0',
+    'widgetsnbextension==4.0.13',
     'xarray==2024.7.0',
     'xorg-libxau==1.0.11',
     'xorg-libxdmcp==1.1.3',
@@ -561,73 +579,81 @@
 ## Linux ----
 
 .scvelo.dependencies.Linux <- list(
-  channels = c("anaconda", "conda-forge", "bioconda"),
+  channels = c("anaconda", "conda-forge"),
   packages = c(
     '_libgcc_mutex==0.1',
-    '_openmp_mutex==4.5',
+    '_openmp_mutex==5.1',
     'absl-py==2.1.0',
     'anndata==0.10.9',
     'array-api-compat==1.8',
+    'asttokens==2.0.5',
     'blas==1.0',
     'bottleneck==1.3.7',
     'brotli==1.0.9',
     'brotli-bin==1.0.9',
+    'brotli-python==1.0.9',
     'bzip2==1.0.8',
     'c-ares==1.19.1',
     'ca-certificates==2024.7.2',
+    'certifi==2024.8.30',
+    'charset-normalizer==3.3.2',
     'chex==0.1.5',
     'click==8.1.7',
+    'comm==0.2.1',
     'contextlib2==21.6.0',
     'contourpy==1.2.0',
     'cycler==0.11.0',
+    'decorator==5.1.1',
     'dm-tree==0.1.7',
     'docrep==0.3.2',
     'et_xmlfile==1.1.0',
     'exceptiongroup==1.2.0',
+    'executing==0.8.3',
     'filelock==3.13.1',
     'flax==0.6.1',
     'fonttools==4.51.0',
     'freetype==2.12.1',
-    'fsspec==2024.3.1',
+    'fsspec==2024.6.1',
     'get-annotations==0.1.2',
     'gmp==6.2.1',
     'gmpy2==2.1.2',
     'h5py==3.11.0',
     'hdf5==1.12.1',
+    'idna==3.7',
+    'ipython==8.25.0',
+    'ipywidgets==8.1.2',
     'jax==0.3.25',
     'jaxlib==0.3.25',
+    'jedi==0.19.1',
     'jinja2==3.1.4',
     'joblib==1.4.2',
     'jpeg==9e',
+    'jupyterlab_widgets==3.0.10',
     'kiwisolver==1.4.4',
     'krb5==1.20.1',
     'lcms2==2.12',
     'ld_impl_linux-64==2.38',
     'legacy-api-wrap==1.4',
     'lerc==3.0',
-    'libblas==3.9.0',
     'libbrotlicommon==1.0.9',
     'libbrotlidec==1.0.9',
     'libbrotlienc==1.0.9',
-    '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',
+    'libgcc-ng==11.2.0',
     'libgfortran-ng==11.2.0',
     'libgfortran5==11.2.0',
-    'libgomp==14.1.0',
+    'libgomp==11.2.0',
     'libllvm14==14.0.6',
     'libnghttp2==1.57.0',
     'libopenblas==0.3.21',
     'libpng==1.6.39',
     'libprotobuf==3.20.3',
     'libssh2==1.11.0',
-    'libstdcxx==14.1.0',
-    'libstdcxx-ng==14.1.0',
+    'libstdcxx-ng==11.2.0',
     'libtiff==4.5.1',
     'libuuid==1.41.5',
     'libwebp-base==1.3.2',
@@ -637,53 +663,62 @@
     'lz4-c==1.9.4',
     'markdown-it-py==2.2.0',
     'markupsafe==2.1.3',
-    'matplotlib-base==3.8.4',
+    'matplotlib-base==3.9.2',
+    'matplotlib-inline==0.1.6',
     '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',
+    'mudata==0.3.1',
     'multipledispatch==0.6.0',
     'natsort==7.1.1',
     'ncurses==6.4',
     'networkx==3.3',
     'numba==0.60.0',
     'numexpr==2.8.7',
-    'numpy==1.26.4',
-    'numpy-base==1.26.4',
+    'numpy==1.23.5',
+    'numpy-base==1.23.5',
     'numpy_groupies==0.11.2',
     'numpyro==0.13.2',
     'openjpeg==2.5.2',
     'openpyxl==3.1.5',
-    'openssl==3.0.14',
+    'openssl==3.0.15',
     'opt_einsum==3.3.0',
     'optax==0.1.4',
     'packaging==24.1',
     'pandas==2.2.2',
+    'parso==0.8.3',
     'patsy==0.5.6',
+    'pexpect==4.8.0',
     'pillow==10.4.0',
     'pip==24.2',
-    'pybind11-abi==4',
+    'platformdirs==3.10.0',
+    'pooch==1.7.0',
+    'prompt-toolkit==3.0.43',
+    'prompt_toolkit==3.0.43',
+    'ptyprocess==0.7.0',
+    'pure_eval==0.2.2',
     'pygments==2.15.1',
     'pynndescent==0.5.10',
-    'pyparsing==3.0.9',
+    'pyparsing==3.1.2',
     'pyro-api==0.1.2',
     'pyro-ppl==1.9.1',
+    'pysocks==1.7.1',
     'python==3.11.9',
     'python-dateutil==2.9.0post0',
     'python-tzdata==2023.3',
-    'python_abi==3.11',
     'pytorch==2.3.0',
     'pytorch-lightning==1.9.5',
     'pytz==2024.1',
     'pyyaml==6.0.1',
     'readline==8.2',
+    'requests==2.32.3',
     'rich==13.7.1',
     'scanpy==1.10.2',
     'scikit-learn==1.1.3',
-    'scipy==1.13.1',
+    'scipy==1.10.0',
     'scvelo==0.3.2',
     'scvi-tools==0.20.3',
     'seaborn==0.13.2',
@@ -691,20 +726,26 @@
     'setuptools==72.1.0',
     'six==1.16.0',
     'sqlite==3.45.3',
+    'stack_data==0.2.0',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'sympy==1.12',
+    'sympy==1.13.2',
+    'tbb==2021.8.0',
     'threadpoolctl==3.5.0',
     'tk==8.6.14',
     'toolz==0.12.0',
     'torchmetrics==1.4.0.post0',
-    'tqdm==4.66.4',
+    'tqdm==4.66.5',
+    'traitlets==5.14.3',
     'typing-extensions==4.11.0',
     'typing_extensions==4.11.0',
     'tzdata==2024a',
-    'umap-learn==0.5.3',
+    'umap-learn==0.5.4',
     'unicodedata2==15.1.0',
+    'urllib3==2.2.2',
+    'wcwidth==0.2.5',
     'wheel==0.43.0',
+    'widgetsnbextension==4.0.10',
     'xz==5.4.6',
     'yaml==0.2.5',
     'zlib==1.2.13',
diff --git a/inst/envs/Linux_x86_64_anaconda.yaml b/inst/envs/Linux_x86_64_anaconda.yaml
index 653d1cd..957d98f 100644
--- a/inst/envs/Linux_x86_64_anaconda.yaml
+++ b/inst/envs/Linux_x86_64_anaconda.yaml
@@ -1,73 +1,81 @@
-name: scvelo_libjpegturbo303
+name: scvelo
 channels:
 - anaconda
 - conda-forge
 dependencies:
-- _libgcc_mutex=0.1=conda_forge
-- _openmp_mutex=4.5=2_gnu
+- _libgcc_mutex=0.1=main
+- _openmp_mutex=5.1=1_gnu
 - absl-py=2.1.0=py311h06a4308_0
 - anndata=0.10.9=pyhd8ed1ab_0
 - array-api-compat=1.8=pyhd8ed1ab_0
+- asttokens=2.0.5=pyhd3eb1b0_0
 - blas=1.0=openblas
 - bottleneck=1.3.7=py311hf4808d0_0
 - brotli=1.0.9=h5eee18b_8
 - brotli-bin=1.0.9=h5eee18b_8
+- brotli-python=1.0.9=py311h6a678d5_8
 - bzip2=1.0.8=h5eee18b_6
 - c-ares=1.19.1=h5eee18b_0
 - ca-certificates=2024.7.2=h06a4308_0
+- certifi=2024.8.30=py311h06a4308_0
+- charset-normalizer=3.3.2=pyhd3eb1b0_0
 - chex=0.1.5=py311h06a4308_0
 - click=8.1.7=py311h06a4308_0
+- comm=0.2.1=py311h06a4308_0
 - contextlib2=21.6.0=py311h06a4308_0
 - contourpy=1.2.0=py311hdb19cb5_0
 - cycler=0.11.0=pyhd3eb1b0_0
+- decorator=5.1.1=pyhd3eb1b0_0
 - dm-tree=0.1.7=py311h6a678d5_1
 - docrep=0.3.2=pyh44b312d_0
 - et_xmlfile=1.1.0=py311h06a4308_0
 - exceptiongroup=1.2.0=py311h06a4308_0
+- executing=0.8.3=pyhd3eb1b0_0
 - filelock=3.13.1=py311h06a4308_0
 - flax=0.6.1=pyhd8ed1ab_1
 - fonttools=4.51.0=py311h5eee18b_0
 - freetype=2.12.1=h4a9f257_0
-- fsspec=2024.3.1=py311h06a4308_0
+- fsspec=2024.6.1=py311h06a4308_0
 - get-annotations=0.1.2=pyhd8ed1ab_0
 - gmp=6.2.1=h295c915_3
 - gmpy2=2.1.2=py311hc9b5ff0_0
 - h5py=3.11.0=py311h865a13c_0
 - hdf5=1.12.1=h2b7332f_3
+- idna=3.7=py311h06a4308_0
+- ipython=8.25.0=py311h06a4308_0
+- ipywidgets=8.1.2=py311h06a4308_0
 - jax=0.3.25=py311h06a4308_0
 - jaxlib=0.3.25=py311h6a678d5_2
+- jedi=0.19.1=py311h06a4308_0
 - jinja2=3.1.4=py311h06a4308_0
 - joblib=1.4.2=py311h06a4308_0
 - jpeg=9e=h5eee18b_3
+- jupyterlab_widgets=3.0.10=py311h06a4308_0
 - kiwisolver=1.4.4=py311h6a678d5_0
 - krb5=1.20.1=h143b758_1
 - lcms2=2.12=h3be6417_0
 - ld_impl_linux-64=2.38=h1181459_1
 - legacy-api-wrap=1.4=pyhd8ed1ab_1
 - lerc=3.0=h295c915_0
-- libblas=3.9.0=16_linux64_openblas
 - libbrotlicommon=1.0.9=h5eee18b_8
 - libbrotlidec=1.0.9=h5eee18b_8
 - libbrotlienc=1.0.9=h5eee18b_8
-- libcblas=3.9.0=16_linux64_openblas
 - libcurl=7.88.1=h251f7ec_2
 - libdeflate=1.17=h5eee18b_1
 - libedit=3.1.20230828=h5eee18b_0
 - libev=4.33=h7f8727e_1
 - libffi=3.4.4=h6a678d5_1
-- libgcc=14.1.0=h77fa898_1
-- libgcc-ng=14.1.0=h69a702a_1
+- libgcc-ng=11.2.0=h1234567_1
 - libgfortran-ng=11.2.0=h00389a5_1
 - libgfortran5=11.2.0=h1234567_1
-- libgomp=14.1.0=h77fa898_1
+- libgomp=11.2.0=h1234567_1
 - libllvm14=14.0.6=hdb19cb5_3
 - libnghttp2=1.57.0=h2d74bed_0
 - libopenblas=0.3.21=h043d6bf_0
 - libpng=1.6.39=h5eee18b_0
 - libprotobuf=3.20.3=he621ea3_0
 - libssh2=1.11.0=h251f7ec_0
-- libstdcxx=14.1.0=hc0a3c3a_1
-- libstdcxx-ng=14.1.0=h4852527_1
+- libstdcxx-ng=11.2.0=h1234567_1
 - libtiff=4.5.1=h6a678d5_0
 - libuuid=1.41.5=h5eee18b_0
 - libwebp-base=1.3.2=h5eee18b_0
@@ -77,53 +85,62 @@ dependencies:
 - lz4-c=1.9.4=h6a678d5_1
 - markdown-it-py=2.2.0=py311h06a4308_1
 - markupsafe=2.1.3=py311h5eee18b_0
-- matplotlib-base=3.8.4=py311ha02d727_0
+- matplotlib-base=3.9.2=py311h6fb44e5_0
+- matplotlib-inline=0.1.6=py311h06a4308_0
 - mdurl=0.1.0=py311h06a4308_0
 - ml-collections=0.1.1=pyhd8ed1ab_0
 - mpc=1.1.0=h10f8cd9_1
 - mpfr=4.0.2=hb69a4c5_1
 - mpmath=1.3.0=py311h06a4308_0
 - msgpack-python=1.0.3=py311hdb19cb5_0
-- mudata=0.3.0=pyhd8ed1ab_0
+- mudata=0.3.1=pyhd8ed1ab_0
 - multipledispatch=0.6.0=py311h06a4308_0
 - natsort=7.1.1=pyhd3eb1b0_0
 - ncurses=6.4=h6a678d5_0
 - networkx=3.3=py311h06a4308_0
-- numba=0.60.0=py311h4bc866e_0
+- numba=0.60.0=py311ha02d727_0
 - numexpr=2.8.7=py311h812550d_0
-- numpy=1.26.4=py311h24aa872_0
-- numpy-base=1.26.4=py311hbfb1bba_0
+- numpy=1.23.5=py311h5585df3_0
+- numpy-base=1.23.5=py311hc9e7d78_0
 - numpy_groupies=0.11.2=pyhd8ed1ab_0
 - numpyro=0.13.2=pyhd8ed1ab_0
 - openjpeg=2.5.2=he7f1fd0_0
 - openpyxl=3.1.5=py311h5eee18b_0
-- openssl=3.0.14=h5eee18b_0
+- openssl=3.0.15=h5eee18b_0
 - opt_einsum=3.3.0=pyhd3eb1b0_1
 - optax=0.1.4=py311h06a4308_0
 - packaging=24.1=py311h06a4308_0
 - pandas=2.2.2=py311ha02d727_0
+- parso=0.8.3=pyhd3eb1b0_0
 - patsy=0.5.6=py311h06a4308_0
+- pexpect=4.8.0=pyhd3eb1b0_3
 - pillow=10.4.0=py311h5eee18b_0
 - pip=24.2=py311h06a4308_0
-- pybind11-abi=4=hd3eb1b0_1
+- platformdirs=3.10.0=py311h06a4308_0
+- pooch=1.7.0=py311h06a4308_0
+- prompt-toolkit=3.0.43=py311h06a4308_0
+- prompt_toolkit=3.0.43=hd3eb1b0_0
+- ptyprocess=0.7.0=pyhd3eb1b0_2
+- pure_eval=0.2.2=pyhd3eb1b0_0
 - pygments=2.15.1=py311h06a4308_1
 - pynndescent=0.5.10=py311h06a4308_0
-- pyparsing=3.0.9=py311h06a4308_0
+- pyparsing=3.1.2=py311h06a4308_0
 - pyro-api=0.1.2=pyhd8ed1ab_0
 - pyro-ppl=1.9.1=pyhd8ed1ab_0
+- pysocks=1.7.1=py311h06a4308_0
 - python=3.11.9=h955ad1f_0
 - python-dateutil=2.9.0post0=py311h06a4308_2
 - python-tzdata=2023.3=pyhd3eb1b0_0
-- python_abi=3.11=2_cp311
 - pytorch=2.3.0=cpu_py311h991c31c_0
 - pytorch-lightning=1.9.5=py311h06a4308_1
 - pytz=2024.1=py311h06a4308_0
 - pyyaml=6.0.1=py311h5eee18b_0
 - readline=8.2=h5eee18b_0
+- requests=2.32.3=py311h06a4308_0
 - rich=13.7.1=py311h06a4308_0
 - scanpy=1.10.2=pyhd8ed1ab_0
-- scikit-learn=1.1.3=py311h3b52e38_1
-- scipy=1.13.1=py311h24aa872_0
+- scikit-learn=1.1.3=py311h6a678d5_1
+- scipy=1.10.0=py311hefedb09_1
 - scvelo=0.3.2=pyhd8ed1ab_1
 - scvi-tools=0.20.3=pyhd8ed1ab_0
 - seaborn=0.13.2=py311h06a4308_0
@@ -131,20 +148,26 @@ dependencies:
 - setuptools=72.1.0=py311h06a4308_0
 - six=1.16.0=pyhd3eb1b0_1
 - sqlite=3.45.3=h5eee18b_0
+- stack_data=0.2.0=pyhd3eb1b0_0
 - statsmodels=0.14.2=py311hf4808d0_0
 - stdlib-list=0.10.0=py311h06a4308_0
-- sympy=1.12=py311h06a4308_0
+- sympy=1.13.2=py311h06a4308_0
+- tbb=2021.8.0=hdb19cb5_0
 - threadpoolctl=3.5.0=py311h92b7b1e_0
 - tk=8.6.14=h39e8969_0
 - toolz=0.12.0=py311h06a4308_0
 - torchmetrics=1.4.0.post0=py311h06a4308_0
-- tqdm=4.66.4=py311h92b7b1e_0
+- tqdm=4.66.5=py311h92b7b1e_0
+- traitlets=5.14.3=py311h06a4308_0
 - typing-extensions=4.11.0=py311h06a4308_0
 - typing_extensions=4.11.0=py311h06a4308_0
 - tzdata=2024a=h04d1e81_0
-- umap-learn=0.5.3=py311h06a4308_0
+- umap-learn=0.5.4=py311h06a4308_0
 - unicodedata2=15.1.0=py311h5eee18b_0
+- urllib3=2.2.2=py311h06a4308_0
+- wcwidth=0.2.5=pyhd3eb1b0_0
 - wheel=0.43.0=py311h06a4308_0
+- widgetsnbextension=4.0.10=py311h06a4308_0
 - xz=5.4.6=h5eee18b_1
 - yaml=0.2.5=h7b6447c_0
 - zlib=1.2.13=h5eee18b_1
diff --git a/inst/envs/M1.yaml b/inst/envs/M1.yaml
index a9fe0be..a0f74f5 100644
--- a/inst/envs/M1.yaml
+++ b/inst/envs/M1.yaml
@@ -6,37 +6,41 @@ dependencies:
 - anndata=0.10.9=pyhd8ed1ab_0
 - aom=3.9.1=h7bae524_0
 - array-api-compat=1.8=pyhd8ed1ab_0
+- asttokens=2.4.1=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
+- brotli=1.1.0=hd74edd7_2
+- brotli-bin=1.1.0=hd74edd7_2
+- brotli-python=1.1.0=py311h3f08180_2
 - 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
+- certifi=2024.8.30=pyhd8ed1ab_0
+- cffi=1.17.1=py311h3a79f62_0
 - 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
+- comm=0.2.2=pyhd8ed1ab_0
 - contextlib2=21.6.0=pyhd8ed1ab_0
-- contourpy=1.3.0=py311h2c37856_0
+- contourpy=1.3.0=py311h2c37856_1
 - cycler=0.12.1=pyhd8ed1ab_0
 - dav1d=1.2.1=hb547adb_0
+- decorator=5.1.1=pyhd8ed1ab_0
 - docrep=0.3.2=pyh44b312d_0
 - et_xmlfile=1.1.0=pyhd8ed1ab_0
-- etils=1.9.2=pyhd8ed1ab_0
+- etils=1.9.4=pyhd8ed1ab_0
 - exceptiongroup=1.2.2=pyhd8ed1ab_0
-- filelock=3.15.4=pyhd8ed1ab_0
+- executing=2.1.0=pyhd8ed1ab_0
+- filelock=3.16.0=pyhd8ed1ab_0
 - flax=0.9.0=pyhd8ed1ab_0
-- fonttools=4.53.1=py311hd3f4193_0
+- fonttools=4.53.1=py311h460d6c5_1
 - freetype=2.12.1=hadb7bae_2
-- fsspec=2024.6.1=pyhff2d567_0
+- fsspec=2024.9.0=pyhff2d567_0
 - get-annotations=0.1.2=pyhd8ed1ab_0
 - gmp=6.3.0=h7bae524_2
-- gmpy2=2.1.5=py311h1e33d93_1
+- gmpy2=2.1.5=py311hb5ce3a2_2
 - h2=4.1.0=pyhd8ed1ab_0
 - h5py=3.11.0=nompi_py311hd41bb03_102
 - hdf5=1.14.3=nompi_hec07895_105
@@ -45,13 +49,16 @@ dependencies:
 - 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
+- ipython=8.27.0=pyh707e725_0
+- ipywidgets=8.1.5=pyhd8ed1ab_0
+- jax=0.4.31=pyhd8ed1ab_1
+- jaxlib=0.4.31=cpu_py311hd54497d_1
+- jedi=0.19.1=pyhd8ed1ab_0
 - jinja2=3.1.4=pyhd8ed1ab_0
 - joblib=1.4.2=pyhd8ed1ab_0
-- kiwisolver=1.4.5=py311h2c37856_2
+- jupyterlab_widgets=3.0.13=pyhd8ed1ab_0
+- kiwisolver=1.4.7=py311h2c37856_0
 - krb5=1.21.3=h237132a_0
 - lcms2=2.16=ha0e7c42_0
 - legacy-api-wrap=1.4=pyhd8ed1ab_1
@@ -60,16 +67,16 @@ dependencies:
 - 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
+- libbrotlicommon=1.1.0=hd74edd7_2
+- libbrotlidec=1.1.0=hd74edd7_2
+- libbrotlienc=1.1.0=hd74edd7_2
 - libcblas=3.9.0=23_osxarm64_openblas
 - libcurl=8.9.1=hfd8ffcc_0
-- libcxx=18.1.8=h3ed4263_6
+- libcxx=18.1.8=h3ed4263_7
 - libdeflate=1.21=h99b78c6_0
 - libedit=3.1.20191231=hc8eb9b7_2
 - libev=4.33=h93a5062_2
-- libexpat=2.6.2=hebf3989_0
+- libexpat=2.6.3=hf9b8971_0
 - libffi=3.4.2=h3422bc3_5
 - libgfortran=5.0.0=13_2_0_hd922786_3
 - libgfortran5=13.2.0=hf226fd6_3
@@ -84,7 +91,7 @@ dependencies:
 - 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
+- libsqlite=3.46.1=hc14010f_0
 - libssh2=1.11.0=h7a5bd25_0
 - libtiff=4.6.0=hf8409c0_4
 - libtorch=2.4.0=cpu_generic_h15ee98c_1
@@ -94,21 +101,22 @@ dependencies:
 - 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
+- lightning-utilities=0.11.7=pyhd8ed1ab_0
 - llvm-openmp=18.1.8=hde57baf_1
-- llvmlite=0.43.0=py311h02e79e2_0
+- llvmlite=0.43.0=py311hc367efa_1
 - 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
+- matplotlib-inline=0.1.7=pyhd8ed1ab_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
+- ml_dtypes=0.4.0=py311h9cb3ce9_2
+- mpc=1.3.1=h8f1351a_1
+- mpfr=4.2.1=hb693164_3
 - mpmath=1.3.0=pyhd8ed1ab_0
-- msgpack-python=1.0.8=py311h6bde47b_0
+- msgpack-python=1.0.8=py311h2c37856_1
 - mudata=0.3.1=pyhd8ed1ab_0
 - multipledispatch=0.6.0=pyhd8ed1ab_1
 - munkres=1.1.4=pyh9f0ad1d_0
@@ -122,19 +130,25 @@ dependencies:
 - 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
+- openpyxl=3.1.5=py311hfb527b5_1
+- openssl=3.3.2=h8359307_0
 - 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
+- parso=0.8.4=pyhd8ed1ab_0
 - patsy=0.5.6=pyhd8ed1ab_0
+- pexpect=4.9.0=pyhd8ed1ab_0
+- pickleshare=0.7.5=py_1003
 - pillow=10.4.0=py311hd7951ec_0
 - pip=24.2=pyh8b19718_1
+- prompt-toolkit=3.0.47=pyha770c72_0
 - protobuf=4.25.3=py311hd7a3543_1
 - pthread-stubs=0.4=h27ca646_1001
+- ptyprocess=0.7.0=pyhd3deb0d_0
+- pure_eval=0.2.3=pyhd8ed1ab_0
 - pybind11-abi=4=hd8ed1ab_3
 - pycparser=2.22=pyhd8ed1ab_0
 - pygments=2.18.0=pyhd8ed1ab_0
@@ -150,7 +164,7 @@ dependencies:
 - 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
+- pyyaml=6.0.2=py311h460d6c5_1
 - qhull=2020.2=h420ef59_5
 - rav1e=0.6.6=h69fbcac_2
 - re2=2023.09.01=h4cba328_2
@@ -165,33 +179,37 @@ dependencies:
 - 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
+- setuptools=73.0.1=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
+- stack_data=0.6.2=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
+- tbb=2021.13.0=h7b3277c_0
+- tensorstore=0.1.62=py311h6f6bbf4_1
 - 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
+- traitlets=5.14.3=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
+- wcwidth=0.2.13=pyhd8ed1ab_0
 - wheel=0.44.0=pyhd8ed1ab_0
+- widgetsnbextension=4.0.13=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
+- zstandard=0.23.0=py311ha60cc69_1
 - 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 3ca1244..7c8fedd 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("inst/envs/M1.yaml")
+yaml_data <- yaml::read_yaml("inst/envs/Linux_x86_64_anaconda.yaml")
 r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies)
 cat(paste0(
   "c(",