Support Julia LTS versions (#15)

Author: Ben J. Ward

.github/workflows/docs.yml

@@ -1,30 +1,25 @@
 name: Documentation
 
 on:
-    push:
-        branches:
-            - 'master'
-            - 'release-'
-        tags: '*'
-    pull_request:
+  push:
+    branches:
+      - master
+      - release/.*
+    tags: '*'
+  pull_request:
 
 jobs:
-    build:
-        runs-on: ${{ matrix.os }}
-        strategy:
-            matrix:
-                julia-version: [1.3.0]
-                julia-arch: [x86]
-                os: [ubuntu-latest]
-        steps:
-            - uses: actions/[email protected]
-            - uses: julia-actions/setup-julia@latest
-              with:
-                  version: ${{ matrix.julia-version }}
-            - name: Install dependencies
-              run: |
-                julia --project=docs -e 'using Pkg; Pkg.add(PackageSpec(path="./")); Pkg.instantiate(); Pkg.update()'
-            - name: Build and deploy
-              env:
-                  DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
-              run: julia --project=docs --color=yes docs/make.jl
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - name: Install dependencies
+        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/testing.yml

@@ -1,17 +1,44 @@
-name: Unit testing
-on: [push, pull_request]
+name: Unit tests
+
+on:
+  - push
+  - pull_request
+
 jobs:
-    test:
-        runs-on: ${{ matrix.os }}
-        strategy:
-            matrix:
-                julia-version: [1.2, 1.3]
-                julia-arch: [x64]
-                os: [ubuntu-latest, macOS-latest]
-        steps:
-            - uses: actions/[email protected]
-            - uses: julia-actions/setup-julia@latest
-              with:
-                  version: ${{ matrix.julia-version }}
-            - name: Install dependencies
-            - uses: julia-actions/julia-runtest@latest
+  test:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version:
+          - '1.0' # LTS
+          - '1'
+        julia-arch: [x86]
+        os: [ubuntu-latest, windows-latest, macOS-latest] # TODO: Work on windows-latest
+        experimental: [false]
+        include:
+          - julia-version: nightly
+            julia-arch: x86
+            os: ubuntu-latest
+            experimental: true
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@latest
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}

.travis.yml

@@ -10,7 +10,7 @@ FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 [compat]
 BioSequences = "2"
 FASTX = "1.1"
-julia = "1.1"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

Project.toml

@@ -127,8 +127,15 @@ function LinkedReads{A}(fwq::FASTQ.Reader, rvq::FASTQ.Reader, outfile::String, n
         # Read in `chunksize` read pairs.
         chunkfill = 0
         while !eof(fwq) && !eof(rvq) && chunkfill < chunksize
-            read!(fwq, fwrec)
-            read!(rvq, rvrec)
+            try # TODO: Get to the bottom of why this is nessecery to fix Windows issues.
+                read!(fwq, fwrec)
+                read!(rvq, rvrec)
+            catch ex
+                if isa(ex, EOFError)
+                    break
+                end
+                rethrow()
+            end
             cd_i = chunk_data[chunkfill + 1]
             _extract_tag_and_sequences!(cd_i, fwrec, rvrec, max_read_len, format)
             if cd_i.tag != zero(UInt32)
@@ -232,7 +239,7 @@ function Base.open(::Type{LinkedReads{A}}, filename::String, name::Union{Symbol,
 
     read_tags = read_flat_vector(fd, UInt32)
 
-    return LinkedReads{A}(filename, isnothing(name) ? default_name : Symbol(name), default_name, max_read_len, chunksize, position(fd), read_tags, fd)
+    return LinkedReads{A}(filename, name === nothing ? default_name : Symbol(name), default_name, max_read_len, chunksize, position(fd), read_tags, fd)
 end
 
 @inline _read_data_begin(prds::LinkedReads) = prds.readpos_offset

src/linked-reads.jl

@@ -101,7 +101,14 @@ function LongReads{A}(rdr::FASTQ.Reader, outfile::String, name::Union{String,Sym
     @info "Writing long reads to datastore"
 
     while !eof(rdr)
-        read!(rdr, record)
+        try # TODO: Get to the bottom of why this is nessecery to fix Windows issues.
+            read!(rdr, record)
+        catch ex
+            if isa(ex, EOFError)
+                break
+            end
+            rethrow()
+        end
         seq_len = FASTQ.seqlen(record)
         if seq_len < min_size
             discarded = discarded + 1
@@ -143,7 +150,7 @@ function Base.open(::Type{LongReads{A}}, filename::String, name::Union{String,Sy
     default_name = Symbol(readuntil(fd, '\0'))
     seek(fd, fpos)
     read_to_file_position = read_flat_vector(fd, ReadPosSize)
-    return LongReads{A}(filename, isnothing(name) ? default_name : Symbol(name), default_name, read_to_file_position, fd)
+    return LongReads{A}(filename, name === nothing ? default_name : Symbol(name), default_name, read_to_file_position, fd)
 end
 
 ###

src/long-reads.jl

@@ -126,14 +126,22 @@ function PairedReads{A}(rdrx::FASTQ.Reader, rdry::FASTQ.Reader,
     readpos = write(fd, UInt64(0)) + sizepos
 
     pairs = discarded = truncated = 0
+    p = 1
 
     @info "Building paired read datastore from FASTQ files"
     @info "Writing paired reads to datastore"
 
     while !eof(rdrx) && !eof(rdry)
         # Read in the two records.
-        read!(rdrx, lread)
-        read!(rdry, rread)
+        try # TODO: Get to the bottom of why this is nessecery to fix Windows issues.
+            read!(rdrx, lread)
+            read!(rdry, rread)
+        catch ex
+            if isa(ex, EOFError)
+                break
+            end
+            rethrow()
+        end
 
         llen = UInt64(FASTQ.seqlen(lread))
         rlen = UInt64(FASTQ.seqlen(rread))
@@ -178,7 +186,7 @@ function PairedReads{A}(rdrx::FASTQ.Reader, rdry::FASTQ.Reader,
 
     seek(fd, sizepos)
     write(fd, nreads)
-    
+    flush(fd)
     close(fd)
 
     @info "Done writing paired read sequences to datastore"
@@ -205,7 +213,7 @@ function Base.open(::Type{PairedReads{A}}, filename::String, name::Union{String,
     nreads = read(fd, UInt64)
     readpos_offset = position(fd)
 
-    return PairedReads{A}(filename, isnothing(name) ? default_name : Symbol(name), default_name,
+    return PairedReads{A}(filename, name === nothing ? default_name : Symbol(name), default_name,
                        max_read_len, chunksize, fragsize,
                        readpos_offset, nreads, orientation, fd)
 end