From e485a80cf7bb81101d3eb3bb50418d38bbbaa1c7 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue, 20 Jun 2023 20:50:23 +0200
Subject: [PATCH 01/18] fix: update deprecated alias `--all` to new argument
 `--workspace`

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 798e181be..8874e17a3 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -131,7 +131,7 @@ jobs:
           use-tool-cache: true
 
       - name: Coverage with tarpaulin
-        run: cargo tarpaulin --all --all-features --timeout 600 --out Lcov -- --test-threads 1
+        run: cargo tarpaulin --workspace --all-features --timeout 600 --out Lcov -- --test-threads 1
 
       - name: Upload coverage
         uses: coverallsapp/github-action@master

From c0b251d775da898e14e444666bb40acb1c7cc37b Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue, 20 Jun 2023 20:53:51 +0200
Subject: [PATCH 02/18] fix: include `doctests` in test coverage calculation,
 see https://github.com/xd009642/tarpaulin/issues/538#issuecomment-675921588

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 8874e17a3..255bee054 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -131,7 +131,7 @@ jobs:
           use-tool-cache: true
 
       - name: Coverage with tarpaulin
-        run: cargo tarpaulin --workspace --all-features --timeout 600 --out Lcov -- --test-threads 1
+        run: cargo tarpaulin --workspace --all-features --run-types Tests,Doctests --timeout 600 --out Lcov -- --test-threads 1
 
       - name: Upload coverage
         uses: coverallsapp/github-action@master

From 052f09c262194555411b7fc670492c3ac1eb0d67 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Mon, 26 Jun 2023 14:35:21 +0200
Subject: [PATCH 03/18] try fixing failing doctest compilation during coverage
 estimation by copying rust-htslib approach

---
 .github/workflows/rust.yml | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 255bee054..135c1aab2 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -116,6 +116,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
+        with:
+          submodules: recursive
 
       - name: Install nightly toolchain
         uses: actions-rs/toolchain@v1
@@ -123,18 +125,18 @@ jobs:
           toolchain: nightly
           override: true
 
-      - name: Install cargo-tarpaulin
-        uses: actions-rs/install@v0.1
+      - uses: Swatinem/rust-cache@v1.3.0
+
+      - name: Install and run cargo-tarpaulin
+        uses: actions-rs/tarpaulin@v0.1
         with:
-          crate: cargo-tarpaulin
-          version: latest
+          # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
+          version: "0.22.0"
           use-tool-cache: true
-
-      - name: Coverage with tarpaulin
-        run: cargo tarpaulin --workspace --all-features --run-types Tests,Doctests --timeout 600 --out Lcov -- --test-threads 1
+          args: "--workspace --all-features --run-types Tests,Doctests --timeout 600 --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
-        uses: coverallsapp/github-action@master
+        uses: coverallsapp/github-action@v1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           path-to-lcov: ./lcov.info

From 57f78b57fe9affab404589dd163cee987aec7bb0 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Mon, 26 Jun 2023 22:18:36 +0200
Subject: [PATCH 04/18] make coverage CI step identical to rust-htslib setup

---
 .github/workflows/rust.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 135c1aab2..93b3a982b 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -125,6 +125,10 @@ jobs:
           toolchain: nightly
           override: true
 
+      - name: Install system dependencies
+        run: |
+          sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
+
       - uses: Swatinem/rust-cache@v1.3.0
 
       - name: Install and run cargo-tarpaulin
@@ -133,7 +137,7 @@ jobs:
           # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
           version: "0.22.0"
           use-tool-cache: true
-          args: "--workspace --all-features --run-types Tests,Doctests --timeout 600 --out Lcov -- --test-threads 1"
+          args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From 046e4d053407a82af7023d9bce67ab721b671292 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue, 27 Jun 2023 10:13:15 +0200
Subject: [PATCH 05/18] remove unused / inexistent tarpaulin option

---
 .github/workflows/rust.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 93b3a982b..b0cca734e 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -136,7 +136,6 @@ jobs:
         with:
           # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
           version: "0.22.0"
-          use-tool-cache: true
           args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage

From 0b7a6878b3824576b25986fff823f830069bbaff Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue, 27 Jun 2023 10:14:04 +0200
Subject: [PATCH 06/18] try updating rust-cache action to address save-state
 deprecation warning

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index b0cca734e..e88604fe4 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -129,7 +129,7 @@ jobs:
         run: |
           sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
-      - uses: Swatinem/rust-cache@v1.3.0
+      - uses: Swatinem/rust-cache@v2.5.0
 
       - name: Install and run cargo-tarpaulin
         uses: actions-rs/tarpaulin@v0.1

From 7630569e1594dcc09b3fe7b927e67dfab38af7f6 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue, 27 Jun 2023 10:24:31 +0200
Subject: [PATCH 07/18] add `--verbose` and `--debug` to tarpaulin, to figure
 out doctest failures

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index e88604fe4..f5518b5a3 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -136,7 +136,7 @@ jobs:
         with:
           # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
           version: "0.22.0"
-          args: "--all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
+          args: "--verbose --debug --all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From f9c778c28516ec49b6f4933f2786a985e839d394 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 13:48:09 +0200
Subject: [PATCH 08/18] fix newick doctest

---
 src/io/newick.rs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/io/newick.rs b/src/io/newick.rs
index f8d252f5c..9e5954840 100644
--- a/src/io/newick.rs
+++ b/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);
 //!  }
 //!  ```

From 7ba5976ffcfcb99ffd0505c683aa4f3923f5515b Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 13:50:29 +0200
Subject: [PATCH 09/18] remove caching for coverage calculation, as this uses
 nightly

for nightly, caching is not very useful, see:
https://github.com/marketplace/actions/rust-cache#cache-effectiveness
---
 .github/workflows/rust.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index f5518b5a3..c7d379fad 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -129,8 +129,6 @@ jobs:
         run: |
           sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
 
-      - uses: Swatinem/rust-cache@v2.5.0
-
       - name: Install and run cargo-tarpaulin
         uses: actions-rs/tarpaulin@v0.1
         with:

From ee7dc77194790fcccef9c68fc9554dfc8a7956c5 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 13:51:22 +0200
Subject: [PATCH 10/18] revert installation of deps that was only added for
 identical syntax with rust-htslib

these are probably not needed...
---
 .github/workflows/rust.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index c7d379fad..9d553e0ca 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -125,10 +125,6 @@ jobs:
           toolchain: nightly
           override: true
 
-      - name: Install system dependencies
-        run: |
-          sudo apt-get install --yes zlib1g-dev libbz2-dev musl musl-dev musl-tools clang libc6-dev
-
       - name: Install and run cargo-tarpaulin
         uses: actions-rs/tarpaulin@v0.1
         with:

From 0bbcb67e9ec4b63ed200d166f8f36eb6efd5f30c Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 13:52:15 +0200
Subject: [PATCH 11/18] remove debugging output from tarpaulin CI step and put
 `--workspace` argument back in

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 9d553e0ca..95c30fe93 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -130,7 +130,7 @@ jobs:
         with:
           # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
           version: "0.22.0"
-          args: "--verbose --debug --all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From d95dcbe4f35f002d80a0219a1a9f13f1a9d13db0 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 14:35:56 +0200
Subject: [PATCH 12/18] increase tarpaulin timeout for tests to 5 minutes
 (instead of 1 minute for default)

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 95c30fe93..990891305 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -130,7 +130,7 @@ jobs:
         with:
           # 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 -- --test-threads 1"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 300 -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From e642b2e008298929f5cb870da9cfc90435a1124b Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 14:52:05 +0200
Subject: [PATCH 13/18] increase `--timeout` back to the original 10 minutes

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 990891305..8b7ce5b17 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -130,7 +130,7 @@ jobs:
         with:
           # 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 -- --test-threads 1"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 600 -- --test-threads 1"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From 1614643e960d8b056ef4289eb0b156e8ce58acff Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 15:13:06 +0200
Subject: [PATCH 14/18] allow tarpaulin multithreading and increase --timeout
 to 15 minutes

---
 .github/workflows/rust.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 8b7ce5b17..58ee01b84 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -130,7 +130,7 @@ jobs:
         with:
           # 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 600 -- --test-threads 1"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 900"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From a86839506a5d4d4703c5e5b43680516001ada634 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 15:50:59 +0200
Subject: [PATCH 15/18] make code coverage CI step run only after successful
 testing, increase --timeout for it to 30 minutes

---
 .github/workflows/rust.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 58ee01b84..8a6637858 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -111,7 +111,7 @@ jobs:
           args: --all --no-fail-fast
 
   Coverage:
-    needs: Formatting
+    needs: Testing
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
@@ -130,7 +130,7 @@ jobs:
         with:
           # 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 900"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 1800"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1

From c9876d2823a12dd8db6e85b07e41ec0ebb6a31f0 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 16:44:14 +0200
Subject: [PATCH 16/18] do not run bio::io::fastq doctests that read from stdin

---
 src/io/fastq.rs | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/io/fastq.rs b/src/io/fastq.rs
index 23067eadb..220cd3718 100644
--- a/src/io/fastq.rs
+++ b/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;

From 17077ebbd04f894cf25d1f9a3324c1fc6bc43906 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 20:37:05 +0200
Subject: [PATCH 17/18] exclude all doctests that read from io::stdin() from
 being run (they are still compiled)

---
 src/io/fasta.rs | 6 +++---
 src/io/gff.rs   | 2 +-
 src/lib.rs      | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/io/fasta.rs b/src/io/fasta.rs
index aa9a4591a..46667780d 100644
--- a/src/io/fasta.rs
+++ b/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;
diff --git a/src/io/gff.rs b/src/io/gff.rs
index a6654ce5e..b34b0d56f 100644
--- a/src/io/gff.rs
+++ b/src/io/gff.rs
@@ -11,7 +11,7 @@
 //!
 //! # Example
 //!
-//! ```
+//! ```no_run
 //! // import functions (at top of script)
 //! use bio::io::gff;
 //! use std::io;
diff --git a/src/lib.rs b/src/lib.rs
index fe9c09a48..e25d2d095 100644
--- a/src/lib.rs
+++ b/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};

From 889e87d9ffbf9f40ddb779ed72d3f8912d8ce4ba Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Wed, 28 Jun 2023 20:38:30 +0200
Subject: [PATCH 18/18] reduce tarpaulin --timeout back to 5 minutes, put
 needs: back to Formatting

---
 .github/workflows/rust.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 8a6637858..a848a1d39 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -111,7 +111,7 @@ jobs:
           args: --all --no-fail-fast
 
   Coverage:
-    needs: Testing
+    needs: Formatting
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
@@ -130,7 +130,7 @@ jobs:
         with:
           # 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 1800"
+          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 300"
 
       - name: Upload coverage
         uses: coverallsapp/github-action@v1