Rather than a git revision.

vdj_ann should depend on published align_tools.

Should fix at least one problem with the CI.

* Upgrade to GitHub-native Dependabot

* Remove ignores.

Co-authored-by: dependabot-preview[bot] <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Adam Azarchs <adam.azarchs@10xgenomics.com>

* Bump rust edition to 2018.

* Remove unused dependencies.

* Deny warnings in CI, and add clippy check.

* Automated clippy fix.

* Fix future-incompatible macro warning.

semicolon-in-expressions-from-macros

* Fix clippy errors.

Remove redundant if cases.

Use `if let Some(x) = y.next()` rather than a loop-and-break.

Don't clone something when cloning doesn't do anything.

These directives control which files are downloaded when someone gets
the crate from crates.io.  It is good practice to exclude test files,
READMEs, and so on in order to minimize the download.

The main impact of this is on the 50+mb of fasta files in vdj_ann, but
there's also a relatively large jpg image for pretty_trace.

Replace the `failure::Error` usage with the concrete (and only) errors for each case.

For `pretty_trace` and `binary_vec_io` I used the errors from `std::io::Error` and `nix::Error` directly.

…f > 2^16 - 1 (#70)

Clippy should never be blanket-disabled.  The deny-level lints are
generally indicating a serious problem, or at least a high likelihood
that the code is confusing.  In cases where it is overly aggressive,
it's reasonable to disable specific lints, but only one at a time.

We've had several production bugs because of this one.

It's not great to make the linker process 25MB of fasta files unless
it's actually required.

Also move the binaries, with their dependency on exons
(which shouldn't have been published, but too late now...).

Move embedded reference data out of vdj_ann.

This is an initial, minimal toolkit for working with eval_expr, and used by enclone. It is unstable at the moment.

* added Gamma and Delta
* some formatting changes
* fixing changes to yml file

Fix a future-incompatible warning in some `io_util` macros due to trailing
semicolons.

Also fix those macros to work properly when expanded in contexts where
the types they're accessing aren't in scope, and allow them to work with
`impl AsRef<Path>` types rather than just `&String`.

Add trait implementations where appropriate, mostly `Default` but also a
few for `From` where it looked like it made sense given existing
conversion functions, in order to bring the APIs into conformance with
common naming conventions.

Fix a bunch of clippy lints around stuff that looks like
```rust
if f.is_err() {
    // thing
} else {
    let f = f.unwrap();
    // other thing
}
```
using `match` instead to avoid checking more than once whether the type
was an error.

Replace uses of `&Vec<T>` with `&[T]` where possible.  In some cases,
the extent to which this was possible is limited until some of the
upstream crates (from this repository) push a new version with their
APIs updated.

Replace uses of `&String` with either `&str` or `impl AsRef<Path>`
as appropriate for the use case.  Again, as with the `&Vec<T>` changes,
in some cases this means temporarily going through fallible steps
allocating String objects until the upstream crates publish versions
with updated APIs.

I could be wrong but I believe that `cargo clippy --fix` will be able
to fix the TODOs from the above two items automatically when the time
comes.

The above two changes _shouldn't_ affect existing users, at least in
most cases (`&Vec<T>` casts implicitly to `&[T]`, `&String` casts
implicitly to `&str`, and both `&String` and `&str` implement
`AsRef<Path>`).  At least, in theory.

Change the `segtype` field of `vdj_ann::refx::RefData` from a vector of
owned `String` to a `&'static str`, since everything added to that
vector is a constant value.  This should significantly reduce memory
consumption, as the vector is now a vector of pointers into constant
memory rather than a vector of pointers each into their own heap-
allocated copy of the source strings.  Because that field is public,
this is a breaking API change (though I don't know how many downstream
users actually access the field directly), so I'm bumping the version
of that crate.

In vdj_ann_ref, don't convert `&'static str` to `String` except in
cases where (similarly to above) we have to in order to satisfy the old
APIs.  Also, change the if-chaining logic to `match` statements to make
the different cases more clear.

* Bump depended-on version for io_utils.

* Remove unused imports.

* Fix TODOs from #78.

Missed from previous PR.

This reverts commit df785d5.

These are dev dependencies, but they were conflicting with the versions
expected by nalgebra.

Hyperbase must use the same version as whatever version its graph_simple
dependency uses, but that's allowed with the widened version range.

Also fix some clippy lints.

many_single_char_names and comparison_chain are both too noisy,
at least for now, and it would be better to focus on more important ones
like ptr_arg.

On the other hand, deny `unused` and `perf` lints.

This should allow dependabot PRs to succeed.

…24 (#81)