IWYU compliant code

Makefile.am

@@ -18,7 +18,7 @@ dist_doc_DATA = README.md LICENSE doc/API.md
 # Custom script for generating files, but not installed
 dist_noinst_SCRIPTS = autogen.sh
 
-# Include all files inside doc/doxygen in the distribution tarball
+# Include all files in the contrib, doc, and examples directories in the distribution tarball
 EXTRA_DIST = \
 	$(wildcard contrib/*) \
 	$(wildcard doc/*) \
@@ -33,32 +33,16 @@ doc/doxygen/.stamp: doc/Doxyfile
 # If Doxygen is available, build the documentation
 if HAVE_DOXYGEN
 docs: doc/doxygen/.stamp
+else
+docs:
+	@echo "error: doxygen not found"
+endif
 
 # Target to clean up the documentation directory
 clean-docs:
 	@echo "Cleaning documentation files..."
 	rm -rf doc/doxygen
 
-# Custom rule to install the entire 'doc' directory
-install-data-local: docs
-	$(MKDIR_P) $(DESTDIR)$(docdir)
-	cp -r doc/doxygen/html $(DESTDIR)$(docdir)
-
-# Remove the installed documentation directory during uninstallation.
-uninstall-local:
-	-rm -rf $(DESTDIR)$(docdir)/html
-
-# Ensure that make docs is run when creating a distribution
-dist-hook:
-	$(MAKE) docs
-
-else
-docs:
-	@echo "error: doxygen not found"
-clean-docs:
-	@echo "error: doxygen not found"
-endif
-
 # Custom clean rule to clean both docs and dist/ directory
 clean-local: clean-docs
 	@echo "Cleaning dist directory..."

doc/Doxyfile.in

@@ -949,7 +949,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = src/include/qyra.h src/include/common.h doc/README_doxygen.md
+INPUT                  = src/include/qyra.h doc/README_doxygen.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

examples/example1.cpp

@@ -7,6 +7,8 @@
 
 #include <iostream>
 #include <stdint.h>
+#include <string>
+#include <vector>
 
 /**
  * @brief Main function that initializes a CQYRA object, sets the header and nonce,

examples/example2.cpp

@@ -6,7 +6,7 @@
 #include "../src/utils.h"
 #include <qyra.h>
 
-#include <cstdint>
+#include <cstddef>
 #include <iostream>
 #include <sstream>
 #include <stdexcept>

src/Makefile.am

@@ -30,17 +30,14 @@ lib_LTLIBRARIES = libqyra.la
 noinst_LTLIBRARIES =
 
 # Header file to be installed for public API access
-include_HEADERS = include/qyra.h include/common.h
+include_HEADERS = include/qyra.h
 
 # Include directories
-QYRA_INCLUDES=-I$(builddir) -I$(srcdir)/include -I$(srcdir)/test -I$(srcdir)/bench
+QYRA_INCLUDES=-I$(builddir) -I$(srcdir)/include -I$(srcdir)/test -I$(srcdir)/bench -I$(srcdir)/bench/data
 
 QYRA_API_H = \
 	include/qyra.h
 
-QYRA_COMMON_H = \
-	include/common.h
-
 QYRA_H = \
 	crypto.h \
 	hash.h \
@@ -58,8 +55,7 @@ libqyra_la_SOURCES = \
 	utils.cpp \
 	qyra.cpp \
 	$(QYRA_H) \
-	$(QYRA_API_H) \
-	$(QYRA_COMMON_H)
+	$(QYRA_API_H)
 
 # Preprocessor flags for libqyra
 libqyra_la_CPPFLAGS = $(AM_CPPFLAGS) $(QYRA_INCLUDES)

src/Makefile.bench.include

@@ -25,8 +25,7 @@ QYRA_BENCH = \
 	utils.cpp \
 	bench/bench.h \
 	bench/bench.cpp \
-	$(QYRA_H) \
-	$(QYRA_COMMON_H)
+	$(QYRA_H)
 
 # Specify source files for the qyra-bench program
 bench_qyra_bench_SOURCES = \

src/bench/bench.cpp

@@ -3,17 +3,23 @@
 // file COPYING or https://www.opensource.org/licenses/mit-license.php.
 
 #include <bench.h>
-#include <common.h>
-#include <data/solutions.json.h>
-#include <fstream>
+
 #include <graph.h>
 #include <path.h>
+#include <qyra.h>
 #include <stream.h>
 #include <utils.h>
 
-#include <chrono>
+#include <data/solutions.json.h>
+
+// IWYU pragma: no_include <bits/chrono.h>
+
+#include <chrono> // IWYU pragma: keep
+#include <cstdio>
 #include <iostream>
+#include <limits>
 #include <random>
+#include <string>
 #include <thread>
 #include <vector>
 

src/bench/bench.h

@@ -5,8 +5,10 @@
 #ifndef QYRA_BENCH_H
 #define QYRA_BENCH_H
 
+// IWYU pragma: no_include <oqs/kem_kyber.h>
+
 #include <cstdint>
-#include <oqs/oqs.h>
+#include <oqs/oqs.h> // IWYU pragma: keep
 
 // Public key.
 uint8_t publicKey[OQS_KEM_kyber_768_length_public_key] =

src/crypto.cpp

@@ -3,18 +3,20 @@
 // file COPYING or https://www.opensource.org/licenses/mit-license.php.
 
 #include <crypto.h>
+
 #include <utils.h>
 
-#include <algorithm>
+// IWYU pragma: no_include <oqs/common.h>
+// IWYU pragma: no_include <oqs/kem_kyber.h>
+
 #include <openssl/evp.h>
 #include <openssl/rand.h>
-#include <oqs/oqs.h>
-#include <random>
-#include <stdexcept>
+#include <openssl/types.h>
+#include <oqs/oqs.h> // IWYU pragma: keep
+#include <stdio.h>
+#include <string>
 #include <vector>
 
-#include <iostream>
-
 // Static method to generate a public/secret key pair for encryption.
 bool CCrypter::GenerateKeyPair(uint8_t* public_key, uint8_t* secret_key)
 {

src/crypto.h

@@ -6,7 +6,6 @@
 #define QYRA_CRYPTO_H
 
 #include <cstdint>
-#include <string>
 #include <vector>
 
 /**

src/graph.cpp

@@ -2,21 +2,22 @@
 // Distributed under the MIT software license, see the accompanying
 // file COPYING or https://www.opensource.org/licenses/mit-license.php.
 
-#include <common.h>
-#include <crypto.h>
 #include <graph.h>
+
+#include <crypto.h>
 #include <hash.h>
+#include <qyra.h>
 #include <stream.h>
 #include <utils.h>
 
 #include <algorithm>
 #include <array>
 #include <cassert>
 #include <fstream>
-#include <iomanip>
-#include <stdexcept>
+#include <stdio.h>
 #include <thread>
 #include <unordered_set>
+#include <utility>
 
 // Constructor of the CGraph class.
 // Initializes the adjacency matrix with a maximum number of nodes.
@@ -51,15 +52,8 @@ bool CGraph::AddEdge(uint16_t from, uint16_t to)
     // Reset the bitset for the 'from' node, clearing all edges from this node.
     adjacencyMatrix[from].reset();
 
-    try {
-        // Set the bit indicating an edge from 'from' to 'to'.
-        adjacencyMatrix[from].set(to);
-    } catch (const std::exception& e) {
-        fprintf(stderr, "ERROR: [%s] Failed to set edge from %u to %u: %s\n", __func__, from, to, e.what());
-
-        // Return false on failure
-        return false;
-    }
+    // Set the bit indicating an edge from 'from' to 'to'.
+    adjacencyMatrix[from].set(to);
 
     // Return true on success
     return true;

src/graph.h

@@ -5,8 +5,12 @@
 #ifndef QYRA_GRAPH_H
 #define QYRA_GRAPH_H
 
+// IWYU pragma: no_include <oqs/kem_kyber.h>
+
 #include <bitset>
-#include <oqs/oqs.h>
+#include <cstddef>
+#include <oqs/oqs.h> // IWYU pragma: keep
+#include <stdint.h>
 #include <string>
 #include <vector>
 

src/hash.h

@@ -5,7 +5,6 @@
 #ifndef QYRA_HASH_H
 #define QYRA_HASH_H
 
-#include <string>
 #include <vector>
 
 /**

src/include/qyra.h

@@ -5,8 +5,7 @@
 #ifndef QYRA_H
 #define QYRA_H
 
-#include <common.h>
-
+#include <cstddef>
 #include <cstdint>
 #include <string>
 #include <vector>
@@ -21,9 +20,53 @@
 #endif
 #endif
 
+/**
+ * @brief Explanation of data structure sizes for encryption
+ *
+ * The plaintext consists of two parts:
+ * - **Header**: 108 bytes
+ * - **Nonce**: 32 bytes
+ *
+ * Together, this makes a total of 140 bytes of plaintext data.
+ *
+ * Since AES-256-CBC operates in 16-byte blocks, and the plaintext size is not a multiple of 16,
+ * 4 bytes of padding will be added to reach a size of 144 bytes.
+ *
+ * The encrypted version of this 140-byte plaintext will always be 144 bytes due to padding.
+ */
+#define ENC_SIZE 144         ///< Size of encrypted data
+#define IV_SIZE 16           ///< Size of initialization vector (AES_BLOCK_SIZE)
+#define CIPHERTEXT_SIZE 1088 ///< Size of ciphertext for Kyber768
+#define HASH_SIZE 32         ///< Size of hash
+
+#define TOTAL_SIZE (ENC_SIZE + IV_SIZE + CIPHERTEXT_SIZE) ///< Define total size for the combined vector
+#define SOLUTION_SIZE (TOTAL_SIZE + HASH_SIZE)            ///< Define total size for the solution vector including the hash
+
+/**
+ * @class CGraph
+ * @brief Forward declaration of the CGraph class.
+ *
+ * This class represents a graph structure used in various graph algorithms.
+ */
 class CGraph;
+
+/**
+ * @class CPath
+ * @brief Forward declaration of the CPath class.
+ *
+ * This class is used to represent a path within a graph, enabling
+ * traversal and pathfinding operations.
+ */
 class CPath;
 
+/**
+ * @namespace LibQYRA
+ * @brief A namespace for the LibQYRA library.
+ *
+ * This namespace encompasses all classes and functions
+ * related to the LibQYRA library, providing modularity and
+ * preventing name collisions.
+ */
 namespace LibQYRA {
 
 /**

src/keygen.cpp

@@ -4,9 +4,13 @@
 
 #include <crypto.h>
 
+// IWYU pragma: no_include <oqs/kem_kyber.h>
+
+#include <cstddef>
 #include <iomanip>
 #include <iostream>
-#include <oqs/oqs.h>
+#include <oqs/oqs.h> // IWYU pragma: keep
+#include <stdint.h>
 
 int main()
 {

src/path.cpp

@@ -2,19 +2,18 @@
 // Distributed under the MIT software license, see the accompanying
 // file COPYING or https://www.opensource.org/licenses/mit-license.php.
 
-#include <crypto.h>
+#include <path.h>
+
 #include <graph.h>
 #include <hash.h>
-#include <path.h>
 #include <stream.h>
 #include <utils.h>
 
-#include <algorithm>
+#include <bitset>
+#include <cstdio>
 #include <fstream>
 #include <iostream>
 #include <mutex>
-#include <numeric>
-#include <sstream>
 #include <thread>
 
 // Constructs a CPath from a set of nodes.

src/path.h

@@ -5,6 +5,7 @@
 #ifndef QYRA_PATH_H
 #define QYRA_PATH_H
 
+#include <cstddef>
 #include <cstdint>
 #include <mutex>
 #include <string>

src/qyra.cpp

@@ -9,6 +9,7 @@
 #include <stream.h>
 #include <utils.h>
 
+#include <stdio.h>
 #include <thread>
 #include <vector>
 

src/test/test.cpp

@@ -6,13 +6,9 @@
 
 #include <test.h>
 
-#include <crypto.h>
-#include <utils.h>
-
+#include <boost/test/included/unit_test.hpp> // IWYU pragma: keep
 #include <vector>
 
-#include <boost/test/included/unit_test.hpp>
-
 BasicTestingSetup::BasicTestingSetup()
 {
     originalData = {'H', 'e', 'l', 'l', 'o', ' ', 'W', 'o', 'r', 'l', 'd'};