Atomic woes, megalinter, and batches (#13)

* fix libCZI dependency w/ atomic woes

* add megalinter

* fix megalinter triggers

* use correct flavor

* build status in readme

* clang-format

* megalinter batch

* disable suggestions

set libCZI options before fetching

Set compile definitions for static libCZI

.github/workflows/mega-linter.yml

@@ -0,0 +1,204 @@
+# MegaLinter GitHub Action configuration file
+# More info at https://megalinter.io
+---
+name: MegaLinter
+
+# Trigger mega-linter at every push. Action will also be visible from
+# Pull Requests to main
+on:
+  # Comment this line to trigger action only on pull-requests
+  # (not recommended if you don't pay for GH Actions)
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+# Comment env block if you do not want to apply fixes
+env:
+  # Apply linter fixes configuration
+  #
+  # When active, APPLY_FIXES must also be defined as environment variable
+  # (in github/workflows/mega-linter.yml or other CI tool)
+  APPLY_FIXES: none
+
+  # Decide which event triggers application of fixes in a commit or a PR
+  # (pull_request, push, all)
+  APPLY_FIXES_EVENT: pull_request
+
+  # If APPLY_FIXES is used, defines if the fixes are directly committed (commit)
+  # or posted in a PR (pull_request)
+  APPLY_FIXES_MODE: commit
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  megalinter:
+    name: MegaLinter
+    runs-on: ubuntu-latest
+
+    # Give the default GITHUB_TOKEN write permission to commit and push, comment
+    # issues, and post new Pull Requests; remove the ones you do not need
+    permissions:
+      contents: write
+      issues: write
+      pull-requests: write
+
+    steps:
+      # Git Checkout
+      - name: Checkout Code
+        uses: actions/checkout@v5
+        with:
+          token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
+
+          # If you use VALIDATE_ALL_CODEBASE = true, you can remove this line to
+          # improve performance
+          fetch-depth: 0
+
+      # MegaLinter
+      - name: MegaLinter
+
+        # You can override MegaLinter flavor used to have faster performances
+        # More info at https://megalinter.io/latest/flavors/
+        uses: oxsecurity/megalinter/flavors/c_cpp@v9.1.0
+
+        id: ml
+
+        # All available variables are described in documentation
+        # https://megalinter.io/latest/config-file/
+        env:
+          # Validates all source when push on main, else just the git diff with
+          # main. Override with true if you always want to lint all sources
+          #
+          # To validate the entire codebase, set to:
+          # VALIDATE_ALL_CODEBASE: true
+          #
+          # To validate only diff with main, set to:
+          # VALIDATE_ALL_CODEBASE: >-
+          #   ${{
+          #     github.event_name == 'push' &&
+          #     github.ref == 'refs/heads/main'
+          #   }}
+          VALIDATE_ALL_CODEBASE: true
+
+          # Disable LLM Advisor for bot PRs (dependabot, renovate, etc.)
+          LLM_ADVISOR_ENABLED: >-
+            ${{
+              github.event_name != 'pull_request' ||
+              (github.event.pull_request.user.login != 'dependabot[bot]' &&
+               github.event.pull_request.user.login != 'renovate[bot]' &&
+               github.event.pull_request.user.login != 'github-actions[bot]' &&
+               !startsWith(github.event.pull_request.user.login, 'dependabot') &&
+               !startsWith(github.event.pull_request.user.login, 'renovate'))
+            }}
+
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+          # Uncomment to use ApiReporter (Grafana)
+          # API_REPORTER: true
+          # API_REPORTER_URL: ${{ secrets.API_REPORTER_URL }}
+          # API_REPORTER_BASIC_AUTH_USERNAME: ${{ secrets.API_REPORTER_BASIC_AUTH_USERNAME }}
+          # API_REPORTER_BASIC_AUTH_PASSWORD: ${{ secrets.API_REPORTER_BASIC_AUTH_PASSWORD }}
+          # API_REPORTER_METRICS_URL: ${{ secrets.API_REPORTER_METRICS_URL }}
+          # API_REPORTER_METRICS_BASIC_AUTH_USERNAME: ${{ secrets.API_REPORTER_METRICS_BASIC_AUTH_USERNAME }}
+          # API_REPORTER_METRICS_BASIC_AUTH_PASSWORD: ${{ secrets.API_REPORTER_METRICS_BASIC_AUTH_PASSWORD }}
+          # API_REPORTER_DEBUG: false
+
+          # ADD YOUR CUSTOM ENV VARIABLES HERE TO OVERRIDE VALUES OF
+          # .mega-linter.yml AT THE ROOT OF YOUR REPOSITORY
+
+      # Upload MegaLinter artifacts
+      - name: Archive production artifacts
+        uses: actions/upload-artifact@v4
+        if: success() || failure()
+        with:
+          name: MegaLinter reports
+          include-hidden-files: "true"
+          path: |
+            megalinter-reports
+            mega-linter.log
+
+      # Create pull request if applicable
+      # (for now works only on PR from same repository, not from forks)
+      - name: Create Pull Request with applied fixes
+        uses: peter-evans/create-pull-request@v7
+        id: cpr
+        if: >-
+          steps.ml.outputs.has_updated_sources == 1 &&
+          (
+            env.APPLY_FIXES_EVENT == 'all' ||
+            env.APPLY_FIXES_EVENT == github.event_name
+          ) &&
+          env.APPLY_FIXES_MODE == 'pull_request' &&
+          (
+            github.event_name == 'push' ||
+            github.event.pull_request.head.repo.full_name == github.repository
+          ) &&
+          !contains(github.event.head_commit.message, 'skip fix')
+        with:
+          token: ${{ secrets.PAT || secrets.GITHUB_TOKEN }}
+          commit-message: "[MegaLinter] Apply linters automatic fixes"
+          title: "[MegaLinter] Apply linters automatic fixes"
+          labels: bot
+
+      - name: Create PR output
+        if: >-
+          steps.ml.outputs.has_updated_sources == 1 &&
+          (
+            env.APPLY_FIXES_EVENT == 'all' ||
+            env.APPLY_FIXES_EVENT == github.event_name
+          ) &&
+          env.APPLY_FIXES_MODE == 'pull_request' &&
+          (
+            github.event_name == 'push' ||
+            github.event.pull_request.head.repo.full_name == github.repository
+          ) &&
+          !contains(github.event.head_commit.message, 'skip fix')
+        run: |
+          echo "PR Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "PR URL - ${{ steps.cpr.outputs.pull-request-url }}"
+
+      # Push new commit if applicable
+      # (for now works only on PR from same repository, not from forks)
+      - name: Prepare commit
+        if: >-
+          steps.ml.outputs.has_updated_sources == 1 &&
+          (
+            env.APPLY_FIXES_EVENT == 'all' ||
+            env.APPLY_FIXES_EVENT == github.event_name
+          ) &&
+          env.APPLY_FIXES_MODE == 'commit' &&
+          github.ref != 'refs/heads/main' &&
+          (
+            github.event_name == 'push' ||
+            github.event.pull_request.head.repo.full_name == github.repository
+          ) &&
+          !contains(github.event.head_commit.message, 'skip fix')
+        run: sudo chown -Rc $UID .git/
+
+      - name: Commit and push applied linter fixes
+        uses: stefanzweifel/git-auto-commit-action@v6
+        if: >-
+          steps.ml.outputs.has_updated_sources == 1 &&
+          (
+            env.APPLY_FIXES_EVENT == 'all' ||
+            env.APPLY_FIXES_EVENT == github.event_name
+          ) &&
+          env.APPLY_FIXES_MODE == 'commit' &&
+          github.ref != 'refs/heads/main' &&
+          (
+            github.event_name == 'push' ||
+            github.event.pull_request.head.repo.full_name == github.repository
+          ) &&
+          !contains(github.event.head_commit.message, 'skip fix')
+        with:
+          branch: >-
+            ${{
+              github.event.pull_request.head.ref ||
+              github.head_ref ||
+              github.ref
+            }}
+          commit_message: "[MegaLinter] Apply linters fixes"
+          commit_user_name: megalinter-bot
+          commit_user_email: 129584137+megalinter-bot@users.noreply.github.com

.gitignore

@@ -2,4 +2,5 @@ build/
 out/
 .vs/
 .cache/
-*~
+*~
+megalinter-reports/

.mega-linter.yml

@@ -0,0 +1,28 @@
+# Configuration file for MegaLinter
+#
+# See all available variables at https://megalinter.io/latest/config-file/ and in
+# linters documentation
+
+# all, none, or list of linter keys
+APPLY_FIXES: none
+
+# If you use ENABLE variable, all other languages/formats/tooling-formats will
+# be disabled by default
+# ENABLE:
+
+# If you use ENABLE_LINTERS variable, all other linters will be disabled by
+# default
+ENABLE_LINTERS:
+  - SPELL
+  - CPP_CLANG_FORMAT
+
+# DISABLE:
+  # - COPYPASTE # Uncomment to disable checks of excessive copy-pastes
+  # - SPELL # Uncomment to disable checks of spelling mistakes
+
+SHOW_ELAPSED_TIME: true
+
+# Uncomment if you want MegaLinter to detect errors but not block CI to pass
+DISABLE_ERRORS: true
+
+FLAVOR_SUGGESTIONS: false

Readme.org

@@ -6,6 +6,9 @@
 #+author: Maximilian Kueffner
 #+exclude_tags: noexport
 
+[[https://github.com/m-aXimilian/pixelarium/actions/workflows/ci-workflow.yml][file:https://github.com/m-aXimilian/pixelarium/actions/workflows/ci-workflow.yml/badge.svg]]
+[[https://github.com/m-aXimilian/pixelarium/actions/workflows/mega-linter.yml][file:https://github.com/m-aXimilian/pixelarium/actions/workflows/mega-linter.yml/badge.svg]]
+
 * Synopsis
 
 Pixelarium strives to be a batteries-included visualizer application used in conjunction with an externally implemented and linked arbitrary functionality.

cmake/libCZI.cmake

@@ -8,13 +8,15 @@ FetchContent_Declare(
 
 if(NOT libCZI_POPULATED)
   message(STATUS "Fetching libCZI")
-  FetchContent_MakeAvailable(libCZI)
 
-  set(LIBCZI_BUILD_CZICMD OFF CACHE BOOL "" FORCE)
+  set(LIBCZI_BUILD_CZICMD                           OFF CACHE BOOL "Don't build commandline libCZI." FORCE)
-  set(LIBCZI_BUILD_DYNLIB OFF CACHE BOOL "" FORCE)
+  set(LIBCZI_BUILD_DYNLIB                           OFF CACHE BOOL "Don't build libCZI as a shared library." FORCE)
-  set(LIBCZI_BUILD_UNITTESTS OFF CACHE BOOL "" FORCE)
+  set(LIBCZI_BUILD_UNITTESTS                        OFF CACHE BOOL "Don't build libCZI unit tests." FORCE)
-  set(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_RAPIDJSON OFF CACHE BOOL "" FORCE)
+  set(LIBCZI_BUILD_PREFER_EXTERNALPACKAGE_RAPIDJSON OFF CACHE BOOL "Use internal rapidjson." FORCE)
-  set(LIBCZI_DO_NOT_SET_MSVC_RUNTIME_LIBRARY  ON CACHE BOOL "" FORCE)
+  set(LIBCZI_DO_NOT_SET_MSVC_RUNTIME_LIBRARY        ON  CACHE BOOL "Consumer sets the runtime." FORCE)
+  set(ADDITIONAL_LIBS_REQUIRED_FOR_ATOMIC           ""  CACHE STRING "Additional atomic libs included." FORCE)
+
+  FetchContent_MakeAvailable(libCZI)
 endif()
 
 FetchContent_GetProperties(libCZI)

lib/imaging/CMakeLists.txt

@@ -22,6 +22,8 @@ set(IMAGELIBLIBNAME pixelariumimagelib)
 add_library(${IMAGELIBLIBNAME}
   STATIC ${IMAGELIBSRC})
 
+target_compile_definitions(${IMAGELIBLIBNAME} PUBLIC _LIBCZISTATICLIB)
+
 target_link_libraries(${IMAGELIBLIBNAME}
   PUBLIC ${OpenCV_LIBS}
   PUBLIC pixelariumutilslib

lib/imaging/IPixelariumImage.hpp

@@ -46,7 +46,7 @@ class IPixelariumImage
     virtual std::unique_ptr<cv::Mat> TryGetImage() = 0;
 
     /// @brief Attempts to retrieve the image.
-    /// @param query The query object defining the images to retrieve./// 
+    /// @param query The query object defining the images to retrieve.
     /// @return A unique pointer to a Mat object containing the image data,
     /// or nullptr if the image is not found or cannot be retrieved.
     virtual std::unique_ptr<cv::Mat> TryGetImage(const IImageQuery& query) = 0;

lib/imaging/PixelariumImageFactory.cpp

@@ -7,7 +7,6 @@
 #include "impl/PixelariumJpg.hpp"
 #include "impl/PixelariumPng.hpp"
 
-
 /*static*/ std::unique_ptr<pixelarium::imaging::IPixelariumImage>
 pixelarium::imaging::PixelariumImageFactory::CreateImage(const std::string& uri, const Log& log)
 {

lib/imaging/impl/PixelariumCzi.cpp

@@ -29,7 +29,6 @@ bool comp_blockinfo_params(const pixelarium::imaging::CziParams& params, const l
     return res;
 }
 
-
 constexpr int try_get_index_match(const pixelarium::imaging::CziParams& params, libCZI::ICZIReader& reader)
 {
     int index{-1};

lib/imaging/impl/PixelariumCzi.hpp

@@ -4,8 +4,8 @@
 #include <string>
 
 #include "../IPixelariumImage.hpp"
-#include "utilities/ILog.hpp"
 #include "libCZI.h"
+#include "utilities/ILog.hpp"
 
 namespace pixelarium::imaging
 {
@@ -21,12 +21,12 @@ struct CziParams : public IImageQuery
 class PixelariumCzi : public IPixelariumImage
 {
     using Log = pixelarium::utils::log::ILog;
+
    public:
     explicit PixelariumCzi(const std::string& uri, const Log& log);
     ~PixelariumCzi()
     {
-        if (this->czi_reader_)
+        if (this->czi_reader_) this->czi_reader_->Close();
-            this->czi_reader_->Close();
     }
 
     // IPixelariumImage member implementations

lib/rendering/RenderImageManager.hpp

@@ -5,7 +5,6 @@
 #include <unordered_set>
 
 #include "ImageViewFactory.hpp"
-#include "PixelariumImageViewDefault.hpp"
 #include "rendering/IPixelariumImageView.hpp"
 #include "resources/resource.hpp"
 #include "utilities/ILog.hpp"
@@ -23,7 +22,6 @@ struct RenderImageStateWrapper
     const bool* show_state;
 };
 
-
 /// @brief Manage instances of IPixelariumImageView.
 ///
 /// This class is used to keep track of what must be rendered.