Various installation issues

[TheLemonPig]

I had been struggling to get PySR working in most environments but was successful in running the Google Colab tutorial. I was hoping to migrate the functionality of the first block of code out of Google Colab into a python or .pytoml file in order to run PySR outside of the Google Colab environment. However I have been struggling understand what the block of code does to make PySR work.

!echo "Runtime started."

%%shell
set -e

#---------------------------------------------------#
JULIA_VERSION="1.7.2"
JULIA_NUM_THREADS=4
export JULIA_PKG_PRECOMPILE_AUTO=0
#---------------------------------------------------#

if [ -z `which julia` ]; then
  # Install Julia
  JULIA_VER=`cut -d '.' -f -2 <<< "$JULIA_VERSION"`
  echo "Installing Julia $JULIA_VERSION on the current Colab Runtime..."
  BASE_URL="https://julialang-s3.julialang.org/bin/linux/x64"
  URL="$BASE_URL/$JULIA_VER/julia-$JULIA_VERSION-linux-x86_64.tar.gz"
  wget -nv $URL -O /tmp/julia.tar.gz # -nv means "not verbose"
  tar -x -f /tmp/julia.tar.gz -C /usr/local --strip-components 1
  rm /tmp/julia.tar.gz

  echo "Installing PyCall.jl..."
  julia -e 'using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
  julia -e 'println("Success")'

fi

Doing this Google Colab specific task was also necessary:
" Use fallback runtime. Run the above cell (!echo "Runtime started.") to start the runtime. Now, open the command pallette (bottom left -> second icon from the bottom), and search for "use fallback runtime", and hit enter. "

[MilesCranmer]

This block of code is colab-specific. It installs Julia within Google Colab, because their VM (based on Ubuntu) doesn't include Julia by default. Note that Google Colab runs in the cloud, rather than on your local machine – so even if Julia is installed locally, it still needs to be installed on the colab VM.

Doing this Google Colab specific task was also necessary:
" Use fallback runtime. Run the above cell (!echo "Runtime started.") to start the runtime. Now, open the command pallette (bottom left -> second icon from the bottom), and search for "use fallback runtime", and hit enter. "

This actually changed only 2 hours ago! See googlecolab/colabtools#3385. I need to update the colab notebook to remove that part, as you have noted 🙂

I had been struggling to get PySR working in most environments but was successful in running the Google Colab tutorial.

Please share where you are struggling and I can try to help

---

Edit: updated the notebook.

[TheLemonPig]

Building PyCall → ~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/62f417f6ad727987c755549e9cd88c46578da562/build.log
ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.

The python executable we tried was /Users/joshuahewson/Developer/venvs/pysrvenv/bin/python (= version 3.10).
Re-building with
ENV["PYCALL_DEBUG_BUILD"] = "yes"
may provide extra information for why it failed.

Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] find_libpython(python::String; _dlopen::typeof(Base.Libc.Libdl.dlopen))
@ Main ~/.julia/packages/PyCall/twYvK/deps/buildutils.jl:72
[3] find_libpython(python::String)
@ Main ~/.julia/packages/PyCall/twYvK/deps/buildutils.jl:40
[4] top-level scope
@ ~/.julia/packages/PyCall/twYvK/deps/build.jl:82
[5] include(fname::String)
@ Base.MainInclude ./client.jl:476
[6] top-level scope
@ none:5
in expression starting at /Users/joshuahewson/.julia/packages/PyCall/twYvK/deps/build.jl:43
ERROR: LoadError: Error building PyCall:

Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67
[2] (::Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String})()
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1060
[3] withenv(::Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
@ Base ./env.jl:172
[4] (::Pkg.Operations.var"#107#112"{String, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec})()
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1619
[5] with_temp_env(fn::Pkg.Operations.var"#107#112"{String, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec}, temp_env::String)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1493
[6] (::Pkg.Operations.var"#105#110"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1582
[7] mktempdir(fn::Pkg.Operations.var"#105#110"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String)
@ Base.Filesystem ./file.jl:764
[8] mktempdir(fn::Function, parent::String) (repeats 2 times)
@ Base.Filesystem ./file.jl:760
[9] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1540
[10] build_versions(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}; verbose::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1041
[11] build(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}, verbose::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:898
[12] build(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; verbose::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:1029
[13] build(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:verbose,), Tuple{Bool}}})
@ Pkg.API ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:156
[14] #build#99
@ ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:144 [inlined]
[15] #build#98
@ ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:143 [inlined]
[16] build_pycall()
@ Main ~/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:54
[17] top-level scope
@ ~/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:115
in expression starting at /Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:73
Traceback (most recent call last):
File "", line 1, in
File "/Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/pysr/julia_helpers.py", line 84, in install
julia.install(quiet=quiet)
File "/Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/tools.py", line 118, in install
raise PyCallInstallError("Installing", output)
julia.tools.PyCallInstallError: Installing PyCall failed.

** Important information from Julia may be printed before Python's Traceback **

Some useful information may also be stored in the build log file
~/.julia/packages/PyCall/*/deps/build.log.

[MilesCranmer]

Very strange...

Can you try to delete your entire ~/.julia and then re-run the installation?

[TheLemonPig]

Same output unfortunately

[MilesCranmer]

It looks like the error:

 ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.

relates to it not being able to find libpython.dylib or libpython.so. Can you check if you have one of those?

[TheLemonPig]

I don't seem to have either one of those in my entire computer. Definitely not within the virtual environment I am working :/