chemfiles / Chemfiles.jl

With julia-1.5.3:

julia> Pkg.test("Chemfiles")

led to:

`Test Summary: | Pass Total
Generics | 1 1
Test Summary: | Pass Total
Atom | 16 16
WARNING: both Chemfiles and Base export "contains"; uses of it in module Main must be qualified
Residue: Error During Test at $HOME/.julia/packages/Chemfiles/uJPdJ/test/Residue.jl:22
Test threw exception
Expression: contains(residue, 56) == true
UndefVarError: contains not defined
Stacktrace:
[1] top-level scope at $HOME.julia/packages/Chemfiles/uJPdJ/test/Residue.jl:22
[2] top-level scope at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Test/src/Test.jl:1115
[3] top-level scope at $HOME/.julia/packages/Chemfiles/uJPdJ/test/Residue.jl:2

Test Summary: | Pass Error Total
Residue | 12 1 13
ERROR: LoadError: LoadError: Some tests did not pass: 12 passed, 0 failed, 1 errored, 0 broken.
in expression starting at $HOME/.julia/packages/Chemfiles/uJPdJ/test/Residue.jl:1
in expression starting at $HOME/.julia/packages/Chemfiles/uJPdJ/test/runtests.jl:28
ERROR: Package Chemfiles errored during testing`

The problem was circumvented in Residue.jl (line: ) by using:
@test **Chemfiles.contains**(residue, 56) == true

Thanks for reporting this error!

I'm a bit puzzled by the warning both Chemfiles and Base export "contains"; uses of it in module Main must be qualified since the export should be guarded by a version check:

Chemfiles.jl/src/Residue.jl

Lines 6 to 8 in 41b963c

    
           if VERSION < v"1.5.0-alpha" 
        
               export contains 
        
           end

.

I'm currently updating this package to chemfiles 0.10, and as part of it I changed this code to use Compat instead, which should be the right thing to do. So the next version should have this fixed.

~~I'll check if I can reproduce this error with julia-1.5.3, it is not happening on 1.5.0 =/~~

Ok, now I remember: this is already fixed in master, but not in the version registered in General.jl. Given that version 0.10 is coming soon, I'd rather not spend the time to do a 0.9.4 release.

If you need the fix in the mean time, you can run Pkg.rm("Chemfiles") and the Pkg.develop("Chemfiles") to get the latest master.

Hello Guillaume, Thank you for your two messages and your work. All my gratitude for indicating me the Pkg.develop("Chemfiles") method. Good work & best regards, Thierry

…

-- Thierry Lepoint chimieetjulia.org La pensée ne doit jamais se soumettre ni à un dogme, ni à un parti, ni à une passion, ni à un intérêt, ni à une idée préconçue, ni à quoi que ce soit, si ce n'est aux faits eux-mêmes, parce que, pour elle, se soumettre, ce serait cesser d'être. (Henri Poincaré) Sent with [ProtonMail](https://protonmail.com) Secure Email. ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ Le lundi 18 janvier 2021 16:24, Guillaume Fraux <notifications@github.com> a écrit :

Ok, now I remember: this is already fixed in master, but not in the version registered in General.jl. Given that version 0.10 is coming soon, I'd rather not spend the time to do a 0.9.4 release. If you need the fix in the mean time, you can run Pkg.rm("Chemfiles") and the Pkg.develop("Chemfiles") to get the latest master. — You are receiving this because you authored the thread. Reply to this email directly, [view it on GitHub](#47 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/ASJNSCFWGTNCVDXDYC3PLPTS2RHDJANCNFSM4WGJ7H2Q).

Now that version 0.10.0 have been released, this should be fixed!

test: UndefVarError: contains not defined