Incompatible with plotting packages

[trahflow]

On my (arch linux) system, python throws the following error if I

• first import a plotting package (I tried CairoMakie, GLMakie, Plots)
• create a WandbLogger and log a simple object using Wandb.log()

ERROR: Python: ImportError: /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/lib-dynload/pyexpat.cpython-312-x86_64-linux-gnu.so: undefined symbol: XML_SetReparseDeferralEnabled

Stacktrace

``` Python stacktrace: [1] @ /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/xml/parsers/expat.py:4 [2] @ /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/plistlib.py:70 [3] @ /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/pkg_resources/__init__.py:40 [4] parse_version @ wandb.util /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/util.py:1891 [5] _server_accepts_client_ids @ wandb.sdk.data_types.base_types.wb_value /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/data_types/base_types/wb_value.py:33 [6] _get_artifact_entry_ref_url @ wandb.sdk.data_types.base_types.wb_value /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/data_types/base_types/wb_value.py:220 [7] to_json @ wandb.sdk.data_types.base_types.media /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/data_types/base_types/media.py:172 [8] to_json @ wandb.data_types /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/data_types.py:554 [9] val_to_json @ wandb.sdk.data_types.utils /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/data_types/utils.py:166 [10] history_dict_to_json @ wandb.sdk.data_types.utils /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/data_types/utils.py:52 [11] publish_partial_history @ wandb.sdk.interface.interface /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/interface/interface.py:572 [12] _partial_history_callback @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:1474 [13] _log @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:1602 [14] log @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:1838 [15] wrapper @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:361 [16] wrapper_fn @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:371 [17] wrapper @ wandb.sdk.wandb_run /tmp/jl_7X2lxa/.CondaPkg/env/lib/python3.12/site-packages/wandb/sdk/wandb_run.py:420 Stacktrace: [1] pythrow() @ PythonCall.Core ~/.julia/packages/PythonCall/bb3ax/src/Core/err.jl:92 [2] errcheck @ ~/.julia/packages/PythonCall/bb3ax/src/Core/err.jl:10 [inlined] [3] pycallargs @ ~/.julia/packages/PythonCall/bb3ax/src/Core/builtins.jl:212 [inlined] [4] pycall(f::PythonCall.Core.Py, args::PythonCall.Core.Py; kwargs::@Kwargs{}) @ PythonCall.Core ~/.julia/packages/PythonCall/bb3ax/src/Core/builtins.jl:230 [5] pycall @ ~/.julia/packages/PythonCall/bb3ax/src/Core/builtins.jl:220 [inlined] [6] Py @ ~/.julia/packages/PythonCall/bb3ax/src/Core/Py.jl:339 [inlined] [7] log(lg::WandbLogger, logs::Dict{String, PythonCall.Core.Py}; kwargs::@Kwargs{}) @ Wandb ~/.julia/packages/Wandb/jByAm/src/main.jl:69 [8] top-level scope @ REPL[10]:1 ```

Note that everything works fine if I don't import any plotting packages.

Minimal example to reproduce the error:

using Wandb, Plots

lg = WandbLogger(project="dummyproject")

x = collect(1.0:20.0)
y = cumsum(rand(20))
s = ones(20)

table = Wandb.Table(data=[x;;y;;s], columns=["Frequency", "FSC", "stroke"])
plt = Wandb.plot_line(table, "Frequency", "FSC", "stroke", "Fourier Shell Correlation")
Wandb.log(lg, Dict("FSC plot" => plt))

close(lg)

versioninfo

julia> versioninfo() Julia Version 1.10.2 Commit bd47eca2c8a (2024-03-01 10:14 UTC) Build Info: Official https://julialang.org/ release Platform Info: OS: Linux (x86_64-linux-gnu) CPU: 8 × 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, tigerlake) Threads: 1 default, 0 interactive, 1 GC (on 8 virtual cores) Environment: JULIA_CONDAPKG_BACKEND = System

[avik-pal]

What happens if you use the default CondaPkg settings (without using system python)? Atleast with CairoMakie, I don't seem to get any issues.

Also maybe use python 3.11 instead of 3.12, quite a few packages have compatibility issues with 3.12 afaik.

[trahflow]

What happens if you use the default CondaPkg settings (without using system python)? Atleast with CairoMakie, I don't seem to get any issues.

Ok I've tried different combinations of CondaPkg backends (System as well as MicroMamba) and Plots and CairoMakie and all seem to work now. Not sure what has fixed this or why the problem appeared in the first place, but it works now :)