Receiving error in collate command using alevin-fry 0.6.0 (possibly lower).

[rob-p]

Q: Using a command that should work properly, like

$ alevin-fry collate -i <input_dir> -r <rad_dir>

I receive unexpected output:

error: The following required arguments were not provided:
    --threads <THREADS>
    --max-records <MAXRECORDS>

USAGE:
    alevin-fry collate --input-dir <INPUTDIR> --rad-dir <RADFILE> --threads <THREADS> --max-records <MAXRECORDS>

For more information try --help

A: You may see this behavior if you are using a recently-compiled alevin-fry of version <0.7.0. This behavior is the result of updates to the argument parsing library which alter the previous behavior regarding the optional status of these arguments. Specifically, these arguments should be optional, and have proper defaults set. However, updates to the argument parsing library have altered the interpretation of the previous code, such that these arguments are now parsed as required. This particular behavior was introduced in clap 3.1.20 (see release notes specifically, "Defaults no longer satisfy required and its variants (clap-rs/clap#3793)"). This release came out 12 days after 0.6.0 was tagged using clap 3.1.18. alevin-fry has been updated in 0.7.0 to conform to the new parsing expectations of clap, and the optional status (with defaults) has been restored to the relevant arguments. The recommended solution is to upgrade to the latest version of alevin-fry.

However, if you cannot upgrade immediately, and need to make use of a newly-compiled 0.6.0, then you may either alter the Cargo.toml file to fix the version of clap being used by replacing:

clap = { version = ">=3.1.18", features = ["derive", "wrap_help", "cargo"] }

with

clap = { version = "=3.1.18", features = ["derive", "wrap_help", "cargo"] }

or, you will have to explicitly pass the -t and -m options to the collate command. For consistency with previous behavior and with newer versions, the default value of the -m option is 30,000,000, so that you should pass -m 30000000 to obtain the memory characteristics of the previous behavior of the collate command. In order to minimize the possibility of such unexpected issues in the future, we are pinning the specific clap version for each release, and also including the Cargo.lock file to allow precise replication of the dependency solve when building from source.