How to compare two fields/columns in a condition?

I am having a hard time trying to figure out how to get a sub-query working.

Imagine I have:

    $schools
        ->select($this->Schools)
        ->select([
            'pupilcount' => $this->Pupils
                ->find()
                ->select([
                    $this->Pupils->find()->func()->count('*')
                ])
                ->where([
                    'Pupils.school_id' => 'Schools.id', 

                ]),

The problem I am experiencing (I think) is that Schools.id is always 0 and so the count is returned as 0. I can pull out the Pupils join and it shows Pupils there.

I tried changing my code to add a:

->select(['SCID' => 'Schools.id'])

and reference that in the sub-query but doesn't work, it will always return 0 for the pupilcount.

What am I doing wrong here?

Whenever encountering query problems, check what queries are actually being generated (for example using DebugKit). Unless being an expression object, the right hand side of a condition will always be bound as a parameter, ie you're comparing against a string literal:

Pupils.school_id = 'Schools.id'

Generally for proper auto quoting compatibility, column names should be identifier expressions. While the left hand side will automatically be handled properly, the right hand side would require to be handled manually.

In your specific case you could easily utilize QueryExpression::equalFields(), which is ment for exactly what you're trying to do, comparing fields/columns:

->where(function (\Cake\Database\Expression\QueryExpression $exp, \Cake\ORM\Query $query) {
    return $exp->equalFields('Pupils.school_id', 'Schools.id');
})

It's also possible to create identifier expressions manually by simply instantiating them:

->where([
    'Pupils.school_id' => new \Cake\Database\Expression\IdentifierExpression('Schools.id')
])

or as of CakePHP 3.6 via the Query::identifier() method:

->where([
    'Pupils.school_id' => $query->identifier('Schools.id')
])

And finally you could also always pass a single string value, which is basically inserted into the query as raw SQL, however in that case the identifiers will not be subject to automatic identifier quoting:

->where([
    'Pupils.school_id = Schools.id'
])