chore(deps): bump linter deps

GenSpectrum · Jun 2, 2024 · 071d3b1 · 071d3b1
1 parent 25c2abf
commit 071d3b1
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Showing 13 changed files with 141 additions and 62 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,15 +19,15 @@ jobs:
     strategy:
       matrix:
         path:
-          - check: 'src'
-          - check: 'include'
-            exclude: '(PerfEvent.hpp)'
+          - check: "src"
+          - check: "include"
+            exclude: "(PerfEvent.hpp)"
     steps:
       - uses: actions/checkout@v4
       - name: Run clang-format style check
         uses: jidicula/[email protected]
         with:
-          clang-format-version: '17'
+          clang-format-version: "17"
           check-path: ${{ matrix.path['check'] }}
           exclude-regex: ${{ matrix.path['exclude'] }}
 
@@ -39,8 +39,17 @@ jobs:
 
       - name: Generate dependency files hash
         id: files-hash
-        run: |
-          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_linter_dependencies') }})
+        run: |-
+          DIR_HASH=$(
+            echo -n ${{
+              hashFiles(
+                'conanfile.py',
+                'conanprofile.docker',
+                '.github/workflows/ci.yml',
+                './Dockerfile_linter_dependencies'
+              )
+            }}
+          )
           echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV
 
       - name: Docker metadata
@@ -91,8 +100,17 @@ jobs:
 
       - name: Generate dependency files hash
         id: files-hash
-        run: |
-          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_linter_dependencies') }})
+        run: |-
+          DIR_HASH=$(
+            echo -n ${{
+              hashFiles(
+                'conanfile.py',
+                'conanprofile.docker',
+                '.github/workflows/ci.yml',
+                './Dockerfile_linter_dependencies'
+              )
+            }}
+          )
           echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV
 
       - name: Set up Docker Buildx
@@ -119,8 +137,18 @@ jobs:
 
       - name: Generate dependency files hash
         id: files-hash
-        run: |
-          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }})
+        run: |-
+          DIR_HASH=$(
+            echo -n ${{
+              hashFiles(
+                'conanfile.py',
+                'conanprofile.docker',
+                'conanprofile.docker_arm',
+                '.github/workflows/ci.yml',
+                './Dockerfile_dependencies'
+              )
+            }}
+          )
           echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV
 
       - name: Docker metadata
@@ -174,8 +202,18 @@ jobs:
 
       - name: Generate dependency files hash
         id: files-hash
-        run: |
-          DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }})
+        run: |-
+          DIR_HASH=$(
+            echo -n ${{
+              hashFiles(
+                'conanfile.py',
+                'conanprofile.docker',
+                'conanprofile.docker_arm',
+                '.github/workflows/ci.yml',
+                './Dockerfile_dependencies'
+              )
+            }}
+          )
           echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV
 
       - name: Docker metadata
@@ -233,10 +271,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        preprocessing-docker-compose: [
-          docker-compose-for-tests-preprocessing-from-tsv.yml,
-          docker-compose-for-tests-preprocessing-from-ndjson.yml
-        ]
+        preprocessing-docker-compose:
+          [
+            docker-compose-for-tests-preprocessing-from-tsv.yml,
+            docker-compose-for-tests-preprocessing-from-ndjson.yml,
+          ]
     steps:
       - uses: actions/checkout@v4
 
@@ -274,4 +313,4 @@ jobs:
           SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }}
 
       - name: Run Tests
-        run: cd endToEndTests && SILO_URL=localhost:8080 npm run test
+        run: cd endToEndTests && SILO_URL=localhost:8080 npm run test
diff --git a/.gitignore b/.gitignore
@@ -62,6 +62,8 @@ conanprofile
 *.out
 *.app
 
+# Debug files
+debug.duckdb
 
 **/output/
 **/logs/

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -67,7 +67,7 @@ list(REMOVE_ITEM SRC_SILO_API ${SRC_TEST})
 # ---------------------------------------------------------------------------
 
 option(BUILD_WITH_CLANG_TIDY "Build process clang-tidy")
-if (NOT CMAKE_BUILD_TYPE STREQUAL Release AND BUILD_WITH_CLANG_TIDY)
+if (NOT CMAKE_BUILD_TYPE STREQUAL Release AND BUILD_WITH_CLANG_TIDY AND NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     find_program(CLANG_TIDY_EXE NAMES clang-tidy-19)
     if (NOT CLANG_TIDY_EXE)
         message(SEND_ERROR "clang-tidy not found, aborting. You can run the build with '-D BUILD_WITH_CLANG_TIDY=OFF' to disable clang-tidy.")

diff --git a/Dockerfile b/Dockerfile
@@ -4,20 +4,24 @@ FROM $DEPENDENCY_IMAGE AS builder
 
 COPY . ./
 
-RUN  \
-    python ./build_with_conan.py --release --parallel 4\
+RUN python ./build_with_conan.py --release --parallel 4 \
     && cp build/silo_test . \
     && cp build/siloApi .
 
 
-FROM alpine:3.18 AS server
+FROM ubuntu:24.04 AS server
+
+RUN apt-get update \
+    && apt-get install -y \
+    curl \
+    jq \
+    && apt-get clean
 
 WORKDIR /app
 COPY docker_default_preprocessing_config.yaml ./default_preprocessing_config.yaml
 COPY docker_runtime_config.yaml ./runtime_config.yaml
 COPY --from=builder /src/siloApi ./
 
-RUN apk update && apk add libtbb=2021.9.0-r0 curl jq
 
 # call /info, extract "seqeunceCount" from the JSON and assert that the value is not 0. If any of those fails, "exit 1".
 HEALTHCHECK --start-period=20s CMD curl --fail --silent localhost:8081/info | jq .sequenceCount | xargs test 0 -ne || exit 1

diff --git a/Dockerfile_dependencies b/Dockerfile_dependencies
@@ -1,23 +1,32 @@
-FROM alpine:3.18
+FROM ubuntu:24.04
 
 ARG TARGETPLATFORM
 
-RUN apk update && apk add --no-cache py3-pip \
-    build-base=0.5-r3 \
-    cmake=3.26.5-r0 \
-    bash=5.2.15-r5 \
-    linux-headers=6.3-r0 \
-    boost-build=1.82.0-r0 \
-    libtbb=2021.9.0-r0
+WORKDIR /src
 
-RUN pip install conan==2.0.17
+RUN apt update \
+    && apt install -y \
+    cmake \
+    pipx \
+    && apt clean
+
+RUN gcc --version
+
+ENV PATH="/root/.local/bin:$PATH"
+RUN pipx install conan --pip-args="--no-cache-dir" --system-site-packages
 
-WORKDIR /src
 COPY conanfile.py conanprofile.docker conanprofile.docker_arm ./
+
 RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
-        mv conanprofile.docker_arm conanprofile; \
+    mv conanprofile.docker_arm conanprofile; \
     else \
-        mv conanprofile.docker conanprofile; \
+    mv conanprofile.docker conanprofile; \
     fi
 
-RUN conan install . --build=missing --profile ./conanprofile --profile:build ./conanprofile --output-folder=build
+RUN apt update \
+    && apt install -y \
+    gcc \
+    g++ \
+    && apt clean
+
+RUN conan install . --build=missing --profile ./conanprofile --profile:build ./conanprofile --output-folder=build
diff --git a/Dockerfile_linter_dependencies b/Dockerfile_linter_dependencies
@@ -1,22 +1,37 @@
-FROM ubuntu:22.04
+FROM ubuntu:23.10
+
+ARG TARGETPLATFORM
 
 WORKDIR /src
 
 RUN apt update \
     && apt install -y \
-    cmake=3.22.1-1ubuntu1.22.04.2 \
-    python3-pip=22.0.2+dfsg-1ubuntu0.4 \
-    software-properties-common=0.99.22.9 \
-    wget=1.21.2-2ubuntu1 \
-    gnupg=2.2.27-3ubuntu2.1 \
-    lsb-release=11.1.0ubuntu4 \
+    cmake \
+    software-properties-common \
+    wget \
+    gnupg \
+    lsb-release \
+    pipx \
     && wget -qO- https://apt.llvm.org/llvm-snapshot.gpg.key | tee /etc/apt/trusted.gpg.d/apt.llvm.org.asc \
-    && add-apt-repository 'deb http://apt.llvm.org/jammy/  llvm-toolchain-jammy main' \
-    && apt install -y clang-tidy-19
+    && add-apt-repository 'deb http://apt.llvm.org/mantic/  llvm-toolchain-mantic main' \
+    && apt update \
+    && apt install -y clang-tidy-19 \
+    && apt-get clean
+
+ENV PATH="/root/.local/bin:$PATH"
+RUN pipx install conan --pip-args="--no-cache-dir" --system-site-packages
+
+COPY conanfile.py conanprofile.docker conanprofile.docker_arm ./
+
+RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then \
+    mv conanprofile.docker_arm conanprofile; \
+    else \
+    mv conanprofile.docker conanprofile; \
+    fi
+
 
-RUN pip install conan==2.0.17
+RUN apt-get update && apt-get install -y gcc g++
 
-COPY conanfile.py conanprofile.docker ./
-RUN mv conanprofile.docker conanprofile
+RUN gcc --version
 
 RUN conan install . --build=missing --profile ./conanprofile --profile:build ./conanprofile --output-folder=build -s build_type=Debug
diff --git a/conanfile.py b/conanfile.py
@@ -5,18 +5,19 @@
 class SiloRecipe(ConanFile):
     settings = "os", "compiler", "build_type", "arch"
 
+    # Update regularly
     requires = [
-        "boost/1.82.0",
-        "duckdb/0.8.1",
-        "poco/1.12.4",
-        "hwloc/2.9.3",
-        "onetbb/2021.10.0",
-        "nlohmann_json/3.11.2",
-        "gtest/cci.20210126",
-        "roaring/1.0.0",
-        "spdlog/1.11.0",
-        "yaml-cpp/0.7.0",
-        "zstd/1.5.5",
+        "boost/1.83.0", # https://conan.io/center/recipes?value=boosta #FIXME: Serialization error with 1.84.0
+        "duckdb/0.8.1", # https://conan.io/center/recipes?value=duckdb #FIXME: test files only compatible with 0.8, need to EXPORT DATABASE in v0.8, then IMPORT DATABASE on the current version of DuckDB
+        "gtest/1.14.0", # https://conan.io/center/recipes?value=gtest
+        "hwloc/2.9.3", # https://conan.io/center/recipes?value=hwloc # BLOCKED: Pinned by onetbb <= 2021.12.0
+        "nlohmann_json/3.11.3", # https://conan.io/center/recipes?value=nlohmann_json
+        "onetbb/2021.12.0", # https://conan.io/center/recipes?value=onetbb
+        "poco/1.13.3", # https://conan.io/center/recipes?value=poco
+        "roaring/4.0.0", # https://conan.io/center/recipes?value=roaring
+        "spdlog/1.11.0", # https://conan.io/center/recipes?value=spdlog #FIXME: 1.12.0 fails with `error: implicit instantiation of undefined template` #TODO: holding back upgrade to 1.14.1
+        "yaml-cpp/0.8.0", # https://conan.io/center/recipes?value=yaml-cpp
+        "zstd/1.5.5", # https://conan.io/center/recipes?value=zstd #BLOCKED: Pinned by boost <=1.85.0
     ]
 
     default_options = {

diff --git a/conanprofile.docker b/conanprofile.docker
@@ -3,6 +3,6 @@ os=Linux
 arch=x86_64
 compiler=gcc
 compiler.libcxx=libstdc++11
-compiler.version=9.3
+compiler.version=12.2
 build_type=Release
 [options]
diff --git a/conanprofile.docker_arm b/conanprofile.docker_arm
@@ -3,6 +3,6 @@ os=Linux
 arch=armv8
 compiler=gcc
 compiler.libcxx=libstdc++11
-compiler.version=9.3
+compiler.version=12.2
 build_type=Release
 [options]
diff --git a/conanprofile.example → conanprofile.linux_x86 b/conanprofile.example → conanprofile.linux_x86
@@ -3,6 +3,6 @@ os=Linux
 arch=x86_64
 compiler=gcc
 compiler.libcxx=libstdc++11
-compiler.version=9.3
+compiler.version=12.2
 build_type=Release
 [options]
diff --git a/conanprofile.mac_arm b/conanprofile.mac_arm
@@ -0,0 +1,8 @@
+[settings]
+os=Macos
+arch=armv8
+compiler=gcc
+compiler.libcxx=libstdc++11
+compiler.version=12.2
+build_type=Release
+[options]
diff --git a/include/silo/config/util/abstract_config_source.h b/include/silo/config/util/abstract_config_source.h
@@ -1,5 +1,6 @@
 #pragma once
 
+#include <cstdint>
 #include <optional>
 #include <string>
 #include <string_view>

diff --git a/src/silo/query_engine/actions/tuple.cpp b/src/silo/query_engine/actions/tuple.cpp
@@ -458,7 +458,7 @@ std::vector<Tuple> TupleFactory::allocateMany(size_t count) {
    const size_t allocation_size = tuple_size * count;
    std::vector<std::byte>& data = all_tuple_data.emplace_back(allocation_size);
    for (unsigned i = 0; i < count; i++) {
-      tuples.emplace_back(&columns, data.data() + i * tuple_size, tuple_size);
+      tuples.emplace_back(&columns, data.data() + (i * tuple_size), tuple_size);
    }
    return tuples;
 }