BifurcationKit doc update

Author: TorkelE

docs/src/catalyst_applications/bifurcation_diagrams.md

@@ -72,7 +72,7 @@ We also bundle the information we have compiled so far into a
 using BifurcationKit, Plots, LinearAlgebra, Setfield
 
 bprob = BifurcationProblem(F, oprob.u0, oprob.p, (@lens _[bif_idx]);
-                           recordFromSolution = (x, p) -> x[plot_idx], J = J)
+                           record_from_solution = (x, p) -> x[plot_idx], J = J)
 nothing   # hide
 ```
 Next, we need to specify the input options for the pseudo-arclength continuation
@@ -81,10 +81,10 @@ method (PACM) which produces the diagram.
 bopts = ContinuationPar(dsmax = 0.05,          # Max arclength in PACM.
                         dsmin = 1e-4,          # Min arclength in PACM.
                         ds = 0.001,            # Initial (positive) arclength in PACM.
-                        maxSteps = 100000,     # Max number of steps.
-                        pMin = p_span[1],      # Min p-val (if hit, the method stops).
-                        pMax = p_span[2],      # Max p-val (if hit, the method stops).
-                        detectBifurcation = 3) # Value in {0,1,2,3}
+                        max_steps = 100000,     # Max number of steps.
+                        p_min = p_span[1],      # Min p-val (if hit, the method stops).
+                        p_max = p_span[2],      # Max p-val (if hit, the method stops).
+                        detect_bifurcation = 3) # Value in {0,1,2,3}
 nothing   # hide
 ```
 Here `detectBifurcation` determines to what extent bifurcation points are
@@ -111,6 +111,24 @@ capable of a lot more. For more details, please see that package's
 documentation:
 [BifurcationKit.jl](https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/).
 
+---
+## [Citation](@id homotopy_continuation_citation)
+If you use this functionality in your research, please cite the following paper to support the author of the BifurcationKit package:
+```
+@misc{veltz:hal-02902346,
+  title = {{BifurcationKit.jl}},
+  author = {Veltz, Romain},
+  url = {https://hal.archives-ouvertes.fr/hal-02902346},
+  institution = {{Inria Sophia-Antipolis}},
+  year = {2020},
+  month = Jul,
+  keywords = {pseudo-arclength-continuation ; periodic-orbits ; floquet ; gpu ; bifurcation-diagram ; deflation ; newton-krylov},
+  pdf = {https://hal.archives-ouvertes.fr/hal-02902346/file/354c9fb0d148262405609eed2cb7927818706f1f.tar.gz},
+  hal_id = {hal-02902346},
+  hal_version = {v1},
+}
+```
+
 ---
 ## References
 [^1]: [Yuri A. Kuznetsov, *Elements of Applied Bifurcation Theory*, Springer (2023).](https://link.springer.com/book/10.1007/978-3-031-22007-4)

docs/src/catalyst_applications/homotopy_continuation.md

@@ -61,8 +61,8 @@ hc_steady_states(two_state_model, ps; u0)
 - `hc_steady_states` supports any systems where all rates are systems of rational polynomials (such as Hill functions with integer Hill coefficients).
 - When providing initial conditions to compute conservation laws, values are only required for those species that are part of conserved quantities. If this set of species is unknown, it is recommended to provide initial conditions for all species. 
 - Additional arguments provided to `hc_steady_states` are automatically passed to HomotopyContinuation's `solve` command. Use e.g. `show_progress=false` to disable the progress bar.
----
 
+---
 ## [Citation](@id homotopy_continuation_citation)
 If you use this functionality in your research, please cite the following paper to support the authors of the HomotopyContinuation package:
 ```
@@ -76,6 +76,7 @@ If you use this functionality in your research, please cite the following paper
 }
 ```
 
+---
 ## References
 [^1]: [Thomas Wilhelm, *The smallest chemical reaction system with bistability*, BMC Systems Biology (2009).](https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-3-90)
 [^2]: [Paul Breiding, Sascha Timme, *HomotopyContinuation.jl: A Package for Homotopy Continuation in Julia*, International Congress on Mathematical Software (2018).](https://link.springer.com/chapter/10.1007/978-3-319-96418-8_54)