Merge pull request #3253 from boutproject/bump-deps

Bump some dependencies

Author: bendudson

.github/workflows/black-fix.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ github.head_ref }}
 

.github/workflows/clang-format.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

.github/workflows/clang-tidy-review.yml

@@ -16,12 +16,12 @@ jobs:
     if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.21.0
+        uses: ZedThree/clang-tidy-review@v0.23.0
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.21.0
+        uses: ZedThree/clang-tidy-review/upload@v0.23.0

.github/workflows/docker.yml

@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Log in to the Container registry
         uses: docker/login-action@master

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -57,7 +57,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -106,7 +106,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true

.github/workflows/tests.yml

@@ -168,7 +168,7 @@ jobs:
                  libparpack2-dev
                  libhypre-dev
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
@@ -182,7 +182,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -205,7 +205,7 @@ jobs:
     timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build Fedora
@@ -219,7 +219,7 @@ jobs:
     container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04

CMakeLists.txt

@@ -729,7 +729,7 @@ endif()
 
 option(BOUT_BUILD_DOCS "Build the documentation" OFF)
 if (BOUT_BUILD_DOCS)
-  add_subdirectory(manual EXCLUDE_FROM_ALL)
+  add_subdirectory(manual)
 endif()
 
 

cmake/SetupBOUTThirdParty.cmake

@@ -164,8 +164,8 @@ if (BOUT_USE_NETCDF)
     include(FetchContent)
     FetchContent_Declare(
       netcdf-cxx4
-      GIT_REPOSITORY https://github.com/ZedThree/netcdf-cxx4
-      GIT_TAG        "ad3e50953190615cb69dcc8a4652f9a88a8499cf"
+      GIT_REPOSITORY https://github.com/Unidata/netcdf-cxx4
+      GIT_TAG        "a43d6d4d415d407712c246faca553bd951730dc1"
       )
     # Don't build the netcdf tests, they have lots of warnings
     set(NCXX_ENABLE_TESTS OFF CACHE BOOL "" FORCE)