From fd0fa36732a1de4db6c6cf241d47cd345a2debce Mon Sep 17 00:00:00 2001
From: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: Thu, 29 Aug 2024 10:08:47 +0100
Subject: [PATCH] try an environment using anaconda

---
 R/basilisk.R                         | 222 ++++++++++-----------------
 inst/envs/Linux_x86_64_anaconda.yaml | 151 ++++++++++++++++++
 inst/envs/format_yaml_to_r.R         |   2 +-
 3 files changed, 234 insertions(+), 141 deletions(-)
 create mode 100644 inst/envs/Linux_x86_64_anaconda.yaml

diff --git a/R/basilisk.R b/R/basilisk.R
index 66df06b..3bdd527 100644
--- a/R/basilisk.R
+++ b/R/basilisk.R
@@ -698,212 +698,154 @@
 ## Linux ----
 
 .scvelo.dependencies.Linux <- list(
-  channels = c("conda-forge", "bioconda"),
+  channels = c("anaconda", "conda-forge", "bioconda"),
   packages = c(
     '_libgcc_mutex==0.1',
     '_openmp_mutex==4.5',
     'absl-py==2.1.0',
-    'anndata==0.10.8',
-    'aom==3.9.1',
+    'anndata==0.10.9',
     'array-api-compat==1.8',
-    'blosc==1.21.6',
-    'brotli==1.1.0',
-    'brotli-bin==1.1.0',
-    'brotli-python==1.1.0',
+    'blas==1.0',
+    'bottleneck==1.3.7',
+    'brotli==1.0.9',
+    'brotli-bin==1.0.9',
     'bzip2==1.0.8',
-    'c-ares==1.33.1',
-    'ca-certificates==2024.7.4',
-    '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',
+    'c-ares==1.19.1',
+    'ca-certificates==2024.7.2',
+    'chex==0.1.5',
     'click==8.1.7',
-    'colorama==0.4.6',
     'contextlib2==21.6.0',
-    'contourpy==1.2.1',
-    'cycler==0.12.1',
-    'dav1d==1.2.1',
+    'contourpy==1.2.0',
+    'cycler==0.11.0',
+    'dm-tree==0.1.7',
     'docrep==0.3.2',
     'et_xmlfile==1.1.0',
-    'etils==1.9.2',
-    'exceptiongroup==1.2.2',
-    'filelock==3.15.4',
-    'flax==0.9.0',
-    'fonttools==4.53.1',
+    'exceptiongroup==1.2.0',
+    'filelock==3.13.1',
+    'flax==0.6.1',
+    'fonttools==4.51.0',
     'freetype==2.12.1',
-    'fsspec==2024.6.1',
+    'fsspec==2024.3.1',
     'get-annotations==0.1.2',
-    'gmp==6.3.0',
-    'gmpy2==2.1.5',
-    'h2==4.1.0',
+    'gmp==6.2.1',
+    'gmpy2==2.1.2',
     'h5py==3.11.0',
-    'hdf5==1.14.3',
-    'hpack==4.0.0',
-    'hyperframe==6.0.1',
-    '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',
+    'hdf5==1.12.1',
+    'jax==0.3.25',
+    'jaxlib==0.3.25',
     'jinja2==3.1.4',
     'joblib==1.4.2',
-    'keyutils==1.6.1',
-    'kiwisolver==1.4.5',
-    'krb5==1.21.3',
-    'lcms2==2.16',
-    'ld_impl_linux-64==2.40',
+    'jpeg==9e',
+    'kiwisolver==1.4.4',
+    'krb5==1.20.1',
+    'lcms2==2.12',
+    'ld_impl_linux-64==2.38',
     'legacy-api-wrap==1.4',
-    'lerc==4.0.0',
-    'libabseil==20240116.2',
-    'libaec==1.1.3',
-    'libavif16==1.1.1',
+    'lerc==3.0',
     'libblas==3.9.0',
-    'libbrotlicommon==1.1.0',
-    'libbrotlidec==1.1.0',
-    'libbrotlienc==1.1.0',
+    'libbrotlicommon==1.0.9',
+    'libbrotlidec==1.0.9',
+    'libbrotlienc==1.0.9',
     'libcblas==3.9.0',
-    'libcurl==8.9.1',
-    'libdeflate==1.21',
-    'libedit==3.1.20191231',
+    'libcurl==7.88.1',
+    'libdeflate==1.17',
+    'libedit==3.1.20230828',
     'libev==4.33',
-    'libexpat==2.6.2',
-    'libffi==3.4.2',
+    'libffi==3.4.4',
     'libgcc==14.1.0',
     'libgcc-ng==14.1.0',
-    'libgfortran==14.1.0',
-    'libgfortran-ng==14.1.0',
-    'libgfortran5==14.1.0',
+    'libgfortran-ng==11.2.0',
+    'libgfortran5==11.2.0',
     'libgomp==14.1.0',
-    'libgrpc==1.62.2',
-    'libhwloc==2.11.1',
-    'libiconv==1.17',
-    'libjpeg-turbo==3.0.0',
-    'liblapack==3.9.0',
     'libllvm14==14.0.6',
-    'libnghttp2==1.58.0',
-    'libnsl==2.0.1',
-    'libopenblas==0.3.27',
-    'libpng==1.6.43',
-    'libprotobuf==4.25.3',
-    'libre2-11==2023.09.01',
-    'libsqlite==3.46.0',
+    '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',
-    'libtiff==4.6.0',
-    'libtorch==2.4.0',
-    'libuuid==2.38.1',
-    'libuv==1.48.0',
-    'libwebp-base==1.4.0',
-    'libxcb==1.16',
-    'libxcrypt==4.4.36',
-    'libxml2==2.12.7',
-    'libzlib==1.3.1',
-    'lightning==2.4.0',
-    'lightning-utilities==0.11.6',
+    'libtiff==4.5.1',
+    'libuuid==1.41.5',
+    'libwebp-base==1.3.2',
+    'lightning-utilities==0.9.0',
     '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==3.9.2',
-    'mdurl==0.1.2',
+    'markdown-it-py==2.2.0',
+    'markupsafe==2.1.3',
+    'matplotlib-base==3.8.4',
+    'mdurl==0.1.0',
     'ml-collections==0.1.1',
-    'ml_dtypes==0.4.0',
-    'mpc==1.3.1',
-    'mpfr==4.2.1',
+    'mpc==1.1.0',
+    'mpfr==4.0.2',
     'mpmath==1.3.0',
-    'msgpack-python==1.0.8',
+    'msgpack-python==1.0.3',
     'mudata==0.3.0',
     'multipledispatch==0.6.0',
-    'munkres==1.1.4',
-    'natsort==8.4.0',
-    'ncurses==6.5',
-    'nest-asyncio==1.6.0',
+    'natsort==7.1.1',
+    'ncurses==6.4',
     'networkx==3.3',
-    'nomkl==1.0',
     'numba==0.60.0',
+    'numexpr==2.8.7',
     'numpy==1.26.4',
+    'numpy-base==1.26.4',
     'numpy_groupies==0.11.2',
-    'numpyro==0.15.2',
+    'numpyro==0.13.2',
     'openjpeg==2.5.2',
     'openpyxl==3.1.5',
-    'openssl==3.3.1',
-    'opt-einsum==3.3.0',
+    'openssl==3.0.14',
     'opt_einsum==3.3.0',
-    'optax==0.2.2',
-    'orbax-checkpoint==0.4.4',
+    'optax==0.1.4',
     'packaging==24.1',
     'pandas==2.2.2',
     'patsy==0.5.6',
     'pillow==10.4.0',
     'pip==24.2',
-    'protobuf==4.25.3',
-    'pthread-stubs==0.4',
     'pybind11-abi==4',
-    'pycparser==2.22',
-    'pygments==2.18.0',
-    'pynndescent==0.5.13',
-    'pyparsing==3.1.4',
+    'pygments==2.15.1',
+    'pynndescent==0.5.10',
+    'pyparsing==3.0.9',
     'pyro-api==0.1.2',
     'pyro-ppl==1.9.1',
-    'pysocks==1.7.1',
     'python==3.11.9',
-    'python-dateutil==2.9.0',
-    'python-tzdata==2024.1',
+    'python-dateutil==2.9.0post0',
+    'python-tzdata==2023.3',
     'python_abi==3.11',
-    'pytorch==2.4.0',
-    'pytorch-lightning==2.4.0',
+    'pytorch==2.3.0',
+    'pytorch-lightning==1.9.5',
     'pytz==2024.1',
-    'pyyaml==6.0.2',
-    'qhull==2020.2',
-    'rav1e==0.6.6',
-    're2==2023.09.01',
+    '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',
     'scvelo==0.3.2',
-    'scvi-tools==1.1.6',
+    'scvi-tools==0.20.3',
     'seaborn==0.13.2',
-    'seaborn-base==0.13.2',
     'session-info==1.0.0',
-    'setuptools==72.2.0',
+    'setuptools==72.1.0',
     'six==1.16.0',
-    'sleef==3.6.1',
-    'snappy==1.2.1',
-    'sparse==0.15.4',
+    'sqlite==3.45.3',
     'statsmodels==0.14.2',
     'stdlib-list==0.10.0',
-    'svt-av1==2.2.1',
-    'sympy==1.13.2',
-    'tbb==2021.12.0',
-    'tensorstore==0.1.62',
+    'sympy==1.12',
     'threadpoolctl==3.5.0',
-    'tk==8.6.13',
-    'toolz==0.12.1',
+    'tk==8.6.14',
+    'toolz==0.12.0',
     'torchmetrics==1.4.0.post0',
-    'tqdm==4.66.5',
-    'typing-extensions==4.12.2',
-    'typing_extensions==4.12.2',
+    'tqdm==4.66.4',
+    'typing-extensions==4.11.0',
+    'typing_extensions==4.11.0',
     'tzdata==2024a',
-    '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',
+    'umap-learn==0.5.3',
+    'unicodedata2==15.1.0',
+    'wheel==0.43.0',
+    'xz==5.4.6',
     'yaml==0.2.5',
-    'zipp==3.20.1',
-    'zstandard==0.23.0',
-    'zstd==1.5.6'
+    'zlib==1.2.13',
+    'zstd==1.5.5'
   )
 )
 
diff --git a/inst/envs/Linux_x86_64_anaconda.yaml b/inst/envs/Linux_x86_64_anaconda.yaml
new file mode 100644
index 0000000..653d1cd
--- /dev/null
+++ b/inst/envs/Linux_x86_64_anaconda.yaml
@@ -0,0 +1,151 @@
+name: scvelo_libjpegturbo303
+channels:
+- anaconda
+- conda-forge
+dependencies:
+- _libgcc_mutex=0.1=conda_forge
+- _openmp_mutex=4.5=2_gnu
+- absl-py=2.1.0=py311h06a4308_0
+- anndata=0.10.9=pyhd8ed1ab_0
+- array-api-compat=1.8=pyhd8ed1ab_0
+- blas=1.0=openblas
+- bottleneck=1.3.7=py311hf4808d0_0
+- brotli=1.0.9=h5eee18b_8
+- brotli-bin=1.0.9=h5eee18b_8
+- bzip2=1.0.8=h5eee18b_6
+- c-ares=1.19.1=h5eee18b_0
+- ca-certificates=2024.7.2=h06a4308_0
+- chex=0.1.5=py311h06a4308_0
+- click=8.1.7=py311h06a4308_0
+- contextlib2=21.6.0=py311h06a4308_0
+- contourpy=1.2.0=py311hdb19cb5_0
+- cycler=0.11.0=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
+- 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
+- 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
+- jax=0.3.25=py311h06a4308_0
+- jaxlib=0.3.25=py311h6a678d5_2
+- jinja2=3.1.4=py311h06a4308_0
+- joblib=1.4.2=py311h06a4308_0
+- jpeg=9e=h5eee18b_3
+- 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
+- libgfortran-ng=11.2.0=h00389a5_1
+- libgfortran5=11.2.0=h1234567_1
+- libgomp=14.1.0=h77fa898_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
+- libtiff=4.5.1=h6a678d5_0
+- libuuid=1.41.5=h5eee18b_0
+- libwebp-base=1.3.2=h5eee18b_0
+- lightning-utilities=0.9.0=py311h06a4308_0
+- llvmlite=0.43.0=py311h6a678d5_0
+- loompy=3.0.6=py_0
+- 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
+- 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
+- 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
+- numexpr=2.8.7=py311h812550d_0
+- numpy=1.26.4=py311h24aa872_0
+- numpy-base=1.26.4=py311hbfb1bba_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
+- opt_einsum=3.3.0=pyhd3eb1b0_1
+- optax=0.1.4=py311h06a4308_0
+- packaging=24.1=py311h06a4308_0
+- pandas=2.2.2=py311ha02d727_0
+- patsy=0.5.6=py311h06a4308_0
+- pillow=10.4.0=py311h5eee18b_0
+- pip=24.2=py311h06a4308_0
+- pybind11-abi=4=hd3eb1b0_1
+- pygments=2.15.1=py311h06a4308_1
+- pynndescent=0.5.10=py311h06a4308_0
+- pyparsing=3.0.9=py311h06a4308_0
+- pyro-api=0.1.2=pyhd8ed1ab_0
+- pyro-ppl=1.9.1=pyhd8ed1ab_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
+- 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
+- scvelo=0.3.2=pyhd8ed1ab_1
+- scvi-tools=0.20.3=pyhd8ed1ab_0
+- seaborn=0.13.2=py311h06a4308_0
+- session-info=1.0.0=pyhd8ed1ab_0
+- setuptools=72.1.0=py311h06a4308_0
+- six=1.16.0=pyhd3eb1b0_1
+- sqlite=3.45.3=h5eee18b_0
+- statsmodels=0.14.2=py311hf4808d0_0
+- stdlib-list=0.10.0=py311h06a4308_0
+- sympy=1.12=py311h06a4308_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
+- 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
+- unicodedata2=15.1.0=py311h5eee18b_0
+- wheel=0.43.0=py311h06a4308_0
+- xz=5.4.6=h5eee18b_1
+- yaml=0.2.5=h7b6447c_0
+- zlib=1.2.13=h5eee18b_1
+- zstd=1.5.5=hc292b87_2
diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R
index 157f9e6..d147eb2 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("Linux_x86_64.yaml")
+yaml_data <- yaml::read_yaml("Linux_x86_64_anaconda.yaml")
 r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies)
 cat(paste0(
   "c(",