# Errors Using PythonCall.jl and PythonPlot.jl with a Python Virtual Environment

**URL:** https://discourse.julialang.org/t/errors-using-pythoncall-jl-and-pythonplot-jl-with-a-python-virtual-environment/124084
**Category:** General Usage
**Tags:** question, plotting, python, pythoncall, pythonplot
**Created:** [December 22, 2024, 4:45am UTC](https://discourse.julialang.org/t/errors-using-pythoncall-jl-and-pythonplot-jl-with-a-python-virtual-environment/124084 "2024-12-22T04:45:23Z")
**Posts on this page:** 3
**Page:** 1

<div class="post-metadata">

### Author: ![ericdammannjr](https://avatars.discourse-cdn.com/v4/letter/e/a4c791/32.png) [@ericdammannjr](https://discourse.julialang.org/u/ericdammannjr)
#### Post date: [December 22, 2024, 4:45am UTC](https://discourse.julialang.org/t/errors-using-pythoncall-jl-and-pythonplot-jl-with-a-python-virtual-environment/124084/1 "2024-12-22T04:45:23Z")

</div>

I really have been struggling with this issue and not sure what to do. For context, I have a brand-new Windows PC, and I have `Julia 1.11.2` and `Python 3.13.1` installed on it. I did the following:

I created a Python virtual environment (in a PowerShell Terminal with PowerShell version `5.1.22621.4391`) called `venv_1` with `venv` (the virtual environment manager that comes with Python) in the following directory:

```julia
"C:\Research Software\Python\Virtual Environments\venv_1"

```

I then activated the Python virtual environment and did:

```julia
pip install numpy
pip install matplotlib

```

When I do `pip list` in the Python virtual environment, I get the following output:

```julia
Package Version
--------------- -----------
contourpy 1.3.1
cycler 0.12.1
fonttools 4.55.3
kiwisolver 1.4.7
matplotlib 3.10.0
numpy 2.2.1
packaging 24.2
pillow 11.0.0
pip 24.3.1
pyparsing 3.2.0
python-dateutil 2.9.0.post0
six 1.17.0

```

I then created a Julia virtual environment called `venv_1` in the following directory:

```julia
"C:\Research Software\Julia\Virtual Environments\venv_1"

```

I then activated the Julia virtual environment and did:

```julia
Pkg.add("Plots.jl")
Pkg.add("PythonCall.jl")
Pkg.add("PythonPlot.jl")

```

I then added the following lines of code to my `startup.jl` file located at `"~\.julia\config\startup.jl"`:

```julia
ENV["JULIA_CONDAPKG_BACKEND"]="Null"
ENV["JULIA_PYTHONCALL_EXE"]=raw"C:/Research Software/Python/Virtual Environments/venv_1/Scripts/python.exe"

```

Here is where the issue arises. When I run the following Julia script (called `test_script.jl`):

```julia
using Plots
pythonplot()

x = [1,2,3,4,5]
y = x

plot(x,y)

```

I get the following error:

```julia
ERROR: InitError: PythonCall.Core.PyException(PythonCall.Core.Py(Ptr{PythonCall.C.PyObject} @0x00007ffe22ec7f20), PythonCall.Core.Py(Ptr{PythonCall.C.PyObject} @0x000002d8339cd6c0), PythonCall.Core.Py(Ptr{PythonCall.C.PyObject} @0x000002d833a24480), false)
Stacktrace:
  [1] pythrow()
    @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:92
  [2] errcheck
    @ C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:10 [inlined]
  [3] pyimport(m::String)
    @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\builtins.jl:1561
  [4] __init__ ()
    @ PythonPlot C:\Users\ericd\.julia\packages\PythonPlot\469aA\src\init.jl:150
  [5] run_module_init(mod::Module, i::Int64)
    @ Base .\loading.jl:1378
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1366
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{…}, ignore_native::Nothing; register::Bool)
    @ Base .\loading.jl:1254
  [8] _include_from_serialized (repeats 2 times)
    @ .\loading.jl:1210 [inlined]
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{…}, DEPOT_PATH::Vector{…})
    @ Base .\loading.jl:2057
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2527
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2388
 [12] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [13] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2375
 [15] macro expansion
    @ .\loading.jl:2314 [inlined]
 [16] macro expansion
    @ .\lock.jl:273 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2271
 [18] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [19] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2260
 [21] top-level scope
    @ C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:1074
during initialization of module PythonPlot
Some type information was truncated. Use `show(err)` to see complete types.

```

When I then type `show(err)`, the following is displayed:

```julia
1-element ExceptionStack:
LoadError: InitError: Python: ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
Python stacktrace:
 [1] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\numpy\ __init__.py:132
 [2] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\matplotlib\cbook.py:24
 [3] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\matplotlib\ __init__.py:161
Stacktrace:
  [1] pythrow()
    @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:92
  [2] errcheck
    @ C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:10 [inlined]
  [3] pyimport(m::String)
    @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\builtins.jl:1561
  [4] __init__ ()
    @ PythonPlot C:\Users\ericd\.julia\packages\PythonPlot\469aA\src\init.jl:150
  [5] run_module_init(mod::Module, i::Int64)
    @ Base .\loading.jl:1378
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1366
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any}, ignore_native::Nothing; register::Bool)
    @ Base .\loading.jl:1254
  [8] _include_from_serialized (repeats 2 times)
    @ .\loading.jl:1210 [inlined]
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})
    @ Base .\loading.jl:2057
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:2527
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2388
 [12] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [13] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:2375
 [15] macro expansion
    @ .\loading.jl:2314 [inlined]
 [16] macro expansion
    @ .\lock.jl:273 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2271
 [18] #invoke_in_world#3
    @ .\essentials.jl:1089 [inlined]
 [19] invoke_in_world
    @ .\essentials.jl:1086 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:2260
 [21] top-level scope
    @ C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:1074
 [22] eval
    @ .\boot.jl:430 [inlined]
 [23] _initialize_backend(pkg::Plots.PythonPlotBackend)
    @ Plots C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:1073
 [24] backend(pkg::Plots.PythonPlotBackend)
    @ Plots C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:245
 [25] pythonplot()
    @ Plots C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:86
 [26] top-level scope
    @ c:\Examples\test_script.jl:2
 [27] eval
    @ .\boot.jl:430 [inlined]
 [28] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base .\loading.jl:2734
 [29] include_string(m::Module, txt::String, fname::String)
    @ Base .\loading.jl:2744
 [30] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
    @ Base .\essentials.jl:1055
 [31] invokelatest(::Any, ::Any, ::Vararg{Any})
    @ Base .\essentials.jl:1052
 [32] inlineeval(m::Module, code::String, code_line::Int64, code_column::Int64, file::String; softscope::Bool)
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:271
 [33] (::VSCodeServer.var"#69#74"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:181
 [34] withpath(f::VSCodeServer.var"#69#74"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams}, path::String)
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\repl.jl:276
 [35] (::VSCodeServer.var"#68#73"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:179
 [36] hideprompt(f::VSCodeServer.var"#68#73"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\repl.jl:38
 [37] #67
    @ c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:150 [inlined]
 [38] with_logstate(f::VSCodeServer.var"#67#72"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams}, logstate::Base.CoreLogging.LogState)
    @ Base.CoreLogging .\logging\logging.jl:522
 [39] with_logger
    @ .\logging\logging.jl:632 [inlined]
 [40] (::VSCodeServer.var"#66#71"{VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:263
 [41] #invokelatest#2
    @ .\essentials.jl:1055 [inlined]
 [42] invokelatest(::Any)
    @ Base .\essentials.jl:1052
 [43] (::VSCodeServer.var"#64#65")()
    @ VSCodeServer c:\Users\ericd\.vscode\extensions\julialang.language-julia-1.127.2\scripts\packages\VSCodeServer\src\eval.jl:34
during initialization of module PythonPlot
in expression starting at c:\Examples\test_script.jl:2

```

If I run `test_script.jl` again in the same Julia session, the following error is returned:

```julia
┌ Warning: You are using Matplotlib 0.0.0, which is no longer
│ officially supported by the Plots community. To ensure smooth Plots.jl
│ integration update your Matplotlib library to a version ≥ 3.4.0
└ @ Plots C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends\pythonplot.jl:12
┌ Warning: You are using Matplotlib 0.0.0, which is no longer
│ officially supported by the Plots community. To ensure smooth Plots.jl
│ integration update your Matplotlib library to a version ≥ 3.4.0
└ @ Plots C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends\pythonplot.jl:12
ERROR: Python: ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
Python stacktrace:
 [1] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\numpy\ __init__.py:132
 [2] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\matplotlib\cbook.py:24
 [3] <module>
   @ C:\Research Software\Python\Virtual Environments\venv_1\Lib\site-packages\matplotlib\ __init__.py:161
Stacktrace:
 [1] pythrow()
   @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:92
 [2] errcheck
   @ C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\err.jl:10 [inlined]
 [3] pyimport(m::String)
   @ PythonCall.Core C:\Users\ericd\.julia\packages\PythonCall\Nr75f\src\Core\builtins.jl:1561
 [4] top-level scope
   @ C:\Users\ericd\.julia\packages\Plots\Ec1L1\src\backends.jl:1055

```

To see if the issue was (exclusively) with my Python installation, I created the following Python script called `test_script.py` and ran it with the Python interpreter found in the `venv_1` python virtual environment:

```julia
import numpy as np
import matplotlib.pyplot at plt

x = np.array([1,2,3,4,5])
y = x 

plt.plot(x,y)

plt.show()

```

This script ran perfectly fine. I am not sure what the issue is. I specifically would like to understand the following and how it can be resolved.

```julia
Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

```

Any help is greatly appreciated!

(I recently posted another post with respect to PyCall.jl and PyPlot.jl. This issue is similar but not identical, so I figured this post was warranted.)

---

<div class="post-metadata">

### Author: ![eldee](https://avatars.discourse-cdn.com/v4/letter/e/b5a626/32.png) [@eldee](https://discourse.julialang.org/u/eldee)
#### Post date: [December 22, 2024, 2:05pm UTC](https://discourse.julialang.org/t/errors-using-pythoncall-jl-and-pythonplot-jl-with-a-python-virtual-environment/124084/2 "2024-12-22T14:05:23Z")

</div>

Hi,

the PythonCall.jl equivalent of [the explicit adding of `site-packages`](https://discourse.julialang.org/t/error-with-importing-matplotlib-pyplot-for-use-with-pycall-jl/124062/5) also seems to work here:

```julia
ENV["JULIA_PYTHONCALL_EXE"] = "C:/Research Software/Python/Virtual Environments/venv_1/Scripts/python.exe"
ENV["JULIA_CONDAPKG_BACKEND"] = "Null"
using Pkg
Pkg.add("PythonCall")
using PythonCall
pyimport("site").addsitedir("C:/Research Software/Python/Virtual Environments/venv_1/Lib/site-packages")
# Alternatively, pyimport("sys").path.insert(0, "C:/Research Software/Python/Virtual Environments/venv_1/Lib/site-packages") also seems to work.
# It's probably safest to add to both site and path.
Pkg.add("PythonPlot")
Pkg.add("Plots")

using Plots
pythonplot()

x = [1,2,3,4,5]
y = x

plot(x,y)
```

---

<div class="post-metadata">

### Author: ![ericdammannjr](https://avatars.discourse-cdn.com/v4/letter/e/a4c791/32.png) [@ericdammannjr](https://discourse.julialang.org/u/ericdammannjr)
#### Post date: [December 22, 2024, 8:40pm UTC](https://discourse.julialang.org/t/errors-using-pythoncall-jl-and-pythonplot-jl-with-a-python-virtual-environment/124084/3 "2024-12-22T20:40:02Z")

</div>

Thank you very much. This worked for me.