fix: include doctests in the test coverage of code that tarpaulin calculates

[dlaehnemann]

Using a syntax found here:
xd009642/tarpaulin#538 (comment)

We are also using this in rust-htslib, now.

[coveralls]

coverage: 85.218% (+4.3%) from 80.932% when pulling 889e87d on include-doctests-in-code-coverage-calculation into e2b2fd8 on master.

[tedil]

This looks quite reasonable to me ;)
I guess while there is a way to somehow mock stdin for doctests, it is not a big issue for now. We could of course manually replace stdin in the examples with some fixed input in the future.

[dlaehnemann]

I guess as an example, the stdin-construct is useful as well. So I'm also not overly concerned about this.

[dcroote]

What a heroic effort @dlaehnemann !

[dlaehnemann]

Thanks for the kind words! 😅

It did take me a while to figure out that tarpaulin + actions-rs was swallowing up the relevant doctest error output and then figuring out how I could run the same setup locally... If anybody comes looking for info on debugging cargo tarpaulin doctest coverage around here:

1. Install the nightly toolchain with rustup (needed for tarpaulin doctest coverage).
2. Turn on --debug and --verbose in the cargo tarpaulin command.
3. Copy-paste the rustdoc command that is now printed out in the CI, to run it locally and get all the output, for example:

Running `/home/runner/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/bin/rustdoc --edition=2018 --crate-type lib --crate-name bio --test src/lib.rs --test-run-directory /home/runner/work/rust-bio/rust-bio -L dependency=/home/runner/work/rust-bio/rust-bio/target/debug/deps -L dependency=/home/runner/work/rust-bio/rust-bio/target/debug/deps --test-args --test-threads --test-args 1 --extern anyhow=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libanyhow-c6cf0643f3c509bb.rlib --extern approx=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libapprox-bfa4e03988db6ef8.rlib --extern bio=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libbio-f8a8caca8f493098.rlib --extern bio_types=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libbio_types-5834d92d1c46e184.rlib --extern bit_set=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libbit_set-26380277f767511f.rlib --extern bv=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libbv-502cf4d8e73630ab.rlib --extern bytecount=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libbytecount-9b439d721f18ee63.rlib --extern csv=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libcsv-3d38631523f1901f.rlib --extern custom_derive=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libcustom_derive-5ff07f976469020f.rlib --extern editdistancek=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libeditdistancek-8c6ff1406d9ca3f4.rlib --extern enum_map=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libenum_map-643d7108588eefc6.rlib --extern fxhash=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libfxhash-b77bbadc3c8ee64c.rlib --extern getset=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libgetset-5d904b9ae15addf1.so --extern itertools=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libitertools-094a968098f292d0.rlib --extern itertools_num=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libitertools_num-995199b6bce6f447.rlib --extern lazy_static=/home/runner/work/rust-bio/rust-bio/target/debug/deps/liblazy_static-d0c2dc85fa90a848.rlib --extern multimap=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libmultimap-5cc0df6d1f5eafcc.rlib --extern ndarray=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libndarray-6c31cbb51e19675f.rlib --extern newtype_derive=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libnewtype_derive-61bcd3628007834a.rlib --extern num_integer=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libnum_integer-cabbc0ef90f1a2e0.rlib --extern num_traits=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libnum_traits-4ed70ee29490e97a.rlib --extern ordered_float=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libordered_float-b407e7b6f8375d07.rlib --extern pest=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libpest-99ec8909eeb71d69.rlib --extern pest_derive=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libpest_derive-e1db1b01905d5ad5.so --extern petgraph=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libpetgraph-21f1893f777ff568.rlib --extern proptest=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libproptest-ae59404c71bd4d08.rlib --extern rand=/home/runner/work/rust-bio/rust-bio/target/debug/deps/librand-f82595de47ce7eac.rlib --extern regex=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libregex-535503b0639f3019.rlib --extern serde=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libserde-f6b47fff014ddb92.rlib --extern serde_derive=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libserde_derive-8449af3a227a832e.so --extern statrs=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libstatrs-635688025de7198c.rlib --extern strum=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libstrum-96436eb227d2763f.rlib --extern strum_macros=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libstrum_macros-9310f4a2b996ea58.so --extern tempfile=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libtempfile-fad2efdb632262d8.rlib --extern thiserror=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libthiserror-e0d424f42cc5b579.rlib --extern triple_accel=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libtriple_accel-d8e30d009751d8d9.rlib --extern vec_map=/home/runner/work/rust-bio/rust-bio/target/debug/deps/libvec_map-f06fa9452ca8d0f8.rlib -C embed-bitcode=no --cfg 'feature="generic-simd"' --cfg 'feature="pest"' --cfg 'feature="pest_derive"' --cfg 'feature="phylogeny"' --cfg 'feature="runtime-dispatch-simd"' -Cdebuginfo=2 --cfg=tarpaulin --persist-doctests /home/runner/work/rust-bio/rust-bio/target/doctests -Zunstable-options -Clink-dead-code --error-format json`

I condensed this down to something like (I think -- I didn't record it while doing it, so this is from memory):

rustdoc --edition=2018 --crate-type lib --crate-name bio --test src/lib.rs --cfg 'feature="generic-simd"' --cfg 'feature="pest"' --cfg 'feature="pest_derive"' --cfg 'feature="phylogeny"' --cfg 'feature="runtime-dispatch-simd"' -Cdebuginfo=2 --cfg=tarpaulin --persist-doctests /home/runner/work/rust-bio/rust-bio/target/doctests -Zunstable-options -Clink-dead-code --error-format human

Also, the setting of --error-format human helps... ;)