Doctests fail if CondaPkg is not installed

[Robbybp]

When trying to run the tests with julia --project=test test/runtests.jl, I get a long error message at the Doctest step:

[ Info: Doctest: running doctests.                                                                                                                                                                                               12:44:06 [384/9299]
┌ Error: doctest failure in ~/research/upstream-dev/MathOptAI.jl/src/predictors/PytorchModel.jl:12-16                     
│                                                                                                                         
│ ```jldoctest                                                                                                            
│ julia> using PythonCall, MathOptAI                                                                                                                                                                                                                
│                                                                                                                         
│ julia> ml_model = PytorchModel("model.pt");                                                                             
│ ```                                                                                                                     
│                                                                                                                         
│ Subexpression:                                                                                                          
│                                                                                                                                                                                                                                                   
│ using PythonCall, MathOptAI                                                                                             
│                                                                                                                                                                                                                                                   
│ Evaluated output:                                                                                                       
│                                                                                                                         
│     CondaPkg Found dependencies: /Users/rbparker/.julia/packages/PythonCall/flx5V/CondaPkg.toml                         
│     CondaPkg Resolving changes                                                                                          
│              ~ python                                                                                                   
│              - torch (pip)                                                                                              
│     CondaPkg Removing Pip packages                                                                                      
│              │ /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env/bin/pip                            
│              │ uninstall                                                                                                
│              │ -y                                                                                                                                                                                                                                 
│              └ torch                                                                                                                                                                                                                              
│ Found existing installation: torch 2.4.0                                                                                
│ Uninstalling torch-2.4.0:                                                                                               
│   Successfully uninstalled torch-2.4.0                                                                                  
│     CondaPkg Installing packages                                                                                        
│              │ /Users/rbparker/.julia/artifacts/98aba21a6802e06a5d2e7c48633d7dc1c3d4a749/bin/micromamba                 
│              │ -r /Users/rbparker/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root                        
│              │ install                                                                                                  
│              │ -y                                                                                                       
│              │ -p /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                                                                                                                                                           
│              │ --override-channels                         
│              │ --no-channel-priority                                                                                    
│              │ openssl[version='>=3, <3.1']                                                                             
│              │ python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']                                       
│              └ -c conda-forge                                                                                           
│ conda-forge/osx-arm64                                       Using cache                                                 
│ conda-forge/noarch                                          Using cache                                                 
│                                                                                                                         
│ Transaction                                                                                                             
│                                                                                                                         
│   Prefix: /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                                         
│                                                                                                                                                                                                                                                   
│   Updating specs:                                                                                                       
│                                                                                                                         
│    - openssl[version='>=3, <3.1']                                                                                       
│    - conda-forge::python[version='>=3.8,<4',build=*cpython*]                                                            
│                                                                                                                         
│                                                                                                                                                                                                                                                   
│   Package   Version  Build               Channel           Size                                                         
│ ─────────────────────────────────────────────────────────────────                                                                                                                                                                                 
│   Reinstall:                                                                                                            
│ ─────────────────────────────────────────────────────────────────                                                       
│                                                                                                                         
│   o python   3.11.0  h3ba56d0_1_cpython  conda-forge     Cached                                                         
│                                                                                                                         
│   Summary:                                                                                                              
│                                                                                                                         
│   Reinstall: 1 packages                                                                                                 
│                                                                                                                         
│   Total download: 0 B                                                                                                                                                                                                                             
│                                                                                                                                                                                                                                                   
│ ─────────────────────────────────────────────────────────────────                                                       
│                                                            
│                                                            
│                                                            
│ Transaction starting                                       
│ Reinstalling python-3.11.0-h3ba56d0_1_cpython              
│                                                            
│ Transaction finished                                       
│                                                            
│ To activate this environment, use:                         
│                                                            
│     micromamba activate /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                           
│                                                            
│ Or to execute a single command in this environment, use:   
│                                                            
│     micromamba run -p /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env mycommand                   
│                                                            
│ Expected output:                                           
│                                                            
│                                                            
│                                                            
│   diff =                                                   
│        CondaPkg Found dependencies: /Users/rbparker/.julia/packages/PythonCall/flx5V/CondaPkg.toml                      
│        CondaPkg Resolving changes                          
│                 ~ python                                   
│                 - torch (pip)                              
│        CondaPkg Removing Pip packages                      
│                 │ /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env/bin/pip                         
│                 │ uninstall                                
│                 │ -y                                       
│                 └ torch                                    
│    Found existing installation: torch 2.4.0                
│    Uninstalling torch-2.4.0:                               
│      Successfully uninstalled torch-2.4.0                  
│        CondaPkg Installing packages                        
│                 │ /Users/rbparker/.julia/artifacts/98aba21a6802e06a5d2e7c48633d7dc1c3d4a749/bin/micromamba              
│                 │ -r /Users/rbparker/.julia/scratchspaces/0b3b1443-0f03-428d-bdfb-f27f9c1191ea/root                     
│                 │ install                                  
│                 │ -y                                       
│                 │ -p /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                              
│                 │ --override-channels                      
│                 │ --no-channel-priority                    
│                 │ openssl[version='>=3, <3.1']             
│                 │ python[version='>=3.8,<4',channel='conda-forge',build='*cpython*']                                    
│                 └ -c conda-forge                           
│    conda-forge/osx-arm64                                       Using cache                                              
│    conda-forge/noarch                                          Using cache                                              
│                                                            
│    Transaction                                             
│                                                            
│      Prefix: /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                                      
│                                                            
│      Updating specs:                                       
│                                                            
│       - openssl[version='>=3, <3.1']                       
│       - conda-forge::python[version='>=3.8,<4',build=*cpython*]                                                         
│                                                            
│                                                            
│      Package   Version  Build               Channel           Size                                                      
│    ─────────────────────────────────────────────────────────────────                                                    
│      Reinstall:                                            
│    ─────────────────────────────────────────────────────────────────                                                    
│                                                            
│      o python   3.11.0  h3ba56d0_1_cpython  conda-forge     Cached                                                      
│                                                            
│      Summary:                                              
│                                                            
│      Reinstall: 1 packages                                 
│                                                            
│      Total download: 0 B                                   
│                                                            
│    ─────────────────────────────────────────────────────────────────                                                    
│                                                            
│                                                            
│                                                            
│    Transaction starting                                    
│    Reinstalling python-3.11.0-h3ba56d0_1_cpython           
│                                                            
│    Transaction finished                                    
│                                                                                                                                                                                                                                                   
│    To activate this environment, use:                                                                                                                                                                                                             
│                                                            
│        micromamba activate /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env                        
│                                                                                                                         
│    Or to execute a single command in this environment, use:                                                             
│                                                                                                                         
│        micromamba run -p /Users/rbparker/research/upstream-dev/MathOptAI.jl/test/.CondaPkg/env mycommand                
└ @ Documenter ~/research/upstream-dev/MathOptAI.jl/src/predictors/PytorchModel.jl:12                                     
┌ Error: Doctesting failed                                   
│   exception =                                              
│    `makedocs` encountered a doctest error. Terminating build                                                            
│    Stacktrace:                                             
│      [1] error(s::String)                                  
│        @ Base ./error.jl:35                                
│      [2] runner(::Type{Documenter.Builder.Doctest}, doc::Documenter.Document)                                           
│        @ Documenter ~/.julia/packages/Documenter/qoyeC/src/builder_pipeline.jl:212                                      
│      [3] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document)                                  
│        @ Documenter.Selectors ~/.julia/packages/Documenter/qoyeC/src/utilities/Selectors.jl:170                         
│      [4] #86                                                                                                            
│        @ ~/.julia/packages/Documenter/qoyeC/src/makedocs.jl:248 [inlined]                                               
│      [5] withenv(::Documenter.var"#86#88"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}})
│        @ Base ./env.jl:257                                                                                              
│      [6] #85                                               
│        @ ~/.julia/packages/Documenter/qoyeC/src/makedocs.jl:247 [inlined]                                               
│      [7] cd(f::Documenter.var"#85#87"{Documenter.Document}, dir::String)                                                
│        @ Base.Filesystem ./file.jl:112                     
│      [8] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{root::String, source::String, sitename::String, doctest::Symbol, modules::Vector{Module}, doctestfilters::Vector{Regex}, remotes::Nothing, plugins::Vector{Do
cumenter.Plugin}})                                           
│        @ Documenter ~/.julia/packages/Documenter/qoyeC/src/makedocs.jl:247                                              
│      [9] (::Documenter.var"#all_doctests#131"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Vector{Module}})()        
│        @ Documenter ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:82                                                
│     [10] macro expansion                                                                                                
│        @ ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:107 [inlined]                                                
│     [11] macro expansion                                   
│        @ ~/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined] 
│     [12] macro expansion                                   
│        @ ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:107 [inlined]                                                
│     [13] macro expansion                                   
│        @ ~/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] 
│     [14] doctest(source::Nothing, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin})
│        @ Documenter ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:107                                               
│     [15] doctest                                           
│        @ ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:66 [inlined]                                                 
│     [16] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{})                                    
│        @ Documenter ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:34                                                
│     [17] macro expansion                                   
│        @ ~/research/upstream-dev/MathOptAI.jl/test/runtests.jl:19 [inlined]                                             
│     [18] macro expansion                                   
│        @ ~/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] 
│     [19] top-level scope                                   
│        @ ~/research/upstream-dev/MathOptAI.jl/test/runtests.jl:19                                                       
│     [20] include(mod::Module, _path::String)               
│        @ Base ./Base.jl:495                                
│     [21] exec_options(opts::Base.JLOptions)                
│        @ Base ./client.jl:318                              
│     [22] _start()                                          
│        @ Base ./client.jl:552                              
└ @ Documenter ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:96                                                       
Doctests: MathOptAI: Test Failed at /Users/rbparker/.julia/packages/Documenter/qoyeC/src/doctest.jl:107                   
  Expression: all_doctests()                                 

Stacktrace:                                                  
 [1] macro expansion                                         
   @ ~/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined]       
 [2] macro expansion                                         
   @ ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:107 [inlined]                                                      
 [3] macro expansion                                         
   @ ~/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]      
 [4] doctest(source::Nothing, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin})
   @ Documenter ~/.julia/packages/Documenter/qoyeC/src/doctest.jl:107                                                     
Test Summary:         | Fail  Total   Time                   
Docstrings            |    1      1  14.1s                   
  Doctests: MathOptAI |    1      1  13.9s                   
ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken.                                       

This goes away if I install CondaPkg in the test environment. My test/Project.toml is then:

diff --git a/test/Project.toml b/test/Project.toml
index d292d27..d851cbd 100644
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DecisionTree = "7806a523-6efd-50cb-b5f6-3fa6f1930dbb"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"

However, the offending line (using PythonCall, MathOptAI, I think) works fine in julia --project=test without CondaPkg explicitly installed. Not sure what's going on here. Feel free to close if there's nothing to be done, but thought I'd open in case this happens to someone else.

[odow]

Hmm. Not sure. It all works for me locally. But this will be much easier to diagnose once the repo is public and we can setup CI etc.