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

.github/workflows/rust.yml

@@ -116,25 +116,24 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
+        with:
+          submodules: recursive
 
       - name: Install nightly toolchain
         uses: actions-rs/toolchain@v1
         with:
           toolchain: nightly
           override: true
 
-      - name: Install cargo-tarpaulin
-        uses: actions-rs/install@v0.1
+      - name: Install and run cargo-tarpaulin
+        uses: actions-rs/tarpaulin@v0.1
         with:
-          crate: cargo-tarpaulin
-          version: latest
-          use-tool-cache: true
-
-      - name: Coverage with tarpaulin
-        run: cargo tarpaulin --all --all-features --timeout 600 --out Lcov -- --test-threads 1
+          # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
+          version: "0.22.0"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 300"
 
       - name: Upload coverage
-        uses: coverallsapp/github-action@master
+        uses: coverallsapp/github-action@v1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info

src/io/fasta.rs

@@ -11,7 +11,7 @@
 //!
 //! In this example, we parse a fasta file from stdin and compute some statistics
 //!
-//! ```
+//! ```no_run
 //! use bio::io::fasta;
 //! use std::io;
 //!
@@ -34,7 +34,7 @@
 //!
 //! We can also use a `while` loop to iterate over records.
 //! This is slightly faster than the `for` loop.
-//! ```
+//! ```no_run
 //! use bio::io::fasta;
 //! use std::io;
 //! let mut records = fasta::Reader::new(io::stdin()).records();
@@ -79,7 +79,7 @@
 //!
 //! In this example we filter reads from stdin on sequence length and write them to stdout
 //!
-//! ```
+//! ```no_run
 //! use bio::io::fasta;
 //! use bio::io::fasta::FastaRead;
 //! use std::io;
@@ -371,7 +371,7 @@
 
     /// Open a FASTA index from a given file path.
     pub fn from_file<P: AsRef<Path> + std::fmt::Debug>(path: &P) -> anyhow::Result<Self> {
         fs::File::open(&path)
             .map_err(csv::Error::from)
             .and_then(Self::new)
             .with_context(|| format!("Failed to read fasta index from {:#?}", path))
@@ -414,7 +414,7 @@
     /// present for FASTA ref.fasta.
     pub fn from_file<P: AsRef<Path> + std::fmt::Debug>(path: &P) -> anyhow::Result<Self> {
         let index = Index::with_fasta_file(path)?;
         fs::File::open(&path)
             .map(|f| Self::with_index(f, index))
             .map_err(csv::Error::from)
             .with_context(|| format!("Failed to read fasta from {:#?}", path))

src/io/fastq.rs

@@ -11,7 +11,7 @@
 //!
 //! In this example, we parse a fastq file from stdin and compute some statistics
 //!
-//! ```
+//! ```no_run
 //! use bio::io::fastq;
 //! use std::io;
 //! let mut reader = fastq::Reader::new(io::stdin());
@@ -31,7 +31,7 @@
 //! ```
 //!
 //! We can also use a `while` loop to iterate over records
-//! ```
+//! ```no_run
 //! use bio::io::fastq;
 //! use std::io;
 //! let mut records = fastq::Reader::new(io::stdin()).records();
@@ -78,7 +78,7 @@
 //!
 //! In this example we filter reads from stdin on mean quality (Phred + 33) and write them to stdout
 //!
-//! ```
+//! ```no_run
 //! use bio::io::fastq;
 //! use bio::io::fastq::FastqRead;
 //! use std::io;

src/io/gff.rs

@@ -11,7 +11,7 @@
 //!
 //! # Example
 //!
-//! ```
+//! ```no_run
 //! // import functions (at top of script)
 //! use bio::io::gff;
 //! use std::io;

src/io/newick.rs

@@ -14,7 +14,7 @@
 //!  use bio::io::newick;
 //!
 //!  let tree = newick::from_string("(A:0.1,B:0.2,(C:0.3,D:0.4)E:0.5)F;").unwrap();
-//!  for taxon in tree.raw_nodes() {
+//!  for taxon in tree.g.raw_nodes() {
 //!      println!("{}", taxon.weight);
 //!  }
 //!  ```

src/lib.rs

@@ -95,7 +95,7 @@
 //!
 //! An example of using `rust-bio`:
 //!
-//! ```rust
+//! ```no_run
 //! // Import some modules
 //! use bio::alphabets;
 //! use bio::data_structures::bwt::{bwt, less, Occ};