Jul 17, 2024: Test actions pt2

.github/workflows/README.md

@@ -0,0 +1,10 @@
+validate is automatically run on pushes to any branch, or pull requests to main
+
+to automatically create a new release and automatically upload mac, ubuntu, and windows builds run:
+`git tag v*`
+`git push origin v*`
+where * is the version number.
+
+Example:
+`git tag v1.2.1`
+`git push origin v1.2.1`

.github/workflows/create_release.yml

@@ -0,0 +1,66 @@
+name: Create Release
+
+on:
+  push:
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+jobs:
+  create_release:
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+      with:
+        submodules: recursive
+    - name: Create Release
+      id: create_release
+      uses: actions/create-release@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+      with:
+        tag_name: ${{ github.ref }}
+        release_name: teloscope ${{ github.ref }}
+        body: |
+          Changes in this Release
+        draft: false
+        prerelease: false
+    outputs:
+      upload_url: ${{ steps.create_release.outputs.upload_url }}
+
+  add_resources:
+    needs: create_release
+    name: Add Resources
+    strategy:
+      matrix:
+        OS: [macos-latest, ubuntu-latest, windows-2019]
+        include:
+        - OS: macos-latest
+          OS_NAME: macOS
+        - OS: ubuntu-latest
+          OS_NAME: linux
+        - OS: windows-2019
+          OS_NAME: win
+    runs-on: ${{ matrix.OS }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+        with:
+            submodules: true
+      - name: Build
+        run: make
+      - name: Zip
+        uses: papeloto/action-zip@v1
+        with:
+          files: build/bin/teloscope
+          dest: result.zip
+      - name: Add binaries
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ needs.create_release.outputs.upload_url }}
+          asset_path: result.zip
+          asset_name: teloscope.${{ github.ref_name }}-${{matrix.OS_NAME}}.zip
+          asset_content_type: application/zip

.github/workflows/val.bat

@@ -0,0 +1 @@
+"build/bin/teloscope-validate.exe" validateFiles

.github/workflows/val.sh

@@ -0,0 +1 @@
+build/bin/teloscope-validate validateFiles

.github/workflows/validate.yml

@@ -0,0 +1,33 @@
+name: Validate
+
+on:
+  push:
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  validate:
+    name: Validate
+    strategy:
+      matrix:
+        include:
+          - os: macos-latest
+            command: ".github/workflows/val.sh"
+          - os: ubuntu-latest
+            command: ".github/workflows/val.sh"
+            chmod: true
+          - os: windows-2019
+            command: ".github/workflows/val.bat"
+      fail-fast: false
+    runs-on: ${{ matrix.os }}
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+      with:
+            submodules: true
+    - name: Build
+      run: make all -j
+    - name: Validate
+      run: |
+        chmod +x .github/workflows/val.sh
+        ${{ matrix.command }}

src/generate-tests.cpp

@@ -36,27 +36,11 @@ int main(int, char **argv) {
 
     const std::map<std::set<std::string>, std::vector<std::string>> file_args = {
         {{"random1.fasta"}, {"-f testFiles/random1.fasta -w 3 -s 1"}},
-        {{"random2.fasta"}, {"-f testFiles/random2.fasta -w 10 -s 5"}}
+        {{"random2.fasta"}, {"-f testFiles/random2.fasta -w 10 -s 5"}},
+        {{"random3.fasta"}, {"-f testFiles/random3.fasta -w 10 -s 5"}}
     //  {{set of test file paths}, {list of command line args to run with}}
     };
 
-    // const std::map<std::set<std::string>, std::vector<std::string>> ext_args = {
-    //     {{"fasta", "fasta.gz", "fastq", "fastq.gz"}, {"", "-s s", "-s c", "-s g", "-b a", "-b s", "-b c", "-b g", "--homopolymer-compress 1 -ofa"}},
-    //     {{"gfa", "gfa.gz", "gfa2", "gfa2.gz"}, {"-o gfa2", "-o gfa", "-o fasta"}}
-    // //  {{set of test file extensions}, {list of command line args to run with}}
-    // };
-
-    // const std::map<std::set<std::string>, std::vector<std::string>> file_args = {
-    //     {{"random1.fasta", "random1.fasta.gz", "random1.fastq", "random1.fastq.gz", "random1.gfa2"}, {"-a testFiles/random1.agp --stats", "-a testFiles/random1.agp -ofa", "-k testFiles/random1.rvcp.sak", "-k testFiles/random1.mask.sak"}},
-    //     {{"random1.fasta"}, {"-k testFiles/random1.instructions.sak", "-ofa -k testFiles/random1.instructions.sak", "-ofa -k testFiles/random1.hc.sak", "-ofa -k testFiles/random1.hdc.sak", "Header2", "-ofa -i testFiles/random1.fasta.bed", "-ofa -e testFiles/random1.fasta.bed"}},
-    //     {{"random2.noseq.gfa"}, {""}},
-    //     {{"random1.gfa2"}, {"-k testFiles/random1.gfa2.instructions.sak"}},
-    //     {{"random4.fasta"}, {""}},
-    //     {{"random5.findovl.gfa"}, {"--discover-terminal-overlaps 3 -ogfa"}}
-
-    // //  {{set of test file paths}, {list of command line args to run with}}
-    // };
-
     const std::set<std::string> exclude {"agp", "sak"};
 
     for(const std::string &file : list_dir("testFiles")) {