search

TencentAILabHealthcare / pysodb

22 stars 4 forks source link

Streamline installation with .yml and conda #2

Closed mattobny closed 1 year ago

mattobny commented 1 year ago

Hello and thank you for putting this package together! I was experiencing the same issues detailed in #1 earlier today. So, I took the dependencies from setup.py and reorganized them into the file pysodb.yml for installation with conda; it worked on the first try! I removed and reinstalled the environment to ensure my first try was not a fluke, and I had success yet again. I then was able to import data according to the README.md without issue.

This PR contains the .yml file I used, pysodb.yml, and a slightly altered README.md to reflect my installation process to the tee. Thank you again for your work - the @drieslab and I look forward to utilizing this package to access the SODB!

Specs:
Windows 11 x64
Conda v22.11.1

For those curious, below is the stdout from conda list in this new environment:

#
# Name                    Version                   Build  Channel
anndata                   0.8.0              pyhd8ed1ab_1    conda-forge
appdirs                   1.4.4              pyh9f0ad1d_0    conda-forge
brotli                    1.0.9                hcfcfb64_8    conda-forge
brotli-bin                1.0.9                hcfcfb64_8    conda-forge
brotlipy                  0.7.0           py38h91455d4_1005    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
ca-certificates           2022.12.7            h5b45459_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38h57701bc_3    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
contourpy                 1.0.7            py38hb1fd069_0    conda-forge
cryptography              39.0.1           py38h95f5157_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
fonttools                 4.38.0           py38h91455d4_1    conda-forge
freetype                  2.12.1               h546665d_1    conda-forge
h5py                      3.8.0           nompi_py38h442309b_101    conda-forge
hdf5                      1.14.0          nompi_h5af7005_102    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.0.0              pyha770c72_0    conda-forge
importlib-resources       5.12.0             pyhd8ed1ab_0    conda-forge
importlib_metadata        6.0.0                hd8ed1ab_0    conda-forge
importlib_resources       5.12.0             pyhd8ed1ab_0    conda-forge
intel-openmp              2023.0.0         h57928b3_25922    conda-forge
joblib                    1.2.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hcfcfb64_3    conda-forge
kiwisolver                1.4.4            py38hb1fd069_1    conda-forge
krb5                      1.20.1               heb0366b_0    conda-forge
lcms2                     2.14                 ha5c8aab_1    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libblas                   3.9.0              16_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_8    conda-forge
libbrotlidec              1.0.9                hcfcfb64_8    conda-forge
libbrotlienc              1.0.9                hcfcfb64_8    conda-forge
libcblas                  3.9.0              16_win64_mkl    conda-forge
libcurl                   7.88.1               h68f0423_0    conda-forge
libdeflate                1.17                 hcfcfb64_0    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libhwloc                  2.9.0                h51c2c0f_0    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
liblapack                 3.9.0              16_win64_mkl    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libsqlite                 3.40.0               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h9a1e1f7_3    conda-forge
libtiff                   4.5.0                hf8721a0_2    conda-forge
libwebp-base              1.2.4                h8ffe710_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.3               hc3477c8_0    conda-forge
libzlib                   1.2.13               hcfcfb64_4    conda-forge
llvmlite                  0.39.1           py38h19421c1_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
matplotlib-base           3.7.0            py38h528a6c7_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.2.0              pyhd8ed1ab_0    conda-forge
networkx                  3.0                pyhd8ed1ab_0    conda-forge
numba                     0.56.4           py38h3873db4_0    conda-forge
numpy                     1.22.4           py38h1d2777f_0    conda-forge
openjpeg                  2.5.0                ha2aaf27_2    conda-forge
openssl                   3.0.8                hcfcfb64_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py38h5846ac1_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pillow                    9.4.0            py38h087119c_1    conda-forge
pip                       23.0.1             pyhd8ed1ab_0    conda-forge
pooch                     1.6.0              pyhd8ed1ab_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pynndescent               0.5.8              pyh1a96a4e_0    conda-forge
pyopenssl                 23.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyh0701188_6    conda-forge
pysodb                    1.0.0                    pypi_0    pypi
python                    3.8.16          h4de0772_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
requests                  2.28.2             pyhd8ed1ab_0    conda-forge
scanpy                    1.9.2              pyhd8ed1ab_0    conda-forge
scikit-learn              1.2.1            py38h69724d7_0    conda-forge
scipy                     1.10.0           py38h0f6ee2a_2    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                67.4.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
statsmodels               0.13.5           py38hbaf524b_2    conda-forge
stdlib-list               0.8.0              pyhd8ed1ab_0    conda-forge
tbb                       2021.8.0             h91493d7_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
tqdm                      4.64.1             pyhd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
umap-learn                0.5.3            py38haa244fe_0    conda-forge
unicodedata2              15.0.0           py38h91455d4_0    conda-forge
urllib3                   1.26.14            pyhd8ed1ab_0    conda-forge
vc                        14.3                hb6edc58_10    conda-forge
vs2015_runtime            14.34.31931         h4c5c07a_10    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyhd8ed1ab_6    conda-forge
xorg-libxau               1.0.9                hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
zipp                      3.14.0             pyhd8ed1ab_0    conda-forge
zstd                      1.5.2                h12be248_6    conda-forge
WinterPan2017 commented 1 year ago

Thanks for your contribution, I will merge this request.