use plotly; fix bitrot

quarto/ODEs/differential_equations.qmd

@@ -384,15 +384,16 @@ Finally, we note that the `ModelingToolkit` package provides symbolic-numeric co
 
 ```{julia}
 #| hold: true
-@parameters t γ g
-@variables x(t) y(t)
+@parameters γ g
+@variables t x(t) y(t)
 D = Differential(t)
 
 eqs = [D(D(x)) ~ -γ * D(x),
        D(D(y)) ~ -g - γ * D(y)]
 
-@named sys = ODESystem(eqs)
+@named sys = ODESystem(eqs, t, [x,y], [γ,g])
 sys = ode_order_lowering(sys) # turn 2nd order into 1st
+sys = structural_simplify(sys)
 
 u0 = [D(x) => vxy₀[1],
       D(y) => vxy₀[2],

quarto/_common_code.qmd

@@ -1,4 +1,5 @@
 ```{julia}
+#| output: false
 #| echo: false
 
 ## Formatting options are included here; not in CalculusWithJulia.WeaveSupport
@@ -7,18 +8,20 @@ nothing
 ```
 
 ```{julia}
+#| output: false
 #| echo: false
 fig_size=(800, 600)
 nothing
 ```
 
 ```{julia}
+#| output: false
 #| echo: false
 
 import Logging
 Logging.disable_logging(Logging.Info) # or e.g. Logging.Info
 Logging.disable_logging(Logging.Warn)
-
+nothing
 ```
 
 ```{julia}
@@ -36,6 +39,7 @@ end
 ```
 
 ```{julia}
+#| output: false
 #| echo: false
 # ImageFile
 ## WeaveSupport from CalculusWithJulia package
@@ -220,4 +224,6 @@ function Base.show(io::IO, m::MIME"text/plain", x::HTMLoutput)
     println(io, caption)
     return nothing
 end
+
+nothing
 ```

quarto/_quarto.yml

@@ -155,4 +155,5 @@ format:
 
 execute:
   error: false
+#  freeze: false
   freeze: auto

quarto/alternatives/SciML.qmd

@@ -173,7 +173,7 @@ We can solve for several parameters at once, by using a matching number of initi
 
 ```{julia}
 ps = [1, 2, 3, 4]
-u0 = @SVector[1, 1, 1, 1]
+u0 = [1, 1, 1, 1]
 prob = NonlinearProblem(f, u0, ps)
 solve(prob, NewtonRaphson())
 ```
@@ -235,13 +235,15 @@ The extra step is to specify a "`NonlinearSystem`." It is a system, as in practi
 
 ```{julia}
 ns = NonlinearSystem([eq], [x], [α], name=:ns);
+ns = complete(ns)
 ```
 
 The `name` argument is special. The name of the object (`ns`) is assigned through `=`, but the system must also know this same name. However, the name on the left is not known when the name on the right is needed, so it is up to the user to keep them synchronized. The `@named` macro handles this behind the scenes by simply rewriting the syntax of the assignment:
 
 
 ```{julia}
 @named ns = NonlinearSystem([eq], [x], [α]);
+ns = complete(ns)
 ```
 
 With the system defined, we can pass this to `NonlinearProblem`, as was done with a function. The parameter is specified here, and in this case is `α => 1.0`. The initial guess is `[1.0]`:
@@ -366,6 +368,7 @@ The above should be self explanatory. To put into a form to pass to `solve` we d
 
 ```{julia}
 @named sys = OptimizationSystem(Area, [x], [P]);
+sys = complete(sys)
 ```
 
 (This step is different, as before an `OptimizationFunction` was defined; we use `@named`, as above, to ensure the system has the same name as the identifier, `sys`.)

quarto/derivatives/alternative_implicit.qmd

@@ -0,0 +1,78 @@
+## THIS IS FAILING
+## Appendix
+
+
+There are other packages in the `Julia` ecosystem that can plot implicit equations.
+
+
+### The ImplicitEquations package
+
+
+The `ImplicitEquations` packages can plot equations and inequalities. The use is somewhat similar to the examples above, but the object plotted is a predicate, not a function. These predicates are created with functions like `Eq` or `Lt`.
+
+
+For example, the `ImplicitPlots` manual shows this function $f(x,y) = (x^4 + y^4 - 1) \cdot (x^2 + y^2 - 2) + x^5 \cdot y$ to plot. Using `ImplicitEquations`, this equation would be plotted with:
+
+
+```{julia}
+#| hold: true
+using ImplicitEquations
+f(x,y) = (x^4 + y^4 - 1) * (x^2 + y^2 - 2) + x^5 * y
+r = Eq(f, 0)  # the equation f(x,y) = 0
+plot(r)
+```
+
+Unlike `ImplicitPlots`, inequalities may be displayed:
+
+
+```{julia}
+#| hold: true
+f(x,y) = (x^4 + y^4 - 1) * (x^2 + y^2 - 2) + x^5 * y
+r = Lt(f, 0)          # the inequality f(x,y) < 0
+plot(r; M=10, N=10)  # less blocky
+```
+
+The rendered plots look "blocky" due to the algorithm used to plot the equations. As there is no rule defining $(x,y)$ pairs to plot, a search by regions is done. A region is initially labeled undetermined. If it can be shown that for any value in the region the equation is true (equations can also be inequalities), the region is colored black. If it can be shown it will never be true, the region is dropped. If a black-and-white answer is not clear, the region is subdivided and each subregion is similarly tested. This continues until the remaining undecided regions are smaller than some threshold. Such regions comprise a boundary, and here are also colored black. Only regions are plotted - not $(x,y)$ pairs - so the results are blocky. Pass larger values of $N=M$ (with defaults of $8$) to `plot` to lower the threshold at the cost of longer computation times, as seen in the last example.
+
+
+### The IntervalConstraintProgramming package
+
+
+The `IntervalConstraintProgramming` package also can be used to graph implicit equations. For certain problem descriptions it is significantly faster and makes better graphs. The usage is slightly more involved. We show the commands, but don't run them here, as there are minor conflicts with the `CalculusWithJulia`package.
+
+
+We specify a problem using the `@constraint` macro. Using a macro allows expressions to involve free symbols, so the problem is specified in an equation-like manner:
+
+
+```{julia}
+#| eval: false
+S = @constraint x^2 + y^2 <= 2
+```
+
+The right hand side must be a number.
+
+
+The area to plot over must be specified as an `IntervalBox`, basically a pair of intervals. The interval $[a,b]$ is expressed through `a..b`:
+
+
+```{julia}
+#| eval: false
+J = -3..3
+X = IntervalArithmetic.IntervalBox(J, J)
+```
+
+The `pave` command does the heavy lifting:
+
+
+```{julia}
+#| eval: false
+region = IntervalConstraintProgramming.pave(S, X)
+```
+
+A plot can be made of either the boundary, the interior, or both.
+
+
+```{julia}
+#| eval: false
+plot(region.inner)       # plot interior; use r.boundary for boundary
+```

quarto/derivatives/curve_sketching.qmd

@@ -9,6 +9,7 @@ This section uses the following add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using SymPy
 using Roots
 using Polynomials # some name clash with SymPy
@@ -38,7 +39,7 @@ With these, a sketch fills in between the points/lines associated with these val
 #| echo: false
 #| cache: true
 ### {{{ sketch_sin_plot }}}
-
+gr()
 
 function sketch_sin_plot_graph(i)
     f(x) = 10*sin(pi/2*x)  # [0,4]
@@ -84,7 +85,7 @@ end
 
 imgfile = tempname() * ".gif"
 gif(anim, imgfile, fps = 1)
-
+plotly()
 ImageFile(imgfile, caption)
 ```
 

quarto/derivatives/derivatives.qmd

@@ -9,6 +9,7 @@ This section uses these add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using SymPy
 ```
 
@@ -218,6 +219,7 @@ The slope of the secant line represents the average rate of change over a given
 #| hold: true
 #| echo: false
 #| cache: true
+gr()
 function secant_line_tangent_line_graph(n)
     f(x) = sin(x)
     c = pi/3
@@ -251,6 +253,7 @@ end
 imgfile = tempname() * ".gif"
 gif(anim, imgfile, fps = 1)
 
+plotly()
 ImageFile(imgfile, caption)
 ```
 
@@ -268,6 +271,7 @@ We will define the tangent line at $(c, f(c))$ to be the line through the point
 #| hold: true
 #| echo: false
 #| cache: true
+gr()
 function line_approx_fn_graph(n)
     f(x) = sin(x)
     c = pi/3
@@ -296,6 +300,7 @@ end
 imgfile = tempname() * ".gif"
 gif(anim, imgfile, fps = 1)
 
+plotly()
 ImageFile(imgfile, caption)
 ```
 

quarto/derivatives/first_second_derivatives.qmd

@@ -9,6 +9,7 @@ This section uses these add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using SymPy
 using Roots
 ```

quarto/derivatives/implicit_differentiation.qmd

@@ -9,6 +9,7 @@ This section uses these add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using Roots
 using SymPy
 ```
@@ -993,81 +994,3 @@ choices = ["concave up", "concave down", "both concave up and down"]
 answ = 3
 radioq(choices, answ, keep_order=true)
 ```
-
-## Appendix
-
-
-There are other packages in the `Julia` ecosystem that can plot implicit equations.
-
-
-### The ImplicitEquations package
-
-
-The `ImplicitEquations` packages can plot equations and inequalities. The use is somewhat similar to the examples above, but the object plotted is a predicate, not a function. These predicates are created with functions like `Eq` or `Lt`.
-
-
-For example, the `ImplicitPlots` manual shows this function $f(x,y) = (x^4 + y^4 - 1) \cdot (x^2 + y^2 - 2) + x^5 \cdot y$ to plot. Using `ImplicitEquations`, this equation would be plotted with:
-
-
-```{julia}
-#| hold: true
-using ImplicitEquations
-f(x,y) = (x^4 + y^4 - 1) * (x^2 + y^2 - 2) + x^5 * y
-r = Eq(f, 0)  # the equation f(x,y) = 0
-plot(r)
-```
-
-Unlike `ImplicitPlots`, inequalities may be displayed:
-
-
-```{julia}
-#| hold: true
-f(x,y) = (x^4 + y^4 - 1) * (x^2 + y^2 - 2) + x^5 * y
-r = Lt(f, 0)          # the inequality f(x,y) < 0
-plot(r; M=10, N=10)  # less blocky
-```
-
-The rendered plots look "blocky" due to the algorithm used to plot the equations. As there is no rule defining $(x,y)$ pairs to plot, a search by regions is done. A region is initially labeled undetermined. If it can be shown that for any value in the region the equation is true (equations can also be inequalities), the region is colored black. If it can be shown it will never be true, the region is dropped. If a black-and-white answer is not clear, the region is subdivided and each subregion is similarly tested. This continues until the remaining undecided regions are smaller than some threshold. Such regions comprise a boundary, and here are also colored black. Only regions are plotted - not $(x,y)$ pairs - so the results are blocky. Pass larger values of $N=M$ (with defaults of $8$) to `plot` to lower the threshold at the cost of longer computation times, as seen in the last example.
-
-
-### The IntervalConstraintProgramming package
-
-
-The `IntervalConstraintProgramming` package also can be used to graph implicit equations. For certain problem descriptions it is significantly faster and makes better graphs. The usage is slightly more involved. We show the commands, but don't run them here, as there are minor conflicts with the `CalculusWithJulia`package.
-
-
-We specify a problem using the `@constraint` macro. Using a macro allows expressions to involve free symbols, so the problem is specified in an equation-like manner:
-
-
-```{julia}
-#| eval: false
-S = @constraint x^2 + y^2 <= 2
-```
-
-The right hand side must be a number.
-
-
-The area to plot over must be specified as an `IntervalBox`, basically a pair of intervals. The interval $[a,b]$ is expressed through `a..b`:
-
-
-```{julia}
-#| eval: false
-J = -3..3
-X = IntervalArithmetic.IntervalBox(J, J)
-```
-
-The `pave` command does the heavy lifting:
-
-
-```{julia}
-#| eval: false
-region = IntervalConstraintProgramming.pave(S, X)
-```
-
-A plot can be made of either the boundary, the interior, or both.
-
-
-```{julia}
-#| eval: false
-plot(region.inner)       # plot interior; use r.boundary for boundary
-```

quarto/derivatives/lhospitals_rule.qmd

@@ -9,8 +9,8 @@ This section uses these add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using SymPy
-
 ```
 
 
@@ -245,6 +245,7 @@ A first proof of L'Hospital's rule takes advantage of Cauchy's [generalization](
 #| echo: false
 #| cache: true
 using Roots
+gr()
 let
 ## {{{lhopitals_picture}}}
 
@@ -293,7 +294,7 @@ imgfile = tempname() * ".gif"
 gif(anim, imgfile, fps = 1)
 
 
-plotly()
+    plotly()
     ImageFile(imgfile, caption)
 end
 ```

quarto/derivatives/linearization.qmd

@@ -9,6 +9,7 @@ This section uses these add-on packages:
 ```{julia}
 using CalculusWithJulia
 using Plots
+plotly()
 using SymPy
 using TaylorSeries
 using DualNumbers