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A conda-smithy repository for graph-tool.

License: BSD 3-Clause "New" or "Revised" License

Shell 89.61% Python 10.39%

graph-tool-feedstock's Introduction

About graph-tool-suite-feedstock

Feedstock license: BSD-3-Clause

Home: https://graph-tool.skewed.de/

Package license: LGPL-3.0-or-later

Summary: Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). The 'graph-tool' conda package installs graph-tool and all dependencies, including drawing dependencies. For users who don't need drawing support, the 'graph-tool-base' conda package installs graph-tool and only essential dependencies (but none for drawing).

Current build status

Azure

Variant	Status
linux_64_numpy1.22python3.10.____cpython
linux_64_numpy1.22python3.8.____cpython
linux_64_numpy1.22python3.9.____cpython
linux_64_numpy1.23python3.11.____cpython
linux_64_numpy1.26python3.12.____cpython
linux_aarch64_numpy1.22python3.10.____cpython
linux_aarch64_numpy1.22python3.8.____cpython
linux_aarch64_numpy1.22python3.9.____cpython
linux_aarch64_numpy1.23python3.11.____cpython
linux_aarch64_numpy1.26python3.12.____cpython
osx_64_numpy1.22python3.10.____cpython
osx_64_numpy1.22python3.8.____cpython
osx_64_numpy1.22python3.9.____cpython
osx_64_numpy1.23python3.11.____cpython
osx_64_numpy1.26python3.12.____cpython
osx_arm64_numpy1.22python3.10.____cpython
osx_arm64_numpy1.22python3.8.____cpython
osx_arm64_numpy1.22python3.9.____cpython
osx_arm64_numpy1.23python3.11.____cpython
osx_arm64_numpy1.26python3.12.____cpython

Current release info

Name	Downloads	Version	Platforms

Installing graph-tool-suite

Installing graph-tool-suite from the conda-forge channel can be achieved by adding conda-forge to your channels with:

conda config --add channels conda-forge
conda config --set channel_priority strict

Once the conda-forge channel has been enabled, graph-tool, graph-tool-base can be installed with conda:

conda install graph-tool graph-tool-base

or with mamba:

mamba install graph-tool graph-tool-base

It is possible to list all of the versions of graph-tool available on your platform with conda:

conda search graph-tool --channel conda-forge

or with mamba:

mamba search graph-tool --channel conda-forge

Alternatively, mamba repoquery may provide more information:

# Search all versions available on your platform:
mamba repoquery search graph-tool --channel conda-forge

# List packages depending on `graph-tool`:
mamba repoquery whoneeds graph-tool --channel conda-forge

# List dependencies of `graph-tool`:
mamba repoquery depends graph-tool --channel conda-forge

About conda-forge

conda-forge is a community-led conda channel of installable packages. In order to provide high-quality builds, the process has been automated into the conda-forge GitHub organization. The conda-forge organization contains one repository for each of the installable packages. Such a repository is known as a feedstock.

A feedstock is made up of a conda recipe (the instructions on what and how to build the package) and the necessary configurations for automatic building using freely available continuous integration services. Thanks to the awesome service provided by Azure, GitHub, CircleCI, AppVeyor, Drone, and TravisCI it is possible to build and upload installable packages to the conda-forge anaconda.org channel for Linux, Windows and OSX respectively.

To manage the continuous integration and simplify feedstock maintenance conda-smithy has been developed. Using the conda-forge.yml within this repository, it is possible to re-render all of this feedstock's supporting files (e.g. the CI configuration files) with conda smithy rerender.

For more information please check the conda-forge documentation.

Terminology

feedstock - the conda recipe (raw material), supporting scripts and CI configuration.

conda-smithy - the tool which helps orchestrate the feedstock. Its primary use is in the construction of the CI .yml files and simplify the management of many feedstocks.

conda-forge - the place where the feedstock and smithy live and work to produce the finished article (built conda distributions)

Updating graph-tool-suite-feedstock

If you would like to improve the graph-tool-suite recipe or build a new package version, please fork this repository and submit a PR. Upon submission, your changes will be run on the appropriate platforms to give the reviewer an opportunity to confirm that the changes result in a successful build. Once merged, the recipe will be re-built and uploaded automatically to the conda-forge channel, whereupon the built conda packages will be available for everybody to install and use from the conda-forge channel. Note that all branches in the conda-forge/graph-tool-suite-feedstock are immediately built and any created packages are uploaded, so PRs should be based on branches in forks and branches in the main repository should only be used to build distinct package versions.

In order to produce a uniquely identifiable distribution:

If the version of a package is not being increased, please add or increase the build/number.
If the version of a package is being increased, please remember to return the build/number back to 0.

Feedstock Maintainers

graph-tool-feedstock's People

Contributors

Stargazers

Watchers

Forkers

stuarteberg regro-cf-autotick-bot count0 conda-forge-linter xhochy isuruf h-vetinari

graph-tool-feedstock's Issues

Boost iostreams symbol not found only in conda-packaged version

Hello,

I am running Conda 4.11.0, this is my conda info:

conda info

     active environment : optimisation
    active env location : /home/alberto/.conda/envs/optimisation
            shell level : 2
       user config file : /home/alberto/.condarc
 populated config files : /home/alberto/.condarc
          conda version : 4.11.0
    conda-build version : not installed
         python version : 3.9.5.final.0
       virtual packages : __linux=5.16.3=0
                          __glibc=2.33=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/miniconda3  (read only)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : http://conda.anaconda.org/gurobi/linux-64
                          http://conda.anaconda.org/gurobi/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /home/alberto/.conda/pkgs
       envs directories : /home/alberto/.conda/envs
                          /opt/miniconda3/envs
               platform : linux-64
             user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.5 Linux/5.16.3-arch1-1 arch/ glibc/2.33
                UID:GID : 1000:1000
             netrc file : /home/alberto/.netrc
           offline mode : False

I installed graph-tool from Conda Forge. For reference, here are all the packages I have installed in my environment, with the respective versions:

conda package list

# packages in environment at /home/alberto/.conda/envs/optimisation:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38h497a2fe_1    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
at-spi2-atk               2.38.0               h0630a04_3    conda-forge
at-spi2-core              2.40.3               h0630a04_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
black                     22.1.0             pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
boost                     1.74.0           py38h2b96118_5    conda-forge
boost-cpp                 1.74.0               h359cf19_6    conda-forge
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            ha00ac49_1009    conda-forge
cairomm                   1.12.2               ha770c72_4    conda-forge
cairomm-1.0               1.12.2               h96a316c_4    conda-forge
certifi                   2021.10.8        py38h578d9bd_1    conda-forge
cffi                      1.15.0           py38h3931269_0    conda-forge
click                     8.0.3            py38h578d9bd_1    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
debugpy                   1.5.1            py38h709712a_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
dill                      0.3.4              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
epoxy                     1.5.9                h7f98852_0    conda-forge
executing                 0.8.2              pyhd8ed1ab_0    conda-forge
expat                     2.4.4                h9c3ff4c_0    conda-forge
flit-core                 3.6.0              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                2.13.94              ha180cfb_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.29.1           py38h497a2fe_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          h73d1719_1008    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glib-tools                2.70.2               h780b84a_1    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
graph-tool                2.44             py38h7041675_2    conda-forge
graph-tool-base           2.44             py38hbc125d9_2    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gst-plugins-base          1.18.5               hf529b03_3    conda-forge
gstreamer                 1.18.5               h9f60fe5_3    conda-forge
gtk3                      3.24.31              habab178_3    conda-forge
gurobi                    9.5.0                    py38_0    gurobi
harfbuzz                  3.3.1                hb4a5f5f_0    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       69.1                 h9c3ff4c_0    conda-forge
importlib-metadata        4.10.1           py38h578d9bd_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.8.0            py38he5a9106_0    conda-forge
ipython                   8.0.1            py38h578d9bd_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1           py38h578d9bd_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py38h578d9bd_7    conda-forge
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.1            py38h578d9bd_1    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.2            py38h1fd1430_1    conda-forge
krb5                      1.19.2               hcc1bbae_3    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.35.1               h7274673_9  
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libclang                  13.0.1          default_hc23dcda_0    conda-forge
libcups                   2.3.3                hf5a7f15_1    conda-forge
libdeflate                1.8                  h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_12    conda-forge
libgfortran-ng            11.2.0              h69a702a_12    conda-forge
libgfortran5              11.2.0              h5c6108e_12    conda-forge
libgirepository           1.70.0               hb520f89_1    conda-forge
libglib                   2.70.2               h174f98d_1    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libimagequant             2.17.0               h7f98852_1    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libllvm13                 13.0.1               hf817b99_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.4                h7f98852_1    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libopus                   1.3.1                h7f98852_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     14.1                 hd57d9b9_1    conda-forge
librsvg                   2.52.5               h0a9e6e8_2    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_12    conda-forge
libtiff                   4.3.0                h6f004c6_2    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h9c3ff4c_0    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h885dcf4_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
llvm-openmp               12.0.1               h4bd325d_1    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
markupsafe                2.0.1            py38h497a2fe_1    conda-forge
matplotlib-base           3.5.1            py38hf4fb855_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py38h497a2fe_1005    conda-forge
multiprocess              0.70.12.2        py38h497a2fe_1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3            py38h578d9bd_4    conda-forge
mysql-common              8.0.28               ha770c72_0    conda-forge
mysql-libs                8.0.28               hfa10184_0    conda-forge
nbclient                  0.5.10             pyhd8ed1ab_1    conda-forge
nbconvert                 6.4.1            py38h578d9bd_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h7f8727e_2  
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
notebook                  6.4.8              pyha770c72_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.74                 hb5efdd6_0    conda-forge
numpy                     1.22.2           py38h6ae9a64_0    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.0            py38h43a58ef_0    conda-forge
pandoc                    2.17.1.1             ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.3               h9967ed3_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathos                    0.2.8              pyhd8ed1ab_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.0.1            py38he2f12e7_0    conda-forge
pip                       21.2.4           py38h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
platformdirs              2.4.1              pyhd8ed1ab_1    conda-forge
ply                       3.11                       py_1    conda-forge
pox                       0.3.0              pyhd8ed1ab_0    conda-forge
ppft                      1.6.6.4            pyhd8ed1ab_0    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.26             pyha770c72_0    conda-forge
prompt_toolkit            3.0.26               hd8ed1ab_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.20.1           py38hf61ee4a_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pygobject                 3.42.0           py38h382169c_1    conda-forge
pyomo                     6.2              py38h709712a_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3           py38h578d9bd_8    conda-forge
pyqt-impl                 5.12.3           py38h0ffb2e6_8    conda-forge
pyqt5-sip                 4.19.18          py38h709712a_8    conda-forge
pyqtchart                 5.12             py38h7400c14_8    conda-forge
pyqtwebengine             5.12.1           py38h7400c14_8    conda-forge
pyrsistent                0.18.1           py38h497a2fe_0    conda-forge
python                    3.8.12          ha38a3c6_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
pyzmq                     22.3.0           py38h2035c66_1    conda-forge
qt                        5.12.9               ha98a1a1_5    conda-forge
qtconsole                 5.2.2              pyhd8ed1ab_1    conda-forge
qtconsole-base            5.2.2              pyhd8ed1ab_1    conda-forge
qtpy                      2.0.1              pyhd8ed1ab_0    conda-forge
readline                  8.1.2                h7f8727e_1  
scipy                     1.8.0            py38h56a6a73_0    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                58.0.4           py38h06a4308_0  
sigcpp-2.0                2.10.7               h9c3ff4c_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sparsehash                2.0.4                h9c3ff4c_0    conda-forge
sqlite                    3.37.0               hc218d9a_0  
stack_data                0.1.4              pyhd8ed1ab_0    conda-forge
terminado                 0.13.1           py38h578d9bd_0    conda-forge
testpath                  0.5.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.11               h1ccaba5_0  
tomli                     2.0.0              pyhd8ed1ab_1    conda-forge
tornado                   6.1              py38h497a2fe_2    conda-forge
tqdm                      4.62.3             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.2            py38h497a2fe_0    conda-forge
typing_extensions         4.0.1              pyha770c72_0    conda-forge
unicodedata2              14.0.0           py38h497a2fe_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.37.1             pyhd3eb1b0_0  
widgetsnbextension        3.5.2            py38h578d9bd_1    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               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxtst              1.2.3             h7f98852_1002    conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h7b6447c_0  
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstandard                 0.17.0           py38h497a2fe_0    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

The following minimal example fails:

from graph_tool.generation import complete_graph

The stack trace is:

Traceback (most recent call last):
  File "run/run_hop.py", line 12, in <module>
    from hop.instance.reduction import InstanceReductor
  File "/home/alberto/local/src/github/public/hazardous-ortienteering-problem/hop/instance/reduction.py", line 6, in <module>
    from graph_tool.generation import complete_graph
  File "/home/alberto/.conda/envs/optimisation/lib/python3.8/site-packages/graph_tool/__init__.py", line 106, in <module>
    dl_import("from . import libgraph_tool_core as libcore")
  File "/home/alberto/.conda/envs/optimisation/lib/python3.8/site-packages/graph_tool/dl_import.py", line 58, in dl_import
    exec(import_expr, local_dict, global_dict)
  File "<string>", line 1, in <module>
ImportError: /home/alberto/.conda/envs/optimisation/lib/python3.8/site-packages/graph_tool/libgraph_tool_core.so: undefined symbol: _ZN5boost9iostreams4zlib6finishE

This looks reasonable, because that symbol (surprisingly) is not in the boost shared object file distributed with conda:

$ nm -gD ~/.conda/envs/optimisation/lib/libboost_iostreams.so | grep _ZN5boost9iostreams4zlib6finishE
<empty output>

By contrast, I have it in my systemwide boost installation:

$ nm -gD /usr/lib/libboost_iostreams.so | grep _ZN5boost9iostreams4zlib6finishE                      
000000000001171c R _ZN5boost9iostreams4zlib6finishE

My system boost is 1.78.0 (as packaged by Arch Linux), vs. 1.74.0 provided by Conda.

cannot import graph_tool.draw

my version==2.29,can you help me?

import graph_tool.draw
Traceback (most recent call last):
File "", line 1, in
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/graph_tool/draw/init.py", line 875, in
from . cairo_draw import graph_draw, cairo_draw, get_hierarchy_control_points, default_cm
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/graph_tool/draw/cairo_draw.py", line 1489, in
from gi.repository import Gtk, Gdk, GdkPixbuf
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 656, in _load_unlocked
File "", line 626, in _load_backward_compatible
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/gi/importer.py", line 144, in load_module
importlib.import_module('gi.repository.' + dep.split("-")[0])
File "/data/miniconda3/envs/openea/lib/python3.6/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 994, in _gcd_import
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 656, in _load_unlocked
File "", line 626, in _load_backward_compatible
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/gi/importer.py", line 145, in load_module
dynamic_module = load_overrides(introspection_module)
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/gi/overrides/init.py", line 118, in load_overrides
override_mod = importlib.import_module(override_package_name)
File "/data/miniconda3/envs/openea/lib/python3.6/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/gi/overrides/Gdk.py", line 83, in
Color = override(Color)
File "/data/miniconda3/envs/openea/lib/python3.6/site-packages/gi/overrides/init.py", line 195, in override
assert g_type != TYPE_NONE
AssertionError

Provide a base package without drawing dependencies

Many of the dependencies of our graph-tool package are solely to provide drawing support. (They are listed in the graph-tool documentation.) Since most of graph-tool's features do not require drawing, it may be useful (for multiple reasons) to offer a smaller package for users who don't need drawing. This is easily supported in conda recipes. The matplotlib feedstock serves as an example. So, in our case, our recipe would emit two packages: graph-tool-base, and graph-tool.

Build for linux_aarch64?

Out of curiosity, I did a quick investigation of what it would take to build this feedstock for the linux-aarch64 platform, which is compatible with Raspberry Pi and also Amazon's Graviton processors, IIUC.

As far as I can tell, there are only two dependencies which DON'T already have linux-aarch64 packages available:

sparsehash
cairomm (note: cairo and pycairo are already supported)

And their dependencies are already available on linux-aarch64. So in principle it might not take much to upgrade those two. Then we'd have to work on the graph-tool feedstock itself, of course.

(I suspect the story is similar for linux-ppc64le, but I didn't actually check.)

If we're lucky, it could be as simple as adding the following lines to conda-forge.yml in the sparsehash, cairomm, and graph-tool feedstocks:

provider:
  linux_ppc64le: default
  linux_aarch64: default

Personally, I do not use the linux-aarch64 platform for my own work, so I'm not highly motivated to add this support. But it might not be too hard... On the other hand, wading through build errors is nobody's idea of a good time.

BTW, I notice that two somewhat analogous packages, igraph and networkit, are already available for linux-aarch64, with modest download counts for that platform (see here and here). One can speculate about whether the graph-tool download counts for that platform would be similar, were it available. That might help us gauge the impact of working on this.

Interactive window freezes when using .draw()

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

Python3 seems to crash every time I try to use the draw() function.

To give an example:

>>>from graph_tool.all import *
>>>g = collection.data["lesmis"]
>>>state = minimize_nested_blockmodel_dl(g)
>>>state.draw()

The interactive window would then freeze, not responding, so I have to kill the program. No error message shows up but in the terminal I get:

((<VertexPropertyMap object with value type 'vector<double>', for Graph 0x1aa8eb520, at 0x1aac43700>, <VertexPropertyMap object with value type 'bool', for Graph 0x1aa8eb520, at 0x1aac42f20>), <Graph object, directed, with 84 vertices and 83 edges, at 0x1aac2b640>, <VertexPropertyMap object with value type 'vector<double>', for Graph 0x1aac2b640, at 0x1aac2ad70>)

Thanks for any help in advance :)

Environment Info

Installed packages

# packages in environment at /Users/yijingch/opt/anaconda3/envs/myenv:
#
# Name                    Version                   Build  Channel
anyio                     3.5.0                    pypi_0    pypi
appnope                   0.1.2           py310h2ec42d9_2    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310he24745e_1    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.36.0               he69c4ee_4    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1                    pypi_0    pypi
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
black                     22.1.0             pyhd8ed1ab_0    conda-forge
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
boost                     1.74.0          py310h509978a_5    conda-forge
boost-cpp                 1.74.0               hdbf7018_7    conda-forge
brotli                    1.0.9                h0d85af4_6    conda-forge
brotli-bin                1.0.9                h0d85af4_6    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2021.10.8            h033912b_0    conda-forge
cairo                     1.16.0            he01c77b_1009    conda-forge
cairomm                   1.12.2               h694c41f_4    conda-forge
cairomm-1.0               1.12.2               h941ccef_4    conda-forge
certifi                   2021.10.8       py310h2ec42d9_1    conda-forge
cffi                      1.15.0          py310hcc37b68_0    conda-forge
charset-normalizer        2.0.12                   pypi_0    pypi
click                     8.0.4           py310h2ec42d9_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
dbus                      1.13.6               h811a1a6_3    conda-forge
debugpy                   1.5.1           py310hba3363e_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
epoxy                     1.5.9                h0d85af4_0    conda-forge
executing                 0.8.2              pyhd8ed1ab_0    conda-forge
expat                     2.4.6                h96cf925_0    conda-forge
flit-core                 3.7.1              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                2.13.96              h10f422b_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.29.1          py310he24745e_0    conda-forge
freetype                  2.10.4               h4cff582_1    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
gdk-pixbuf                2.42.6               h2e6141f_0    conda-forge
gettext                   0.19.8.1          hd1a6beb_1008    conda-forge
giflib                    5.2.1                hbcb3906_2    conda-forge
glib-tools                2.70.2               hcf210ce_4    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
graph-tool                2.44            py310h6327fc9_2    conda-forge
graph-tool-base           2.44            py310h8287337_2    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
gtk3                      3.24.31              h967bb29_3    conda-forge
harfbuzz                  3.4.0                h447b35c_0    conda-forge
hicolor-icon-theme        0.17                 h694c41f_2    conda-forge
icu                       69.1                 he49afe7_0    conda-forge
idna                      3.3                      pypi_0    pypi
importlib-metadata        4.11.1          py310h2ec42d9_0    conda-forge
importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge
infomap                   2.1.0                    pypi_0    pypi
ipykernel                 6.9.1           py310ha188af9_0    conda-forge
ipython                   8.0.1           py310h2ec42d9_2    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.6.5              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h0d85af4_2003    conda-forge
jedi                      0.18.1          py310h2ec42d9_0    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0                    pypi_0    pypi
jpeg                      9e                   h0d85af4_0    conda-forge
json5                     0.9.6                    pypi_0    pypi
jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0           py310h2ec42d9_7    conda-forge
jupyter-server            1.13.5                   pypi_0    pypi
jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.2           py310h2ec42d9_0    conda-forge
jupyterlab                3.2.9                    pypi_0    pypi
jupyterlab-server         2.10.3                   pypi_0    pypi
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.0.2              pyhd8ed1ab_0    conda-forge
kiwisolver                1.3.2           py310h2fea185_1    conda-forge
krb5                      1.19.2               hcfbf3a7_3    conda-forge
krippendorff              0.5.1                    pypi_0    pypi
lcms2                     2.12                 h577c468_0    conda-forge
lerc                      3.0                  he49afe7_0    conda-forge
libblas                   3.9.0           13_osx64_openblas    conda-forge
libbrotlicommon           1.0.9                h0d85af4_6    conda-forge
libbrotlidec              1.0.9                h0d85af4_6    conda-forge
libbrotlienc              1.0.9                h0d85af4_6    conda-forge
libcblas                  3.9.0           13_osx64_openblas    conda-forge
libclang                  13.0.1          default_he082bbe_0    conda-forge
libcxx                    12.0.1               habf9029_1    conda-forge
libdeflate                1.10                 h0d85af4_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               5.0.0           9_3_0_h6c81a4c_23    conda-forge
libgfortran5              9.3.0               h6c81a4c_23    conda-forge
libgirepository           1.70.0               h128b86d_1    conda-forge
libglib                   2.70.2               hf1fb8c0_4    conda-forge
libiconv                  1.16                 haf1e3a3_0    conda-forge
liblapack                 3.9.0           13_osx64_openblas    conda-forge
libllvm13                 13.0.1               h64f94b2_2    conda-forge
libopenblas               0.3.18          openmp_h3351f45_0    conda-forge
libpng                    1.6.37               h7cec526_2    conda-forge
libpq                     14.2                 hea3049e_0    conda-forge
librsvg                   2.52.5               h5e5d7d9_2    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libtiff                   4.3.0                h17f2ce3_3    conda-forge
libwebp                   1.2.2                h28dabe5_0    conda-forge
libwebp-base              1.2.2                h0d85af4_1    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.9.12               h7e28ab6_1    conda-forge
libzlib                   1.2.11            h9173be1_1013    conda-forge
llvm-openmp               13.0.1               hda6cdc1_0    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
markupsafe                2.1.0           py310h1961e1f_0    conda-forge
matplotlib-base           3.5.1           py310hfc59cd6_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py310he24745e_1005    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           0.4.3           py310h2ec42d9_4    conda-forge
mysql-common              8.0.28               h694c41f_0    conda-forge
mysql-libs                8.0.28               h115446f_0    conda-forge
nbclassic                 0.3.5                    pypi_0    pypi
nbclient                  0.5.11             pyhd8ed1ab_0    conda-forge
nbconvert                 6.4.2           py310h2ec42d9_0    conda-forge
nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  he49afe7_0    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
networkx                  2.6.3                    pypi_0    pypi
notebook                  6.4.8              pyha770c72_0    conda-forge
nspr                      4.32                 hcd9eead_1    conda-forge
nss                       3.74                 h31e2bf1_0    conda-forge
numpy                     1.22.2          py310hfbbbacf_0    conda-forge
openjpeg                  2.4.0                h6e7aa92_1    conda-forge
openssl                   1.1.1l               h0d85af4_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.1                    pypi_0    pypi
pandoc                    2.17.1.1             h694c41f_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.3               h7f27720_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.0.1           py310h382dc3b_2    conda-forge
pip                       22.0.3             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               hbcb3906_0    conda-forge
platformdirs              2.5.1              pyhd8ed1ab_0    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
prompt_toolkit            3.0.27               hd8ed1ab_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.20.1          py310h31a7ac3_1    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pygobject                 3.42.0          py310hf93f9e7_1    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyqt                      5.12.3          py310h2ec42d9_8    conda-forge
pyqt-impl                 5.12.3          py310hea9ccf3_8    conda-forge
pyqt5-sip                 4.19.18         py310hd046c34_8    conda-forge
pyqtchart                 5.12            py310hea9ccf3_8    conda-forge
pyqtwebengine             5.12.1          py310hea9ccf3_8    conda-forge
pyrsistent                0.18.1          py310he24745e_0    conda-forge
python                    3.10.2          h1dd9edd_3_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2021.3                   pypi_0    pypi
pyzmq                     22.3.0          py310hcce64c8_1    conda-forge
qt                        5.12.9               h2a607e2_5    conda-forge
qtconsole                 5.2.2              pyhd8ed1ab_1    conda-forge
qtconsole-base            5.2.2              pyhd8ed1ab_1    conda-forge
qtpy                      2.0.1              pyhd8ed1ab_0    conda-forge
readline                  8.1                  h05e3726_0    conda-forge
requests                  2.27.1                   pypi_0    pypi
scikit-learn              1.0.2                    pypi_0    pypi
scipy                     1.8.0           py310h47774c9_1    conda-forge
seaborn                   0.11.2                   pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                60.9.3          py310h2ec42d9_0    conda-forge
sigcpp-2.0                2.10.7               he49afe7_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sklearn                   0.0                      pypi_0    pypi
sniffio                   1.2.0                    pypi_0    pypi
sparsehash                2.0.4                he49afe7_0    conda-forge
sqlite                    3.37.0               h23a322b_0    conda-forge
src                       0.1                       dev_0    <develop>
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
terminado                 0.13.1          py310h2ec42d9_0    conda-forge
testpath                  0.6.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.1.0                    pypi_0    pypi
tk                        8.6.12               h5dbffcc_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.1             py310he24745e_2    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.2           py310he24745e_0    conda-forge
typing_extensions         4.1.1              pyha770c72_0    conda-forge
tzdata                    2021e                he74cb21_0    conda-forge
unicodedata2              14.0.0          py310he24745e_0    conda-forge
urllib3                   1.26.8                   pypi_0    pypi
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.2.3                    pypi_0    pypi
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.5.2           py310h2ec42d9_1    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h9173be1_1013    conda-forge
zstandard                 0.17.0          py310he24745e_0    conda-forge
zstd                      1.5.2                h582d3a0_0    conda-forge

Environment info

active environment : myenv
    active env location : /Users/yijingch/opt/anaconda3/envs/myenv
            shell level : 2
       user config file : /Users/yijingch/.condarc
 populated config files : /Users/yijingch/.condarc
          conda version : 4.11.0
    conda-build version : 3.21.7
         python version : 3.9.7.final.0
       virtual packages : __osx=10.16=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/yijingch/opt/anaconda3  (writable)
      conda av data dir : /Users/yijingch/opt/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-arm64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-arm64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/yijingch/opt/anaconda3/pkgs
                          /Users/yijingch/.conda/pkgs
       envs directories : /Users/yijingch/opt/anaconda3/envs
                          /Users/yijingch/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.11.0 requests/2.27.1 CPython/3.9.7 Darwin/21.3.0 OSX/10.16
                UID:GID : 501:20
             netrc file : None
           offline mode : False

PackagesNotFoundError: The following packages are not available from current channels

Hi,

I am trying to install the graph tool package via conda. I already created a new environment and added the conda forge channels.

But whenever I try to install the package with conda install -c conda-forge graph-tool I receive the following error:

PackagesNotFoundError: The following packages are not available from current channels:

graph-tool

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Drop Python 2 support

Currently the build is failing due to Python 2 incompatibility. I can patch it, but my plan was to make the current release (2.30) the last one supporting Python 2. But it might be easier just to drop it, since this has already happened with matplotlib, scipy, numpy, etc.

@conda-forge-admin,please add bot automerge

Issue: ModuleNotFoundError: No module named 'graph_tool'

Environment (conda list):

Even installing, in the conda following the documentation, when I try to import in the spider or in the Qt Console, the module is not found. When I go to Environments, the graph-tool appears as installed

$ conda search graph-tool --channel conda-forge
</details>

<br/>
Details about  <code>$ conda search graph-tool --channel conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.
</code> and system ( <code>conda info</code> ):
<details>

$ conda info

</details>

git recipe?

It would be nice if we could have an additional recipe that pulls from git head instead of a full release.

This would allow us to do testing before a new release hits, and give users access to the bleeding edge.

We don't have to provide binary packages, just the ability for users to build locally. (We could also consider periodic "snapshot" packages)

@stuarteberg Is this something that is easily supported in conda-forge at all?

Maintainers

Good news! Thanks to this year's improvements to conda-forge's infrastructure (e.g. C++17 compilers, longer build times), it has become feasible to maintain a conda-forge feedstock for graph-tool. So here we are.

Is anyone else interested in helping me maintain this package? If so, let me know and I'll add you to the maintainers list, which will automatically give you commit permissions to this feedstock.

@ostrokach, you've maintained your own recipe for some time now. Care to help out with this one?

And of course, if the man himself wants to help out, that would be great. So, any interest, @count0?

Cannot import graph_tool

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

I installed graph_tool through conda enviroment, and then I installed to pytorch and PyG packages, the list is as beow. But when I import graph_tool, thr error is:
ImportError: /USERS/usr/miniconda3/envs/gt2/lib/python3.12/site-packages/torch/lib/libgomp-a34b3233.so.1: version GOMP_5.0' not found (required by /USERS/usr/miniconda3/envs/gt2/lib/python3.12/site-packages/graph_tool/libgraph_tool_core.so)`

Installed packages

conda list
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
aiohttp                   3.9.4                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
at-spi2-atk               2.38.0               h0630a04_3    conda-forge
at-spi2-core              2.40.3               h0630a04_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     23.2.0                   pypi_0    pypi
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cairo                     1.18.0               h3faef2a_0    conda-forge
cairomm-1.16              1.16.2               h7e731d7_1    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py312hf06ca03_0    conda-forge
charset-normalizer        3.3.2                    pypi_0    pypi
contourpy                 1.2.1           py312h8572e83_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
epoxy                     1.5.10               h166bdaf_1    conda-forge
expat                     2.6.2                h59595ed_0    conda-forge
filelock                  3.13.4                   pypi_0    pypi
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                 h77eed37_1    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.51.0          py312h98912ed_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2024.3.1                 pypi_0    pypi
gdk-pixbuf                2.42.10              h829c605_5    conda-forge
gettext                   0.22.5               h59595ed_2    conda-forge
gettext-tools             0.22.5               h59595ed_2    conda-forge
glib-tools                2.80.0               hde27a5a_4    conda-forge
gmp                       6.3.0                h59595ed_1    conda-forge
graph-tool                2.59            py312hf63df81_1    conda-forge
graph-tool-base           2.59            py312h2c0dc93_1    conda-forge
graphite2                 1.3.13            h59595ed_1003    conda-forge
gtk3                      3.24.41              h280cfa0_0    conda-forge
harfbuzz                  8.3.0                h3d44ed6_0    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.7                      pypi_0    pypi
jinja2                    3.1.3                    pypi_0    pypi
joblib                    1.4.0                    pypi_0    pypi
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py312h8572e83_1    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libasprintf               0.22.5               h661eb56_2    conda-forge
libasprintf-devel         0.22.5               h661eb56_2    conda-forge
libblas                   3.9.0           22_linux64_openblas    conda-forge
libboost                  1.84.0               h8013b2b_2    conda-forge
libboost-python           1.84.0          py312hfb10629_2    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           22_linux64_openblas    conda-forge
libcups                   2.3.3                h4637d8d_4    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgettextpo              0.22.5               h59595ed_2    conda-forge
libgettextpo-devel        0.22.5               h59595ed_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libgirepository           1.80.1               h003a4f0_0    conda-forge
libglib                   2.80.0               hf2295e7_4    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
liblapack                 3.9.0           22_linux64_openblas    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.27          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
librsvg                   2.58.0               hce6bd6c_0    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_1    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxkbcommon              1.7.0                h662e7e4_0    conda-forge
libxml2                   2.12.6               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
markupsafe                2.1.5                    pypi_0    pypi
matplotlib-base           3.8.4           py312he5832f3_0    conda-forge
mpmath                    1.3.0                    pypi_0    pypi
multidict                 6.0.5                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.4.20240210         h59595ed_0    conda-forge
networkx                  3.3                      pypi_0    pypi
numpy                     1.26.4          py312heda63a1_0    conda-forge
nvidia-cublas-cu12        12.1.3.1                 pypi_0    pypi
nvidia-cuda-cupti-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-nvrtc-cu12    12.1.105                 pypi_0    pypi
nvidia-cuda-runtime-cu12  12.1.105                 pypi_0    pypi
nvidia-cudnn-cu12         8.9.2.26                 pypi_0    pypi
nvidia-cufft-cu12         11.0.2.54                pypi_0    pypi
nvidia-curand-cu12        10.3.2.106               pypi_0    pypi
nvidia-cusolver-cu12      11.4.5.107               pypi_0    pypi
nvidia-cusparse-cu12      12.1.0.106               pypi_0    pypi
nvidia-nccl-cu12          2.19.3                   pypi_0    pypi
nvidia-nvjitlink-cu12     12.4.127                 pypi_0    pypi
nvidia-nvtx-cu12          12.1.105                 pypi_0    pypi
openjpeg                  2.5.2                h488ebb8_0    conda-forge
openssl                   3.2.1                hd590300_1    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pango                     1.52.2               ha41ecd1_0    conda-forge
pcre2                     10.43                hcad00b1_0    conda-forge
pillow                    10.3.0          py312hdcec9eb_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h59595ed_0    conda-forge
psutil                    5.9.8                    pypi_0    pypi
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycairo                   1.26.0          py312he48a392_0    conda-forge
pycparser                 2.22               pyhd8ed1ab_0    conda-forge
pyg-lib                   0.4.0+pt22cu121          pypi_0    pypi
pygobject                 3.48.2          py312h15a1d3f_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
python                    3.12.2          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python_abi                3.12                    4_cp312    conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.31.0                   pypi_0    pypi
scikit-learn              1.4.2                    pypi_0    pypi
scipy                     1.13.0          py312heda63a1_0    conda-forge
setuptools                69.5.1             pyhd8ed1ab_0    conda-forge
sigcpp-3.0                3.6.0                h59595ed_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sparsehash                2.0.4                hcb278e6_1    conda-forge
sqlite                    3.45.2               h2c6b66d_0    conda-forge
sympy                     1.12                     pypi_0    pypi
threadpoolctl             3.4.0                    pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
torch                     2.2.2                    pypi_0    pypi
torch-cluster             1.6.3+pt22cu121          pypi_0    pypi
torch-geometric           2.5.2                    pypi_0    pypi
torch-scatter             2.1.2+pt22cu121          pypi_0    pypi
torch-sparse              0.6.18+pt22cu121          pypi_0    pypi
torch-spline-conv         1.2.2+pt22cu121          pypi_0    pypi
torchaudio                2.2.2                    pypi_0    pypi
torchvision               0.17.2                   pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.11.0                   pypi_0    pypi
tzdata                    2024a                h0c530f3_0    conda-forge
urllib3                   2.2.1                    pypi_0    pypi
wayland                   1.22.0               h8c25dac_1    conda-forge
wheel                     0.43.0             pyhd8ed1ab_1    conda-forge
xkeyboard-config          2.41                 hd590300_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               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.9                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxcomposite        0.4.6                h0b41bf4_1    conda-forge
xorg-libxcursor           1.2.0                h0b41bf4_1    conda-forge
xorg-libxdamage           1.1.5                h7f98852_1    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxinerama          1.1.5                h27087fc_0    conda-forge
xorg-libxrandr            1.5.2                h7f98852_1    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-libxtst              1.2.3             h7f98852_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             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yarl                      1.9.4                    pypi_0    pypi
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.22.0          py312hd58854c_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge
torch_sparse             0.6.18+pt22cu121
torch_spline_conv        1.2.2+pt22cu121
torchaudio               2.2.2
torchvision              0.17.2

pip list
aiohttp                  3.9.4
aiosignal                1.3.1
attrs                    23.2.0
certifi                  2024.2.2
cffi                     1.16.0
charset-normalizer       3.3.2
contourpy                1.2.1
cycler                   0.12.1
filelock                 3.13.4
fonttools                4.51.0
frozenlist               1.4.1
fsspec                   2024.3.1
idna                     3.7
Jinja2                   3.1.3
joblib                   1.4.0
kiwisolver               1.4.5
MarkupSafe               2.1.5
matplotlib               3.8.4
mpmath                   1.3.0
multidict                6.0.5
munkres                  1.1.4
networkx                 3.3
numpy                    1.26.4
nvidia-cublas-cu12       12.1.3.1
nvidia-cuda-cupti-cu12   12.1.105
nvidia-cuda-nvrtc-cu12   12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12        8.9.2.26
nvidia-cufft-cu12        11.0.2.54
nvidia-curand-cu12       10.3.2.106
nvidia-cusolver-cu12     11.4.5.107
nvidia-cusparse-cu12     12.1.0.106
nvidia-nccl-cu12         2.19.3
nvidia-nvjitlink-cu12    12.4.127
nvidia-nvtx-cu12         12.1.105
packaging                24.0
pillow                   10.3.0
pip                      24.0
psutil                   5.9.8
pycairo                  1.26.0
pycparser                2.22
pyg_lib                  0.4.0+pt22cu121
PyGObject                3.48.2
pyparsing                3.1.2
python-dateutil          2.9.0
requests                 2.31.0
scikit-learn             1.4.2
scipy                    1.13.0
setuptools               69.5.1
six                      1.16.0
sympy                    1.12
threadpoolctl            3.4.0
torch                    2.2.2
torch_cluster            1.6.3+pt22cu121
torch_geometric          2.5.2
torch_scatter            2.1.2+pt22cu121
torch_sparse             0.6.18+pt22cu121
torch_spline_conv        1.2.2+pt22cu121
torchaudio               2.2.2
torchvision              0.17.2
tqdm                     4.66.2
typing_extensions        4.11.0
urllib3                  2.2.1
wheel                    0.43.0
yarl                     1.9.4
zstandard                0.22.0

Environment info

active environment : gt2
    active env location : /USERS/usr/miniconda3/envs/gt2
            shell level : 2
       user config file : /export_home/usr/.condarc
 populated config files : /export_home/usr/.condarc
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.10.8.final.0
       virtual packages : __archspec=1=x86_64
                          __cuda=12.2=0
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /USERS/usr/miniconda3  (writable)
      conda av data dir : /USERS/usr/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /USERS/usr/miniconda3/pkgs
                          /export_home/usr/.conda/pkgs
       envs directories : /USERS/usr/miniconda3/envs/manifold2
                          /USERS/usr/miniconda3/envs
                          /export_home/usr/.conda/envs
               platform : linux-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.10.8 Linux/5.15.0-92-generic ubuntu/22.04.3 glibc/2.35
                UID:GID : 1028:1006
             netrc file : None
           offline mode : False

conda cannot search graph-tool

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

Dear manager,

When I install the graph-tool, I see the problem as below. I think the conda can't find the package.
My machine OS is window11, and I tried at Anacaconda prompt.

Command output

(base) C:\Users\Kicet>conda install -c conda-forge graph-tool
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

graph-tool

Current channels:

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

How can I fix it??

Installed packages

# Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0            py39haa95532_0
aioitertools              0.11.0                   pypi_0    pypi
aiosignal                 1.2.0                    pypi_0    pypi
alabaster                 0.7.12             pyhd3eb1b0_0
anaconda                  2022.10                 py310_0
anaconda-client           1.11.0           py39haa95532_0
anaconda-navigator        2.3.2            py39haa95532_0
anaconda-project          0.11.1           py39haa95532_0
anyio                     3.5.0            py39haa95532_0
appdirs                   1.4.4              pyhd3eb1b0_0
argon2-cffi               21.3.0             pyhd3eb1b0_0
argon2-cffi-bindings      21.2.0           py39h2bbff1b_0
arrow                     1.2.2              pyhd3eb1b0_0
ase                       3.22.1             pyhd8ed1ab_1    conda-forge
astroid                   2.11.7           py39haa95532_0
astropy                   5.1              py39h080aedc_0
atomicwrites              1.4.0                      py_0
attrs                     21.4.0             pyhd3eb1b0_0
automat                   20.2.0                     py_0
autopep8                  1.6.0              pyhd3eb1b0_1
babel                     2.9.1              pyhd3eb1b0_0
backcall                  0.2.0              pyhd3eb1b0_0
backports                 1.1                pyhd3eb1b0_0
backports.functools_lru_cache 1.6.4              pyhd3eb1b0_0
backports.tempfile        1.0                pyhd3eb1b0_1
backports.weakref         1.0.post1                  py_1
bcrypt                    3.2.0            py39h2bbff1b_1
beautifulsoup4            4.11.1           py39haa95532_0
binaryornot               0.4.4              pyhd3eb1b0_1
bitarray                  2.5.1            py39h2bbff1b_0
bkcharts                  0.2              py39haa95532_1
black                     22.6.0           py39haa95532_0
blas                      1.0                         mkl
bleach                    4.1.0              pyhd3eb1b0_0
blosc                     1.21.0               h19a0ad4_1
bokeh                     2.4.3            py39haa95532_0
boto3                     1.24.28          py39haa95532_0
botocore                  1.27.28          py39haa95532_0
bottleneck                1.3.5            py39h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py39h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.07.19           haa95532_0
certifi                   2022.9.24        py39haa95532_0
cffi                      1.15.1           py39h2bbff1b_0
cfitsio                   3.470                h2bbff1b_7
cftime                    1.6.1            py39h5d4886f_0    conda-forge
chardet                   4.0.0           py39haa95532_1003
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py39haa95532_0
cloudpickle               2.0.0              pyhd3eb1b0_0
clyent                    1.2.2            py39haa95532_1
colorama                  0.4.5            py39haa95532_0
colorcet                  3.0.0            py39haa95532_0
comtypes                  1.1.10          py39haa95532_1002
conda                     22.9.0           py39haa95532_0
conda-build               3.22.0           py39haa95532_0
conda-content-trust       0.1.3            py39haa95532_0
conda-env                 2.6.0                haa95532_1
conda-pack                0.6.0              pyhd3eb1b0_0
conda-package-handling    1.9.0            py39h8cc25b3_0
conda-repo-cli            1.0.20           py39haa95532_0
conda-token               0.4.0              pyhd3eb1b0_0
conda-verify              3.4.2                      py_1
console_shortcut          0.1.1                         4
constantly                15.1.0             pyh2b92418_0
cookiecutter              1.7.3              pyhd3eb1b0_0
cryptography              37.0.1           py39h21b164f_0
cssselect                 1.1.0              pyhd3eb1b0_0
curl                      7.84.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cython                    0.29.32          py39hd77b12b_0
cytoolz                   0.11.0           py39h2bbff1b_0
daal4py                   2021.6.0         py39h757b272_1
dal                       2021.6.0           h59b6b97_874
dask                      2022.7.0         py39haa95532_0
dask-core                 2022.7.0         py39haa95532_0
dataclasses               0.8                pyh6d0b6a4_7
datashader                0.14.1           py39haa95532_0
datashape                 0.5.4            py39haa95532_1
debugpy                   1.5.1            py39hd77b12b_0
decorator                 5.1.1              pyhd3eb1b0_0
defusedxml                0.7.1              pyhd3eb1b0_0
diff-match-patch          20200713           pyhd3eb1b0_0
dill                      0.3.4              pyhd3eb1b0_0
distlib                   0.3.6                    pypi_0    pypi
distributed               2022.7.0         py39haa95532_0
dnspython                 2.2.1                    pypi_0    pypi
docutils                  0.18.1           py39haa95532_3
double-conversion         3.2.0                h0e60522_0    conda-forge
eigen                     3.4.0                h2d74725_0    conda-forge
emmet-core                0.37.0                   pypi_0    pypi
entrypoints               0.4              py39haa95532_0
et_xmlfile                1.1.0            py39haa95532_0
expat                     2.4.8                h39d44d4_0    conda-forge
fastapi                   0.85.1                   pypi_0    pypi
fftw                      3.3.9                h2bbff1b_1
filelock                  3.6.0              pyhd3eb1b0_0
fireworks                 2.0.3                    pypi_0    pypi
flake8                    4.0.1              pyhd3eb1b0_1
flask                     1.1.2              pyhd3eb1b0_0
flask-paginate            2022.1.8                 pypi_0    pypi
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.10.4               hd328e21_0
frozenlist                1.3.1                    pypi_0    pypi
fsspec                    2022.7.1         py39haa95532_0
future                    0.18.2           py39haa95532_1
gensim                    4.1.2            py39hd77b12b_0
giflib                    5.2.1                h62dcd97_0
gl2ps                     1.4.2                h0597ee9_0    conda-forge
glew                      2.1.0                h39d44d4_2    conda-forge
glob2                     0.7                pyhd3eb1b0_0
greenlet                  1.1.1            py39hd77b12b_0
grpcio                    1.43.0                   pypi_0    pypi
gunicorn                  20.1.0                   pypi_0    pypi
h5py                      3.7.0            py39h3de5c98_0
hdf4                      4.2.13            h0e5069d_1005    conda-forge
hdf5                      1.10.6               h1756f20_1
heapdict                  1.0.1              pyhd3eb1b0_0
holoviews                 1.15.0           py39haa95532_0
hvplot                    0.8.0            py39haa95532_0
hyperlink                 21.0.0             pyhd3eb1b0_0
icc_rt                    2022.1.0             h6049295_2
icu                       58.2                 ha925a31_3
idna                      3.3                pyhd3eb1b0_0
imagecodecs               2021.8.26        py39hc0a7faf_1
imageio                   2.19.3           py39haa95532_0
imagesize                 1.4.1            py39haa95532_0
importlib-metadata        4.11.3           py39haa95532_0
importlib_metadata        4.11.3               hd3eb1b0_0
incremental               21.3.0             pyhd3eb1b0_0
inflection                0.5.1            py39haa95532_0
iniconfig                 1.1.1              pyhd3eb1b0_0
intake                    0.6.5              pyhd3eb1b0_0
intel-openmp              2021.4.0          haa95532_3556
intervaltree              3.1.0              pyhd3eb1b0_0
ipykernel                 6.15.2           py39haa95532_0
ipython                   7.31.1           py39haa95532_1
ipython_genutils          0.2.0              pyhd3eb1b0_1
ipywidgets                7.6.5              pyhd3eb1b0_1
isort                     5.9.3              pyhd3eb1b0_0
itemadapter               0.3.0              pyhd3eb1b0_0
itemloaders               1.0.4              pyhd3eb1b0_1
itsdangerous              2.0.1              pyhd3eb1b0_0
jdcal                     1.4.1              pyhd3eb1b0_0
jedi                      0.18.1           py39haa95532_1
jellyfish                 0.9.0            py39h2bbff1b_0
jinja2                    2.11.3             pyhd3eb1b0_0
jinja2-time               0.2.0              pyhd3eb1b0_3
jmespath                  0.10.0             pyhd3eb1b0_0
joblib                    1.1.0              pyhd3eb1b0_0
jpeg                      9e                   h2bbff1b_0
jq                        1.6                  haa95532_1
json5                     0.9.6              pyhd3eb1b0_0
jsoncpp                   1.9.4                h2d74725_3    conda-forge
jsonschema                4.16.0           py39haa95532_0
jupyter                   1.0.0            py39haa95532_8
jupyter_client            7.3.4            py39haa95532_0
jupyter_console           6.4.3              pyhd3eb1b0_0
jupyter_core              4.11.1           py39haa95532_0
jupyter_server            1.18.1           py39haa95532_0
jupyterlab                3.4.4            py39haa95532_0
jupyterlab_pygments       0.1.2                      py_0
jupyterlab_server         2.10.3             pyhd3eb1b0_1
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1
keyring                   23.4.0           py39haa95532_0
kiwisolver                1.4.2            py39hd77b12b_0
latexcodec                2.0.1              pyh9f0ad1d_0    conda-forge
lazy-object-proxy         1.6.0            py39h2bbff1b_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libarchive                3.6.1                hebabd0d_0
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libcurl                   7.84.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libiconv                  1.16                 h2bbff1b_2
liblief                   0.11.5               hd77b12b_1
libnetcdf                 4.8.1                h6685c40_1
libogg                    1.3.4                h8ffe710_1    conda-forge
libpng                    1.6.37               h2a8f88b_0
libsodium                 1.0.18               h62dcd97_0
libspatialindex           1.9.3                h6c2663c_0
libssh2                   1.10.0               hcd4344a_0
libtheora                 1.1.1             h8d14728_1005    conda-forge
libtiff                   4.4.0                h8a3f274_0
libwebp                   1.2.2                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
libzip                    1.8.0                hfed4ece_1    conda-forge
libzopfli                 1.0.3                ha925a31_0
llvmlite                  0.39.1                   pypi_0    pypi
locket                    1.0.0            py39haa95532_0
loguru                    0.6.0            py39hcbf5309_1    conda-forge
lxml                      4.9.1            py39h1985fb9_0
lz4                       3.1.3            py39h2bbff1b_0
lz4-c                     1.9.3                h2bbff1b_1
lzo                       2.10                 he774522_2
m2-msys2-runtime          2.5.0.17080.65c939c               3
m2-patch                  2.7.5                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
maggma                    0.49.5                   pypi_0    pypi
markdown                  3.3.4            py39haa95532_0
markupsafe                2.0.1            py39h2bbff1b_0
matplotlib                3.5.2            py39haa95532_0
matplotlib-base           3.5.2            py39hd77b12b_0
matplotlib-inline         0.1.6            py39haa95532_0
mccabe                    0.6.1            py39haa95532_2
menuinst                  1.4.19           py39h59b6b97_0
mistune                   0.8.4           py39h2bbff1b_1000
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py39h2bbff1b_0
mkl_fft                   1.3.1            py39h277e83a_0
mkl_random                1.2.2            py39hf11a4ad_0
mock                      4.0.3              pyhd3eb1b0_0
mongogrant                0.3.3                    pypi_0    pypi
mongomock                 4.1.2                    pypi_0    pypi
monty                     2022.9.9           pyhd8ed1ab_0    conda-forge
mp-api                    0.29.2                   pypi_0    pypi
mpmath                    1.2.1            py39haa95532_0
msgpack-python            1.0.3            py39h59b6b97_0
msys2-conda-epoch         20160418                      1
multipledispatch          0.6.0            py39haa95532_0
munkres                   1.1.4                      py_0
mypy_extensions           0.4.3            py39haa95532_1
navigator-updater         0.3.0            py39haa95532_0
nbclassic                 0.3.5              pyhd3eb1b0_0
nbclient                  0.5.13           py39haa95532_0
nbconvert                 6.4.4            py39haa95532_0
nbformat                  5.5.0            py39haa95532_0
nest-asyncio              1.5.5            py39haa95532_0
netcdf4                   1.5.7           nompi_py39ha89693b_101    conda-forge
networkx                  2.8.4            py39haa95532_0
nltk                      3.7                pyhd3eb1b0_0
nose                      1.3.7           pyhd3eb1b0_1008
notebook                  6.4.12           py39haa95532_0
numba                     0.56.3                   pypi_0    pypi
numexpr                   2.8.3            py39hb80d3ca_0
numpy                     1.21.5           py39h7a0a035_3
numpy-base                1.21.5           py39hca35cd5_3
numpydoc                  1.4.0            py39haa95532_0
olefile                   0.46               pyhd3eb1b0_0
openjpeg                  2.4.0                h4fc8c34_0
openpyxl                  3.0.10           py39h2bbff1b_0
openssl                   1.1.1q               h2bbff1b_0
orjson                    3.8.0                    pypi_0    pypi
packaging                 21.3               pyhd3eb1b0_0
palettable                3.3.0                      py_0    conda-forge
pandas                    1.4.4            py39hd77b12b_0
pandocfilters             1.5.0              pyhd3eb1b0_0
panel                     0.13.1           py39haa95532_0
param                     1.12.0             pyhd3eb1b0_0
paramiko                  2.8.1              pyhd3eb1b0_0
parsel                    1.6.0            py39haa95532_0
parso                     0.8.3              pyhd3eb1b0_0
partd                     1.2.0              pyhd3eb1b0_1
pathlib                   1.0.1              pyhd3eb1b0_1
pathspec                  0.9.0            py39haa95532_0
patsy                     0.5.2            py39haa95532_1
pep8                      1.7.1            py39haa95532_1
pexpect                   4.8.0              pyhd3eb1b0_3
pickleshare               0.7.5           pyhd3eb1b0_1003
pillow                    9.2.0            py39hdc2b20a_1
pip                       22.2.2           py39haa95532_0
pkginfo                   1.8.2              pyhd3eb1b0_0
platformdirs              2.5.2            py39haa95532_0
plotly                    5.9.0            py39haa95532_0
pluggy                    1.0.0            py39haa95532_1
powershell_shortcut       0.0.1                         3
poyo                      0.5.0              pyhd3eb1b0_0
proj                      6.2.1                ha7a8c7b_0    conda-forge
prometheus_client         0.14.1           py39haa95532_0
prompt-toolkit            3.0.20             pyhd3eb1b0_0
prompt_toolkit            3.0.20               hd3eb1b0_0
protego                   0.1.16                     py_0
protobuf                  3.20.3                   pypi_0    pypi
psutil                    5.9.0            py39h2bbff1b_0
ptyprocess                0.7.0              pyhd3eb1b0_2
py                        1.11.0             pyhd3eb1b0_0
py-lief                   0.11.5           py39hd77b12b_1
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pybtex                    0.24.0             pyhd8ed1ab_2    conda-forge
pycodestyle               2.8.0              pyhd3eb1b0_0
pycosat                   0.6.3            py39h2bbff1b_0
pycparser                 2.21               pyhd3eb1b0_0
pyct                      0.4.8            py39haa95532_1
pycurl                    7.45.1           py39hcd4344a_0
pydantic                  1.10.2                   pypi_0    pypi
pydash                    5.1.1                    pypi_0    pypi
pydispatcher              2.0.5            py39haa95532_2
pydocstyle                6.1.1              pyhd3eb1b0_0
pyerfa                    2.0.0            py39h2bbff1b_0
pyflakes                  2.4.0              pyhd3eb1b0_0
pygments                  2.11.2             pyhd3eb1b0_0
pyhamcrest                2.0.2              pyhd3eb1b0_2
pyjwt                     2.4.0            py39haa95532_0
pylint                    2.14.5           py39haa95532_0
pyls-spyder               0.4.0              pyhd3eb1b0_0
pymatgen                  2022.9.21                pypi_0    pypi
pymongo                   4.3.2                    pypi_0    pypi
pynacl                    1.5.0            py39h8cc25b3_0
pyodbc                    4.0.34           py39hd77b12b_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py39haa95532_0
pyqt                      5.9.2            py39hd77b12b_6
pyrsistent                0.18.0           py39h196d8e1_0
pysocks                   1.7.1            py39haa95532_0
pytables                  3.6.1            py39h56d22b6_1
pytest                    7.1.2            py39haa95532_0
python                    3.9.13               h6244533_1
python-dateutil           2.8.2              pyhd3eb1b0_0
python-fastjsonschema     2.16.2           py39haa95532_0
python-libarchive-c       2.9                pyhd3eb1b0_1
python-lsp-black          1.0.0              pyhd3eb1b0_0
python-lsp-jsonrpc        1.0.0              pyhd3eb1b0_0
python-lsp-server         1.3.3              pyhd3eb1b0_0
python-slugify            5.0.2              pyhd3eb1b0_0
python-snappy             0.6.0            py39hd77b12b_3
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1           py39haa95532_0
pyviz_comms               2.0.2              pyhd3eb1b0_0
pywavelets                1.3.0            py39h2bbff1b_0
pywin32                   302              py39h2bbff1b_2
pywin32-ctypes            0.2.0           py39haa95532_1000
pywinpty                  2.0.2            py39h5da7b33_0
pyyaml                    6.0              py39h2bbff1b_1
pyzmq                     24.0.1                   pypi_0    pypi
qdarkstyle                3.0.2              pyhd3eb1b0_0
qstylizer                 0.1.10             pyhd3eb1b0_0
qt                        5.9.7            vc14h73c81de_0
qtawesome                 1.0.3              pyhd3eb1b0_0
qtconsole                 5.2.2              pyhd3eb1b0_0
qtpy                      2.2.0            py39haa95532_0
queuelib                  1.5.0            py39haa95532_0
ray                       2.0.0                    pypi_0    pypi
reaction-network          5.1.0                    pypi_0    pypi
regex                     2022.7.9         py39h2bbff1b_0
requests                  2.28.1           py39haa95532_0
requests-file             1.5.1              pyhd3eb1b0_0
rope                      0.22.0             pyhd3eb1b0_0
rtree                     0.9.7            py39h2eaa2aa_1
ruamel.yaml               0.17.21          py39hb82d6ee_1    conda-forge
ruamel.yaml.clib          0.2.6            py39hb82d6ee_1    conda-forge
ruamel_yaml               0.15.100         py39h2bbff1b_0
s3transfer                0.6.0            py39haa95532_0
scikit-image              0.19.2           py39hf11a4ad_0
scikit-learn              1.0.2            py39hf11a4ad_1
scikit-learn-intelex      2021.6.0         py39haa95532_0
scipy                     1.9.1            py39he11b74f_0
scrapy                    2.6.2            py39haa95532_0
seaborn                   0.11.2             pyhd3eb1b0_0
send2trash                1.8.0              pyhd3eb1b0_1
sentinels                 1.0.0                    pypi_0    pypi
service_identity          18.1.0             pyhd3eb1b0_1
setuptools                63.4.1           py39haa95532_0
sip                       4.19.13          py39hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
smart_open                5.2.1            py39haa95532_0
snappy                    1.1.9                h6c2663c_0
sniffio                   1.2.0            py39haa95532_1
snowballstemmer           2.2.0              pyhd3eb1b0_0
sortedcollections         2.1.0              pyhd3eb1b0_0
sortedcontainers          2.4.0              pyhd3eb1b0_0
soupsieve                 2.3.1              pyhd3eb1b0_0
spglib                    2.0.0            py39h5d4886f_0    conda-forge
sphinx                    5.0.2            py39haa95532_0
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0
spyder                    5.2.2            py39haa95532_1
spyder-kernels            2.2.1            py39haa95532_0
sqlalchemy                1.4.39           py39h2bbff1b_0
sqlite                    3.39.3               h2bbff1b_0
sshtunnel                 0.4.0                    pypi_0    pypi
starlette                 0.20.4                   pypi_0    pypi
statsmodels               0.13.2           py39h2bbff1b_0
sympy                     1.10.1           py39haa95532_0
tabulate                  0.8.10           py39haa95532_0
tbb                       2021.6.0             h59b6b97_0
tbb4py                    2021.6.0         py39h59b6b97_0
tblib                     1.7.0              pyhd3eb1b0_0
tenacity                  8.0.1            py39haa95532_1
terminado                 0.13.1           py39haa95532_0
testpath                  0.6.0            py39haa95532_0
text-unidecode            1.3                pyhd3eb1b0_0
textdistance              4.2.1              pyhd3eb1b0_0
threadpoolctl             2.2.0              pyh0d69192_0
three-merge               0.1.1              pyhd3eb1b0_0
tifffile                  2021.7.2           pyhd3eb1b0_2
tinycss                   0.4             pyhd3eb1b0_1002
tk                        8.6.12               h2bbff1b_0
tldextract                3.2.0              pyhd3eb1b0_0
toml                      0.10.2             pyhd3eb1b0_0
tomli                     2.0.1            py39haa95532_0
tomlkit                   0.11.1           py39haa95532_0
toolz                     0.11.2             pyhd3eb1b0_0
tornado                   6.1              py39h2bbff1b_0
tqdm                      4.64.1           py39haa95532_0
traitlets                 5.1.1              pyhd3eb1b0_0
twisted                   22.2.0           py39h2bbff1b_1
twisted-iocpsupport       1.0.2            py39h2bbff1b_0
typing-extensions         4.3.0            py39haa95532_0
typing_extensions         4.3.0            py39haa95532_0
tzdata                    2022c                h04d1e81_0
ujson                     5.4.0            py39hd77b12b_0
uncertainties             3.1.7              pyhd8ed1ab_0    conda-forge
unidecode                 1.2.0              pyhd3eb1b0_0
urllib3                   1.26.11          py39haa95532_0
utfcpp                    3.2.1                h57928b3_0    conda-forge
vc                        14.2                 h21ff451_1
virtualenv                20.16.5                  pypi_0    pypi
vs2015_runtime            14.27.29016          h5e58377_2
vtk                       9.0.3           py39h84a6d72_201
w3lib                     1.21.0             pyhd3eb1b0_0
watchdog                  2.1.6            py39haa95532_0
wcwidth                   0.2.5              pyhd3eb1b0_0
webencodings              0.5.1            py39haa95532_1
websocket-client          0.58.0           py39haa95532_4
werkzeug                  2.0.3              pyhd3eb1b0_0
wheel                     0.37.1             pyhd3eb1b0_0
widgetsnbextension        3.5.2            py39haa95532_0
win32_setctime            1.1.0              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0            py39haa95532_0
win_unicode_console       0.5              py39haa95532_0
wincertstore              0.2              py39haa95532_2
winpty                    0.4.3                         4
wrapt                     1.14.1           py39h2bbff1b_0
xarray                    0.20.1             pyhd3eb1b0_1
xlrd                      2.0.1              pyhd3eb1b0_0
xlsxwriter                3.0.3              pyhd3eb1b0_0
xlwings                   0.27.15          py39haa95532_0
xz                        5.2.6                h8cc25b3_0
yaml                      0.2.5                he774522_0
yapf                      0.31.0             pyhd3eb1b0_0
zeromq                    4.3.4                hd77b12b_0
zfp                       0.5.5                hd77b12b_6
zict                      2.1.0            py39haa95532_0
zipp                      3.8.0            py39haa95532_0
zlib                      1.2.12               h8cc25b3_3
zope                      1.0              py39haa95532_1
zope.interface            5.4.0            py39h2bbff1b_0
zstd                      1.5.2                h19a0ad4_0

Environment info

active environment : base
    active env location : C:\Users\Kicet\anaconda3
            shell level : 1
       user config file : C:\Users\Kicet\.condarc
 populated config files : C:\Users\Kicet\.condarc
          conda version : 22.9.0
    conda-build version : 3.22.0
         python version : 3.9.13.final.0
       virtual packages : __win=0=0
                          __archspec=1=x86_64
       base environment : C:\Users\Kicet\anaconda3  (writable)
      conda av data dir : C:\Users\Kicet\anaconda3\etc\conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/rwest/win-64
                          https://conda.anaconda.org/rwest/noarch
                          https://conda.anaconda.org/vgauthier/win-64
                          https://conda.anaconda.org/vgauthier/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\Kicet\anaconda3\pkgs
                          C:\Users\Kicet\.conda\pkgs
                          C:\Users\Kicet\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\Kicet\anaconda3\envs
                          C:\Users\Kicet\.conda\envs
                          C:\Users\Kicet\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/22.9.0 requests/2.28.1 CPython/3.9.13 Windows/10 Windows/10.0.22000
          administrator : False
             netrc file : None
           offline mode : False

Cannot install graph-tool

Comment:

Hello,

I am currently trying to install graph-tool in my Anaconda environment and keep running into errors.

As suggested, I have tried to create a new environment and installed graph-tool using the following command:
conda create --name gt -c conda-forge graph-tool

However, I receive the following error:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

graph-tool

Current channels:

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Please let me know if I am missing anything?

AssertionError in gobject-introspection?

I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

Fresh gt environment, only installed ipykernel

conda create --name gt -c conda-forge graph-tool
conda activate gt
conda install ipykernel

when I run

import graph_tool.all as gt

I get

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-5-f96fce82bbfd> in <module>
----> 1 import graph_tool.all as gt

~/anaconda3/envs/gt/lib/python3.9/site-packages/graph_tool/all.py in <module>
     32 import graph_tool.centrality
     33 try:
---> 34     from graph_tool.draw import *
     35     import graph_tool.draw
     36 except ImportError as e:

~/anaconda3/envs/gt/lib/python3.9/site-packages/graph_tool/draw/__init__.py in <module>
    833 
    834 try:
--> 835     from . cairo_draw import graph_draw, cairo_draw, \
    836         get_hierarchy_control_points, default_cm, default_clrs, draw_hierarchy
    837     __all__ += ["draw_hierarchy"]

~/anaconda3/envs/gt/lib/python3.9/site-packages/graph_tool/draw/cairo_draw.py in <module>
   1494     import gi
   1495     gi.require_version('Gtk', '3.0')
-> 1496     from gi.repository import Gtk, Gdk, GdkPixbuf
   1497     from gi.repository import GObject as gobject
   1498     from .gtk_draw import *

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _find_and_load(name, import_)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _load_unlocked(spec)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _load_backward_compatible(spec)

~/anaconda3/envs/gt/lib/python3.9/site-packages/gi/importer.py in load_module(self, fullname)
    142             # https://bugzilla.gnome.org/show_bug.cgi?id=656314
    143             for dep in repository.get_immediate_dependencies(namespace):
--> 144                 importlib.import_module('gi.repository.' + dep.split("-")[0])
    145             dynamic_module = load_overrides(introspection_module)
    146 

~/anaconda3/envs/gt/lib/python3.9/importlib/__init__.py in import_module(name, package)
    125                 break
    126             level += 1
--> 127     return _bootstrap._gcd_import(name[level:], package, level)
    128 
    129 

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _gcd_import(name, package, level)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _find_and_load(name, import_)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _find_and_load_unlocked(name, import_)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _load_unlocked(spec)

~/anaconda3/envs/gt/lib/python3.9/importlib/_bootstrap.py in _load_backward_compatible(spec)

~/anaconda3/envs/gt/lib/python3.9/site-packages/gi/importer.py in load_module(self, fullname)
    143             for dep in repository.get_immediate_dependencies(namespace):
    144                 importlib.import_module('gi.repository.' + dep.split("-")[0])
--> 145             dynamic_module = load_overrides(introspection_module)
    146 
    147         dynamic_module.__file__ = '<%s>' % fullname

~/anaconda3/envs/gt/lib/python3.9/site-packages/gi/overrides/__init__.py in load_overrides(introspection_module)
    116             return introspection_module
    117 
--> 118         override_mod = importlib.import_module(override_package_name)
    119 
    120     finally:

~/anaconda3/envs/gt/lib/python3.9/importlib/__init__.py in import_module(name, package)
    125                 break
    126             level += 1
--> 127     return _bootstrap._gcd_import(name[level:], package, level)
    128 
    129 

~/anaconda3/envs/gt/lib/python3.9/site-packages/gi/overrides/Gdk.py in <module>
     81                          int(blue * Color.MAX_VALUE))
     82 
---> 83     Color = override(Color)
     84     __all__.append('Color')
     85 

~/anaconda3/envs/gt/lib/python3.9/site-packages/gi/overrides/__init__.py in override(type_)
    193 
    194         g_type = info.get_g_type()
--> 195         assert g_type != TYPE_NONE
    196         if g_type != TYPE_INVALID:
    197             g_type.pytype = type_

AssertionError:

Environment (conda list):

$ conda list
# packages in environment at /home/deklan/anaconda3/envs/gt:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
at-spi2-atk               2.38.0               h0630a04_3    conda-forge
at-spi2-core              2.40.3               h0630a04_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
backcall                  0.2.0              pyhd3eb1b0_0
boost                     1.74.0           py39h5472131_3    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2021.7.5             h06a4308_1
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        py39h06a4308_0
cffi                      1.14.6           py39he32792d_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
dbus                      1.13.6               h48d8840_2    conda-forge
decorator                 5.0.9              pyhd3eb1b0_0
epoxy                     1.5.8                h7f98852_0    conda-forge
expat                     2.4.1                h9c3ff4c_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                2.43             py39hc4320a7_0    conda-forge
graph-tool-base           2.43             py39h8160539_0    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
gtk3                      3.24.29              h8879c87_1    conda-forge
harfbuzz                  2.8.2                h83ec7ef_0    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       68.1                 h58526e2_0    conda-forge
ipykernel                 5.3.4            py39hb070fc8_0
ipython                   7.22.0           py39hb070fc8_0
ipython_genutils          0.2.0              pyhd3eb1b0_1
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.17.2           py39h06a4308_1
jpeg                      9d                   h36c2ea0_0    conda-forge
jupyter_client            6.1.12             pyhd3eb1b0_0
jupyter_core              4.7.1            py39h06a4308_0
kiwisolver                1.3.1            py39h1a9c180_1    conda-forge
krb5                      1.19.2               hcc1bbae_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      2.2.1                h9c3ff4c_0    conda-forge
libblas                   3.9.0               10_openblas    conda-forge
libcblas                  3.9.0               10_openblas    conda-forge
libcups                   2.3.3                hf5a7f15_0    conda-forge
libdeflate                1.7                  h7f98852_5    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libffi                    3.3                  h58526e2_2    conda-forge
libgcc-ng                 11.1.0               hc902ee8_6    conda-forge
libgfortran-ng            11.1.0               h69a702a_6    conda-forge
libgfortran5              11.1.0               h6c583b3_6    conda-forge
libglib                   2.68.3               h3e27bee_0    conda-forge
libgomp                   11.1.0               hc902ee8_6    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0               10_openblas    conda-forge
libopenblas               0.3.17          pthreads_h8fe5266_1    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
librsvg                   2.50.7               hc3c00ef_0    conda-forge
libsodium                 1.0.18               h7b6447c_0
libstdcxx-ng              11.1.0               h56837e0_6    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_1    conda-forge
matplotlib-base           3.4.2            py39h2fa2bec_0    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
numpy                     1.21.1           py39hdbf815f_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1k               h27cfd23_0
pango                     1.48.7               hb8ff022_0    conda-forge
parso                     0.7.0                      py_0
pcre                      8.45                 h9c3ff4c_0    conda-forge
pexpect                   4.8.0              pyhd3eb1b0_3
pickleshare               0.7.5           pyhd3eb1b0_1003
pillow                    8.3.1            py39ha612740_0    conda-forge
pip                       21.2.2             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
prompt-toolkit            3.0.17             pyh06a4308_0
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2
pycairo                   1.20.1           py39hedcb9fc_0    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.9.0              pyhd3eb1b0_0
pygobject                 3.40.1           py39he5105b2_1    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
python                    3.9.6           h49503c6_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pyzmq                     20.0.0           py39h2531618_1
readline                  8.1                  h46c0cb4_0    conda-forge
scipy                     1.7.0            py39hee8e79c_1    conda-forge
setuptools                49.6.0           py39hf3d152e_3    conda-forge
sigcpp-2.0                2.10.7               h9c3ff4c_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
tk                        8.6.10               h21135ba_1    conda-forge
tornado                   6.1              py39h3811e60_1    conda-forge
traitlets                 5.0.5              pyhd3eb1b0_0
tzdata                    2021a                he74cb21_1    conda-forge
wcwidth                   0.2.5                      py_0
wheel                     0.36.2             pyhd3deb0d_0    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               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxtst              1.2.3             h7f98852_1002    conda-forge
xorg-recordproto          1.14.2            h7f98852_1002    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    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
zeromq                    4.3.4                h2531618_0
zlib                      1.2.11            h516909a_1010    conda-forge
zstandard                 0.15.2           py39h3811e60_0    conda-forge
zstd                      1.5.0                ha95c52a_0    conda-forge

Details about conda and system ( conda info ):

$ conda info
     active environment : gt
    active env location : /home/deklan/anaconda3/envs/gt
            shell level : 2
       user config file : /home/deklan/.condarc
 populated config files :
          conda version : 4.10.3
    conda-build version : 3.21.4
         python version : 3.8.8.final.0
       virtual packages : __linux=5.10.16.3=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/deklan/anaconda3  (writable)
      conda av data dir : /home/deklan/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/deklan/anaconda3/pkgs
                          /home/deklan/.conda/pkgs
       envs directories : /home/deklan/anaconda3/envs
                          /home/deklan/.conda/envs
               platform : linux-64
             user-agent : conda/4.10.3 requests/2.25.1 CPython/3.8.8 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.2 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

graph-tool not available on M1 via conda

I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

graph-tool is not available on M1.

$ uname -m
arm64
$ wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh
$ chmod +x Miniforge3-MacOSX-arm64.sh
$ ./Miniforge3-MacOSX-arm64.sh
$ exit # exit to get a conda base environment
(base) $ conda install graph-tool graph-tool-base
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  - graph-tool-base
  - graph-tool

Current channels:

  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch

Note that there seems to be no fundamental obstacle to getting graph-tool on M1, as brew install graph-tool succeeds.

Environment (conda list):

$ conda list
# packages in environment at /Users/nathompson7/miniforge3:
#
# Name                    Version                   Build  Channel
brotlipy                  0.7.0           py39h5161555_1001    conda-forge
ca-certificates           2021.5.30            h4653dfc_0    conda-forge
certifi                   2021.5.30        py39h2804cbe_0    conda-forge
cffi                      1.14.6           py39hda8b47f_0    conda-forge
chardet                   4.0.0            py39h2804cbe_1    conda-forge
charset-normalizer        2.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.10.3           py39h2804cbe_0    conda-forge
conda-package-handling    1.7.3            py39h5161555_0    conda-forge
cryptography              3.4.7            py39h73257c9_0    conda-forge
idna                      3.1                pyhd3deb0d_0    conda-forge
libcxx                    12.0.1               h168391b_0    conda-forge
libffi                    3.3                  h9f76cd9_2    conda-forge
ncurses                   6.2                  h9aa5885_4    conda-forge
openssl                   1.1.1k               h27ca646_0    conda-forge
pip                       21.2.2             pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py39h5161555_1006    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pyopenssl                 20.0.1             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py39h2804cbe_3    conda-forge
python                    3.9.6           h54d631c_1_cpython    conda-forge
python_abi                3.9                      2_cp39    conda-forge
readline                  8.1                  hedafd6a_0    conda-forge
requests                  2.26.0             pyhd8ed1ab_0    conda-forge
ruamel_yaml               0.15.80         py39h5161555_1004    conda-forge
setuptools                49.6.0           py39h2804cbe_3    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.36.0               h72a2b83_0    conda-forge
tk                        8.6.10               hf7e6567_1    conda-forge
tqdm                      4.62.0             pyhd8ed1ab_0    conda-forge
tzdata                    2021a                he74cb21_1    conda-forge
urllib3                   1.26.6             pyhd8ed1ab_0    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xz                        5.2.5                h642e427_1    conda-forge
yaml                      0.2.5                h642e427_0    conda-forge
zlib                      1.2.11            h31e879b_1009    conda-forge

Details about conda and system ( conda info ):

$ conda info
(base) ➜  reproduce conda info

     active environment : base
    active env location : /Users/nathompson7/miniforge3
            shell level : 1
       user config file : /Users/nathompson7/.condarc
 populated config files : /Users/nathompson7/miniforge3/.condarc
                          /Users/nathompson7/.condarc
          conda version : 4.10.3
    conda-build version : not installed
         python version : 3.9.6.final.0
       virtual packages : __osx=11.5.1=0
                          __unix=0=0
                          __archspec=1=arm64
       base environment : /Users/nathompson7/miniforge3  (writable)
      conda av data dir : /Users/nathompson7/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/nathompson7/miniforge3/pkgs
                          /Users/nathompson7/.conda/pkgs
       envs directories : /Users/nathompson7/miniforge3/envs
                          /Users/nathompson7/.conda/envs
               platform : osx-arm64
             user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.6 Darwin/20.6.0 OSX/11.5.1
                UID:GID : 501:20
             netrc file : None
           offline mode : False

Conda on AWS Sagemaker

Issue: Cannot install graph-tool in AWS Sagemaker
I tried the following:

conda create --name gt -c conda-forge graph-tool

to create my graph-tool environment
but I got this:

Error log

ERROR conda.core.link:_execute(700): An error occurred while installing package 'conda-forge::gtk3-3.24.21-h45fd312_0'.
Rolling back transaction: done
LinkError: post-link script failed for package conda-forge::gtk3-3.24.21-h45fd312_0
location of failed script: /home/ec2-user/anaconda3/envs/gt/bin/.gtk3-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: /home/ec2-user/anaconda3/envs/gt/bin/gtk-query-immodules-3.0: error while loading shared libraries: libXcursor.so.1: cannot open shared object file: No such file or directory

return code: 127

()

Full Log:
## Package Plan ##

  environment location: /home/ec2-user/anaconda3/envs/gt

  added / updated specs:
    - graph-tool


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |           1_llvm           5 KB  conda-forge
    at-spi2-atk-2.32.0         |       h1369247_0         301 KB  conda-forge
    at-spi2-core-2.35.1        |       h1369247_0         543 KB  conda-forge
    atk-2.36.0                 |                0          12 KB  conda-forge
    atk-1.0-2.36.0             |       haf93ef1_0         519 KB  conda-forge
    boost-1.72.0               |   py38h9de70de_0         341 KB  conda-forge
    boost-cpp-1.72.0           |       h7b93d67_2        16.3 MB  conda-forge
    bzip2-1.0.8                |       h516909a_2         396 KB  conda-forge
    cairo-1.16.0               |    h3fc0475_1005         1.5 MB  conda-forge
    cairomm-1.12.2             |                2          11 KB  conda-forge
    cairomm-1.0-1.12.2         |       h0069156_2         671 KB  conda-forge
    certifi-2020.6.20          |   py38h32f6830_0         151 KB  conda-forge
    cycler-0.10.0              |             py_2           9 KB  conda-forge
    epoxy-1.5.4                |       h516909a_1         1.5 MB  conda-forge
    expat-2.2.9                |       he1b5a44_2         191 KB  conda-forge
    fontconfig-2.13.1          |    h1056068_1002         365 KB  conda-forge
    freetype-2.10.2            |       he06d7ca_0         905 KB  conda-forge
    fribidi-1.0.10             |       h516909a_0         113 KB  conda-forge
    gdk-pixbuf-2.38.2          |       h3f25603_4         653 KB  conda-forge
    glib-2.65.0                |       h6f030ca_0         3.5 MB  conda-forge
    gmp-6.2.0                  |       he1b5a44_2         811 KB  conda-forge
    gobject-introspection-1.64.1|   py38h03d966d_1         1.4 MB  conda-forge
    graph-tool-2.33            |   py38hed06623_0        70.5 MB  conda-forge
    graphite2-1.3.13           |    he1b5a44_1001         102 KB  conda-forge
    gtk3-3.24.21               |       h45fd312_0        19.8 MB  conda-forge
    harfbuzz-2.4.0             |       hee91db6_5         1.5 MB  conda-forge
    hicolor-icon-theme-0.17    |                0          13 KB  conda-forge
    icu-67.1                   |       he1b5a44_0        12.9 MB  conda-forge
    kiwisolver-1.2.0           |   py38hbf85e49_0          87 KB  conda-forge
    krb5-1.17.1                |       hfafb76e_1         1.5 MB  conda-forge
    ld_impl_linux-64-2.34      |       h53a641e_7         616 KB  conda-forge
    libblas-3.8.0              |      17_openblas          11 KB  conda-forge
    libcblas-3.8.0             |      17_openblas          11 KB  conda-forge
    libcroco-0.6.13            |       h8d621e5_1         138 KB  conda-forge
    libcups-2.2.12             |       hf10b501_1         6.3 MB  conda-forge
    libedit-3.1.20191231       |       h46ee950_1         122 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
    libgcc-ng-9.2.0            |       h24d8f2e_2         8.2 MB  conda-forge
    liblapack-3.8.0            |      17_openblas          11 KB  conda-forge
    libopenblas-0.3.10         |       h5ec1e0e_0         7.8 MB  conda-forge
    libpng-1.6.37              |       hed695b0_1         308 KB  conda-forge
    librsvg-2.49.3             |       h33a7fed_0        16.6 MB  conda-forge
    libstdcxx-ng-9.2.0         |       hdf63c60_2         4.5 MB  conda-forge
    libtiff-4.1.0              |       hc7e4089_6         668 KB  conda-forge
    libwebp-base-1.1.0         |       h516909a_3         845 KB  conda-forge
    libxcb-1.13                |    h14c3975_1002         396 KB  conda-forge
    libxml2-2.9.10             |       h72b56ed_1         1.3 MB  conda-forge
    llvm-openmp-10.0.0         |       hc9558a2_0         2.8 MB  conda-forge
    lz4-c-1.9.2                |       he1b5a44_1         226 KB  conda-forge
    matplotlib-base-3.2.2      |   py38h5d868c9_1         7.1 MB  conda-forge
    ncurses-6.1                |    hf484d3e_1002         1.3 MB  conda-forge
    numpy-1.18.5               |   py38h8854b6b_0         5.2 MB  conda-forge
    pango-1.42.4               |       h7062337_4         521 KB  conda-forge
    pcre-8.44                  |       he1b5a44_0         261 KB  conda-forge
    pip-20.1.1                 |             py_1         1.1 MB  conda-forge
    pixman-0.38.0              |    h516909a_1003         594 KB  conda-forge
    pthread-stubs-0.4          |    h14c3975_1001           5 KB  conda-forge
    pycairo-1.19.1             |   py38h323dad1_3          78 KB  conda-forge
    pygobject-3.36.1           |   py38h2faf24e_0         286 KB  conda-forge
    python-3.8.3               |cpython_he5300dc_0        71.0 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    python_abi-3.8             |           1_cp38           4 KB  conda-forge
    readline-8.0               |       h46ee950_1         287 KB  conda-forge
    scipy-1.5.0                |   py38h18bccfc_0        18.7 MB  conda-forge
    setuptools-49.2.0          |   py38h32f6830_0         949 KB  conda-forge
    sigcpp-2.0-2.10.3          |       he1b5a44_0         4.3 MB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    sparsehash-2.0.3           |    hf484d3e_1000          85 KB  conda-forge
    sqlite-3.32.3              |       hcee41ef_1         1.4 MB  conda-forge
    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge
    tornado-6.0.4              |   py38h1e0a361_1         642 KB  conda-forge
    wheel-0.34.2               |             py_1          24 KB  conda-forge
    xorg-libxau-1.0.9          |       h14c3975_0          13 KB  conda-forge
    xorg-libxdmcp-1.1.3        |       h516909a_0          18 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zlib-1.2.11                |    h516909a_1006         105 KB  conda-forge
    zstd-1.4.4                 |       h6597ccf_3         991 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       305.5 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_llvm
  at-spi2-atk        conda-forge/linux-64::at-spi2-atk-2.32.0-h1369247_0
  at-spi2-core       conda-forge/linux-64::at-spi2-core-2.35.1-h1369247_0
  atk                conda-forge/linux-64::atk-2.36.0-0
  atk-1.0            conda-forge/linux-64::atk-1.0-2.36.0-haf93ef1_0
  boost              conda-forge/linux-64::boost-1.72.0-py38h9de70de_0
  boost-cpp          conda-forge/linux-64::boost-cpp-1.72.0-h7b93d67_2
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_2
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  cairo              conda-forge/linux-64::cairo-1.16.0-h3fc0475_1005
  cairomm            conda-forge/linux-64::cairomm-1.12.2-2
  cairomm-1.0        conda-forge/linux-64::cairomm-1.0-1.12.2-h0069156_2
  certifi            conda-forge/linux-64::certifi-2020.6.20-py38h32f6830_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  dbus               conda-forge/linux-64::dbus-1.13.6-he372182_0
  epoxy              conda-forge/linux-64::epoxy-1.5.4-h516909a_1
  expat              conda-forge/linux-64::expat-2.2.9-he1b5a44_2
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h1056068_1002
  freetype           conda-forge/linux-64::freetype-2.10.2-he06d7ca_0
  fribidi            conda-forge/linux-64::fribidi-1.0.10-h516909a_0
  gdk-pixbuf         conda-forge/linux-64::gdk-pixbuf-2.38.2-h3f25603_4
  gettext            conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
  glib               conda-forge/linux-64::glib-2.65.0-h6f030ca_0
  gmp                conda-forge/linux-64::gmp-6.2.0-he1b5a44_2
  gobject-introspec~ conda-forge/linux-64::gobject-introspection-1.64.1-py38h03d966d_1
  graph-tool         conda-forge/linux-64::graph-tool-2.33-py38hed06623_0
  graphite2          conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001
  gtk3               conda-forge/linux-64::gtk3-3.24.21-h45fd312_0
  harfbuzz           conda-forge/linux-64::harfbuzz-2.4.0-hee91db6_5
  hicolor-icon-theme conda-forge/linux-64::hicolor-icon-theme-0.17-0
  icu                conda-forge/linux-64::icu-67.1-he1b5a44_0
  jpeg               conda-forge/linux-64::jpeg-9d-h516909a_0
  kiwisolver         conda-forge/linux-64::kiwisolver-1.2.0-py38hbf85e49_0
  krb5               conda-forge/linux-64::krb5-1.17.1-hfafb76e_1
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_7
  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libcroco           conda-forge/linux-64::libcroco-0.6.13-h8d621e5_1
  libcups            conda-forge/linux-64::libcups-2.2.12-hf10b501_1
  libedit            conda-forge/linux-64::libedit-3.1.20191231-h46ee950_1
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6
  libiconv           conda-forge/linux-64::libiconv-1.15-h516909a_1006
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-h5ec1e0e_0
  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_1
  librsvg            conda-forge/linux-64::librsvg-2.49.3-h33a7fed_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
  libtiff            conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libwebp-base       conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3
  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002
  libxml2            conda-forge/linux-64::libxml2-2.9.10-h72b56ed_1
  llvm-openmp        conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0
  lz4-c              conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1
  matplotlib-base    conda-forge/linux-64::matplotlib-base-3.2.2-py38h5d868c9_1
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  numpy              conda-forge/linux-64::numpy-1.18.5-py38h8854b6b_0
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_0
  pango              conda-forge/linux-64::pango-1.42.4-h7062337_4
  pcre               conda-forge/linux-64::pcre-8.44-he1b5a44_0
  pip                conda-forge/noarch::pip-20.1.1-py_1
  pixman             conda-forge/linux-64::pixman-0.38.0-h516909a_1003
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  pycairo            conda-forge/linux-64::pycairo-1.19.1-py38h323dad1_3
  pygobject          conda-forge/linux-64::pygobject-3.36.1-py38h2faf24e_0
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  python             conda-forge/linux-64::python-3.8.3-cpython_he5300dc_0
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.8-1_cp38
  readline           conda-forge/linux-64::readline-8.0-h46ee950_1
  scipy              conda-forge/linux-64::scipy-1.5.0-py38h18bccfc_0
  setuptools         conda-forge/linux-64::setuptools-49.2.0-py38h32f6830_0
  sigcpp-2.0         conda-forge/linux-64::sigcpp-2.0-2.10.3-he1b5a44_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  sparsehash         conda-forge/linux-64::sparsehash-2.0.3-hf484d3e_1000
  sqlite             conda-forge/linux-64::sqlite-3.32.3-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  tornado            conda-forge/linux-64::tornado-6.0.4-py38h1e0a361_1
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1006
  zstd               conda-forge/linux-64::zstd-1.4.4-h6597ccf_3


Proceed ([y]/n)? y


Downloading and Extracting Packages
wheel-0.34.2         | 24 KB     | #################################################################################### | 100%
gobject-introspectio | 1.4 MB    | #################################################################################### | 100%
matplotlib-base-3.2. | 7.1 MB    | #################################################################################### | 100%
_openmp_mutex-4.5    | 5 KB      | #################################################################################### | 100%
fontconfig-2.13.1    | 365 KB    | #################################################################################### | 100%
libcblas-3.8.0       | 11 KB     | #################################################################################### | 100%
certifi-2020.6.20    | 151 KB    | #################################################################################### | 100%
gtk3-3.24.21         | 19.8 MB   | #################################################################################### | 100%
cairomm-1.0-1.12.2   | 671 KB    | #################################################################################### | 100%
libffi-3.2.1         | 47 KB     | #################################################################################### | 100%
graph-tool-2.33      | 70.5 MB   | #################################################################################### | 100%
gmp-6.2.0            | 811 KB    | #################################################################################### | 100%
python_abi-3.8       | 4 KB      | #################################################################################### | 100%
setuptools-49.2.0    | 949 KB    | #################################################################################### | 100%
zstd-1.4.4           | 991 KB    | #################################################################################### | 100%
libpng-1.6.37        | 308 KB    | #################################################################################### | 100%
libgcc-ng-9.2.0      | 8.2 MB    | #################################################################################### | 100%
atk-2.36.0           | 12 KB     | #################################################################################### | 100%
libblas-3.8.0        | 11 KB     | #################################################################################### | 100%
tk-8.6.10            | 3.2 MB    | #################################################################################### | 100%
six-1.15.0           | 14 KB     | #################################################################################### | 100%
cairomm-1.12.2       | 11 KB     | #################################################################################### | 100%
atk-1.0-2.36.0       | 519 KB    | #################################################################################### | 100%
pygobject-3.36.1     | 286 KB    | #################################################################################### | 100%
xorg-libxau-1.0.9    | 13 KB     | #################################################################################### | 100%
harfbuzz-2.4.0       | 1.5 MB    | #################################################################################### | 100%
sqlite-3.32.3        | 1.4 MB    | #################################################################################### | 100%
libcroco-0.6.13      | 138 KB    | #################################################################################### | 100%
libopenblas-0.3.10   | 7.8 MB    | #################################################################################### | 100%
krb5-1.17.1          | 1.5 MB    | #################################################################################### | 100%
glib-2.65.0          | 3.5 MB    | #################################################################################### | 100%
at-spi2-atk-2.32.0   | 301 KB    | #################################################################################### | 100%
epoxy-1.5.4          | 1.5 MB    | #################################################################################### | 100%
tornado-6.0.4        | 642 KB    | #################################################################################### | 100%
expat-2.2.9          | 191 KB    | #################################################################################### | 100%
llvm-openmp-10.0.0   | 2.8 MB    | #################################################################################### | 100%
pip-20.1.1           | 1.1 MB    | #################################################################################### | 100%
python-3.8.3         | 71.0 MB   | #################################################################################### | 100%
readline-8.0         | 287 KB    | #################################################################################### | 100%
kiwisolver-1.2.0     | 87 KB     | #################################################################################### | 100%
gdk-pixbuf-2.38.2    | 653 KB    | #################################################################################### | 100%
libcups-2.2.12       | 6.3 MB    | #################################################################################### | 100%
python-dateutil-2.8. | 220 KB    | #################################################################################### | 100%
bzip2-1.0.8          | 396 KB    | #################################################################################### | 100%
liblapack-3.8.0      | 11 KB     | #################################################################################### | 100%
_libgcc_mutex-0.1    | 3 KB      | #################################################################################### | 100%
zlib-1.2.11          | 105 KB    | #################################################################################### | 100%
libwebp-base-1.1.0   | 845 KB    | #################################################################################### | 100%
fribidi-1.0.10       | 113 KB    | #################################################################################### | 100%
scipy-1.5.0          | 18.7 MB   | #################################################################################### | 100%
pixman-0.38.0        | 594 KB    | #################################################################################### | 100%
boost-1.72.0         | 341 KB    | #################################################################################### | 100%
pycairo-1.19.1       | 78 KB     | #################################################################################### | 100%
pango-1.42.4         | 521 KB    | #################################################################################### | 100%
pthread-stubs-0.4    | 5 KB      | #################################################################################### | 100%
xorg-libxdmcp-1.1.3  | 18 KB     | #################################################################################### | 100%
boost-cpp-1.72.0     | 16.3 MB   | #################################################################################### | 100%
libxml2-2.9.10       | 1.3 MB    | #################################################################################### | 100%
ld_impl_linux-64-2.3 | 616 KB    | #################################################################################### | 100%
freetype-2.10.2      | 905 KB    | #################################################################################### | 100%
sigcpp-2.0-2.10.3    | 4.3 MB    | #################################################################################### | 100%
sparsehash-2.0.3     | 85 KB     | #################################################################################### | 100%
xz-5.2.5             | 343 KB    | #################################################################################### | 100%
lz4-c-1.9.2          | 226 KB    | #################################################################################### | 100%
libedit-3.1.20191231 | 122 KB    | #################################################################################### | 100%
graphite2-1.3.13     | 102 KB    | #################################################################################### | 100%
numpy-1.18.5         | 5.2 MB    | #################################################################################### | 100%
icu-67.1             | 12.9 MB   | #################################################################################### | 100%
cycler-0.10.0        | 9 KB      | #################################################################################### | 100%
pcre-8.44            | 261 KB    | #################################################################################### | 100%
libtiff-4.1.0        | 668 KB    | #################################################################################### | 100%
hicolor-icon-theme-0 | 13 KB     | #################################################################################### | 100%
libxcb-1.13          | 396 KB    | #################################################################################### | 100%
libstdcxx-ng-9.2.0   | 4.5 MB    | #################################################################################### | 100%
at-spi2-core-2.35.1  | 543 KB    | #################################################################################### | 100%
ncurses-6.1          | 1.3 MB    | #################################################################################### | 100%
cairo-1.16.0         | 1.5 MB    | #################################################################################### | 100%
librsvg-2.49.3       | 16.6 MB   | #################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(700): An error occurred while installing package 'conda-forge::gtk3-3.24.21-h45fd312_0'.
Rolling back transaction: done

LinkError: post-link script failed for package conda-forge::gtk3-3.24.21-h45fd312_0
location of failed script: /home/ec2-user/anaconda3/envs/gt/bin/.gtk3-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr: /home/ec2-user/anaconda3/envs/gt/bin/gtk-query-immodules-3.0: error while loading shared libraries: libXcursor.so.1: cannot open shared object file: No such file or directory

return code: 127

()


</details>

Build wheel and encapsulate with auditwheel

It would be really nice if together with the conda builds we could generate wheel packages as well, which could be made self-contained with auditwheel (or delocate for macos). This would mean that people could do a pip install graph-tool (and hell would freeze over).

How much would we need to change in the build recipe? Is there any other package that does this?

Stuck at Solving the Environment

Issue: The conda installation is stick at solving the environment part and not going further.

Environment (conda list):

Anaconda 3.5.2, Python 3.6.5, Platform: Linux (ubuntu) ``` $ conda list

</details>

<br/>
Details about  <code>conda</code> and system ( <code>conda info</code> ):
<details>

$ conda info

</details>

from graph_tool import draw hang stuck

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

Hi, when I try to import draw function, it hang there
from graph_tool import draw as gt_draw
output Unable to revert mtime: /opt/conda/fonts
then I installed libmagic
conda install -c conda-forge libmagic
the output was gone, but it still hang there
no error, warning so I tried following to investigate, seems it trapped into an infinity loop
python -m trace --trace test.py
here are part of these ouputs from above (btw I believe this related with conda environment because it works in other conda env)

trace output

inspect.py(624):     return cleandoc(doc)
 --- modulename: inspect, funcname: cleandoc
inspect.py(631):     try:
inspect.py(632):         lines = doc.expandtabs().split('\n')
inspect.py(637):         margin = sys.maxsize
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(638):         for line in lines[1:]:
inspect.py(644):         if lines:
inspect.py(645):             lines[0] = lines[0].lstrip()
inspect.py(646):         if margin < sys.maxsize:
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(649):         while lines and not lines[-1]:
inspect.py(650):             lines.pop()
inspect.py(649):         while lines and not lines[-1]:
inspect.py(651):         while lines and not lines[0]:
inspect.py(652):             lines.pop(0)
inspect.py(651):         while lines and not lines[0]:
inspect.py(653):         return '\n'.join(lines)
artist.py(1390):         if docstring is None:
artist.py(1393):         if docstring.startswith('Alias for '):
artist.py(1396):         match = self._get_valid_values_regex.search(docstring)
artist.py(1397):         if match is not None:
artist.py(1402):         param_name = func.__code__.co_varnames[1]
artist.py(1405):         match = re.search(r"(?m)^ *\*?{} : (.+)".format(param_name), docstring)
 --- modulename: re, funcname: search
re.py(201):     return _compile(pattern, flags).search(string)
 --- modulename: re, funcname: _compile
re.py(291):     if isinstance(flags, RegexFlag):
re.py(293):     try:
re.py(294):         return _cache[type(pattern), pattern, flags]
artist.py(1406):         if match:
artist.py(1407):             return match.group(1)
artist.py(1511):             name = self.aliased_name(prop)
 --- modulename: artist, funcname: aliased_name
artist.py(1456):         aliases = ''.join(' or %s' % x for x in sorted(self.aliasd.get(s, [])))
 --- modulename: artist, funcname: <genexpr>
artist.py(1456):         aliases = ''.join(' or %s' % x for x in sorted(self.aliasd.get(s, [])))
artist.py(1457):         return s + aliases
artist.py(1512):             lines.append('%s%s: %s' % (pad, name, accepts))
artist.py(1509):         for prop in sorted(self.get_setters()):
artist.py(1510):             accepts = self.get_valid_values(prop)
 --- modulename: artist, funcname: get_valid_values
artist.py(1384):         name = 'set_%s' % attr
artist.py(1385):         if not hasattr(self.o, name):
artist.py(1387):         func = getattr(self.o, name)
artist.py(1389):         docstring = inspect.getdoc(func)
 --- modulename: inspect, funcname: getdoc
inspect.py(613):     try:
inspect.py(614):         doc = object.__doc__
inspect.py(617):     if doc is None:
inspect.py(622):     if not isinstance(doc, str):
inspect.py(624):     return cleandoc(doc)
 --- modulename: inspect, funcname: cleandoc
inspect.py(631):     try:
inspect.py(632):         lines = doc.expandtabs().split('\n')
inspect.py(637):         margin = sys.maxsize
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(638):         for line in lines[1:]:
inspect.py(644):         if lines:
inspect.py(645):             lines[0] = lines[0].lstrip()
inspect.py(646):         if margin < sys.maxsize:
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(647):             for i in range(1, len(lines)): lines[i] = lines[i][margin:]
inspect.py(649):         while lines and not lines[-1]:
inspect.py(650):             lines.pop()
inspect.py(649):         while lines and not lines[-1]:
inspect.py(651):         while lines and not lines[0]:
inspect.py(652):             lines.pop(0)
inspect.py(651):         while lines and not lines[0]:
inspect.py(653):         return '\n'.join(lines)
artist.py(1390):         if docstring is None:
artist.py(1393):         if docstring.startswith('Alias for '):
artist.py(1396):         match = self._get_valid_values_regex.search(docstring)
artist.py(1397):         if match is not None:
artist.py(1402):         param_name = func.__code__.co_varnames[1]
artist.py(1405):         match = re.search(r"(?m)^ *\*?{} : (.+)".format(param_name), docstring)
 --- modulename: re, funcname: search
re.py(201):     return _compile(pattern, flags).search(string)
 --- modulename: re, funcname: _compile
re.py(291):     if isinstance(flags, RegexFlag):
re.py(293):     try:
re.py(294):         return _cache[type(pattern), pattern, flags]
artist.py(1406):         if match:
artist.py(1407):             return match.group(1)
artist.py(1511):             name = self.aliased_name(prop)
 --- modulename: artist, funcname: aliased_name
artist.py(1456):         aliases = ''.join(' or %s' % x for x in sorted(self.aliasd.get(s, [])))
 --- modulename: artist, funcname: <genexpr>
artist.py(1456):         aliases = ''.join(' or %s' % x for x in sorted(self.aliasd.get(s, [])))
artist.py(1457):         return s + aliases
artist.py(1512):             lines.append('%s%s: %s' % (pad, name, accepts))
artist.py(1509):         for prop in sorted(self.get_setters()):
artist.py(1510):             accepts = self.get_valid_values(prop)
 --- modulename: artist, funcname: get_valid_values
artist.py(1384):         name = 'set_%s' % attr
artist.py(1385):         if not hasattr(self.o, name):
artist.py(1387):         func = getattr(self.o, name)
artist.py(1389):         docstring = inspect.getdoc(func)
 --- modulename: inspect, funcname: getdoc
inspect.py(613):     try:
inspect.py(614):         doc = object.__doc__
inspect.py(617):     if doc is None:
inspect.py(622):     if not isinstance(doc, str):
inspect.py(624):     return cleandoc(doc)
 --- modulename: inspect, funcname: cleandoc
inspect.py(631):     try:
inspect.py(632):         lines = doc.expandtabs().split('\n')
inspect.py(637):         margin = sys.maxsize
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(641):                 indent = len(line) - content
inspect.py(642):                 margin = min(margin, indent)
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content = len(line.lstrip())
inspect.py(640):             if content:
inspect.py(638):         for line in lines[1:]:
inspect.py(639):             content

Installed packages

# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
aniso8601                 9.0.1                    pypi_0    pypi
at-spi2-atk               2.38.0               h0630a04_3    conda-forge
at-spi2-core              2.40.3               h0630a04_0    conda-forge
atk-1.0                   2.36.0               h3371d22_4    conda-forge
attrs                     22.2.0                   pypi_0    pypi
boost                     1.74.0           py39h5472131_5    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
boto3                     1.26.84            pyhd8ed1ab_0    conda-forge
botocore                  1.29.84            pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h166bdaf_8    conda-forge
brotli-bin                1.0.9                h166bdaf_8    conda-forge
brotlipy                  0.7.0           py39h27cfd23_1003  
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2022.12.7            ha878542_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    conda-forge
cairomm                   1.14.4               ha770c72_0    conda-forge
cairomm-1.0               1.14.4               h09cb3b9_0    conda-forge
certifi                   2022.12.7          pyhd8ed1ab_0    conda-forge
cffi                      1.15.0           py39hd667e15_1  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
chemrouter                0.0.2                    pypi_0    pypi
click                     8.1.3                    pypi_0    pypi
colorama                  0.4.4              pyhd3eb1b0_0  
conda                     4.12.0           py39h06a4308_0  
conda-content-trust       0.1.1              pyhd3eb1b0_0  
conda-package-handling    1.8.1            py39h7f8727e_0  
cryptography              36.0.0           py39h9ce1e76_0  
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
epoxy                     1.5.10               h166bdaf_1    conda-forge
exceptiongroup            1.1.0                    pypi_0    pypi
expat                     2.5.0                h27087fc_0    conda-forge
flask                     2.2.2                    pypi_0    pypi
flask-cors                3.0.10                   pypi_0    pypi
flask-restful             0.3.9                    pypi_0    pypi
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                2.14.0               hc2a2eb6_1    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0           py39hb9d737c_1    conda-forge
freetype                  2.12.1               hca18f0e_0    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
gdk-pixbuf                2.42.8               hff1cb4f_0    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
glib-tools                2.74.0               h6239696_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
graph-tool                2.45             py39h7b6895e_2    conda-forge
graph-tool-base           2.45             py39h2fa1a2d_2    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
greenlet                  2.0.2            py39h227be39_0    conda-forge
gtk3                      3.24.34              h4d20fae_1    conda-forge
gunicorn                  20.1.0                   pypi_0    pypi
harfbuzz                  5.3.0                h418a68e_0    conda-forge
hicolor-icon-theme        0.17                 ha770c72_2    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
idna                      3.3                pyhd3eb1b0_0  
importlib-metadata        6.0.0                    pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
itsdangerous              2.1.2                    pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
jmespath                  1.0.1              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.4            py39hf939315_1    conda-forge
krb5                      1.19.3               h08a2579_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_8    conda-forge
libbrotlidec              1.0.9                h166bdaf_8    conda-forge
libbrotlienc              1.0.9                h166bdaf_8    conda-forge
libcblas                  3.9.0           16_linux64_openblas    conda-forge
libcups                   2.3.3                h3e49a29_2    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgfortran-ng            12.2.0              h69a702a_19    conda-forge
libgfortran5              12.2.0              h337968e_19    conda-forge
libgirepository           1.74.0               ha2a38d2_1    conda-forge
libglib                   2.74.0               h7a41b64_0    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libimagequant             2.17.0               h7f98852_1    conda-forge
liblapack                 3.9.0           16_linux64_openblas    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    conda-forge
libpng                    1.6.38               h753d276_0    conda-forge
libpq                     14.5                 he2d8382_0    conda-forge
librsvg                   2.54.4               h7abd40a_0    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
libtiff                   4.3.0                h0fcbabc_4    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.9.14               h22db469_4    conda-forge
libzlib                   1.2.12               h166bdaf_1    conda-forge
llvm-openmp               14.0.4               he0ac6c6_0    conda-forge
markupsafe                2.1.2                    pypi_0    pypi
matplotlib-base           3.5.1            py39h2fa2bec_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h7f8727e_2  
numpy                     1.22.4           py39hc58783e_0    conda-forge
openjpeg                  2.5.0                h7d73246_0    conda-forge
openssl                   3.0.8                h0b41bf4_0    conda-forge
packaging                 23.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.3            py39h2ad29b5_0    conda-forge
pango                     1.50.11              h382ae3d_0    conda-forge
pcre2                     10.37                hc3806b6_1    conda-forge
pillow                    9.0.1            py39he69867a_1    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
platformdirs              3.1.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.0.0                    pypi_0    pypi
pooch                     1.7.0              pyhd8ed1ab_0    conda-forge
psycopg2                  2.9.3            py39hb9d737c_1    conda-forge
psycopg2-binary           2.9.3              pyhd8ed1ab_2    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycairo                   1.23.0           py39h23c5bb2_0    conda-forge
pycosat                   0.6.3            py39h27cfd23_0  
pycparser                 2.21               pyhd3eb1b0_0  
pygobject                 3.42.2           py39habf54e5_0    conda-forge
pyjwt                     2.6.0                    pypi_0    pypi
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyprind                   2.11.3                   pypi_0    pypi
pysocks                   1.7.1            py39h06a4308_0  
pytest                    7.2.0                    pypi_0    pypi
python                    3.9.10          hc74c709_2_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dotenv             0.21.0                   pypi_0    pypi
python_abi                3.9                      3_cp39    conda-forge
pytz                      2022.7.1           pyhd8ed1ab_0    conda-forge
rdkit                     2022.09.1        py39h79face8_0    conda-forge
readline                  8.1.2                h7f8727e_1  
reportlab                 3.6.12           py39h8bbe095_2    conda-forge
requests                  2.27.1             pyhd3eb1b0_0  
ruamel_yaml               0.15.100         py39h27cfd23_0  
s3transfer                0.6.0              pyhd8ed1ab_0    conda-forge
scipy                     1.10.1           py39h7360e5f_0    conda-forge
setuptools                61.2.0           py39h06a4308_0  
sigcpp-2.0                2.10.8               h27087fc_0    conda-forge
six                       1.16.0             pyhd3eb1b0_1  
smilite                   2.3.0                    pypi_0    pypi
sparsehash                2.0.4                h9c3ff4c_0    conda-forge
sqlalchemy                2.0.4            py39h72bdee0_0    conda-forge
sqlite                    3.38.2               hc218d9a_0  
tk                        8.6.11               h1ccaba5_0  
tomli                     2.0.1                    pypi_0    pypi
tqdm                      4.63.0             pyhd3eb1b0_0  
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022a                hda174b7_0  
unicodedata2              15.0.0           py39hb9d737c_0    conda-forge
urllib3                   1.26.8             pyhd3eb1b0_0  
werkzeug                  2.2.3                    pypi_0    pypi
wheel                     0.37.1             pyhd3eb1b0_0  
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               1.8.4                h0b41bf4_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxcomposite        0.4.6                h0b41bf4_1    conda-forge
xorg-libxcursor           1.2.0                h0b41bf4_1    conda-forge
xorg-libxdamage           1.1.5                h7f98852_1    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxfixes            5.0.3             h7f98852_1004    conda-forge
xorg-libxi                1.7.10               h7f98852_0    conda-forge
xorg-libxinerama          1.1.5                h27087fc_0    conda-forge
xorg-libxrandr            1.5.2                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-libxtst              1.2.3             h7f98852_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             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.5                h7b6447c_0  
yaml                      0.2.5                h7b6447c_0  
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.12               h7f8727e_1  
zstandard                 0.19.0           py39h29414ee_1    conda-forge
zstd                      1.5.2                h6239696_4    conda-forge

Environment info

active environment : None
            shell level : 0
       user config file : /home/vscode/.condarc
 populated config files : 
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.10.final.0
       virtual packages : __linux=5.15.49=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/conda/pkgs
                          /home/vscode/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/vscode/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.10 Linux/5.15.49-linuxkit debian/11 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Drawing support

Currently, our build of graph-tool doesn't support drawing, since one of the dependencies (gtk+3) is not yet available via conda-forge. Once that changes, we should update this recipe.

In the meantime, it may be possible for users to enable drawing support by installing the required dependencies themselves, as described here.

~~Something like this might work:~~

conda install -c conda-forge -c pkgw/label/superseded graph-tool pygobject cairo gtk3

Can not install

Issue:
When I try to install using conda it fails.
When I install graph-tool it also install 2.29 and I need 2.32.

Environment (conda list):

Conda install graph-tool=2.32 Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

$ conda list

Details about conda and system ( conda info ):

$ conda info

What is the final solution to install graph-tool in an already conda env?

I read the conda-forge documentation and could not find the solution for my problem there.

Issue: For so many ways I've tried to install graph-tool in an environment I've been worked, and it has been impossible. I've tryed these:

conda install -c conda-forge graph-tool
conda install -c conda-forge/label/cf202003 graph-tool
conda config --add channels conda-forge
conda install graph-tool

I'm not interested to create another env, so Is it possible to use graph-tool without create another env?
Thanks in advance.

Environment (conda list):

$ conda list

Details about conda and system ( conda info ):

$ conda info

gtk3 error when including in another package (X11 libs not found)

Issue: When including this as a dependency in another recipe I am getting a post-link error in gtk3 due to various missing X11 libraries. I need to add the following to dependencies to get the environment to install:

xorg-libxi
xorg-libxcursor
xorg-libxdamage
xorg-libxcomposite
xorg-libxrandr
xorg-libxinerama
xorg-libxpm
xorg-libxaw
xorg-libxfixes

See bioconda/bioconda-recipes#23350

Any idea whether this is a problem here, or perhaps with the gtk3 package? If #28 was done (like matplotlib-base) that might also solve this issue.

Environment (conda list):

16:58:57 BIOCONDA INFO (OUT) The following NEW packages will be INSTALLED:
16:58:57 BIOCONDA INFO (OUT) 
16:58:57 BIOCONDA INFO (OUT)     _libgcc_mutex:         0.1-conda_forge               conda-forge
16:58:57 BIOCONDA INFO (OUT)     _openmp_mutex:         4.5-0_gnu                     conda-forge
16:58:57 BIOCONDA INFO (OUT)     at-spi2-atk:           2.34.2-h1369247_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     at-spi2-core:          2.36.0-h1369247_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     atk-1.0:               2.36.0-haf93ef1_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     boost:                 1.72.0-py38h9de70de_0         conda-forge
16:58:57 BIOCONDA INFO (OUT)     boost-cpp:             1.72.0-h7b93d67_2             conda-forge
16:58:57 BIOCONDA INFO (OUT)     bzip2:                 1.0.8-h516909a_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     ca-certificates:       2020.6.20-hecda079_0          conda-forge
16:58:57 BIOCONDA INFO (OUT)     cairo:                 1.16.0-h3fc0475_1005          conda-forge
16:58:57 BIOCONDA INFO (OUT)     cairomm:               1.12.2-2                      conda-forge
16:58:57 BIOCONDA INFO (OUT)     cairomm-1.0:           1.12.2-h0069156_2             conda-forge
16:58:57 BIOCONDA INFO (OUT)     capnproto:             0.6.1-hfc679d8_1              conda-forge
16:58:57 BIOCONDA INFO (OUT)     certifi:               2020.6.20-py38h32f6830_0      conda-forge
16:58:57 BIOCONDA INFO (OUT)     cycler:                0.10.0-py_2                   conda-forge
16:58:57 BIOCONDA INFO (OUT)     dbus:                  1.13.6-he372182_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     dendropy:              4.4.0-py_1                    bioconda
16:58:57 BIOCONDA INFO (OUT)     epoxy:                 1.5.4-h516909a_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     expat:                 2.2.9-he1b5a44_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     fontconfig:            2.13.1-h1056068_1002          conda-forge
16:58:57 BIOCONDA INFO (OUT)     freetype:              2.10.2-he06d7ca_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     fribidi:               1.0.10-h516909a_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     gdk-pixbuf:            2.38.2-h3f25603_4             conda-forge
16:58:57 BIOCONDA INFO (OUT)     gettext:               0.19.8.1-hc5be6a0_1002        conda-forge
16:58:57 BIOCONDA INFO (OUT)     glib:                  2.65.0-h6f030ca_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     gmp:                   6.2.0-he1b5a44_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     gobject-introspection: 1.64.1-py38h03d966d_1         conda-forge
16:58:57 BIOCONDA INFO (OUT)     graph-tool:            2.33-py38hed06623_0           conda-forge
16:58:57 BIOCONDA INFO (OUT)     graphite2:             1.3.13-he1b5a44_1001          conda-forge
16:58:57 BIOCONDA INFO (OUT)     gsl:                   2.6-h294904e_0                conda-forge
16:58:57 BIOCONDA INFO (OUT)     gtk3:                  3.24.21-h45fd312_0            conda-forge
16:58:57 BIOCONDA INFO (OUT)     h5py:                  2.10.0-nompi_py38hfb01d0b_104 conda-forge
16:58:57 BIOCONDA INFO (OUT)     harfbuzz:              2.4.0-hee91db6_5              conda-forge
16:58:57 BIOCONDA INFO (OUT)     hdbscan:               0.8.26-py38h8790de6_1         conda-forge
16:58:57 BIOCONDA INFO (OUT)     hdf5:                  1.10.6-nompi_h3c11f04_100     conda-forge
16:58:57 BIOCONDA INFO (OUT)     hicolor-icon-theme:    0.17-1                        conda-forge
16:58:57 BIOCONDA INFO (OUT)     icu:                   67.1-he1b5a44_0               conda-forge
16:58:57 BIOCONDA INFO (OUT)     joblib:                0.16.0-py_0                   conda-forge
16:58:57 BIOCONDA INFO (OUT)     jpeg:                  9d-h516909a_0                 conda-forge
16:58:57 BIOCONDA INFO (OUT)     kiwisolver:            1.2.0-py38hbf85e49_0          conda-forge
16:58:57 BIOCONDA INFO (OUT)     krb5:                  1.17.1-hfafb76e_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     lcms2:                 2.11-hbd6801e_0               conda-forge
16:58:57 BIOCONDA INFO (OUT)     ld_impl_linux-64:      2.34-h53a641e_7               conda-forge
16:58:57 BIOCONDA INFO (OUT)     libblas:               3.8.0-11_openblas             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libcblas:              3.8.0-11_openblas             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libcroco:              0.6.13-h8d621e5_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libcups:               2.2.12-hf10b501_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libedit:               3.1.20191231-h46ee950_1       conda-forge
16:58:57 BIOCONDA INFO (OUT)     libffi:                3.2.1-he1b5a44_1007           conda-forge
16:58:57 BIOCONDA INFO (OUT)     libgcc-ng:             9.2.0-h24d8f2e_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libgfortran-ng:        7.5.0-hdf63c60_6              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libgomp:               9.2.0-h24d8f2e_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libiconv:              1.15-h516909a_1006            conda-forge
16:58:57 BIOCONDA INFO (OUT)     liblapack:             3.8.0-11_openblas             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libopenblas:           0.3.6-h6e990d7_6              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libpng:                1.6.37-hed695b0_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     librsvg:               2.49.3-h33a7fed_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     libstdcxx-ng:          9.2.0-hdf63c60_2              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libtiff:               4.1.0-hc7e4089_6              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libuuid:               2.32.1-h14c3975_1000          conda-forge
16:58:57 BIOCONDA INFO (OUT)     libwebp-base:          1.1.0-h516909a_3              conda-forge
16:58:57 BIOCONDA INFO (OUT)     libxcb:                1.13-h14c3975_1002            conda-forge
16:58:57 BIOCONDA INFO (OUT)     libxml2:               2.9.10-h72b56ed_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     lz4-c:                 1.9.2-he1b5a44_1              conda-forge
16:58:57 BIOCONDA INFO (OUT)     mash:                  2.2.2-ha61e061_2              bioconda
16:58:57 BIOCONDA INFO (OUT)     matplotlib:            3.3.0-1                       conda-forge
16:58:57 BIOCONDA INFO (OUT)     matplotlib-base:       3.3.0-py38h91b0d89_1          conda-forge
16:58:57 BIOCONDA INFO (OUT)     ncurses:               6.2-he1b5a44_1                conda-forge
16:58:57 BIOCONDA INFO (OUT)     numpy:                 1.19.1-py38h8854b6b_0         conda-forge
16:58:57 BIOCONDA INFO (OUT)     olefile:               0.46-py_0                     conda-forge
16:58:57 BIOCONDA INFO (OUT)     openblas:              0.3.6-h6e990d7_6              conda-forge
16:58:57 BIOCONDA INFO (OUT)     openssl:               1.1.1g-h516909a_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     pandas:                1.0.5-py38hcb8c335_0          conda-forge
16:58:57 BIOCONDA INFO (OUT)     pango:                 1.42.4-h7062337_4             conda-forge
16:58:57 BIOCONDA INFO (OUT)     pcre:                  8.44-he1b5a44_0               conda-forge
16:58:57 BIOCONDA INFO (OUT)     pillow:                7.2.0-py38h9776b28_1          conda-forge
16:58:57 BIOCONDA INFO (OUT)     pip:                   20.1.1-py_1                   conda-forge
16:58:57 BIOCONDA INFO (OUT)     pixman:                0.38.0-h516909a_1003          conda-forge
16:58:57 BIOCONDA INFO (OUT)     poppunk:               2.1.1-py_0                    local
16:58:57 BIOCONDA INFO (OUT)     pp-sketchlib:          1.4.0-py38h212a85b_0          conda-forge
16:58:57 BIOCONDA INFO (OUT)     pthread-stubs:         0.4-h14c3975_1001             conda-forge
16:58:57 BIOCONDA INFO (OUT)     pycairo:               1.19.1-py38h323dad1_3         conda-forge
16:58:57 BIOCONDA INFO (OUT)     pygobject:             3.36.1-py38h2faf24e_1         conda-forge
16:58:57 BIOCONDA INFO (OUT)     pyparsing:             2.4.7-pyh9f0ad1d_0            conda-forge
16:58:57 BIOCONDA INFO (OUT)     python:                3.8.5-h425cb1d_1_cpython      conda-forge
16:58:57 BIOCONDA INFO (OUT)     python-dateutil:       2.8.1-py_0                    conda-forge
16:58:57 BIOCONDA INFO (OUT)     python_abi:            3.8-1_cp38                    conda-forge
16:58:57 BIOCONDA INFO (OUT)     pytz:                  2020.1-pyh9f0ad1d_0           conda-forge
16:58:57 BIOCONDA INFO (OUT)     rapidnj:               v2.3.2-hc9558a2_2             bioconda
16:58:57 BIOCONDA INFO (OUT)     readline:              8.0-he28a2e2_2                conda-forge
16:58:57 BIOCONDA INFO (OUT)     scikit-learn:          0.23.1-py38h3a94b23_0         conda-forge
16:58:57 BIOCONDA INFO (OUT)     scipy:                 1.5.2-py38h8c5af15_0          conda-forge
16:58:57 BIOCONDA INFO (OUT)     setuptools:            49.2.0-py38h32f6830_0         conda-forge
16:58:57 BIOCONDA INFO (OUT)     sigcpp-2.0:            2.10.3-he1b5a44_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     six:                   1.15.0-pyh9f0ad1d_0           conda-forge
16:58:57 BIOCONDA INFO (OUT)     sparsehash:            2.0.3-hf484d3e_1000           conda-forge
16:58:57 BIOCONDA INFO (OUT)     sqlite:                3.32.3-hcee41ef_1             conda-forge
16:58:57 BIOCONDA INFO (OUT)     threadpoolctl:         2.1.0-pyh5ca1d4c_0            conda-forge
16:58:57 BIOCONDA INFO (OUT)     tk:                    8.6.10-hed695b0_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     tornado:               6.0.4-py38h1e0a361_1          conda-forge
16:58:57 BIOCONDA INFO (OUT)     wheel:                 0.34.2-py_1                   conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-kbproto:          1.0.7-h14c3975_1002           conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libice:           1.0.10-h516909a_0             conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libsm:            1.2.3-h84519dc_1000           conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libx11:           1.6.9-h516909a_0              conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libxau:           1.0.9-h14c3975_0              conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libxdmcp:         1.1.3-h516909a_0              conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libxext:          1.3.4-h516909a_0              conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-libxrender:       0.9.10-h516909a_1002          conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-renderproto:      0.11.1-h14c3975_1002          conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-xextproto:        7.3.0-h14c3975_1002           conda-forge
16:58:57 BIOCONDA INFO (OUT)     xorg-xproto:           7.0.31-h14c3975_1007          conda-forge
16:58:57 BIOCONDA INFO (OUT)     xz:                    5.2.5-h516909a_1              conda-forge
16:58:57 BIOCONDA INFO (OUT)     zlib:                  1.2.11-h516909a_1006          conda-forge
16:58:57 BIOCONDA INFO (OUT)     zstd:                  1.4.5-h6597ccf_1              conda-forge

Details about conda and system ( conda info ):

$ conda info

@conda-forge-admin, please re-render

linux installation: gtk-query-immodules-3.0

I read the conda-forge documentation and could not find the solution for my problem there.

Issue:

i ran into the following issue while installing graph-tool on a linux server

after running

conda create --name gt -c conda-forge graph-tool

i received the message

anaconda3/envs/gt/bin/gtk-query-immodules-3.0: error while loading shared libraries:
libXcursor.so.1: cannot open shared object file: No such file or directory
ERROR: Failed to complete gtk3's post-link script.
To fix this, activate the environment and run:
    glib-compile-schemas "/home/anaconda3/envs/gt/share/glib-2.0/schemas"
    gtk-update-icon-cache -f -t "/home/anaconda3/envs/gt/share/icons/hicolor"
    gtk-query-immodules-3.0 --update-cache

unfortunately running the three suggested lines gives another error

gtk-query-immodules-3.0: error while loading shared libraries: libXcursor.so.1: cannot open shared object file: No such file or directory

i did not get the same error when i installed graph-tool-base, so i think the issue is with one of the extraneous dependencies

Python versions

Currently, we skip all python configurations except 3.7. That's just because this package takes super long to build (5+ hours), and I'm a little afraid of overloading conda-forge's build queues.

But at some point we should take the time to add support for other python versions, assuming the conda-forge core team doesn't mind us soaking up more build time every now and then.

Overlinking?

(This is a relatively minor issue.)

Currently, we list the following runtime dependencies explicitly, even though they are not listed as explicit dependencies in the graph-tool documentation:

gmp
llvm-openmp (mac only)

We list them to avoid warnings from conda-build:

WARNING (graph-tool,lib/python3.7/site-packages/graph_tool/generation/libgraph_tool_generation.so): Needed DSO lib/libgmp.so.10 found in ['gmp']
WARNING (graph-tool,lib/python3.7/site-packages/graph_tool/generation/libgraph_tool_generation.so): .. but ['gmp'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely)

WARNING (graph-tool,lib/python3.7/site-packages/graph_tool/stats/libgraph_tool_stats.0.so): Needed DSO lib/libomp.dylib found in ['llvm-openmp']
WARNING (graph-tool,lib/python3.7/site-packages/graph_tool/stats/libgraph_tool_stats.0.so): .. but ['llvm-openmp'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely)

That is, I "fixed" the warning by introducing a new runtime dependency, but the true issue may in fact be "overlinking" in the graph-tool build flags. For gmp, the overlinking appears to be coming from this line in the configure scripts. I think we could use a patch to remove the -lgmp flag if it isn't really necessary (or patch upstream), and then remove the explicit dependency on gmp.

I'm less clear on whether or not llvm-openmp is being "overlinked".

conda search cannot find graph-tool

Solution to issue cannot be found in the documentation.

I checked the documentation.

Issue

I have a docker linux image that includes graph-tool, which gets rebuilt periodically. The build broke today, and it appears that graph-tool can no longer be found. See conda search results below:

> conda search graph-tool

Loading channels: done
No match found for: graph-tool. Search: *graph-tool*

PackagesNotFoundError: The following packages are not available from current channels:

  - graph-tool

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-aarch64
  - https://conda.anaconda.org/conda-forge/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

If I run conda search graph-tool on my Mac, however, it is successfully found as expected.

Click for Environment details

Installed packages

# packages in environment at /opt/conda:
#
# Name                    Version                   Build  Channel
_openmp_mutex             4.5                       2_gnu    conda-forge
alembic                   1.8.0              pyhd8ed1ab_0    conda-forge
anyio                     3.6.1           py310hbbe02a8_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h761cc84_2    conda-forge
asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
babel                     2.10.1             pyhd8ed1ab_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
brotlipy                  0.7.0           py310h761cc84_1004    conda-forge
bzip2                     1.0.8                hf897c2e_4    conda-forge
c-ares                    1.18.1               hf897c2e_0    conda-forge
ca-certificates           2022.5.18.1          h4fd8a4c_0    conda-forge
certifi                   2022.5.18.1     py310h4c7bcd0_0    conda-forge
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.15.0          py310h8915cd8_0    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
conda                     4.13.0          py310h4c7bcd0_1    conda-forge
conda-package-handling    1.8.1           py310h761cc84_1    conda-forge
configurable-http-proxy   4.5.1           node17_hfaf594c_1    conda-forge
cryptography              37.0.2          py310h07dd38e_0    conda-forge
debugpy                   1.6.0           py310h130cc07_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 0.8.3              pyhd8ed1ab_0    conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge
greenlet                  1.1.2           py310h130cc07_2    conda-forge
icu                       70.1                 ha18d298_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4          py310hbbe02a8_0    conda-forge
importlib_metadata        4.11.4               hd8ed1ab_0    conda-forge
importlib_resources       5.7.1              pyhd8ed1ab_1    conda-forge
ipykernel                 6.13.1          py310h7d5ade6_0    conda-forge
ipython                   8.4.0           py310h4c7bcd0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.18.1          py310hbbe02a8_1    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.6.0              pyhd8ed1ab_0    conda-forge
jupyter_client            7.3.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.10.0          py310h4c7bcd0_0    conda-forge
jupyter_server            1.17.1             pyhd8ed1ab_0    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub                2.3.1              pyhd8ed1ab_0    conda-forge
jupyterhub-base           2.3.1              pyhd8ed1ab_0    conda-forge
jupyterlab                3.4.3              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.14.0             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h4e544f5_0    conda-forge
krb5                      1.19.3               h7c456eb_0    conda-forge
ld_impl_linux-aarch64     2.36.1               h02ad14f_2    conda-forge
libarchive                3.5.2                h610d84a_2    conda-forge
libcurl                   7.83.1               h8fd98b7_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h3557bc0_5    conda-forge
libgcc-ng                 12.1.0              h3242a24_16    conda-forge
libgomp                   12.1.0              h3242a24_16    conda-forge
libiconv                  1.16                 h6dd45c4_0    conda-forge
libmamba                  0.24.0               h8683862_1    conda-forge
libmambapy                0.24.0          py310h76fea7e_1    conda-forge
libnghttp2                1.47.0               h75cb1c7_0    conda-forge
libnsl                    2.0.0                hf897c2e_0    conda-forge
libsodium                 1.0.18               hb9de7d4_1    conda-forge
libsolv                   0.7.22               h7866ba4_0    conda-forge
libssh2                   1.10.0               h1ab2c7b_2    conda-forge
libstdcxx-ng              12.1.0              hd01590b_16    conda-forge
libuuid                   2.32.1            hf897c2e_1000    conda-forge
libuv                     1.43.0               hf897c2e_0    conda-forge
libxml2                   2.9.14               h370961a_0    conda-forge
libzlib                   1.2.12               h4e544f5_0    conda-forge
lz4-c                     1.9.3                h01db608_1    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mako                      1.2.0              pyhd8ed1ab_1    conda-forge
mamba                     0.24.0          py310hcf12e44_1    conda-forge
markupsafe                2.1.1           py310hdc54845_1    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mistune                   0.8.4           py310h7cee911_1005    conda-forge
nbclassic                 0.3.7              pyhd8ed1ab_0    conda-forge
nbclient                  0.6.4              pyhd8ed1ab_1    conda-forge
nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  headf329_1    conda-forge
nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge
nodejs                    17.9.0               he850d6a_0    conda-forge
notebook                  6.4.12             pyha770c72_0    conda-forge
notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge
oauthlib                  3.2.0              pyhd8ed1ab_0    conda-forge
openssl                   1.1.1o               h4e544f5_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandoc                    2.18                 h8af1aa0_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       22.1.2             pyhd8ed1ab_0    conda-forge
prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.29             pyha770c72_0    conda-forge
psutil                    5.9.1           py310h761cc84_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.3           py310h761cc84_1010    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pycurl                    7.45.1          py310h0dc3a97_1    conda-forge
pygments                  2.12.0             pyhd8ed1ab_0    conda-forge
pyjwt                     2.4.0              pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.1          py310hdc54845_1    conda-forge
pysocks                   1.7.1           py310hbbe02a8_5    conda-forge
python                    3.10.4          h2eada40_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyzmq                     23.1.0          py310h7c6bb8d_0    conda-forge
readline                  8.1.2                h38e3740_0    conda-forge
reproc                    14.2.3               hf897c2e_0    conda-forge
reproc-cpp                14.2.3               h01db608_0    conda-forge
requests                  2.28.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.21         py310h761cc84_1    conda-forge
ruamel.yaml.clib          0.2.6           py310h761cc84_1    conda-forge
ruamel_yaml               0.15.80         py310h761cc84_1007    conda-forge
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                62.3.4          py310hbbe02a8_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.2.0           py310h4c7bcd0_3    conda-forge
soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge
sqlalchemy                1.4.37          py310hdc54845_0    conda-forge
sqlite                    3.38.5               hc74f5b8_0    conda-forge
stack_data                0.2.0              pyhd8ed1ab_0    conda-forge
terminado                 0.15.0          py310hbbe02a8_0    conda-forge
tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               hd8af866_0    conda-forge
tornado                   6.1             py310hdc54845_3    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
traitlets                 5.2.2.post1        pyhd8ed1ab_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.3.2              pyhd8ed1ab_0    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xz                        5.2.5                h6dd45c4_1    conda-forge
yaml                      0.2.5                hf897c2e_2    conda-forge
yaml-cpp                  0.7.0                h4de3ea5_1    conda-forge
zeromq                    4.3.4                h01db608_1    conda-forge
zipp                      3.8.0              pyhd8ed1ab_0    conda-forge
zlib                      1.2.12               h4e544f5_0    conda-forge
zstd                      1.5.2                haad177d_1    conda-forge

Environment info

active environment : base
    active env location : /opt/conda
            shell level : 1
       user config file : /home/jovyan/.condarc
 populated config files : /opt/conda/.condarc
          conda version : 4.13.0
    conda-build version : not installed
         python version : 3.10.4.final.0
       virtual packages : __linux=5.10.104=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=aarch64
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-aarch64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /opt/conda/pkgs
                          /home/jovyan/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/jovyan/.conda/envs
               platform : linux-aarch64
             user-agent : conda/4.13.0 requests/2.28.0 CPython/3.10.4 Linux/5.10.104-linuxkit ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:100
             netrc file : None
           offline mode : False

# conda environments:
#
base                  *  /opt/conda

sys.version: 3.10.4 | packaged by conda-forge | (main...
sys.prefix: /opt/conda
sys.executable: /opt/conda/bin/python
conda location: /opt/conda/lib/python3.10/site-packages/conda
conda-build: None
conda-env: /opt/conda/bin/conda-env
user site dirs: 

CIO_TEST: <not set>
CONDA_DEFAULT_ENV: base
CONDA_DIR: /opt/conda
CONDA_EXE: /opt/conda/bin/conda
CONDA_PREFIX: /opt/conda
CONDA_PROMPT_MODIFIER: (base) 
CONDA_PYTHON_EXE: /opt/conda/bin/python
CONDA_ROOT: /opt/conda
CONDA_SHLVL: 1
CURL_CA_BUNDLE: <not set>
PATH: /opt/conda/bin:/opt/conda/bin:/opt/conda/condabin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
REQUESTS_CA_BUNDLE: <not set>
SSL_CERT_FILE: <not set>

@conda-forge-admin, please re-render

@conda-forge-admin, please re-render.

Differences between linux and osx behaviour (but bug for all)

Hi all, I am experiencing some issues with graph_tool version 2.43 on two different systems. In both cases I have installed via conda-forge. On the linux system I have

import graph_tool.all as gt
gt.__version__
'2.43 (commit 5778eb10, )'

for python 3.8 (package version py38hdc7f20d_0). On os x I have

import graph_tool.all as gt
gt.__version__
'2.43 (commit , )'

for python 3.8 (package version py38haa49ee5_0).
Since I'm interested in edge prediction on LayeredBlockState I have tried a simple code which I also reported on graph-tool official issue tracker. The problem is that the same code is returning two different errors on both systems.
On OSX I have

g = gt.collection.ns["new_guinea_tribes"]
state = gt.minimize_nested_blockmodel_dl(g,
                                         state_args=dict(base_type=gt.LayeredBlockState,
                                                         state_args=dict(ec=g.ep.weight, layers=True)))

missing = [(0, 6, 1), (0, 6, -1)]
state.get_edges_prob(missing)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-3-fadd85695711> in <module>
      5 
      6 missing = [(0, 6, 1), (0, 6, -1)]
----> 7 state.get_edges_prob(missing)

~/anaconda3/envs/experimental/lib/python3.8/site-packages/graph_tool/inference/nested_blockmodel.py in get_edges_prob(self, missing, spurious, entropy_args)
    441                 lstate._state.clear_egroups()
    442 
--> 443             L += lstate.get_edges_prob(missing, spurious, entropy_args=eargs)
    444             if isinstance(self.levels[0], LayeredBlockState):
    445                 missing = [(lstate.b[u], lstate.b[v], l_) for u, v, l_ in missing]

~/anaconda3/envs/experimental/lib/python3.8/site-packages/graph_tool/inference/layered_blockmodel.py in get_edges_prob(self, missing, spurious, entropy_args)
    788 
    789             nes.append((u, v, (l, False)))
--> 790             nes.append((self._get_lvertex(u, l),
    791                         self._get_lvertex(v, l), (l, True)))
    792 

~/anaconda3/envs/experimental/lib/python3.8/site-packages/graph_tool/inference/layered_blockmodel.py in _get_lvertex(self, v, l)
    748     def _get_lvertex(self, v, l):
    749         i = numpy.searchsorted(self.vc[v].a, l)
--> 750         if i >= len(self.vc[v]) or l != self.vc[v][i]:
    751             raise ValueError("vertex %d not present in layer %d" % (v, l))
    752         u = self.vmap[v][i]

TypeError: Invalid index type

whereas on linux I have

g = gt.collection.ns["new_guinea_tribes"]
state = gt.minimize_nested_blockmodel_dl(g,
                                         state_args=dict(base_type=gt.LayeredBlockState,
                                                         state_args=dict(ec=g.ep.weight, layers=True)))

missing = [(0, 6, 1), (0, 6, -1)]
state.get_edges_prob(missing)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/beegfs/scratch/tmp/ipykernel_16854/740866967.py in <module>
      5 
      6 missing = [(0, 6, 1), (0, 6, -1)]
----> 7 state.get_edges_prob(missing)

~/miniforge3/envs/singlecell/lib/python3.8/site-packages/graph_tool/inference/nested_blockmodel.py in get_edges_prob(self, missing, spurious, entropy_args)
    441                 lstate._state.clear_egroups()
    442 
--> 443             L += lstate.get_edges_prob(missing, spurious, entropy_args=eargs)
    444             if isinstance(self.levels[0], LayeredBlockState):
    445                 missing = [(lstate.b[u], lstate.b[v], l_) for u, v, l_ in missing]

~/miniforge3/envs/singlecell/lib/python3.8/site-packages/graph_tool/inference/layered_blockmodel.py in get_edges_prob(self, missing, spurious, entropy_args)
    789             nes.append((u, v, (l, False)))
    790             nes.append((self._get_lvertex(u, l),
--> 791                         self._get_lvertex(v, l), (l, True)))
    792 
    793         edge_list = nes

~/miniforge3/envs/singlecell/lib/python3.8/site-packages/graph_tool/inference/layered_blockmodel.py in _get_lvertex(self, v, l)
    749         i = numpy.searchsorted(self.vc[v].a, l)
    750         if i >= len(self.vc[v]) or l != self.vc[v][i]:
--> 751             raise ValueError("vertex %d not present in layer %d" % (v, l))
    752         u = self.vmap[v][i]
    753         return u

ValueError: vertex 6 not present in layer 1

According to Tiago's comments here it may be an issue with a proper compilation of the library.
Of course I may recompile myself graph-tool on os x, but having a fully functional package would save me a lot of time.

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