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Update SBMLNetwork. #49

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2 changes: 1 addition & 1 deletion third_party/SBMLNetwork
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Submodule SBMLNetwork updated 80 files
+1 −1 .github/workflows/build.yml
+5 −5 CMakeLists.txt
+2 −0 README.md
+1 −1 VERSION.txt
+0 −12 examples/paper/data_integration/reaction_fluxes.py
+342 −347 examples/paper/figure_2_sbgn_compliant/figure_2_sbgn_compliant.xml
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/__init__.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/__init__.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_1d_element_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_2d_element_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/__init__.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_catalysis.py
+1 −0 ...les/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_connecting_arc_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_consumption.py
+0 −0 ...s/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_necessary_stimulation.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_production.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_connecting_arcs/sbgn_stimulation.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_container_nodes/__init__.py
+4 −1 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_container_nodes/sbgn_compartment.py
+0 −0 ...les/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_container_nodes/sbgn_container_node_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_element_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/__init__.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/complex.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/macromolecule.py
+0 −0 ...les/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/macromolecule_multimer.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/nucleic_acid_feature.py
+18 −1 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/sbgn_empty_set.py
+0 −0 ...paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/sbgn_entity_pool_node_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/simple_chemical.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/state_variable.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_entity_pool_nodes/unit_of_information.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_logical_operators/__init__.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_logical_operators/sbgn_and_operator.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_logical_operators/sbgn_logic_arc.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_logical_operators/sbgn_logic_port.py
+0 −0 ...paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_logical_operators/sbgn_logical_operator_base.py
+7 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_node_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_process_nodes/__init__.py
+6 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_process_nodes/sbgn_port.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_process_nodes/sbgn_port_base.py
+8 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_process_nodes/sbgn_process.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/sbgn_process_nodes/sbgn_process_node_base.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgn_elements/utils.py
+0 −0 examples/paper/figure_2_sbgn_compliant/sbgntosbml/sbgntosbml.py
+653 −0 examples/paper/figure_2_sbgn_compliant/script.py
+0 −0 examples/paper/figure_3_visual_styling/ecoli.xml
+349 −354 examples/paper/figure_3_visual_styling/figure_3_visual_styling.xml
+7 −0 examples/paper/figure_3_visual_styling/script.py
+ − examples/paper/figure_4_alignment/figure_4_alignment.xml
+74 −0 examples/paper/figure_4_alignment/script.py
+158 −156 examples/paper/figure_5_data_integration/figure_5_data_integration.xml
+0 −0 examples/paper/figure_5_data_integration/glycolysis_pathway_map.xml
+16 −0 examples/paper/figure_5_data_integration/script.py
+0 −177 examples/paper/network_arrangement/tca_cycle.py
+0 −2,220 examples/paper/network_arrangement/tca_cycle.xml
+ − examples/paper/sbgn_compliant/iNOS_SBGN_ED.pdf
+0 −1 examples/paper/sbgn_compliant/src/__init__.py
+0 −11 examples/paper/visual_styling/ecoli_set_escher_style.py
+1 −1 src/CMakeLists.txt
+33 −34 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/features/align.py
+13 −6 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/features/color_bar/color_bar.py
+4 −1 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/features/data_integration.py
+1 −3 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/network_elements/compartment.py
+21 −21 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/network_elements/network_element_base.py
+20 −0 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/network_elements/network_element_lists/reaction_list.py
+23 −25 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/network_elements/reaction.py
+20 −22 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/network_elements/species.py
+14 −5 src/bindings/python/ctypes/sbmlnetwork/src/sbmlnetwork/sbmlnetwork.py
+1 −1 src/bindings/python/ctypes/sbmlnetwork/tests/test_user_interface_layer.py
+1 −7 src/features/autolayout/libsbmlnetwork_autolayout_node.cpp
+3 −4 src/features/defaults/libsbmlnetwork_defaults_render.cpp
+4 −1 src/features/set_layout_features/libsbmlnetwork_set_layout_features.cpp
+18 −18 src/features/styles/libsbmlnetwork_styles.cpp
+5 −3 src/libsbmlnetwork_layout.cpp
+1 −1 src/libsbmlnetwork_layout_helpers.cpp
+1 −1 src/libsbmlnetwork_layout_render.cpp
+1 −1 src/libsbmlnetwork_render.cpp
+8 −5 src/libsbmlnetwork_render_helpers.cpp
+1 −1 src/libsbmlnetwork_sbmldocument_layout.cpp
+4 −4 src/libsbmlnetwork_sbmldocument_render.cpp