Test format

.github/workflows/clang_format_check.yaml

@@ -12,8 +12,12 @@ jobs:
         - name: Fetch repository
           uses: actions/checkout@v4
           with:
-            fetch-depth: 2
+            fetch-depth: 0
+
         - name: Install packages
           run: sudo apt-get update && sudo apt-get install python3-venv
+
         - name: check_clang_format
-          run: ci/check_clang_format.sh
+          run: |
+            git fetch origin master
+            ci/check_clang_format.sh

ci/check_clang_format.sh

@@ -19,7 +19,13 @@ set +u  # ignore errors in virtualenv's activate
 source "$VENV/bin/activate"
 set -u
 
-changes=$(git-clang-format 'HEAD~1' $DIRS_TO_FORMAT)
+git branch --all
+git merge-base HEAD remotes/origin/master
+
+changes_from="$(git merge-base HEAD remotes/origin/master)"
+echo "Changes from: $changes_from"
+git-clang-format --diff $changes_from HEAD $DIRS_TO_FORMAT
+changes=$(git-clang-format --diff $changes_from HEAD $DIRS_TO_FORMAT)
 if [[ $(echo "$changes" | grep -n1 'changed files') ]]; then
     echo "The following files require changes to pass the current clang-format"
     echo "$changes"

include/bbp/sonata/compartment_sets.h

@@ -30,55 +30,75 @@ class CompartmentSets;
 struct CompartmentLocation {
   public:
     uint64_t nodeId = 0;
-    uint64_t sectionIndex = 0;
+    uint64_t sectionId = 0;
     double offset = 0.0;
 
     /// Comparator. Used to compare vectors in CompartmentSet. More idiomatic than defining a
     /// comaprator on the fly
     bool operator==(const CompartmentLocation& other) const {
-        return nodeId == other.nodeId && sectionIndex == other.sectionIndex &&
-               offset == other.offset;
+        return nodeId == other.nodeId && sectionId == other.sectionId && offset == other.offset;
     }
 
     bool operator!=(const CompartmentLocation& other) const {
         return !(*this == other);
     }
+
+    bool operator<(const CompartmentLocation& other) const {
+        if (nodeId != other.nodeId)
+            return nodeId < other.nodeId;
+        if (sectionId != other.sectionId)
+            return sectionId < other.sectionId;
+        return offset < other.offset;
+    }
+
+    bool operator>(const CompartmentLocation& other) const {
+        return other < *this;
+    }
+
+    bool operator<=(const CompartmentLocation& other) const {
+        return !(other < *this);
+    }
+
+    bool operator>=(const CompartmentLocation& other) const {
+        return !(*this < other);
+    }
 };
 
 /// Ostream << operator used by catch2 when there are problems for example
 inline std::ostream& operator<<(std::ostream& os, const CompartmentLocation& cl) {
     os << "CompartmentLocation("
        << "nodeId: " << cl.nodeId << ", "
-       << "sectionIndex: " << cl.sectionIndex << ", "
+       << "sectionId: " << cl.sectionId << ", "
        << "offset: " << cl.offset << ")";
     return os;
 }
 
-class SONATA_API CompartmentSetFilteredIterator {
-public:
-  using iterator_category = std::forward_iterator_tag;
-  using value_type = CompartmentLocation;
-  using difference_type = std::ptrdiff_t;
-  using pointer = const CompartmentLocation*;
-  using reference = const CompartmentLocation&;
-
-  explicit CompartmentSetFilteredIterator(
-      std::unique_ptr<detail::CompartmentSetFilteredIterator> impl);
-  CompartmentSetFilteredIterator(const CompartmentSetFilteredIterator& other);
-  CompartmentSetFilteredIterator& operator=(const CompartmentSetFilteredIterator& other);
-  CompartmentSetFilteredIterator(CompartmentSetFilteredIterator&&) noexcept;
-  CompartmentSetFilteredIterator& operator=(CompartmentSetFilteredIterator&&) noexcept;
-  ~CompartmentSetFilteredIterator();
-
-  const CompartmentLocation& operator*() const;
-  const CompartmentLocation* operator->() const;
-
-  CompartmentSetFilteredIterator& operator++();    // prefix ++
-  CompartmentSetFilteredIterator operator++(int);  // postfix ++
-  bool operator==(const CompartmentSetFilteredIterator& other) const;
-  bool operator!=(const CompartmentSetFilteredIterator& other) const;
-
-private:
+class SONATA_API CompartmentSetFilteredIterator
+{
+  public:
+    using iterator_category = std::forward_iterator_tag;
+    using value_type = CompartmentLocation;
+    using difference_type = std::ptrdiff_t;
+    using pointer = const CompartmentLocation*;
+    using reference = const CompartmentLocation&;
+
+    explicit CompartmentSetFilteredIterator(
+        std::unique_ptr<detail::CompartmentSetFilteredIterator> impl);
+    CompartmentSetFilteredIterator(const CompartmentSetFilteredIterator& other);
+    CompartmentSetFilteredIterator& operator=(const CompartmentSetFilteredIterator& other);
+    CompartmentSetFilteredIterator(CompartmentSetFilteredIterator&&) noexcept;
+    CompartmentSetFilteredIterator& operator=(CompartmentSetFilteredIterator&&) noexcept;
+    ~CompartmentSetFilteredIterator();
+
+    const CompartmentLocation& operator*() const;
+    const CompartmentLocation* operator->() const;
+
+    CompartmentSetFilteredIterator& operator++();    // prefix ++
+    CompartmentSetFilteredIterator operator++(int);  // postfix ++
+    bool operator==(const CompartmentSetFilteredIterator& other) const;
+    bool operator!=(const CompartmentSetFilteredIterator& other) const;
+
+  private:
     std::unique_ptr<detail::CompartmentSetFilteredIterator> impl_;
 };
 
@@ -140,8 +160,7 @@ class SONATA_API CompartmentSet
  */
 class SONATA_API CompartmentSets
 {
-public:
-
+  public:
     CompartmentSets(const std::string& content);
     CompartmentSets(std::unique_ptr<detail::CompartmentSets>&& impl);
     CompartmentSets(detail::CompartmentSets&& impl);
@@ -181,9 +200,9 @@ class SONATA_API CompartmentSets
     bool operator==(const CompartmentSets& other) const;
     bool operator!=(const CompartmentSets& other) const;
 
-private:
+  private:
     std::unique_ptr<detail::CompartmentSets> impl_;
 };
 
 }  // namespace sonata
-}  // namespace bbp
+}  // namespace bbp

include/bbp/sonata/config.h

@@ -382,10 +382,11 @@ class SONATA_API SimulationConfig
      */
     struct Report {
         enum class Sections { invalid = -1, soma, axon, dend, apic, all };
-        enum class Type { invalid = -1, compartment, lfp, summation, synapse };
+        enum class Type { invalid = -1, compartment, lfp, summation, synapse, compartment_set };
         enum class Scaling { invalid = -1, none, area };
         enum class Compartments { invalid = -1, center, all };
 
+
         /// Node sets on which to report
         std::string cells;
         /// Sections on which to report. Default value: "soma"
@@ -398,6 +399,8 @@ class SONATA_API SimulationConfig
         /// For compartment type, select compartments to report.
         /// Default value: "center"(for sections: soma), "all"(for other sections)
         Compartments compartments;
+        /// Name of the compartment set (from compartment_set.json) used for generating the report.
+        std::string compartment_set;
         /// The simulation variable to access. The variables available are model dependent. For
         /// summation type, it supports multiple variables by comma separated strings. E.g. “ina”,
         /// "AdEx.V_M, v", "i_membrane, IClamp".

python/bindings.cpp

@@ -551,19 +551,23 @@ PYBIND11_MODULE(_libsonata, m) {
     py::class_<CompartmentLocation>(m, "CompartmentLocation")
         .def("__eq__", &CompartmentLocation::operator==)
         .def("__ne__", &CompartmentLocation::operator!=)
+        .def("__lt__", &CompartmentLocation::operator<)
+        .def("__le__", &CompartmentLocation::operator<=)
+        .def("__gt__", &CompartmentLocation::operator>)
+        .def("__ge__", &CompartmentLocation::operator>=)
         .def("__repr__",
              [](const CompartmentLocation& self) {
                  return fmt::format("CompartmentLocation({}, {}, {})",
                                     self.nodeId,
-                                    self.sectionIndex,
+                                    self.sectionId,
                                     self.offset);
              })
         .def("__str__",
              [](const CompartmentLocation& self) { return py::str(py::repr(py::cast(self))); })
         .def_readonly("node_id", &CompartmentLocation::nodeId, DOC_COMPARTMENTLOCATION(nodeId))
-        .def_readonly("section_index",
-                      &CompartmentLocation::sectionIndex,
-                      DOC_COMPARTMENTLOCATION(sectionIndex))
+        .def_readonly("section_id",
+                      &CompartmentLocation::sectionId,
+                      DOC_COMPARTMENTLOCATION(sectionId))
         .def_readonly("offset", &CompartmentLocation::offset, DOC_COMPARTMENTLOCATION(offset));
 
     py::class_<CompartmentSet>(m, "CompartmentSet")
@@ -632,7 +636,7 @@ PYBIND11_MODULE(_libsonata, m) {
 
     py::class_<CompartmentSets>(m, "CompartmentSets")
         .def(py::init<const std::string&>())
-        .def_static("fromFile", &CompartmentSets::fromFile, py::arg("path"))
+        .def_static("from_file", &CompartmentSets::fromFile, py::arg("path"))
         .def("__contains__",
              &CompartmentSets::contains,
              py::arg("key"),
@@ -869,6 +873,9 @@ PYBIND11_MODULE(_libsonata, m) {
         .def_readonly("cells",
                       &SimulationConfig::Report::cells,
                       DOC_SIMULATIONCONFIG(Report, cells))
+        .def_readonly("compartment_set",
+                      &SimulationConfig::Report::compartment_set,
+                      DOC_SIMULATIONCONFIG(Report, compartmentSet))
         .def_readonly("sections",
                       &SimulationConfig::Report::sections,
                       DOC_SIMULATIONCONFIG(Report, sections))
@@ -898,6 +905,7 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(Report, enabled));
 
     py::enum_<SimulationConfig::Report::Sections>(report, "Sections")
+        .value("invalid", SimulationConfig::Report::Sections::invalid)
         .value("soma",
                SimulationConfig::Report::Sections::soma,
                DOC_SIMULATIONCONFIG(Report, Sections, soma))
@@ -918,13 +926,15 @@ PYBIND11_MODULE(_libsonata, m) {
         .value("compartment", SimulationConfig::Report::Type::compartment)
         .value("lfp", SimulationConfig::Report::Type::lfp)
         .value("summation", SimulationConfig::Report::Type::summation)
-        .value("synapse", SimulationConfig::Report::Type::synapse);
+        .value("synapse", SimulationConfig::Report::Type::synapse)
+        .value("compartment_set", SimulationConfig::Report::Type::compartment_set);
 
     py::enum_<SimulationConfig::Report::Scaling>(report, "Scaling")
         .value("none", SimulationConfig::Report::Scaling::none)
         .value("area", SimulationConfig::Report::Scaling::area);
 
     py::enum_<SimulationConfig::Report::Compartments>(report, "Compartments")
+        .value("invalid", SimulationConfig::Report::Compartments::invalid)
         .value("center", SimulationConfig::Report::Compartments::center)
         .value("all", SimulationConfig::Report::Compartments::all);
 

python/generated/docstrings.h

@@ -383,7 +383,7 @@ static const char *__doc_bbp_sonata_NodeSets_toJSON = R"doc(Return the nodesets
 
 static const char *__doc_bbp_sonata_CompartmentLocation_nodeId = R"doc(Id of the node.)doc";
 
-static const char *__doc_bbp_sonata_CompartmentLocation_sectionIndex = R"doc(Absolute section index. Progressive index that uniquely identifies the section. There is a mapping between neuron section names (i.e. dend[10]) and this index.)doc";
+static const char *__doc_bbp_sonata_CompartmentLocation_sectionId = R"doc(Absolute section id. Progressive index that uniquely identifies the section. It is different from the relative section index. There is a mapping between neuron section names (i.e. dend[10]) and this index.)doc";
 
 static const char *__doc_bbp_sonata_CompartmentLocation_offset = R"doc(Offset of the compartment along the section)doc";
 
@@ -1156,6 +1156,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_Report_Type_synapse = R"doc
 
 static const char *__doc_bbp_sonata_SimulationConfig_Report_cells = R"doc(Node sets on which to report)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_Report_compartmentSet = R"doc(Compartment set on which to report)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_Report_compartments =
 R"doc(For compartment type, select compartments to report. Default value:
 "center"(for sections: soma), "all"(for other sections))doc";