libsonata 0.2.0__tar.gz → 0.2.2__tar.gz

{libsonata-0.2.0 → libsonata-0.2.2}/.github/workflows/publish-sdist-wheels.yml

@@ -73,7 +73,8 @@ jobs:
         if: runner.os == 'macOS'
 
         env:
-          CIBW_ENVIRONMENT_PASS: "CMAKE_ARGS CMAKE_PREFIX_PATH"
+          MACOSX_DEPLOYMENT_TARGET: "10.15"
+          CIBW_ENVIRONMENT_PASS: "CMAKE_ARGS CMAKE_PREFIX_PATH MACOSX_DEPLOYMENT_TARGET"
           CIBW_BEFORE_BUILD: |
             # CMake complains if the dependencies come from within the same tree
             # as the source, so we'll just pretend they are elsewhere

{libsonata-0.2.0 → libsonata-0.2.2}/.readthedocs.yaml

@@ -10,11 +10,11 @@ submodules:
   recursive: true
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   apt_packages:
     - libhdf5-dev
   tools:
-    python: "3.9"
+    python: "3.12"
 
 sphinx:
   configuration: docs/source/conf.py

{libsonata-0.2.0 → libsonata-0.2.2}/CMakeLists.txt

@@ -59,7 +59,7 @@ option(SONATA_CXX_WARNINGS "Compile C++ with warnings as errors, for glibcxx tur
 
 set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
 
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set(SONATA_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include)

{libsonata-0.2.0 → libsonata-0.2.2}/MANIFEST.in

@@ -21,9 +21,6 @@ recursive-include extlib/HighFive/include *
 include extlib/HighFive/CMakeLists.txt
 include extlib/HighFive/LICENSE
 
-# ghc::filesystem
-include extlib/filesystem.hpp
-
 # pybind11
 recursive-include python/pybind11/include *
 recursive-include python/pybind11/tools *.cmake

{libsonata-0.2.0 → libsonata-0.2.2}/PKG-INFO

@@ -1,14 +1,15 @@
 Metadata-Version: 2.4
 Name: libsonata
-Version: 0.2.0
+Version: 0.2.2
 Summary: SONATA files reader
-Author: Blue Brain Project, EPFL
+Author: Open Brain Institute
 License-Expression: LGPL-3.0-or-later
 Project-URL: Homepage, https://github.com/openbraininstitute/libsonata
 Requires-Python: >=3.9
 Requires-Dist: numpy>=1.17.3
 Provides-Extra: docs
-Requires-Dist: sphinx-bluebrain-theme; extra == "docs"
+Requires-Dist: sphinx<10,>=8.2; extra == "docs"
+Requires-Dist: obi-sphinx-theme>=2.0.0; extra == "docs"
 Description-Content-Type: text/x-rst
 
 |banner|
@@ -49,11 +50,6 @@ Building the C++ library
    cmake -DCMAKE_BUILD_TYPE=Release -DEXTLIB_FROM_SUBMODULES=ON ..
    make -j
 
-Since `libsonata` uses backports for `std::optional` and `std::variant` which
-turn into their actual STL implementation once available, it's recommended to compile
-`libsonata` with the same C++ standard as the project linking to `libsonata`. This
-is done by passing `-DCMAKE_CXX_STANDARD={14,17}` to the `cmake` command above.
-
 Usage (Python)
 --------------
 

{libsonata-0.2.0 → libsonata-0.2.2}/README.rst

@@ -36,11 +36,6 @@ Building the C++ library
    cmake -DCMAKE_BUILD_TYPE=Release -DEXTLIB_FROM_SUBMODULES=ON ..
    make -j
 
-Since `libsonata` uses backports for `std::optional` and `std::variant` which
-turn into their actual STL implementation once available, it's recommended to compile
-`libsonata` with the same C++ standard as the project linking to `libsonata`. This
-is done by passing `-DCMAKE_CXX_STANDARD={14,17}` to the `cmake` command above.
-
 Usage (Python)
 --------------
 

{libsonata-0.2.0 → libsonata-0.2.2}/ci/check_generated_docstrings.sh

@@ -44,6 +44,7 @@ $VENV/bin/python -m pybind11_mkdoc \
   ./include/bbp/sonata/*.h \
   -Wno-pragma-once-outside-header \
   -ferror-limit=100000 \
+  -std=c++17 \
   -I/usr/include/hdf5/serial \
   -I./extlib/HighFive/include \
   -I./extlib/nlohmann/ \

libsonata-0.2.2/docs/source/_templates/navbar-version.html

@@ -0,0 +1,3 @@
+<span class="navbar-version" style="color: #fff" aria-label="Documentation version">
+  v{{ release }}
+</span>

{libsonata-0.2.0 → libsonata-0.2.2}/docs/source/conf.py

@@ -17,8 +17,8 @@
 
 # -- Project information -----------------------------------------------------
 
+from importlib.metadata import version as package_version
 from pathlib import Path
-import pkg_resources
 import re
 import shutil
 import subprocess
@@ -26,8 +26,8 @@ import subprocess
 from jinja2 import Template
 
 project = "libsonata"
-author = "Blue Brain Project, EPFL"
-version = pkg_resources.get_distribution("libsonata").version
+author = "Open Brain Institute"
+version = package_version("libsonata")
 release = version
 
 # -- General configuration ---------------------------------------------------
@@ -51,19 +51,19 @@ master_doc = "index"
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = "sphinx-bluebrain-theme"
+html_theme = "obi_sphinx_theme"
 html_title = "libsonata"
 html_show_sourcelink = False
 html_extra_path = ["doxygen"]
-html_theme_options = {
-    "repo_url": "https://github.com/openbraininstitute/libsonata/",
-    "repo_name": "openbraininstitute/libsonata",
-}
 
 autodoc_default_options = {"members": True, "imported-members": True}
+
+html_theme_options = {
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "navbar_persistent": ["navbar-version", "search-button-field"],
+}
 autodoc_docstring_signature = True
-# work around changes to `sphinx` 9 that are incompatible with `sphinx-bluebrain-theme`
-autodoc_use_legacy_class_based = True
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

{libsonata-0.2.0 → libsonata-0.2.2}/include/bbp/sonata/config.h

@@ -18,17 +18,17 @@
 
 #include <bbp/sonata/edges.h>
 #include <bbp/sonata/nodes.h>
-#include <bbp/sonata/optional.hpp>
+#include <optional>
 
 #include "common.h"
-#include "optional.hpp"
-#include "variant.hpp"
+
+#include <variant>
 
 
 namespace bbp {
 namespace sonata {
 
-using variantValueType = nonstd::variant<bool, std::string, int, double>;
+using variantValueType = std::variant<bool, std::string, int, double>;
 
 enum class SimulatorType { invalid = -1, NEURON, CORENEURON, LEARNINGENGINE, BRIAN2, UNSPECIFIED };
 
@@ -91,19 +91,19 @@ struct SONATA_API NodePopulationProperties: public CommonPopulationProperties {
      * Path to the .h5 file containing the vasculature morphology. Only for vasculature node
      * populations where it is mandatory.
      */
-    nonstd::optional<std::string> vasculatureFile{nonstd::nullopt};
+    std::optional<std::string> vasculatureFile{std::nullopt};
 
     /**
      *Path to the .obj file containing the mesh of a vasculature morphology. Only for vasculature
      *node populations where it is mandatory.
      */
-    nonstd::optional<std::string> vasculatureMesh{nonstd::nullopt};
+    std::optional<std::string> vasculatureMesh{std::nullopt};
 
     /**
      * Path to the .h5 storing microdomain data. Only for astrocyte node populations where it is
      * mandatory.
      */
-    nonstd::optional<std::string> microdomainsFile{nonstd::nullopt};
+    std::optional<std::string> microdomainsFile{std::nullopt};
 };
 
 /**
@@ -118,12 +118,12 @@ struct SONATA_API EdgePopulationProperties: public CommonPopulationProperties {
     /**
      * Path to spatial_segment_index
      */
-    nonstd::optional<std::string> endfeetMeshesFile{nonstd::nullopt};
+    std::optional<std::string> endfeetMeshesFile{std::nullopt};
 
     /**
      * Path to the directory containing the dendritic spine morphologies.
      */
-    nonstd::optional<std::string> spineMorphologiesDir{nonstd::nullopt};
+    std::optional<std::string> spineMorphologiesDir{std::nullopt};
 };
 
 /**
@@ -251,11 +251,11 @@ class SONATA_API CircuitConfig
         std::string pointNeuronModelsDir;
         std::string mechanismsDir;
 
-        nonstd::optional<std::string> vasculatureFile{nonstd::nullopt};
-        nonstd::optional<std::string> vasculatureMesh{nonstd::nullopt};
-        nonstd::optional<std::string> endfeetMeshesFile{nonstd::nullopt};
-        nonstd::optional<std::string> microdomainsFile{nonstd::nullopt};
-        nonstd::optional<std::string> spineMorphologiesDir{nonstd::nullopt};
+        std::optional<std::string> vasculatureFile{std::nullopt};
+        std::optional<std::string> vasculatureMesh{std::nullopt};
+        std::optional<std::string> endfeetMeshesFile{std::nullopt};
+        std::optional<std::string> microdomainsFile{std::nullopt};
+        std::optional<std::string> spineMorphologiesDir{std::nullopt};
     };
 
     class Parser;
@@ -417,11 +417,11 @@ class SONATA_API SimulationConfig
         std::string sectionConfigure;
     };
 
-    using Modification = nonstd::variant<ModificationTTX,
-                                         ModificationConfigureAllSections,
-                                         ModificationSectionList,
-                                         ModificationSection,
-                                         ModificationCompartmentSet>;
+    using Modification = std::variant<ModificationTTX,
+                                      ModificationConfigureAllSections,
+                                      ModificationSectionList,
+                                      ModificationSection,
+                                      ModificationCompartmentSet>;
 
     /**
      * Parameters defining global experimental conditions.
@@ -441,7 +441,7 @@ class SONATA_API SimulationConfig
         SpikeLocation spikeLocation = DEFAULT_spikeLocation;
         /// Extracellular calcium concentration, being applied to the synapse uHill parameter in
         /// order to scale the U parameter of synapses. Default is None.
-        nonstd::optional<double> extracellularCalcium{nonstd::nullopt};
+        std::optional<double> extracellularCalcium{std::nullopt};
         /// Enable legacy behavior to randomize the GABA_A rise time in the helper functions.
         /// Default is false
         bool randomizeGabaRiseTime = DEFAULT_randomizeGabaRiseTime;
@@ -519,8 +519,8 @@ class SONATA_API SimulationConfig
             ornstein_uhlenbeck,
             relative_ornstein_uhlenbeck,
             spatially_uniform_e_field,
-            poisson
-
+            poisson,
+            replay
         };
 
         enum class InputType {
@@ -533,17 +533,17 @@ class SONATA_API SimulationConfig
         };
 
         /// Type of stimulus
-        Module module;
+        Module module{Module::invalid};
         /// Type of input
-        InputType inputType;
+        InputType inputType{InputType::invalid};
         /// Time when input is activated (ms)
         double delay{};
         /// Time duration for how long input is activated (ms)
         double duration{};
         /// Node set which is affected by input. Not allowed in case of CompartmentSet
-        nonstd::optional<std::string> nodeSet{nonstd::nullopt};
+        std::optional<std::string> nodeSet{std::nullopt};
         /// CompartmentSet which is affected by the input. It has priority over nodeSet
-        nonstd::optional<std::string> compartmentSet{nonstd::nullopt};
+        std::optional<std::string> compartmentSet{std::nullopt};
     };
 
     struct InputLinear: public InputBase {
@@ -617,9 +617,9 @@ class SONATA_API SimulationConfig
 
     struct InputNoise: public InputBase {
         /// The mean value of current to inject (nA), default = None
-        nonstd::optional<double> mean{nonstd::nullopt};
+        std::optional<double> mean{std::nullopt};
         /// The mean value of current to inject as a percentage of threshold current, default = None
-        nonstd::optional<double> meanPercent{nonstd::nullopt};
+        std::optional<double> meanPercent{std::nullopt};
         /// State var to track whether the value of injected noise current is mean or
         /// mean_percent
         double variance{};
@@ -633,7 +633,7 @@ class SONATA_API SimulationConfig
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
         /// Override the random seed to introduce correlations between cells, default = None
-        nonstd::optional<int> randomSeed{nonstd::nullopt};
+        std::optional<int> randomSeed{std::nullopt};
         /// Reversal potential for conductance injection in mV. Default is 0
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
@@ -655,7 +655,7 @@ class SONATA_API SimulationConfig
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
         /// Override the random seed to introduce correlations between cells, default = None
-        nonstd::optional<int> randomSeed{nonstd::nullopt};
+        std::optional<int> randomSeed{std::nullopt};
         /// Reversal potential for conductance injection in mV. Default is 0
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
@@ -680,7 +680,7 @@ class SONATA_API SimulationConfig
         /// The decay time of the bi-exponential shots (ms)
         double decayTime{};
         /// Override the random seed to introduce correlations between cells, default = None
-        nonstd::optional<int> randomSeed{nonstd::nullopt};
+        std::optional<int> randomSeed{std::nullopt};
         /// Reversal potential for conductance injection in mV. Default is 0
         double reversal{};
         /// Timestep of generated signal in ms. Default is 0.25 ms
@@ -705,7 +705,7 @@ class SONATA_API SimulationConfig
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
         /// Override the random seed to introduce correlations between cells, default = None
-        nonstd::optional<int> randomSeed{nonstd::nullopt};
+        std::optional<int> randomSeed{std::nullopt};
         /// Signal mean in nA (current_clamp) or uS (conductance)
         double mean{};
         /// Signal std dev in nA (current_clamp) or uS (conductance)
@@ -722,7 +722,7 @@ class SONATA_API SimulationConfig
         /// Timestep of generated signal in ms. Default is 0.25 ms
         double dt{};
         /// Override the random seed to introduce correlations between cells, default = None
-        nonstd::optional<int> randomSeed{nonstd::nullopt};
+        std::optional<int> randomSeed{std::nullopt};
         /// Signal mean as percentage of a cell’s threshold current (current_clamp) or inverse input
         /// resistance (conductance)
         double meanPercent{};
@@ -773,22 +773,32 @@ class SONATA_API SimulationConfig
         double weight{};
     };
 
-    using Input = nonstd::variant<InputLinear,
-                                  InputRelativeLinear,
-                                  InputPulse,
-                                  InputSinusoidal,
-                                  InputSubthreshold,
-                                  InputHyperpolarizing,
-                                  InputSynapseReplay,
-                                  InputSeclamp,
-                                  InputNoise,
-                                  InputShotNoise,
-                                  InputRelativeShotNoise,
-                                  InputAbsoluteShotNoise,
-                                  InputOrnsteinUhlenbeck,
-                                  InputRelativeOrnsteinUhlenbeck,
-                                  InputSpatiallyUniformEField,
-                                  InputPoissonSpike>;
+    struct InputReplay: public InputBase {
+        /// Path to the input file to replay.
+        std::string path;
+
+        /// Whether the signal should be interpolated.
+        bool interpolate;
+    };
+
+    using Input = std::variant<std::monostate,
+                               InputLinear,
+                               InputRelativeLinear,
+                               InputPulse,
+                               InputSinusoidal,
+                               InputSubthreshold,
+                               InputHyperpolarizing,
+                               InputSynapseReplay,
+                               InputSeclamp,
+                               InputNoise,
+                               InputShotNoise,
+                               InputRelativeShotNoise,
+                               InputAbsoluteShotNoise,
+                               InputOrnsteinUhlenbeck,
+                               InputRelativeOrnsteinUhlenbeck,
+                               InputSpatiallyUniformEField,
+                               InputPoissonSpike,
+                               InputReplay>;
 
     using InputMap = std::unordered_map<std::string, Input>;
 
@@ -806,25 +816,25 @@ class SONATA_API SimulationConfig
         /// Scalar to adjust synaptic strength, default = 1.
         double weight{1.};
         /// Rate to spontaneously trigger the synapses in this connection_override, default = None
-        nonstd::optional<double> spontMinis{nonstd::nullopt};
+        std::optional<double> spontMinis{std::nullopt};
         /// Snippet of hoc code to be executed on the synapses in this connection_override, default
         /// = None
-        nonstd::optional<std::string> synapseConfigure{nonstd::nullopt};
+        std::optional<std::string> synapseConfigure{std::nullopt};
         /// Synapse helper files to instantiate the synapses in this connection_override, default =
         /// None
-        nonstd::optional<std::string> modoverride{nonstd::nullopt};
+        std::optional<std::string> modoverride{std::nullopt};
         /// Value to override the synaptic delay time originally set in the edge file (ms),
         /// default = None.
-        nonstd::optional<double> synapseDelayOverride{nonstd::nullopt};
+        std::optional<double> synapseDelayOverride{std::nullopt};
         /// Adjustments from weight of this connection_override are applied after the specified
         /// delay has elapsed in ms, default = 0.
         double delay{0.};
         /// To override the neuromod_dtc values between the selected source and target neurons for
         /// the neuromodulatory projection. Given in ms.
-        nonstd::optional<double> neuromodulationDtc{nonstd::nullopt};
+        std::optional<double> neuromodulationDtc{std::nullopt};
         /// To override the neuromod_strength values between the selected source and target neurons
         /// for the neuromodulatory projection. Given in muM.
-        nonstd::optional<double> neuromodulationStrength{nonstd::nullopt};
+        std::optional<double> neuromodulationStrength{std::nullopt};
     };
 
     /**
@@ -928,12 +938,12 @@ class SONATA_API SimulationConfig
     /**
      * Returns the name of the node set to be instantiated for the simulation, default = None
      */
-    const nonstd::optional<std::string>& getNodeSet() const noexcept;
+    const std::optional<std::string>& getNodeSet() const noexcept;
 
     /**
      * Returns the name of the compartment set to be instantiated for the simulation, default = None
      */
-    const nonstd::optional<std::string>& getCompartmentSet() const noexcept;
+    const std::optional<std::string>& getCompartmentSet() const noexcept;
 
     /**
      * Returns the metadata section
@@ -981,7 +991,7 @@ class SONATA_API SimulationConfig
     // Path of compartment sets file
     std::string _compartmentSetsFile;
     // Name of node set
-    nonstd::optional<std::string> _nodeSet{nonstd::nullopt};
+    std::optional<std::string> _nodeSet{std::nullopt};
     // Remarks on the simulation
     std::unordered_map<std::string, variantValueType> _metaData;
     // Variables for a new feature in development, to be moved to other sections once in production

{libsonata-0.2.0 → libsonata-0.2.2}/include/bbp/sonata/electrode_reader.h

@@ -8,8 +8,8 @@
 #include <highfive/H5File.hpp>
 
 #include <bbp/sonata/common.h>
-#include <bbp/sonata/optional.hpp>
 #include <bbp/sonata/selection.h>
+#include <optional>
 
 namespace bbp {
 namespace sonata {
@@ -65,8 +65,8 @@ class SONATA_API ElectrodeReader
          * \return ElectrodeScalingFactors with the submatrix of scaling factors.
          */
         ElectrodeScalingFactors get(
-            const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-            const nonstd::optional<Selection>& electrode_ids = nonstd::nullopt) const;
+            const std::optional<Selection>& node_ids = std::nullopt,
+            const std::optional<Selection>& electrode_ids = std::nullopt) const;
 
         /**
          * Return electrode names ordered by column index.

{libsonata-0.2.0 → libsonata-0.2.2}/include/bbp/sonata/report_reader.h

@@ -7,8 +7,8 @@
 
 #include <highfive/H5File.hpp>
 
-#include <bbp/sonata/optional.hpp>
 #include <bbp/sonata/population.h>
+#include <optional>
 
 namespace bbp {
 namespace sonata {
@@ -51,9 +51,9 @@ class SONATA_API SpikeReader
         /**
          * Return spikes with all those node_ids between 'tstart' and 'tstop'
          */
-        Spikes get(const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-                   const nonstd::optional<double>& tstart = nonstd::nullopt,
-                   const nonstd::optional<double>& tstop = nonstd::nullopt) const;
+        Spikes get(const std::optional<Selection>& node_ids = std::nullopt,
+                   const std::optional<double>& tstart = std::nullopt,
+                   const std::optional<double>& tstop = std::nullopt) const;
 
         /**
          * Return the raw node_ids and timestamps vectors
@@ -63,9 +63,9 @@ class SONATA_API SpikeReader
         /**
          * Return the node_ids and timestamps vectors with all node_ids between 'tstart' and 'tstop'
          */
-        SpikeTimes getArrays(const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-                             const nonstd::optional<double>& tstart = nonstd::nullopt,
-                             const nonstd::optional<double>& tstop = nonstd::nullopt) const;
+        SpikeTimes getArrays(const std::optional<Selection>& node_ids = std::nullopt,
+                             const std::optional<double>& tstart = std::nullopt,
+                             const std::optional<double>& tstop = std::nullopt) const;
 
         /**
          * Return the way data are sorted ('none', 'by_id', 'by_time')
@@ -158,23 +158,22 @@ class SONATA_API ReportReader
          * \param block_gap_limit gap limit between each IO block while fetching data from storage
          */
         typename DataFrame<KeyType>::DataType getNodeIdElementIdMapping(
-            const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-            const nonstd::optional<size_t>& block_gap_limit = nonstd::nullopt) const;
+            const std::optional<Selection>& node_ids = std::nullopt,
+            const std::optional<size_t>& block_gap_limit = std::nullopt) const;
 
         /**
          * \param node_ids limit the report to the given selection.
-         * \param tstart return voltages occurring on or after tstart. tstart=nonstd::nullopt
+         * \param tstart return voltages occurring on or after tstart. tstart=std::nullopt
          * indicates no limit. \param tstop return voltages occurring on or before tstop.
-         * tstop=nonstd::nullopt indicates no limit. \param tstride indicates every how many
-         * timesteps we read data. tstride=nonstd::nullopt indicates that all timesteps are read.
+         * tstop=std::nullopt indicates no limit. \param tstride indicates every how many
+         * timesteps we read data. tstride=std::nullopt indicates that all timesteps are read.
          * \param block_gap_limit gap limit between each IO block while fetching data from storage.
          */
-        DataFrame<KeyType> get(
-            const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-            const nonstd::optional<double>& tstart = nonstd::nullopt,
-            const nonstd::optional<double>& tstop = nonstd::nullopt,
-            const nonstd::optional<size_t>& tstride = nonstd::nullopt,
-            const nonstd::optional<size_t>& block_gap_limit = nonstd::nullopt) const;
+        DataFrame<KeyType> get(const std::optional<Selection>& node_ids = std::nullopt,
+                               const std::optional<double>& tstart = std::nullopt,
+                               const std::optional<double>& tstop = std::nullopt,
+                               const std::optional<size_t>& tstride = std::nullopt,
+                               const std::optional<size_t>& block_gap_limit = std::nullopt) const;
 
       private:
         struct NodeIdElementLayout {
@@ -186,8 +185,8 @@ class SONATA_API ReportReader
         };
 
         Population(const HighFive::File& file, const std::string& populationName);
-        std::pair<size_t, size_t> getIndex(const nonstd::optional<double>& tstart,
-                                           const nonstd::optional<double>& tstop) const;
+        std::pair<size_t, size_t> getIndex(const std::optional<double>& tstart,
+                                           const std::optional<double>& tstop) const;
         /**
          * Return the element IDs for the given selection, alongside the filtered node pointers
          * and the range of positions where they fit in the file. This latter two are necessary
@@ -198,8 +197,8 @@ class SONATA_API ReportReader
          * \param block_gap_limit gap limit between each IO block while fetching data from storage
          */
         NodeIdElementLayout getNodeIdElementLayout(
-            const nonstd::optional<Selection>& node_ids = nonstd::nullopt,
-            const nonstd::optional<size_t>& block_gap_limit = nonstd::nullopt) const;
+            const std::optional<Selection>& node_ids = std::nullopt,
+            const std::optional<size_t>& block_gap_limit = std::nullopt) const;
 
         HighFive::Group pop_group_;
         std::vector<NodeID> node_ids_;

{libsonata-0.2.0 → libsonata-0.2.2}/pyproject.toml

@@ -9,11 +9,11 @@ description = "SONATA files reader"
 readme = "README.rst"
 license = "LGPL-3.0-or-later"
 requires-python = ">=3.9"
-authors = [{name = "Blue Brain Project, EPFL"}]
+authors = [{name = "Open Brain Institute"}]
 dependencies = ["numpy>=1.17.3"]
 
 [project.optional-dependencies]
-docs = ["sphinx-bluebrain-theme"]
+docs = ["sphinx>=8.2,<10", "obi-sphinx-theme>=2.0.0"]
 
 [project.urls]
 Homepage = "https://github.com/openbraininstitute/libsonata"