Re-enable golangci-lint.yml, turn on linters, and lint.

[carreter]

No description provided.

[TimothyStiles]

I think we started doing this to make it easier to mock tests?

[Koeng101]

I think the big changes to the parsers remove this anyway - since gzip gets tossed into generics, its easier to test

[carreter]

I think we started doing this to make it easier to mock tests?

IMO, you shouldn't need to reach into a module and change its state to mock it, especially given how Go handles errors. We should favor onion architecture keep I/O as high up in the call chain as possible. This allows inner functions to be pure. The gzipReaderFn variable was unused anyway, that's why I removed it.

[carreter]

Go's interfaces are the solution for testing, IMO. If a function/object needs to perform I/O operations, it should take io.Reader and io.Writer interfaces as an argument/field. These interfaces can then be easily be mocked:

import "bufio"
import "bytes"

const someData = ";alskjdf;lkajsdlf"

func main() {
    var b bytes.Buffer
    mockedWriter := bufio.NewWriter(&b)
    FunctionThatTakesAWriter(mockedWriter)
    got := b.String()

    mockedReader := bytes.NewReader([]byte(someData))
    FunctionThatTakesAReader(mockedReader)
}

[Koeng101]

I agree here! Much more readable too. This is how the bio parsers work, and is how I mock test to completion fasta in ioToBio.

[TimothyStiles]

@Koeng101 wasn't buildMultiNth meant to deal with some annoying corner case?

[Koeng101]

Hmmm not entirely sure, I don't quite remember

[Koeng101]

The build functions will mostly be moved into bio once we get there though, I just haven't started on genbank compatibility because it's gonna be quite sizable and deserves its own PR

[carreter]

The underlying logic is the same, it was just being buried a few function calls deep for some reason.

Before: Build(gbk) makes a single element slice gbks and passes it to BuildMulti(gbks), which immediately calls buildMultiNth(gbks, -1). The count argument is unused in buildMultiNth() and all its clients pass -1 as a value anyway.

After: Build(gbk) makes a single element slice gbks and passes it to BuildMulti(gbks), which holds same the logic buildMultiNth() used to.

IMHO, this (Build() calling BuildMulti()) is a little backward, but it seems reasonable to avoid having to append results.

[Koeng101]

Looks good! Mostly just style changes (obviously, since this turns on linter), and the non-style changes make sense.

[Koeng101]

I agree here! Much more readable too. This is how the bio parsers work, and is how I mock test to completion fasta in ioToBio.

[TimothyStiles]

Excellent pull request. Thanks @carreter for submitting and thanks @Koeng101 for reviewing!

MERGED