Restructure base directory & add GitHub Actions builds/releases (smit…

…h-chem-wisc#577)

* restructure base directory

* add github action workflows

.github/workflows/dotnet.yml

@@ -0,0 +1,51 @@
+name: Build and Test
+
+on:
+  push:
+    branches: [ restructureBaseDir ]
+  pull_request:
+    branches: [ restructureBaseDir ]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up .NET
+      uses: actions/setup-dotnet@v1
+      with:
+        dotnet-version: 5.0.x
+    - name: Restore dependencies
+      run: cd mzLib; dotnet restore
+    - name: Build
+      run:
+        cd mzLib;
+        dotnet build --no-restore;
+        dotnet build --no-restore ./Test/Test.csproj;
+        dotnet build --no-restore ./TestFlashLFQ/TestFlashLFQ.csproj;
+    - name: Add msbuild
+      run:
+        cd mzLib;
+        dotnet add Test/Test.csproj package coverlet.msbuild;
+        dotnet add TestFlashLFQ/TestFlashLFQ.csproj package coverlet.msbuild;
+    - name: Test
+      run:
+        cd mzLib;
+        dotnet test --no-build --verbosity normal
+          /p:CollectCoverage=true /p:CoverletOutputFormat=cobertura
+          /p:CoverletOutput='../../coberturatest.xml'
+          ./Test/Test.csproj;
+        dotnet test --no-build --verbosity normal
+          /p:CollectCoverage=true /p:CoverletOutputFormat=cobertura
+          /p:CoverletOutput='../../coberturatestlfq.xml'
+          ./TestFlashLFQ/TestFlashLFQ.csproj;
+    - name: Directory lists
+      run:
+        ls;
+        ls mzLib;
+    - name: Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        verbose: true
+        files: ./coberturatest.xml,./coberturatestlfq.xml

.github/workflows/release.yml

@@ -0,0 +1,50 @@
+name: Release
+
+on:
+  push:
+    tags:
+    - "[0-9]+.[0-9]+.[0-9]+"
+
+jobs:
+  build:
+    runs-on: windows-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup .NET
+        uses: actions/setup-dotnet@v1
+        with:
+          dotnet-version: 5.0.x
+
+      - name: Verify commit exists in origin/master
+        run: |
+          git fetch --no-tags --prune --depth=1 origin +refs/heads/*:refs/remotes/origin/*
+          git branch --remote --contains | grep origin/${env:RELEASE_BRANCH}
+        env:
+          RELEASE_BRANCH: master
+
+      - name: Restore dependencies
+        run: dotnet restore
+
+      - name: Build
+        run: |
+          $version= &git describe --tags
+          cd mzLib
+          dotnet build --no-restore --configuration Release /p:Version=${version}
+      - name: Test
+        run: |
+          $version= &git describe --tags
+          cd mzLib
+          dotnet test --configuration Release /p:Version=${version} --no-build
+      - name: Pack
+        run: |
+          $version= &git describe --tags
+          cd mzLib
+          dotnet pack --configuration Release /p:Version=${version} --no-build --output .
+      - name: Push
+        run: |
+          $version= &git describe --tags
+          cd mzLib
+          dotnet nuget push mzLib/mzLib.${version}.nupkg --source https://api.nuget.org/v3/index.json --api-key ${env:GITHUB_TOKEN}
+        env:
+          GITHUB_TOKEN: ${{ secrets.NUGET_KEY }}

.gitignore

@@ -246,3 +246,7 @@ ModelManifest.xml
 
 # FAKE - F# Make
 .fake/
+
+# Macintosh files
+**/.DS_Store
+

README.md

@@ -3,12 +3,11 @@
 A library for mass spectrometry projects.
 
 
-
- [![Build status](https://ci.appveyor.com/api/projects/status/s4wix633hmjv0jx4/branch/master?svg=true)](https://ci.appveyor.com/project/smith-chem-wisc/mzlib/branch/master)
- [![codecov](https://codecov.io/gh/smith-chem-wisc/mzLib/branch/master/graph/badge.svg)](https://codecov.io/gh/smith-chem-wisc/mzLib)
- [![Coverity Scan Build Status](https://scan.coverity.com/projects/10000/badge.svg)](https://scan.coverity.com/projects/mzlib)
- [![Codacy Badge](https://api.codacy.com/project/badge/Grade/1047dac2ae8d4d94b104c3cb3ca44926)](https://www.codacy.com/app/solntsev_2/mzLib?utm_source=github.com&utm_medium=referral&utm_content=smith-chem-wisc/mzLib&utm_campaign=Badge_Grade)
- [![NuGet version (mzLib)](https://img.shields.io/nuget/v/mzLib.svg?style=flat-square)](https://www.nuget.org/packages/mzLib/)
+[![GitHub Action Builds](https://github.com/smith-chem-wisc/mzLib/actions/workflows/dotnet.yml/badge.svg)](https://github.com/smith-chem-wisc/mzLib/actions/workflows/dotnet.yml)
+[![codecov](https://codecov.io/gh/smith-chem-wisc/mzLib/branch/master/graph/badge.svg)](https://codecov.io/gh/smith-chem-wisc/mzLib)
+[![Coverity Scan Build Status](https://scan.coverity.com/projects/10000/badge.svg)](https://scan.coverity.com/projects/mzlib)
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/1047dac2ae8d4d94b104c3cb3ca44926)](https://www.codacy.com/app/solntsev_2/mzLib?utm_source=github.com&utm_medium=referral&utm_content=smith-chem-wisc/mzLib&utm_campaign=Badge_Grade)
+[![NuGet version (mzLib)](https://img.shields.io/nuget/v/mzLib.svg?style=flat-square)](https://www.nuget.org/packages/mzLib/)
 
 
 Releases are here: https://www.nuget.org/packages/mzLib/
@@ -52,3 +51,4 @@ IEnumerable<ModificationWithLocation> ptms = PtmListLoader.ReadMods("ptms.txt")
 ```
 # License
 Code heavily borrowed from https://github.com/dbaileychess/CSMSL and distrubuted under the appropriate license, LGPL.
+