From 6756e0d381d475d0c8d6e3d07d79165063ff326d Mon Sep 17 00:00:00 2001 From: Kevin Rue-Albrecht Date: Tue, 10 Sep 2024 12:33:56 +0100 Subject: [PATCH] fix env --- R/basilisk.R | 100 +++++++++++++++++++++++++++++++++++ inst/envs/M1.yaml | 100 +++++++++++++++++++++++++++++++++++ inst/envs/format_yaml_to_r.R | 2 +- 3 files changed, 201 insertions(+), 1 deletion(-) diff --git a/R/basilisk.R b/R/basilisk.R index a47eddf..b1f5be7 100644 --- a/R/basilisk.R +++ b/R/basilisk.R @@ -237,6 +237,106 @@ 'libev==4.33', 'libexpat==2.6.3', 'libffi==3.4.2', + 'libgfortran==5.0.0', + 'libgfortran5==13.2.0', + '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', + 'libopenblas==0.3.27', + 'libpng==1.6.43', + 'libprotobuf==4.25.3', + 'libre2-11==2023.09.01', + 'libsqlite==3.46.1', + 'libssh2==1.11.0', + 'libtiff==4.6.0', + 'libtorch==2.4.0', + 'libuv==1.48.0', + 'libwebp-base==1.4.0', + 'libxcb==1.16', + 'libxml2==2.12.7', + 'libzlib==1.3.1', + 'lightning==2.4.0', + 'lightning-utilities==0.11.7', + '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==3.9.2', + 'matplotlib-inline==0.1.7', + 'mdurl==0.1.2', + 'ml-collections==0.1.1', + 'ml_dtypes==0.4.0', + 'mpc==1.3.1', + 'mpfr==4.2.1', + 'mpmath==1.3.0', + 'msgpack-python==1.0.8', + '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==3.3', + 'nomkl==1.0', + 'numba==0.60.0', + 'numpy==1.26.4', + 'numpy_groupies==0.11.2', + 'numpyro==0.15.2', + 'openjpeg==2.5.2', + 'openpyxl==3.1.5', + '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', + 'pynndescent==0.5.13', + 'pyparsing==3.1.4', + '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_abi==3.11', + 'pytorch==2.4.0', + 'pytorch-lightning==2.4.0', + 'pytz==2024.1', + 'pyyaml==6.0.2', + 'qhull==2020.2', + 'rav1e==0.6.6', + 're2==2023.09.01', + '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', + 'seaborn==0.13.2', + 'seaborn-base==0.13.2', 'session-info==1.0.0', 'setuptools==73.0.1', 'six==1.16.0', diff --git a/inst/envs/M1.yaml b/inst/envs/M1.yaml index 4c3ffd4..fc48be0 100644 --- a/inst/envs/M1.yaml +++ b/inst/envs/M1.yaml @@ -78,6 +78,106 @@ dependencies: - libev=4.33=h93a5062_2 - 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 +- 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=3.46.1=hc14010f_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=0.11.7=pyhd8ed1ab_0 +- llvm-openmp=18.1.8=hde57baf_1 +- 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=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=py311h2c37856_1 +- 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=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 +- 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=py311h460d6c5_1 +- 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=73.0.1=pyhd8ed1ab_0 - six=1.16.0=pyh6c4a22f_0 diff --git a/inst/envs/format_yaml_to_r.R b/inst/envs/format_yaml_to_r.R index 7c8fedd..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("inst/envs/Linux_x86_64_anaconda.yaml") +yaml_data <- yaml::read_yaml("inst/envs/M1.yaml") r_data <- gsub("([[:alnum:]_]+)=([[:alnum:].]+)=.+", "\\1==\\2" , yaml_data$dependencies) cat(paste0( "c(",