similar names due to features? (and features of optional features)

[brentp]

I think this is a general rust question regarding features rather than specific to noodles but I am not able to find the solution.

I have in my Cargo.toml this:

noodles = { version = "0.48.0" }
noodles-util = { version = "0.19.0", features = ['variant'] }

and later, I have:

[features]
default = ["bed", "vcf", "bcf", "csi", "core", "bam", "sam", "bgzf"]
bam = ["noodles/bam"]
bed = ["noodles/bed"]
bgzf = ["noodles/bgzf"]
sam = ["noodles/sam"]
vcf = ["noodles/vcf"]
csi = ["noodles/csi"]
core = ["noodles/core"]
bcf = ["noodles/bcf"]

Since I need the features on noodles-util, I specified it that way.
However doing so causes problems. I see:

error[E0308]: mismatched types
  --> src/sniff.rs:76:73
   |
76 |             let bed_vcf = bedder_vcf::BedderVCF::new(Box::new(wrapper), hdr)?;
   |                           --------------------------                    ^^^ expected `noodles::noodles_vcf::Header`, found `noodles_vcf::header::Header`
   |                           |
   |                           arguments to this function are incorrect
   |
   = note: `noodles_vcf::header::Header` and `noodles::noodles_vcf::Header` have similar names, but are actually distinct types
note: `noodles_vcf::header::Header` is defined in crate `noodles_vcf`
  --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.35.0/src/header.rs:48:1
   |
48 | pub struct Header {
   | ^^^^^^^^^^^^^^^^^
note: `noodles::noodles_vcf::Header` is defined in crate `noodles_vcf`
  --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.36.0/src/header.rs:48:1
   |
48 | pub struct Header {
   | ^^^^^^^^^^^^^^^^^
   = note: perhaps two different versions of crate `noodles_vcf` are being used?
note: associated function defined here
  --> src/bedder_vcf.rs:60:12
   |
60 |     pub fn new(r: Box<dyn VCFReader + 'a>, header: vcf::Header) -> io::Result<BedderVCF<'a>> {
   |            ^^^                             -------------------

error[E0308]: mismatched types
  --> src/bedder_vcf.rs:43:39
   |
43 |         let mut q = self.reader.query(header, region)?;
   |                                 ----- ^^^^^^ expected `noodles_vcf::header::Header`, found `noodles::noodles_vcf::Header`
   |                                 |
   |                                 arguments to this method are incorrect
   |
   = note: `noodles::noodles_vcf::Header` and `noodles_vcf::header::Header` have similar names, but are actually distinct types
note: `noodles::noodles_vcf::Header` is defined in crate `noodles_vcf`
  --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.36.0/src/header.rs:48:1
   |
48 | pub struct Header {
   | ^^^^^^^^^^^^^^^^^
note: `noodles_vcf::header::Header` is defined in crate `noodles_vcf`
  --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.35.0/src/header.rs:48:1
   |
48 | pub struct Header {
   | ^^^^^^^^^^^^^^^^^
   = note: perhaps two different versions of crate `noodles_vcf` are being used?
note: method defined here
  --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-util-0.19.0/src/variant/indexed_reader.rs:53:12
   |
53 |     pub fn query<'r, 'h: 'r>(
   |            ^^^^^

error[E0308]: mismatched types
   --> src/bedder_vcf.rs:46:37
    |
46  |                 self.variant = Some(variant);
    |                                ---- ^^^^^^^ expected `noodles::noodles_vcf::Record`, found `noodles_vcf::record::Record`
    |                                |
    |                                arguments to this enum variant are incorrect
    |
    = note: `noodles_vcf::record::Record` and `noodles::noodles_vcf::Record` have similar names, but are actually distinct types
note: `noodles_vcf::record::Record` is defined in crate `noodles_vcf`
   --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.35.0/src/record.rs:38:1
    |
38  | pub struct Record {
    | ^^^^^^^^^^^^^^^^^
note: `noodles::noodles_vcf::Record` is defined in crate `noodles_vcf`
   --> /home/brentp/.cargo/registry/src/index.crates.io-6f17d22bba15001f/noodles-vcf-0.36.0/src/record.rs:38:1
    |
38  | pub struct Record {
    | ^^^^^^^^^^^^^^^^^
    = note: perhaps two different versions of crate `noodles_vcf` are being used?
help: the type constructed contains `noodles_vcf::record::Record` due to the type of the argument passed
   --> src/bedder_vcf.rs:46:32

where rust thinks these are different types (not sure how version 0.35.0 and version 0.36.0 are getting chosen).

Can you help me with this? I think if I can figure how to specify the features of noodles-util this will be resolved.

thanks in advance.

[zaeleus]

noodles 0.48.0 and noodles-util 0.19.{0,1} are pulling in two different versions of noodles-vcf.

$ cargo tree
[...]
├── noodles v0.48.0
│   └── noodles-vcf v0.36.0 (*)
└── noodles-util v0.19.1
    └── noodles-vcf v0.35.0 (*)

cargo does not consider 0.x releases to be semver compatible and tries to include both. In this case, the usages overlap.

noodles and noodles-util need to be kept in sync, i.e., use noodles 0.48.0 and noodles-util 0.20.0.

[brentp]

Thank you!
Is there a reason why util must be imported as noodles_util and the rest I can import as e.g. noodles::bam?

[zaeleus]

Is there a reason why util must be imported as noodles_util and the rest I can import as e.g. noodles::bam?

All features in noodles-util are disabled by default, meaning you always have to include it as an direct dependency to enable features.

[brentp]

understood. thanks again.