Clean up defunct dependencies

ConnectedSystems commented 3 months ago

Used Aqua to help identify issues.

Added Aqua to tests
Removed undefined exports
Moved unused dependencies to [weakdeps] section as they will be used by extension packages later, or
Removed dependencies altogether as they are no longer needed
Also bumped the version number in prep for next release

Cleaning this up results in a substantial improvement to precompilation times. Previously it was ~30 seconds for ADRIA. It is now between 8 - 10 seconds.

(sandbox) pkg> activate --temp
  Activating new project at `C:\Users\tiwanaga\AppData\Local\Temp\jl_HZP6j3`

# Add ADRIA as a development dependency
(jl_HZP6j3) pkg> dev .
   Resolving package versions...
    Updating `C:\Users\tiwanaga\AppData\Local\Temp\jl_HZP6j3\Project.toml` 

(jl_HZP6j3) pkg> ^C

julia> @time using ADRIA
  8.696201 seconds (9.55 M allocations: 571.700 MiB, 2.02% gc time, 8.13% compilation time: 32% of which was recompilation)

Things will only improve as we split functionality out into extension packages.

ConnectedSystems commented 3 months ago

Also note that OrdinaryDiffEq is also slated for removal, pending the new model being finalized.

Zapiano commented 3 months ago

@ConnectedSystems I tried to run some scenarios and got an error in the line https://github.com/open-AIMS/ADRIA.jl/blob/d1c066453b13e62935d6f13a7bfed4fccf7a65d4/src/scenario.jl#L441

ConnectedSystems commented 3 months ago

Aaaah my bad, I moved one dependency out after my test run thinking it wasn't needed either. Will fix soon

ConnectedSystems commented 3 months ago

Should be all good now!

Zapiano commented 3 months ago

Hum, now I got an error when loading the extensions.

ConnectedSystems commented 3 months ago

Hum, now I got an error when loading the extensions.

Could I confirm you updated the ADRIA environment?

Zapiano commented 3 months ago

Could I confirm you updated the ADRIA environment?

Yes, I did... but I didn't restart the REPL after updating. I can try that, give me a second.

Zapiano commented 3 months ago

Could I confirm you updated the ADRIA environment?

Yes, I did... but I didn't restart the REPL after updating. I can try that, give me a second.

but then, same error when I run using ADRIA

ConnectedSystems commented 3 months ago

Could you do a status in the package manager for the ADRIA environment?

Zapiano commented 3 months ago

Could you do a status in the package manager for the ADRIA environment?

(ADRIA) pkg> status
Project ADRIA v0.12.0
Status `C:\Users\pribeiro\AIMS\Code\ADRIA.jl\Project.toml`
  [c9ce4bd3] ArchGDAL v0.10.4
  [e28b5b4c] Bootstrap v2.4.0
  [336ed68f] CSV v0.10.14
  [aaaa29a8] Clustering v0.15.7
  [861a8166] Combinatorics v1.0.2
  [adafc99b] CpuId v0.3.1
  [a93c6f00] DataFrames v1.6.1
  [864edb3b] DataStructures v0.18.20
  [0703355e] DimensionalData v0.27.3
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.109
  [cc61a311] FLoops v0.2.1
  [5789e2e9] FileIO v1.16.3
  [62cb38b5] GeoDataFrames v0.3.8
  [68eda718] GeoFormatTypes v0.4.2
  [cf35fbd7] GeoInterface v1.3.4
  [86223c79] Graphs v1.11.1
  [09f84164] HypothesisTests v0.11.0
  [82e4d734] ImageIO v0.6.8
  [a98d9a8b] Interpolations v0.15.1
  [358108f5] JMcDM v0.7.16
  [682c06a0] JSON v0.21.4
  [5cadff95] JuliennedArrays v0.4.0
  [23992714] MAT v0.10.7
  [add582a8] MLJ v0.20.6
  [4744a3fa] ModelParameters v0.4.2
  [30363a11] NetCDF v0.12.0
  [a15396b6] OnlineStats v1.7.0
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.82.0
  [eebad327] PkgVersion v0.3.3
  [aea7be01] PrecompileTools v1.2.1
  [92933f4c] ProgressMeter v1.10.0
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [cdeec39e] SIRUS v2.0.1
  [0bca4576] SciMLBase v2.41.2
  [efcf1570] Setfield v1.1.1
  [47aef6b3] SimpleWeightedGraphs v1.4.0
  [276daf66] SpecialFunctions v2.4.0
  [860ef19b] StableRNGs v1.0.2
  [90137ffa] StaticArrays v1.9.5
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.1
  [6fc51010] Surrogates v6.9.0
  [c21b50f5] YAXArrays v0.5.7
  [0a941bbe] Zarr v0.9.4
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [9a3f8284] Random
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [fa267f1f] TOML v1.0.3

ConnectedSystems commented 3 months ago

Oh sorry, I'll also need the versions of GeoMakie, GraphMakie and WGLMakie (or GLMakie, whichever you're using)

ConnectedSystems commented 3 months ago

Reverted dependency of GeoMakie to v0.6.x - ADRIA now correctly precompiles for me now.

open-AIMS / ADRIA.jl

Clean up defunct dependencies #776