From 687d285cb7cc8cb468c81a0a2cfdec513349efd3 Mon Sep 17 00:00:00 2001 From: adelhpour Date: Fri, 19 Sep 2025 10:54:38 -0700 Subject: [PATCH 1/2] update docs - add newly added api functions - add a new version of the escher styling figure with larger fonts --- docs/_static/escher_ecoli.svg | 5653 ++++++++++++++------------ docs/api_reference/c_api_index.rst | 4 + docs/api_reference/cpp_api_index.rst | 8 + 3 files changed, 3177 insertions(+), 2488 deletions(-) diff --git a/docs/_static/escher_ecoli.svg b/docs/_static/escher_ecoli.svg index c159805e..62066ad4 100644 --- a/docs/_static/escher_ecoli.svg +++ b/docs/_static/escher_ecoli.svg @@ -1,2489 +1,3166 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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PPCK + + + PIt2r + + + AKGt2r + + + FBA + + + TPI + + + CYTBD + + + RPI + + + MALS + + + PTAr + + + GLNabc + + + ME1 + + + G6PDH2r + + + EX_ac_e + + + GLUN + + + ATPM + + + LDH_D + + + MDH + + + H2Ot + + + EX_h2o_e + + + TKT1 + + + CO2t + + + EX_akg_e + + + PPS + + + EX_glc__D_e + + + ETOHt2r + + + PGM + + + EX_etoh_e + + + ACKr + + + EX_nh4_e + + + GLUSy + + + EX_pi_e + + + FUMt2_2 + + + ACt2r + + + GLCpts + + + SUCCt3 + + + PGL + + + GAPD + + + EX_fum_e + + + SUCCt2_2 + + + GLUDy + + + ATPS4r + + + CS + + + PYRt2 + + + ME2 + + + EX_for_e + + + ACALD + + + ACALDt + + + EX_acald_e + + + ALCD2x + + + FORt2 + + + FORti + + + FRD7 + + + FRUpts2 + + + EX_fru_e + + + MALt2_2 + + + EX_mal__L_e + + + NADH16 + + + SUCDi + + + D_LACt2 + + + BIOMASS_Ecoli_core_w_GAM + + + ACONTa + + + ACONTb + diff --git a/docs/api_reference/c_api_index.rst b/docs/api_reference/c_api_index.rst index 7badd5e6..fe5e1f4b 100644 --- a/docs/api_reference/c_api_index.rst +++ b/docs/api_reference/c_api_index.rst @@ -211,6 +211,10 @@ Functions .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::c_api_isSpeciesReferenceCurveSegmentCubicBezier(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex = 0, int speciesReferenceIndex = 0, int curveSegmentIndex = 0, int layoutIndex = 0) +.. doxygenfunction:: LIBSBMLNETWORK_EXTERN int c_api_convertSpeciesReferenceCurveSegmentToLine(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex = 0, int speciesReferenceIndex = 0, int curveSegmentIndex = 0, int layoutIndex = 0) + +.. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE:int c_api_convertSpeciesReferenceCurveSegmentToCubicBezier(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex = 0, int speciesReferenceIndex = 0, int curveSegmentIndex = 0, int layoutIndex = 0) + .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::c_api_getSpeciesReferenceCurveSegmentStartPointX(SBMLDocument* document, const char* reactionId, int reactionGlyphIndex = 0, int speciesReferenceIndex = 0, int curveSegmentIndex = 0, int layoutIndex = 0) .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::c_api_setSpeciesReferenceCurveSegmentStartPointX(SBMLDocument* document, const char* reactionId, const double x, int reactionGlyphIndex = 0, int speciesReferenceIndex = 0, int curveSegmentIndex = 0, int layoutIndex = 0) diff --git a/docs/api_reference/cpp_api_index.rst b/docs/api_reference/cpp_api_index.rst index 3b088497..46323ef3 100644 --- a/docs/api_reference/cpp_api_index.rst +++ b/docs/api_reference/cpp_api_index.rst @@ -340,6 +340,14 @@ Layout Functions .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::isSpeciesReferenceCurveSegmentCubicBezier(SBMLDocument* document, unsigned int layoutIndex, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) +.. doxygenfunction:: LIBSBMLNETWORK_EXTERN int convertSpeciesReferenceCurveSegmentToLine(SBMLDocument* document, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) + +.. doxygenfunction:: LIBSBMLNETWORK_EXTERN int convertSpeciesReferenceCurveSegmentToLine(SBMLDocument* document, unsigned int layoutIndex, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) + +.. doxygenfunction:: LIBSBMLNETWORK_EXTERN int convertSpeciesReferenceCurveSegmentToCubicBezier(SBMLDocument* document, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) + +.. doxygenfunction:: LIBSBMLNETWORK_EXTERN int convertSpeciesReferenceCurveSegmentToCubicBezier(SBMLDocument* document, unsigned int layoutIndex, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) + .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getSpeciesReferenceCurveSegmentStartPointX(SBMLDocument* document, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) .. doxygenfunction:: LIBSBMLNETWORK_CPP_NAMESPACE::getSpeciesReferenceCurveSegmentStartPointX(SBMLDocument* document, unsigned int layoutIndex, const std::string& reactionId, unsigned int reactionGlyphIndex = 0, unsigned int speciesReferenceIndex = 0, unsigned int curveSegmentIndex = 0) From d096fa625119592a51d615d0477fc6a79bc272f5 Mon Sep 17 00:00:00 2001 From: adelhpour Date: Fri, 19 Sep 2025 10:54:57 -0700 Subject: [PATCH 2/2] bump version to 0.5.12 --- VERSION.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION.txt b/VERSION.txt index cacdf3bd..12697f71 100755 --- a/VERSION.txt +++ b/VERSION.txt @@ -1 +1 @@ -0.5.11 \ No newline at end of file +0.5.12 \ No newline at end of file