Merge pull request #47 from alyst/new_ci

New CI based on GH-actions

Author: jakobnissen

.codecov.yml

@@ -0,0 +1,68 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.version == 'nightly' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.0'
+          - '1'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        include:
+          - os: windows-latest
+            version: '1'
+            arch: x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Documentation.yml

@@ -977,9 +977,13 @@ end
         seq2 = aa"EPSHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA"
         model = AffineGapScoreModel(BLOSUM62, gap_open=-10, gap_extend=-1)
         aln = alignment(pairalign(GlobalAlignment(), seq1, seq2, model))
+        # julia 1.6+ uses shorter type aliases when printing types
+        seqtype = VERSION >= v"1.6" ?
+            "BioSequences.LongAminoAcidSeq" :
+            "BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}"
         @test sprint(show, aln) ==
         """
-        PairwiseAlignment{BioSequences.LongSequence{BioSequences.AminoAcidAlphabet},BioSequences.LongSequence{BioSequences.AminoAcidAlphabet}}:
+        PairwiseAlignment{$(seqtype),$(VERSION >= v"1.6" ? " " : "")$(seqtype)}:
           seq:  1 EPVTSHPKAVSPTETK--PTEKGQHLPVSAPPKITQSLKAEASKDIAKLTCAVESSALCA 58
                   ||  ||||||||||||  |||| ||||||||||||| ||||||| |||||| |||| | |
           ref:  1 EP--SHPKAVSPTETKRCPTEKVQHLPVSAPPKITQFLKAEASKEIAKLTCVVESSVLRA 58