environment.yml not working for mac

[emarsh25]

I am struggling to get the conda environment set up on my Mac M1. I am only really raising this issue because the repo says it has been tested on MacOS. Originally this was the error:

ResolvePackageNotFound:

• certifi==2021.10.8=py37h06a4308_2
• xorg-libxau==1.0.9=h7f98852_0
• kiwisolver==1.3.2=py37h2527ec5_0
• openssl==3.0.0=h7f98852_1
• xorg-libxdmcp==1.1.3=h7f98852_0
• tornado==6.1=py37h5e8e339_1
• nbconvert==6.2.0=py37h89c1867_0
• libopenblas==0.3.18=pthreads_h8fe5266_0
• markupsafe==2.0.1=py37h5e8e339_0
• _openmp_mutex==4.5=1_gnu
• fontconfig==2.13.1=hba837de_1005
• freetype==2.10.4=h0708190_1
• liblapack==3.9.0=12_linux64_openblas
• libgomp==11.2.0=h1d223b6_11
• xz==5.2.5=h516909a_1
• tenacity==8.0.1=py37h06a4308_0
• zeromq==4.3.4=h9c3ff4c_1
• libpng==1.6.37=h21135ba_2
• xorg-libice==1.0.10=h7f98852_0
• scikit-learn==1.0=py37hf0f1638_1
• xorg-xextproto==7.3.0=h7f98852_1002
• pixman==0.38.0=h516909a_1003
• xorg-renderproto==0.11.1=h7f98852_1002
• libzlib==1.2.11=h36c2ea0_1013
• pyrsistent==0.17.3=py37h5e8e339_2
• libxml2==2.9.12=h03d6c58_0
• libgcc-ng==11.2.0=h1d223b6_11
• ld_impl_linux-64==2.36.1=hea4e1c9_2
• debugpy==1.4.1=py37hcd2ae1e_0
• libgfortran-ng==11.2.0=h69a702a_11
• sqlite==3.36.0=h9cd32fc_2
• xorg-xproto==7.0.31=h7f98852_1007
• mistune==0.8.4=py37h5e8e339_1004
• pcre==8.45=h9c3ff4c_0
• py-boost==1.73.0=py37ha9443f7_11
• icu==58.2=hf484d3e_1000
• xorg-kbproto==1.0.7=h7f98852_1002
• lz4-c==1.9.3=h9c3ff4c_1
• glib==2.70.0=h780b84a_0
• pthread-stubs==0.4=h36c2ea0_1001
• libblas==3.9.0=12_linux64_openblas
• _libgcc_mutex==0.1=conda_forge
• statsmodels==0.13.0=py37hb1e94ed_0
• libxcb==1.13=h7f98852_1003
• jedi==0.18.0=py37h89c1867_2
• tk==8.6.11=h27826a3_1
• xorg-libxext==1.3.4=h7f98852_1
• libsodium==1.0.18=h36c2ea0_1
• bzip2==1.0.8=h7f98852_4
• libiconv==1.16=h516909a_0
• ipython==7.28.0=py37h6531663_0
• readline==8.1=h46c0cb4_0
• libboost==1.73.0=h3ff78a5_11
• libglib==2.70.0=h174f98d_0
• jpeg==9d=h36c2ea0_0
• libtiff==4.0.10=hc3755c2_1005
• zlib==1.2.11=h36c2ea0_1013
• libstdcxx-ng==11.2.0=he4da1e4_11
• jupyter_core==4.8.1=py37h89c1867_0

After I removed the versions and things, I got the following error:

ResolvePackageNotFound:

• _libgcc_mutex
• _openmp_mutex
• libgomp
• libstdcxx-ng
• libnsl
• libgcc-ng
• libgfortran-ng

Any help would be great!

[wjm41]

Thanks for raising the issue! Let me look into this over the weekend and get back to you :)

[wjm41]

My bad, I forgot to include a separate environment .yml for macOS - I've updated the repo with a .yml file, could you check if that works for you?

fyi I am using an Intel-based Macbook but that shouldn't lead to any discrepancies since I'm not utilising any GPU-dependent packages.

[emarsh25]

So it looks a lot better but I still got the following error:

ResolvePackageNotFound:

• pip==22.3.1=py37hecd8cb5_0
• ncurses==6.3=hca72f7f_3
• zlib==1.2.13=h4dc903c_0
• openssl==1.1.1s=hca72f7f_0
• certifi==2022.12.7=py37hecd8cb5_0
• ca-certificates==2022.10.11=hecd8cb5_0
• libffi==3.4.2=hecd8cb5_6
• sqlite==3.40.1=h880c91c_0
• readline==8.2=hca72f7f_0
• setuptools==65.6.3=py37hecd8cb5_0
• python==3.7.15=h218abb5_1
• tk==8.6.12=h5d9f67b_0
• xz==5.2.8=h6c40b1e_0

[wjm41]

Interesting! Could you try the updated .yml in the repo, as well as these instructions I found here for making an x86 environment on Apple Silicon macs?

Specifically, I think the line should be this:

CONDA_SUBDIR=osx-64 conda create -f environment_mac.yml
conda activate fresco
conda config --env --set subdir osx-64

Let me know if that works!

[wjm41]

Just updated the yml file again to fix some incompatibilities - it looks like running pip install kdepy won't work so you'll have to install that separately after creating the conda environment by running:

git clone [email protected]:tommyod/KDEpy.git
cd KDEpy
pip install .

as detailed here. Fingers crossed, that should mean you can import v1.1.0 of kdepy in python.

Let me know if that works!