From 7ef3eabba58795f3df68c1f8f6a418e31a7fbf84 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Mon, 21 Oct 2024 16:14:52 +0200
Subject: [PATCH] Prepare for release

---
 .github/workflows/documentation.yml | 20 ++++++-----------
 .github/workflows/unittest.yml      | 27 ++++++++++++-----------
 src/PairwiseMappingFormat.jl        | 34 ++++++++++++++---------------
 3 files changed, 37 insertions(+), 44 deletions(-)

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 4c7bd84..bee37bc 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -8,22 +8,16 @@ on:
   pull_request:
 
 jobs:
-  build:
-    permissions:
-      contents: write
-      pull-requests: read
-      statuses: write
+  Documenter:
+    name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
-          version: 'nightly'
-      - uses: julia-actions/cache@v1
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+          version: '1'
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-docdeploy@latest
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/unittest.yml b/.github/workflows/unittest.yml
index 03206a0..031c8cb 100644
--- a/.github/workflows/unittest.yml
+++ b/.github/workflows/unittest.yml
@@ -8,38 +8,39 @@ on:
 
 jobs:
   test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: false
       matrix:
-        julia-version:
-          - 'nightly'
-        os: [ ubuntu-latest, windows-latest ]
-        arch: [ x64 ]
+        julia-version: ['1', '1.11']
+        os: [ubuntu-latest, macOS-latest, windows-latest]
+        experimental: [false]
         include:
+          # Include nightly, but experimental, so it's allowed to fail without
+          # failing CI.
           - julia-version: nightly
-            julia-arch: x86
             os: ubuntu-latest
             experimental: true
-         # - julia-version: 1
-         #   os: macOS-latest
-         #   experimental: false
+            fail_ci_if_error: false
+
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Setup Julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@latest
         with:
           version: ${{ matrix.julia-version }}
       - name: Run Tests
         uses: julia-actions/julia-runtest@latest
       - name: Create CodeCov
-        uses: julia-actions/julia-processcoverage@v1
+        uses: julia-actions/julia-processcoverage@latest
       - name: Upload CodeCov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         with:
           file: ./lcov.info
           flags: unittests
           name: codecov-umbrella
           fail_ci_if_error: false
           token: ${{ secrets.CODECOV_TOKEN }}
+
diff --git a/src/PairwiseMappingFormat.jl b/src/PairwiseMappingFormat.jl
index 02c16c8..30315c9 100644
--- a/src/PairwiseMappingFormat.jl
+++ b/src/PairwiseMappingFormat.jl
@@ -749,6 +749,8 @@ function read_buffer!(reader::PAFReader)::Int
             remaining = length(mem) - reader.filled
         end
     end
+
+    @assert !iszero(remaining)
     # This part annoys me a lot. Julia has no efficient API to read bytes
     # into a byte buffer. How on Earth can that be true?
     # * read! will throw EOF if the memory is too short, and there is no
@@ -759,26 +761,22 @@ function read_buffer!(reader::PAFReader)::Int
     # It uses bytesavailable to check how many bytes to read and avoid buffer overflows etc,
     # and when there are zero bytes available, it reads a single byte, hoping that
     # more bytes will be available.
-    if !iszero(remaining)
-        n_available = bytesavailable(reader.io)
+    n_available = bytesavailable(reader.io)
+    if iszero(n_available) && !eof(reader.io)
         # Read one byte and hope more bytes become available
-        if iszero(n_available) && !eof(reader.io)
-            byte = read(reader.io, UInt8)
-            @inbounds mem[reader.filled + 1] = byte
-            reader.filled += 1
-            remaining -= 1
-            n_available = bytesavailable(reader.io)
-        end
-        # Read with unsafe_read
-        n_bytes = min(n_available, remaining)
-        if !iszero(n_bytes)
-            GC.@preserve mem unsafe_read(reader.io, pointer(mem, reader.filled + 1), n_bytes)
-            reader.filled += n_bytes
-        end
-        return n_bytes
-    else
-        return 0
+        byte = read(reader.io, UInt8)
+        @inbounds mem[reader.filled + 1] = byte
+        reader.filled += 1
+        remaining -= 1
+        n_available = bytesavailable(reader.io)
+    end
+    # Read with unsafe_read
+    n_bytes = min(n_available, remaining)
+    if !iszero(n_bytes)
+        GC.@preserve mem unsafe_read(reader.io, pointer(mem, reader.filled + 1), n_bytes)
+        reader.filled += n_bytes
     end
+    return n_bytes
 end
 
 """