Merge pull request #12 from lbl-cbg/fix-gh-actions

update GitHub Actions

.github/workflows/codespell.yml

@@ -0,0 +1,21 @@
+name: Codespell
+
+on:
+  push:
+    branches:
+    - main
+
+  pull_request:
+    branches:
+    - main
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+        - name: Checkout repository
+          uses: actions/checkout@v4
+        - name: Codespell
+          uses: codespell-project/actions-codespell@v2

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Linter
+
+on:
+  push:
+    branches:
+    - main
+
+  pull_request:
+    branches:
+    - main
+  workflow_dispatch:
+
+jobs:
+  lint:
+    name: Run linter
+    runs-on: ubuntu-latest
+    steps:
+        - name: Checkout repository
+          uses: actions/checkout@v4
+        - name: Lint
+          run: cmake -D FORMAT_COMMAND=clang-format-14 -P cmake/lint.cmake

.github/workflows/tests.yml

@@ -0,0 +1,59 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+    - main
+
+  pull_request:
+    branches:
+    - main
+  workflow_dispatch:
+
+jobs:
+  tests:
+    defaults:
+      run:
+        shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
+      cancel-in-progress: true
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Install dependencies - ubuntu
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libhdf5-dev libboost-all-dev
+        git clone https://github.com/catchorg/Catch2.git
+        cd Catch2
+        git checkout "v3.5.3"
+        cmake -Bbuild -H. -DBUILD_TESTING=OFF
+        sudo cmake --build build/ --target install
+    
+    - name: Install dependencies - macos
+      if: matrix.os == 'macos-latest'
+      run: brew install hdf5 boost catch2
+
+    - name: Configure
+      shell: pwsh
+      run: cmake "--preset=ci-$("${{ matrix.os }}".split("-")[0])"
+
+    - name: Build
+      run: cmake --build build --config Release -j 2
+
+    - name: Install
+      run: cmake --install build --config Release --prefix prefix
+
+    - name: Test
+      working-directory: build
+      run: ctest --output-on-failure --no-tests=error -C Release -j 2

CMakePresets.json

@@ -144,7 +144,7 @@
     },
     {
       "name": "ci-ubuntu",
-      "inherits": ["ci-build", "ci-linux", "clang-tidy", "cppcheck", "dev-mode"]
+      "inherits": ["ci-build", "ci-linux", "dev-mode"]
     },
     {
       "name": "ci-windows",

cmake/dev-mode.cmake

@@ -12,7 +12,7 @@ add_custom_target(
 )
 add_dependencies(run-exe aq-nwb_exe)
 
-option(BUILD_DOCS "Build documentation using Doxygen" ON)
+option(BUILD_DOCS "Build documentation using Doxygen" OFF)
 if(BUILD_DOCS)
   include(cmake/docs.cmake)
 endif()

src/io/BaseIO.hpp

@@ -1,7 +1,9 @@
 #pragma once
 
+#include <cstdint>
 #include <iostream>
 #include <string>
+#include <vector>
 
 #include "Types.hpp"