fix env

kevinrue · Sep 10, 2024 · 6756e0d · 6756e0d
1 parent db20318
commit 6756e0d
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diff --git 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
@@ -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
@@ -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(",