error using development version of package

[lmiq]

I am getting this error when trying to use a development version of a package:

In [6]: jl.Pkg.develop("CellListMap")                                                                 
   Resolving package versions...
    Updating `~/.julia/environments/PythonCall/Project.toml`
  [69e1c6dd] + CellListMap v0.7.0-DEV `~/.julia/dev/CellListMap`
    Updating `~/.julia/environments/PythonCall/Manifest.toml`
  [a4c015fc] + ANSIColoredPrinters v0.0.1
  [69e1c6dd] + CellListMap v0.7.0-DEV `~/.julia/dev/CellListMap`
  [187b0558] + ConstructionBase v1.3.0
  [ffbed154] + DocStringExtensions v0.8.6
  [e30172f5] + Documenter v0.27.10
  [b5f81e59] + IOCapture v0.2.2
  [bac558e1] + OrderedCollections v1.4.1
  [d96e819e] + Parameters v0.12.3
  [92933f4c] + ProgressMeter v1.7.1
  [efcf1570] + Setfield v0.7.1
  [90137ffa] + StaticArrays v1.2.13
  [3a884ed6] + UnPack v1.0.2
  [8ba89e20] + Distributed
  [9fa8497b] + Future
  [2f01184e] + SparseArrays
  [10745b16] + Statistics

In [7]: jl.seval("using CellListMap")                                                                 
---------------------------------------------------------------------------
JuliaError                                Traceback (most recent call last)
<ipython-input-7-53a2dfd17fba> in <module>
----> 1 jl.seval("using CellListMap")

~/.local/lib/python3.8/site-packages/juliacall/__init__.py in seval(self, expr)

JuliaError: MethodError: no method matching rawhandle(::PythonCall.PyIO)
Closest candidates are:
  rawhandle(!Matched::Base.LibuvStream) at ~/programs/julia/julia-1.7.0/share/julia/base/stream.jl:285
  rawhandle(!Matched::Base.Filesystem.File) at ~/programs/julia/julia-1.7.0/share/julia/base/filesystem.jl:94
  rawhandle(!Matched::Base.DevNull) at ~/programs/julia/julia-1.7.0/share/julia/base/cmd.jl:163
  ...

There is no error if using one stable version from the repo:

In [8]: jl.Pkg.rm("CellListMap")                                                                      
    Updating `~/.julia/environments/PythonCall/Project.toml`
  [69e1c6dd] - CellListMap v0.7.0-DEV `~/.julia/dev/CellListMap`
    Updating `~/.julia/environments/PythonCall/Manifest.toml`
  [a4c015fc] - ANSIColoredPrinters v0.0.1
  [69e1c6dd] - CellListMap v0.7.0-DEV `~/.julia/dev/CellListMap`
  [187b0558] - ConstructionBase v1.3.0
  [ffbed154] - DocStringExtensions v0.8.6
  [e30172f5] - Documenter v0.27.10
  [b5f81e59] - IOCapture v0.2.2
  [bac558e1] - OrderedCollections v1.4.1
  [d96e819e] - Parameters v0.12.3
  [92933f4c] - ProgressMeter v1.7.1
  [efcf1570] - Setfield v0.7.1
  [90137ffa] - StaticArrays v1.2.13
  [3a884ed6] - UnPack v1.0.2
  [8ba89e20] - Distributed
  [9fa8497b] - Future
  [2f01184e] - SparseArrays
  [10745b16] - Statistics

In [9]: jl.Pkg.add("CellListMap")                                                                     
    Updating registry at `~/.julia/registries/General.toml`
   Resolving package versions...
    Updating `~/.julia/environments/PythonCall/Project.toml`
  [69e1c6dd] + CellListMap v0.6.7
    Updating `~/.julia/environments/PythonCall/Manifest.toml`
  [69e1c6dd] + CellListMap v0.6.7
  [187b0558] + ConstructionBase v1.3.0
  [ffbed154] + DocStringExtensions v0.8.6
  [bac558e1] + OrderedCollections v1.4.1
  [d96e819e] + Parameters v0.12.3
  [92933f4c] + ProgressMeter v1.7.1
  [efcf1570] + Setfield v0.7.1
  [90137ffa] + StaticArrays v1.2.13
  [3a884ed6] + UnPack v1.0.2
  [8ba89e20] + Distributed
  [9fa8497b] + Future
  [2f01184e] + SparseArrays
  [10745b16] + Statistics

In [10]: jl.seval("using CellListMap")                                                                

In [11]:       

[cjdoris]

Curious bug! I can't reproduce it myself.

From the presence of PyIO in the error, I'm guessing you're using JuliaCall from IPython? If so, doing the following may work around the issue:

jl.PythonCall.CONFIG.auto_ipython_display = False

(By default if PythonCall detects you're in IPython, it changes Julia's Base.stdout to point to Python's sys.stdout so that Julia output appears in IPython, but this is a somewhat experimental feature.)

It seems a bit like a bug in Julia though - somewhere some code is assuming that Base.stdout is a certain kind of IO object. Can you please do the following to figure out where the error is (I haven't yet got Python to show the stacktrace of Julia exceptions)?

jl.seval('try; using CellListMap; catch e; (e, stacktrace(catch_backtrace())); end')

[cjdoris]

Ok I know what the bug is. I need to remove this stdout override.

[cjdoris]

Fixed on master.