Merge pull request #133 from bkryza/fix-add-compile-commands-flags

Fix add compile commands flags

.gitignore

@@ -6,7 +6,7 @@ CMakeScripts
 Testing
 cmake_install.cmake
 install_manifest.txt
-compile_commands.json
+/compile_commands.json
 CTestTestfile.cmake
 Session.vim
 _deps

CHANGELOG.md

@@ -1,5 +1,6 @@
 # CHANGELOG
 
+  * Fixed add_compile_flags and added remove_compile_flags config options (#130)
   * Added rendering of template specialization fields and methods (#128)
   * Improved template specialization/instantiation matching based on deduced
     context

docs/configuration_file.md

@@ -16,6 +16,8 @@
 * `diagrams` - the map of diagrams to be generated, each diagram name is provided as
              the key of the diagram YAML node
 * `debug_mode` - add inline debug information in the generated diagrams
+* `add_compile_flags` - add compile flags to all compilation database entries
+* `remove_compile_flags` - remove compile flags from all compilation database entries
 
 ### Diagram options
 * `type` - type of diagram, one of [`class`, `sequence`, `package`, `include`]
@@ -56,6 +58,9 @@ compilation_database_dir: debug
 # Inject additional compile commands to the compilation database entries
 add_compile_flags:
   - '-Wno-vla-extension'
+# Remove specified compile flags from all compilation database entries
+remove_compile_flags:
+  - '-Wshadow'
 # The directory where *.puml files will be generated
 output_directory: docs/diagrams
 # Set this as default for all diagrams

docs/troubleshooting.md

@@ -4,6 +4,7 @@
 
 * [General issues](#general-issues)
   * [Diagram generated with PlantUML is cropped](#diagram-generated-with-plantuml-is-cropped)
+  * [`clang` produces several warnings during diagram generation](#clang-produces-several-warnings-during-diagram-generation)
   * [YAML anchors and aliases are not fully supported](#yaml-anchors-and-aliases-are-not-fully-supported)
 * [Class diagrams](#class-diagrams)
   * ["fatal error: 'stddef.h' file not found"](#fatal-error-stddefh-file-not-found)
@@ -24,6 +25,43 @@ $ plantuml -tsvg mydiagram.puml
 $ convert +antialias mydiagram.svg mydiagram.png
 ```
 
+### `clang` produces several warnings during diagram generation
+During the generation of the diagram `clang` may report a lot of warnings, which
+do not occur during the compilation with other compiler (e.g. GCC). This can be
+fixed easily by using the `add_compile_flags` config option. For instance,
+assuming that the warnings are as follows:
+
+```
+... warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion]
+... warning: declaration shadows a variable in namespace 'YAML' [-Wshadow]
+```
+
+simply add the following to your `.clang-uml` configuration file:
+
+```
+add_compile_flags:
+  - -Wno-implicit-const-int-float-conversion
+  - -Wno-shadow
+```
+
+Alternatively, the same can be passed through the `clang-uml` command line, e.g.
+
+```bash
+$ clang-uml --add-compile-flag -Wno-implicit-const-int-float-conversion \
+            --add-compile-flag -Wno-shadow ...
+```
+
+Please note that if your `compile_commands.json` already contains - for instance
+`-Wshadow` - then you also have to remove it, i.e.:
+
+```
+add_compile_flags:
+  - -Wno-implicit-const-int-float-conversion
+  - -Wno-shadow
+remove_compile_flags:
+  - -Wshadow
+```
+
 ### YAML anchors and aliases are not fully supported
 `clang-uml` uses [yaml-cpp](https://github.com/jbeder/yaml-cpp) library, which
 currently does not support
@@ -76,6 +114,25 @@ project), e.g.:
 apt install clang
 ```
 
+If this doesn't help the include paths can be customized using config options:
+ * `add_compile_flags` - which adds a list of compile flags such as include paths to each entry of the compilation database
+ * `remove_compile_flags` - which removes existing compile flags from each entry of the compilation database
+
+For instance:
+
+```yaml
+add_compile_flags:
+  - -I/opt/my_toolchain/include
+remove_compile_flags:
+  - -I/usr/include
+```
+
+These options can be also passed on the command line, for instance:
+
+```bash
+$ clang-uml --add-compile-flag -I/opt/my_toolchain/include \
+            --remove-compile-flag -I/usr/include ...
+```
 ## Sequence diagrams
 ### Generated diagram is empty
 In order to generate sequence diagram the `start_from` configuration option must have a valid starting point

src/cli/cli_handler.cc

@@ -83,6 +83,11 @@ cli_flow_t cli_handler::parse(int argc, const char **argv)
     app.add_flag("-l,--list-diagrams", list_diagrams,
         "Print list of diagrams defined in the config file");
     app.add_flag("--init", initialize, "Initialize example config file");
+    app.add_option("--add-compile-flag", add_compile_flag,
+        "Add a compilation flag to each entry in the compilation database");
+    app.add_option("--remove-compile-flag", remove_compile_flag,
+        "Remove a compilation flag from each entry in the compilation "
+        "database");
     app.add_option(
         "--add-class-diagram", add_class_diagram, "Add class diagram config");
     app.add_option("--add-sequence-diagram", add_sequence_diagram,
@@ -269,6 +274,21 @@ cli_flow_t cli_handler::handle_post_config_options()
     if (!ensure_output_directory_exists(effective_output_directory))
         return cli_flow_t::kError;
 
+    //
+    // Append add_compile_flags and remove_compile_flags to the config
+    //
+    if (add_compile_flag) {
+        std::copy(add_compile_flag->begin(), add_compile_flag->end(),
+            std::back_inserter(config.add_compile_flags.value));
+        config.add_compile_flags.has_value = true;
+    }
+
+    if (remove_compile_flag) {
+        std::copy(remove_compile_flag->begin(), remove_compile_flag->end(),
+            std::back_inserter(config.remove_compile_flags.value));
+        config.remove_compile_flags.has_value = true;
+    }
+
     return cli_flow_t::kContinue;
 }
 

src/cli/cli_handler.h

@@ -121,6 +121,8 @@ public:
     bool list_diagrams{false};
     bool quiet{false};
     bool initialize{false};
+    std::optional<std::vector<std::string>> add_compile_flag;
+    std::optional<std::vector<std::string>> remove_compile_flag;
     std::optional<std::string> add_class_diagram;
     std::optional<std::string> add_sequence_diagram;
     std::optional<std::string> add_package_diagram;

src/common/compilation_database.cc

@@ -0,0 +1,104 @@
+/**
+ * src/common/compilation_database.cc
+ *
+ * Copyright (c) 2021-2023 Bartek Kryza <bkryza@gmail.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include "compilation_database.h"
+
+namespace clanguml::common {
+
+std::unique_ptr<compilation_database>
+compilation_database::auto_detect_from_directory(
+    const clanguml::config::config &cfg)
+{
+    std::string error_message;
+    auto res = clang::tooling::CompilationDatabase::autoDetectFromDirectory(
+        cfg.compilation_database_dir(), error_message);
+
+    if (!error_message.empty())
+        throw compilation_database_error(error_message);
+
+    return std::make_unique<compilation_database>(std::move(res), cfg);
+}
+
+compilation_database::compilation_database(
+    std::unique_ptr<clang::tooling::CompilationDatabase> base,
+    const clanguml::config::config &cfg)
+    : base_{std::move(base)}
+    , config_{cfg}
+{
+}
+
+const clanguml::config::config &compilation_database::config() const
+{
+    return config_;
+}
+
+const clang::tooling::CompilationDatabase &compilation_database::base() const
+{
+    return *base_;
+}
+
+std::vector<std::string> compilation_database::getAllFiles() const
+{
+    return base().getAllFiles();
+}
+
+std::vector<clang::tooling::CompileCommand>
+compilation_database::getCompileCommands(clang::StringRef FilePath) const
+{
+    auto commands = base().getCompileCommands(FilePath);
+
+    adjust_compilation_database(commands);
+
+    return commands;
+}
+
+std::vector<clang::tooling::CompileCommand>
+compilation_database::getAllCompileCommands() const
+{
+    auto commands = base().getAllCompileCommands();
+
+    adjust_compilation_database(commands);
+
+    return commands;
+}
+
+void compilation_database::adjust_compilation_database(
+    std::vector<clang::tooling::CompileCommand> &commands) const
+{
+    if (config().add_compile_flags && !config().add_compile_flags().empty()) {
+        for (auto &compile_command : commands) {
+            compile_command.CommandLine.insert(
+                // Add flags after argv[0]
+                compile_command.CommandLine.begin() + 1,
+                config().add_compile_flags().begin(),
+                config().add_compile_flags().end());
+        }
+    }
+
+    if (config().remove_compile_flags &&
+        !config().remove_compile_flags().empty()) {
+        for (auto &compile_command : commands) {
+            for (const auto &flag : config().remove_compile_flags()) {
+                util::erase_if(compile_command.CommandLine,
+                    [&flag](const auto &arg) { return flag == arg; });
+            }
+        }
+    }
+}
+
+} // namespace clanguml::common

src/common/compilation_database.h

@@ -0,0 +1,78 @@
+/**
+ * src/common/compilation_database.h
+ *
+ * Copyright (c) 2021-2023 Bartek Kryza <bkryza@gmail.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#pragma once
+
+#include "common/model/enums.h"
+#include "common/model/namespace.h"
+#include "common/model/template_parameter.h"
+#include "config/config.h"
+#include "types.h"
+#include "util/util.h"
+
+#include <clang/Frontend/CompilerInstance.h>
+#include <clang/Tooling/CompilationDatabase.h>
+#include <clang/Tooling/Tooling.h>
+
+#include <deque>
+#include <filesystem>
+#include <string>
+
+namespace clanguml::common {
+
+class compilation_database_error : public std::runtime_error {
+    using std::runtime_error::runtime_error;
+};
+
+class compilation_database : public clang::tooling::CompilationDatabase {
+public:
+    compilation_database(
+        std::unique_ptr<clang::tooling::CompilationDatabase> base,
+        const clanguml::config::config &cfg);
+
+    ~compilation_database() override = default;
+
+    static std::unique_ptr<compilation_database> auto_detect_from_directory(
+        const clanguml::config::config &cfg);
+
+    std::vector<clang::tooling::CompileCommand> getCompileCommands(
+        clang::StringRef FilePath) const override;
+
+    std::vector<std::string> getAllFiles() const override;
+
+    std::vector<clang::tooling::CompileCommand>
+    getAllCompileCommands() const override;
+
+    const clanguml::config::config &config() const;
+
+    const clang::tooling::CompilationDatabase &base() const;
+
+private:
+    void adjust_compilation_database(
+        std::vector<clang::tooling::CompileCommand> &commands) const;
+
+    // Actual instance of the compilation database is stored in here
+    // The inheritance is just to keep the interface
+    std::unique_ptr<clang::tooling::CompilationDatabase> base_;
+
+    // Reference to the clang-uml config
+    const clanguml::config::config &config_;
+};
+
+using compilation_database_ptr = std::unique_ptr<compilation_database>;
+
+} // namespace clanguml::common

src/common/generators/generators.cc

@@ -79,7 +79,7 @@ void generate_diagram_select_generator(const std::string &od,
 template <typename DiagramConfig>
 void generate_diagram_impl(const std::string &od, const std::string &name,
     std::shared_ptr<clanguml::config::diagram> diagram,
-    const clang::tooling::CompilationDatabase &db,
+    const common::compilation_database &db,
     const std::vector<std::string> &translation_units,
     const std::vector<clanguml::common::generator_type_t> &generators,
     bool verbose)
@@ -107,7 +107,7 @@ void generate_diagram_impl(const std::string &od, const std::string &name,
 
 void generate_diagram(const std::string &od, const std::string &name,
     std::shared_ptr<clanguml::config::diagram> diagram,
-    const clang::tooling::CompilationDatabase &db,
+    const common::compilation_database &db,
     const std::vector<std::string> &translation_units,
     const std::vector<clanguml::common::generator_type_t> &generators,
     bool verbose)
@@ -139,9 +139,9 @@ void generate_diagram(const std::string &od, const std::string &name,
 }
 
 void generate_diagrams(const std::vector<std::string> &diagram_names,
-    clanguml::config::config &config, const std::string &od,
+    config::config &config, const std::string &od,
-    const std::unique_ptr<clang::tooling::CompilationDatabase> &db,
+    const common::compilation_database_ptr &db, const int verbose,
-    const int verbose, const unsigned int thread_count,
+    const unsigned int thread_count,
     const std::vector<clanguml::common::generator_type_t> &generators,
     const std::map<std::string, std::vector<std::string>>
         &translation_units_map)
@@ -184,17 +184,4 @@ void generate_diagrams(const std::vector<std::string> &diagram_names,
     }
 }
 
-void adjust_compilation_database(const clanguml::config::config &config,
-    clang::tooling::CompilationDatabase &db)
-{
-    if (config.add_compile_flags && !config.add_compile_flags().empty()) {
-        for (auto &compile_command : db.getAllCompileCommands()) {
-            compile_command.CommandLine.insert(
-                compile_command.CommandLine.begin() + 1,
-                config.add_compile_flags().begin(),
-                config.add_compile_flags().end());
-        }
-    }
-}
-
 } // namespace clanguml::common::generators

src/common/generators/generators.h

@@ -20,6 +20,7 @@
 #include "class_diagram/generators/json/class_diagram_generator.h"
 #include "class_diagram/generators/plantuml/class_diagram_generator.h"
 #include "cli/cli_handler.h"
+#include "common/compilation_database.h"
 #include "common/generators/generators.h"
 #include "common/model/diagram_filter.h"
 #include "config/config.h"
@@ -33,7 +34,6 @@
 #include "version.h"
 
 #include <clang/Frontend/CompilerInstance.h>
-#include <clang/Tooling/CompilationDatabase.h>
 #include <clang/Tooling/Tooling.h>
 
 #include <cstring>
@@ -139,9 +139,6 @@ void find_translation_units_for_diagrams(
     const std::vector<std::string> &compilation_database_files,
     std::map<std::string, std::vector<std::string>> &translation_units_map);
 
-void adjust_compilation_database(const clanguml::config::config &config,
-    clang::tooling::CompilationDatabase &db);
-
 template <typename DiagramModel, typename DiagramConfig,
     typename TranslationUnitVisitor>
 class diagram_ast_consumer : public clang::ASTConsumer {
@@ -229,10 +226,9 @@ private:
 
 template <typename DiagramModel, typename DiagramConfig,
     typename DiagramVisitor>
-std::unique_ptr<DiagramModel> generate(
+std::unique_ptr<DiagramModel> generate(const common::compilation_database &db,
-    const clang::tooling::CompilationDatabase &db, const std::string &name,
+    const std::string &name, DiagramConfig &config,
-    DiagramConfig &config, const std::vector<std::string> &translation_units,
+    const std::vector<std::string> &translation_units, bool /*verbose*/ = false)
-    bool /*verbose*/ = false)
 {
     LOG_INFO("Generating diagram {}", name);
 
@@ -262,14 +258,14 @@ std::unique_ptr<DiagramModel> generate(
 
 void generate_diagram(const std::string &od, const std::string &name,
     std::shared_ptr<clanguml::config::diagram> diagram,
-    const clang::tooling::CompilationDatabase &db,
+    const common::compilation_database &db,
     const std::vector<std::string> &translation_units,
     const std::vector<clanguml::common::generator_type_t> &generators,
     bool verbose);
 
 void generate_diagrams(const std::vector<std::string> &diagram_names,
     clanguml::config::config &config, const std::string &od,
-    const std::unique_ptr<clang::tooling::CompilationDatabase> &db, int verbose,
+    const common::compilation_database_ptr &db, int verbose,
     unsigned int thread_count,
     const std::vector<clanguml::common::generator_type_t> &generators,
     const std::map<std::string, std::vector<std::string>>

src/config/config.h

@@ -226,6 +226,8 @@ struct config : public inheritable_diagram_options {
     option<std::string> compilation_database_dir{
         "compilation_database_dir", "."};
     option<std::vector<std::string>> add_compile_flags{"add_compile_flags"};
+    option<std::vector<std::string>> remove_compile_flags{
+        "remove_compile_flags"};
     option<std::string> output_directory{"output_directory"};
 
     option<std::map<std::string, diagram_template>> diagram_templates{

src/config/yaml_decoders.cc

@@ -588,6 +588,7 @@ template <> struct convert<config> {
         get_option(node, rhs.output_directory);
         get_option(node, rhs.compilation_database_dir);
         get_option(node, rhs.add_compile_flags);
+        get_option(node, rhs.remove_compile_flags);
         get_option(node, rhs.include_relations_also_as_members);
         get_option(node, rhs.puml);
         get_option(node, rhs.generate_method_arguments);

src/config/yaml_emitters.cc

@@ -188,6 +188,7 @@ YAML::Emitter &operator<<(YAML::Emitter &out, const config &c)
     out << c.compilation_database_dir;
     out << c.output_directory;
     out << c.add_compile_flags;
+    out << c.remove_compile_flags;
 
     out << dynamic_cast<const inheritable_diagram_options &>(c);
 

src/main.cc

@@ -17,6 +17,7 @@
  */
 
 #include "cli/cli_handler.h"
+#include "common/compilation_database.h"
 #include "common/generators/generators.h"
 #include "include_diagram/generators/plantuml/include_diagram_generator.h"
 #include "util/util.h"
@@ -53,38 +54,33 @@ int main(int argc, const char *argv[])
     if (res == cli::cli_flow_t::kError)
         return 1;
 
-    std::string err{};
+    try {
-    auto db = clang::tooling::CompilationDatabase::autoDetectFromDirectory(
+        const auto db =
-        cli.config.compilation_database_dir(), err);
+            clanguml::common::compilation_database::auto_detect_from_directory(
+                cli.config);
 
-    if (!err.empty()) {
+        const auto compilation_database_files = db->getAllFiles();
-        LOG_ERROR("Failed to load compilation database from {}",
+
-            cli.config.compilation_database_dir());
+        std::map<std::string /* diagram name */,
+            std::vector<std::string> /*translation units*/>
+            translation_units_map;
+
+        // We have to generate the translation units list for each diagram
+        // before scheduling tasks, because std::filesystem::current_path cannot
+        // be trusted with multiple threads
+        clanguml::common::generators::find_translation_units_for_diagrams(
+            cli.diagram_names, cli.config, compilation_database_files,
+            translation_units_map);
+
+        clanguml::common::generators::generate_diagrams(cli.diagram_names,
+            cli.config, cli.effective_output_directory, db, cli.verbose,
+            cli.thread_count, cli.generators, translation_units_map);
+    }
+    catch (clanguml::common::compilation_database_error &e) {
+        LOG_ERROR("Failed to load compilation database from {} due to: {}",
+            cli.config.compilation_database_dir(), e.what());
         return 1;
     }
 
-    const auto compilation_database_files = db->getAllFiles();
-
-    std::map<std::string /* diagram name */,
-        std::vector<std::string> /*translation units*/>
-        translation_units_map;
-
-    // We have to generate the translation units list for each diagram before
-    // scheduling tasks, because std::filesystem::current_path cannot be trusted
-    // with multiple threads
-    clanguml::common::generators::find_translation_units_for_diagrams(
-        cli.diagram_names, cli.config, compilation_database_files,
-        translation_units_map);
-
-    //
-    // Inject any additional compilation flags from the config to the
-    // compilation database
-    //
-    clanguml::common::generators::adjust_compilation_database(cli.config, *db);
-
-    clanguml::common::generators::generate_diagrams(cli.diagram_names,
-        cli.config, cli.effective_output_directory, db, cli.verbose,
-        cli.thread_count, cli.generators, translation_units_map);
-
     return 0;
 }

tests/CMakeLists.txt

@@ -1,7 +1,9 @@
 
 file(GLOB_RECURSE TEST_CASE_SOURCES t*/*.cc t*/*.c t*/src/*.c)
 file(GLOB_RECURSE TEST_CASE_CONFIGS t*/.clang-uml)
-file(GLOB_RECURSE TEST_CONFIG_YMLS test_config_data/*.yml)
+file(GLOB_RECURSE TEST_CONFIG_YMLS test_config_data/*.yml
+                                   test_compilation_database_data/*.yml
+                                   test_compilation_database_data/*.json)
 
 set(TEST_CASES_REQUIRING_CXX20 t00056 t00058 t00059)
 
@@ -36,6 +38,7 @@ set(TEST_CASES
         test_util
         test_model
         test_cases
+        test_compilation_database
         test_decorator_parser
         test_config
         test_cli_handler

tests/test_cases.cc

@@ -19,6 +19,7 @@
 #include "test_cases.h"
 
 #include "cli/cli_handler.h"
+#include "common/compilation_database.h"
 #include "common/generators/generators.h"
 
 #include <spdlog/spdlog.h>
@@ -33,32 +34,28 @@ void inject_diagram_options(std::shared_ptr<clanguml::config::diagram> diagram)
     diagram->generate_links.set(links_config);
 }
 
-std::pair<clanguml::config::config,
+std::pair<clanguml::config::config, clanguml::common::compilation_database_ptr>
-    std::unique_ptr<clang::tooling::CompilationDatabase>>
 load_config(const std::string &test_name)
 {
-    auto config = clanguml::config::load(test_name + "/.clang-uml", true);
+    std::pair<clanguml::config::config,
+        clanguml::common::compilation_database_ptr>
+        res;
+
+    res.first = clanguml::config::load(test_name + "/.clang-uml", true);
 
     LOG_DBG("Loading compilation database from {}",
-        config.compilation_database_dir());
+        res.first.compilation_database_dir());
 
-    std::string err{};
+    res.second =
-    auto compilation_database =
+        clanguml::common::compilation_database::auto_detect_from_directory(
-        clang::tooling::CompilationDatabase::autoDetectFromDirectory(
+            res.first);
-            config.compilation_database_dir(), err);
 
-    if (!err.empty()) {
+    return res;
-        LOG_ERROR("Failed to load compilation database from {}",
-            config.compilation_database_dir());
-        throw std::runtime_error{err};
-    }
-
-    return std::make_pair(std::move(config), std::move(compilation_database));
 }
 
 namespace detail {
 template <typename DiagramConfig>
-auto generate_diagram_impl(clang::tooling::CompilationDatabase &db,
+auto generate_diagram_impl(clanguml::common::compilation_database &db,
     std::shared_ptr<clanguml::config::diagram> diagram)
 {
     using diagram_config = DiagramConfig;
@@ -117,7 +114,7 @@ auto generate_diagram_json(
 }
 
 std::unique_ptr<clanguml::class_diagram::model::diagram> generate_class_diagram(
-    clang::tooling::CompilationDatabase &db,
+    clanguml::common::compilation_database &db,
     std::shared_ptr<clanguml::config::diagram> diagram)
 {
     return detail::generate_diagram_impl<clanguml::config::class_diagram>(
@@ -125,7 +122,7 @@ std::unique_ptr<clanguml::class_diagram::model::diagram> generate_class_diagram(
 }
 
 std::unique_ptr<clanguml::sequence_diagram::model::diagram>
-generate_sequence_diagram(clang::tooling::CompilationDatabase &db,
+generate_sequence_diagram(clanguml::common::compilation_database &db,
     std::shared_ptr<clanguml::config::diagram> diagram)
 {
     return detail::generate_diagram_impl<clanguml::config::sequence_diagram>(
@@ -133,7 +130,7 @@ generate_sequence_diagram(clang::tooling::CompilationDatabase &db,
 }
 
 std::unique_ptr<clanguml::package_diagram::model::diagram>
-generate_package_diagram(clang::tooling::CompilationDatabase &db,
+generate_package_diagram(clanguml::common::compilation_database &db,
     std::shared_ptr<clanguml::config::diagram> diagram)
 {
     return detail::generate_diagram_impl<clanguml::config::package_diagram>(
@@ -141,7 +138,7 @@ generate_package_diagram(clang::tooling::CompilationDatabase &db,
 }
 
 std::unique_ptr<clanguml::include_diagram::model::diagram>
-generate_include_diagram(clang::tooling::CompilationDatabase &db,
+generate_include_diagram(clanguml::common::compilation_database &db,
     std::shared_ptr<clanguml::config::diagram> diagram)
 {
     return detail::generate_diagram_impl<clanguml::config::include_diagram>(

tests/test_cases.h

@@ -23,6 +23,7 @@
 #include "class_diagram/model/diagram.h"
 #include "class_diagram/visitor/translation_unit_visitor.h"
 #include "common/clang_utils.h"
+#include "common/compilation_database.h"
 #include "config/config.h"
 #include "include_diagram/generators/plantuml/include_diagram_generator.h"
 #include "include_diagram/visitor/translation_unit_visitor.h"
@@ -54,8 +55,7 @@ using Catch::Matchers::VectorContains;
 
 using namespace clanguml::util;
 
-std::pair<clanguml::config::config,
+std::pair<clanguml::config::config, clanguml::common::compilation_database_ptr>
-    std::unique_ptr<clang::tooling::CompilationDatabase>>
 load_config(const std::string &test_name);
 
 std::string generate_sequence_puml(

tests/test_cli_handler.cc

@@ -156,4 +156,31 @@ TEST_CASE("Test cli handler print_diagram_template", "[unit-test]")
     namespaces: [{{ namespace_name }}]
 
 )");
+}
+
+TEST_CASE(
+    "Test cli handler add_compile_flag and remove_compile_flag", "[unit-test]")
+{
+    using clanguml::cli::cli_flow_t;
+    using clanguml::cli::cli_handler;
+    using clanguml::util::contains;
+
+    std::vector<const char *> argv{"clang-uml", "--config",
+        "./test_config_data/simple.yml", "--add-compile-flag", "-Wno-error",
+        "--add-compile-flag", "-Wno-warning", "--remove-compile-flag",
+        "-I/usr/include"};
+
+    std::ostringstream ostr;
+    cli_handler cli{ostr, make_sstream_logger(ostr)};
+
+    auto res = cli.handle_options(argv.size(), argv.data());
+
+    REQUIRE(res == cli_flow_t::kContinue);
+
+    REQUIRE(cli.config.add_compile_flags.has_value);
+    REQUIRE(cli.config.remove_compile_flags.has_value);
+
+    REQUIRE(contains(cli.config.add_compile_flags(), "-Wno-error"));
+    REQUIRE(contains(cli.config.add_compile_flags(), "-Wno-warning"));
+    REQUIRE(contains(cli.config.remove_compile_flags(), "-I/usr/include"));
 }

tests/test_compilation_database.cc

@@ -0,0 +1,86 @@
+/**
+ * tests/test_compilation_database.cc
+ *
+ * Copyright (c) 2021-2023 Bartek Kryza <bkryza@gmail.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#define CATCH_CONFIG_MAIN
+
+#include "common/compilation_database.h"
+
+#include "util/util.h"
+
+#include "catch.h"
+#include <spdlog/sinks/ostream_sink.h>
+#include <spdlog/spdlog.h>
+
+std::shared_ptr<spdlog::logger> make_sstream_logger(std::ostream &ostr)
+{
+    auto oss_sink = std::make_shared<spdlog::sinks::ostream_sink_mt>(ostr);
+    return std::make_shared<spdlog::logger>(
+        "clanguml-logger", std::move(oss_sink));
+}
+
+TEST_CASE("Test compilation_database should work", "[unit-test]")
+{
+    using clanguml::common::compilation_database;
+    using clanguml::common::compilation_database_ptr;
+    using clanguml::common::model::access_t;
+    using clanguml::common::model::relationship_t;
+    using clanguml::util::contains;
+
+    auto cfg =
+        clanguml::config::load("./test_compilation_database_data/config.yml");
+
+    try {
+        const auto db =
+            clanguml::common::compilation_database::auto_detect_from_directory(
+                cfg);
+
+        auto all_files = db->getAllFiles();
+
+        REQUIRE(all_files.size() == 3);
+        REQUIRE(all_files.at(0) ==
+            "src/class_diagram/generators/json/class_diagram_generator.cc");
+        REQUIRE(all_files.at(1) ==
+            "src/class_diagram/generators/plantuml/"
+            "class_diagram_generator.cc");
+        REQUIRE(all_files.at(2) == "src/class_diagram/model/class.cc");
+
+        auto ccs = db->getAllCompileCommands();
+
+        REQUIRE(contains(ccs.at(0).CommandLine, "-Wno-error"));
+        REQUIRE(contains(ccs.at(0).CommandLine, "-Wno-unknown-warning-option"));
+        REQUIRE(
+            !contains(ccs.at(0).CommandLine, "-Wno-deprecated-declarations"));
+    }
+    catch (clanguml::common::compilation_database_error &e) {
+        REQUIRE(false);
+    }
+}
+
+TEST_CASE("Test compilation_database should throw", "[unit-test]")
+{
+    using clanguml::common::compilation_database;
+    using clanguml::common::compilation_database_error;
+    using clanguml::common::compilation_database_ptr;
+    using clanguml::util::contains;
+
+    auto cfg = clanguml::config::load(
+        "./test_compilation_database_data/config_bad.yml");
+
+    REQUIRE_THROWS_AS(
+        clanguml::common::compilation_database::auto_detect_from_directory(cfg),
+        compilation_database_error);
+}

tests/test_compilation_database_data/compile_commands.json

@@ -0,0 +1,17 @@
+[
+  {
+    "directory": ".",
+    "command": "/usr/bin/c++  -I/usr/lib/llvm-15/include -Werror -Wall -Wextra -Wno-unused-parameter -Wno-unused-private-field -Wno-deprecated-declarations -std=c++17 -o CMakeFiles/clang-umllib.dir/class_diagram/generators/json/class_diagram_generator.cc.o -c ./src/class_diagram/generators/json/class_diagram_generator.cc",
+    "file": "./src/class_diagram/generators/json/class_diagram_generator.cc"
+  },
+  {
+    "directory": ".",
+    "command": "/usr/bin/c++  -I/usr/lib/llvm-15/include -Werror -Wall -Wextra -Wno-unused-parameter -Wno-unused-private-field -Wno-deprecated-declarations -std=c++17 -o CMakeFiles/clang-umllib.dir/class_diagram/generators/plantuml/class_diagram_generator.cc.o -c ./src/class_diagram/generators/plantuml/class_diagram_generator.cc",
+    "file": "./src/class_diagram/generators/plantuml/class_diagram_generator.cc"
+  },
+  {
+    "directory": ".",
+    "command": "/usr/bin/c++  -I/usr/lib/llvm-15/include -Werror -Wall -Wextra -Wno-unused-parameter -Wno-unused-private-field -Wno-deprecated-declarations -std=c++17 -o CMakeFiles/clang-umllib.dir/class_diagram/model/class.cc.o -c ./src/class_diagram/model/class.cc",
+    "file": "./src/class_diagram/model/class.cc"
+  }
+]

tests/test_compilation_database_data/config.yml

@@ -0,0 +1,7 @@
+compilation_database_dir: .
+output_directory: .
+add_compile_flags: [-Wno-unknown-warning-option, -Wno-error]
+remove_compile_flags: [-Wno-deprecated-declarations]
+diagrams:
+  class_main:
+    type: class

tests/test_compilation_database_data/config_bad.yml

@@ -0,0 +1,5 @@
+compilation_database_dir: /tmp/no_such_directory___
+output_directory: .
+diagrams:
+  class_main:
+    type: class