Feature/modernize firmware

.github/workflows/ci.yml

@@ -23,24 +23,21 @@ jobs:
 
       - name: Build and Start Docker Compose
         run: |
-          docker-compose up -d --build
+          docker-compose up -d 
 
       - name: Run C Static Analysis
         run: |
-          docker-compose exec -T app bash -c "dos2unix /workspace/ContinuousIntegration/run_c_static_code_analysis.sh && bash /workspace/ContinuousIntegration/run_c_static_code_analysis.sh"
+          docker-compose exec -T ionizationchamber bash -c "python3 -m venv /workspace/venv && source /workspace/venv/bin/activate && cd /workspace/build && cmake .. && make cstatic"
 
       - name: Copy C Analysis Reports to Host
         run: |
-          docker cp app:/workspace/build/C_Lint_ReportApplicationOnly.txt .
-          docker cp app:/workspace/build/C_Lint_ReportFull.txt .
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/CStaticAnalysis .
 
       - name: Archive C Analysis Reports
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: c-lint-reports
-          path: |
-            C_Lint_ReportApplicationOnly.txt
-            C_Lint_ReportFull.txt
+          path: CStaticAnalysis
 
       - name: Clean Up Containers
         run: |
@@ -60,28 +57,28 @@ jobs:
 
       - name: Build and Start Docker Compose
         run: |
-          docker-compose up -d --build
+          docker-compose up -d 
 
       - name: Run Python Static Analysis
         run: |
-          docker-compose exec -T app bash -c "dos2unix /workspace/ContinuousIntegration/run_python_static_code_analysis.sh && bash /workspace/ContinuousIntegration/run_python_static_code_analysis.sh"
+          docker-compose exec -T ionizationchamber bash -c "python3 -m venv /workspace/venv && source /workspace/venv/bin/activate && pip install -e /workspace/Software/MeasurementAcquisition && cd /workspace/build/ && cmake .. && make pystatic"
 
       - name: Copy Python Analysis Reports to Host
         run: |
-          docker cp app:/workspace/build/python_lint_report ./python_lint_report
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/PyStaticAnalysis .
 
       - name: Archive Python Analysis Reports
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-lint-reports
-          path: python_lint_report
+          path: PyStaticAnalysis
 
       - name: Clean Up Containers
         run: |
           docker-compose down
 
-  run-shell-static-analysis:
-    name: Run Shell Static Analysis
+  run-r-static-analysis:
+    name: Run R Static Analysis
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Code
@@ -94,21 +91,21 @@ jobs:
 
       - name: Build and Start Docker Compose
         run: |
-          docker-compose up -d --build
+          docker-compose up -d 
 
-      - name: Run Shell Static Analysis
+      - name: Run R Static Analysis
         run: |
-          docker-compose exec -T app bash -c "dos2unix /workspace/ContinuousIntegration/run_shellscripts_static_code_analysis.sh && bash /workspace/ContinuousIntegration/run_shellscripts_static_code_analysis.sh"
+          docker-compose exec -T ionizationchamber bash -c "source /workspace/venv/bin/activate && cd /workspace/build && cmake .. && make rstatic"
 
-      - name: Copy Shell Analysis Report to Host
+      - name: Copy R Analysis Reports to Host
         run: |
-          docker cp app:/workspace/build/Shell_Script_Lint_Report.txt Shell_Script_Lint_Report.txt
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/RStaticAnalysis .
 
-      - name: Archive Shell Analysis Report
-        uses: actions/upload-artifact@v3
+      - name: Archive R Analysis Reports
+        uses: actions/upload-artifact@v4
         with:
-          name: shell-lint-report
-          path: Shell_Script_Lint_Report.txt
+          name: r-lint-reports
+          path: RStaticAnalysis
 
       - name: Clean Up Containers
         run: |
@@ -128,29 +125,129 @@ jobs:
 
       - name: Build and Start Docker Compose
         run: |
-          docker-compose up -d --build
+          docker-compose up -d 
 
       - name: Build Firmware
         run: |
-          docker-compose exec -T app bash -c "cd /workspace/build && cmake ../Software/Firmware/ && make -j$(nproc)"
+          docker-compose exec -T ionizationchamber bash -c "mkdir -p /workspace/build/firmware && cd /workspace/build/firmware && cmake -DCMAKE_TOOLCHAIN_FILE=/workspace/Software/Firmware/sdcc-stm8.cmake -B . -S /workspace/Software/Firmware/ && cmake --build . -j$(nproc)"
 
       - name: Copy Firmware Files to Host
         run: |
-          docker cp app:/workspace/build/IonizationChamber.cdb .
-          docker cp app:/workspace/build/IonizationChamber.lk .
-          docker cp app:/workspace/build/IonizationChamber.ihx .
-          docker cp app:/workspace/build/IonizationChamber.map .
+          docker cp ionizationchamber:/workspace/build/firmware/IonizationChamber.lk .
+          docker cp ionizationchamber:/workspace/build/firmware/IonizationChamber.ihx .
+          docker cp ionizationchamber:/workspace/build/firmware/IonizationChamber.map .
 
       - name: Archive Firmware Build Artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: firmware-build-artifacts
           path: |
-            IonizationChamber.cdb
             IonizationChamber.lk
             IonizationChamber.ihx
             IonizationChamber.map
 
       - name: Clean Up Containers
         run: |
           docker-compose down
+
+  docs-coverage:
+    name: Documentation Coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Install Docker Compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+
+      - name: Build and Start Docker Compose
+        run: |
+          docker-compose up -d 
+
+      - name: Generate Documentation
+        run: |
+          docker-compose exec -T ionizationchamber bash -c "python3 -m venv /workspace/venv && source /workspace/venv/bin/activate && cd /workspace/build/ && cmake .. && make docs"
+
+      - name: Copy Documentation Coverage Report
+        run: |
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/DocsCoverage .
+
+      - name: Archive Documentation Coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-coverage-report
+          path: DocsCoverage
+
+      - name: Clean Up Containers
+        run: |
+          docker-compose down
+
+  c-code-coverage:
+    name: C Code Coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Install Docker Compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+
+      - name: Build and Start Docker Compose
+        run: |
+          docker-compose up -d 
+
+      - name: Generate C Code Coverage
+        run: |
+          docker-compose exec -T ionizationchamber bash -c "mkdir -p /workspace/build/ut && cd /workspace/build/ut && cmake -DCMAKE_BUILD_TYPE=Debug /workspace/Software/Firmware/UnitTest/ && make -j$(nproc) && make run_all_tests  && make coverage"
+
+      - name: Copy C Code Coverage Report
+        run: |
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/CCodeCoverage .
+
+      - name: Archive C Code Coverage
+        uses: actions/upload-artifact@v4
+        with:
+          name: c-code-coverage-report
+          path: CCodeCoverage
+
+      - name: Clean Up Containers
+        run: |
+          docker-compose down
+
+  run-python-code-coverage:
+    name: Run Python Code Coverage
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v3
+
+      - name: Install Docker Compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+
+      - name: Build and Start Docker Compose
+        run: |
+          docker-compose up -d 
+
+      - name: Run Python Code Coverage
+        run: |
+          docker-compose exec -T ionizationchamber bash -c "source /workspace/venv/bin/activate && cd /workspace/build && cmake .. && make pycoverage"
+
+      - name: Copy Python Analysis Reports to Host
+        run: |
+          docker cp ionizationchamber:/workspace/DevOps/BuildArtifacts/PyCodeCoverage .
+
+      - name: Archive Python Analysis Reports
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-code-coverage-reports
+          path: PyCodeCoverage
+
+      - name: Clean Up Containers
+        run: |
+          docker-compose down

CMakeLists.txt

@@ -0,0 +1,11 @@
+cmake_minimum_required(VERSION 3.31)
+project(IoninizationChamberCodeQuality)
+
+add_subdirectory(Software/Firmware/UnitTest/)
+
+include(DevOps/Cmake/DocsCoverage.cmake)
+include(DevOps/Cmake/PyStaticAnalysis.cmake)
+include(DevOps/Cmake/PyCodeCoverage.cmake)
+include(DevOps/Cmake/CStaticAnalysis.cmake)
+include(DevOps/Cmake/RStaticAnalysis.cmake)
+include(DevOps/Cmake/CodeBeautifier.cmake)

DevOps/BuildArtifacts/.gitignore

@@ -0,0 +1,8 @@
+DocsCoverage/
+PyStaticAnalysis/
+PyCodeCoverage/
+CStaticAnalysis/
+CCodeCoverage/
+RStaticAnalysis/
+*.png
+*.svg

DevOps/Cmake/CStaticAnalysis.cmake

@@ -0,0 +1,88 @@
+cmake_minimum_required(VERSION 3.31)
+
+# Get the number of available processors
+include(ProcessorCount)
+ProcessorCount(NPROC)
+if(NOT NPROC OR NPROC EQUAL 0)
+    set(NPROC 1) # Fallback to 1 if ProcessorCount fails
+endif()
+
+# Define the source directories to analyze
+set(CODECHECKER_SOURCE_DIRS
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Application"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Device"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Driver"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/UnitTest")
+
+# Define the output directories for CodeChecker analysis and reports
+set(CODECHECKER_ANALYZE_DIR /tmp/StaticAnalysisIntermediary)
+set(CODECHECKER_REPORT_DIR ${CMAKE_SOURCE_DIR}/DevOps/BuildArtifacts/CStaticAnalysis)
+set(CODECHECKER_SKIP_FILE ${CMAKE_SOURCE_DIR}/DevOps/Scripts/CodeCheckerSkipList)
+
+# Ensure the output directories exist
+file(MAKE_DIRECTORY ${CODECHECKER_ANALYZE_DIR})
+file(MAKE_DIRECTORY ${CODECHECKER_REPORT_DIR})
+
+# Add a custom target for CodeChecker analysis
+add_custom_target(cstatic
+
+    COMMAND CodeChecker analyze compile_commands.json
+        --output ${CODECHECKER_ANALYZE_DIR}
+        --file ${CODECHECKER_SOURCE_DIRS}
+        --skip ${CODECHECKER_SKIP_FILE}
+        --jobs ${NPROC}
+        --enable-all
+        #--disable checker:clang-diagnostic-c++98-compat
+        #--disable modernize-use-trailing-return-type
+        #--disable readability-identifier-length
+        #--disable readability-uppercase-literal-suffix
+        #--disable modernize-avoid-c-arrays
+        #--disable modernize-use-auto
+        --disable altera-unroll-loops
+        #--disable cppcheck-missingIncludeSystem
+        #--disable cppcheck-toomanyconfigs
+        #--disable checker:clang-diagnostic-padded
+        --disable altera-struct-pack-align
+        #--disable clang-diagnostic-weak-vtables
+        #--disable altera-id-dependent-backward-branch
+        --disable bugprone-easily-swappable-parameters
+        #--disable clang-diagnostic-covered-switch-default
+        # project specific
+        --disable modernize-macro-to-enum
+        --disable clang-diagnostic-declaration-after-statement
+        --disable optin.core.EnumCastOutOfRange # https://github.com/llvm/llvm-project/issues/76208
+        --disable checker:clang-diagnostic-unsafe-buffer-usage # https://stackoverflow.com/questions/77017567/how-to-fix-code-to-avoid-warning-wunsafe-buffer-usage
+        --disable security.insecureAPI.DeprecatedOrUnsafeBufferHandling # we dont use string-related functions due to STM8 binary size limitation 
+    COMMENT "Running CodeChecker analysis..."
+
+    COMMAND CodeChecker parse ${CODECHECKER_ANALYZE_DIR}
+        --skip ${CODECHECKER_SKIP_FILE}
+        --export html
+        --output ${CODECHECKER_REPORT_DIR}
+    COMMENT "Generating CodeChecker HTML report..."
+
+    VERBATIM
+)
+
+# Add a custom command to generate the HTML report
+add_custom_command(TARGET cstatic POST_BUILD
+    COMMAND CodeChecker parse ${CODECHECKER_ANALYZE_DIR}
+        --skip ${CODECHECKER_SKIP_FILE}
+        --export html
+        --output ${CODECHECKER_REPORT_DIR}
+    COMMENT "Generating CodeChecker HTML report..."
+    VERBATIM
+)
+
+# Add a custom command to check for errors and fail the build if any are found
+add_custom_command(TARGET cstatic POST_BUILD
+    COMMAND bash -c "if [ -n \"\$(CodeChecker parse ${CODECHECKER_ANALYZE_DIR} | grep -i 'error')\" ]; then echo 'CodeChecker found errors!'; exit 1; fi"
+    COMMENT "Failing the build if CodeChecker finds errors..."
+    VERBATIM
+)
+
+# Message if CodeChecker is not found (optional)
+find_program(CODECHECKER_EXECUTABLE CodeChecker)
+if(NOT CODECHECKER_EXECUTABLE)
+    message(WARNING "CodeChecker not found. Skipping static analysis.")
+endif()

DevOps/Cmake/CodeBeautifier.cmake

@@ -0,0 +1,42 @@
+cmake_minimum_required(VERSION 3.31)
+
+find_program(UNCRUSTIFY uncrustify)
+find_program(RSCRIPT Rscript)
+find_program(BLACK black)
+# Get all files
+file(GLOB MODIFY_FILES 
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/*.c"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Application/*.h"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Application/*.c"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Device/*.h"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Device/*.c"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Driver/*.h"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/Driver/*.c"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/UnitTest/*.h"
+    "${CMAKE_SOURCE_DIR}/Software/Firmware/UnitTest/*.c"
+)
+
+# Files to exclude
+set(EXCLUDE_FILES
+#    "${CMAKE_SOURCE_DIR}/Software/Firmware/Driver/interrupt_handler.h"
+#    "${CMAKE_SOURCE_DIR}/Software/Firmware/Driver/interrupt_handler.c"
+)
+
+# Remove excluded files
+list(REMOVE_ITEM MODIFY_FILES ${EXCLUDE_FILES})
+
+add_custom_target(style
+    COMMAND ${UNCRUSTIFY} -c "${CMAKE_SOURCE_DIR}/DevOps/Scripts/uncrustify.cfg" --replace --no-backup ${MODIFY_FILES}
+    WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+    COMMENT "Running uncrustify on source directories"
+
+    COMMAND ${BLACK} "${CMAKE_SOURCE_DIR}/Software/MeasurementAcquisition" 
+    COMMAND ${BLACK} "${CMAKE_SOURCE_DIR}/Simulation"
+    WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+    COMMENT "Running black on source directories"
+
+    COMMAND  ${RSCRIPT} "${CMAKE_SOURCE_DIR}/Software/MeasurementAnalysis"
+    WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+    COMMENT "Running styler (R language formatter) on source directories"
+    VERBATIM
+)