search

bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
88 stars 18 forks source link

cannot import name 'gcd' from 'fractions' #169

Closed cizydorczyk closed 2 years ago

cizydorczyk commented 3 years ago

Versions

Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge apscheduler 3.7.0 py39hf3d152e_0 conda-forge at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.2 h0630a04_0 conda-forge atk-1.0 2.36.0 h3371d22_4 conda-forge boost 1.74.0 py39h5472131_3 conda-forge boost-cpp 1.74.0 h312852a_4 conda-forge brotlipy 0.7.0 py39h3811e60_1001 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h7f98852_1 conda-forge ca-certificates 2021.5.30 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge cairomm 1.12.2 ha770c72_3 conda-forge cairomm-1.0 1.12.2 h56b4340_3 conda-forge certifi 2021.5.30 py39hf3d152e_0 conda-forge cffi 1.14.5 py39he32792d_0 conda-forge chardet 4.0.0 py39hf3d152e_1 conda-forge click 8.0.1 py39hf3d152e_0 conda-forge cryptography 3.4.7 py39hbca0aa6_0 conda-forge cycler 0.10.0 py_2 conda-forge dataclasses 0.8 pyhc8e2a94_1 conda-forge dbus 1.13.6 h48d8840_2 conda-forge decorator 5.0.9 pyhd8ed1ab_0 conda-forge dendropy 4.5.2 pyh3252c3a_0 bioconda epoxy 1.5.8 h7f98852_0 conda-forge expat 2.4.1 h9c3ff4c_0 conda-forge flask 2.0.1 pyhd8ed1ab_0 conda-forge flask-apscheduler 1.11.0 py_0 conda-forge flask-cors 3.0.10 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.13.1 hba837de_1005 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.10.4 h0708190_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gdk-pixbuf 2.42.6 h04a7f16_0 conda-forge gettext 0.19.8.1 h0b5b191_1005 conda-forge glib 2.68.3 h9c3ff4c_0 conda-forge glib-tools 2.68.3 h9c3ff4c_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gobject-introspection 1.68.0 py39hcb793ab_1 conda-forge graph-tool 2.37 py39hc2c1061_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge gtk3 3.24.29 h8879c87_1 conda-forge gunicorn 20.1.0 py39hf3d152e_0 conda-forge h5py 3.3.0 nompi_py39h98ba4bc_100 conda-forge harfbuzz 2.8.1 h83ec7ef_0 conda-forge hdbscan 0.8.27 py39hce5d2b2_0 conda-forge hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge hicolor-icon-theme 0.17 ha770c72_2 conda-forge icu 68.1 h58526e2_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge itsdangerous 2.0.1 pyhd8ed1ab_0 conda-forge jbig 2.1 h7f98852_2003 conda-forge jinja2 3.0.1 pyhd8ed1ab_0 conda-forge joblib 1.0.1 pyhd8ed1ab_0 conda-forge jpeg 9d h36c2ea0_0 conda-forge kiwisolver 1.3.1 py39h1a9c180_1 conda-forge krb5 1.19.1 hcc1bbae_0 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.35.1 hea4e1c9_2 conda-forge lerc 2.2.1 h9c3ff4c_0 conda-forge libblas 3.9.0 9_openblas conda-forge libcblas 3.9.0 9_openblas conda-forge libcups 2.3.3 hf5a7f15_0 conda-forge libcurl 7.77.0 h2574ce0_0 conda-forge libdeflate 1.7 h7f98852_5 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.3 h58526e2_2 conda-forge libgcc-ng 9.3.0 h2828fa1_19 conda-forge libgfortran-ng 9.3.0 hff62375_19 conda-forge libgfortran5 9.3.0 hff62375_19 conda-forge libglib 2.68.3 h3e27bee_0 conda-forge libgomp 9.3.0 h2828fa1_19 conda-forge libiconv 1.16 h516909a_0 conda-forge liblapack 3.9.0 9_openblas conda-forge libnghttp2 1.43.0 h812cca2_0 conda-forge libopenblas 0.3.15 pthreads_h8fe5266_1 conda-forge libpng 1.6.37 h21135ba_2 conda-forge librsvg 2.50.7 hc3c00ef_0 conda-forge libssh2 1.9.0 ha56f1ee_6 conda-forge libstdcxx-ng 9.3.0 h6de172a_19 conda-forge libtiff 4.3.0 hf544144_1 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.0 h7f98852_2 conda-forge libxcb 1.13 h7f98852_1003 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge lz4-c 1.9.3 h9c3ff4c_0 conda-forge markupsafe 2.0.1 py39h3811e60_0 conda-forge matplotlib-base 3.4.2 py39h2fa2bec_0 conda-forge ncurses 6.2 h58526e2_4 conda-forge networkx 2.3 py_0 conda-forge numpy 1.21.0 py39hdbf815f_0 conda-forge olefile 0.46 pyh9f0ad1d_1 conda-forge openblas 0.3.15 pthreads_h4748800_1 conda-forge openjpeg 2.4.0 hb52868f_1 conda-forge openssl 1.1.1k h7f98852_0 conda-forge pandas 1.2.5 py39hde0f152_0 conda-forge pango 1.48.5 hb8ff022_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pillow 8.2.0 py39hf95b381_1 conda-forge pip 21.1.2 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge poppunk 2.4.0 py39h7f0572b_0 bioconda pp-sketchlib 1.7.3 py39h85fd282_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycairo 1.20.1 py39hedcb9fc_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygobject 3.40.1 py39he5105b2_1 conda-forge pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pysocks 1.7.1 py39hf3d152e_3 conda-forge python 3.9.5 h49503c6_0_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.9 2_cp39 conda-forge pytz 2021.1 pyhd8ed1ab_0 conda-forge rapidnj 2.3.2 h7d875b9_1 bioconda readline 8.1 h46c0cb4_0 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge scikit-learn 0.24.2 py39h4dfa638_0 conda-forge scipy 1.6.3 py39hee8e79c_0 conda-forge setuptools 49.6.0 py39hf3d152e_3 conda-forge sigcpp-2.0 2.10.3 h58526e2_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sparsehash 2.0.4 h9c3ff4c_0 conda-forge sqlite 3.36.0 h9cd32fc_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge tornado 6.1 py39h3811e60_1 conda-forge tqdm 4.61.1 pyhd8ed1ab_0 conda-forge tzdata 2021a he74cb21_0 conda-forge tzlocal 2.0.0 py_0 conda-forge urllib3 1.26.5 pyhd8ed1ab_0 conda-forge werkzeug 2.0.1 pyhd8ed1ab_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.6.12 h36c2ea0_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxaw 1.0.14 h7f98852_0 conda-forge xorg-libxcomposite 0.4.5 h7f98852_0 conda-forge xorg-libxcursor 1.2.0 h516909a_0 conda-forge xorg-libxdamage 1.1.5 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxfixes 5.0.3 h516909a_1004 conda-forge xorg-libxi 1.7.10 h516909a_0 conda-forge xorg-libxinerama 1.1.4 h9c3ff4c_1001 conda-forge xorg-libxmu 1.1.3 h516909a_0 conda-forge xorg-libxpm 3.5.13 h516909a_0 conda-forge xorg-libxrandr 1.5.2 h516909a_1 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxt 1.1.5 h516909a_1003 conda-forge xorg-libxtst 1.2.3 h516909a_1002 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.5 h516909a_1 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstandard 0.15.2 py39h3811e60_0 conda-forge zstd 1.5.0 ha95c52a_0 conda-forge

$ poppunk_assign --db h_flu_poppunk --query sample_list.txt --output poppunk_clusters --threads 8

PopPUNK: assign (with backend: sketchlib v1.7.3 sketchlib: /home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/pp_sketchlib.cpython-39-x86_64-linux-gnu.so)

Graph-tools OpenMP parallelisation enabled: with 8 threads Traceback (most recent call last): File "/home/conrad/anaconda3/envs/poppunk_env/bin/poppunk_assign", line 11, in sys.exit(main()) File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/assign.py", line 519, in main assign_query(dbFuncs, File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/assign.py", line 82, in assign_query from .web import sketch_to_hdf5 File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/web.py", line 10, in import networkx as nx File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/networkx/init.py", line 114, in import networkx.generators File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/networkx/generators/init.py", line 14, in from networkx.generators.intersection import File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/networkx/generators/intersection.py", line 13, in from networkx.algorithms import bipartite File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/networkx/algorithms/init.py", line 16, in from networkx.algorithms.dag import File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/networkx/algorithms/dag.py", line 23, in from fractions import gcd ImportError: cannot import name 'gcd' from 'fractions' (/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/fractions.py)

Describe the bug

I read somewhere that gcd is now maths in python 3.9.X. This problem does not occur if I downgrade python to 3.8.2, but then I get other errors that end with:

ImportError: cannot import name 'gcd' from 'fractions' (/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/fractions.py)

So I stuck with python v. 3.9.0 but I get the original (above) error.

Any help is greatly appreciated.

Thank you, Conrad

johnlees commented 3 years ago

I believe this is a networkx error, please upgrade to v2.5 or higher

cizydorczyk commented 3 years ago

Updated networkx to 2.5.1 and the previous error disappears, but I get the following new error:

(poppunk_env) conrad@conrad-Precision-Tower-3620:~/hinfluenzae/i36_poppunk$ poppunk_assign --db h_flu_poppunk --query sample_list.txt --output poppunk_clusters --threads 4
PopPUNK: assign
    (with backend: sketchlib v1.7.3
     sketchlib: /home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/pp_sketchlib.cpython-39-x86_64-linux-gnu.so)

Graph-tools OpenMP parallelisation enabled: with 4 threads
Mode: Assigning clusters of query sequences

Traceback (most recent call last):
  File "/home/conrad/anaconda3/envs/poppunk_env/bin/poppunk_assign", line 11, in <module>
    sys.exit(main())
  File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/assign.py", line 519, in main
    assign_query(dbFuncs,
  File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/assign.py", line 106, in assign_query
    model = loadClusterFit(model_file + '.pkl',
  File "/home/conrad/anaconda3/envs/poppunk_env/lib/python3.9/site-packages/PopPUNK/models.py", line 92, in loadClusterFit
    fit_object, fit_type = pickle.load(pickle_obj)
ModuleNotFoundError: No module named 'sklearn.mixture.bayesian_mixture'

Conda-env:

(poppunk_env) conrad@conrad-Precision-Tower-3620:~/hinfluenzae/i36_poppunk$ conda list
packages in environment at /home/conrad/anaconda3/envs/poppunk_env:

Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
apscheduler               3.7.0            py39hf3d152e_0    conda-forge
at-spi2-atk               2.38.0               h0630a04_3    conda-forge
at-spi2-core              2.40.2               h0630a04_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
boost                     1.74.0           py39h5472131_3    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
brotlipy                  0.7.0           py39h3811e60_1001    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.17.1               h7f98852_1    conda-forge
ca-certificates           2021.5.30            ha878542_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h6cf1ce9_1008    conda-forge
cairomm                   1.12.2               ha770c72_3    conda-forge
cairomm-1.0               1.12.2               h56b4340_3    conda-forge
certifi                   2021.5.30        py39hf3d152e_0    conda-forge
cffi                      1.14.5           py39he32792d_0    conda-forge
chardet                   4.0.0            py39hf3d152e_1    conda-forge
click                     8.0.1            py39hf3d152e_0    conda-forge
cryptography              3.4.7            py39hbca0aa6_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dataclasses               0.8                pyhc8e2a94_1    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
decorator                 4.4.2                      py_0    conda-forge
dendropy                  4.5.2              pyh3252c3a_0    bioconda
epoxy                     1.5.8                h7f98852_0    conda-forge
expat                     2.4.1                h9c3ff4c_0    conda-forge
flask                     2.0.1              pyhd8ed1ab_0    conda-forge
flask-apscheduler         1.11.0                     py_0    conda-forge
flask-cors                3.0.10             pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.1            hba837de_1005    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
freetype                  2.10.4               h0708190_1    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gdk-pixbuf                2.42.6               h04a7f16_0    conda-forge
gettext                   0.19.8.1          h0b5b191_1005    conda-forge
glib                      2.68.3               h9c3ff4c_0    conda-forge
glib-tools                2.68.3               h9c3ff4c_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gobject-introspection     1.68.0           py39hcb793ab_1    conda-forge
graph-tool                2.37             py39hc2c1061_1    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gtk3                      3.24.29              h8879c87_1    conda-forge
gunicorn                  20.1.0           py39hf3d152e_0    conda-forge
h5py                      3.3.0           nompi_py39h98ba4bc_100    conda-forge
harfbuzz                  2.8.1                h83ec7ef_0    conda-forge
hdbscan                   0.8.27           py39hce5d2b2_0    conda-forge
hdf5                      1.10.6          nompi_h6a2412b_1114    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
idna                      2.10               pyh9f0ad1d_0    conda-forge
itsdangerous              2.0.1              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jinja2                    3.0.1              pyhd8ed1ab_0    conda-forge
joblib                    1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h36c2ea0_0    conda-forge
kiwisolver                1.3.1            py39h1a9c180_1    conda-forge
krb5                      1.19.1               hcc1bbae_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0                9_openblas    conda-forge
libcblas                  3.9.0                9_openblas    conda-forge
libcups                   2.3.3                hf5a7f15_0    conda-forge
libcurl                   7.77.0               h2574ce0_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_19    conda-forge
libgfortran-ng            9.3.0               hff62375_19    conda-forge
libgfortran5              9.3.0               hff62375_19    conda-forge
libglib                   2.68.3               h3e27bee_0    conda-forge
libgomp                   9.3.0               h2828fa1_19    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0                9_openblas    conda-forge
libnghttp2                1.43.0               h812cca2_0    conda-forge
libopenblas               0.3.15          pthreads_h8fe5266_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
librsvg                   2.50.7               hc3c00ef_0    conda-forge
libssh2                   1.9.0                ha56f1ee_6    conda-forge
libstdcxx-ng              9.3.0               h6de172a_19    conda-forge
libtiff                   4.3.0                hf544144_1    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp-base              1.2.0                h7f98852_2    conda-forge
libxcb                    1.13              h7f98852_1003    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
lz4-c                     1.9.3                h9c3ff4c_0    conda-forge
markupsafe                2.0.1            py39h3811e60_0    conda-forge
matplotlib-base           3.4.2            py39h2fa2bec_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
networkx                  2.5.1              pyhd8ed1ab_0    conda-forge
numpy                     1.21.0           py39hdbf815f_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openblas                  0.3.15          pthreads_h4748800_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1k               h7f98852_0    conda-forge
pandas                    1.2.5            py39hde0f152_0    conda-forge
pango                     1.48.5               hb8ff022_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    8.2.0            py39hf95b381_1    conda-forge
pip                       21.1.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
poppunk                   2.4.0            py39h7f0572b_0    bioconda
pp-sketchlib              1.7.3            py39h85fd282_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycairo                   1.20.1           py39hedcb9fc_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygobject                 3.40.1           py39he5105b2_1    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_3    conda-forge
python                    3.9.5           h49503c6_0_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2021.1             pyhd8ed1ab_0    conda-forge
rapidnj                   2.3.2                h7d875b9_1    bioconda
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.25.1             pyhd3deb0d_0    conda-forge
scikit-learn              0.24.2           py39h4dfa638_0    conda-forge
scipy                     1.6.3            py39hee8e79c_0    conda-forge
setuptools                49.6.0           py39hf3d152e_3    conda-forge
sigcpp-2.0                2.10.3               h58526e2_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sparsehash                2.0.4                h9c3ff4c_0    conda-forge
sqlite                    3.36.0               h9cd32fc_0    conda-forge
threadpoolctl             2.1.0              pyh5ca1d4c_0    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
tqdm                      4.61.1             pyhd8ed1ab_0    conda-forge
tzdata                    2021a                he74cb21_0    conda-forge
tzlocal                   2.0.0                      py_0    conda-forge
urllib3                   1.26.5             pyhd8ed1ab_0    conda-forge
werkzeug                  2.0.1              pyhd8ed1ab_0    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xorg-compositeproto       0.4.2             h7f98852_1001    conda-forge
xorg-damageproto          1.2.1             h7f98852_1002    conda-forge
xorg-fixesproto           5.0               h7f98852_1002    conda-forge
xorg-inputproto           2.3.2             h7f98852_1002    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.6.12               h36c2ea0_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxaw               1.0.14               h7f98852_0    conda-forge
xorg-libxcomposite        0.4.5                h7f98852_0    conda-forge
xorg-libxcursor           1.2.0                h516909a_0    conda-forge
xorg-libxdamage           1.1.5                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxinerama          1.1.4             h9c3ff4c_1001    conda-forge
xorg-libxmu               1.1.3                h516909a_0    conda-forge
xorg-libxpm               3.5.13               h516909a_0    conda-forge
xorg-libxrandr            1.5.2                h516909a_1    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxt                1.1.5             h516909a_1003    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-randrproto           1.5.0             h7f98852_1001    conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-util-macros          1.19.3               h7f98852_0    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge
zstandard                 0.15.2           py39h3811e60_0    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

Notably, installing networkx 2.5.1 downgraded:

(poppunk_env) conrad@conrad-Precision-Tower-3620:~/hinfluenzae/i36_poppunk$ conda install networkx=2.5Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

  environment location: /home/conrad/anaconda3/envs/poppunk_env

  added / updated specs:
    - networkx=2.5

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    networkx-2.5.1             |     pyhd8ed1ab_0         1.2 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         1.2 MB

The following packages will be UPDATED:

  networkx                                         2.3-py_0 --> 2.5.1-pyhd8ed1ab_0

The following packages will be DOWNGRADED:

  decorator                              5.0.9-pyhd8ed1ab_0 --> 4.4.2-py_0

Not really sure why I am having so much trouble -- thank you for your help.

johnlees commented 3 years ago

Where did you get the h_flu_poppunk database from, particularly the .pkl file? It looks like this may have been made by an old version of sklearn. I think the module should be called sklearn.mixture.BayesianGaussianMixture. Can you refit the original data (if it was your fit originally)?

johnlees commented 2 years ago

Closing issue for now, but let us know if further help required