Inconsistent config scope resolution when using profiles

[nathan-wan]

Bug report

Expected behavior and actual behavior

When combining . or { syntax for config scopes, expected to see all properties configured for a given scope, especially if they are disjoint. Works as expected outside of profiles, but resolution are different when syntaxes are combined when declared in a profile.

Steps to reproduce the problem

% cat << EOF > nextflow.config && nextflow config 
alpha.p = 1
alpha {
    q = 2
}
beta {
    p = 1
}
beta.q = 2
EOF
alpha {
   p = 1
   q = 2
}

beta {
   p = 1
   q = 2
}
% cat << EOF > nextflow.config && nextflow config -profile foo
profiles {
    foo {
        alpha.p = 1
        alpha {
            q = 2
        }
        beta {
            p = 1
        }
        beta.q = 2
    }
}
EOF
alpha {
   q = 2
}

beta {
   p = 1
   q = 2
}
% nextflow -v
nextflow version 23.04.3.5875

Program output

See above

Environment

• Nextflow version: 23.04.3.5875
• Java version: openjdk 20.0.2 2023-07-18
• Operating system: macOS
• Bash version: zsh 5.8.1 (x86_64-apple-darwin21.0)

Additional context

Reproduced on Linux and macOS

[mribeirodantas]

According to some tests I ran on my side, this seems to happen only within profiles when you set some with . and then afterward with {. If you start with {, the next ones with . will apply as expected.

By changing slightly your second example, it works:

cat << EOF > nextflow.config && nextflow config -profile foo
profiles {
    foo {
        alpha {
            q = 2
        }
        alpha.p = 1
        beta {
            p = 1
        }
        beta.q = 2
    }
}
EOF
alpha {
   q = 2
   p = 1
}

beta {
   p = 1
   q = 2
}

While it's not fixed, I opened a PR to update the warning we have in the documentation here.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[bentsherman]

Should be resolved by #4744