refactor: panic: prefix all macros with SILO_

To avoid clashing with gtest's `ASSERT_EQ` and potentially
more. Prefix all macros at once.

CMakeLists.txt

@@ -8,13 +8,13 @@ endif ()
 message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
 
 set(CMAKE_CXX_FLAGS "-Wall")
-set(CMAKE_CXX_FLAGS_DEBUG "-g -fsanitize=address -D DEBUG_ASSERTIONS=1")
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -D DEBUG_ASSERTIONS=0")
+set(CMAKE_CXX_FLAGS_DEBUG "-g -fsanitize=address -D SILO_DEBUG_ASSERTIONS=1")
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -D SILO_DEBUG_ASSERTIONS=0")
 
 # Work-around only for MacOS
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
-    set(CMAKE_CXX_FLAGS_DEBUG "-g -D DEBUG_ASSERTIONS=1")
-    set(CMAKE_CXX_FLAGS_RELEASE "-O3 -D DEBUG_ASSERTIONS=0")
+    set(CMAKE_CXX_FLAGS_DEBUG "-g -D SILO_DEBUG_ASSERTIONS=1")
+    set(CMAKE_CXX_FLAGS_RELEASE "-O3 -D SILO_DEBUG_ASSERTIONS=0")
 endif ()
 
 set(CMAKE_CXX_STANDARD 20)

include/silo/common/panic.h

@@ -29,31 +29,31 @@ namespace silo::common {
 /// Passes arguments to `fmt::format` (at least a format string
 /// argument is required) and adds file and line information, then
 /// calls `panic`.
-#define PANIC(...) silo::common::panic(fmt::format(__VA_ARGS__), __FILE__, __LINE__)
+#define SILO_PANIC(...) silo::common::panic(fmt::format(__VA_ARGS__), __FILE__, __LINE__)
 
 /// Denotes a place that isn't implemented *yet*, during
 /// development. Follows the same path as `PANIC` when reached.
-#define TODO() silo::common::todo(__FILE__, __LINE__)
+#define SILO_TODO() silo::common::todo(__FILE__, __LINE__)
 
 [[noreturn]] void todo(const char* file, int line);
 
 /// Denotes a place that theoretically can't be reached. Follows the
 /// same path as `PANIC` when reached.
-#define UNREACHABLE() silo::common::unreachable(__FILE__, __LINE__)
+#define SILO_UNREACHABLE() silo::common::unreachable(__FILE__, __LINE__)
 
 [[noreturn]] void unreachable(const char* file, int line);
 
 /// Denotes a missing implementation. Follows the same path as `PANIC`
 /// when reached.
-#define UNIMPLEMENTED() silo::common::unimplemented(__FILE__, __LINE__)
+#define SILO_UNIMPLEMENTED() silo::common::unimplemented(__FILE__, __LINE__)
 
 [[noreturn]] void unimplemented(const char* file, int line);
 
 /// Asserts that the expression `e` evaluates to true. On failure
 /// calls `panic` with the stringification of the code `e` and
-/// file/line information. `ASSERT` is always compiled in; if
-/// performance overrides safety, use `DEBUG_ASSERT` instead.
-#define ASSERT(e)                                             \
+/// file/line information. `SILO_ASSERT` is always compiled in; if
+/// performance overrides safety, use `SILO_DEBUG_ASSERT` instead.
+#define SILO_ASSERT(e)                                             \
    do {                                                       \
       if (!(e)) {                                             \
          silo::common::assertFailure(#e, __FILE__, __LINE__); \
@@ -62,7 +62,7 @@ namespace silo::common {
 
 [[noreturn]] void assertFailure(const char* msg, const char* file, int line);
 
-#define INTERNAL_ASSERT_OP_(prefix_str, e1, op, e2)                                       \
+#define SILO_INTERNAL_ASSERT_OP_(prefix_str, e1, op, e2)                                       \
    do {                                                                                   \
       auto internal_assert_op__v1 = (e1);                                                 \
       auto internal_assert_op__v2 = (e2);                                                 \
@@ -79,8 +79,8 @@ namespace silo::common {
       }                                                                                   \
    } while (0)
 
-#define ASSERT_OP_(partial_prefix, e1, op, e2) \
-   INTERNAL_ASSERT_OP_("ASSERT_" #partial_prefix, e1, op, e2)
+#define SILO_ASSERT_OP_(partial_prefix, e1, op, e2) \
+   SILO_INTERNAL_ASSERT_OP_("ASSERT_" #partial_prefix, e1, op, e2)
 
 [[noreturn]] void assertOpFailure(
    const char* prefix,
@@ -96,49 +96,49 @@ namespace silo::common {
 /// value, compared via `==`. On failure calls `panic` with the stringification of the code and the
 /// two values passed through fmt::format, plus file/line information. Always compiled in, if
 /// performance overrides safety, use `DEBUG_ASSERT_EQ` instead.
-#define ASSERT_EQ(e1, e2) ASSERT_OP_(EQ, e1, ==, e2)
+#define SILO_ASSERT_EQ(e1, e2) SILO_ASSERT_OP_(EQ, e1, ==, e2)
 
 /// Like ASSERT_EQ but asserts that `e1 <= e2`.
-#define ASSERT_LE(e1, e2) ASSERT_OP_(LE, e1, <=, e2)
+#define SILO_ASSERT_LE(e1, e2) SILO_ASSERT_OP_(LE, e1, <=, e2)
 
 /// Like ASSERT_EQ but asserts that `e1 < e2`.
-#define ASSERT_LT(e1, e2) ASSERT_OP_(LT, e1, <, e2)
+#define SILO_ASSERT_LT(e1, e2) SILO_ASSERT_OP_(LT, e1, <, e2)
 
 /// Like ASSERT_EQ but asserts that `e1 >= e2`.
-#define ASSERT_GE(e1, e2) ASSERT_OP_(GE, e1, >=, e2)
+#define SILO_ASSERT_GE(e1, e2) SILO_ASSERT_OP_(GE, e1, >=, e2)
 
 /// Like ASSERT_EQ but asserts that `e1 > e2`.
-#define ASSERT_GT(e1, e2) ASSERT_OP_(GT, e1, >, e2)
+#define SILO_ASSERT_GT(e1, e2) SILO_ASSERT_OP_(GT, e1, >, e2)
 
-/// Like ASSERT_EQ but asserts that `e1 != e2`.
-#define ASSERT_NE(e1, e2) ASSERT_OP_(NE, e1, !=, e2)
+/// Like SILO_ASSERT_EQ but asserts that `e1 != e2`.
+#define SILO_ASSERT_NE(e1, e2) SILO_ASSERT_OP_(NE, e1, !=, e2)
 
-/// `DEBUG_ASSERT` is like `ASSERT`, but for cases where performance
+/// `SILO_DEBUG_ASSERT` is like `SILO_ASSERT`, but for cases where performance
 /// is more important than verification in production: instantiations
 /// are only active when compiling SILO in debug (via
 /// `CMakeLists.txt`; concretely, they are compiled to be active when
-/// the preprocessor variable `DEBUG_ASSERTIONS` is set to 1, and
+/// the preprocessor variable `SILO_DEBUG_ASSERTIONS` is set to 1, and
 /// ignored if that variable is set to 0; if the variable is missing,
-/// a compilation warning is printed and `DEBUG_ASSERT` is ignored, if
+/// a compilation warning is printed and `SILO_DEBUG_ASSERT` is ignored, if
 /// present with another value, a compilation error results. Note that
-/// `DEBUG_ASSERTIONS` must be set to 1 for debug builds or
-/// `DEBUG_ASSERT` won't even check the assertion in debug builds. The
+/// `SILO_DEBUG_ASSERTIONS` must be set to 1 for debug builds or
+/// `SILO_DEBUG_ASSERT` won't even check the assertion in debug builds. The
 /// SILO `CMakeLists.txt` does set it up that way.)
-#ifndef DEBUG_ASSERTIONS
+#ifndef SILO_DEBUG_ASSERTIONS
 #warning \
-   "DEBUG_ASSERTIONS is not set, should be 0 to ignore DEBUG_ASSERT, 1 to compile it in, assuming 0"
-#define DEBUG_ASSERTIONS 0
+   "SILO_DEBUG_ASSERTIONS is not set, should be 0 to ignore SILO_DEBUG_ASSERT, 1 to compile it in, assuming 0"
+#define SILO_DEBUG_ASSERTIONS 0
 #else
-#if DEBUG_ASSERTIONS == 0   /* never */
-#elif DEBUG_ASSERTIONS == 1 /* always */
+#if SILO_DEBUG_ASSERTIONS == 0   /* never */
+#elif SILO_DEBUG_ASSERTIONS == 1 /* always */
 #else
-#error "DEBUG_ASSERTIONS should be 0 to ignore DEBUG_ASSERT, 1 to compile it in"
+#error "SILO_DEBUG_ASSERTIONS should be 0 to ignore SILO_DEBUG_ASSERT, 1 to compile it in"
 #endif
 #endif
 
-#define DEBUG_ASSERT(e)                                               \
+#define SILO_DEBUG_ASSERT(e)                                               \
    do {                                                               \
-      if (DEBUG_ASSERTIONS) {                                         \
+      if (SILO_DEBUG_ASSERTIONS) {                                         \
          if (!(e)) {                                                  \
             silo::common::debugAssertFailure(#e, __FILE__, __LINE__); \
          }                                                            \
@@ -147,30 +147,30 @@ namespace silo::common {
 
 [[noreturn]] void debugAssertFailure(const char* msg, const char* file, int line);
 
-#define DEBUG_ASSERT_OP_(partial_prefix, e1, op, e2)                       \
+#define SILO_DEBUG_ASSERT_OP_(partial_prefix, e1, op, e2)                       \
    do {                                                                    \
-      if (DEBUG_ASSERTIONS) {                                              \
-         INTERNAL_ASSERT_OP_("DEBUG_ASSERT_" #partial_prefix, e1, op, e2); \
+      if (SILO_DEBUG_ASSERTIONS) {                                              \
+         SILO_INTERNAL_ASSERT_OP_("DEBUG_ASSERT_" #partial_prefix, e1, op, e2); \
       }                                                                    \
    } while (0)
 
-/// Like `ASSERT_EQ`, but like `DEBUG_ASSERT`, for cases where
+/// Like `SILO_ASSERT_EQ`, but like `SILO_DEBUG_ASSERT`, for cases where
 /// performance is more important than verification in production.
-#define DEBUG_ASSERT_EQ(e1, e2) DEBUG_ASSERT_OP_(EQ, e1, ==, e2)
+#define SILO_DEBUG_ASSERT_EQ(e1, e2) SILO_DEBUG_ASSERT_OP_(EQ, e1, ==, e2)
 
 /// Like DEBUG_ASSERT_EQ but asserts that `e1 <= e2`.
-#define DEBUG_ASSERT_LE(e1, e2) DEBUG_ASSERT_OP_(LE, e1, <=, e2)
+#define SILO_DEBUG_ASSERT_LE(e1, e2) SILO_DEBUG_ASSERT_OP_(LE, e1, <=, e2)
 
 /// Like DEBUG_ASSERT_EQ but asserts that `e1 < e2`.
-#define DEBUG_ASSERT_LT(e1, e2) DEBUG_ASSERT_OP_(LT, e1, <, e2)
+#define SILO_DEBUG_ASSERT_LT(e1, e2) SILO_DEBUG_ASSERT_OP_(LT, e1, <, e2)
 
 /// Like DEBUG_ASSERT_EQ but asserts that `e1 >= e2`.
-#define DEBUG_ASSERT_GE(e1, e2) DEBUG_ASSERT_OP_(GE, e1, >=, e2)
+#define SILO_DEBUG_ASSERT_GE(e1, e2) SILO_DEBUG_ASSERT_OP_(GE, e1, >=, e2)
 
 /// Like DEBUG_ASSERT_EQ but asserts that `e1 > e2`.
-#define DEBUG_ASSERT_GT(e1, e2) DEBUG_ASSERT_OP_(GT, e1, >, e2)
+#define SILO_DEBUG_ASSERT_GT(e1, e2) SILO_DEBUG_ASSERT_OP_(GT, e1, >, e2)
 
 /// Like DEBUG_ASSERT_EQ but asserts that `e1 != e2`.
-#define DEBUG_ASSERT_NE(e1, e2) DEBUG_ASSERT_OP_(NE, e1, !=, e2)
+#define SILO_DEBUG_ASSERT_NE(e1, e2) SILO_DEBUG_ASSERT_OP_(NE, e1, !=, e2)
 
 }  // namespace silo::common

src/silo/common/aa_symbols.cpp

@@ -61,7 +61,7 @@ char AminoAcid::symbolToChar(AminoAcid::Symbol symbol) {
       case AminoAcid::Symbol::STOP:
          return '*';
    }
-   UNREACHABLE();
+   SILO_UNREACHABLE();
 }
 
 std::optional<AminoAcid::Symbol> AminoAcid::charToSymbol(char character) {

src/silo/common/lineage_tree.cpp

@@ -46,8 +46,8 @@ Graph::Graph(size_t number_of_vertices)
       adjacency_list(number_of_vertices) {}
 
 void Graph::addEdge(Idx vertex_from, Idx vertex_to) {
-   ASSERT_LT(vertex_from, number_of_vertices);
-   ASSERT_LT(vertex_to, number_of_vertices);
+   SILO_ASSERT_LT(vertex_from, number_of_vertices);
+   SILO_ASSERT_LT(vertex_to, number_of_vertices);
    adjacency_list.at(vertex_from).emplace_back(vertex_to);
 }
 
@@ -100,11 +100,11 @@ std::optional<std::vector<Idx>> Graph::getCycle() const {
          if (witness_lasso.has_value()) {
             // We found a witness lasso of the form 1 -> 2 -> 3 -> 4 -> 5 -> 3
             // We need to remove leading vertices up until the cycle
-            ASSERT_GE(witness_lasso.value().size(), 2);
+            SILO_ASSERT_GE(witness_lasso.value().size(), 2);
             const Idx cycle_node = witness_lasso.value().back();
             auto cycle_node_first_occurrence =
                std::find(witness_lasso.value().begin(), witness_lasso.value().end(), cycle_node);
-            ASSERT(cycle_node_first_occurrence < witness_lasso.value().end());
+            SILO_ASSERT(cycle_node_first_occurrence < witness_lasso.value().end());
             witness_lasso.value().erase(witness_lasso.value().begin(), cycle_node_first_occurrence);
             return witness_lasso;
          }
@@ -201,7 +201,7 @@ std::unordered_map<Idx, Idx> assignAliasIdsAndGetAliasMapping(
    std::unordered_map<Idx, Idx> alias_mapping;
    for (const auto& lineage : file.lineages) {
       const auto lineage_id = lookup.getId(lineage.lineage_name.string);
-      ASSERT(lineage_id.has_value());
+      SILO_ASSERT(lineage_id.has_value());
       for (const auto& alias : lineage.aliases) {
          if (lookup.getId(alias.string).has_value()) {
             throw silo::preprocessing::PreprocessingException(fmt::format(
@@ -225,7 +225,7 @@ std::vector<std::pair<Idx, Idx>> getParentChildEdges(
    std::vector<std::pair<Idx, Idx>> edge_list;
    for (const auto& lineage : file.lineages) {
       const auto child_id = lookup.getId(lineage.lineage_name.string);
-      ASSERT(child_id.has_value());
+      SILO_ASSERT(child_id.has_value());
 
       for (const auto& parent_lineage : lineage.parents) {
          auto parent_id = lookup.getId(parent_lineage.string);
@@ -270,4 +270,4 @@ LineageTreeAndIdMap LineageTreeAndIdMap::fromLineageDefinitionFilePath(
    return fromLineageDefinitionFile(definition_file);
 }
 
-}  // namespace silo::common
+}  // namespace silo::common

src/silo/common/nucleotide_symbols.cpp

@@ -38,7 +38,7 @@ char Nucleotide::symbolToChar(Nucleotide::Symbol symbol) {
       case Symbol::N:
          return 'N';
    }
-   UNREACHABLE();
+   SILO_UNREACHABLE();
 }
 
 std::optional<Nucleotide::Symbol> Nucleotide::charToSymbol(char character) {

src/silo/common/optional_bool.cpp

@@ -45,7 +45,7 @@ std::optional<bool> OptionalBool::value() const noexcept {
       case Representation::TRUE:
          return true;
    }
-   UNREACHABLE();
+   SILO_UNREACHABLE();
 }
 
 std::string_view OptionalBool::asStr() const noexcept {
@@ -57,7 +57,7 @@ std::string_view OptionalBool::asStr() const noexcept {
       case Representation::TRUE:
          return "true";
    }
-   UNREACHABLE();
+   SILO_UNREACHABLE();
 }
 
 }  // namespace silo::common

src/silo/common/panic.test.cpp

@@ -47,18 +47,18 @@ void nullCapableSetenv(const char* name, const char* value, int overwrite) {
 
 // NOLINTNEXTLINE(readability-identifier-naming,readability-function-cognitive-complexity)
 TEST(panic, assertEqPanicModes) {
-   ASSERT_EQ(1 + 1, 2);
+   SILO_ASSERT_EQ(1 + 1, 2);
 
    const char* old_env = getenv("SILO_PANIC");
    setenv("SILO_PANIC", "", 1);
    try {
-      ASSERT_EQ(1 + 1, 3);
+      SILO_ASSERT_EQ(1 + 1, 3);
    } catch (const std::exception& ex) {
       assertMsg(ex.what(), "ASSERT_EQ failure: 1 + 1 == 3: 2 == 3");
    };
 
    setenv("SILO_PANIC", "abort", 1);
-   ASSERT_DEATH(ASSERT_EQ(1 + 1, 3), "ASSERT_EQ failure: 1 \\+ 1 == 3: 2 == 3");
+   ASSERT_DEATH(SILO_ASSERT_EQ(1 + 1, 3), "ASSERT_EQ failure: 1 \\+ 1 == 3: 2 == 3");
 
    // revert it back
    nullCapableSetenv("SILO_PANIC", old_env, 1);
@@ -67,42 +67,42 @@ TEST(panic, assertEqPanicModes) {
 // NOLINTNEXTLINE(readability-identifier-naming,readability-function-cognitive-complexity)
 TEST(panic, debugAssertBehavesAsPerCompilationMode) {
    // should never complain
-   DEBUG_ASSERT(1 + 1 == 2);
+   SILO_DEBUG_ASSERT(1 + 1 == 2);
 
-   // Check that DEBUG_ASSERT is active if DEBUG_ASSERTIONS==1, off
+   // Check that DEBUG_ASSERT is active if SILO_DEBUG_ASSERTIONS==1, off
    // otherwise; each of those branches is only tested when compiling
    // the unit tests in debug or release mode, respectively.
 
-#if DEBUG_ASSERTIONS
+#if SILO_DEBUG_ASSERTIONS
 
    const char* old_env = getenv("SILO_PANIC");
    setenv("SILO_PANIC", "", 1);
    try {
-      DEBUG_ASSERT(1 + 1 == 3);
+      SILO_DEBUG_ASSERT(1 + 1 == 3);
    } catch (const std::exception& ex) {
       assertMsg(ex.what(), "DEBUG_ASSERT failure: 1 + 1 == 3");
    };
    nullCapableSetenv("SILO_PANIC", old_env, 1);
 
 #else
-   // check that DEBUG_ASSERT is disabled
-   DEBUG_ASSERT(1 + 1 == 3);
+   // check that SILO_DEBUG_ASSERT is disabled
+   SILO_DEBUG_ASSERT(1 + 1 == 3);
 #endif
 }
 
 // NOLINTNEXTLINE(readability-identifier-naming,readability-function-cognitive-complexity)
 TEST(panic, debugAssertGeWorks) {
    // stand-in for all the DEBUG_ASSERT_* variants
 
-   DEBUG_ASSERT_GE(1 + 5, 6);
-   DEBUG_ASSERT_GE(1 + 5, 5);
+   SILO_DEBUG_ASSERT_GE(1 + 5, 6);
+   SILO_DEBUG_ASSERT_GE(1 + 5, 5);
 
-#if DEBUG_ASSERTIONS
+#if SILO_DEBUG_ASSERTIONS
 
    const char* old_env = getenv("SILO_PANIC");
    setenv("SILO_PANIC", "", 1);
    try {
-      DEBUG_ASSERT_GE(1 + 5, 7);
+      SILO_DEBUG_ASSERT_GE(1 + 5, 7);
    } catch (const std::exception& ex) {
       assertMsg(ex.what(), "DEBUG_ASSERT_GE failure: 1 + 5 >= 7: 6 >= 7");
    };

src/silo/common/string_utils.cpp

@@ -64,7 +64,7 @@ std::vector<std::string> tie(
    const std::vector<std::string>& elements2,
    std::string_view suffix
 ) {
-   ASSERT(elements1.size() == elements2.size());
+   SILO_ASSERT(elements1.size() == elements2.size());
    std::vector<std::string> output;
    output.reserve(elements1.size());
    for (size_t i = 0; i < elements1.size(); ++i) {

src/silo/common/table_reader.cpp

@@ -39,7 +39,7 @@ silo::TableReader::TableReader(
 
 size_t silo::TableReader::read() {
    loadTable();
-   ASSERT(query_result->ColumnCount() == column_functions.size() + 1);
+   SILO_ASSERT(query_result->ColumnCount() == column_functions.size() + 1);
    size_t current_start_of_chunk = 0;
    std::unique_ptr<duckdb::DataChunk> current_chunk = query_result->Fetch();
    while (current_chunk) {

src/silo/database.cpp

@@ -201,7 +201,7 @@ BitmapContainerSize& BitmapContainerSize::operator+=(const BitmapContainerSize&
 
 BitmapSizePerSymbol& BitmapSizePerSymbol::operator+=(const BitmapSizePerSymbol& other) {
    for (const auto& symbol : Nucleotide::SYMBOLS) {
-      ASSERT(size_in_bytes.contains(symbol));
+      SILO_ASSERT(size_in_bytes.contains(symbol));
       size_in_bytes.at(symbol) += other.size_in_bytes.at(symbol);
    }
    return *this;
@@ -225,7 +225,7 @@ BitmapSizePerSymbol Database::calculateBitmapSizePerSymbol(
 
       for (const SequenceStorePartition<SymbolType>& seq_store_partition : seq_store.partitions) {
          for (const auto& position : seq_store_partition.positions) {
-            ASSERT(bitmap_size_per_symbol.size_in_bytes.contains(symbol));
+            SILO_ASSERT(bitmap_size_per_symbol.size_in_bytes.contains(symbol));
             bitmap_size_per_symbol.size_in_bytes[symbol] +=
                position.getBitmap(symbol)->getSizeInBytes();
          }
@@ -651,7 +651,7 @@ void Database::initializeColumn(const config::DatabaseMetadata& metadata) {
          }
          return;
    }
-   UNREACHABLE();
+   SILO_UNREACHABLE();
 }
 
 void Database::initializeColumns() {