Remove all notions of morphology equality (#91)

This is now handled in morph-tool

binds/python/bind_immutable.cpp

@@ -23,21 +23,6 @@ static void bind_immutable_module(py::module &m) {
         .def(py::init<const morphio::URI&, unsigned int>(),
              "filename"_a, "options"_a=morphio::enums::Option::NO_MODIFIER)
         .def(py::init<morphio::mut::Morphology&>())
-        .def("__eq__", [](const morphio::Morphology& a, const morphio::Morphology& b) {
-                return a.operator==(b);
-            }, py::is_operator(),
-            "Are considered equal, 2 morphologies with the same:\n"
-            "- point vector\n"
-            "- diameter vector\n"
-            "- perimeter vector\n"
-            "- cell family\n"
-            "- section types\n"
-            "- topology (children/parent relationship)\n\n"
-            "Note: the soma types are NOT required to be equal")
-        .def("__ne__", [](const morphio::Morphology& a, const morphio::Morphology& b) {
-                return a.operator!=(b);
-            }, py::is_operator())
-        .def(py::self != py::self)
 
         .def("as_mutable", [](const morphio::Morphology* morph) { return morphio::mut::Morphology(*morph); })
 
@@ -146,12 +131,6 @@ static void bind_immutable_module(py::module &m) {
                                "Note: the soma surface computation depends on the soma type");
 
     py::class_<morphio::Section>(m, "Section")
-        .def("__eq__", [](const morphio::Section& a, const morphio::Section& b) {
-                return a.operator==(b);
-            }, py::is_operator())
-        .def("__ne__", [](const morphio::Section& a, const morphio::Section& b) {
-                return a.operator!=(b);
-            }, py::is_operator())
         .def("__str__", [](const morphio::Section& section) {
                 std::stringstream ss;
                 ss << section;

binds/python/bind_misc.cpp

@@ -217,16 +217,4 @@ static void bind_misc(py::module &m) {
              "neuronal_section_ids"_a, "distances_to_section_start"_a, "diameters"_a);
 
     m.doc() = "pybind11 example plugin"; // optional module docstring
-
-
-  m.def("diff", static_cast<bool (*)(const morphio::Morphology& left, const morphio::Morphology& right, morphio::enums::LogLevel logLevel)>(&morphio::diff),
-        "Perform a diff on 2 morphologies, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
-  m.def("diff", static_cast<bool (*)(const morphio::Section& left, const morphio::Section& right, morphio::enums::LogLevel logLevel)>(&morphio::diff),
-        "Perform a diff on 2 sections, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
-
-  m.def("diff", static_cast<bool (*)(const morphio::mut::Morphology& left, const morphio::mut::Morphology& right, morphio::enums::LogLevel logLevel)>(&morphio::mut::diff),
-        "Perform a diff on 2 morphologies, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
-  m.def("diff", static_cast<bool (*)(const morphio::mut::Section& left, const morphio::mut::Section& right, morphio::enums::LogLevel logLevel)>(&morphio::mut::diff),
-        "Perform a diff on 2 sections, returns True if items differ", "left"_a, "right"_a, "log_level"_a=morphio::enums::LogLevel::INFO);
-
 }

binds/python/bind_mutable.cpp

@@ -20,23 +20,6 @@ static void bind_mutable_module(py::module &m) {
         .def(py::init<const morphio::mut::Morphology&, unsigned int>(),
              "morphology"_a, "options"_a=morphio::enums::Option::NO_MODIFIER)
 
-        .def("__eq__", [](const morphio::mut::Morphology& a, const morphio::mut::Morphology& b) {
-                return a.operator==(b);
-            }, py::is_operator(),
-            "Are considered equal, 2 morphologies with the same:\n"
-            "- root sections\n"
-            "- section topology\n"
-            "- cell family\n"
-            "For each section:"
-            "- same points\n"
-            "- same diameters\n"
-            "- same perimeters\n"
-            "- same type\n"
-            "Note: the soma types are NOT required to be equal")
-        .def("__ne__", [](const morphio::mut::Morphology& a, const morphio::mut::Morphology& b) {
-                return a.operator!=(b);
-            }, py::is_operator())
-
         // Cell sub-part accessors
         .def_property_readonly("sections", &morphio::mut::Morphology::sections,
                                "Returns a list containing IDs of all sections. "
@@ -226,12 +209,6 @@ static void bind_mutable_module(py::module &m) {
              "immutable_section"_a, "recursive"_a=false);
 
     py::class_<morphio::mut::Section, std::shared_ptr<morphio::mut::Section>>(m, "Section")
-        .def("__eq__", [](const morphio::mut::Section& a, const morphio::mut::Section& b) {
-                return a.operator==(b);
-            }, py::is_operator())
-        .def("__ne__", [](const morphio::mut::Section& a, const morphio::mut::Section& b) {
-                return a.operator!=(b);
-                }, py::is_operator())
         .def("__str__", [](const morphio::mut::Section& section) {
                 std::stringstream ss;
                 ss << section;

binds/python/bind_vasculature.cpp

@@ -20,19 +20,6 @@ static void bind_vasculature(py::module &m) {
         .def(py::init<const morphio::URI&>(),
              "filename"_a)
         // .def(py::init<morphio::mut::Morphology&>())
-        .def("__eq__", [](const morphio::vasculature::Vasculature& a, const morphio::vasculature::Vasculature& b) {
-                return a.operator==(b);
-            }, py::is_operator(),
-            "Are considered equal, 2 morphologies with the same:\n"
-            "- point vector\n"
-            "- diameter vector\n"
-            "- section types\n"
-            "- topology\n")
-        .def("__ne__", [](const morphio::vasculature::Vasculature& a, const morphio::vasculature::Vasculature& b) {
-                return a.operator!=(b);
-            }, py::is_operator())
-        .def(py::self != py::self)
-
         // .def("as_mutable", [](const morphio::vasculature::VasculatureMorphology* morph) { return morphio::mut::Morphology(*morph); })
 
         .def_property_readonly("sections", &morphio::vasculature::Vasculature::sections,

include/morphio/morphology.h

@@ -26,22 +26,6 @@ class Morphology
     Morphology(Morphology&&);
     Morphology& operator=(Morphology&&);
 
-    /**
-       Equality operator:
-           Are considered equal, 2 morphologies with the same:
-               - point vector
-               - diameter vector
-               - perimeter vector
-               - cell family
-               - section types
-               - topology (children/parent relationship)
-
-           Note: the soma types are NOT required to be equal
-     **/
-    bool operator==(const Morphology& other) const;
-    bool operator!=(const Morphology& other) const;
-
-
     /** @name Read API */
     //@{
     /** Open the given source to a morphology file and parse it.

include/morphio/mut/morphology.h

@@ -56,21 +56,6 @@ class Morphology
 
     virtual ~Morphology();
 
-    /**
-    Are considered equal, 2 morphologies with the same:\n
-     - root sections
-     - section topology
-     - cell family
-     For each section:
-     - same points
-     - same diameters
-     - same perimeters
-     - same type
-     Note: the soma types are NOT required to be equal
-     **/
-    bool operator==(const Morphology& other) const;
-    bool operator!=(const Morphology& other) const;
-
     /**
        Returns all section ids at the tree root
     **/

include/morphio/mut/section.h

@@ -96,16 +96,6 @@ class Section : public std::enable_shared_from_this<Section>
         const Property::PointLevel&,
         SectionType sectionType = SectionType::SECTION_UNDEFINED);
 
-    /**
-    Two sections are equal if they have same:
-    - points
-    - diameters
-    - perimeters
-    - type
-    **/
-    bool operator==(const Section& other) const;
-    bool operator!=(const Section& other) const;
-
 private:
     friend class Morphology;
 

include/morphio/section.h

@@ -33,18 +33,6 @@ class Section : public SectionBase<Section>
     using PointAttribute = Property::Point;
 
 public:
-    /**
-       Equality operator:
-       Are considered equal, 2 sections with the same:
-       - point vector
-       - diameter vector
-       - perimeter vector
-       - section types
-       - topology (children/parent relationship)
-    **/
-    bool operator==(const Section& other) const;
-    bool operator!=(const Section& other) const;
-
     /**
        Depth first search iterator
     **/

include/morphio/vasc/vasculature.h

@@ -15,17 +15,6 @@ class Vasculature
     Vasculature(Vasculature&&);
     Vasculature& operator=(Vasculature&&);
 
-    /**
-        Equality operators :
-        Two vasculature morphologies are considered equal if they have the same:
-            - point vector
-            - diameter vector
-            - section types
-            - topology (successor / predecessor relationship)
-    **/
-    bool operator==(const Vasculature& other) const;
-    bool operator!=(const Vasculature& other) const;
-
     /** @name Read API */
     /** Open the given source to a vasculature file and parse it.
      */

src/CMakeLists.txt

@@ -13,7 +13,6 @@ set(MORPHIO_SOURCES
   morphology.cpp
   soma.cpp
   section.cpp
-  tools.cpp
   vasc/section.cpp
   vasc/vasculature.cpp
   vasc/properties.cpp

src/morphology.cpp

@@ -79,16 +79,6 @@ Morphology::~Morphology()
 {
 }
 
-bool Morphology::operator==(const Morphology& other) const
-{
-    return !diff(*this, other, LogLevel::ERROR);
-}
-
-bool Morphology::operator!=(const Morphology& other) const
-{
-    return diff(*this, other, LogLevel::ERROR);
-}
-
 const Soma Morphology::soma() const
 {
     return Soma(_properties);

src/mut/morphology.cpp

@@ -417,15 +417,5 @@ void Morphology::write(const std::string& filename)
         LBTHROW(UnknownFileType(_err.ERROR_WRONG_EXTENSION(filename)));
 }
 
-bool Morphology::operator==(const Morphology& other) const
-{
-    return !diff(*this, other, LogLevel::ERROR);
-}
-
-bool Morphology::operator!=(const Morphology& other) const
-{
-    return diff(*this, other, LogLevel::ERROR);
-}
-
 } // end namespace mut
 } // end namespace morphio

src/mut/section.cpp

@@ -203,16 +203,6 @@ std::shared_ptr<Section> Section::appendSection(
     return ptr;
 }
 
-bool Section::operator==(const Section& other) const
-{
-    return !diff(*this, other, LogLevel::ERROR);
-}
-
-bool Section::operator!=(const Section& other) const
-{
-    return diff(*this, other, LogLevel::ERROR);
-}
-
 } // end namespace mut
 } // end namespace morphio
 

src/section.cpp

@@ -5,16 +5,6 @@
 
 namespace morphio {
 
-bool Section::operator==(const Section& other) const
-{
-    return !diff(*this, other, LogLevel::ERROR);
-}
-
-bool Section::operator!=(const Section& other) const
-{
-    return diff(*this, other, LogLevel::ERROR);
-}
-
 SectionType Section::type() const
 {
     auto val = _properties->get<Property::SectionType>()[_id];