Packages with symlinks have issues

[ericphanson]

Problem 1:

In [25]: analyze("Mads"; version= v"0.9.1")
┌ Debug: Downloading code via github api
└ @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/obtain_code.jl:106
┌ Debug: Must be download corruption; tree hash of download does not match expected
│   get_tree_hash(dest) = "8b5971b5b9b32a2f45cacda47a0e5fd4849981d9"
│   tree_hash = "488a8dfcddf4e1c0fef21a59f62e7e52b32f0888"
└ @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/obtain_code.jl:77
Out[25]: PackageV1 Mads:
  * repo: https://github.com/madsjulia/Mads.jl.git
  * uuid: d6bdc55b-bd94-5012-933c-1f73fc2ee992
  * version: 0.9.1
  * is reachable: false

Problem 2: if I manually clone,

❯ git clone https://github.com/madsjulia/Mads.jl.git
❯ cd Mads.jl
❯ git log --pretty=raw | grep -B 1 488a8dfcddf4e1c0fef21a59f62e7e52b32f0888 # tree hash from error above
commit 191bee6213169df94c4d20dfd3c65907ac8e4833
tree 488a8dfcddf4e1c0fef21a59f62e7e52b32f0888
❯ git reset --hard 191bee6213169df94c4d20dfd3c65907ac8e4833

then start Julia and analyze:

In [4]: using PackageAnalyzer

In [5]: analyze(".")
ERROR: SystemError: opening file "./examples/model_analysis/models/internal-polynomial.jl": No such file or directory
Stacktrace:
  [1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
    @ Base ./error.jl:176
  [2] #systemerror#82
    @ ./error.jl:175 [inlined]
  [3] systemerror
    @ ./error.jl:175 [inlined]
  [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing)
    @ Base ./iostream.jl:293
  [5] open
    @ ./iostream.jl:275 [inlined]
  [6] open(f::Base.var"#418#419"{String}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:393
  [7] open
    @ ./io.jl:392 [inlined]
  [8] read
    @ ./io.jl:473 [inlined]
  [9] parse_green_node(file_path::String)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/count_loc.jl:102
 [10] count_julia_lines_of_code(dir::String)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/count_loc.jl:146
 [11] count_lines_of_code(dir::String)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/count_loc.jl:16
 [12] analyze_code(dir::String; repo::String, reachable::Bool, subdir::String, auth::GitHub.AnonymousAuth, sleep::Int64, only_subdir::Bool, version::Nothing)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:263
 [13] analyze_code
    @ ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:221 [inlined]
 [14] #analyze#41
    @ ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:185 [inlined]
 [15] analyze
    @ ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:177 [inlined]
 [16] analyze(name_or_dir_or_url::String; registries::Vector{RegistryInstances.RegistryInstance}, auth::GitHub.AnonymousAuth, sleep::Int64, version::Nothing, root::String, subdir::String)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:76
 [17] analyze(name_or_dir_or_url::String)
    @ PackageAnalyzer ~/.julia/packages/PackageAnalyzer/GHakA/src/analyze.jl:58
 [18] top-level scope
    @ REPL[5]:1
 [19] top-level scope
    @ ~/.julia/juliaup/julia-1.9.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.9/REPL/src/REPL.jl:1416

The file in question seems to be a symlink:

❯ ls -alh ./examples/model_analysis/models/
total 600
drwxr-xr-x  13 eph  staff   416B Jul  6 02:24 .
drwxr-xr-x  28 eph  staff   896B Jul  6 02:24 ..
-rw-r--r--   1 eph  staff   461B Jul  6 02:24 internal-exp-polynomial.jl
-rw-r--r--   1 eph  staff   550B Jul  6 02:24 internal-exp-polynomial.mads
-rw-r--r--   1 eph  staff   399B Jul  6 02:24 internal-linear.jl
-rw-r--r--   1 eph  staff   435B Jul  6 02:24 internal-linear.mads
-rw-r--r--   1 eph  staff   129K Jul  6 02:24 internal-polynomial-efast-385.png
-rw-r--r--   1 eph  staff    52K Jul  6 02:24 internal-polynomial-w13a-model-100-spaghetti.png
-rw-r--r--   1 eph  staff    87K Jul  6 02:24 internal-polynomial-w13a-svr-100-spaghetti.png
lrwxr-xr-x   1 eph  staff    54B Jul  6 02:24 internal-polynomial.jl -> ../../internal-polynomial-model/internal-polynomial.jl
lrwxr-xr-x   1 eph  staff    56B Jul  6 02:24 internal-polynomial.mads -> ../../internal-polynomial-model/internal-polynomial.mads
-rw-r--r--   1 eph  staff   437B Jul  6 02:24 internal-polynomial3.jl
-rw-r--r--   1 eph  staff   549B Jul  6 02:24 internal-polynomial3.mads

[giordano]

I reported also in #90, the problem isn't the symlink per se, but the fact it has a nonsense target: they dumped the content of the file as the target....