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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
GNU General Public License v3.0
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Conda install of smc++ version 0.0.0? #253

Open dmacguigan opened 8 months ago

dmacguigan commented 8 months ago

Hello,

I recently installed smc++ using conda.

conda create --name smcpp_env
conda install -c terhorst smcpp

The install is successful and I can use smc++. However, it lists the version as 0.0.0. Any idea what's going on?

Also, it would be helpful if the SMC++ GitHub README could be updated. It still says "Anaconda support has been discontinued"

(smcpp_env) dmacguig@pop-os:~$ smc++ version
SMC++ v0.0.0
(smcpp_env) dmacguig@pop-os:~$ conda list
# packages in environment at /home/dmacguig/miniconda3/envs/smcpp_env:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
appdirs                   1.4.4                    pypi_0    pypi
brotli-python             1.1.0            py38h17151c0_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
charset-normalizer        3.3.0              pyhd8ed1ab_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
icu                       67.1                 he1b5a44_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
joblib                    1.3.2                    pypi_0    pypi
kiwisolver                1.4.5            py38h7f3f72f_1    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libblas                   3.9.0           19_linux64_openblas    conda-forge
libcblas                  3.9.0           19_linux64_openblas    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
liblapack                 3.9.0           19_linux64_openblas    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsqlite                 3.43.2               h2797004_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
matplotlib                3.2.2                         1    conda-forge
matplotlib-base           3.2.2            py38h5d868c9_1    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
numpy                     1.24.4           py38h59b608b_0    conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.0.3            py38h01efb38_1    conda-forge
pip                       23.3               pyhd8ed1ab_0    conda-forge
platformdirs              3.11.0             pyhd8ed1ab_0    conda-forge
pooch                     1.7.0              pyhd8ed1ab_4    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysam                     0.22.0                   pypi_0    pypi
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.8.18          hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.8                      4_cp38    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
scikit-learn              1.3.1                    pypi_0    pypi
scipy                     1.10.1           py38h59b608b_3    conda-forge
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smcpp                     0.0.0                    pypi_0    pypi
sqlite                    3.43.2               h2c6b66d_0    conda-forge
threadpoolctl             3.2.0                    pypi_0    pypi
tk                        8.6.13               h2797004_0    conda-forge
tornado                   6.3.3            py38h01eb140_1    conda-forge
tqdm                      4.66.1                   pypi_0    pypi
typing-extensions         4.8.0                hd8ed1ab_0    conda-forge
typing_extensions         4.8.0              pyha770c72_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
urllib3                   2.0.7              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
terhorst commented 8 months ago

Hello, I no longer support building SMC++ with Anaconda precisely due to weird issues like this one (see #164). It's possible you may be able to get it to work; however I am unable to do so. For this reason I switched over to Docker.

dmacguigan commented 8 months ago

Ah I see. Is there a way to use SMC++ v.1.15.5 with Docker? The latest release I can see on Github is 1.15.2. And when I use Docker, it the latest version is 1.15.4.

(base) ***@***.***:~$ sudo docker run --rm -v $PWD:/mnt terhorst/smcpp:latest version
SMC++ v1.15.4.dev18+gca077da.d20210316