test MFGnet fails because Test is missing in Project.toml

[finmod]

Nice package and acquisition to Julia.
Immediately after installing MFGnet.jl, I tried to Pkg> test MFGnet
It produces the following error:

           _

_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.3.1 (2019-12-30)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

(v1.3) pkg> test MFGnet
Testing MFGnet
Status C:\Users\Denis\AppData\Local\Temp\jl_oAcD2q\Manifest.toml
[621f4979] AbstractFFTs v0.5.0
[1520ce14] AbstractTrees v0.2.1
[79e6a3ab] Adapt v1.0.0
[b99e7846] BinaryProvider v0.5.8
[944b1d66] CodecZlib v0.6.0
[3da002f7] ColorTypes v0.9.0
[5ae59095] Colors v0.11.2
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.2.0
[9a962f9c] DataAPI v1.1.0
[864edb3b] DataStructures v0.17.7
[163ba53b] DiffResults v0.0.4
[b552c78f] DiffRules v1.0.0
[7a1cc6ca] FFTW v1.2.0
[f5851436] FFTW_jll v3.3.9+3
[1a297f60] FillArrays v0.8.2
[53c48c17] FixedPointNumbers v0.6.1
[587475ba] Flux v0.8.3
[f6369f11] ForwardDiff v0.10.8
[7869d1d1] IRTools v0.3.0
[1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
[e5e0dc1b] Juno v0.7.2
[97b447e0] MFGnet v0.0.3 #master (https://github.com/EmoryMLIP/MFGnet.jl)
[856f044c] MKL_jll v2019.0.117+0
[1914dd2f] MacroTools v0.5.3
[e89f7d12] Media v0.5.0
[e1d29d7a] Missings v0.4.3
[872c559c] NNlib v0.6.2
[77ba4419] NaNMath v0.3.3
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[bac558e1] OrderedCollections v1.1.0
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[9f7883ad] Tracker v0.2.6
[3bb67fe8] TranscodingStreams v0.9.5
[a5390f91] ZipFile v0.9.0
[83775a58] Zlib_jll v1.2.11+7
[e88e6eb3] Zygote v0.4.4
[700de1a5] ZygoteRules v0.2.0
[2a0f44e3] Base64 [@stdlib/Base64]
[ade2ca70] Dates [@stdlib/Dates]
[8bb1440f] DelimitedFiles [@stdlib/DelimitedFiles]
[8ba89e20] Distributed [@stdlib/Distributed]
[b77e0a4c] InteractiveUtils [@stdlib/InteractiveUtils]
[76f85450] LibGit2 [@stdlib/LibGit2]
[8f399da3] Libdl [@stdlib/Libdl]
[37e2e46d] LinearAlgebra [@stdlib/LinearAlgebra]
[56ddb016] Logging [@stdlib/Logging]
[d6f4376e] Markdown [@stdlib/Markdown]
[a63ad114] Mmap [@stdlib/Mmap]
[44cfe95a] Pkg [@stdlib/Pkg]
[de0858da] Printf [@stdlib/Printf]
[9abbd945] Profile [@stdlib/Profile]
[3fa0cd96] REPL [@stdlib/REPL]
[9a3f8284] Random [@stdlib/Random]
[ea8e919c] SHA [@stdlib/SHA]
[9e88b42a] Serialization [@stdlib/Serialization]
[1a1011a3] SharedArrays [@stdlib/SharedArrays]
[6462fe0b] Sockets [@stdlib/Sockets]
[2f01184e] SparseArrays [@stdlib/SparseArrays]
[10745b16] Statistics [@stdlib/Statistics]
[8dfed614] Test [@stdlib/Test]
[cf7118a7] UUIDs [@stdlib/UUIDs]
[4ec0a83e] Unicode [@stdlib/Unicode]
ERROR: LoadError: ArgumentError: Package Test not found in current path:

• Run import Pkg; Pkg.add("Test") to install the Test package.

Stacktrace:
[1] require(::Module, ::Symbol) at .\loading.jl:887
[2] include at .\boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at .\loading.jl:1105
[4] include(::Module, ::String) at .\Base.jl:31
[5] include(::String) at .\client.jl:424
[6] top-level scope at none:6
in expression starting at C:\Users\Denis.julia\packages\MFGnet\p0gHj\test\runtests.jl:1
ERROR: Package MFGnet errored during testing

(v1.3) pkg>

[finmod]

Let me add that in the same Project.toml file, Revise.jl should be added as a [deps]. Then Pkg> test MFGnet passes.

[finmod]

@lruthotto Noted your update of Project and Manifest. However, Pkg> test MFGnet still errors because
the Project.toml should read something like this:

[compat]
julia = "1.2"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Test"]

With these additions, Pkg> test MFGnet passes and this issue can be closed.

[lruthotto]

Yes, I've been starting to implement your changes. Thanks btw for starting this issue. Will do the others later.

[finmod]

With the latest commit, an issue remains with the compatibility of various packages: Flux#master, Tracker, Zygote etc. This is a bit strange because at first test MFGnet passed. After restart, update and build the error message is:

           _

_ _ ()_ | Documentation: https://docs.julialang.org
() | () () |
_ _ | | __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 1.3.1 (2019-12-30)
/ |_'|||_'_| | Official https://julialang.org/ release
|__/ |

(v1.3) pkg> test MFGnet
Testing MFGnet
Resolving package versions...
Status C:\Users\Denis\AppData\Local\Temp\jl_rRESVx\Manifest.toml
[621f4979] AbstractFFTs v0.5.0
[1520ce14] AbstractTrees v0.3.1
[79e6a3ab] Adapt v1.0.0
[9e28174c] BinDeps v1.0.0
[b99e7846] BinaryProvider v0.5.8
[a74b3585] Blosc v0.5.1
[e1450e63] BufferedStreams v1.0.0
[fa961155] CEnum v0.2.0
[631607c0] CMake v1.1.2
[d5fb7624] CMakeWrapper v0.2.3
[3895d2a7] CUDAapi v2.1.0
[c5f51814] CUDAdrv v5.0.1
[be33ccc6] CUDAnative v2.8.1
[da1fd8a2] CodeTracking v0.5.8
[944b1d66] CodecZlib v0.6.0
[3da002f7] ColorTypes v0.8.1
[5ae59095] Colors v0.9.6
[bbf7d656] CommonSubexpressions v0.2.0
[34da2185] Compat v2.2.0
[3a865a2d] CuArrays v1.6.0
[9a962f9c] DataAPI v1.1.0
[864edb3b] DataStructures v0.17.9
[163ba53b] DiffResults v1.0.2
[b552c78f] DiffRules v1.0.0
[7a1cc6ca] FFTW v1.2.0
[f5851436] FFTW_jll v3.3.9+3
[1a297f60] FillArrays v0.8.4
[53c48c17] FixedPointNumbers v0.6.1
[587475ba] Flux v0.10.1 #master (https://github.com/FluxML/Flux.jl.git)
[f6369f11] ForwardDiff v0.10.9
[0c68f7d7] GPUArrays v2.0.1
[f67ccb44] HDF5 v0.12.5
[7869d1d1] IRTools v0.3.0
[1d5cc7b8] IntelOpenMP_jll v2018.0.3+0
[aa1ae85d] JuliaInterpreter v0.7.8
[e5e0dc1b] Juno v0.7.2
[9a2cd570] KrylovMethods v0.6.0
[929cbde3] LLVM v1.3.3
[6f1432cf] LoweredCodeUtils v0.4.2
[23992714] MAT v0.7.0
[97b447e0] MFGnet v0.0.3 #master (https://github.com/EmoryMLIP/MFGnet.jl)
[856f044c] MKL_jll v2019.0.117+2
[1914dd2f] MacroTools v0.5.3
[e89f7d12] Media v0.5.0
[e1d29d7a] Missings v0.4.3
[872c559c] NNlib v0.6.4
[77ba4419] NaNMath v0.3.3
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[bac558e1] OrderedCollections v1.1.0
[ccf9b6e2] ParSpMatVec v0.1.1
[d96e819e] Parameters v0.12.0
[189a3867] Reexport v0.2.0
[ae029012] Requires v0.5.2
[295af30f] Revise v2.5.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[90137ffa] StaticArrays v0.12.1
[2913bbd2] StatsBase v0.32.0
[a759f4b9] TimerOutputs v0.5.3
[9f7883ad] Tracker v0.2.6
[3bb67fe8] TranscodingStreams v0.9.5
[30578b45] URIParser v0.4.0
[a5390f91] ZipFile v0.9.1
[83775a58] Zlib_jll v1.2.11+7
[e88e6eb3] Zygote v0.4.6
[700de1a5] ZygoteRules v0.2.0
[3dacf901] jInv v1.0.0
[2a0f44e3] Base64 [@stdlib/Base64]
[ade2ca70] Dates [@stdlib/Dates]
[8bb1440f] DelimitedFiles [@stdlib/DelimitedFiles]
[8ba89e20] Distributed [@stdlib/Distributed]
[7b1f6079] FileWatching [@stdlib/FileWatching]
[b77e0a4c] InteractiveUtils [@stdlib/InteractiveUtils]
[76f85450] LibGit2 [@stdlib/LibGit2]
[8f399da3] Libdl [@stdlib/Libdl]
[37e2e46d] LinearAlgebra [@stdlib/LinearAlgebra]
[56ddb016] Logging [@stdlib/Logging]
[d6f4376e] Markdown [@stdlib/Markdown]
[a63ad114] Mmap [@stdlib/Mmap]
[44cfe95a] Pkg [@stdlib/Pkg]
[de0858da] Printf [@stdlib/Printf]
[9abbd945] Profile [@stdlib/Profile]
[3fa0cd96] REPL [@stdlib/REPL]
[9a3f8284] Random [@stdlib/Random]
[ea8e919c] SHA [@stdlib/SHA]
[9e88b42a] Serialization [@stdlib/Serialization]
[1a1011a3] SharedArrays [@stdlib/SharedArrays]
[6462fe0b] Sockets [@stdlib/Sockets]
[2f01184e] SparseArrays [@stdlib/SparseArrays]
[10745b16] Statistics [@stdlib/Statistics]
[8dfed614] Test [@stdlib/Test]
[cf7118a7] UUIDs [@stdlib/UUIDs]
[4ec0a83e] Unicode [@stdlib/Unicode]
ERROR: LoadError: LoadError: UndefVarError: TrackedArray not defined
Stacktrace:
[1] top-level scope at C:\Users\Denis.julia\packages\MFGnet\XOqZI\src\layers.jl:98
[2] include at .\boot.jl:328 [inlined]
[3] include_relative(::Module, ::String) at .\loading.jl:1105
[4] include at .\Base.jl:31 [inlined]
[5] include(::String) at C:\Users\Denis.julia\packages\MFGnet\XOqZI\src\MFGnet.jl:15
[6] top-level scope at C:\Users\Denis.julia\packages\MFGnet\XOqZI\src\MFGnet.jl:22
[7] include at .\boot.jl:328 [inlined]
[8] include_relative(::Module, ::String) at .\loading.jl:1105
[9] include(::Module, ::String) at .\Base.jl:31
[10] top-level scope at none:2
[11] eval at .\boot.jl:330 [inlined]
[12] eval(::Expr) at .\client.jl:425
[13] top-level scope at .\none:3
in expression starting at C:\Users\Denis.julia\packages\MFGnet\XOqZI\src\layers.jl:98
in expression starting at C:\Users\Denis.julia\packages\MFGnet\XOqZI\src\MFGnet.jl:22
ERROR: LoadError: Failed to precompile MFGnet [97b447e0-6553-5d69-bee2-d3681083803f] to C:\Users\Denis.julia\compiled\v1.3\MFGnet\T4wuO_7OhxH.ji.
Stacktrace:
[1] error(::String) at .\error.jl:33
[2] compilecache(::Base.PkgId, ::String) at .\loading.jl:1283
[3] _require(::Base.PkgId) at .\loading.jl:1024
[4] require(::Base.PkgId) at .\loading.jl:922
[5] require(::Module, ::Symbol) at .\loading.jl:917
[6] include at .\boot.jl:328 [inlined]
[7] include_relative(::Module, ::String) at .\loading.jl:1105
[8] include(::Module, ::String) at .\Base.jl:31
[9] include(::String) at .\client.jl:424
[10] top-level scope at none:6
in expression starting at C:\Users\Denis.julia\packages\MFGnet\XOqZI\test\runtests.jl:4
ERROR: Package MFGnet errored during testing

(v1.3) pkg>

[lruthotto]

At first glance, our Flux seems to be too new for our code to run. Can you try this with the Manifest we provide?

We'll update the dependencies soon, but for now the goal is to use the (very nice) Manifest framework in julia to allow reproducibility with the same package version that we used to develop the first version of the project.

[dlml]

@lruthotto Do you have a python version ？

[lruthotto]

We don't have an exact match in python, but for the optimal transport problems, you can look at https://github.com/EmoryMLIP/OT-Flow which follows the same principles here.