@ladybugmem/icebug 0.1.0 → 0.1.1

package/vendor/include/networkit/io/METISParser.hpp

@@ -1,63 +0,0 @@
-/*
- * METISParser.hpp
- *
- *  Created on: 27.11.2012
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_IO_METIS_PARSER_HPP_
-#define NETWORKIT_IO_METIS_PARSER_HPP_
-
-#include <fstream>
-#include <string>
-#include <tuple>
-#include <vector>
-
-#include <networkit/Globals.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- * Parser for the METIS file format.
- */
-class METISParser final {
-
-    std::ifstream graphFile;
-
-public:
-    /**
-     * Constructor for the METIS Parser.
-     *
-     * @param[in]  path  file path
-     */
-    METISParser(std::string_view path);
-
-    /**
-     * Get the METIS graph file header
-     */
-    std::tuple<count, count, index, count> getHeader();
-
-    /**
-     * Test if graph file has a next line.
-     */
-    bool hasNext();
-
-    /**
-     * Get adjacencies from the next line in the METIS graph file.
-     *
-     * @param[in]  ignoreFirst  number of values to ignore [in case the METIS file contains node
-     * weightes]
-     */
-    std::vector<node> getNext(count ignoreFirst = 0);
-
-    /**
-     * Get adjacencies with edge weights from the next line in the METIS graph file.
-     *
-     * @param[in]  ignoreFirst  number of values to ignore [in case the METIS file contains node
-     * weightes]
-     */
-    std::vector<std::pair<node, double>> getNextWithWeights(count ignoreFirst = 0);
-};
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_METIS_PARSER_HPP_

package/vendor/include/networkit/io/MTXGraphReader.hpp

@@ -1,31 +0,0 @@
-#ifndef NETWORKIT_IO_MTX_GRAPH_READER_HPP_
-#define NETWORKIT_IO_MTX_GRAPH_READER_HPP_
-
-#include <networkit/io/GraphReader.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- *
- * Reader for the matrix market file format documented in
- * https://networkrepository.com/mtx-matrix-market-format.html
- *
- * Does not allow complex fields.
- *
- */
-class MTXGraphReader final : public GraphReader {
-public:
-    MTXGraphReader() = default;
-
-    /**
-     * Takes a file path as parameter and returns a graph.
-     *
-     * @param path
-     * @return Graph
-     */
-    GraphW read(std::string_view path) override;
-};
-
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_MTX_GRAPH_READER_HPP_

package/vendor/include/networkit/io/MTXParser.hpp

@@ -1,87 +0,0 @@
-#ifndef NETWORKIT_IO_MTX_PARSER_HPP_
-#define NETWORKIT_IO_MTX_PARSER_HPP_
-
-#include <fstream>
-#include <optional>
-#include <string>
-#include <tuple>
-#include <unordered_map>
-#include <vector>
-
-#include <networkit/Globals.hpp>
-#include <networkit/graph/Graph.hpp>
-
-namespace NetworKit {
-/**
- * @ingroup io
- * Parser for the MTX file format.
- */
-class MTXParser final {
-
-    std::ifstream graphFile;
-    std::string currentLine;
-
-public:
-    enum class Object { Matrix, Vector };
-    enum class Format { Coordinate, Array };
-    enum class Field { Real, Double, Complex, Integer, Pattern };
-    enum class Symmetry { General, Symmetric, SkewSymmetric, Hermitian };
-
-    std::unordered_map<std::string, Object> objectMap = {{"matrix", Object::Matrix},
-                                                         {"vector", Object::Vector}};
-    std::unordered_map<std::string, Format> formatMap = {{"coordinate", Format::Coordinate},
-                                                         {"array", Format::Array}};
-    std::unordered_map<std::string, Field> fieldMap = {{"real", Field::Real},
-                                                       {"double", Field::Double},
-                                                       {"integer", Field::Integer},
-                                                       {"pattern", Field::Pattern}};
-    std::unordered_map<std::string, Symmetry> symmetryMap = {
-        {"general", Symmetry::General},
-        {"symmetric", Symmetry::Symmetric},
-        {"skew-symmetric", Symmetry::SkewSymmetric}};
-
-    struct MTXHeader {
-        Object object;
-        Format format;
-        Field field;
-        Symmetry symmetry;
-    };
-
-    struct MatrixSize {
-        count rows;
-        count columns;
-        count nonzeros;
-
-        MatrixSize(count r, count c, count nz) : rows(r), columns(c), nonzeros(nz) {}
-    };
-
-    struct Edge {
-        node from;
-        node to;
-        std::optional<double> weight;
-
-        Edge(node f, node t, std::optional<double> w) : from(f), to(t), weight(w) {}
-    };
-
-    MTXParser(const std::string &path);
-
-    /**
-     * Get the MTX graph file header.
-     */
-    MTXHeader getHeader();
-
-    /**
-     * Get the MTX graph file matrix size header.
-     */
-    MatrixSize getMatrixSize();
-
-    /**
-     * Get the (weighted) edge from the next line in the MTX graph file if present.
-     *
-     * @param weighted
-     * @return std::optional<std::pair<NetworKit::Edge, NetworKit::edgeweight>>
-     */
-    std::optional<NetworKit::WeightedEdge> getNext(bool weighted);
-};
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_MTX_PARSER_HPP_

package/vendor/include/networkit/io/MatrixMarketReader.hpp

@@ -1,33 +0,0 @@
-/*
- * MatrixMarketReader.hpp
- *
- *  Created on: 25.07.2014
- *      Author: dhoske
- */
-
-#ifndef NETWORKIT_IO_MATRIX_MARKET_READER_HPP_
-#define NETWORKIT_IO_MATRIX_MARKET_READER_HPP_
-
-#include <networkit/io/MatrixReader.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- * Reader for the matrix market file format as described in
- * http://math.nist.gov/MatrixMarket/reports/MMformat.ps.
- *
- * Only allows real, symmetric matrices.
- */
-class MatrixMarketReader final : public MatrixReader {
-public:
-    MatrixMarketReader() = default;
-
-    CSRMatrix read(std::string_view path) override;
-
-    /** Reads the matrix in @a in. */
-    CSRMatrix read(std::istream &in);
-};
-
-} // namespace NetworKit
-#endif // NETWORKIT_IO_MATRIX_MARKET_READER_HPP_

package/vendor/include/networkit/io/MatrixReader.hpp

@@ -1,33 +0,0 @@
-/*
- * MatrixReader.hpp
- *
- *  Created on: 17.01.2013
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_IO_MATRIX_READER_HPP_
-#define NETWORKIT_IO_MATRIX_READER_HPP_
-
-#include <networkit/algebraic/CSRMatrix.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- * Abstract base class for matrix readers.
- */
-class MatrixReader {
-public:
-    virtual ~MatrixReader() = default;
-
-    /**
-     * Reads the matrix in @a path.
-     */
-    virtual CSRMatrix read(std::string_view path) = 0;
-
-    /** only to be used by Cython - this eliminates an unnecessary copy */
-    CSRMatrix *_read(std::string_view path) { return new CSRMatrix{read(path)}; };
-};
-
-} // namespace NetworKit
-#endif // NETWORKIT_IO_MATRIX_READER_HPP_

package/vendor/include/networkit/io/MemoryMappedFile.hpp

@@ -1,80 +0,0 @@
-/*
- * MemoryMappedFile.hpp
- *
- *  Created on: 16.07.2018
- *      Author: Manuel Penschuck (networkit@manuel.jetzt)
- */
-
-#ifndef NETWORKIT_IO_MEMORY_MAPPED_FILE_HPP_
-#define NETWORKIT_IO_MEMORY_MAPPED_FILE_HPP_
-
-#include <memory>
-#include <string>
-
-namespace NetworKit {
-struct MemoryMappedFileState;
-
-/**
- * This class is a wrapper to os-dependend file mapping implementations.
- * It supports to map a read-only file into virtual address space.
- * After successful opening, pointers to the begin/end of the virtual
- * address space are accessible via cbegin() / cend(). All file and mapping
- * handlers are freed automatically.
- *
- * This wrapper is non-copyable but can be cheaply moved and swapped.
- */
-class MemoryMappedFile final {
-public:
-    using value_type = char;
-    using const_iterator = const value_type *;
-
-    //! Creates a MemoryMappedFile instance in an unmapped state.
-    //! A call to open() is required.
-    MemoryMappedFile();
-
-    //! Invokes open(path) automatically
-    explicit MemoryMappedFile(std::string_view path);
-
-    //! Invokes close
-    ~MemoryMappedFile();
-
-    //! It's non copy-able
-    MemoryMappedFile(const MemoryMappedFile &) = delete;
-    MemoryMappedFile &operator=(const MemoryMappedFile &) = delete;
-
-    //! Takes over the mapping (if any) from o, leaves o in a "closed"
-    //! state ready to be opened again.
-    MemoryMappedFile(MemoryMappedFile &&o) noexcept;
-
-    //! If *this currently holds a mapping, it is closed and replaced
-    //! the other's state which in turn is left closed.
-    MemoryMappedFile &operator=(MemoryMappedFile &&o) noexcept;
-
-    //! Opens the file and maps it to cbegin() ... cend()
-    //! Opening an empty file is considered an error.
-    void open(std::string_view file);
-
-    //! If a file is mapped, it is closed. Otherwise, operation is carried out.
-    //! @note This function is automatically called by the destructor.
-    void close() noexcept;
-
-    //! If a file is opened, a random-access iterator to the first byte mapped is returned.
-    //! If no file is opened, nullptr is returned.
-    const_iterator cbegin() const { return beginIt; }
-
-    //! Analogously to cbegin()
-    const_iterator cend() const { return endIt; }
-
-    //! Number of bytes mapped
-    size_t size() const { return std::distance(beginIt, endIt); }
-
-private:
-    const_iterator beginIt{nullptr};
-    const_iterator endIt{nullptr};
-
-    //!< used only by Windows implementation to keep handlers around.
-    std::unique_ptr<MemoryMappedFileState> state;
-};
-
-} // namespace NetworKit
-#endif // NETWORKIT_IO_MEMORY_MAPPED_FILE_HPP_

package/vendor/include/networkit/io/NetworkitBinaryGraph.hpp

@@ -1,144 +0,0 @@
-/*
- * NetworkitBinaryGraph.hpp
- *
- *      Author: Charmaine Ndolo <charmaine.ndolo@hu-berlin.de>
- */
-
-#ifndef NETWORKIT_IO_NETWORKIT_BINARY_GRAPH_HPP_
-#define NETWORKIT_IO_NETWORKIT_BINARY_GRAPH_HPP_
-
-#include <cstddef>
-#include <cstdint>
-
-#include <tlx/define/likely.hpp>
-#include <tlx/math/clz.hpp>
-#include <tlx/math/ffs.hpp>
-
-namespace NetworKit {
-namespace nkbg {
-
-struct Header {
-    char magic[8];
-    uint64_t checksum;
-    uint64_t features;
-    uint64_t nodes;
-    uint64_t chunks;
-    uint64_t offsetBaseData;
-    uint64_t offsetAdjLists;
-    uint64_t offsetAdjTranspose;
-    uint64_t offsetWeightLists;
-    uint64_t offsetWeightTranspose;
-    uint64_t offsetAdjIdLists;
-    uint64_t offsetAdjIdTranspose;
-};
-
-enum class WeightFormat : int { NONE = 0, VARINT = 1, SIGNED_VARINT = 2, DOUBLE = 3, FLOAT = 4 };
-
-using WEIGHT_FORMAT = WeightFormat; // enum alias for backwards compatibility
-
-static constexpr uint8_t DELETED_BIT = 0x1; // bit 0
-static constexpr uint64_t DIR_MASK = 0x1;   // bit 0
-static constexpr uint64_t WGHT_MASK = 0xE;  // bit 1-3
-static constexpr uint64_t WGHT_SHIFT = 0x1;
-static constexpr uint64_t INDEX_MASK = 0x10; // bit 4
-static constexpr uint64_t INDEX_SHIFT = 0x4;
-
-/**
- * Serializes value into a buffer and returns the number of bytes written.
- * The space required to store an integer x ranges between 1 and 9 bytes.
- *
- * The first byte (buffer[0]) encodes the number of following data bytes
- * in the position y in [0, 7] of the least significant bit that is asserted.
- * If the header byte is zero (i.e., it contains no asserted bits), exactly
- * y=8 data bytes follow.
- * Possibly remaining bits in the header are used to store the least
- * significant bits of x. The subsequent data bytes store the remainder of x
- * in little endian, i.e. * the eight least significant bits (not stored in
- * the header) are stored in buffer[1], the next higher eight bits in
- * buffer[2] and so on.
- *
- * Example:
- * x = 0b0GFE'DCBA with G=1 requires 7 bits of storage. Hence it fits
- * completely into the header which is
- * buffer[0] = 0bGFED'CBA|1 where bit 0 encodes that no
- * data bytes follow while bits 1 to 7 store x.
- *
- * x = 0bHGFE'DCBA with H=1 requires 8 bits of storage. Hence an
- * additional data byte is required:
- *
- * buffer[0] = 0bFEDC'BA|10 where bits 0 and 1 encode that one data byte will follow
- * buffer[1] = 0b0000'00|HG where bits 0 and 1 encode the remaining two bits
- * of x, and bits 2 to 7 are filled as zeros
- */
-
-inline size_t varIntEncode(uint64_t value, uint8_t *buffer) noexcept {
-    if (!value) {
-        buffer[0] = 1;
-        return 1;
-    }
-
-    int dataBytes;
-
-    if (TLX_UNLIKELY(value >= (1llu << 56))) {
-        // We have more than 56 bits of data, i.e. we need 8 data bytes.
-        buffer[0] = 0;
-        dataBytes = 8;
-
-    } else {
-        const auto bits = 64 - tlx::clz(value);
-        dataBytes = static_cast<int>((bits - 1) / 7);
-
-        // number of bytes is encode by the number of trailing zeros
-        buffer[0] = static_cast<uint8_t>(1 << dataBytes);
-
-        // put the 8 - (dataBytes - 1) least significant bits into the remainder of the buffer byte
-        buffer[0] |= static_cast<uint8_t>(value << (dataBytes + 1));
-        value >>= 7 - dataBytes;
-    }
-
-    for (int i = 0; i < dataBytes; i++) {
-        buffer[i + 1] = static_cast<uint8_t>(value & 0xFF);
-        value >>= 8;
-    }
-
-    return dataBytes + 1;
-}
-
-/// Converts a serialized varint into an uint64_t value and returns the number of bytes consumed.
-inline size_t varIntDecode(const uint8_t *data, uint64_t &value) noexcept {
-    int n = 8;
-    int bitsRecovered = 0;
-    uint64_t decoded = 0;
-
-    if (data[0]) {
-        n = static_cast<int>(tlx::ffs(data[0]) - 1);
-        decoded = data[0] >> (n + 1);
-        bitsRecovered = 7 - n;
-    }
-
-    for (int i = 0; i < n; i++) {
-        decoded |= static_cast<uint64_t>(data[i + 1]) << bitsRecovered;
-        bitsRecovered += 8;
-    }
-
-    value = decoded;
-    return n + 1;
-}
-
-/**
- * Encodes a singed value, s.t. the sign bit is in the LSB bit, while the absolute value is
- * stored in the remaining upper 63 bits. This allows more effective compression using varint.
- */
-inline uint64_t zigzagEncode(int64_t value) noexcept {
-    return (static_cast<uint64_t>(value) << 1) ^ (int64_t(-1) * (value < 0));
-}
-
-//! Reverses zigzagEncode.
-inline int64_t zigzagDecode(uint64_t value) noexcept {
-    return (value >> 1) ^ (-(value & 1));
-}
-
-} // namespace nkbg
-} // namespace NetworKit
-
-#endif // NETWORKIT_IO_NETWORKIT_BINARY_GRAPH_HPP_

package/vendor/include/networkit/io/NetworkitBinaryReader.hpp

@@ -1,50 +0,0 @@
-/*
- * NetworkitBinaryReader.hpp
- *
- *      Author: Charmaine Ndolo <charmaine.ndolo@hu-berlin.de>
- */
-
-#ifndef NETWORKIT_IO_NETWORKIT_BINARY_READER_HPP_
-#define NETWORKIT_IO_NETWORKIT_BINARY_READER_HPP_
-
-#include <cstring>
-#include <string>
-#include <networkit/graph/Graph.hpp>
-#include <networkit/io/GraphReader.hpp>
-#include <networkit/io/MemoryMappedFile.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- *
- * Reads a graph written in the custom Networkit binary format.
- * Note that there are multiple versions of the Networkit binary format.
- * This Reader can read files that are written with format version 2 and 3.
- * Format version 3 was released with Networkit 9.1 (December 2021).
- * Further information can be found here:
- * https://github.com/networkit/networkit/blob/master/networkit/cpp/io/NetworkitBinaryGraph.md
- */
-
-class NetworkitBinaryReader final : public GraphReader {
-
-public:
-    NetworkitBinaryReader(){};
-
-    GraphW read(std::string_view path) override;
-    GraphW readFromBuffer(const std::vector<uint8_t> &data);
-
-private:
-    count nodes;
-    count chunks;
-    bool directed;
-    bool weighted;
-    bool indexed;
-    count version;
-
-    template <class T>
-    GraphW readData(const T &source);
-};
-} // namespace NetworKit
-
-#endif // NETWORKIT_IO_NETWORKIT_BINARY_READER_HPP_

package/vendor/include/networkit/io/NetworkitBinaryWriter.hpp

@@ -1,71 +0,0 @@
-/*
- * NetworkitBinaryWriter.hpp
- *
- *      Author: Charmaine Ndolo <charmaine.ndolo@hu-berlin.de>
- */
-
-#ifndef NETWORKIT_IO_NETWORKIT_BINARY_WRITER_HPP_
-#define NETWORKIT_IO_NETWORKIT_BINARY_WRITER_HPP_
-
-#include <networkit/graph/Graph.hpp>
-#include <networkit/io/GraphWriter.hpp>
-
-namespace NetworKit {
-
-enum class NetworkitBinaryWeights : int {
-    NONE,
-    UNSIGNED_FORMAT,
-    SIGNED_FORMAT,
-    DOUBLE_FORMAT,
-    FLOAT_FORMAT,
-    AUTO_DETECT,
-    none = NONE, // this + following added for backwards compatibility
-    unsignedFormat = UNSIGNED_FORMAT,
-    signedFormat = SIGNED_FORMAT,
-    doubleFormat = DOUBLE_FORMAT,
-    floatFormat = FLOAT_FORMAT,
-    autoDetect = AUTO_DETECT
-};
-
-enum class NetworkitBinaryEdgeIDs : int {
-    NO_EDGE_IDS,
-    WIRTE_EDGE_IDS,
-    AUTO_DETECT,
-    noEdgeIDs = NO_EDGE_IDS, // this + following added for backwards compatibility
-    writeEdgeIDs = WIRTE_EDGE_IDS,
-    autoDetect = AUTO_DETECT
-};
-
-/**
- * @ingroup io
- *
- * Writes a graph written in the custom Networkit format.
- * Note that there are multiple versions of the Networkit binary format.
- * Since Networkit 9.1 (December 2021), the writer always writes files using format version 3.
- * Reading a binary file with version < 3 and re-writing it, implicitly upgrades the format to the
- * current version. Further information can be found here:
- * https://github.com/networkit/networkit/blob/master/networkit/cpp/io/NetworkitBinaryGraph.md
- */
-class NetworkitBinaryWriter final : public GraphWriter {
-
-public:
-    NetworkitBinaryWriter(uint64_t chunks = 32,
-                          NetworkitBinaryWeights weightsType = NetworkitBinaryWeights::AUTO_DETECT,
-                          NetworkitBinaryEdgeIDs edgeIndex = NetworkitBinaryEdgeIDs::AUTO_DETECT);
-
-    void write(const Graph &G, std::string_view path) override;
-    std::vector<uint8_t> writeToBuffer(const Graph &G);
-
-private:
-    count chunks;
-    NetworkitBinaryWeights weightsType;
-    NetworkitBinaryEdgeIDs edgeIndex;
-    bool preserveEdgeIndex;
-
-    template <class T>
-    void writeData(T &outStream, const Graph &G);
-};
-
-} // namespace NetworKit
-
-#endif // NETWORKIT_IO_NETWORKIT_BINARY_WRITER_HPP_

package/vendor/include/networkit/io/PartitionReader.hpp

@@ -1,34 +0,0 @@
-/*
- * PartitionReader.hpp
- *
- *  Created on: 15.02.2013
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_IO_PARTITION_READER_HPP_
-#define NETWORKIT_IO_PARTITION_READER_HPP_
-
-#include <fstream>
-
-#include <networkit/graph/Graph.hpp>
-#include <networkit/structures/Partition.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- */
-class PartitionReader final {
-
-public:
-    /**
-     * Read a clustering from a file. File format:
-     *     line n contains cluster id of node (n - 1)
-     *
-     * @param[in]  path  Path to file.
-     */
-    Partition read(std::string_view path);
-};
-
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_PARTITION_READER_HPP_

package/vendor/include/networkit/io/PartitionWriter.hpp

@@ -1,31 +0,0 @@
-/*
- * PartitionWriter.hpp
- *
- *  Created on: 22.01.2013
- *      Author: Christian Staudt
- */
-
-#ifndef NETWORKIT_IO_PARTITION_WRITER_HPP_
-#define NETWORKIT_IO_PARTITION_WRITER_HPP_
-
-#include <fstream>
-
-#include <networkit/structures/Partition.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- * Write a clustering to a file.
- */
-class PartitionWriter final {
-
-public:
-    void write(const Partition &zeta, std::string_view path) const {
-        std::ofstream file{path.data()};
-        zeta.forEntries([&](node, const index c) { file << c << '\n'; });
-    }
-};
-
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_PARTITION_WRITER_HPP_

package/vendor/include/networkit/io/RBGraphReader.hpp

@@ -1,37 +0,0 @@
-/*
- * RBGraphReader.hpp
- *
- *  Created on: 16.10.2024
- *      Author: bernlu
- */
-
-#ifndef NETWORKIT_IO_RB_GRAPH_READER_HPP_
-#define NETWORKIT_IO_RB_GRAPH_READER_HPP_
-
-#include <networkit/io/GraphReader.hpp>
-
-namespace NetworKit {
-
-/**
- * @ingroup io
- * Reader for the Rutherford Boeing (RB) matrix file format as described in
- * http://sparse-files.engr.tamu.edu/files/DOC/rb.pdf.
- *
- * @note currently the reader only supports compressed column format for real, integer, or pattern
- * data types.
- */
-class RBGraphReader final : public GraphReader {
-public:
-    RBGraphReader() = default;
-
-    /**
-     * Takes a file path as parameter and returns a graph.
-     *
-     * @param path
-     * @return Graph
-     */
-    GraphW read(std::string_view path) override;
-};
-
-} /* namespace NetworKit */
-#endif // NETWORKIT_IO_RB_GRAPH_READER_HPP_